Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007776.1 Hibiscus syriacus cultivar Beakdansim tig00110057_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: 2207776
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1664096 original size:35 final size:36
Alignment explanation
Indices: 1664056--1664129 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 36
1664046 TATACTATAC
*
1664056 ATAGTTT-ATACATACATGTACTATAAGTTACATAT
1 ATAGTTTAATACATACATATACTATAAGTTACATAT
** *
1664091 ATAGTTTACATGTATACATATATTATAAGTTACATAT
1 ATAGTTTA-ATACATACATATACTATAAGTTACATAT
1664128 AT
1 AT
1664130 TAACTATTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 7 0.21
37 26 0.79
ACGTcount: A:0.41, C:0.09, G:0.08, T:0.42
Consensus pattern (36 bp):
ATAGTTTAATACATACATATACTATAAGTTACATAT
Found at i:1664339 original size:29 final size:29
Alignment explanation
Indices: 1664307--1664405 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
1664297 TACATACATA
*
1664307 TATATACTATATTAATATAAATTATAATT
1 TATAAACTATATTAATATAAATTATAATT
* * *
1664336 TATAAACTATA-TACTTTATATAGTT-T-ATA
1 TATAAACTATATTA--ATATA-AATTATAATT
* * *
1664365 TATATACTATATTAACATAAATTATAGTT
1 TATAAACTATATTAATATAAATTATAATT
1664394 TATAAACTATAT
1 TATAAACTATAT
1664406 ACTTTTTATA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
27 3 0.06
28 6 0.11
29 34 0.64
30 7 0.13
31 3 0.06
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (29 bp):
TATAAACTATATTAATATAAATTATAATT
Found at i:1664379 original size:58 final size:58
Alignment explanation
Indices: 1664304--1664428 Score: 214
Period size: 58 Copynumber: 2.2 Consensus size: 58
1664294 TTATACATAC
*
1664304 ATATATATACTATATTAATATAAATTATAATTTATAAACTATATACTTTATATAGTTT
1 ATATATATACTATATTAACATAAATTATAATTTATAAACTATATACTTTATATAGTTT
* *
1664362 ATATATATACTATATTAACATAAATTATAGTTTATAAACTATATACTTTTTATAGTTT
1 ATATATATACTATATTAACATAAATTATAATTTATAAACTATATACTTTATATAGTTT
*
1664420 ATACATATA
1 ATATATATA
1664429 TAGTTTACGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 63 1.00
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.47
Consensus pattern (58 bp):
ATATATATACTATATTAACATAAATTATAATTTATAAACTATATACTTTATATAGTTT
Found at i:1664457 original size:13 final size:13
Alignment explanation
Indices: 1664412--1664514 Score: 64
Period size: 13 Copynumber: 7.3 Consensus size: 13
1664402 ATATACTTTT
1664412 TATAGTTTATACATA
1 TATAGTTTAT--ATA
**
1664427 TATAGTTTACGTA
1 TATAGTTTATATA
*
1664440 CATAGTTTATATA
1 TATAGTTTATATA
*
1664453 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
1664468 CATAATTTATATA
1 TATAGTTTATATA
1664481 TATAGCTTATAATAATTA
1 TATAG-TT-T-AT-A-TA
1664499 TATAGTTTATA-A
1 TATAGTTTATATA
1664511 TATA
1 TATA
1664515 AATAAAGTTT
Statistics
Matches: 69, Mismatches: 12, Indels: 17
0.70 0.12 0.17
Matches are distributed among these distances:
12 5 0.07
13 26 0.38
14 3 0.04
15 22 0.32
16 3 0.04
17 3 0.04
18 7 0.10
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.46
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:1664595 original size:2 final size:2
Alignment explanation
Indices: 1664584--1664645 Score: 63
Period size: 2 Copynumber: 30.5 Consensus size: 2
1664574 TATGCATTTA
* * * *
1664584 AT AT ACT AT AT AT AT AA ACT AT AT AC AT AA AT CT -T AT AT AT AT
1 AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
1664627 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1664646 AAGTACATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
1 1 0.02
2 46 0.92
3 3 0.06
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1664679 original size:11 final size:11
Alignment explanation
Indices: 1664663--1664687 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1664653 TAGTTTATTA
1664663 ATAAACTACAT
1 ATAAACTACAT
1664674 ATAAACTACAT
1 ATAAACTACAT
1664685 ATA
1 ATA
1664688 TTATATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (11 bp):
ATAAACTACAT
Found at i:1666881 original size:31 final size:31
Alignment explanation
Indices: 1666789--1666881 Score: 141
Period size: 31 Copynumber: 3.0 Consensus size: 31
1666779 CGATCATACT
* *
1666789 AAGGGTCATCAAAGGGAATTACACTAGTAGA
1 AAGGATCATCAAAGGGAATTACACTAGTGGA
* *
1666820 AAGGATCATCAAAGAGAATTACACTTGTGGA
1 AAGGATCATCAAAGGGAATTACACTAGTGGA
*
1666851 AAGGATCATCAAAGGGAATTACACTGGTGGA
1 AAGGATCATCAAAGGGAATTACACTAGTGGA
1666882 TGTGATTCAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.20
Consensus pattern (31 bp):
AAGGATCATCAAAGGGAATTACACTAGTGGA
Found at i:1670916 original size:24 final size:24
Alignment explanation
Indices: 1670888--1670937 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1670878 TAAGTTTTGA
1670888 TAAATTTT-TAAGTCTCCACTAATT
1 TAAATTTTATAA-TCTCCACTAATT
* *
1670912 TAAATTTTATAATCTCGATTAATT
1 TAAATTTTATAATCTCCACTAATT
1670936 TA
1 TA
1670938 GTAAGAATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 20 0.87
25 3 0.13
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (24 bp):
TAAATTTTATAATCTCCACTAATT
Found at i:1671119 original size:28 final size:28
Alignment explanation
Indices: 1671088--1671148 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
1671078 TTTTAATATT
1671088 TTTAATATGTATATTTAAT-TTTTTATAA
1 TTTAATATGTATATTTAATATTTTTAT-A
* * * *
1671116 TTTAATTTTTATTTTTAGTATTTTTATA
1 TTTAATATGTATATTTAATATTTTTATA
1671144 TTTAA
1 TTTAA
1671149 AATTTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (28 bp):
TTTAATATGTATATTTAATATTTTTATA
Found at i:1671147 original size:21 final size:21
Alignment explanation
Indices: 1671097--1671147 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
1671087 TTTTAATATG
1671097 TATATTTAATTTTTTATAATTT
1 TATATTT-ATTTTTTATAATTT
* * *
1671119 AATTTTTA-TTTTTAGTATTTT
1 TATATTTATTTTTTA-TAATTT
1671140 TATATTTA
1 TATATTTA
1671148 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 6 0.26
21 12 0.52
22 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TATATTTATTTTTTATAATTT
Found at i:1671153 original size:15 final size:14
Alignment explanation
Indices: 1671097--1671149 Score: 54
Period size: 15 Copynumber: 3.7 Consensus size: 14
1671087 TTTTAATATG
*
1671097 TATATTTAATTTTT
1 TATATTTAAATTTT
1671111 TATAATTT-AATTTT
1 TAT-ATTTAAATTTT
* *
1671125 TATTTTTAGTATTTT
1 TATATTTA-AATTTT
1671140 TATATTTAAA
1 TATATTTAAA
1671150 ATTTAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 3 0.10
14 12 0.39
15 16 0.52
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TATATTTAAATTTT
Found at i:1671896 original size:10 final size:10
Alignment explanation
Indices: 1671881--1671914 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1671871 TTTTATGTTC
1671881 GTTCGTTTAT
1 GTTCGTTTAT
*
1671891 GTTCGTTTAC
1 GTTCGTTTAT
*
1671901 GGTCGTTTAT
1 GTTCGTTTAT
1671911 GTTC
1 GTTC
1671915 ATTCGATTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.09, C:0.15, G:0.24, T:0.53
Consensus pattern (10 bp):
GTTCGTTTAT
Found at i:1682394 original size:20 final size:21
Alignment explanation
Indices: 1682347--1682398 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 21
1682337 TGGTGAATTA
1682347 AAAATAATTTATATGATGATT
1 AAAATAATTTATATGATGATT
1682368 GAAAAATAATTTATATGATGATT
1 --AAAATAATTTATATGATGATT
*
1682391 AAATTAAT
1 AAAATAAT
1682399 ATTTTAAGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 7 0.25
23 21 0.75
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (21 bp):
AAAATAATTTATATGATGATT
Found at i:1682402 original size:23 final size:23
Alignment explanation
Indices: 1682346--1682390 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1682336 TTGGTGAATT
1682346 AAAAATAATTTATATGATGATTG
1 AAAAATAATTTATATGATGATTG
1682369 AAAAATAATTTATATGATGATT
1 AAAAATAATTTATATGATGATT
1682391 AAATTAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.40
Consensus pattern (23 bp):
AAAAATAATTTATATGATGATTG
Found at i:1693069 original size:21 final size:20
Alignment explanation
Indices: 1693030--1693069 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1693020 GTGGTCTTGT
*
1693030 AACATTATACAAAAGCTTTG
1 AACACTATACAAAAGCTTTG
*
1693050 AACACTATGCAAAGAGCTTT
1 AACACTATACAAA-AGCTTT
1693070 ATTGATGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (20 bp):
AACACTATACAAAAGCTTTG
Found at i:1693587 original size:22 final size:22
Alignment explanation
Indices: 1693559--1693637 Score: 122
Period size: 22 Copynumber: 3.6 Consensus size: 22
1693549 ACATCTACAT
1693559 TCTTCAAAGATGATATATTCTC
1 TCTTCAAAGATGATATATTCTC
* *
1693581 TCTTCAAAGATGATAGATTCTA
1 TCTTCAAAGATGATATATTCTC
*
1693603 TCTTCAAAGATGATATATTATC
1 TCTTCAAAGATGATATATTCTC
*
1693625 TTTTCAAAGATGA
1 TCTTCAAAGATGA
1693638 AAACTTTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATATATTCTC
Found at i:1694416 original size:36 final size:35
Alignment explanation
Indices: 1694364--1694563 Score: 139
Period size: 36 Copynumber: 5.5 Consensus size: 35
1694354 TTCAAATAGC
*
1694364 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 AATTTGTCTCACTTGAGATTGTTTTTCTTAAAACA
* * ** ** **
1694399 AATTGCGTCTCGCTTGAGACAGTTTCACTCGAAACA
1 AATT-TGTCTCACTTGAGATTGTTTTTCTTAAAACA
* *
1694435 TCAATTTATCTCACTTGAGATTATTTTTCTTAAAACAA
1 --AATTTGTCTCACTTGAGATTGTTTTTCTTAAAAC-A
* * ** ** **
1694473 AATTTGTTTCGCTTGAGACAGTTTCACTCGAAACAA
1 AATTTGTCTCACTTGAGATTGTTTTTCTTAAAAC-A
*
1694509 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACA
1 -AATTTGTCTCACTTGAGATTGTTTTTCTTAAAACA
* *
1694545 AGATTCGTCTCGCTTGAGA
1 A-ATTTGTCTCACTTGAGA
1694564 CAGTTTCACT
Statistics
Matches: 118, Mismatches: 41, Indels: 11
0.69 0.24 0.06
Matches are distributed among these distances:
35 5 0.04
36 63 0.53
37 45 0.38
38 5 0.04
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (35 bp):
AATTTGTCTCACTTGAGATTGTTTTTCTTAAAACA
Found at i:1694485 original size:73 final size:73
Alignment explanation
Indices: 1694363--1694581 Score: 368
Period size: 73 Copynumber: 3.0 Consensus size: 73
1694353 TTTCAAATAG
1694363 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AAATTGCGTCTCGCTTGAGACAGTTTCAC
1 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATT-CGTCTCGCTTGAGACAGTTTCAC
*
1694427 TCGAAACAT
65 TCGAAACAA
* * *
1694436 CAATTTATCTCACTTGAGATTATTTTTCTTAAAACAAAATTTGTTTCGCTTGAGACAGTTTCACT
1 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCACT
1694501 CGAAACAA
66 CGAAACAA
*
1694509 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCGTCTCGCTTGAGACAGTTTCACT
1 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCACT
*
1694574 AGAAACAA
66 CGAAACAA
1694582 AAAATTTCAT
Statistics
Matches: 136, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
73 131 0.96
74 5 0.04
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (73 bp):
CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTCGTCTCGCTTGAGACAGTTTCACT
CGAAACAA
Found at i:1694580 original size:36 final size:35
Alignment explanation
Indices: 1694394--1694582 Score: 123
Period size: 36 Copynumber: 5.2 Consensus size: 35
1694384 GTTTTTCTTA
* *
1694394 AAACAAATTGCGTCTCGCTTGAGACAGTTTCACTCG
1 AAACAAATT-TGTCTCGCTTGAGACAGTTTCACTAG
* * * * *
1694430 AAACATCAATTTATCTCACTTGAGATTATTTTTC-TTA-
1 AAACA--AATTTGTCTCGCTTGAGA-CA-GTTTCACTAG
* *
1694467 AAACAAAATTTGTTTCGCTTGAGACAGTTTCACTCG
1 AAAC-AAATTTGTCTCGCTTGAGACAGTTTCACTAG
* * ** **
1694503 AAACAACAATTTATCTCACTTGAGATTGTTTTTCTTA-
1 AAAC-A-AATTTGTCTCGCTTGAGACAGTTTCAC-TAG
*
1694540 AAACAAGATTCGTCTCGCTTGAGACAGTTTCACTAG
1 AAACAA-ATTTGTCTCGCTTGAGACAGTTTCACTAG
1694576 AAACAAA
1 AAACAAA
1694583 AAATTTCATC
Statistics
Matches: 113, Mismatches: 29, Indels: 23
0.68 0.18 0.14
Matches are distributed among these distances:
34 4 0.04
35 6 0.05
36 52 0.46
37 39 0.35
38 8 0.07
39 4 0.04
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (35 bp):
AAACAAATTTGTCTCGCTTGAGACAGTTTCACTAG
Found at i:1694826 original size:123 final size:122
Alignment explanation
Indices: 1694605--1695291 Score: 877
Period size: 122 Copynumber: 5.7 Consensus size: 122
1694595 TCGATGGATC
* *
1694605 AACATTTCCAGAGGAAGTTCATAATGAGCAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
1 AACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
* * *
1694670 AGAAGAACTTGTTCAACCTTTTTCTCGACTCTATCACAGAATGAGATAGATCAGCACT
65 AGAAGAACTTGTTCAACCTTTTGCTCGAGTCTATCACAAAATGAGATAGATCAGCACT
* * *
1694728 AACATTTCCAAATAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATG
1 AACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
* * * *
1694793 AGAAGAATTTGTTCAACCTTTTGCTCAAGTCTATCAC----TCA-ATGGAT-----C-
65 AGAAGAACTTGTTCAACCTTTTGCTCGAGTCTATCACAAAATGAGATAGATCAGCACT
* * *
1694840 AACATTTCCAGAGGAAGTTCATAATGAGAAGAATTCATCTGAAGAGGAATG-AGAAGTTTATAAT
1 AACATTTCCAGA-AAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAA-GAAGAAGTTCATAAT
* * * *
1694904 GAGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCCCAAAAGGAGATAGATCAGCACC
64 GAGAAGAACTTGTTCAACCTTTTGCTCGAGTCTATCACAAAATGAGATAGATCAGCACT
**
1694963 AACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
1 AACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
* *
1695028 GAAGAACTTGTTCAACCTTTTGCTCGAAG-CTATCACAGAA-GCATATAGATCAGCA-T
66 GAAGAACTTGTTCAACCTTTTGCTCG-AGTCTATCACAAAATG-AGATAGATCAGCACT
** * *
1695084 CAACATTTCCAGAAGTGTTCATAATGAGAAAAACTCATCTGAAGAGGAAGAATAAGTTCATAATG
1 -AACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
* * * *
1695149 AGAAGAACTTGTTCAACCTTTTGAAT-GATTCTATCACAAAAAGAGATAGATCAACA-T
65 AGAAGAACTTGTTCAACCTTTTG-CTCGAGTCTATCACAAAATGAGATAGATCAGCACT
*
1695206 CAACATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAGGAAGTTCATAAT
1 -AACATTTCCAGAAA-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT
1695271 GAGAAGAACTTGTTCAACCTT
64 GAGAAGAACTTGTTCAACCTT
1695292 GCCTTAATTC
Statistics
Matches: 496, Mismatches: 48, Indels: 40
0.85 0.08 0.07
Matches are distributed among these distances:
112 89 0.18
113 2 0.00
116 1 0.00
117 5 0.01
118 5 0.01
119 2 0.00
121 3 0.01
122 216 0.44
123 173 0.35
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (122 bp):
AACATTTCCAGAAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACCTTTTGCTCGAGTCTATCACAAAATGAGATAGATCAGCACT
Found at i:1696489 original size:2 final size:2
Alignment explanation
Indices: 1696477--1696516 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
1696467 ATATCTTATT
*
1696477 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1696517 TTACTTCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1696800 original size:23 final size:22
Alignment explanation
Indices: 1696774--1696827 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
1696764 TTCTAAGTAA
*
1696774 ATAAATATCTTATTTATAAAAAT
1 ATAAATAT-ATATTTATAAAAAT
*
1696797 ATAAAAAATATATTTATAAAAAT
1 AT-AAATATATATTTATAAAAAT
1696820 -T-AATATAT
1 ATAAATATAT
1696828 TTTCTTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 6 0.22
22 1 0.04
23 15 0.56
24 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAAATATATATTTATAAAAAT
Found at i:1705798 original size:17 final size:17
Alignment explanation
Indices: 1705772--1705806 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1705762 GATAGTTAAA
* *
1705772 AGAATGACAATTGATTC
1 AGAATAACAAATGATTC
1705789 AGAATAACAAATGATTC
1 AGAATAACAAATGATTC
1705806 A
1 A
1705807 CCTGATCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.26
Consensus pattern (17 bp):
AGAATAACAAATGATTC
Found at i:1706297 original size:30 final size:30
Alignment explanation
Indices: 1706261--1706325 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
1706251 CGGTGCTCTA
1706261 GGCATATAGTTTAATCTGGTAGACCATCTT
1 GGCATATAGTTTAATCTGGTAGACCATCTT
1706291 GGCATATAGTTTAATCTGGTAGACCATCTT
1 GGCATATAGTTTAATCTGGTAGACCATCTT
1706321 GGCAT
1 GGCAT
1706326 TTTCTTTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (30 bp):
GGCATATAGTTTAATCTGGTAGACCATCTT
Found at i:1706929 original size:15 final size:15
Alignment explanation
Indices: 1706909--1706939 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1706899 CAACAAATAG
1706909 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
1706924 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
1706939 A
1 A
1706940 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:1720874 original size:12 final size:12
Alignment explanation
Indices: 1720840--1720899 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
1720830 AACATAATAA
1720840 AAATTTAAAAAT
1 AAATTTAAAAAT
*
1720852 AAGCA-TAAAAAAT
1 AA--ATTTAAAAAT
1720865 AAATTTAAAAAT
1 AAATTTAAAAAT
** *
1720877 TTATTAAAAAAT
1 AAATTTAAAAAT
1720889 AAATTTAAAAA
1 AAATTTAAAAA
1720900 ATTACTTTTC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
11 1 0.03
12 26 0.70
13 9 0.24
14 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (12 bp):
AAATTTAAAAAT
Found at i:1720874 original size:25 final size:24
Alignment explanation
Indices: 1720840--1720899 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
1720830 AACATAATAA
1720840 AAATTTAAAAA-TAAGCATAAAAAAT
1 AAATTTAAAAATTAA--ATAAAAAAT
* *
1720865 AAATTTAAAAATTTATTAAAAAAT
1 AAATTTAAAAATTAAATAAAAAAT
1720889 AAATTTAAAAA
1 AAATTTAAAAA
1720900 ATTACTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 19 0.59
25 11 0.34
26 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AAATTTAAAAATTAAATAAAAAAT
Found at i:1722108 original size:21 final size:22
Alignment explanation
Indices: 1722068--1722120 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
1722058 GTTTTGATAT
*
1722068 TTTTTTAAAATTTTATAAATTAA
1 TTTTTTAAAA-TTTAAAAATTAA
*
1722091 TTTTTTAAAA-TTAAAAATTTA
1 TTTTTTAAAATTTAAAAATTAA
*
1722112 TATTTTAAA
1 TTTTTTAAA
1722121 CGAACTTATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 17 0.63
23 10 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTTTAAAATTTAAAAATTAA
Found at i:1722116 original size:23 final size:23
Alignment explanation
Indices: 1722068--1722117 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1722058 GTTTTGATAT
* *
1722068 TTTTTTAAAATTTTATAAATTAA
1 TTTTTTAAAATTTAAAAAATTAA
*
1722091 TTTTTTAAAA-TTAAAAATTTATA
1 TTTTTTAAAATTTAAAAAATTA-A
1722114 TTTT
1 TTTT
1722118 AAACGAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTTTAAAATTTAAAAAATTAA
Found at i:1726133 original size:17 final size:17
Alignment explanation
Indices: 1726111--1726145 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1726101 AAATTATTTT
*
1726111 AAAAATTTGAAATATAG
1 AAAAATATGAAATATAG
1726128 AAAAATATGAAATATAG
1 AAAAATATGAAATATAG
1726145 A
1 A
1726146 TTTTTAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (17 bp):
AAAAATATGAAATATAG
Found at i:1728973 original size:18 final size:18
Alignment explanation
Indices: 1728947--1729033 Score: 129
Period size: 18 Copynumber: 4.8 Consensus size: 18
1728937 TGAATGGTTT
1728947 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
1728965 TCTCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
1728983 TCCCGAAGGATCACTATG
1 TCCCGAAGGACCACTATG
* *
1729001 TCCCAAAGGATCACTATG
1 TCCCGAAGGACCACTATG
*
1729019 TTCCGAAGGACCACT
1 TCCCGAAGGACCACT
1729034 GATAATCCCT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.21
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:1729300 original size:2 final size:2
Alignment explanation
Indices: 1729293--1729350 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
1729283 TATATCCATA
1729293 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1729335 AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT
1729351 GCATGTACAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1736500 original size:26 final size:26
Alignment explanation
Indices: 1736470--1736555 Score: 127
Period size: 26 Copynumber: 3.3 Consensus size: 26
1736460 CTTAAGGTTG
*
1736470 TAGGAGCTACGAGAGTAGCCTTTCCT
1 TAGGAGGTACGAGAGTAGCCTTTCCT
*
1736496 TAGGAGGTACGAGAGTAGTCTTTCCT
1 TAGGAGGTACGAGAGTAGCCTTTCCT
* * *
1736522 TATGAGGTACGAGAGTAACCTTTCTT
1 TAGGAGGTACGAGAGTAGCCTTTCCT
1736548 TAGGAGGT
1 TAGGAGGT
1736556 CTTGAGGGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.30
Consensus pattern (26 bp):
TAGGAGGTACGAGAGTAGCCTTTCCT
Found at i:1736999 original size:2 final size:2
Alignment explanation
Indices: 1736992--1737018 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1736982 AAAGCTAGTC
1736992 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1737019 ATCCAATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1737793 original size:18 final size:18
Alignment explanation
Indices: 1737765--1737815 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
1737755 TGAATGGTTT
*
1737765 TCCCAAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
1737783 TCTCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
*
1737801 TCCCGAAGGATCACT
1 TCCCGAAGGACCACT
1737816 GATAATCCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:1738867 original size:26 final size:24
Alignment explanation
Indices: 1738822--1738869 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
1738812 CAAATTTAAC
*
1738822 TTCCAATTTTAGTTATGAACTCTA
1 TTCCAATTTTAGTTAAGAACTCTA
*
1738846 TTCCAATATTTCATTTAAGAACTC
1 TTCCAAT-TTT-AGTTAAGAACTC
1738870 CTAATCTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 3 0.15
26 10 0.50
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (24 bp):
TTCCAATTTTAGTTAAGAACTCTA
Found at i:1745476 original size:101 final size:102
Alignment explanation
Indices: 1745289--1745717 Score: 300
Period size: 101 Copynumber: 4.0 Consensus size: 102
1745279 AATCATTTTC
* * * * * * *
1745289 CTCTTCAGATGAGTTCTTCTCATTATGAACTCTTTCTGGAAATGTTGATGATAATATATCTCTTT
1 CTCTTCAAATGAGTTATTCTCATTATGAACACATTCTGGAAATGTTGATGCTGATATATCTCCTT
* * *
1745354 CTATGATAGAATC-ACGTAAAAGGTTGAACAAGTTCTT
66 ATATGATAGAGTCGA-GCAAAAGGTTGAACAAGTTCTT
*
1745391 CTCTTCAAATGAGTTATTCTCATTATGAACAC-TTCTGGAAATGTTGATGCTGATCTATCTCCTT
1 CTCTTCAAATGAGTTATTCTCATTATGAACACATTCTGGAAATGTTGATGCTGATATATCTCCTT
** *
1745455 ATGGGATAGCGTCGAGCAAAAGGTTGAACAAGCTT-TT
66 ATATGATAGAGTCGAGCAAAAGGTTGAACAAG-TTCTT
** * *
1745492 CTCATT-ATGAACT-TCTTCACCTTCTTCA-TATGAGTTATTCTCATTAT-GAACACT-TCTGGA
1 CTC-TTCA--AA-TGAGTT-A--TTC-TCATTATGA---A--CACATTCTGGAA-A-TGT-T-G-
* * * * *
1745552 AATGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCGAGCAAAAAGTTGAACAAGTTCTT
48 -ATGCTGA---T-A--TATCTCCTTATATGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTT
* * * *
1745614 CTCTTCATATGAGTTCTTCTCATTATGAACAC-TTTTAGAAATGTTGATGCTGATATATCTCCTT
1 CTCTTCAAATGAGTTATTCTCATTATGAACACATTCTGGAAATGTTGATGCTGATATATCTCCTT
*
1745678 ATATGATAGCGTCGAGCAAAAGGTTGAACAAGTTCTT
66 ATATGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTT
1745715 CTC
1 CTC
1745718 ATTATGAACT
Statistics
Matches: 257, Mismatches: 36, Indels: 69
0.71 0.10 0.19
Matches are distributed among these distances:
101 102 0.40
102 34 0.13
103 5 0.02
104 3 0.01
106 8 0.03
107 9 0.04
109 2 0.01
110 2 0.01
111 10 0.04
112 10 0.04
113 2 0.01
114 2 0.01
116 9 0.04
117 8 0.03
119 2 0.01
120 3 0.01
121 4 0.02
122 42 0.16
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (102 bp):
CTCTTCAAATGAGTTATTCTCATTATGAACACATTCTGGAAATGTTGATGCTGATATATCTCCTT
ATATGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTT
Found at i:1745543 original size:122 final size:122
Alignment explanation
Indices: 1745392--1745616 Score: 371
Period size: 122 Copynumber: 1.8 Consensus size: 122
1745382 CAAGTTCTTC
*
1745392 TCTTCAAATGAGTTATTCTCATTATGAACACTTCTGGAAATGTTGATGCTGATCTATCTCCTTAT
1 TCTTCAAATGAGTTATTCTCATTATGAACACTTCTGGAAATGTTGATGCTGATCTATCTCATTAT
* *
1745457 GGGATAGCGTCGAGCAAAAGGTTGAACAAGCTT-TTCTCATTATGAACTTCTTCACCT
66 GGGATAGAGTCGAGCAAAAAGTTGAACAAG-TTCTTCTCATTATGAACTTCTTCACCT
* * *
1745514 TCTTCATATGAGTTATTCTCATTATGAACACTTCTGGAAATGTTGATGTTGATCTATCTCATTCT
1 TCTTCAAATGAGTTATTCTCATTATGAACACTTCTGGAAATGTTGATGCTGATCTATCTCATTAT
*
1745579 GTGATAGAGTCGAGCAAAAAGTTGAACAAGTTCTTCTC
66 GGGATAGAGTCGAGCAAAAAGTTGAACAAGTTCTTCTC
1745617 TTCATATGAG
Statistics
Matches: 95, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
121 2 0.02
122 93 0.98
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (122 bp):
TCTTCAAATGAGTTATTCTCATTATGAACACTTCTGGAAATGTTGATGCTGATCTATCTCATTAT
GGGATAGAGTCGAGCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCACCT
Found at i:1745639 original size:223 final size:223
Alignment explanation
Indices: 1745250--1745839 Score: 871
Period size: 223 Copynumber: 2.6 Consensus size: 223
1745240 GAATTAAGGC
* ** *
1745250 AAGGTTGAACAAGTTCTTTTCATTATGAAAATCATTTTCC-TCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTC-TTCTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * * * * *
1745314 TGAACTCTTTCTGGAAATGTTGATGATAATATATCTCTTTCTATGATAGAATC-ACGTAAAAGGT
65 TGAACAC-TTCTGGAAATGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCGA-GTAAAAAGT
*
1745378 TGAACAAGTTCTTCTCTTCAAATGAGTTATTCTCATTATGAACACTTCTGGAAATGTTGATGCTG
128 TGAACAAGTTCTTCTCTTCAAATGAGTTATTCTCATTATGAACACTTCTAGAAATGTTGATGCTG
* *
1745443 ATCTATCTCCTTATGGGATAGCGTCGAGCAA
193 ATATATCTCCTTATAGGATAGCGTCGAGCAA
* * *
1745474 AAGGTTGAACAAGCTT-TTCTCATTATGAACTTCTTCACCTTCTTCATATGAGTTATTCTCATTA
1 AAGGTTGAACAAG-TTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTA
*
1745538 TGAACACTTCTGGAAATGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCGAGCAAAAAGTTG
65 TGAACACTTCTGGAAATGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCGAGTAAAAAGTTG
* * *
1745603 AACAAGTTCTTCTCTTCATATGAGTTCTTCTCATTATGAACACTTTTAGAAATGTTGATGCTGAT
130 AACAAGTTCTTCTCTTCAAATGAGTTATTCTCATTATGAACACTTCTAGAAATGTTGATGCTGAT
*
1745668 ATATCTCCTTATATGATAGCGTCGAGCAA
195 ATATCTCCTTATAGGATAGCGTCGAGCAA
*
1745697 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCATTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
* * * *
1745762 GAACACTTCTTGAAATATTGATGTTGATCTATATCCTTCTGTGATAGAGTCGAGTAAAAAGTTGA
66 GAACACTTCTGGAAATGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCGAGTAAAAAGTTGA
1745827 ACAAGTTCTTCTC
131 ACAAGTTCTTCTC
1745840 ATTATGAACT
Statistics
Matches: 330, Mismatches: 32, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
222 2 0.01
223 270 0.82
224 56 0.17
225 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.38
Consensus pattern (223 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTAT
GAACACTTCTGGAAATGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCGAGTAAAAAGTTGA
ACAAGTTCTTCTCTTCAAATGAGTTATTCTCATTATGAACACTTCTAGAAATGTTGATGCTGATA
TATCTCCTTATAGGATAGCGTCGAGCAA
Found at i:1746020 original size:113 final size:113
Alignment explanation
Indices: 1745802--1746116 Score: 533
Period size: 113 Copynumber: 2.8 Consensus size: 113
1745792 ATATCCTTCT
* * * * *
1745802 GTGATAGAGTCGAGTAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAG
1 GTGATGGATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAG
* *
1745866 ATCAGTTCTTCTCATTATGAACTCTACCCGGCAATGCTGATCCATCGG
66 ATGAGTTCTTCTCATTATGAACTCTACCCGACAATGCTGATCCATCGG
1745914 GTGATGGATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAG
1 GTGATGGATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAG
* * *
1745979 ATGAGTTCTTCTCATTATGAACTCTACCTGATAATGTTGATCCATCGG
66 ATGAGTTCTTCTCATTATGAACTCTACCCGACAATGCTGATCCATCGG
1746027 GTGATGGATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAG
1 GTGATGGATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAG
1746092 ATGAGTTCTTCTCATTATGAACTCT
66 ATGAGTTCTTCTCATTATGAACTCT
1746117 TTCTGGCAAT
Statistics
Matches: 192, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
112 48 0.25
113 144 0.75
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (113 bp):
GTGATGGATTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTCTACCCGACAATGCTGATCCATCGG
Found at i:1746321 original size:73 final size:73
Alignment explanation
Indices: 1746129--1746603 Score: 756
Period size: 73 Copynumber: 6.5 Consensus size: 73
1746119 CTGGCAATGC
* * *
1746129 TTTAAGAAAAACAATCTCAAATGAGATAAATGGATATTTCAAGTGAAACTTCCTCTAGAGAGAAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTTCAAGTGAAACTTTCTCTAGAGAGAAA
1746194 TAGTTTG-
66 TAGTTTGT
* *
1746201 TTTAAGAAAAACAATCGCAAGTGAGATAAATGGATATTTCAAGTGAAACTTTCTCTAGAGAGAAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTTCAAGTGAAACTTTCTCTAGAGAGAAA
1746266 TAGTTTGT
66 TAGTTTGT
* *
1746274 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAATTGAAACTTTCTCTAGAGAGAAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTTCAAGTGAAACTTTCTCTAGAGAGAAA
1746339 TAGTTTG-
66 TAGTTTGT
* * *
1746346 TTTAAGAAAAACAATCGCAAGTGAGATAAATGGATATTTCAAGTGAATCTTTCTCTAGAGAGAAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTTCAAGTGAAACTTTCTCTAGAGAGAAA
1746411 TAGTTTGT
66 TAGTTTGT
* * * *
1746419 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAATTGAAACTTTCTCAAGCGAGAAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTTCAAGTGAAACTTTCTCTAGAGAGAAA
*
1746484 CAGTTTGT
66 TAGTTTGT
* * *
1746492 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAATTGAAACTTTCTCTAGGGAGAAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTTCAAGTGAAACTTTCTCTAGAGAGAAA
*
1746557 CAGTTTGT
66 TAGTTTGT
*
1746565 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTT
1746604 GAAAACATCT
Statistics
Matches: 378, Mismatches: 23, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
72 136 0.36
73 242 0.64
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (73 bp):
TTTAAGAAAAACAATCTCAAGTGAGATAAATTGATATTTCAAGTGAAACTTTCTCTAGAGAGAAA
TAGTTTGT
Found at i:1746392 original size:145 final size:145
Alignment explanation
Indices: 1746129--1746603 Score: 797
Period size: 145 Copynumber: 3.3 Consensus size: 145
1746119 CTGGCAATGC
* * * * *
1746129 TTTAAGAAAAACAATCTCAAATGAGATAAATGGATATTTCAAGTGAAACTTCCTCTAGAGAGAAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAATTGAAACTTTCTCTAGAGAGAAA
1746194 TAGTTTGTTTAAGAAAAACAATCGCAAGTGAGATAAATGGATATTTCAAGTGAAACTTTCTCTAG
66 TAGTTTGTTTAAGAAAAACAATCGCAAGTGAGATAAATGGATATTTCAAGTGAAACTTTCTCTAG
1746259 AGAGAAATAGTTTGT
131 AGAGAAATAGTTTGT
1746274 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAATTGAAACTTTCTCTAGAGAGAAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAATTGAAACTTTCTCTAGAGAGAAA
*
1746339 TAGTTTGTTTAAGAAAAACAATCGCAAGTGAGATAAATGGATATTTCAAGTGAATCTTTCTCTAG
66 TAGTTTGTTTAAGAAAAACAATCGCAAGTGAGATAAATGGATATTTCAAGTGAAACTTTCTCTAG
1746404 AGAGAAATAGTTTGT
131 AGAGAAATAGTTTGT
* * *
1746419 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAATTGAAACTTTCTCAAGCGAGAAA
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAATTGAAACTTTCTCTAGAGAGAAA
* * * * *
1746484 CAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTTATTTCAATTGAAACTTTCTCTA
66 TAGTTTG-TTTAAGAAAAACAATCGCAAGTGAGATAAATGGATATTTCAAGTGAAACTTTCTCTA
* *
1746549 GGGAGAAACAGTTTGT
130 GAGAGAAATAGTTTGT
1746565 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTT
1746604 GAAAACATCT
Statistics
Matches: 311, Mismatches: 18, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
145 207 0.67
146 104 0.33
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (145 bp):
TTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAATTGAAACTTTCTCTAGAGAGAAA
TAGTTTGTTTAAGAAAAACAATCGCAAGTGAGATAAATGGATATTTCAAGTGAAACTTTCTCTAG
AGAGAAATAGTTTGT
Found at i:1746512 original size:36 final size:35
Alignment explanation
Indices: 1746188--1746590 Score: 175
Period size: 36 Copynumber: 11.1 Consensus size: 35
1746178 TTCCTCTAGA
*
1746188 GAGAAATAGTTTG-TTTAAGAAAAACAATCGCAAGT
1 GAGAAA-AGTTTGTTTTAAGAAAAACAATCTCAAGT
** * * ** ** * *
1746223 GAGATAAATGGATATTTCAAGTGAAACTTTCTCTAGA
1 GAGA-AAA-GTTTGTTTTAAGAAAAACAATCTCAAGT
1746260 GAGAAATAGTTTGTTTTAAGAAAAACAATCTCAAGT
1 GAGAAA-AGTTTGTTTTAAGAAAAACAATCTCAAGT
*** ** * *
1746296 GAGATAAA--TTGCTATTTCAATTGAAACTTTCTCTAGA
1 GAGA-AAAGTTTG-T-TTT-AAGAAAAACAATCTCAAGT
*
1746333 GAGAAATAGTTTG-TTTAAGAAAAACAATCGCAAGT
1 GAGAAA-AGTTTGTTTTAAGAAAAACAATCTCAAGT
** * * ** * ** * *
1746368 GAGATAAATGGATATTTCAAGTGAATCTTTCTCTAGA
1 GAGA-AAA-GTTTGTTTTAAGAAAAACAATCTCAAGT
1746405 GAGAAATAGTTTGTTTTAAGAAAAACAATCTCAAGT
1 GAGAAA-AGTTTGTTTTAAGAAAAACAATCTCAAGT
* * * *** ** *
1746441 GAGATAAATTGTTATTTCAATTGAAACTTTCTCAAGC
1 GAGA-AAAGT-TTGTTTTAAGAAAAACAATCTCAAGT
1746478 GAGAAACAGTTTGTTTTAAGAAAAACAATCTCAAGT
1 GAGAAA-AGTTTGTTTTAAGAAAAACAATCTCAAGT
* * * *** ** * *
1746514 GAGATAAATTGTTATTTCAATTGAAACTTTCTCTAGG
1 GAGA-AAAGT-TTGTTTTAAGAAAAACAATCTCAAGT
1746551 GAGAAACAGTTTGTTTTAAGAAAAACAATCTCAAGT
1 GAGAAA-AGTTTGTTTTAAGAAAAACAATCTCAAGT
1746587 GAGA
1 GAGA
1746591 TAAATTGCTA
Statistics
Matches: 250, Mismatches: 97, Indels: 41
0.64 0.25 0.11
Matches are distributed among these distances:
34 3 0.01
35 22 0.09
36 115 0.46
37 107 0.43
39 3 0.01
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.32
Consensus pattern (35 bp):
GAGAAAAGTTTGTTTTAAGAAAAACAATCTCAAGT
Found at i:1747341 original size:22 final size:22
Alignment explanation
Indices: 1747290--1747346 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
1747280 AATAAAGCCT
* *
1747290 TCATCTTCGAAAAGAGAATATA
1 TCATCTTTGAAGAGAGAATATA
*
1747312 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATATA
1747334 TCATCTTTGAAGA
1 TCATCTTTGAAGA
1747347 ATGTAGATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATATA
Found at i:1747900 original size:55 final size:55
Alignment explanation
Indices: 1747716--1748043 Score: 446
Period size: 55 Copynumber: 6.0 Consensus size: 55
1747706 ATCACTGGTT
* * *
1747716 CGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTATGCTCAGATGTT-
1 CGTAAAACATTTGACAACACATTTATCCTTTCCTGTGGCTTCTGCACAGATGTTC
* * * ** *
1747770 CATAAAACATTTGACAACACATTCA-CACTTTCCTGTGGATTCTGCTTAGATATT-
1 CGTAAAACATTTGACAACACATTTATC-CTTTCCTGTGGCTTCTGCACAGATGTTC
* * * * *
1747824 CATAAAACATTTGAAAACACATTTATCATTTTCTGTGGCTTCTGCACATATGTTC
1 CGTAAAACATTTGACAACACATTTATCCTTTCCTGTGGCTTCTGCACAGATGTTC
*
1747879 CGTAAAACATTTGACAACACATTTATCCTTTCCTGTGGCTTCTACACAGATGTTC
1 CGTAAAACATTTGACAACACATTTATCCTTTCCTGTGGCTTCTGCACAGATGTTC
1747934 CGTAAAACATTTGACAACACATTTATCCTTTCCTGTGGCTTCTGCACAGATGTTC
1 CGTAAAACATTTGACAACACATTTATCCTTTCCTGTGGCTTCTGCACAGATGTTC
* * * * *
1747989 CGTAAAACATTTGACAACACATTCATTCTTTCCTATGGCTTCTTCTCAGATGTTC
1 CGTAAAACATTTGACAACACATTTATCCTTTCCTGTGGCTTCTGCACAGATGTTC
1748044 TAAATCATTG
Statistics
Matches: 245, Mismatches: 26, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
53 1 0.00
54 90 0.37
55 154 0.63
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (55 bp):
CGTAAAACATTTGACAACACATTTATCCTTTCCTGTGGCTTCTGCACAGATGTTC
Found at i:1749036 original size:75 final size:75
Alignment explanation
Indices: 1748913--1749083 Score: 227
Period size: 75 Copynumber: 2.3 Consensus size: 75
1748903 ACATGATGAT
* * * *
1748913 ATGGGCCTTCAGCATGCCCCAATATTTGTTGATACAGACGTTCAAAATGCACCAACATTCCTGA-
1 ATGGGCTTTCAGCATGCCCCAATATTTGCTGATACAAACGTTCAAAATGCACCAACATTCC-AAT
1748977 TTATGATTAAA
65 TTATGATTAAA
* * ** *
1748988 ATGGGCTTTCAACATGCCCCAATATTTGCTGATATAAACGTTCAAAATGCGTCAATATTCCAATT
1 ATGGGCTTTCAGCATGCCCCAATATTTGCTGATACAAACGTTCAAAATGCACCAACATTCCAATT
* *
1749053 TCTGATTGAA
66 TATGATTAAA
1749063 ATGGGCTTTCAGCATGCCCCA
1 ATGGGCTTTCAGCATGCCCCA
1749084 CATGGATCTG
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
74 1 0.01
75 82 0.99
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (75 bp):
ATGGGCTTTCAGCATGCCCCAATATTTGCTGATACAAACGTTCAAAATGCACCAACATTCCAATT
TATGATTAAA
Found at i:1749316 original size:77 final size:76
Alignment explanation
Indices: 1749167--1749341 Score: 206
Period size: 77 Copynumber: 2.2 Consensus size: 76
1749157 TTGCTTCTTG
* * * * * * *
1749167 CTGAGATGAGCCTCCAAGAATGCCCAAATATTCATATTGCTGTGAGACTTCAAAATACCCTACAT
1 CTGA-ATGAGCCTTCAA-AATACCCAAATATTCAAACTGATGTGACACTTCAAAATACCCCACAT
1749232 GGATCATTTCTAT
64 GGATCATTTCTAT
* *
1749245 CTGGAATGAGCCTTCAAAATACCCAAATATTCAAACTGATGTGACCCTTCAAAATGCCCCACATG
1 CT-GAATGAGCCTTCAAAATACCCAAATATTCAAACTGATGTGACACTTCAAAATACCCCACATG
* *
1749310 GATCATTTTTGT
65 GATCATTTCTAT
*
1749322 CTGAATTGGGCCTTCAAAAT
1 CTGAA-TGAGCCTTCAAAAT
1749342 GCCTCAACAT
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
76 3 0.04
77 65 0.78
78 13 0.16
79 2 0.02
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (76 bp):
CTGAATGAGCCTTCAAAATACCCAAATATTCAAACTGATGTGACACTTCAAAATACCCCACATGG
ATCATTTCTAT
Found at i:1753465 original size:14 final size:14
Alignment explanation
Indices: 1753446--1753559 Score: 68
Period size: 14 Copynumber: 7.5 Consensus size: 14
1753436 AAATGTAATT
1753446 ATGCAAAAATGAAA
1 ATGCAAAAATGAAA
1753460 ATGCAAAAATGAAA
1 ATGCAAAAATGAAA
* *
1753474 ATGTAAATACAAACGTAAAA
1 ATG--CA-A-AAA--TGAAA
* *
1753494 ATGCAAAGATGCAA
1 ATGCAAAAATGAAA
* *
1753508 ATGCAATAATGAAT
1 ATGCAAAAATGAAA
1753522 ATGCAAAAAATGTAGAA
1 ATGC-AAAAATG-A-AA
*
1753539 ATACAAAAAT-AAGA
1 ATGCAAAAATGAA-A
1753553 ATGCAAA
1 ATGCAAA
1753560 TTGTGCAATA
Statistics
Matches: 76, Mismatches: 14, Indels: 20
0.69 0.13 0.18
Matches are distributed among these distances:
13 1 0.01
14 42 0.55
15 6 0.08
16 10 0.13
17 6 0.08
18 4 0.05
20 7 0.09
ACGTcount: A:0.60, C:0.09, G:0.14, T:0.18
Consensus pattern (14 bp):
ATGCAAAAATGAAA
Found at i:1753476 original size:20 final size:20
Alignment explanation
Indices: 1753451--1753530 Score: 56
Period size: 20 Copynumber: 3.9 Consensus size: 20
1753441 TAATTATGCA
1753451 AAAATGAAAATGCAAAAATG
1 AAAATGAAAATGCAAAAATG
* * ** *
1753471 AAAATGTAAATACAAACGTA
1 AAAATGAAAATGCAAAAATG
1753491 AAAATGCAAAGATGC--AAATG
1 AAAATG-AAA-ATGCAAAAATG
*
1753511 CAATAATGAATATGCAAAAA
1 -AA-AATGAAAATGCAAAAA
1753531 ATGTAGAAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 10
0.67 0.17 0.16
Matches are distributed among these distances:
20 27 0.63
21 6 0.14
22 10 0.23
ACGTcount: A:0.60, C:0.09, G:0.14, T:0.17
Consensus pattern (20 bp):
AAAATGAAAATGCAAAAATG
Found at i:1754251 original size:36 final size:36
Alignment explanation
Indices: 1754204--1754275 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
1754194 TCTTATCGTA
* *
1754204 GAATACTTTTGGTATCAATCTAACATGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
1754240 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
1754276 TGCATAGCTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.40
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
Found at i:1755799 original size:22 final size:22
Alignment explanation
Indices: 1755772--1755831 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
1755762 TTTCTGGGCT
1755772 AGGGGAATCGGTACCCATTCAA
1 AGGGGAATCGGTACCCATTCAA
* *
1755794 GGGGGAATCGGTACTCATTCAA
1 AGGGGAATCGGTACCCATTCAA
* *
1755816 AGGGTAATCGATACCC
1 AGGGGAATCGGTACCC
1755832 CCTCAACCGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (22 bp):
AGGGGAATCGGTACCCATTCAA
Found at i:1757242 original size:106 final size:106
Alignment explanation
Indices: 1757047--1757472 Score: 762
Period size: 106 Copynumber: 4.0 Consensus size: 106
1757037 TCAAGAGATA
* * *
1757047 TAAGTTAAGGGATATCTGTGAATTACATGAAAATATGCTATGTGTAAGTGAATTACGTGATTATA
1 TAAGCTAAGGGATATATGTGAATTACATGAAAATGTGCTATGTGTAAGTGAATTACGTGATTATA
1757112 TGAATATGAAATCATATGAGAATTGACATGAACTACGTGAT
66 TGAATATGAAATCATATGAGAATTGACATGAACTACGTGAT
* *
1757153 TAAACTAAGGGATATCTGTGAATTACATGAAAATGTGCTATGTGTAAGTGAATTACGTGATTATA
1 TAAGCTAAGGGATATATGTGAATTACATGAAAATGTGCTATGTGTAAGTGAATTACGTGATTATA
*
1757218 TGAATATGAAATCATATGACAATTGACATGAACTACGTGAT
66 TGAATATGAAATCATATGAGAATTGACATGAACTACGTGAT
*
1757259 TAAGCTAAGGGATATATGTGAATTACATGAAAATGTGATATGTGTAAGTGAATTACGTGATTATA
1 TAAGCTAAGGGATATATGTGAATTACATGAAAATGTGCTATGTGTAAGTGAATTACGTGATTATA
1757324 TGAATATGAAATCATATGAGAATTGACATGAACTACGTGAT
66 TGAATATGAAATCATATGAGAATTGACATGAACTACGTGAT
* *
1757365 TAAGCTAAGGGATATATATGAATTACATAAAAATGTGCTATGTGTAAGTGAATTACGTGATTATA
1 TAAGCTAAGGGATATATGTGAATTACATGAAAATGTGCTATGTGTAAGTGAATTACGTGATTATA
*
1757430 TGAATATGAAATCATATGAGAATTGATATGAACTACGTGAT
66 TGAATATGAAATCATATGAGAATTGACATGAACTACGTGAT
1757471 TA
1 TA
1757473 CATGTATGTG
Statistics
Matches: 308, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 308 1.00
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (106 bp):
TAAGCTAAGGGATATATGTGAATTACATGAAAATGTGCTATGTGTAAGTGAATTACGTGATTATA
TGAATATGAAATCATATGAGAATTGACATGAACTACGTGAT
Found at i:1757385 original size:53 final size:53
Alignment explanation
Indices: 1757115--1757386 Score: 166
Period size: 53 Copynumber: 5.1 Consensus size: 53
1757105 GATTATATGA
* *
1757115 ATATGAAATCATATGAGAATTGACATGAACTACGTGATTAAACTAAGGGATAT
1 ATATGAAATCATATGAAAATTGACATGAACTACGTGATTAAGCTAAGGGATAT
* * * * ** * * * **
1757168 CTGTG-AATTACATGAAAATGTG-CTATG-TGTAAGTGAATTACG-TGA-TTATAT
1 ATATGAAATCATATGAAAAT-TGAC-ATGAACTACGTG-ATTAAGCTAAGGGATAT
*
1757219 GAATATGAAATCATATGACAATTGACATGAACTACGTGATTAAGCTAAGGGATAT
1 --ATATGAAATCATATGAAAATTGACATGAACTACGTGATTAAGCTAAGGGATAT
* * * * ** * * * **
1757274 ATGTG-AATTACATGAAAATGTGATATG-TGTAAGTGAATTACG-TGA-TTATAT
1 ATATGAAATCATATGAAAAT-TGACATGAACTACGTG-ATTAAGCTAAGGGATAT
*
1757325 GAATATGAAATCATATGAGAATTGACATGAACTACGTGATTAAGCTAAGGGATAT
1 --ATATGAAATCATATGAAAATTGACATGAACTACGTGATTAAGCTAAGGGATAT
1757380 ATATGAA
1 ATATGAA
1757387 TTACATAAAA
Statistics
Matches: 152, Mismatches: 49, Indels: 36
0.64 0.21 0.15
Matches are distributed among these distances:
51 8 0.05
52 37 0.24
53 62 0.41
54 37 0.24
55 8 0.05
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (53 bp):
ATATGAAATCATATGAAAATTGACATGAACTACGTGATTAAGCTAAGGGATAT
Found at i:1757437 original size:53 final size:53
Alignment explanation
Indices: 1757171--1757439 Score: 148
Period size: 53 Copynumber: 5.1 Consensus size: 53
1757161 GGGATATCTG
*
1757171 TGAATTACATGAAAATGTGCTATGTGTAAGTGAATTACGTGATTATATGAATA
1 TGAATTACATAAAAATGTGCTATGTGTAAGTGAATTACGTGATTATATGAATA
* * ** * * * ** *
1757224 TGAAAT-CATATGACAAT-TGAC-ATGAACTACGTG-ATTAAGCTAAGGGATAT--ATG
1 TGAATTACATA--AAAATGTG-CTATG-TGTAAGTGAATTACG-TGA-TTATATGAATA
* *
1757277 TGAATTACATGAAAATGTGATATGTGTAAGTGAATTACGTGATTATATGAATA
1 TGAATTACATAAAAATGTGCTATGTGTAAGTGAATTACGTGATTATATGAATA
* * ** * * * **
1757330 TGAAAT-CATATGAGAAT-TGAC-ATGAACTACGTG-ATTAAGCTAAGGGATAT--ATA
1 TGAATTACATA--AAAATGTG-CTATG-TGTAAGTGAATTACG-TGA-TTATATGAATA
1757383 TGAATTACATAAAAATGTGCTATGTGTAAGTGAATTACGTGATTATATGAATA
1 TGAATTACATAAAAATGTGCTATGTGTAAGTGAATTACGTGATTATATGAATA
1757436 TGAA
1 TGAA
1757440 ATCATATGAG
Statistics
Matches: 149, Mismatches: 43, Indels: 48
0.62 0.18 0.20
Matches are distributed among these distances:
51 8 0.05
52 29 0.19
53 74 0.50
54 30 0.20
55 8 0.05
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (53 bp):
TGAATTACATAAAAATGTGCTATGTGTAAGTGAATTACGTGATTATATGAATA
Found at i:1757801 original size:105 final size:104
Alignment explanation
Indices: 1757613--1757835 Score: 250
Period size: 105 Copynumber: 2.1 Consensus size: 104
1757603 GAGTCGAGGG
*
1757613 TCTACGCGGTCCTTCGGAACATATAGGTATCATATGGAACATCTATGAGGTCCTTTGAGACACGT
1 TCTACGTGGTCCTTCGGAACATATAGGTATCATATGGAACATCTATGAGGTCCTTTGAGACACGT
** * * *
1757678 ATTTGGTCTTTAGCATATGTATATGATTCTTGAGGAATTT
66 ACGTGATCCTTAGCATATGTATATGATTCTTAAGGAA-TT
* * * * * * * *
1757718 TCTACGTGGTCCTTCGGGACGTATATGTATTC-TTTGGAGCATGTATGAGGTCTTTTGAGACACT
1 TCTACGTGGTCCTTCGGAACATATAGGTA-TCATATGGAACATCTATGAGGTCCTTTGAGACACG
* * *
1757782 TACGTGATCCTTGGTATATGTATATGGTTCTTAAGGAATT
65 TACGTGATCCTTAGCATATGTATATGATTCTTAAGGAATT
* *
1757822 TATATGTGGTCCTT
1 TCTACGTGGTCCTT
1757836 ATAGACAATC
Statistics
Matches: 98, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
104 14 0.14
105 82 0.84
106 2 0.02
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (104 bp):
TCTACGTGGTCCTTCGGAACATATAGGTATCATATGGAACATCTATGAGGTCCTTTGAGACACGT
ACGTGATCCTTAGCATATGTATATGATTCTTAAGGAATT
Found at i:1757897 original size:23 final size:24
Alignment explanation
Indices: 1757852--1757897 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1757842 AATCTTATAT
*
1757852 GGCACTACGGTGCAAATTCTACGC
1 GGCACTACGGTGCAAATTATACGC
*
1757876 GGCACTTCGGTGC-AATTATACG
1 GGCACTACGGTGCAAATTATACG
1757898 AGCTATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (24 bp):
GGCACTACGGTGCAAATTATACGC
Found at i:1759556 original size:24 final size:25
Alignment explanation
Indices: 1759512--1759559 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1759502 ATAATTATTG
1759512 AATATAAAAAGACTAAATTAAAATA
1 AATATAAAAAGACTAAATTAAAATA
*
1759537 AATA-AAAAATAC-AAAGTTAAAAT
1 AATATAAAAAGACTAAA-TTAAAAT
1759560 TAAAGCATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 14 0.67
25 4 0.19
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (25 bp):
AATATAAAAAGACTAAATTAAAATA
Found at i:1765929 original size:19 final size:20
Alignment explanation
Indices: 1765886--1765937 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
1765876 ATTATAATTT
*
1765886 ATATTATTTTTATTTTTAGA
1 ATATTATTTTTAGTTTTAGA
1765906 A-ATTATCTTTT-GTTTT-GA
1 ATATTAT-TTTTAGTTTTAGA
1765924 ATATTAATTTTTAG
1 ATATT-ATTTTTAG
1765938 GGTTTTTGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
18 3 0.11
19 16 0.59
20 8 0.30
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.62
Consensus pattern (20 bp):
ATATTATTTTTAGTTTTAGA
Found at i:1767562 original size:23 final size:23
Alignment explanation
Indices: 1767535--1767579 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1767525 CCTTAGTCTC
1767535 TGTGAGATCGACCCTTACTTCTA
1 TGTGAGATCGACCCTTACTTCTA
1767558 TGTGAGATCGACCCTTACTTCT
1 TGTGAGATCGACCCTTACTTCT
1767580 CTTTTACTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (23 bp):
TGTGAGATCGACCCTTACTTCTA
Found at i:1767695 original size:31 final size:31
Alignment explanation
Indices: 1767657--1767715 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1767647 ACGCTCGTCA
*
1767657 AGTTCCTAGTGAGAATGACATATTGAATGGG
1 AGTTCCTAGTGAAAATGACATATTGAATGGG
*
1767688 AGTTCCTAGTGAAAATGACATGTTGAAT
1 AGTTCCTAGTGAAAATGACATATTGAAT
1767716 TCTCCGAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (31 bp):
AGTTCCTAGTGAAAATGACATATTGAATGGG
Found at i:1778452 original size:24 final size:24
Alignment explanation
Indices: 1778416--1778462 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1778406 CTTGTTGGTT
* *
1778416 ATCATGAAAATCATCGTACACATC
1 ATCAAGAAAATCACCGTACACATC
* *
1778440 ATCAAGAACATCACCGTGCACAT
1 ATCAAGAAAATCACCGTACACAT
1778463 TATCCTGAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.40, C:0.28, G:0.11, T:0.21
Consensus pattern (24 bp):
ATCAAGAAAATCACCGTACACATC
Found at i:1786447 original size:7 final size:7
Alignment explanation
Indices: 1786435--1786464 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1786425 GGTCAAAGGA
1786435 GGTCAAC
1 GGTCAAC
1786442 GGTCAAC
1 GGTCAAC
*
1786449 GGTCAAT
1 GGTCAAC
1786456 GGTCAAC
1 GGTCAAC
1786463 GG
1 GG
1786465 GTCGGGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.27, C:0.23, G:0.33, T:0.17
Consensus pattern (7 bp):
GGTCAAC
Found at i:1795978 original size:260 final size:263
Alignment explanation
Indices: 1795496--1795992 Score: 643
Period size: 260 Copynumber: 1.9 Consensus size: 263
1795486 AGAGAGCAAA
* * * *
1795496 TTCTTTGTCCACCATTGTGTCCTTGAGTTTGCCTTATCCTTGATAAAATCGAAGACTTCGGTCTT
1 TTCTTTGTCCACCATTGTATCCTCGAGTTTGCCTTATCCTTGACAAAATCAAAGACTTCGGTCTT
1795561 GTTTCTACCAACCGTAAGTGGCAAACCAAGATAGGATCTCGATTCTTCCTGTTCATGCACTCTAA
66 GTTTCTACCAACC------GGC-AA-CAAGATAGGATCTCGATTCTTCCTGTTCATGCACTCTAA
* *
1795626 TAATGCCAAAGATTTCTCTTATGTGCTCCCTGTTGGTGTTATGACTGAAGTAAATATGGACTTGT
123 TAATGCCAAAGATTTCTCTTATGTGCTCCCTATCGGTGTTATGACTGAAGTAAATATGGACTTGT
1795691 CAAAAATAATCTTTTGTCCCAAAGAGTTTTCATACAGAGTCATATCTCTTCAAGGCGTCTAACTT
188 CAAAAATAATCTTTTGTCCCAAAGAGTTTTCATACAGAGTCATATCTCTTCAAGGCGTCTAACTT
1795756 CATTAGGGGAG
253 CATTAGGGGAG
* *
1795767 TTCTTTGTCCACCTTTGTATCCTCGAGTTTGCCTTATCCTTGGCAAAATCAAAGAC-TCTGGTCT
1 TTCTTTGTCCACCATTGTATCCTCGAGTTTGCCTTATCCTTGACAAAATCAAAGACTTC-GGTCT
* * *
1795831 TGTTTCTACCAACC-GC-A-AAGATTGGATC-CTGGTTCTTCCTGTTTATGCACTCTAATAATGC
65 TGTTTCTACCAACCGGCAACAAGATAGGATCTC-GATTCTTCCTGTTCATGCACTCTAATAATGC
** *
1795892 C-AAGAATTTCTCTT-TCGTGCTCTTTATCGGTGTT-TGGATTGAAGTAAATCATGGAC-TGTCA
129 CAAAG-ATTTCTCTTAT-GTGCTCCCTATCGGTGTTAT-GACTGAAGTAAAT-ATGGACTTGTCA
* * * *
1795953 AAATTAATCTTTTGTTCCGAAGAGTTTTCATACATAGTCA
190 AAAATAATCTTTTGTCCCAAAGAGTTTTCATACAGAGTCA
1795993 AAATTTCTTT
Statistics
Matches: 202, Mismatches: 18, Indels: 23
0.83 0.07 0.09
Matches are distributed among these distances:
259 6 0.03
260 116 0.57
261 6 0.03
262 1 0.00
264 2 0.01
270 2 0.01
271 69 0.34
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (263 bp):
TTCTTTGTCCACCATTGTATCCTCGAGTTTGCCTTATCCTTGACAAAATCAAAGACTTCGGTCTT
GTTTCTACCAACCGGCAACAAGATAGGATCTCGATTCTTCCTGTTCATGCACTCTAATAATGCCA
AAGATTTCTCTTATGTGCTCCCTATCGGTGTTATGACTGAAGTAAATATGGACTTGTCAAAAATA
ATCTTTTGTCCCAAAGAGTTTTCATACAGAGTCATATCTCTTCAAGGCGTCTAACTTCATTAGGG
GAG
Found at i:1798952 original size:17 final size:17
Alignment explanation
Indices: 1798930--1798964 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1798920 TGAAGCTTGC
*
1798930 AATGGCTTTCTGTTATA
1 AATGGCCTTCTGTTATA
1798947 AATGGCCTTCTGTTATA
1 AATGGCCTTCTGTTATA
1798964 A
1 A
1798965 GGCTTAACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (17 bp):
AATGGCCTTCTGTTATA
Found at i:1800966 original size:34 final size:34
Alignment explanation
Indices: 1800920--1800985 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
1800910 AGCAGCAAGT
*
1800920 ATGATCACTGGTGTCAAAGTTGGCGGCAATTGAA
1 ATGATCACTGGTGTCAAAGTTGGCGACAATTGAA
* * *
1800954 ATGATCATTGGTGTCTAAGTTGGTGACAATTG
1 ATGATCACTGGTGTCAAAGTTGGCGACAATTG
1800986 TAATTAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.32
Consensus pattern (34 bp):
ATGATCACTGGTGTCAAAGTTGGCGACAATTGAA
Found at i:1812363 original size:2 final size:2
Alignment explanation
Indices: 1812356--1812386 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1812346 AAGATTGAAG
1812356 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1812387 AAAAGAATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1815390 original size:17 final size:16
Alignment explanation
Indices: 1815368--1815463 Score: 72
Period size: 17 Copynumber: 5.8 Consensus size: 16
1815358 GATGAAGTTA
1815368 AAAATATATAATAAAAT
1 AAAATA-ATAATAAAAT
*
1815385 AAAATAAATAATTATAATT
1 AAAAT-AATAA-TA-AAAT
*
1815404 AAAA-AATAATAATAAA
1 AAAATAATAATAA-AAT
1815420 AAAATAATAATAAAA-
1 AAAATAATAATAAAAT
*
1815435 AAAGGAAAATAATAAAAT
1 AAA--ATAATAATAAAAT
*
1815453 AATA-AATAATA
1 AAAATAATAATA
1815464 GTAGTAAAGA
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
15 11 0.17
16 10 0.15
17 33 0.50
18 5 0.08
19 7 0.11
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (16 bp):
AAAATAATAATAAAAT
Found at i:1815416 original size:3 final size:3
Alignment explanation
Indices: 1815370--1815463 Score: 51
Period size: 3 Copynumber: 32.3 Consensus size: 3
1815360 TGAAGTTAAA
*
1815370 AAT ATAT AAT AA- AAT AA- AAT AAAT AAT TAT AATT AA- AA- AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT AA-T AAT AAT AAT AAT
* * *
1815414 AAT AA- AAA AAT AAT AAT AA- AAA AAGG AA- AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
1815456 AAAT AAT A
1 -AAT AAT A
1815464 GTAGTAAAGA
Statistics
Matches: 75, Mismatches: 4, Indels: 24
0.73 0.04 0.23
Matches are distributed among these distances:
2 16 0.21
3 45 0.60
4 14 0.19
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:1815425 original size:31 final size:29
Alignment explanation
Indices: 1815377--1815463 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 29
1815367 AAAAATATAT
*
1815377 AATAA-AATAAAATAAATAATTATAATTAAAA
1 AATAATAATAAAA-AAATAATAATAA--AAAA
1815408 AATAATAATAAAAAAATAATAATAAAAAA
1 AATAATAATAAAAAAATAATAATAAAAAA
* *
1815437 AGGAAAATAATAAAATAATAAATAATA
1 A--ATAATAATAAAAAAAT-AATAATA
1815464 GTAGTAAAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
29 5 0.10
31 30 0.61
32 14 0.29
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (29 bp):
AATAATAATAAAAAAATAATAATAAAAAA
Found at i:1815437 original size:14 final size:14
Alignment explanation
Indices: 1815367--1815457 Score: 84
Period size: 14 Copynumber: 6.8 Consensus size: 14
1815357 AGATGAAGTT
1815367 AAAAAT-AT-ATAA
1 AAAAATAATAATAA
*
1815379 TAAAATAA-AAT-A
1 AAAAATAATAATAA
* * *
1815391 AATAATTATAATTA
1 AAAAATAATAATAA
1815405 AAAAATAATAATAA
1 AAAAATAATAATAA
1815419 AAAAATAATAATAA
1 AAAAATAATAATAA
*
1815433 AAAAAGGAA-AATAA
1 AAAAA-TAATAATAA
*
1815447 TAAAATAATAA
1 AAAAATAATAA
1815458 ATAATAGTAG
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
12 11 0.17
13 8 0.13
14 42 0.67
15 2 0.03
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (14 bp):
AAAAATAATAATAA
Found at i:1815524 original size:18 final size:18
Alignment explanation
Indices: 1815503--1815545 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1815493 GTTGTTTTTA
*
1815503 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
**
1815521 AAATAAAAGAAAATTATT
1 AAATAAAAGAAAAGAATT
1815539 AAATAAA
1 AAATAAA
1815546 TAATTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1815909 original size:9 final size:9
Alignment explanation
Indices: 1815883--1815950 Score: 61
Period size: 9 Copynumber: 7.6 Consensus size: 9
1815873 ACCCCGATTA
*
1815883 TATATATATA
1 TATATAT-TT
1815893 TATAATATTT
1 TAT-ATATTT
1815903 TATATATTT
1 TATATATTT
*
1815912 TATAT-TAAT
1 TATATAT-TT
*
1815921 TATATA-TA
1 TATATATTT
1815929 TA-ATATTT
1 TATATATTT
1815937 TATATATTT
1 TATATATTT
1815946 TATAT
1 TATAT
1815951 TAATTATATA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
7 3 0.06
8 6 0.12
9 28 0.58
10 7 0.15
11 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATATATTT
Found at i:1815926 original size:34 final size:34
Alignment explanation
Indices: 1815887--1815970 Score: 159
Period size: 34 Copynumber: 2.5 Consensus size: 34
1815877 CGATTATATA
1815887 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
1815921 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
*
1815955 TATATATAAAATATTT
1 TATATATATAATATTT
1815971 GTGGGTTCGG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:1815957 original size:18 final size:18
Alignment explanation
Indices: 1815902--1815961 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
1815892 ATATAATATT
1815902 TTATATATTTTATATTAA
1 TTATATATTTTATATTAA
* *
1815920 TTATATATATAATATT--
1 TTATATATTTTATATTAA
1815936 TTATATATTTTATATTAA
1 TTATATATTTTATATTAA
1815954 TTATATAT
1 TTATATAT
1815962 AAAATATTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.39
18 22 0.61
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATATTTTATATTAA
Found at i:1816666 original size:19 final size:19
Alignment explanation
Indices: 1816638--1816748 Score: 61
Period size: 19 Copynumber: 5.8 Consensus size: 19
1816628 AAATAATATT
*
1816638 CTAAATCCTAATTAAAATA
1 CTAAAACCTAATTAAAATA
* *
1816657 CTAAAACCTATTTAAACTA
1 CTAAAACCTAATTAAAATA
* *
1816676 --AAATACCTAA-AACAAAGA
1 CTAAA-ACCTAATTA-AAATA
** *
1816694 -TAAAATATAA-AAATAATA
1 CTAAAACCTAATTAA-AATA
*
1816712 TCCTAAAACTTAATTAAAATA
1 -C-TAAAACCTAATTAAAATA
1816733 CTAAAACCTAATTAAA
1 CTAAAACCTAATTAAA
1816749 TTAAAATACA
Statistics
Matches: 70, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
17 5 0.07
18 17 0.24
19 33 0.47
20 1 0.01
21 12 0.17
22 2 0.03
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.27
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:1816750 original size:24 final size:24
Alignment explanation
Indices: 1816647--1816757 Score: 84
Period size: 24 Copynumber: 4.5 Consensus size: 24
1816637 TCTAAATCCT
*
1816647 AATTAAAATACTAAAACCTATTTA
1 AATTAAAATACTAAAACCTAATTA
* ** *
1816671 AACTAAAATACCTAAAACAAAGATAA
1 AATTAAAATA-CTAAAACCTA-ATTA
*
1816697 AATATAAAA-A-TAATATCCTAAAACTT-
1 AAT-TAAAATACTAA-AACCT--AA-TTA
1816723 AATTAAAATACTAAAACCTAATTA
1 AATTAAAATACTAAAACCTAATTA
1816747 AATTAAAATAC
1 AATTAAAATAC
1816758 AAAGATAAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
23 2 0.03
24 25 0.38
25 15 0.23
26 14 0.21
27 10 0.15
ACGTcount: A:0.59, C:0.13, G:0.01, T:0.27
Consensus pattern (24 bp):
AATTAAAATACTAAAACCTAATTA
Found at i:1816781 original size:76 final size:75
Alignment explanation
Indices: 1816569--1816757 Score: 228
Period size: 76 Copynumber: 2.6 Consensus size: 75
1816559 TAAAACATCT
* * * * *
1816569 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCT-AAA-AATGAT---ATTTA
1 TAAAACCTAATTAAAATAC-TAAAACCTAATTAAACTAAAATACCTAAAACAAAGATAAAATATA
*
1816628 AAATAATATTC
65 AAATAATATCC
* *
1816639 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTAATTAAACTAAAATACCTAAAACAAAGATAAAATAT-A
1816704 AAATAATATCC
65 AAATAATATCC
* *
1816715 TAAAACTTAATTAAAATACTAAAACCTAATTAAATTAAAATAC
1 TAAAACCTAATTAAAATACTAAAACCTAATTAAACTAAAATAC
1816758 AAAGATAAAA
Statistics
Matches: 104, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
69 5 0.05
70 38 0.37
71 3 0.03
72 5 0.05
75 3 0.03
76 50 0.48
ACGTcount: A:0.56, C:0.13, G:0.01, T:0.30
Consensus pattern (75 bp):
TAAAACCTAATTAAAATACTAAAACCTAATTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AATAATATCC
Found at i:1817895 original size:30 final size:30
Alignment explanation
Indices: 1817861--1817921 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1817851 TTTAAACAGG
*
1817861 AAACATAGATCTATCGGCATCTTTAGTAGA
1 AAACATAGATCTATCGGCATCTTTAGCAGA
* *
1817891 AAACATGGATCTATCGGCGTCTTTAGCAGA
1 AAACATAGATCTATCGGCATCTTTAGCAGA
1817921 A
1 A
1817922 TTTGCATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (30 bp):
AAACATAGATCTATCGGCATCTTTAGCAGA
Found at i:1818256 original size:81 final size:82
Alignment explanation
Indices: 1818155--1818338 Score: 228
Period size: 84 Copynumber: 2.2 Consensus size: 82
1818145 AAAATAGCAC
* * *
1818155 AAAATAAAAAAAAGTAAAAGAAAAGGTAATAATGCATGTGATAATGGAC-A-ATCCATCTAAAAC
1 AAAATAAACAAAAGCAAAAGAAAAGGTAATAATGCATGTGATAATGGACAATATCCATCAAAAAC
1818218 AGAACACAAAACAACAT
66 AGAACACAAAACAACAT
* *
1818235 AAAATAAACCAAAAGCAAAAGAAAGGGTAATAATGCATGTGATAATGGGCAATTATCCATCAAAA
1 AAAATAAA-CAAAAGCAAAAGAAAAGGTAATAATGCATGTGATAATGGACAA-TATCCATCAAAA
* * * *
1818300 ACAGCACACCAAATAGCAT
64 ACAGAACACAAAACAACAT
* *
1818319 AAAACAAAGCAAAAACAAAA
1 AAAATAAA-CAAAAGCAAAA
1818339 ACAAAAATAC
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
80 8 0.09
81 37 0.42
82 1 0.01
84 42 0.48
ACGTcount: A:0.58, C:0.15, G:0.13, T:0.15
Consensus pattern (82 bp):
AAAATAAACAAAAGCAAAAGAAAAGGTAATAATGCATGTGATAATGGACAATATCCATCAAAAAC
AGAACACAAAACAACAT
Found at i:1821589 original size:42 final size:42
Alignment explanation
Indices: 1821542--1821800 Score: 432
Period size: 42 Copynumber: 6.2 Consensus size: 42
1821532 GTACATATTT
* * *
1821542 AATAATAATTATTTAACTTTAATGATTTAATTTTAATGATTC
1 AATAATAATTACTTGACTTTAATGATTTAACTTTAATGATTC
1821584 AATAATAATTACTTGACTTTAATGATTTAACTTTAATGATTC
1 AATAATAATTACTTGACTTTAATGATTTAACTTTAATGATTC
*
1821626 AATAATAATTACTTGACTTTAATGATTTAATTTTAATGATTC
1 AATAATAATTACTTGACTTTAATGATTTAACTTTAATGATTC
1821668 AATAATAATTACTTGACTTTAATGATTTAACTTTAATGATTC
1 AATAATAATTACTTGACTTTAATGATTTAACTTTAATGATTC
1821710 AATAATAATTACTTGACTTTAATGATTTAACTTTAATGATTC
1 AATAATAATTACTTGACTTTAATGATTTAACTTTAATGATTC
* *
1821752 AATAATAATTAATTGACTTTAATGATTTGTA-TTTAATGATAT-
1 AATAATAATTACTTGACTTTAATGATTT-AACTTTAATGAT-TC
1821794 AATAATA
1 AATAATA
1821801 CTAAATATAT
Statistics
Matches: 208, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
42 206 0.99
43 2 0.01
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (42 bp):
AATAATAATTACTTGACTTTAATGATTTAACTTTAATGATTC
Found at i:1821749 original size:14 final size:14
Alignment explanation
Indices: 1821547--1821750 Score: 137
Period size: 14 Copynumber: 14.6 Consensus size: 14
1821537 TATTTAATAA
*
1821547 TAATTATTTAACTT
1 TAATGATTTAACTT
*
1821561 TAATGATTTAATTT
1 TAATGATTTAACTT
* *
1821575 TAATGATTCAA-TAA
1 TAATGATTTAACT-T
* * *
1821589 TAATTACTTGACTT
1 TAATGATTTAACTT
1821603 TAATGATTTAACTT
1 TAATGATTTAACTT
* *
1821617 TAATGATTCAA-TAA
1 TAATGATTTAACT-T
* * *
1821631 TAATTACTTGACTT
1 TAATGATTTAACTT
*
1821645 TAATGATTTAATTT
1 TAATGATTTAACTT
* *
1821659 TAATGATTCAA-TAA
1 TAATGATTTAACT-T
* * *
1821673 TAATTACTTGACTT
1 TAATGATTTAACTT
1821687 TAATGATTTAACTT
1 TAATGATTTAACTT
* *
1821701 TAATGATTCAA-TAA
1 TAATGATTTAACT-T
* * *
1821715 TAATTACTTGACTT
1 TAATGATTTAACTT
1821729 TAATGATTTAACTT
1 TAATGATTTAACTT
1821743 TAATGATT
1 TAATGATT
1821751 CAATAATAAT
Statistics
Matches: 139, Mismatches: 43, Indels: 16
0.70 0.22 0.08
Matches are distributed among these distances:
13 4 0.03
14 131 0.94
15 4 0.03
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.48
Consensus pattern (14 bp):
TAATGATTTAACTT
Found at i:1824443 original size:31 final size:32
Alignment explanation
Indices: 1824405--1824489 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
1824395 TGCATTATTA
1824405 TGAAGAAGACGCCGA-TACATCC-CCTCCCAA-C
1 TGAAGAAGACGCCGAGTA-ATCCACC-CCCAATC
* * *
1824436 TGAAGAAGACGTCGAGTATTCCACCCCCAATG
1 TGAAGAAGACGCCGAGTAATCCACCCCCAATC
*
1824468 TGAAGAAGACGCCGAGAAATCC
1 TGAAGAAGACGCCGAGTAATCC
1824490 TCTACTTAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
31 22 0.49
32 23 0.51
ACGTcount: A:0.34, C:0.31, G:0.21, T:0.14
Consensus pattern (32 bp):
TGAAGAAGACGCCGAGTAATCCACCCCCAATC
Found at i:1824586 original size:19 final size:20
Alignment explanation
Indices: 1824542--1824586 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1824532 CCCATACATC
1824542 TTTCTCTGCTCACCCCGTGAA
1 TTTC-CTGCTCACCCCGTGAA
*
1824563 TTTCCTGCTCACCTCGTG-A
1 TTTCCTGCTCACCCCGTGAA
1824582 TTTCC
1 TTTCC
1824587 CACGTCCAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 13 0.57
21 4 0.17
ACGTcount: A:0.11, C:0.38, G:0.13, T:0.38
Consensus pattern (20 bp):
TTTCCTGCTCACCCCGTGAA
Found at i:1824781 original size:40 final size:39
Alignment explanation
Indices: 1824705--1824805 Score: 130
Period size: 40 Copynumber: 2.6 Consensus size: 39
1824695 GACCTCCATG
* * * * *
1824705 AATTGTATTAAAGATGCCGAGGCCTCATGTTCGAATGGA
1 AATTGTGTTAAAGACGCCTAGACCTCATGTTCGAATGCA
* *
1824744 AGTTGTGTTAAAGACGCCTAGACCTCCATGTTTGAATGCA
1 AATTGTGTTAAAGACGCCTAGACCT-CATGTTCGAATGCA
1824784 AATTGTGTTAAAGACGCCTAGA
1 AATTGTGTTAAAGACGCCTAGA
1824806 GCACCATTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 20 0.38
40 33 0.62
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (39 bp):
AATTGTGTTAAAGACGCCTAGACCTCATGTTCGAATGCA
Found at i:1825499 original size:38 final size:38
Alignment explanation
Indices: 1825444--1825517 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
1825434 ATAAACAACG
* *
1825444 TTTGGACGGTTGAGATTTTG-TTAGTGCAAAAGTGTAAA
1 TTTGGACGGCTGAGA-TTTGATTACTGCAAAAGTGTAAA
* *
1825482 TTTGGACGGCTGTGATTTGATTTCTGCAAAAGTGTA
1 TTTGGACGGCTGAGATTTGATTACTGCAAAAGTGTA
1825518 GCTTCGCTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 4 0.13
38 27 0.87
ACGTcount: A:0.26, C:0.08, G:0.28, T:0.38
Consensus pattern (38 bp):
TTTGGACGGCTGAGATTTGATTACTGCAAAAGTGTAAA
Found at i:1837392 original size:22 final size:21
Alignment explanation
Indices: 1837356--1837396 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1837346 CATCTCCATT
1837356 TCATCATCAACACCATCAACA
1 TCATCATCAACACCATCAACA
*
1837377 TCATCCATCAAGACCATCAA
1 TCAT-CATCAACACCATCAA
1837397 TTCTGCAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.41, C:0.37, G:0.02, T:0.20
Consensus pattern (21 bp):
TCATCATCAACACCATCAACA
Found at i:1855797 original size:13 final size:13
Alignment explanation
Indices: 1855779--1855827 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 13
1855769 CTTAGCATGT
1855779 TTAAAAATAAAAC
1 TTAAAAATAAAAC
1855792 TT-AAAATAAAA-
1 TTAAAAATAAAAC
1855803 -TAAAAATGAAAAC
1 TTAAAAAT-AAAAC
* *
1855816 TTGAAAAGAAAA
1 TTAAAAATAAAA
1855828 GAAAAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 1 0.03
11 5 0.17
12 13 0.43
13 6 0.20
14 5 0.17
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.20
Consensus pattern (13 bp):
TTAAAAATAAAAC
Found at i:1855814 original size:24 final size:24
Alignment explanation
Indices: 1855780--1855832 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
1855770 TTAGCATGTT
*
1855780 TAAAAATAAAACTT-AAAATAAAA
1 TAAAAATAAAACTTGAAAAGAAAA
1855803 TAAAAATGAAAACTTGAAAAGAAAA
1 TAAAAAT-AAAACTTGAAAAGAAAA
*
1855828 GAAAA
1 TAAAA
1855833 GAAAAGAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 7 0.27
24 7 0.27
25 12 0.46
ACGTcount: A:0.72, C:0.04, G:0.08, T:0.17
Consensus pattern (24 bp):
TAAAAATAAAACTTGAAAAGAAAA
Found at i:1857017 original size:21 final size:21
Alignment explanation
Indices: 1856991--1857041 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1856981 ACTTGATACA
1856991 TTGAGCCTATTATTGTGAACT
1 TTGAGCCTATTATTGTGAACT
*
1857012 TTGAGCCTATTCTTGTGAACT
1 TTGAGCCTATTATTGTGAACT
1857033 TTGAGCCTA
1 TTGAGCCTA
1857042 ATGATCATTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (21 bp):
TTGAGCCTATTATTGTGAACT
Found at i:1859635 original size:17 final size:18
Alignment explanation
Indices: 1859602--1859637 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1859592 AATTCCAAGA
1859602 AAATATATTAATTTTTAT
1 AAATATATTAATTTTTAT
*
1859620 AAATATA-TATTTTTTAT
1 AAATATATTAATTTTTAT
1859637 A
1 A
1859638 TTTTTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATATTAATTTTTAT
Found at i:1859927 original size:2 final size:2
Alignment explanation
Indices: 1859920--1859951 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1859910 AAAAATGAAG
1859920 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1859952 AATGAGATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1861418 original size:122 final size:123
Alignment explanation
Indices: 1861154--1861606 Score: 696
Period size: 123 Copynumber: 3.7 Consensus size: 123
1861144 TTAAGGAAAT
* *
1861154 GTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAT
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
1861219 C-TCTTTCTGGAAATGTTGATGTTGATCTATCTCTTTCTGTGATAGAATC-ATTCAAAAG
66 CTTC-CTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGA-TCAAAAG
1861277 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * * * *
1861342 C-ACTTCTGGAAATTTTGATGCTGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAAG
66 CTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGATCAAAAG
* * *
1861399 GTTGAACAAGTTCATCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATAAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
1861464 CTTCCTCTAGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAGTTGATCAAAAG
66 CTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGATCAAAAG
*
1861522 GTTGAACAAGTTCTTCTCATTATGAACTTCATCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
*
1861587 CTTCCTCTGGAAATATTGAT
66 CTTCCTCTGGAAATGTTGAT
1861607 CCATCGAGTG
Statistics
Matches: 301, Mismatches: 27, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
122 109 0.36
123 192 0.64
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.40
Consensus pattern (123 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAA
CTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCGATCAAAAG
Found at i:1861584 original size:245 final size:246
Alignment explanation
Indices: 1861154--1861606 Score: 723
Period size: 245 Copynumber: 1.8 Consensus size: 246
1861144 TTAAGGAAAT
* * *
1861154 GTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAT
1 GTTGAACAAGTTCATCTCATTATGAACTTCCTCTTCCTCTTCAGATGAGTTCTTCTCATTATAAA
* * * *
1861219 CTCTTTCTGGAAATGTTGATGTTGATCTATCTCTTTCTGTGATAGAATCATTCAAAAGGTTGAAC
66 CTCTCTCTAGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCATTCAAAAGGTTGAAC
* *
1861284 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAAC-ACTTC
131 AAGTTCTTCTCATTATGAACTTCATCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTACCTC
*
1861348 TGGAAATTTTGATGCTGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAAG
196 TGGAAATATTGATGCTGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAAG
* *
1861399 GTTGAACAAGTTCATCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTATAAA
1 GTTGAACAAGTTCATCTCATTATGAACTTCCTCTTCCTCTTCAGATGAGTTCTTCTCATTATAAA
* * *
1861464 CT-TCCTCTAGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAGTTGA-TCAAAAGGTTGA
66 CTCT-CTCTAGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGA-ATCATTCAAAAGGTTGA
*
1861527 ACAAGTTCTTCTCATTATGAACTTCATCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTCC
129 ACAAGTTCTTCTCATTATGAACTTCATCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTACC
1861592 TCTGGAAATATTGAT
194 TCTGGAAATATTGAT
1861607 CCATCGAGTG
Statistics
Matches: 189, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
244 1 0.01
245 171 0.90
246 17 0.09
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.40
Consensus pattern (246 bp):
GTTGAACAAGTTCATCTCATTATGAACTTCCTCTTCCTCTTCAGATGAGTTCTTCTCATTATAAA
CTCTCTCTAGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCATTCAAAAGGTTGAAC
AAGTTCTTCTCATTATGAACTTCATCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTACCTC
TGGAAATATTGATGCTGATCTATCTCCTTCTGTGATAGCGTCGAGCAAAAG
Found at i:1861685 original size:36 final size:36
Alignment explanation
Indices: 1861645--1861843 Score: 211
Period size: 36 Copynumber: 5.5 Consensus size: 36
1861635 AGTGAAACTG
* * *
1861645 TCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGATAAATGTTGTTTTAAGAAAAACAA
* * **
1861681 TCTCAAGTGAGATAAATTGTTGTTTTGAGTAAAACTG
1 TCTCAAGTGAGATAAA-TGTTGTTTTAAGAAAAACAA
* * *
1861718 TCTCAAGCGAGATAAATTTTGTTTTAAGAAAAATAA
1 TCTCAAGTGAGATAAATGTTGTTTTAAGAAAAACAA
** ** **
1861754 TCTCAAGTGAGATAAATTGTTGTTTCGAGTGAAACTG
1 TCTCAAGTGAGATAAA-TGTTGTTTTAAGAAAAACAA
*
1861791 TCTCAAGTGAGATGCAAT-TTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGAT-AAATGTTGTTTTAAGAAAAACAA
1861827 TCTCAAGTGAGATAAAT
1 TCTCAAGTGAGATAAAT
1861844 TTTTATTTGA
Statistics
Matches: 129, Mismatches: 31, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
35 3 0.02
36 68 0.53
37 56 0.43
38 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.33
Consensus pattern (36 bp):
TCTCAAGTGAGATAAATGTTGTTTTAAGAAAAACAA
Found at i:1861705 original size:73 final size:72
Alignment explanation
Indices: 1861628--1861844 Score: 353
Period size: 73 Copynumber: 3.0 Consensus size: 72
1861618 TGGAAATTTC
*
1861628 TGTTTCCAGTGAAACTGTCTCAAGCGAGATGAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGATGAAT-TTGTTTTAAGAAAAACAATCTCAAGTGAGA
1861693 TAAATTGT
65 TAAATTGT
* * * *
1861701 TGTTTTGAGTAAAACTGTCTCAAGCGAGATAAATTTTGTTTTAAGAAAAATAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGATGAA-TTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1861766 TAAATTGT
65 TAAATTGT
*
1861774 TGTTTCGAGTGAAACTGTCTCAAGTGAGATGCAATTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTGTCTCAAGCGAGATG-AATTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1861839 TAAATT
65 TAAATT
1861845 TTTATTTGAA
Statistics
Matches: 132, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
73 129 0.98
74 3 0.02
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (72 bp):
TGTTTCGAGTGAAACTGTCTCAAGCGAGATGAATTTGTTTTAAGAAAAACAATCTCAAGTGAGAT
AAATTGT
Found at i:1862607 original size:20 final size:22
Alignment explanation
Indices: 1862571--1862649 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
1862561 AATAAAGTTT
* *
1862571 TCATATTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
*
1862593 TCATCTTTGAAGAGAGAATTTA
1 TCATCTTTGAAGAGAGAATCTA
1862615 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
1862637 TCATCTTTGAAGA
1 TCATCTTTGAAGA
1862650 ATGTAGATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:1870266 original size:36 final size:36
Alignment explanation
Indices: 1870202--1870273 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
1870192 TCTTACCGTA
* *
1870202 GAATGCTTTTGGTATCAATCTAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
* *
1870238 GAATACTTTTGGTATTAATATAATAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
1870274 TGCATAGCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
Found at i:1871747 original size:23 final size:23
Alignment explanation
Indices: 1871694--1871748 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1871684 ATTCCAAGAA
1871694 AATATATTA-ATTTTTATAAATAT
1 AATAT-TTATATTTTTATAAATAT
* *
1871717 ATTTTTTATATTTTTATAAATA-
1 AATATTTATATTTTTATAAATAT
1871739 AGATATTTAT
1 A-ATATTTAT
1871749 TTACTTAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
AATATTTATATTTTTATAAATAT
Found at i:1871965 original size:16 final size:18
Alignment explanation
Indices: 1871944--1871977 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1871934 CATTTCTTTG
1871944 ATATTAA-AATAA-ATAA
1 ATATTAAGAATAATATAA
1871960 ATATTAAGAATAATATAA
1 ATATTAAGAATAATATAA
1871978 TAAATTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (18 bp):
ATATTAAGAATAATATAA
Found at i:1872015 original size:2 final size:2
Alignment explanation
Indices: 1872008--1872055 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1871998 TAAAATGAAG
1872008 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1872050 TT TA TA
1 TA TA TA
1872056 AATTATTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1877989 original size:41 final size:41
Alignment explanation
Indices: 1877933--1878015 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
1877923 TAATTTATGG
** *
1877933 TTTTTAGAAGGCTATAAATTCCCTCTTAGGGTAAGCCTAAT
1 TTTTTAGAAGGCTATAAACACCCCCTTAGGGTAAGCCTAAT
*
1877974 TTTTTATAAGGCTATAAACACCCCCTTAGGGTAAGCCTAAT
1 TTTTTAGAAGGCTATAAACACCCCCTTAGGGTAAGCCTAAT
1878015 T
1 T
1878016 CATTATTCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (41 bp):
TTTTTAGAAGGCTATAAACACCCCCTTAGGGTAAGCCTAAT
Found at i:1884428 original size:16 final size:15
Alignment explanation
Indices: 1884400--1884449 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
1884390 TTTAAAATTT
1884400 AAAATTAAAATATAAA
1 AAAATT-AAATATAAA
* *
1884416 TATATTCAAATATTAAA
1 AAAATT-AAATA-TAAA
1884433 AAAATTAAATATAAA
1 AAAATTAAATATAAA
1884448 AA
1 AA
1884450 TACGAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 6 0.21
16 14 0.50
17 8 0.29
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATTAAATATAAA
Found at i:1903151 original size:30 final size:30
Alignment explanation
Indices: 1903115--1903183 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 30
1903105 CCAAAGGACC
* *
1903115 TATGTAACTGTCCATATGTTTCGAAGAACA
1 TATGTAACTGTCCATATATTCCGAAGAACA
* * *
1903145 TATGTAAAATGTCTATATATTCCGTAGAACA
1 TATGT-AACTGTCCATATATTCCGAAGAACA
*
1903176 TAGGTAAC
1 TATGTAAC
1903184 CCTCGACTCT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (30 bp):
TATGTAACTGTCCATATATTCCGAAGAACA
Found at i:1906469 original size:19 final size:19
Alignment explanation
Indices: 1906445--1906484 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1906435 TTTCGTCACT
1906445 GCCTCTTTGATCTTTAATA
1 GCCTCTTTGATCTTTAATA
1906464 GCCTCTTTGATCTTTAATA
1 GCCTCTTTGATCTTTAATA
1906483 GC
1 GC
1906485 TTCTCTGGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (19 bp):
GCCTCTTTGATCTTTAATA
Found at i:1912533 original size:17 final size:17
Alignment explanation
Indices: 1912511--1912544 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1912501 GTGGATCTAT
1912511 TCTATCGAGTTATTTGA
1 TCTATCGAGTTATTTGA
*
1912528 TCTATCGGGTTATTTGA
1 TCTATCGAGTTATTTGA
1912545 AGATGCAAGG
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:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (17 bp):
TCTATCGAGTTATTTGA
Found at i:1912634 original size:10 final size:11
Alignment explanation
Indices: 1912617--1912643 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1912607 TAATGATATT
1912617 CTTTTTTTTTA
1 CTTTTTTTTTA
1912628 CTTTTTTTTTA
1 CTTTTTTTTTA
1912639 CTTTT
1 CTTTT
1912644 CTTATATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (11 bp):
CTTTTTTTTTA
Found at i:1912849 original size:2 final size:2
Alignment explanation
Indices: 1912833--1912911 Score: 128
Period size: 2 Copynumber: 41.0 Consensus size: 2
1912823 ATTTTTAGAA
*
1912833 AT AT -T AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1912874 AT -T AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1912912 GTAATGTATG
Statistics
Matches: 72, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
1 3 0.04
2 69 0.96
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1913353 original size:20 final size:20
Alignment explanation
Indices: 1913315--1913353 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1913305 TTTATGATAT
*
1913315 ATATTCATTCTTAATTTTTA
1 ATATTAATTCTTAATTTTTA
1913335 ATATTAATT-TTAATATTTT
1 ATATTAATTCTTAAT-TTTT
1913354 TAAAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
ATATTAATTCTTAATTTTTA
Found at i:1913424 original size:7 final size:7
Alignment explanation
Indices: 1913397--1913456 Score: 65
Period size: 7 Copynumber: 9.0 Consensus size: 7
1913387 TTCGTATTAT
*
1913397 ATTTTAA
1 ATTTAAA
*
1913404 ATATAAA
1 ATTTAAA
1913411 TATTTAAA
1 -ATTTAAA
1913419 ATTTAAA
1 ATTTAAA
1913426 ATTT-AA
1 ATTTAAA
1913432 ATTTAAA
1 ATTTAAA
1913439 A-TT-AA
1 ATTTAAA
1913444 A-TTAAA
1 ATTTAAA
1913450 ATTTAAA
1 ATTTAAA
1913457 TTTTTTATAT
Statistics
Matches: 46, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
5 5 0.11
6 11 0.24
7 24 0.52
8 6 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATTTAAA
Found at i:1913435 original size:6 final size:6
Alignment explanation
Indices: 1913412--1913459 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
1913402 AAATATAAAT
* *
1913412 ATTTAAA ATTTAAA ATTTAA ATTTAA AATTAA ATTAAA ATTTAA ATTT
1 ATTT-AA ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT
1913460 TTTATATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
6 26 0.70
7 11 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATTTAA
Found at i:1913445 original size:12 final size:13
Alignment explanation
Indices: 1913399--1913459 Score: 81
Period size: 13 Copynumber: 4.7 Consensus size: 13
1913389 CGTATTATAT
*
1913399 TTTAAATATAAATA
1 TTTAAATTTAAA-A
1913413 TTTAAAATTTAAAA
1 TTT-AAATTTAAAA
1913427 TTTAAATTTAAAA
1 TTTAAATTTAAAA
1913440 -TTAAA-TTAAAA
1 TTTAAATTTAAAA
1913451 TTTAAATTT
1 TTTAAATTT
1913460 TTTATATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
11 6 0.14
12 10 0.23
13 12 0.28
14 7 0.16
15 8 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TTTAAATTTAAAA
Found at i:1917399 original size:74 final size:74
Alignment explanation
Indices: 1917310--1917459 Score: 282
Period size: 74 Copynumber: 2.0 Consensus size: 74
1917300 ACATTGTCTC
*
1917310 GATATTTTAGAAATCATGATGCGGTCTTTAAAATGATGTCGACCTATTTTGGGAATCACCAGTAG
1 GATATTTTAGAAATCATGATGCGGTCTTTAAAATGATGTCAACCTATTTTGGGAATCACCAGTAG
1917375 TCACCCCTT
66 TCACCCCTT
*
1917384 GATATTTTAGAAATCATGATGTGGTCTTTAAAATGATGTCAACCTATTTTGGGAATCACCAGTAG
1 GATATTTTAGAAATCATGATGCGGTCTTTAAAATGATGTCAACCTATTTTGGGAATCACCAGTAG
1917449 TCACCCCTT
66 TCACCCCTT
1917458 GA
1 GA
1917460 GCATACTTGT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (74 bp):
GATATTTTAGAAATCATGATGCGGTCTTTAAAATGATGTCAACCTATTTTGGGAATCACCAGTAG
TCACCCCTT
Found at i:1917501 original size:62 final size:62
Alignment explanation
Indices: 1917430--1917554 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
1917420 TGTCAACCTA
**
1917430 TTTTGGGAATCACCAGTAGTCACCCCTTGAGCATACTTGTGGGAGATAGACTATCGACTCCC
1 TTTTGGGAATCACCAGTAGTCACCCCTTGAGCATACTTGCAGGAGATAGACTATCGACTCCC
1917492 TTTTGGGAATCACCAGTAGTCACCCCTTGAGCATACTTGCAGGAGATAGACTATCGACTCCC
1 TTTTGGGAATCACCAGTAGTCACCCCTTGAGCATACTTGCAGGAGATAGACTATCGACTCCC
1917554 T
1 T
1917555 AATAAGTGAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (62 bp):
TTTTGGGAATCACCAGTAGTCACCCCTTGAGCATACTTGCAGGAGATAGACTATCGACTCCC
Found at i:1919864 original size:17 final size:17
Alignment explanation
Indices: 1919842--1919875 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1919832 GTGGATCTAT
1919842 TCTATCGAGTTATTTGA
1 TCTATCGAGTTATTTGA
*
1919859 TCTATCGGGTTATTTGA
1 TCTATCGAGTTATTTGA
1919876 AGTGCAAGGT
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:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (17 bp):
TCTATCGAGTTATTTGA
Found at i:1920665 original size:21 final size:22
Alignment explanation
Indices: 1920639--1920686 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
1920629 TAAAATAAAT
1920639 ATTTTTTAGTAATTTA-ATTTA
1 ATTTTTTAGTAATTTATATTTA
*
1920660 ATTTTTTAGTATTTTATATTTA
1 ATTTTTTAGTAATTTATATTTA
1920682 ATTTT
1 ATTTT
1920687 AAATATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
ATTTTTTAGTAATTTATATTTA
Found at i:1920695 original size:20 final size:20
Alignment explanation
Indices: 1920650--1920696 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
1920640 TTTTTTAGTA
* *
1920650 ATTTAATTTAATTTTTTAGT
1 ATTTAATTTAATTTTTAAAT
1920670 ATTTTATATTTAA-TTTTAAAT
1 A-TTTA-ATTTAATTTTTAAAT
1920691 ATTTAA
1 ATTTAA
1920697 ATATTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 1 0.04
20 5 0.22
21 11 0.48
22 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTAATTTAATTTTTAAAT
Found at i:1920725 original size:7 final size:8
Alignment explanation
Indices: 1920675--1920710 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
1920665 TTAGTATTTT
1920675 ATATTT-A
1 ATATTTAA
1920682 AT-TTTAA
1 ATATTTAA
1920689 ATATTTAA
1 ATATTTAA
1920697 ATATTTAA
1 ATATTTAA
1920705 ATATTT
1 ATATTT
1920711 TTAAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 3 0.11
7 5 0.19
8 19 0.70
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
ATATTTAA
Found at i:1921842 original size:36 final size:36
Alignment explanation
Indices: 1921795--1921866 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
1921785 ATGCACGTTG
1921795 GTTCAAATTTTATAAAAAAAATAACTTAATGAATAT
1 GTTCAAATTTTATAAAAAAAATAACTTAATGAATAT
1921831 GTTCAAATTTTATAAAAAAAATAACTTAATGAATAT
1 GTTCAAATTTTATAAAAAAAATAACTTAATGAATAT
1921867 ATCTTTCTAG
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:0.53, C:0.06, G:0.06, T:0.36
Consensus pattern (36 bp):
GTTCAAATTTTATAAAAAAAATAACTTAATGAATAT
Found at i:1928042 original size:2 final size:2
Alignment explanation
Indices: 1928037--1928076 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1928027 ATTATGCATA
1928037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1928077 CTAATGTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1928576 original size:21 final size:22
Alignment explanation
Indices: 1928550--1928597 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
1928540 TAAAATAAAT
1928550 ATTTTTTAGTAATTTA-ATTTA
1 ATTTTTTAGTAATTTATATTTA
*
1928571 ATTTTTTAGTATTTTATATTTA
1 ATTTTTTAGTAATTTATATTTA
1928593 ATTTT
1 ATTTT
1928598 AAAATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
ATTTTTTAGTAATTTATATTTA
Done.