Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397277.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_2.0, 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: 2651878
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.33
Warning! 95949 characters in sequence are not A, C, G, or T
File 5 of 6
Found at i:1984913 original size:22 final size:22
Alignment explanation
Indices: 1984888--1984943 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1984878 GAGTAACTGA
* *
1984888 TTTTTAGGCCTTATATGACTAG
1 TTTTTAGGCATTACATGACTAG
* *
1984910 TTTTTAGGTATTGCATGACTAG
1 TTTTTAGGCATTACATGACTAG
*
1984932 TTTTTAGTCATT
1 TTTTTAGGCATT
1984944 GCGTGATTGG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (22 bp):
TTTTTAGGCATTACATGACTAG
Found at i:1985031 original size:45 final size:44
Alignment explanation
Indices: 1984982--1985090 Score: 128
Period size: 45 Copynumber: 2.5 Consensus size: 44
1984972 ACCGATGTTT
* ** *
1984982 GGGCATTGCATGATTGGTTTTGAGTCATTGTATGACTAGTTTGTA
1 GGGCATTGCATGATTGGTTTTGAGACATTACATGACGAGTTT-TA
* * * * *
1985027 GGGCATTACATTATCGGTTTTTAGACATTACGTGACGAGTTTTA
1 GGGCATTGCATGATTGGTTTTGAGACATTACATGACGAGTTTTA
1985071 GGGCATTGCATGATTGGTTT
1 GGGCATTGCATGATTGGTTT
1985091 CTAGGCATTG
Statistics
Matches: 52, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
44 19 0.37
45 33 0.63
ACGTcount: A:0.21, C:0.11, G:0.28, T:0.40
Consensus pattern (44 bp):
GGGCATTGCATGATTGGTTTTGAGACATTACATGACGAGTTTTA
Found at i:1985090 original size:22 final size:22
Alignment explanation
Indices: 1984982--1985101 Score: 68
Period size: 22 Copynumber: 5.4 Consensus size: 22
1984972 ACCGATGTTT
1984982 GGGCATTGCATGATTGGTTTT-
1 GGGCATTGCATGATTGGTTTTA
* * * *
1985003 GAGTCATTGTATGACTAGTTTGTA
1 G-GGCATTGCATGATTGGTTT-TA
* * *
1985027 GGGCATTACATTATCGGTTTTTA
1 GGGCATTGCATGATTGG-TTTTA
* * * *
1985050 -GACATTACGTGA-CGAGTTTTA
1 GGGCATTGCATGATTG-GTTTTA
1985071 GGGCATTGCATGATTGGTTTCTA
1 GGGCATTGCATGATTGGTTT-TA
1985094 -GGCATTGC
1 GGGCATTGC
1985102 TTGGATATTA
Statistics
Matches: 73, Mismatches: 18, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
21 8 0.11
22 46 0.63
23 15 0.21
24 4 0.05
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.39
Consensus pattern (22 bp):
GGGCATTGCATGATTGGTTTTA
Found at i:1986594 original size:305 final size:305
Alignment explanation
Indices: 1986037--1986671 Score: 957
Period size: 305 Copynumber: 2.1 Consensus size: 305
1986027 TCACATAAGA
* * *
1986037 TTTTACTAGGTGATTATAATATTTATAATTGACTTGTAGTTCTGGGCGTCGGAGGGCATTCTTGC
1 TTTTATTAGGTGATTATAATATTTATAATTGACTTGCAGTTCTGGGCGTCGGAGGCCATTCTTGC
* * * *
1986102 TATCCAAAGATAATTTGGATCTCATTGTGAGTCTAAAGACGCTTATCCACGAATTCTTAGATGGA
66 TATCCAAAGATAATTTGGATCCCAATGTGAGTCTAAAGACACTTATCCACGAATGCTTAGATGGA
* * *
1986167 ATTGCAAGGAGAAGCCCACAAGCTCCCACAAGATCATTACAGATTCAAAAAGTGAAGACAAGGTG
131 ATTGCAAGAAGAAGCCCACAAGCTCCCACAAGATCATTACAAATTCAAAAAGTGAAGACAAAGTG
* * *
1986232 AGGAGCGAAATGATACTATTTTTATTTTTTATATTAGGTGATTATACTATTTATAATTGACTTGC
196 AGGAGCGAAATGATACTATTTTTATTTTTTATATTAAGTGATTATAATATTTATAATTGACTTGA
*
1986297 AGTTCTAATTTATAATTGGTTATAATATTTATACTATTTTTATTT
261 AGTTCTAATTTATAATTGATTATAATATTTATACTATTTTTATTT
*
1986342 TTTTATTAGGTGATTATAATATTTATAATTGACTTGCAGTTTTGGGCGTCGGAGGCCATTCTTGC
1 TTTTATTAGGTGATTATAATATTTATAATTGACTTGCAGTTCTGGGCGTCGGAGGCCATTCTTGC
* * * ** *
1986407 TATCCAAAGCTACTTTGGATCCCAATGCT-AGTTTGTAGACACTTATCCATGAATGCTTAGATGG
66 TATCCAAAGATAATTTGGATCCCAATG-TGAGTCTAAAGACACTTATCCACGAATGCTTAGATGG
* * * * * * *** *
1986471 AATTGCAAGAAGAGGCCCATAGGTTTCCACAAGATCATTGCAAATTTGGAGAGTGAAGACAAAGT
130 AATTGCAAGAAGAAGCCCACAAGCTCCCACAAGATCATTACAAATTCAAAAAGTGAAGACAAAGT
1986536 GAGGAGCGAAATGATACTATTTTTATTTTTTATATTAAGTGATTATAATATTTATAATTGACTTG
195 GAGGAGCGAAATGATACTATTTTTATTTTTTATATTAAGTGATTATAATATTTATAATTGACTTG
*
1986601 AAGTTCTAATTTATAATTGATTATAATATTTATACTATTTTTGTTT
260 AAGTTCTAATTTATAATTGATTATAATATTTATACTATTTTTATTT
*
1986647 TTATATTAGGTGATTATAATATTTA
1 TTTTATTAGGTGATTATAATATTTA
1986672 AAGAAGTGAT
Statistics
Matches: 296, Mismatches: 33, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
305 295 1.00
306 1 0.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (305 bp):
TTTTATTAGGTGATTATAATATTTATAATTGACTTGCAGTTCTGGGCGTCGGAGGCCATTCTTGC
TATCCAAAGATAATTTGGATCCCAATGTGAGTCTAAAGACACTTATCCACGAATGCTTAGATGGA
ATTGCAAGAAGAAGCCCACAAGCTCCCACAAGATCATTACAAATTCAAAAAGTGAAGACAAAGTG
AGGAGCGAAATGATACTATTTTTATTTTTTATATTAAGTGATTATAATATTTATAATTGACTTGA
AGTTCTAATTTATAATTGATTATAATATTTATACTATTTTTATTT
Found at i:1986631 original size:19 final size:19
Alignment explanation
Indices: 1986575--1986634 Score: 57
Period size: 24 Copynumber: 2.9 Consensus size: 19
1986565 TTATATTAAG
1986575 TGATTATAATATTTATAAT
1 TGATTATAATATTTATAAT
**
1986594 TGACTTGAAGTTCTAATTTATAAT
1 TGA-TT--A-TAAT-ATTTATAAT
1986618 TGATTATAATATTTATA
1 TGATTATAATATTTATA
1986635 CTATTTTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
19 10 0.31
20 4 0.12
21 1 0.03
22 1 0.03
23 4 0.12
24 12 0.38
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.50
Consensus pattern (19 bp):
TGATTATAATATTTATAAT
Found at i:1987974 original size:62 final size:62
Alignment explanation
Indices: 1987867--1988037 Score: 225
Period size: 62 Copynumber: 2.8 Consensus size: 62
1987857 TATCCTCAAA
*
1987867 TTCACTCTAATGAGAACTGGATTTGTGCTATCTTCACCTTCATAAATGGGCACAAAACCAAC
1 TTCACTCTAATGAGAACTAGATTTGTGCTATCTTCACCTTCATAAATGGGCACAAAACCAAC
* * * * ** * **
1987929 TTCACTCTAATGGGAACAAAATTTATGCTATCTTCGTCTTTATAAATGGGCACAAAATGAAC
1 TTCACTCTAATGAGAACTAGATTTGTGCTATCTTCACCTTCATAAATGGGCACAAAACCAAC
* * *
1987991 TTCACTCTAACGAGAACTAGATTTGTGCTATCTTCACTTTTATAAAT
1 TTCACTCTAATGAGAACTAGATTTGTGCTATCTTCACCTTCATAAAT
1988038 CGGTATGCCC
Statistics
Matches: 91, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
62 91 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (62 bp):
TTCACTCTAATGAGAACTAGATTTGTGCTATCTTCACCTTCATAAATGGGCACAAAACCAAC
Found at i:1992676 original size:31 final size:31
Alignment explanation
Indices: 1992634--1992717 Score: 95
Period size: 31 Copynumber: 2.7 Consensus size: 31
1992624 TAATTTTTAA
1992634 ATATTTT-TTCAATTTAATCCCTTA-AC-AT
1 ATATTTTATTCAATTTAATCCCTTATACTAT
*
1992662 CTCAATTTTATTCAATTTAAT-CCTTATACTAT
1 AT--ATTTTATTCAATTTAATCCCTTATACTAT
*
1992694 ATATTTTAGTTCAATTTAGTCCCT
1 ATATTTTA-TTCAATTTAATCCCT
1992718 ATGACGTGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
28 1 0.02
30 16 0.35
31 23 0.50
32 6 0.13
ACGTcount: A:0.30, C:0.18, G:0.02, T:0.50
Consensus pattern (31 bp):
ATATTTTATTCAATTTAATCCCTTATACTAT
Found at i:1999966 original size:35 final size:37
Alignment explanation
Indices: 1999919--2000011 Score: 136
Period size: 35 Copynumber: 2.5 Consensus size: 37
1999909 TTTTTAAAAT
*
1999919 ATTGAAAAATAATTTATTAATGATGT-ATTGTTTAAG
1 ATTGAAAAATAATTTATTAATGATATAATTGTTTAAG
* *
1999955 ATTG-AAAATAATTTATTAATTATATAATTTTTTAAG
1 ATTGAAAAATAATTTATTAATGATATAATTGTTTAAG
1999991 ATTGAAAATATAATTTATTAA
1 ATTGAAAA-ATAATTTATTAA
2000012 ATATATATTG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
35 19 0.37
36 17 0.33
37 3 0.06
38 12 0.24
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.46
Consensus pattern (37 bp):
ATTGAAAAATAATTTATTAATGATATAATTGTTTAAG
Found at i:2000017 original size:38 final size:37
Alignment explanation
Indices: 1999919--2000018 Score: 134
Period size: 36 Copynumber: 2.7 Consensus size: 37
1999909 TTTTTAAAAT
*
1999919 ATTGAAAAATAATTTATT-AATGATGT-ATTGTTTAAG
1 ATTGAAAAATAATTTATTAAAT-ATATAATTGTTTAAG
* *
1999955 ATTG-AAAATAATTTATTAATTATATAATTTTTTAAG
1 ATTGAAAAATAATTTATTAAATATATAATTGTTTAAG
1999991 ATTGAAAATATAATTTATTAAATATATA
1 ATTGAAAA-ATAATTTATTAAATATATA
2000019 TTGAAAAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
35 16 0.29
36 19 0.34
37 3 0.05
38 18 0.32
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (37 bp):
ATTGAAAAATAATTTATTAAATATATAATTGTTTAAG
Found at i:2000724 original size:16 final size:18
Alignment explanation
Indices: 2000703--2000739 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
2000693 ATGAACAAAT
2000703 AATATAAAT-A-AATATA
1 AATATAAATAATAATATA
2000719 AATATAAATAATAATATA
1 AATATAAATAATAATATA
2000737 AAT
1 AAT
2000740 TGAAAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.47
17 1 0.05
18 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATATAAATAATAATATA
Found at i:2001317 original size:4 final size:4
Alignment explanation
Indices: 2001310--2001334 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2001300 AAAAAAAAAC
2001310 ACAG ACAG ACAG ACAG ACAG ACAG A
1 ACAG ACAG ACAG ACAG ACAG ACAG A
2001335 GGAAGCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.24, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:2002320 original size:8 final size:8
Alignment explanation
Indices: 2002309--2002333 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2002299 AATCCAAAAA
2002309 TCTTTGCT
1 TCTTTGCT
2002317 TCTTTGCT
1 TCTTTGCT
2002325 TCTTTGCT
1 TCTTTGCT
2002333 T
1 T
2002334 TTTCACTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.12, T:0.64
Consensus pattern (8 bp):
TCTTTGCT
Found at i:2004582 original size:9 final size:9
Alignment explanation
Indices: 2004568--2004593 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2004558 ATTTGATAGA
2004568 AGAAGAATG
1 AGAAGAATG
2004577 AGAAGAATG
1 AGAAGAATG
2004586 AGAAGAAT
1 AGAAGAAT
2004594 AGACGTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.31, T:0.12
Consensus pattern (9 bp):
AGAAGAATG
Found at i:2007411 original size:2 final size:2
Alignment explanation
Indices: 2007404--2007431 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2007394 ATGATAAAGA
2007404 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
2007432 TTGTTATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2014626 original size:2 final size:2
Alignment explanation
Indices: 2014621--2014657 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2014611 CCCCCCCCCC
2014621 CT CT CT CT CT CT CT CT CT CT CT -T CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2014658 TTTATATCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:2016374 original size:20 final size:20
Alignment explanation
Indices: 2016351--2016390 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2016341 TGGATAAATA
* *
2016351 ACCCAATTTATCGATAGATG
1 ACCCAATCTATAGATAGATG
2016371 ACCCAATCTATAGATAGATG
1 ACCCAATCTATAGATAGATG
2016391 GCACTATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (20 bp):
ACCCAATCTATAGATAGATG
Found at i:2018143 original size:33 final size:32
Alignment explanation
Indices: 2018101--2018180 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 32
2018091 ACTAAAGTTT
*
2018101 CCAATGAAATTTTTTGTCCG-AAAAGAATATTA
1 CCAATGAAATTTTTTAT-CGAAAAAGAATATTA
** *
2018133 CCAATAGAAATTTTCCATCGAAAAAGGATATTA
1 CCAAT-GAAATTTTTTATCGAAAAAGAATATTA
*
2018166 CCAATGAAAATTTTT
1 CCAATGAAATTTTTT
2018181 CAACAGATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
32 14 0.36
33 25 0.64
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (32 bp):
CCAATGAAATTTTTTATCGAAAAAGAATATTA
Found at i:2025768 original size:68 final size:68
Alignment explanation
Indices: 2025676--2025855 Score: 204
Period size: 68 Copynumber: 2.6 Consensus size: 68
2025666 TTAGATAGTG
* * * *
2025676 GTGTTTTTCCAATAATCACCTTATAAAAAGATAACTTCT-CATATCAT-AGACATAAGCTTTGAA
1 GTGTTTTTCCAATAATCACTTTATAAAAAGACAACTT-TACATAT-ATAAGACATAAACTTTCAA
*
2025739 TTGAA
64 TTCAA
*
2025744 GTGTTTTTCCAATAGTCACTTTATAAAAAGACAACTTTACATATATAAGACATAAACTTTCAATT
1 GTGTTTTTCCAATAATCACTTTATAAAAAGACAACTTTACATATATAAGACATAAACTTTCAATT
*
2025809 CTA
66 CAA
* * * * *
2025812 GTGGCTTTT-CAATAATCACTTTATCAAGAGGCATCTTTACATAT
1 GT-GTTTTTCCAATAATCACTTTATAAAAAGACAACTTTACATAT
2025856 GGAAATATAT
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
67 3 0.03
68 88 0.92
69 5 0.05
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (68 bp):
GTGTTTTTCCAATAATCACTTTATAAAAAGACAACTTTACATATATAAGACATAAACTTTCAATT
CAA
Found at i:2029866 original size:1 final size:1
Alignment explanation
Indices: 2029860--2029888 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
2029850 ATGAAAGAGA
2029860 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2029889 TGTGGCGGCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2037701 original size:15 final size:15
Alignment explanation
Indices: 2037681--2037724 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
2037671 TTTACAATGC
2037681 AATGTGATTACAGGT
1 AATGTGATTACAGGT
* *
2037696 AATGTGATTGCAAGT
1 AATGTGATTACAGGT
*
2037711 AATATGATTACAGG
1 AATGTGATTACAGG
2037725 GAAAATAACA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (15 bp):
AATGTGATTACAGGT
Found at i:2037975 original size:33 final size:34
Alignment explanation
Indices: 2037934--2037997 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
2037924 TTTTAATGTC
*
2037934 ATATATTTTATTTTCATTTC-TTATTATAATCTT
1 ATATATTTTATTTTCATTTCTTTAATATAATCTT
2037967 ATATATTTTATTTTCATTTCTTTAATATAAT
1 ATATATTTTATTTTCATTTCTTTAATATAAT
2037998 TTTTGATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 20 0.69
34 9 0.31
ACGTcount: A:0.30, C:0.08, G:0.00, T:0.62
Consensus pattern (34 bp):
ATATATTTTATTTTCATTTCTTTAATATAATCTT
Found at i:2038077 original size:26 final size:28
Alignment explanation
Indices: 2038059--2038120 Score: 53
Period size: 26 Copynumber: 2.3 Consensus size: 28
2038049 TTTAATTTCT
*
2038059 TATATTTTAT-TTTATT-TTTTGA-TTCT
1 TATATTTTATATTT-TTATTTTAATTTCT
2038085 TATATTTTATA-TTTTATTTTAATATT-T
1 TATATTTTATATTTTTATTTTAAT-TTCT
*
2038112 TTTATTTTA
1 TATATTTTA
2038121 ATTATAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 2 0.07
26 17 0.57
27 9 0.30
28 2 0.07
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (28 bp):
TATATTTTATATTTTTATTTTAATTTCT
Found at i:2038111 original size:20 final size:20
Alignment explanation
Indices: 2038066--2038120 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
2038056 TCTTATATTT
*
2038066 TATTTTATTTTTTGATTCTTA
1 TATTTTATATTTT-ATTCTTA
2038087 TATTTTATATTTTATT-TTAA
1 TATTTTATATTTTATTCTT-A
*
2038107 TATTTTTTATTTTA
1 TATTTTATATTTTA
2038121 ATTATAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 2 0.06
20 17 0.55
21 12 0.39
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (20 bp):
TATTTTATATTTTATTCTTA
Found at i:2055382 original size:21 final size:22
Alignment explanation
Indices: 2055336--2055382 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
2055326 TTCATATGGC
*
2055336 TATCTATCGATAAATTCCACGA
1 TATCTATCAATAAATTCCACGA
**
2055358 -ATCTATCAATAGTTTCCA-GA
1 TATCTATCAATAAATTCCACGA
2055378 TATCT
1 TATCT
2055383 CTGCTTTACA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (22 bp):
TATCTATCAATAAATTCCACGA
Found at i:2056474 original size:20 final size:21
Alignment explanation
Indices: 2056433--2056474 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2056423 ATTAATGACT
* *
2056433 TTTTTAAAAACAATCTTGTTA
1 TTTTTAAAAAAAATCTTATTA
2056454 TTTTTAAAAAAAAT-TTATTA
1 TTTTTAAAAAAAATCTTATTA
2056474 T
1 T
2056475 ATTAAAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (21 bp):
TTTTTAAAAAAAATCTTATTA
Found at i:2068455 original size:15 final size:15
Alignment explanation
Indices: 2068435--2068463 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2068425 CACTAAAATC
2068435 TCAATAAATTAATAT
1 TCAATAAATTAATAT
2068450 TCAATAAATTAATA
1 TCAATAAATTAATA
2068464 ATTTCGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
TCAATAAATTAATAT
Found at i:2072146 original size:355 final size:355
Alignment explanation
Indices: 2071491--2072150 Score: 867
Period size: 355 Copynumber: 1.9 Consensus size: 355
2071481 GATAACTCAT
* * * *
2071491 CATGAGCTCATTCTTCCTAACTGTAGTGGGTGGTGATCATAATAAATCCCAAGAATCCCATATAC
1 CATGAGCTCATTCTTCCTAACTGTAATGGGTGGCGATCATAATAAATCCCAAGAATACCAAATAC
* *** * **** *
2071556 ATTATTAGGTTACACATAAGGTTTGGGATTGAATTCTTTTGTTGTATTTATTTGTAGAACCCTGA
66 ATTATTAGGTTACACATAAGGTTTGGGATTGAATTCTTTTATCACATCTAACCATAGAACCCTAA
* * * * *
2071621 TTTTATATGTAAGGGTAAAATGGTTAATTTACTTGGTGAACTGAAGAGAGAACCTTATCTTGAGC
131 ATTTATATGAAAGGGTAAAATGGTGAATGTACTTGATGAACTGAAGAGAGAACCTTATCTTGAGC
*
2071686 TCAAATTATGAGAAATTAACTTTAGAGATGCTAAAAGGAGTGAGAGGGGACATTTGAAAGGCAAA
196 TCAAATTATGAGAAATTAACTTTAGAGATACTAAAAGGAGTGAGAGGGGACATTTGAAAGGCAAA
* *
2071751 AGGAGTAGAGAAATCAAAAGACAAGGCTTAAAAACCATTTTGCCTCAAAAGAATTGGCATTCACA
261 AGAAATAGAGAAATCAAAAGACAAGGCTTAAAAACCATTTTGCCTCAAAAGAATTGGCATTCACA
2071816 AGCTTAAAAAAACCTTAGAAGGGCATTCTA
326 AGCTTAAAAAAACCTTAGAAGGGCATTCTA
* ** * * *
2071846 CATGAGCTTATTCTTTTTTACTGTAATGGGTGGCGGTCATAATAAATCCCAAGAATACCAAATCC
1 CATGAGCTCATTCTTCCTAACTGTAATGGGTGGCGATCATAATAAATCCCAAGAATACCAAATAC
* * * *
2071911 ATTATTATGTTGCTCATAAGGTTTGGGATTGAATTTTTTTATCACATCTAACCATAGAACCCTAA
66 ATTATTAGGTTACACATAAGGTTTGGGATTGAATTCTTTTATCACATCTAACCATAGAACCCTAA
* * *
2071976 ATTTATATGAAAGGTTAAAATGGTGAATGTACTTTATGAGA-T-AGAGAGATAACCTTATCTTGA
131 ATTTATATGAAAGGGTAAAATGGTGAATGTACTTGATGA-ACTGA-AGAGAGAACCTTATCTTGA
* * * * *
2072039 GCTCAAATTGTGAGGAATTAACTTTAGAGATACTAAAATGAGTGAGAGGGGACATTTGAAGGGTA
194 GCTCAAATTATGAGAAATTAACTTTAGAGATACTAAAAGGAGTGAGAGGGGACATTTGAAAGGCA
* * ** *
2072104 AGAGAACAT-GATAAATCAAGGGACAAGGCTTAAAATCCATTTTGCCT
259 AAAGAA-ATAGAGAAATCAAAAGACAAGGCTTAAAAACCATTTTGCCT
2072151 TAGAAAGATC
Statistics
Matches: 257, Mismatches: 45, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
354 1 0.00
355 254 0.99
356 2 0.01
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (355 bp):
CATGAGCTCATTCTTCCTAACTGTAATGGGTGGCGATCATAATAAATCCCAAGAATACCAAATAC
ATTATTAGGTTACACATAAGGTTTGGGATTGAATTCTTTTATCACATCTAACCATAGAACCCTAA
ATTTATATGAAAGGGTAAAATGGTGAATGTACTTGATGAACTGAAGAGAGAACCTTATCTTGAGC
TCAAATTATGAGAAATTAACTTTAGAGATACTAAAAGGAGTGAGAGGGGACATTTGAAAGGCAAA
AGAAATAGAGAAATCAAAAGACAAGGCTTAAAAACCATTTTGCCTCAAAAGAATTGGCATTCACA
AGCTTAAAAAAACCTTAGAAGGGCATTCTA
Found at i:2073072 original size:44 final size:44
Alignment explanation
Indices: 2072982--2073078 Score: 101
Period size: 44 Copynumber: 2.2 Consensus size: 44
2072972 TACAATCTCG
* * *
2072982 ATTGTGGATGGCATATGCAAGGTGAAAGGTACATGAACGTGGTT
1 ATTGTGGATAGCATATGCAAGGTGAAAGGTACATGAACATGATT
*
2073026 ATTGTGGATAGCATGT-CTAAGGTG-AAGGATACATG-ACTATGATT
1 ATTGTGGATAGCATATGC-AAGGTGAAAGG-TACATGAAC-ATGATT
*
2073070 ATTATGGAT
1 ATTGTGGAT
2073079 GACACGTGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
43 7 0.16
44 38 0.84
ACGTcount: A:0.31, C:0.08, G:0.30, T:0.31
Consensus pattern (44 bp):
ATTGTGGATAGCATATGCAAGGTGAAAGGTACATGAACATGATT
Found at i:2075910 original size:20 final size:20
Alignment explanation
Indices: 2075873--2075910 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2075863 GAAACATGTG
*
2075873 CAAATGTATCGATGCATTCT
1 CAAATGTATCGATACATTCT
*
2075893 CAAATGTATGGATACATT
1 CAAATGTATCGATACATT
2075911 ATTGGGTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (20 bp):
CAAATGTATCGATACATTCT
Found at i:2080170 original size:15 final size:15
Alignment explanation
Indices: 2080150--2080190 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2080140 CACACGTAAA
* *
2080150 GTGTTATAGTATAAT
1 GTGTTATAGCATAAG
2080165 GTGTTATAGCATAAG
1 GTGTTATAGCATAAG
*
2080180 GTGTTACAGCA
1 GTGTTATAGCA
2080191 CAAAATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (15 bp):
GTGTTATAGCATAAG
Found at i:2080598 original size:15 final size:15
Alignment explanation
Indices: 2080561--2080600 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
2080551 ATTTTTTCAC
2080561 TTATACCTTTTTCTT
1 TTATACCTTTTTCTT
2080576 TT-TACCTTTTTCTT
1 TTATACCTTTTTCTT
*
2080590 TTATTCCTTTT
1 TTATACCTTTT
2080601 CACATACACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.61
15 9 0.39
ACGTcount: A:0.10, C:0.20, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATACCTTTTTCTT
Found at i:2082168 original size:17 final size:17
Alignment explanation
Indices: 2082142--2082186 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
2082132 CCCCAAGGCA
*
2082142 CAAGATGACTTACTTTC
1 CAAGACGACTTACTTTC
2082159 CAAGACGACTTACTTTC
1 CAAGACGACTTACTTTC
*
2082176 CAAGACAACTT
1 CAAGACGACTT
2082187 TACTACACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (17 bp):
CAAGACGACTTACTTTC
Found at i:2083328 original size:53 final size:53
Alignment explanation
Indices: 2083248--2083351 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
2083238 CCAAATCTAG
2083248 CAATACATGTTTTTCATGTATAAATACATTTTGATAAGTATTGATAGATTCAT
1 CAATACATGTTTTTCATGTATAAATACATTTTGATAAGTATTGATAGATTCAT
2083301 CAATACATGTTTTTCATGTATAAATACATTTTGATAAGTATTGATAGATTC
1 CAATACATGTTTTTCATGTATAAATACATTTTGATAAGTATTGATAGATTC
2083352 CAAAATCTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (53 bp):
CAATACATGTTTTTCATGTATAAATACATTTTGATAAGTATTGATAGATTCAT
Found at i:2083499 original size:20 final size:20
Alignment explanation
Indices: 2083471--2083508 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2083461 CTTGCTAACT
*
2083471 TAAAAGTATCGATACATTAG
1 TAAAAGTATAGATACATTAG
*
2083491 TAAATGTATAGATACATT
1 TAAAAGTATAGATACATT
2083509 TTAAGTAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (20 bp):
TAAAAGTATAGATACATTAG
Found at i:2083567 original size:20 final size:20
Alignment explanation
Indices: 2083542--2083579 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
2083532 GCAGGTAAGT
2083542 TCAAATGTATCAATACATGC
1 TCAAATGTATCAATACATGC
2083562 TCAAATGTATCAATACAT
1 TCAAATGTATCAATACAT
2083580 CTCGGTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (20 bp):
TCAAATGTATCAATACATGC
Found at i:2089506 original size:47 final size:47
Alignment explanation
Indices: 2089437--2089532 Score: 192
Period size: 47 Copynumber: 2.0 Consensus size: 47
2089427 CCATTGTATC
2089437 ATGATACTTTAACTCTTTCATTAGAACATGCAATTGTTAATCACTCT
1 ATGATACTTTAACTCTTTCATTAGAACATGCAATTGTTAATCACTCT
2089484 ATGATACTTTAACTCTTTCATTAGAACATGCAATTGTTAATCACTCT
1 ATGATACTTTAACTCTTTCATTAGAACATGCAATTGTTAATCACTCT
2089531 AT
1 AT
2089533 CATCTGGGTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (47 bp):
ATGATACTTTAACTCTTTCATTAGAACATGCAATTGTTAATCACTCT
Found at i:2091399 original size:22 final size:23
Alignment explanation
Indices: 2091371--2091422 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
2091361 AATCAATTTT
2091371 AACTTT-AAAATGTTCTAAAGTA
1 AACTTTAAAAATGTTCTAAAGTA
* *
2091393 AACTTTAAAAAATGTTCTAAGGTG
1 AACTTT-AAAAATGTTCTAAAGTA
2091417 AACTTT
1 AACTTT
2091423 TATAAGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 6 0.23
24 20 0.77
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (23 bp):
AACTTTAAAAATGTTCTAAAGTA
Found at i:2091409 original size:24 final size:24
Alignment explanation
Indices: 2091377--2091422 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2091367 TTTTAACTTT
2091377 AAAATGTTCTAAAGTAAACTTTAA
1 AAAATGTTCTAAAGTAAACTTTAA
* *
2091401 AAAATGTTCTAAGGTGAACTTT
1 AAAATGTTCTAAAGTAAACTTT
2091423 TATAAGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (24 bp):
AAAATGTTCTAAAGTAAACTTTAA
Found at i:2091941 original size:16 final size:16
Alignment explanation
Indices: 2091910--2091946 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
2091900 AAATAATTTT
2091910 ATTATTATTTTATCAA
1 ATTATTATTTTATCAA
2091926 ATTAGTTATTTT-TC-A
1 ATTA-TTATTTTATCAA
2091941 ATTATT
1 ATTATT
2091947 TGATGGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 2 0.10
15 5 0.25
16 6 0.30
17 7 0.35
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (16 bp):
ATTATTATTTTATCAA
Found at i:2092962 original size:19 final size:19
Alignment explanation
Indices: 2092938--2092974 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2092928 ATTTTCTTTA
2092938 ATTATTTT-TTTATATTTTG
1 ATTATTTTATTT-TATTTTG
2092957 ATTATTTTATTTTATTTT
1 ATTATTTTATTTTATTTT
2092975 TTTAAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (19 bp):
ATTATTTTATTTTATTTTG
Found at i:2096546 original size:48 final size:48
Alignment explanation
Indices: 2096436--2096995 Score: 497
Period size: 48 Copynumber: 11.6 Consensus size: 48
2096426 CAAAATGAGT
* * * *
2096436 CTACTTAACTTTAAAATGATTGAAAAAAGCTCCTTATCTTTAAAC-ATGG
1 CTACGTAACTTTAAAATGATTG-GAAAAGCTCCTCATCTCTAAACGA-GG
** * * *
2096485 CTACACAAATTTAAAATGATTGGAAAAGGTCCTCATCTCTAAACGAGT
1 CTACGTAACTTTAAAATGATTGGAAAAGCTCCTCATCTCTAAACGAGG
* * *
2096533 CTACGTAACTTTAAAATGA-TAGATAAAGCTCCTTATCTCTAAACGAGA
1 CTACGTAACTTTAAAATGATTGGA-AAAGCTCCTCATCTCTAAACGAGG
**
2096581 CTACACAACTTTAAAATGATTGGAAAAAGC-CCTTCATCTCTAAACGAGG
1 CTACGTAACTTTAAAATGATTGG-AAAAGCTCC-TCATCTCTAAACGAGG
* * * ** * * *
2096630 CTACGCAATTTTAAAATGATGGGAAAAAAATCCTCATCTTTAAAAGAAG
1 CTACGTAACTTTAAAATGATTGG-AAAAGCTCCTCATCTCTAAACGAGG
* * * * * *
2096679 -TCACTATAACTTAAAAATGATTAGAAAAGCTCCTTATTTCTAAATGAGG
1 CT-AC-GTAACTTTAAAATGATTGGAAAAGCTCCTCATCTCTAAACGAGG
* * * * * *
2096728 CTATGCATCTTTAAAATAATT-GAAAAGGCTCCTCATCTCTAAAGGAAG
1 CTACGTAACTTTAAAATGATTGGAAAA-GCTCCTCATCTCTAAACGAGG
* * * *
2096776 CTAC-TACAACTTTAAAATGATTAGAAAAGCTCTTAATCTCTAAACAAGG
1 CTACGT--AACTTTAAAATGATTGGAAAAGCTCCTCATCTCTAAACGAGG
* * **
2096825 CTACGTAACTTTAAAATGATTGAAAAAGCTCATCATCTCTAAATAAGG
1 CTACGTAACTTTAAAATGATTGGAAAAGCTCCTCATCTCTAAACGAGG
* * *
2096873 CTACGTAACTTTAGAATGATTGAAAAAACT-CTACATCTCTAAACGAGG
1 CTACGTAACTTTAAAATGATTGGAAAAGCTCCT-CATCTCTAAACGAGG
* * *
2096921 CTACTTGACTTTAAAATGATTGGAAACA-CTCCTCATCTCTAAACGATG
1 CTACGTAACTTTAAAATGATTGGAAA-AGCTCCTCATCTCTAAACGAGG
**
2096969 CTACCCAACTTTAAAATGATTGGAAAA
1 CTACGTAACTTTAAAATGATTGGAAAA
2096996 CATTTTCCTT
Statistics
Matches: 416, Mismatches: 78, Indels: 36
0.78 0.15 0.07
Matches are distributed among these distances:
47 10 0.02
48 247 0.59
49 136 0.33
50 23 0.06
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (48 bp):
CTACGTAACTTTAAAATGATTGGAAAAGCTCCTCATCTCTAAACGAGG
Found at i:2096576 original size:96 final size:95
Alignment explanation
Indices: 2096436--2096995 Score: 536
Period size: 97 Copynumber: 5.8 Consensus size: 95
2096426 CAAAATGAGT
* * * *
2096436 CTACTTAACTTTAAAATGATTGAAAAAAGCTCCTTATCTTTAAACATGGCTACACAAATTTAAAA
1 CTACGTAACTTTAAAATGATTG-AAAAAGCTCCTCATCTCTAAACA-GGCTACACAACTTTAAAA
* *
2096501 TGATTGGAAAAGGTCCTCATCTCTAAACGAGT
64 TGATTGGAAAAGCTCCTCATCTCTAAACGAGG
* * * *
2096533 CTACGTAACTTTAAAATGATAGATAAAGCTCCTTATCTCTAAACGAGACTACACAACTTTAAAAT
1 CTACGTAACTTTAAAATGATTGAAAAAGCTCCTCATCTCTAAAC-AGGCTACACAACTTTAAAAT
2096598 GATTGGAAAAAGC-CCTTCATCTCTAAACGAGG
65 GATTGG-AAAAGCTCC-TCATCTCTAAACGAGG
* * * ** * * *
2096630 CTACGCAATTTTAAAATGATGGGAAAAAAATCCTCATCTTTAAA-AGAAG-TCACTATAACTTAA
1 CTACGTAACTTTAAAATGAT-TGAAAAAGCTCCTCATCTCTAAACAG--GCT-AC-ACAACTTTA
* * * *
2096693 AAATGATTAGAAAAGCTCCTTATTTCTAAATGAGG
61 AAATGATTGGAAAAGCTCCTCATCTCTAAACGAGG
* * * * * * *
2096728 CTATGCATCTTTAAAATAATTGAAAAGGCTCCTCATCTCTAAAGGAAGCTACTACAACTTTAAAA
1 CTACGTAACTTTAAAATGATTGAAAAAGCTCCTCATCTCTAAA-CAGGCTAC-ACAACTTTAAAA
* * * *
2096793 TGATTAGAAAAGCTCTTAATCTCTAAACAAGG
64 TGATTGGAAAAGCTCCTCATCTCTAAACGAGG
* * ** *
2096825 CTACGTAACTTTAAAATGATTGAAAAAGCTCATCATCTCTAAATAAGGCTACGTAACTTTAGAAT
1 CTACGTAACTTTAAAATGATTGAAAAAGCTCCTCATCTCTAAA-CAGGCTACACAACTTTAAAAT
* *
2096890 GATTGAAAAAACT-CTACATCTCTAAACGAGG
65 GATTGGAAAAGCTCCT-CATCTCTAAACGAGG
* * * * *
2096921 CTACTTGACTTTAAAATGATTGGAAACA-CTCCTCATCTCTAAACGATGCTACCCAACTTTAAAA
1 CTACGTAACTTTAAAATGATT-GAAAAAGCTCCTCATCTCTAAAC-AGGCTACACAACTTTAAAA
2096985 TGATTGGAAAA
64 TGATTGGAAAA
2096996 CATTTTCCTT
Statistics
Matches: 380, Mismatches: 68, Indels: 31
0.79 0.14 0.06
Matches are distributed among these distances:
95 1 0.00
96 138 0.36
97 167 0.44
98 55 0.14
99 19 0.05
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (95 bp):
CTACGTAACTTTAAAATGATTGAAAAAGCTCCTCATCTCTAAACAGGCTACACAACTTTAAAATG
ATTGGAAAAGCTCCTCATCTCTAAACGAGG
Found at i:2100373 original size:12 final size:11
Alignment explanation
Indices: 2100350--2100391 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
2100340 TATATAATTA
2100350 TTATT-ATTTT
1 TTATTAATTTT
2100360 TTATTAACTTTT
1 TTATTAA-TTTT
*
2100372 TTATTAATTTA
1 TTATTAATTTT
2100383 TTATTAATT
1 TTATTAATT
2100392 AAAAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.17
11 13 0.45
12 11 0.38
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (11 bp):
TTATTAATTTT
Found at i:2101001 original size:13 final size:13
Alignment explanation
Indices: 2100968--2101004 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
2100958 ATTTTCTTAA
2100968 TTATT-TTTTATT
1 TTATTATTTTATT
2100980 TTGATTATTTTATT
1 TT-ATTATTTTATT
2100994 TTATTATTTTA
1 TTATTATTTTA
2101005 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 2 0.09
13 12 0.52
14 9 0.39
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
TTATTATTTTATT
Found at i:2101394 original size:13 final size:13
Alignment explanation
Indices: 2101376--2101402 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2101366 ATTTGCAAAA
2101376 ATTTTGAATATAT
1 ATTTTGAATATAT
2101389 ATTTTGAATATAT
1 ATTTTGAATATAT
2101402 A
1 A
2101403 AATAAATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (13 bp):
ATTTTGAATATAT
Found at i:2102473 original size:28 final size:28
Alignment explanation
Indices: 2102442--2102496 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
2102432 ATGTTACAAA
* * *
2102442 CAAATAAATTATACCATATATAAATAAG
1 CAAATAAATTACACCAAACATAAATAAG
*
2102470 CAAATACATTACACCAAACATAAATAA
1 CAAATAAATTACACCAAACATAAATAA
2102497 AATTTCAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.58, C:0.16, G:0.02, T:0.24
Consensus pattern (28 bp):
CAAATAAATTACACCAAACATAAATAAG
Found at i:2109450 original size:110 final size:110
Alignment explanation
Indices: 2109255--2109452 Score: 245
Period size: 110 Copynumber: 1.8 Consensus size: 110
2109245 ATTTGAGCAT
* * ** * *
2109255 AAATGCAGGTCTAATTGATATTCAAAGAAAATTTATTTTCTTTAGACTTAATATAATCTTGGTAT
1 AAATGCAAGTCCAATTGATACACAAAGAAAATTTATTTTCTTTAGACTTAATATAATCTTAGCAT
** * ***
2109320 TATTGATTTTAAGGGGAAAAAAAACTTTATATGCGCTTTACATGA
66 TATCAATTTCAAGAAAAAAAAAAACTTTATATGCGCTTTACATGA
* * *
2109365 AAATGCAAGTCCAATTGATACACAAAGAAAATTTCTTTTCTTT-GAACTTAATATTATTTTAGCA
1 AAATGCAAGTCCAATTGATACACAAAGAAAATTTATTTTCTTTAG-ACTTAATATAATCTTAGCA
2109429 TTATCAATTTCAAGAAAAAAAAAA
65 TTATCAATTTCAAGAAAAAAAAAA
2109453 GTTTGATGTA
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
109 1 0.01
110 71 0.99
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (110 bp):
AAATGCAAGTCCAATTGATACACAAAGAAAATTTATTTTCTTTAGACTTAATATAATCTTAGCAT
TATCAATTTCAAGAAAAAAAAAAACTTTATATGCGCTTTACATGA
Found at i:2120100 original size:20 final size:21
Alignment explanation
Indices: 2120075--2120115 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2120065 CCTTCTTCCA
*
2120075 ATTGATT-AATCTTCCCTTTC
1 ATTGATTGAAGCTTCCCTTTC
*
2120095 ATTGATTGAAGCTTCTCTTTC
1 ATTGATTGAAGCTTCCCTTTC
2120116 TTCAACTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.49
Consensus pattern (21 bp):
ATTGATTGAAGCTTCCCTTTC
Found at i:2133137 original size:54 final size:54
Alignment explanation
Indices: 2133074--2133176 Score: 197
Period size: 54 Copynumber: 1.9 Consensus size: 54
2133064 AACATAAGCA
*
2133074 TGAAAATCATAAACATATAAATTTAAAAAATTCCCCCTAAACTTAAAATATGCG
1 TGAAAATCATAAACATATAAATTTAAAAAATTCCCCCGAAACTTAAAATATGCG
2133128 TGAAAATCATAAACATATAAATTTAAAAAATTCCCCCGAAACTTAAAAT
1 TGAAAATCATAAACATATAAATTTAAAAAATTCCCCCGAAACTTAAAAT
2133177 GAACATTGTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.51, C:0.17, G:0.05, T:0.27
Consensus pattern (54 bp):
TGAAAATCATAAACATATAAATTTAAAAAATTCCCCCGAAACTTAAAATATGCG
Found at i:2135488 original size:35 final size:35
Alignment explanation
Indices: 2135391--2135488 Score: 94
Period size: 35 Copynumber: 2.9 Consensus size: 35
2135381 ATTGTTGAAA
* *
2135391 GGTTTCGCTTGATCCCATAAAATGC--ATTGTAAG
1 GGTTTCACTTGATCCCATAAAAAGCATATTGTAAG
* * * *
2135424 GATTTCATTTGATCCCACAAAAAAG-ATATTGTGAG
1 GGTTTCACTTGATCCCA-TAAAAAGCATATTGTAAG
* *
2135459 GGTTTCACTTAATCCCATAAAAGGCATATT
1 GGTTTCACTTGATCCCATAAAAAGCATATT
2135489 ACTCTTAATG
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
33 14 0.28
34 10 0.20
35 26 0.52
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (35 bp):
GGTTTCACTTGATCCCATAAAAAGCATATTGTAAG
Found at i:2137718 original size:113 final size:116
Alignment explanation
Indices: 2137593--2137812 Score: 302
Period size: 119 Copynumber: 1.9 Consensus size: 116
2137583 TGATAATAAA
* * * *
2137593 ATAAAAAATATCATTTTTATAAATCAATGAAAATT-AAAA-AA-AAGTATTTAAATGGGTCAATT
1 ATAAAAAATATCATTTCTATAAATCAATGAAAATTAAAAATAAGAAGCAATTAAATGGATCAATT
2137655 GAGTTAAGTCGAGACATTACAACAGAATCAAATTATATTACATTATATCAT
66 GAGTTAAGTCGAGACATTACAACAGAATCAAATTATATTACATTATATCAT
* **
2137706 ATAAAAAATATCATTTCTATAAATTAATGAAAATTAAAAAAAATAAGAAGCAATTAAATGGATTG
1 ATAAAAAATATCATTTCTATAAATCAATGAAAATT---AAAAATAAGAAGCAATTAAATGGATCA
* **
2137771 ATTGAGTTAGGTCGAGACATTATGACAGAATCAAATTATATT
63 ATTGAGTTAAGTCGAGACATTACAACAGAATCAAATTATATT
2137813 TAATTACATT
Statistics
Matches: 91, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
113 33 0.36
117 4 0.04
118 2 0.02
119 52 0.57
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (116 bp):
ATAAAAAATATCATTTCTATAAATCAATGAAAATTAAAAATAAGAAGCAATTAAATGGATCAATT
GAGTTAAGTCGAGACATTACAACAGAATCAAATTATATTACATTATATCAT
Found at i:2137828 original size:5 final size:5
Alignment explanation
Indices: 2137805--2137856 Score: 70
Period size: 5 Copynumber: 10.4 Consensus size: 5
2137795 ACAGAATCAA
* *
2137805 ATTAT ATT-T AATTAC ATTAT ATTAT GTTAT ATTAT ATTAT ATTAT ATTAT
1 ATTAT ATTAT -ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
2137855 AT
1 AT
2137857 ACGATTTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 1 0.02
5 40 0.98
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (5 bp):
ATTAT
Found at i:2138741 original size:19 final size:19
Alignment explanation
Indices: 2138699--2138741 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2138689 TTAAATAAAT
2138699 TTTTACTTTTTTATATTTA
1 TTTTACTTTTTTATATTTA
* *
2138718 ATTTATTTTTTTAT-TTTCA
1 TTTTACTTTTTTATATTT-A
2138737 TTTTA
1 TTTTA
2138742 GATTAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTACTTTTTTATATTTA
Found at i:2138777 original size:20 final size:21
Alignment explanation
Indices: 2138745--2138786 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
2138735 CATTTTAGAT
2138745 TAATTATATTTTTATAA-TAAA
1 TAATTATATTTTT-TAATTAAA
2138766 TAATTA-ATTTTTTAATTAAA
1 TAATTATATTTTTTAATTAAA
2138786 T
1 T
2138787 CGTCACTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.15
20 11 0.55
21 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATTATATTTTTTAATTAAA
Found at i:2138954 original size:24 final size:24
Alignment explanation
Indices: 2138927--2138976 Score: 77
Period size: 22 Copynumber: 2.2 Consensus size: 24
2138917 TCACGTAAAT
2138927 TTAAAATAACAAGTGATATTTTAC
1 TTAAAATAACAAGTGATATTTTAC
*
2138951 TT--AATGACAAGTGATATTTTAC
1 TTAAAATAACAAGTGATATTTTAC
2138973 TTAA
1 TTAA
2138977 TGACAATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 21 0.91
24 2 0.09
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (24 bp):
TTAAAATAACAAGTGATATTTTAC
Found at i:2138960 original size:22 final size:22
Alignment explanation
Indices: 2138935--2138982 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
2138925 ATTTAAAATA
2138935 ACAAGTGATATTTTACTTAATG
1 ACAAGTGATATTTTACTTAATG
2138957 ACAAGTGATATTTTACTTAATG
1 ACAAGTGATATTTTACTTAATG
2138979 ACAA
1 ACAA
2138983 TTAGCAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (22 bp):
ACAAGTGATATTTTACTTAATG
Found at i:2140716 original size:200 final size:200
Alignment explanation
Indices: 2140365--2140765 Score: 495
Period size: 200 Copynumber: 2.0 Consensus size: 200
2140355 CCATCAACTA
*
2140365 TTCAAAGTTGAATCCTTGCTTGACTCAAGCTAAAATTTCTTCTCTCACTACACCCAAGCTAAAAT
1 TTCAAAGTTGAATCCTTACTTGACTCAAGCTAAAATTTCTTCTCTCACTACACCCAAGCTAAAAT
* * * * *
2140430 CGCTAGCATCTAATCTTTGTGAAGCAAATCGTCACTATTATTTCTTTGTACATACATCTTGTAAA
66 CGCTAACATCTAACCTTTGTGAAGCAAATCGTCACTATTATTCCTTTGTACACACATCTTATAAA
* * * * *
2140495 AGTTCTATCTTAGTATTGAAAAGCTATCCTGTAAAGGCTATCGCTTGCT-ATTTAAAAAGTAAGA
131 AGTTCTAACTTACTATTGAAAAGCTATCCTATAAAAGCTATCGCTT-CTCATTTAAAAAGTAAAA
2140559 ATCCTT
195 ATCCTT
* * * * * *
2140565 TTCAAAGTTGAATTCTTACTCT-ATTTAAGCTGAAATTTCTTCTCTCACTACACCTAAGTTAAAA
1 TTCAAAGTTGAATCCTTACT-TGACTCAAGCTAAAATTTCTTCTCTCACTACACCCAAGCTAAAA
* * * *
2140629 TCTCTAACATCTAGCCTTTGTGAAGCAAATTC-TTACTATTATTCCTTTGTACACATATCTTATA
65 TCGCTAACATCTAACCTTTGTGAAGCAAA-TCGTCACTATTATTCCTTTGTACACACATCTTATA
* * * * * *
2140693 AAGGTTTTAACTTAACT-TTGAAAAGTTATCTTATAAAAGTTATCTCTTCTCATTTAAAAAGTAA
129 AAAGTTCTAACTT-ACTATTGAAAAGCTATCCTATAAAAGCTATCGCTTCTCATTTAAAAAGTAA
2140757 AAATCCTT
193 AAATCCTT
2140765 T
1 T
2140766 GTGAATTATG
Statistics
Matches: 170, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
199 2 0.01
200 163 0.96
201 5 0.03
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.38
Consensus pattern (200 bp):
TTCAAAGTTGAATCCTTACTTGACTCAAGCTAAAATTTCTTCTCTCACTACACCCAAGCTAAAAT
CGCTAACATCTAACCTTTGTGAAGCAAATCGTCACTATTATTCCTTTGTACACACATCTTATAAA
AGTTCTAACTTACTATTGAAAAGCTATCCTATAAAAGCTATCGCTTCTCATTTAAAAAGTAAAAA
TCCTT
Found at i:2145117 original size:2 final size:2
Alignment explanation
Indices: 2145110--2145144 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2145100 TGTATGTGTT
2145110 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2145145 TACAGCAGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2147323 original size:2 final size:2
Alignment explanation
Indices: 2147316--2147340 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2147306 AGGGAAAGTA
2147316 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 A
2147341 CACACACACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2147345 original size:2 final size:2
Alignment explanation
Indices: 2147340--2147375 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2147330 ATATATATAT
2147340 AC AC AC AC AC AC AC AC AC AC AC A- AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2147376 TACATGGAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2155111 original size:21 final size:21
Alignment explanation
Indices: 2155069--2155122 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
2155059 AGTACTACTC
* *
2155069 TTAATTTAATTTAAAATAAAA
1 TTAAATTAAATTAAAATAAAA
* *
2155090 TTAAATTAAATTAAACTCAAA
1 TTAAATTAAATTAAAATAAAA
*
2155111 -TAACTTAAATTA
1 TTAAATTAAATTA
2155123 CATATTCAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (21 bp):
TTAAATTAAATTAAAATAAAA
Found at i:2156024 original size:18 final size:17
Alignment explanation
Indices: 2155998--2156041 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2155988 TTATTCAAAT
*
2155998 GTGATTATTCAAATTAAA
1 GTGACTATTCAAATT-AA
*
2156016 GTGACTATTTAAATTAA
1 GTGACTATTCAAATTAA
*
2156033 GTGTCTATT
1 GTGACTATT
2156042 TAGATTAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (17 bp):
GTGACTATTCAAATTAA
Found at i:2156040 original size:17 final size:17
Alignment explanation
Indices: 2155998--2156050 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
2155988 TTATTCAAAT
* *
2155998 GTGATTATTCAAATTAAA
1 GTGACTATTTAAATT-AA
2156016 GTGACTATTTAAATTAA
1 GTGACTATTTAAATTAA
* *
2156033 GTGTCTATTTAGATTAA
1 GTGACTATTTAAATTAA
2156050 G
1 G
2156051 ACATGACTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.42
Consensus pattern (17 bp):
GTGACTATTTAAATTAA
Found at i:2160392 original size:18 final size:18
Alignment explanation
Indices: 2160369--2160414 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
2160359 CTTGCACTGA
2160369 TTTTCATCAAATGAGTCT
1 TTTTCATCAAATGAGTCT
*
2160387 TTTTCAGCAAATGAGTCT
1 TTTTCATCAAATGAGTCT
2160405 TTTTCATCAA
1 TTTTCATCAA
2160415 TTTCCTACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.43
Consensus pattern (18 bp):
TTTTCATCAAATGAGTCT
Found at i:2167091 original size:17 final size:17
Alignment explanation
Indices: 2167051--2167100 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 17
2167041 CATACAATAA
*
2167051 AACCTCAATAAATTAAT
1 AACCTCGATAAATTAAT
2167068 -A-CTCGATAAATTAAT
1 AACCTCGATAAATTAAT
2167083 AACCTCGATTAAA-TAAT
1 AACCTCGA-TAAATTAAT
2167100 A
1 A
2167101 TTTTTAACCA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 13 0.45
16 2 0.07
17 10 0.34
18 4 0.14
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (17 bp):
AACCTCGATAAATTAAT
Found at i:2167933 original size:8 final size:8
Alignment explanation
Indices: 2167885--2167962 Score: 52
Period size: 8 Copynumber: 10.0 Consensus size: 8
2167875 ACCTTGATAA
2167885 ATTAATTT
1 ATTAATTT
* *
2167893 -TTTATTA
1 ATTAATTT
2167900 ATTAATTT
1 ATTAATTT
*
2167908 ATAAATTT
1 ATTAATTT
*
2167916 A-TAAATT
1 ATTAATTT
2167923 ATTAATTT
1 ATTAATTT
* *
2167931 ATTGATTA
1 ATTAATTT
* **
2167939 AATAATAG
1 ATTAATTT
2167947 ATTAATTT
1 ATTAATTT
*
2167955 ATAAATTT
1 ATTAATTT
2167963 TCATAGTCCC
Statistics
Matches: 50, Mismatches: 18, Indels: 4
0.69 0.25 0.06
Matches are distributed among these distances:
7 10 0.20
8 40 0.80
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (8 bp):
ATTAATTT
Found at i:2167950 original size:27 final size:27
Alignment explanation
Indices: 2167878--2167950 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 27
2167868 AAAAAATACC
***
2167878 TTGATAAATTAATTTTTTATTAATTAA
1 TTGATAAATTAATAAATTATTAATTAA
* * *
2167905 TTTATAAATTTATAAATTATTAATTTA
1 TTGATAAATTAATAAATTATTAATTAA
*
2167932 TTGATTAAA-TAATAGATTA
1 TTGA-TAAATTAATAAATTA
2167951 ATTTATAAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
27 32 0.89
28 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (27 bp):
TTGATAAATTAATAAATTATTAATTAA
Found at i:2167954 original size:39 final size:38
Alignment explanation
Indices: 2167885--2167961 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 38
2167875 ACCTTGATAA
* * **
2167885 ATTAATTTTTTATTAATTAATTTATAAATTTATAAATT
1 ATTAATTTTTGATTAAATAATAGATAAATTTATAAATT
*
2167923 ATTAATTTATTGATTAAATAATAGATTAATTTATAAATT
1 ATTAATTT-TTGATTAAATAATAGATAAATTTATAAATT
2167962 TTCATAGTCC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
38 8 0.24
39 25 0.76
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (38 bp):
ATTAATTTTTGATTAAATAATAGATAAATTTATAAATT
Found at i:2172569 original size:15 final size:14
Alignment explanation
Indices: 2172533--2172571 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
2172523 TTCTTTTTTC
*
2172533 TTTTCTTCTAATTCT
1 TTTTC-TCTTATTCT
2172548 TTTTCTCTTATTCT
1 TTTTCTCTTATTCT
2172562 TCTTTCTCTT
1 T-TTTCTCTT
2172572 TTTATGTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCTCTTATTCT
Found at i:2172574 original size:23 final size:21
Alignment explanation
Indices: 2172523--2172564 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 21
2172513 TATTTTCGCT
2172523 TTCTTTTTTCTTTTCTTCTAA
1 TTCTTTTTTCTTTTCTTCTAA
2172544 TTCTTTTTCTCTTATTCTTCT
1 TTCTTTTT-TCTT-TTCTTCT
2172565 TTCTCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 7 0.37
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.71
Consensus pattern (21 bp):
TTCTTTTTTCTTTTCTTCTAA
Found at i:2175067 original size:13 final size:13
Alignment explanation
Indices: 2175025--2175067 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
2175015 AGAATTTCAT
*
2175025 AAAAAGCTCTTAA
1 AAAAAGATCTTAA
2175038 AAAAA-ATC-TAA
1 AAAAAGATCTTAA
2175049 AAAAAGATCTTAA
1 AAAAAGATCTTAA
2175062 AAAAAG
1 AAAAAG
2175068 TTCTAATTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 8 0.30
12 5 0.19
13 14 0.52
ACGTcount: A:0.65, C:0.09, G:0.07, T:0.19
Consensus pattern (13 bp):
AAAAAGATCTTAA
Found at i:2175333 original size:15 final size:14
Alignment explanation
Indices: 2175311--2175350 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 14
2175301 TCTTTTTTAG
2175311 TTTTTTTTTTCATT
1 TTTTTTTTTTCATT
2175325 TTATTTTTTTTCATT
1 TT-TTTTTTTTCATT
2175340 TTTTTTCTTTT
1 TTTTTT-TTTT
2175351 GAGTTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTTCATT
Found at i:2183060 original size:21 final size:21
Alignment explanation
Indices: 2183035--2183078 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2183025 ATTTCAATGA
*
2183035 TTGATTATATTTTGTATTGAT
1 TTGATTATATTTTGTACTGAT
2183056 TTGATTATATTTTGTACTGAT
1 TTGATTATATTTTGTACTGAT
2183077 TT
1 TT
2183079 AAGTATTCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.02, G:0.14, T:0.61
Consensus pattern (21 bp):
TTGATTATATTTTGTACTGAT
Found at i:2188732 original size:19 final size:19
Alignment explanation
Indices: 2188709--2188746 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
2188699 CTTTTCTTCT
2188709 TTTTC-CTTTCCTTTCTTTC
1 TTTTCTCTTTCC-TTCTTTC
*
2188728 TTTTCTCTTTTCTTCTTTC
1 TTTTCTCTTTCCTTCTTTC
2188747 AAAGGTGCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTCTCTTTCCTTCTTTC
Found at i:2192363 original size:23 final size:23
Alignment explanation
Indices: 2192333--2192381 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
2192323 TAGCACTGCA
*
2192333 TGACTTATTGAT-AGATCATTGCG
1 TGACTTATTGATAAG-GCATTGCG
2192356 TGACTTATTGATAAGGCATTGCG
1 TGACTTATTGATAAGGCATTGCG
2192379 TGA
1 TGA
2192382 TTGTTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (23 bp):
TGACTTATTGATAAGGCATTGCG
Found at i:2199464 original size:9 final size:9
Alignment explanation
Indices: 2199450--2199474 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2199440 ATAGGTGATG
2199450 TAAAACTCA
1 TAAAACTCA
2199459 TAAAACTCA
1 TAAAACTCA
2199468 TAAAACT
1 TAAAACT
2199475 GCACTAGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.20, G:0.00, T:0.24
Consensus pattern (9 bp):
TAAAACTCA
Found at i:2208636 original size:11 final size:11
Alignment explanation
Indices: 2208620--2208658 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2208610 TTAATTATCT
2208620 TAATTTTTATA
1 TAATTTTTATA
*
2208631 TAATTTTAATA
1 TAATTTTTATA
*
2208642 TAATTAATTATA
1 TAATT-TTTATA
2208654 TAATT
1 TAATT
2208659 ATAAAATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 15 0.62
12 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:2218575 original size:74 final size:74
Alignment explanation
Indices: 2218304--2218564 Score: 299
Period size: 74 Copynumber: 3.5 Consensus size: 74
2218294 TAGACAGAGT
* * * * * *
2218304 GCTCTTACTTAACTAACCATACTTCTTAGTCGATTAAG-TCTTCTCTATCTTATAATTGAATTTT
1 GCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTTC-TCTCTATCTTGTAATTGAAATCT
* * *
2218368 CTAGTAGAGA
65 CTGGCAGTGA
* * * *
2218378 ACTCTTAATTGACTAATCATGCTTCTTAATCGATTAAGTTCTCTCTATCTTGTAATTGAAATCTC
1 GCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTTCTCTCTATCTTGTAATTGAAATCTC
* *
2218443 TGGCAATTA
66 TGGCAGTGA
* * * * *
2218452 GATCTTAGTTGACTAACCTTGCTTCTTAGTCGATTAAGTTCTCTGTGTCTTGTAATTGAAGTCTC
1 GCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTTCTCTCTATCTTGTAATTGAAATCTC
2218517 TGGCAGTGA
66 TGGCAGTGA
* * *
2218526 GCTCTTAGTTGACTAACCATGCTTTTTATTCGACTAAGT
1 GCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGT
2218565 CTTCTTTGTC
Statistics
Matches: 156, Mismatches: 30, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
74 154 0.99
75 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.41
Consensus pattern (74 bp):
GCTCTTAGTTGACTAACCATGCTTCTTAGTCGATTAAGTTCTCTCTATCTTGTAATTGAAATCTC
TGGCAGTGA
Found at i:2220869 original size:100 final size:100
Alignment explanation
Indices: 2220696--2220898 Score: 388
Period size: 100 Copynumber: 2.0 Consensus size: 100
2220686 CAAGAATTTC
2220696 ATACTCTCCCTCATTACTCTCAATATTCAGCAAATTTCTCAAATCTATAGTATTAACCACAAATT
1 ATACTCTCCCTCATTACTCTCAATATTCAGCAAATTTCTCAAATCTATAGTATTAACCACAAATT
2220761 CCTTCTCATTTAAAAATACATTAATATCATCCTTA
66 CCTTCTCATTTAAAAATACATTAATATCATCCTTA
* *
2220796 ATACTCTCCCTCATTACTCTTAATATTCAGCAAATTTCTCAAATCTATAGTATTAACCATAAATT
1 ATACTCTCCCTCATTACTCTCAATATTCAGCAAATTTCTCAAATCTATAGTATTAACCACAAATT
2220861 CCTTCTCATTTAAAAATACATTAATATCATCCTTA
66 CCTTCTCATTTAAAAATACATTAATATCATCCTTA
2220896 ATA
1 ATA
2220899 AAGTCTTCTG
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (100 bp):
ATACTCTCCCTCATTACTCTCAATATTCAGCAAATTTCTCAAATCTATAGTATTAACCACAAATT
CCTTCTCATTTAAAAATACATTAATATCATCCTTA
Found at i:2227520 original size:74 final size:74
Alignment explanation
Indices: 2227395--2227639 Score: 330
Period size: 74 Copynumber: 3.3 Consensus size: 74
2227385 TAGAGTGCTT
* * * * * * * * * *
2227395 TTAGTTTACTAACCATGCTTCTTAGTCGATTAAATTTTCTTTGTCTAGTAATTGAATTCTTTGGG
1 TTAGTTGACTAACCATGCTTCTTAGTCAATTAAGTTCTCTCTATCTTGTAATTGAAGTCTCTGGC
*
2227460 AGTGAGCTC
66 AATGAGCTC
* * *
2227469 ATAGTTGGCTAACCATGTTTCTTAGTCAATTAAGTTCTCTCTATCTTGTAATTGAAGTCTCTGGC
1 TTAGTTGACTAACCATGCTTCTTAGTCAATTAAGTTCTCTCTATCTTGTAATTGAAGTCTCTGGC
2227534 AATGAGCTC
66 AATGAGCTC
* *
2227543 TTAGTTGACT-ACCATGCTTTTTAGTCAATTAAGTTCTCTCTATCTTGTAATTGAAGTCTCTAGC
1 TTAGTTGACTAACCATGCTTCTTAGTCAATTAAGTTCTCTCTATCTTGTAATTGAAGTCTCTGGC
*
2227607 ACTGAGCTC
66 AATGAGCTC
2227616 TTAGTTGACTAACCATGCTTCTTA
1 TTAGTTGACTAACCATGCTTCTTA
2227640 ATCGACTAAG
Statistics
Matches: 149, Mismatches: 21, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
73 69 0.46
74 80 0.54
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (74 bp):
TTAGTTGACTAACCATGCTTCTTAGTCAATTAAGTTCTCTCTATCTTGTAATTGAAGTCTCTGGC
AATGAGCTC
Found at i:2230413 original size:63 final size:63
Alignment explanation
Indices: 2230280--2230413 Score: 144
Period size: 63 Copynumber: 2.1 Consensus size: 63
2230270 GTTGTGGAAA
* * * * * * *
2230280 AATCGACATCTTAAGAAAGAAGAATCAATTCTTTATAAATAGAAAGTTCCAAAGTTTATGAAG
1 AATCGACATCTCAAAAAAGAAGAATCAACTCTTTATAAAAAAAAAGTACCAAACTTTATGAAG
** * * *
2230343 AGCCGACATCTCAAAAAAGAAGAATCGACTCTTTA-AAGAAAAAAAGTACTAGACTTTATGAAG
1 AATCGACATCTCAAAAAAGAAGAATCAACTCTTTATAA-AAAAAAAGTACCAAACTTTATGAAG
2230406 AATCGACA
1 AATCGACA
2230414 ACTTATAATC
Statistics
Matches: 56, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
62 2 0.04
63 54 0.96
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (63 bp):
AATCGACATCTCAAAAAAGAAGAATCAACTCTTTATAAAAAAAAAGTACCAAACTTTATGAAG
Found at i:2233951 original size:17 final size:19
Alignment explanation
Indices: 2233918--2233954 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2233908 TTCCATAATT
2233918 AAAACTCTTTTTAATTTTG
1 AAAACTCTTTTTAATTTTG
*
2233937 AAAA-TCTTTTTATTTTTG
1 AAAACTCTTTTTAATTTTG
2233955 GTAAATTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (19 bp):
AAAACTCTTTTTAATTTTG
Found at i:2234199 original size:67 final size:69
Alignment explanation
Indices: 2234125--2234305 Score: 181
Period size: 76 Copynumber: 2.5 Consensus size: 69
2234115 ATTACATAAC
**
2234125 TTTAGGAATTTCTTTCAAAGTAGGAAACAATTCC-A-ATGAATTTCCC-AAATTAAA-TGCTATC
1 TTTAGGAATTTCTTT-AAAGTAGGAAACAATTCCTATATGAATCACCCAAAATTAAATTG-TATC
*
2234186 TTTAAT
64 CTTAAT
* *
2234192 TTTAGGAATTTCTTTTAAAGTAGAAAAGAATTTCCTATTCTTTATGAATCACCCAAAATTAAATT
1 TTTAGGAATTTC-TTTAAAGTAGGAAACAA-TTCCTA-----TATGAATCACCCAAAATTAAATT
2234257 GTATCCTTAAT
59 GTATCCTTAAT
*
2234268 TTTAGGAATTCACTTTAAAGTAGGAAACAATTTCCTAT
1 TTTAGGAATT-TCTTTAAAGTAGGAAACAA-TTCCTAT
2234306 TTTTTATGAA
Statistics
Matches: 94, Mismatches: 8, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
67 24 0.26
68 7 0.07
69 1 0.01
71 1 0.01
75 9 0.10
76 49 0.52
77 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (69 bp):
TTTAGGAATTTCTTTAAAGTAGGAAACAATTCCTATATGAATCACCCAAAATTAAATTGTATCCT
TAAT
Found at i:2234285 original size:76 final size:76
Alignment explanation
Indices: 2234171--2234330 Score: 234
Period size: 76 Copynumber: 2.1 Consensus size: 76
2234161 TGAATTTCCC
* * *
2234171 AAATTAAATGCTATCTTTAATTTTAGGAATTTCTTTTAAAGTAGAAAAGAATTTCCTATTCTTTA
1 AAATTAAATGCTATCCTTAATTTTAGGAATTTCCTTTAAAGTAGAAAACAATTTCCTATTCTTTA
*
2234236 TGAATCACCCA
66 TGAACCACCCA
* *
2234247 AAATTAAATTG-TATCCTTAATTTTAGGAA-TTCACTTTAAAGTAGGAAACAATTTCCTATTTTT
1 AAATTAAA-TGCTATCCTTAATTTTAGGAATTTC-CTTTAAAGTAGAAAACAATTTCCTATTCTT
2234310 TATGAACCACCCA
64 TATGAACCACCCA
2234323 AAATTAAA
1 AAATTAAA
2234331 CTAGATGGCA
Statistics
Matches: 76, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
75 3 0.04
76 71 0.93
77 2 0.03
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.39
Consensus pattern (76 bp):
AAATTAAATGCTATCCTTAATTTTAGGAATTTCCTTTAAAGTAGAAAACAATTTCCTATTCTTTA
TGAACCACCCA
Found at i:2235095 original size:40 final size:40
Alignment explanation
Indices: 2235040--2235118 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
2235030 TCAAACAGTT
* *
2235040 GAATCCCACAAGATCAATGTTTTTGTTTTTTCATGTAATC
1 GAATCCCACAAGATCAATGTTTGTGTTTTCTCATGTAATC
2235080 GAATCCCACAAGATCAATGTTTGTGTTTTCTCATGTAAT
1 GAATCCCACAAGATCAATGTTTGTGTTTTCTCATGTAAT
2235119 TTTCAAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.41
Consensus pattern (40 bp):
GAATCCCACAAGATCAATGTTTGTGTTTTCTCATGTAATC
Found at i:2241014 original size:73 final size:73
Alignment explanation
Indices: 2240912--2241073 Score: 225
Period size: 73 Copynumber: 2.2 Consensus size: 73
2240902 GACCAAGAGA
* *
2240912 CATTGTTAGTCGACTAAGAGCTTACTGCCAAAAACTGAGTTCAGAAACAGAAACGACTTAATCGA
1 CATTGTTAGTCGACTAAAAGCTTACTGCCAAAAACTGAGTTCAGAAACAGAAACGACTTAATCAA
2240977 CTAAGAAG
66 CTAAGAAG
* * * * * * *
2240985 TATTGTTAGTCAACTAAAAGCTTATTGCCAGAAACTGAGTTCAGAGACATAAATGACTTAATCAA
1 CATTGTTAGTCGACTAAAAGCTTACTGCCAAAAACTGAGTTCAGAAACAGAAACGACTTAATCAA
*
2241050 CTAAGTAG
66 CTAAGAAG
*
2241058 CAATGTTAGTCGACTA
1 CATTGTTAGTCGACTA
2241074 GGAGCATTCT
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (73 bp):
CATTGTTAGTCGACTAAAAGCTTACTGCCAAAAACTGAGTTCAGAAACAGAAACGACTTAATCAA
CTAAGAAG
Found at i:2264663 original size:4 final size:4
Alignment explanation
Indices: 2264646--2264676 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
2264636 TATACATGCA
*
2264646 TATG TATA TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
2264677 TTCATAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.29, C:0.00, G:0.19, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:2265102 original size:12 final size:12
Alignment explanation
Indices: 2265062--2265091 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2265052 TCTAATGACA
2265062 TATATACATATG
1 TATATACATATG
*
2265074 TACATACATATG
1 TATATACATATG
2265086 TATATA
1 TATATA
2265092 TGTATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (12 bp):
TATATACATATG
Found at i:2265404 original size:13 final size:15
Alignment explanation
Indices: 2265369--2265421 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
2265359 TGAATGTATC
* *
2265369 TATATATATACTAAT
1 TATATATATATTATT
*
2265384 AATATATATTATTATT
1 TATATATA-TATTATT
*
2265400 T-TATATATATTGTT
1 TATATATATATTATT
2265414 TATATATA
1 TATATATA
2265422 CATACATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 7 0.23
15 19 0.61
16 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (15 bp):
TATATATATATTATT
Found at i:2268769 original size:24 final size:25
Alignment explanation
Indices: 2268729--2268776 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
2268719 TTATATTTAG
2268729 TTAAAAGAAAATTATCTTGAGTATA
1 TTAAAAGAAAATTATCTTGAGTATA
2268754 TTAAAAG-AAATTATCTTGAGTAT
1 TTAAAAGAAAATTATCTTGAGTAT
2268777 TTAGTCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (25 bp):
TTAAAAGAAAATTATCTTGAGTATA
Found at i:2268881 original size:20 final size:23
Alignment explanation
Indices: 2268842--2268886 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
2268832 TATTTAACTA
2268842 TTTATATTTTATGCATTAT-AGT
1 TTTATATTTTATGCATTATAAGT
*
2268864 TTTATA-TTTA-GTATTATAAGT
1 TTTATATTTTATGCATTATAAGT
2268885 TT
1 TT
2268887 AAATAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 9 0.43
22 6 0.29
ACGTcount: A:0.29, C:0.02, G:0.09, T:0.60
Consensus pattern (23 bp):
TTTATATTTTATGCATTATAAGT
Found at i:2271759 original size:2 final size:2
Alignment explanation
Indices: 2271748--2271778 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2271738 TTATCATCGT
2271748 TA TA -A 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
2271779 AATGTGCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2274230 original size:28 final size:28
Alignment explanation
Indices: 2274173--2274226 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
2274163 ATACATATTG
*
2274173 AAAACAAAGTTATTTACATGCTATGTTA
1 AAAAAAAAGTTATTTACATGCTATGTTA
2274201 AAAAAAAAGTTA-TTACATGCTATGTT
1 AAAAAAAAGTTATTTACATGCTATGTT
2274227 TAAAGTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (28 bp):
AAAAAAAAGTTATTTACATGCTATGTTA
Found at i:2274339 original size:24 final size:25
Alignment explanation
Indices: 2274283--2274340 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 25
2274273 GATAGAGATC
**
2274283 AAGTTATATGCCATGTTGAAAAAAA
1 AAGTTATACACCATGTTGAAAAAAA
2274308 AATTGTTATACACCATGTT-AAAAAAA
1 AA--GTTATACACCATGTTGAAAAAAA
2274334 AAGTTAT
1 AAGTTAT
2274341 TGCACGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
24 5 0.17
25 2 0.07
26 9 0.31
27 13 0.45
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (25 bp):
AAGTTATACACCATGTTGAAAAAAA
Found at i:2274626 original size:117 final size:121
Alignment explanation
Indices: 2274414--2274839 Score: 427
Period size: 126 Copynumber: 3.5 Consensus size: 121
2274404 TATTTTTAAG
* * * * * *
2274414 TGTTTAACTCCAAGAGTTTATATCTTAGTGATATATAAAGATAAAGACTAAGTTACATGCCATTT
1 TGTTTAACTCTAAGAGTTTATATCCTAGTGAAATACAAAGATAAAGAC-AAGTTATATGCCATGT
* * * *
2274479 TGAAAAAAAAAAATTGTTACACATCATGTTGAAAAAAAGTTG-T-TA-G-ATG-CCA
65 TGAAAAAAAAAAATTATTACACGTCATGTTGAAAAAAAATTGTTATACGCATGTACA
* * *
2274531 TGTTTAACTTTAAGAGTTTATGTCCTAATGAAATACAAAGATAAAGATCAAGTTATATGCCATGT
1 TGTTTAACTCTAAGAGTTTATATCCTAGTGAAATACAAAGATAAAGA-CAAGTTATATGCCATGT
* * * *
2274596 TGAAAAAAAAAAATTATTACAGGCCGTGTTGAAAAAAAATTGTTATACGCTATGTTTAAGA
65 TGAAAAAAAAAAATTATTACACGTCATGTTGAAAAAAAATTGTTATACGC-ATG--T-ACA
* *
2274657 TATTTAACTCTAAGAATTTATATCCTAGTGAAATACAAAGATAAA-ACCAAGTTATATGCCATGT
1 TGTTTAACTCTAAGAGTTTATATCCTAGTGAAATACAAAGATAAAGA-CAAGTTATATGCCATGT
* * * *
2274721 TG--AAAAAAAAATTATTACATGTCATGTTGAAAAAAAAAAGTTATTACACGTCATGTTTAAGA
65 TGAAAAAAAAAAATTATTACACGTCATGTTG--AAAAAAAA-TTGTTATACG-CATG--T-ACA
* * *
2274783 TGTTTAATTCTAAGAGTTTATGTCCTAGTGAAATACAAAGATAAAGATTAAGTTATA
1 TGTTTAACTCTAAGAGTTTATATCCTAGTGAAATACAAAGATAAAGA-CAAGTTATA
2274840 CACTATATTT
Statistics
Matches: 260, Mismatches: 34, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
117 90 0.35
118 2 0.01
119 2 0.01
120 1 0.00
122 3 0.01
123 24 0.09
125 28 0.11
126 100 0.38
127 10 0.04
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (121 bp):
TGTTTAACTCTAAGAGTTTATATCCTAGTGAAATACAAAGATAAAGACAAGTTATATGCCATGTT
GAAAAAAAAAAATTATTACACGTCATGTTGAAAAAAAATTGTTATACGCATGTACA
Found at i:2274683 original size:126 final size:127
Alignment explanation
Indices: 2274533--2274839 Score: 442
Period size: 126 Copynumber: 2.4 Consensus size: 127
2274523 AGATGCCATG
* *
2274533 TTTAACTTTAAGAGTTTATGTCCTAATGAAATACAAAGATAAAGATCAAGTTATATGCCATGTTG
1 TTTAACTCTAAGAGTTTATGTCCTAGTGAAATACAAAGATAAAGATCAAGTTATATGCCATGTTG
* ** *
2274598 AAAAAAAAAAATTATTACAGGCCGTGTTGAAAAAAAATTGTTA-TACGC-T-ATGTTTAAGATA
66 --AAAAAAAAATTATTACAGGCCATGTTGAAAAAAAAAAGTTATTACACGTCATGTTTAAGATA
* * *
2274659 TTTAACTCTAAGAATTTATATCCTAGTGAAATACAAAGATAAA-ACCAAGTTATATGCCATGTTG
1 TTTAACTCTAAGAGTTTATGTCCTAGTGAAATACAAAGATAAAGATCAAGTTATATGCCATGTTG
* * *
2274723 AAAAAAAAATTATTACATGTCATGTTGAAAAAAAAAAGTTATTACACGTCATGTTTAAGATG
66 AAAAAAAAATTATTACAGGCCATGTTGAAAAAAAAAAGTTATTACACGTCATGTTTAAGATA
* *
2274785 TTTAATTCTAAGAGTTTATGTCCTAGTGAAATACAAAGATAAAGATTAAGTTATA
1 TTTAACTCTAAGAGTTTATGTCCTAGTGAAATACAAAGATAAAGATCAAGTTATA
2274840 CACTATATTT
Statistics
Matches: 160, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
123 36 0.22
124 4 0.03
125 21 0.13
126 90 0.56
127 9 0.06
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (127 bp):
TTTAACTCTAAGAGTTTATGTCCTAGTGAAATACAAAGATAAAGATCAAGTTATATGCCATGTTG
AAAAAAAAATTATTACAGGCCATGTTGAAAAAAAAAAGTTATTACACGTCATGTTTAAGATA
Found at i:2274746 original size:27 final size:29
Alignment explanation
Indices: 2274716--2274777 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
2274706 AGTTATATGC
*
2274716 CATGTTG-AAAAAAAAA-TTATTACATGT
1 CATGTTGAAAAAAAAAAGTTATTACACGT
2274743 CATGTTGAAAAAAAAAAGTTATTACACGT
1 CATGTTGAAAAAAAAAAGTTATTACACGT
2274772 CATGTT
1 CATGTT
2274778 TAAGATGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 7 0.22
28 9 0.28
29 16 0.50
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (29 bp):
CATGTTGAAAAAAAAAAGTTATTACACGT
Found at i:2274883 original size:126 final size:124
Alignment explanation
Indices: 2274530--2274900 Score: 390
Period size: 126 Copynumber: 2.9 Consensus size: 124
2274520 GTTAGATGCC
*
2274530 ATGTTTAACTT-TAAGAGTTTATGTCCTAATGAAATACAAAGATAAAGATCAAGTTATATGCCAT
1 ATGTTTAA-TTCTAAGAGTTTATGTCCTAGTGAAATACAAAGATAAAGATCAAGTTATATGCCAT
* * * * * *
2274594 GTTGAAAAAAAAAAATTATTACAGGCCGTGTTGAAAAAAAA-TTGTTATACG-CTATGTTTAAG
65 -TT-TAAAAAAAAAATTATTACAAGTCATGTT-AAAAAAAAGTTATTACACGTC-ATGTTTAAG
* * * * * *
2274656 ATATTTAACTCTAAGAATTTATATCCTAGTGAAATACAAAGATAAA-ACCAAGTTATATGCCATG
1 ATGTTTAATTCTAAGAGTTTATGTCCTAGTGAAATACAAAGATAAAGATCAAGTTATATGCCATT
* *
2274720 TTGAAAAAAAAATTATTACATGTCATGTTGAAAAAAAAAAGTTATTACACGTCATGTTTAAG
66 TTAAAAAAAAAATTATTACAAGTCATGTT---AAAAAAAAGTTATTACACGTCATGTTTAAG
* ** *
2274782 ATGTTTAATTCTAAGAGTTTATGTCCTAGTGAAATACAAAGATAAAGATTAAGTTATACACTATA
1 ATGTTTAATTCTAAGAGTTTATGTCCTAGTGAAATACAAAGATAAAGATCAAGTTATATGC--CA
* *** * * *
2274847 TTTTAAAAATATTGTTGTTACAAGTCATGTTTAAAAAACGTTATTACACGTCAT
64 TTTTAAAAAAAAAATTATTACAAGTCATGTTAAAAAAAAGTTATTACACGTCAT
2274901 ATTGAAAAAA
Statistics
Matches: 203, Mismatches: 34, Indels: 16
0.80 0.13 0.06
Matches are distributed among these distances:
123 23 0.11
124 1 0.00
125 25 0.12
126 119 0.59
127 11 0.05
129 24 0.12
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (124 bp):
ATGTTTAATTCTAAGAGTTTATGTCCTAGTGAAATACAAAGATAAAGATCAAGTTATATGCCATT
TTAAAAAAAAAATTATTACAAGTCATGTTAAAAAAAAGTTATTACACGTCATGTTTAAG
Found at i:2277820 original size:36 final size:37
Alignment explanation
Indices: 2277734--2277828 Score: 113
Period size: 36 Copynumber: 2.6 Consensus size: 37
2277724 TACGTATTCA
* * *
2277734 TGTGATACAATGCCCTACATCATGGCCCTTATATGTG
1 TGTGGTACAATGCCCCACATCATGGACCTTATATGTG
** *
2277771 TGTGGTATTATGCCCCAAATCAT-GACCTTCATAT-TG
1 TGTGGTACAATGCCCCACATCATGGACCTT-ATATGTG
2277807 TGTGGTACAATGCCCCACATCA
1 TGTGGTACAATGCCCCACATCA
2277829 AAGCACTCAT
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
36 26 0.54
37 22 0.46
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (37 bp):
TGTGGTACAATGCCCCACATCATGGACCTTATATGTG
Found at i:2278976 original size:33 final size:32
Alignment explanation
Indices: 2278939--2279016 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 32
2278929 TCATGTCACA
* *
2278939 TTAGTATACCACATTATCATCAATTATGATAT
1 TTAGTATGCCACATCATCATCAATTATGATAT
*
2278971 GTTAGTATGCCACATCATCATTAATTATGATAT
1 -TTAGTATGCCACATCATCATCAATTATGATAT
2279004 TTCAGTATGCCAC
1 TT-AGTATGCCAC
2279017 GTTAGTGTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 2 0.05
33 39 0.95
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.38
Consensus pattern (32 bp):
TTAGTATGCCACATCATCATCAATTATGATAT
Found at i:2279933 original size:26 final size:27
Alignment explanation
Indices: 2279903--2279969 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
2279893 CAATTTTTCT
2279903 TTGTTATTCTTTTTTTTTCCTCTTT-A
1 TTGTTATTCTTTTTTTTTCCTCTTTAA
*** *
2279929 TTGTT-TTCAAAATTTTTTCCTTTTTAA
1 TTGTTATTC-TTTTTTTTTCCTCTTTAA
2279956 TT-TTATTCTTTTTT
1 TTGTTATTCTTTTTT
2279970 CACTTGAGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
25 3 0.10
26 22 0.71
27 6 0.19
ACGTcount: A:0.13, C:0.12, G:0.03, T:0.72
Consensus pattern (27 bp):
TTGTTATTCTTTTTTTTTCCTCTTTAA
Found at i:2286204 original size:42 final size:42
Alignment explanation
Indices: 2286155--2286247 Score: 177
Period size: 42 Copynumber: 2.2 Consensus size: 42
2286145 TAAAGGGGTT
*
2286155 AGAAGGAATAAGAGAGCTTATACGTAGCATTTCAATAAAGGA
1 AGAAGGAATAAGAGAGCCTATACGTAGCATTTCAATAAAGGA
2286197 AGAAGGAATAAGAGAGCCTATACGTAGCATTTCAATAAAGGA
1 AGAAGGAATAAGAGAGCCTATACGTAGCATTTCAATAAAGGA
2286239 AGAAGGAAT
1 AGAAGGAAT
2286248 CGAAGCTACG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.46, C:0.10, G:0.25, T:0.19
Consensus pattern (42 bp):
AGAAGGAATAAGAGAGCCTATACGTAGCATTTCAATAAAGGA
Found at i:2286404 original size:11 final size:11
Alignment explanation
Indices: 2286388--2286414 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2286378 GCTTTTCCCT
2286388 ATTCTCTCATC
1 ATTCTCTCATC
2286399 ATTCTCTCATC
1 ATTCTCTCATC
2286410 ATTCT
1 ATTCT
2286415 GCGCCGGTTT
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:0.19, C:0.33, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTCTCTCATC
Found at i:2288949 original size:25 final size:26
Alignment explanation
Indices: 2288915--2288964 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2288905 AAGGCATAAA
2288915 TGAA-CTTTTTTATCAACTT-TGTTCG
1 TGAATCTTTTTTATCAA-TTCTGTTCG
*
2288940 TGAATTTTTTTTATCAATTCTGTTC
1 TGAATCTTTTTTATCAATTCTGTTC
2288965 TTGACACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.20, C:0.14, G:0.10, T:0.56
Consensus pattern (26 bp):
TGAATCTTTTTTATCAATTCTGTTCG
Found at i:2289228 original size:15 final size:15
Alignment explanation
Indices: 2289208--2289237 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2289198 GTTCATGTTC
2289208 AGGAAACTTATTTGT
1 AGGAAACTTATTTGT
*
2289223 AGGAAACTTGTTTGT
1 AGGAAACTTATTTGT
2289238 TGTTTTAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (15 bp):
AGGAAACTTATTTGT
Found at i:2289777 original size:15 final size:14
Alignment explanation
Indices: 2289741--2289778 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
2289731 GAGGAACTAA
2289741 ATTGGACATTGTTT
1 ATTGGACATTGTTT
2289755 ATTGGACATTGTTT
1 ATTGGACATTGTTT
*
2289769 TTGTGGACAT
1 AT-TGGACAT
2289779 ACATATTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.21, C:0.08, G:0.24, T:0.47
Consensus pattern (14 bp):
ATTGGACATTGTTT
Found at i:2304297 original size:17 final size:17
Alignment explanation
Indices: 2304275--2304307 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2304265 TTAATAATAA
2304275 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
2304292 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
2304308 TTATCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:2307654 original size:80 final size:79
Alignment explanation
Indices: 2307510--2307816 Score: 370
Period size: 80 Copynumber: 3.9 Consensus size: 79
2307500 ATAACATCTC
* * * * * *
2307510 CATAAATCATCTT-CATGCTTAGCCTATAGTGTATATGACTATTTCAACGCATACAACTCGTGGC
1 CATAAATCA-CTTACATGCTTAGCCCATAGTGTACATGACTATCTCAACACATACATCTCATGGC
2307574 ATACATTTCATAGTCT
65 ATACATTTCATAG-CT
* * *
2307590 CATAAATCACTTACAAGCTTAGCCCATAGTGTATATGACTATCTCAACACATGCATCTCATGGCA
1 CATAAATCACTTACATGCTTAGCCCATAGTGTACATGACTATCTCAACACATACATCTCATGGCA
*
2307655 TACATTTCATA--A
66 TACATTTCATAGCT
* ** * *
2307667 CATAAATCACTTACATGCTTAGCCCATAGTGTGCATGACTGGCACAACATATACATCTCATGGCA
1 CATAAATCACTTACATGCTTAGCCCATAGTGTACATGACTATCTCAACACATACATCTCATGGCA
*
2307732 TACATTTAATAGCCT
66 TACATTTCATAG-CT
* * * *
2307747 CGTAAATTACTTACATGCTTAGTCCATAGTGTACATGA-TATACTTAACACATACATCTCATGGC
1 CATAAATCACTTACATGCTTAGCCCATAGTGTACATGACTAT-CTCAACACATACATCTCATGGC
2307811 ATACAT
65 ATACAT
2307817 GTTACAATCT
Statistics
Matches: 195, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
77 67 0.34
79 4 0.02
80 124 0.64
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (79 bp):
CATAAATCACTTACATGCTTAGCCCATAGTGTACATGACTATCTCAACACATACATCTCATGGCA
TACATTTCATAGCT
Found at i:2307796 original size:157 final size:157
Alignment explanation
Indices: 2307510--2307816 Score: 402
Period size: 157 Copynumber: 2.0 Consensus size: 157
2307500 ATAACATCTC
* * *** * *
2307510 CATAAATCATCTTCATGCTTAGCCTATAGTGTATATGACTATTTCAACGCATACAACTCGTGGCA
1 CATAAATCATCTTCATGCTTAGCCCATAGTGTACATGACTAGCACAACACATACAACTCATGGCA
* * *
2307575 TACATTTCATAGTCTCATAAATCACTTACAAGCTTAGCCCATAGTGTATATGACTATCTCAACAC
66 TACATTTAATAGCCTCATAAATCACTTACAAGCTTAGCCCATAGTGTACATGACTATCTCAACAC
*
2307640 ATGCATCTCATGGCATACATTTCATAA
131 ATACATCTCATGGCATACATTTCATAA
* * * *
2307667 CATAAATCA-CTTACATGCTTAGCCCATAGTGTGCATGACTGGCACAACATATACATCTCATGGC
1 CATAAATCATCTT-CATGCTTAGCCCATAGTGTACATGACTAGCACAACACATACAACTCATGGC
* * * * *
2307731 ATACATTTAATAGCCTCGTAAATTACTTACATGCTTAGTCCATAGTGTACATGA-TATACTTAAC
65 ATACATTTAATAGCCTCATAAATCACTTACAAGCTTAGCCCATAGTGTACATGACTAT-CTCAAC
2307795 ACATACATCTCATGGCATACAT
129 ACATACATCTCATGGCATACAT
2307817 GTTACAATCT
Statistics
Matches: 128, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
156 6 0.05
157 122 0.95
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.32
Consensus pattern (157 bp):
CATAAATCATCTTCATGCTTAGCCCATAGTGTACATGACTAGCACAACACATACAACTCATGGCA
TACATTTAATAGCCTCATAAATCACTTACAAGCTTAGCCCATAGTGTACATGACTATCTCAACAC
ATACATCTCATGGCATACATTTCATAA
Found at i:2315833 original size:14 final size:15
Alignment explanation
Indices: 2315814--2315842 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2315804 AATATATTTG
2315814 AATTTGA-TATGAAT
1 AATTTGATTATGAAT
2315828 AATTTGATTATGAAT
1 AATTTGATTATGAAT
2315843 CCCTTGGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (15 bp):
AATTTGATTATGAAT
Found at i:2319248 original size:80 final size:80
Alignment explanation
Indices: 2319127--2319308 Score: 260
Period size: 80 Copynumber: 2.3 Consensus size: 80
2319117 ATCTTTATAT
*
2319127 TTAGCCCATAGTGTATATGACCATATCAACACATACATCTCATGGCATATA-TTCTATAAGCTCA
1 TTAGCCCATAGTGTATATGACCATATCAACACATACATCTCATGGCATACATTTC-ATAAGCTCA
2319191 TAAATCACTTACATG-
65 TAAATCACTTACATGC
* * * * * *
2319206 TGTAGCCCATAATGTATATGACTATCTCGACACATACTTCTCATGGCATACATTTCATAATCTCA
1 T-TAGCCCATAGTGTATATGACCATATCAACACATACATCTCATGGCATACATTTCATAAGCTCA
2319271 TAAATCACTTACATGC
65 TAAATCACTTACATGC
*
2319287 TTAGCCCATAGTATATATGACC
1 TTAGCCCATAGTGTATATGACC
2319309 TTTCATAGCC
Statistics
Matches: 90, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
79 1 0.01
80 85 0.94
81 4 0.04
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.32
Consensus pattern (80 bp):
TTAGCCCATAGTGTATATGACCATATCAACACATACATCTCATGGCATACATTTCATAAGCTCAT
AAATCACTTACATGC
Found at i:2319322 original size:51 final size:51
Alignment explanation
Indices: 2319258--2319358 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
2319248 ATGGCATACA
* *
2319258 TTTCATAATCTCATAAATCACTTACATGCTTAGCCCATAGTATATATGACC
1 TTTCATAACCTCATAAATCACTTACATGCTTAGCCCATAATATATATGACC
* * *
2319309 TTTCATAGCCTCATAAATCACTTACATGCTTAGCCTATAATGTATATGAC
1 TTTCATAACCTCATAAATCACTTACATGCTTAGCCCATAATATATATGAC
2319359 TATCTCAACA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.36
Consensus pattern (51 bp):
TTTCATAACCTCATAAATCACTTACATGCTTAGCCCATAATATATATGACC
Found at i:2319421 original size:131 final size:131
Alignment explanation
Indices: 2319187--2319426 Score: 385
Period size: 131 Copynumber: 1.8 Consensus size: 131
2319177 ATTCTATAAG
* *
2319187 CTCATAAATCACTTACATGTGTAGCCCATAATGTATATGACTATCTCGACACATACTTCTCATGG
1 CTCATAAATCACTTACATGTGTAGCCCATAATGTATATGACTATCTCAACACATACATCTCATGG
* *
2319252 CATACATTTCATAATCTCATAAATCACTTACATGCTTAGCCCATAGTATATATGACCTTTCATAG
66 CATACATTCCATAATCTCATAAATCACTTACAAGCTTAGCCCATAGTATATATGACCTTTCATAG
2319317 C
131 C
* *
2319318 CTCATAAATCACTTACATGCT-TAGCCTATAATGTATATGACTATCTCAACATATACATCTCATG
1 CTCATAAATCACTTACATG-TGTAGCCCATAATGTATATGACTATCTCAACACATACATCTCATG
*
2319382 GCATACATTCCATAATGCT-ATATATCACTTACAAGCTTAGCCCAT
65 GCATACATTCCATAAT-CTCATAAATCACTTACAAGCTTAGCCCAT
2319427 TGTGTACATG
Statistics
Matches: 100, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
131 97 0.97
132 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (131 bp):
CTCATAAATCACTTACATGTGTAGCCCATAATGTATATGACTATCTCAACACATACATCTCATGG
CATACATTCCATAATCTCATAAATCACTTACAAGCTTAGCCCATAGTATATATGACCTTTCATAG
C
Found at i:2319492 original size:80 final size:80
Alignment explanation
Indices: 2319312--2319549 Score: 262
Period size: 80 Copynumber: 3.0 Consensus size: 80
2319302 TATGACCTTT
* * * *
2319312 CATAGCCTCATAAATCACTTACATGCTTAGCCTATAATGTATATGACTATCTCAACATATACATC
1 CATAGCCCCATAAATCACTTACATGCTTAGCCTATAGTGTACATGACTAACTCAACATATACATC
2319377 TCATGGCATACATTC
66 TCATGGCATACATTC
*** * * * * * * *
2319392 CATAATGCTATATATCACTTACAAGCTTAGCCCATTGTGTACATGACTACCTCAACATATACATT
1 CATAGCCCCATAAATCACTTACATGCTTAGCCTATAGTGTACATGACTAACTCAACATATACATC
*
2319457 TCATGGCATACATTT
66 TCATGGCATACATTC
* * * * * *
2319472 TATAGCCCCGTAAATGACTTACATGTTTAGCCTATAGTGTACATGA-TATACTTAACACATACAT
1 CATAGCCCCATAAATCACTTACATGCTTAGCCTATAGTGTACATGACTA-ACTCAACATATACAT
*
2319536 CTCTTGGCATACAT
65 CTCATGGCATACAT
2319550 GTTACAATCT
Statistics
Matches: 126, Mismatches: 31, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
79 2 0.02
80 124 0.98
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.33
Consensus pattern (80 bp):
CATAGCCCCATAAATCACTTACATGCTTAGCCTATAGTGTACATGACTAACTCAACATATACATC
TCATGGCATACATTC
Found at i:2328824 original size:15 final size:16
Alignment explanation
Indices: 2328804--2328836 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2328794 CTCAAGAGAA
*
2328804 AAAGGGTT-TTCAATG
1 AAAGGGTTAATCAATG
2328819 AAAGGGTTAATCAATG
1 AAAGGGTTAATCAATG
2328835 AA
1 AA
2328837 GTTGTAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (16 bp):
AAAGGGTTAATCAATG
Found at i:2332067 original size:22 final size:23
Alignment explanation
Indices: 2332036--2332082 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2332026 ATATAGAGTT
*
2332036 ATTTAAGCTTAATTTTTATAGTA
1 ATTTAAGCTTAATTCTTATAGTA
*
2332059 ATTT-AGCTTAGTTCTTATAGTA
1 ATTTAAGCTTAATTCTTATAGTA
2332081 AT
1 AT
2332083 ACATAGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.32, C:0.06, G:0.11, T:0.51
Consensus pattern (23 bp):
ATTTAAGCTTAATTCTTATAGTA
Found at i:2345164 original size:20 final size:20
Alignment explanation
Indices: 2345141--2345179 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2345131 CACTATTGGA
* *
2345141 TGTCATATTATCATATTCAG
1 TGTCACATTACCATATTCAG
2345161 TGTCACATTACCATATTCA
1 TGTCACATTACCATATTCA
2345180 ATATCACGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.41
Consensus pattern (20 bp):
TGTCACATTACCATATTCAG
Found at i:2345186 original size:20 final size:20
Alignment explanation
Indices: 2345147--2345186 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2345137 TGGATGTCAT
* * *
2345147 ATTATCATATTCAGTGTCAC
1 ATTACCATATTCAATATCAC
2345167 ATTACCATATTCAATATCAC
1 ATTACCATATTCAATATCAC
2345187 GTTAGTAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.38
Consensus pattern (20 bp):
ATTACCATATTCAATATCAC
Found at i:2347305 original size:2 final size:2
Alignment explanation
Indices: 2347298--2347325 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2347288 CCTCTATGGA
2347298 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
2347326 TTATCAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2349143 original size:2 final size:2
Alignment explanation
Indices: 2349136--2349169 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2349126 TGAATGGTAT
2349136 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
2349170 ACATTTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.