Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 19 of 171
Found at i:8728415 original size:63 final size:63
Alignment explanation
Indices: 8728311--8728431 Score: 197
Period size: 63 Copynumber: 1.9 Consensus size: 63
8728301 TTCTCAAATA
* *
8728311 TTGAGCTAGAAATGATAAAGACATGAGAACATTAGAACTTGAAACCAGCACTATCTTTATTAT
1 TTGAGCTAAAAATGATAAAGACATGAGAACATTAGAACTTGAAACCAGCACTACCTTTATTAT
* * *
8728374 TTGAGTTAAAAATGATAAATACATGAGAACATTAGAGCTTGAAACCAGCACTACCTTT
1 TTGAGCTAAAAATGATAAAGACATGAGAACATTAGAACTTGAAACCAGCACTACCTTT
8728432 GCAACAAAGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (63 bp):
TTGAGCTAAAAATGATAAAGACATGAGAACATTAGAACTTGAAACCAGCACTACCTTTATTAT
Found at i:8728447 original size:63 final size:63
Alignment explanation
Indices: 8728320--8728447 Score: 161
Period size: 63 Copynumber: 2.0 Consensus size: 63
8728310 ATTGAGCTAG
* ** **
8728320 AAATGATAAAGACATGAGAACATTAGAACTTGAAACCAGCACTATCTTTATTATTTGAGTTAA
1 AAATGATAAAGACATGAGAACATTAGAACTTGAAACCAGCACTACCTTTAACATAAGAGTTAA
* *
8728383 AAATGATAAATACATGAGAACATTAGAGCTTGAAACCAGCACTACCTTTGCAACA-AAGAG-TAA
1 AAATGATAAAGACATGAGAACATTAGAACTTGAAACCAGCACTACCTTT--AACATAAGAGTTAA
8728446 AA
1 AA
8728448 CCATTAGAGT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 51 0.91
64 3 0.05
65 2 0.04
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (63 bp):
AAATGATAAAGACATGAGAACATTAGAACTTGAAACCAGCACTACCTTTAACATAAGAGTTAA
Found at i:8728682 original size:19 final size:19
Alignment explanation
Indices: 8728642--8728683 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
8728632 GGTTGGTGAG
*
8728642 AAAAATAAATATAAATTGT
1 AAAAATAAATATAAATTAT
*
8728661 AAAAAGTAAA-ATACATTAT
1 AAAAA-TAAATATAAATTAT
8728680 AAAA
1 AAAA
8728684 CTTTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAAATAAATATAAATTAT
Found at i:8735511 original size:13 final size:13
Alignment explanation
Indices: 8735476--8735501 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8735466 ATTGTGAAAC
8735476 TGAAATTGATATT
1 TGAAATTGATATT
8735489 TGAAATTGATATT
1 TGAAATTGATATT
8735502 CTAGATTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TGAAATTGATATT
Found at i:8741931 original size:5 final size:5
Alignment explanation
Indices: 8741921--8741967 Score: 80
Period size: 5 Copynumber: 9.8 Consensus size: 5
8741911 TTTGCCCCAT
8741921 TCTCA TCTCA TCTCA TCTCA TCTCA TCTCA TCTCA TCTC- TCTC- TCTC
1 TCTCA TCTCA TCTCA TCTCA TCTCA TCTCA TCTCA TCTCA TCTCA TCTC
8741968 TCTTAATCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 8 0.19
5 34 0.81
ACGTcount: A:0.15, C:0.43, G:0.00, T:0.43
Consensus pattern (5 bp):
TCTCA
Found at i:8749480 original size:21 final size:22
Alignment explanation
Indices: 8749455--8749504 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
8749445 GGAGGGAGTG
*
8749455 GGGAGAGACAT-GAGTGGGAGA
1 GGGAGAGAAATGGAGTGGGAGA
*
8749476 GGGAGAGAAATGGAGTGGGATA
1 GGGAGAGAAATGGAGTGGGAGA
*
8749498 AGGAGAG
1 GGGAGAG
8749505 GTAAGGGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.36, C:0.02, G:0.52, T:0.10
Consensus pattern (22 bp):
GGGAGAGAAATGGAGTGGGAGA
Found at i:8749993 original size:23 final size:23
Alignment explanation
Indices: 8749967--8750010 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
8749957 AAATCATAAA
8749967 TTAATATATAAAAAAATTATATT
1 TTAATATATAAAAAAATTATATT
* * *
8749990 TTAATTTCTCAAAAAATTATA
1 TTAATATATAAAAAAATTATA
8750011 ATTGGATTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (23 bp):
TTAATATATAAAAAAATTATATT
Found at i:8750387 original size:33 final size:33
Alignment explanation
Indices: 8750340--8750402 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
8750330 AATTACTCTT
* *
8750340 TTTTTTCCCGTATAGT-AGGCTAAATAGTTATAA
1 TTTTTTCCCCTATAGTAAGG-TAAACAGTTATAA
8750373 TTTTTTCCCCTATAGTAAGGTAAACAGTTA
1 TTTTTTCCCCTATAGTAAGGTAAACAGTTA
8750403 CCTTAATGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 24 0.89
34 3 0.11
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (33 bp):
TTTTTTCCCCTATAGTAAGGTAAACAGTTATAA
Found at i:8751605 original size:18 final size:20
Alignment explanation
Indices: 8751569--8751605 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
8751559 AAAACAAAAA
*
8751569 AAAAAACACTGAATGTTGTC
1 AAAAAACACTGAATCTTGTC
8751589 AAAAAA-ACT-AATCTTGT
1 AAAAAACACTGAATCTTGT
8751606 TTCCCAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 7 0.44
19 3 0.19
20 6 0.38
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (20 bp):
AAAAAACACTGAATCTTGTC
Found at i:8757088 original size:16 final size:15
Alignment explanation
Indices: 8757051--8757090 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
8757041 TTTATTTTAA
*
8757051 TAATCATTTAAAAAT
1 TAATAATTTAAAAAT
*
8757066 TAATAATTTAAAATT
1 TAATAATTTAAAAAT
8757081 TAAATAATTT
1 T-AATAATTT
8757091 TATTGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATAATTTAAAAAT
Found at i:8757146 original size:20 final size:21
Alignment explanation
Indices: 8757107--8757146 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
8757097 AAAATATTTT
*
8757107 ATATTAATATTTTAATAATAA
1 ATATAAATATTTTAATAATAA
8757128 ATATAAATATTTT-ATAATA
1 ATATAAATATTTTAATAATA
8757147 TAGATACAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATAAATATTTTAATAATAA
Found at i:8758974 original size:18 final size:16
Alignment explanation
Indices: 8758951--8758985 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
8758941 AATAAGATTA
8758951 AATTTATCATTTAGTCTT
1 AATTTATC-TTTAG-CTT
8758969 AATTTATCTTTAGCTT
1 AATTTATCTTTAGCTT
8758985 A
1 A
8758986 TAAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 5 0.29
18 8 0.47
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (16 bp):
AATTTATCTTTAGCTT
Found at i:8760506 original size:20 final size:20
Alignment explanation
Indices: 8760481--8760519 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
8760471 TTTGAAGTTT
*
8760481 ATTGATGAATATTTTATATA
1 ATTGATAAATATTTTATATA
8760501 ATTGATAAATATTTTATAT
1 ATTGATAAATATTTTATAT
8760520 TTAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTGATAAATATTTTATATA
Found at i:8760569 original size:23 final size:24
Alignment explanation
Indices: 8760505--8760573 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 24
8760495 TATATAATTG
*
8760505 ATAAATATTTTATATTT-AAATATT
1 ATAAATATATTA-ATTTAAAATATT
* *
8760529 ATTTAATATCATTCATTTAAAATATT
1 A-TAAATAT-ATTAATTTAAAATATT
8760555 A-AAATATATTAATTTAAAA
1 ATAAATATATTAATTTAAAA
8760574 AATTTAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 11 0.30
24 6 0.16
25 10 0.27
26 10 0.27
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (24 bp):
ATAAATATATTAATTTAAAATATT
Found at i:8760930 original size:15 final size:15
Alignment explanation
Indices: 8760910--8760943 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
8760900 GATTAAAAAT
8760910 TAATAA-AAATTTAAA
1 TAATAATAAA-TTAAA
8760925 TAATAATAAATTAAA
1 TAATAATAAATTAAA
8760940 TAAT
1 TAAT
8760944 TTTGATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.83
16 3 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAATAATAAATTAAA
Found at i:8771925 original size:109 final size:109
Alignment explanation
Indices: 8771734--8771952 Score: 429
Period size: 109 Copynumber: 2.0 Consensus size: 109
8771724 GTTAGAGTGC
8771734 GTTCATGTAATTTGCCACCTGATTTTTATTTAAAAAAAATTAATGGTGAAATGAGCTGTAAGTTG
1 GTTCATGTAATTTGCCACCTGATTTTTATTTAAAAAAAATTAATGGTGAAATGAGCTGTAAGTTG
8771799 TCTCCAGTTTTTATACTCCCCAAAGAATTGGGAAATTAGGAGGA
66 TCTCCAGTTTTTATACTCCCCAAAGAATTGGGAAATTAGGAGGA
*
8771843 GTTCATGTAATTTGCCACCTGATTTTTATTTTAAAAAAATTAATGGTGAAATGAGCTGTAAGTTG
1 GTTCATGTAATTTGCCACCTGATTTTTATTTAAAAAAAATTAATGGTGAAATGAGCTGTAAGTTG
8771908 TCTCCAGTTTTTATACTCCCCAAAGAATTGGGAAATTAGGAGGA
66 TCTCCAGTTTTTATACTCCCCAAAGAATTGGGAAATTAGGAGGA
8771952 G
1 G
8771953 ATTGAATGTT
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
109 109 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.35
Consensus pattern (109 bp):
GTTCATGTAATTTGCCACCTGATTTTTATTTAAAAAAAATTAATGGTGAAATGAGCTGTAAGTTG
TCTCCAGTTTTTATACTCCCCAAAGAATTGGGAAATTAGGAGGA
Found at i:8771989 original size:109 final size:108
Alignment explanation
Indices: 8771766--8771989 Score: 310
Period size: 109 Copynumber: 2.0 Consensus size: 108
8771756 TTTTTATTTA
8771766 AAAAAAATTAATGGTGAAATGAGCTGTAAGTTGTCTCCAGTTTTTATACTCCCCAAAGAATTGGG
1 AAAAAAATTAATGGTGAAATGAGCTGTAAGTTGTCTCCAGTTTTTATACTCCCCAAAGAATTGGG
* * * * ***
8771831 AAATTAGGAGGAGTTCATGTAATTTGCCACCTGATTTTTATTTT
66 AAATTAGGAGGAGAT-ATGTAATTTGCAACATGATTCTTAAAAT
8771875 AAAAAAATTAATGGTGAAATGAGCTGTAAGTTGTCTCCAGTTTTTATACTCCCCAAAGAATTGGG
1 AAAAAAATTAATGGTGAAATGAGCTGTAAGTTGTCTCCAGTTTTTATACTCCCCAAAGAATTGGG
8771940 AAATTAGGAGGAGAT-TG-AATGTT-CTAACAATCGAGTTCTTAAAAT
66 AAATTAGGAGGAGATATGTAAT-TTGC-AAC-AT-GA-TTCTTAAAAT
8771985 AAAAA
1 AAAAA
8771990 TCAGAAAATT
Statistics
Matches: 103, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
106 4 0.04
107 6 0.06
108 1 0.01
109 81 0.79
110 11 0.11
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (108 bp):
AAAAAAATTAATGGTGAAATGAGCTGTAAGTTGTCTCCAGTTTTTATACTCCCCAAAGAATTGGG
AAATTAGGAGGAGATATGTAATTTGCAACATGATTCTTAAAAT
Found at i:8790999 original size:58 final size:58
Alignment explanation
Indices: 8790921--8791057 Score: 188
Period size: 58 Copynumber: 2.3 Consensus size: 58
8790911 AATTTTTGCT
* *
8790921 AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATT-ATATATTA-TTTTATTA
1 AATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAAT-TAATATTTTTATTA
* *
8790981 AATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTAATTAATATTTTTATTA
1 AATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAATATTTTTATTA
8791039 AATTATATTTAATAATAAT
1 AATTATATTTAATAATAAT
8791058 CATTAAAATT
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
57 19 0.27
58 45 0.64
59 2 0.03
60 4 0.06
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (58 bp):
AATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAATATTTTTATTA
Found at i:8791196 original size:39 final size:44
Alignment explanation
Indices: 8791153--8791245 Score: 106
Period size: 46 Copynumber: 2.2 Consensus size: 44
8791143 TTACAACATC
*
8791153 ATTCCATT-CAATCAA-ACATAA-GAA-TA-TTATTACAGCTCT
1 ATTCCATTCCAATCAACAAATAATGAATTACTTATTACAGCTCT
* *
8791192 ATTCCATTCCAATTAACCAAATAATTGAATTACTTATTACAGTTCT
1 ATTCCATTCCAATCAA-CAAATAA-TGAATTACTTATTACAGCTCT
8791238 ATTCCATT
1 ATTCCATT
8791246 ACAGCTCCAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
39 8 0.18
40 6 0.14
42 5 0.11
44 3 0.07
45 2 0.05
46 20 0.45
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (44 bp):
ATTCCATTCCAATCAACAAATAATGAATTACTTATTACAGCTCT
Found at i:8791273 original size:16 final size:16
Alignment explanation
Indices: 8791235--8791278 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
8791225 TTATTACAGT
* *
8791235 TCTATTCCATTACAGC
1 TCTATTCTATTACACC
* *
8791251 TCCATTCTATTATACC
1 TCTATTCTATTACACC
8791267 TCTATTCTATTA
1 TCTATTCTATTA
8791279 GAGCGAACCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.25, C:0.27, G:0.02, T:0.45
Consensus pattern (16 bp):
TCTATTCTATTACACC
Found at i:8792720 original size:20 final size:22
Alignment explanation
Indices: 8792691--8792737 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
8792681 AATTTCATTT
8792691 AAAT-TATTAAATA-T-AATTC
1 AAATATATTAAATATTCAATTC
*
8792710 AAATATATTAACTATTCAATTC
1 AAATATATTAAATATTCAATTC
8792732 AAATAT
1 AAATAT
8792738 TATAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 8 0.33
21 1 0.04
22 11 0.46
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATATTAAATATTCAATTC
Found at i:8792767 original size:21 final size:21
Alignment explanation
Indices: 8792729--8792773 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
8792719 AACTATTCAA
8792729 TTCAAATATTATAATAAAAAAT
1 TTCAAATA-TATAATAAAAAAT
*
8792751 TTCAAATA-ATAATTAAAATAT
1 TTCAAATATATAA-TAAAAAAT
8792772 TT
1 TT
8792774 TTAACGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 9 0.43
22 8 0.38
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
TTCAAATATATAATAAAAAAT
Found at i:8793385 original size:16 final size:17
Alignment explanation
Indices: 8793366--8793401 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
8793356 TATTATTCAA
8793366 AATAATAATTAAG-TAT
1 AATAATAATTAAGTTAT
*
8793382 AATATTAATTAAGTTAT
1 AATAATAATTAAGTTAT
8793399 AAT
1 AAT
8793402 TAAGGCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
AATAATAATTAAGTTAT
Found at i:8798294 original size:183 final size:183
Alignment explanation
Indices: 8797986--8798355 Score: 533
Period size: 183 Copynumber: 2.0 Consensus size: 183
8797976 CAAATGGCAC
8797986 AAATTGTCCCATAAACCCATTCTGTCTTCTAAGGGGATCTTTGACTGATTTGAAACCTCAACTAC
1 AAATTGTCCCATAAACCCATTCTGTCTTCTAAGGGGATCTTTGACTGATTTGAAACCTCAACTAC
* * * *
8798051 ATCCTGAGACCTGACAGACTGAGTAACAGGCCCCTTTCGCAACTCTTGCTGCTCTTCAAACTCAC
66 ATCCTGAAACCTGACAGACTGAGTAACAGACCCCTTTCGCAACCCTTGCAGCTCTTCAAACTCAC
* *
8798116 AGAGGGCATATTGAATTCCTTGGCCATGTTCCAAGCTAGCACTAGTCTTTGAT
131 AGAGGGCATATTGAATTCCTTGGCCATATTCCAAGCTAGCACTAGTCTTTAAT
* *** ** * **
8798169 AAATTGTCCCATGAACTGGTTCTGTCTTCTAAGGGGATCTTTGGTTGCTTTGAAGTCTCAACTAC
1 AAATTGTCCCATAAACCCATTCTGTCTTCTAAGGGGATCTTTGACTGATTTGAAACCTCAACTAC
* * * *
8798234 ATCTTGAAACCTGGCAGACTGAGTAACAGACCCCTTTTGCAACCCTTGCAGCTCTTCAAACTCGC
66 ATCCTGAAACCTGACAGACTGAGTAACAGACCCCTTTCGCAACCCTTGCAGCTCTTCAAACTCAC
* ** *
8798299 TGAGGGCATATTGAATTCCTTGGCCATATTCTGAGCTATCACTAGTCTTTAAT
131 AGAGGGCATATTGAATTCCTTGGCCATATTCCAAGCTAGCACTAGTCTTTAAT
8798352 AAAT
1 AAAT
8798356 GACTGATTCT
Statistics
Matches: 164, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
183 164 1.00
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (183 bp):
AAATTGTCCCATAAACCCATTCTGTCTTCTAAGGGGATCTTTGACTGATTTGAAACCTCAACTAC
ATCCTGAAACCTGACAGACTGAGTAACAGACCCCTTTCGCAACCCTTGCAGCTCTTCAAACTCAC
AGAGGGCATATTGAATTCCTTGGCCATATTCCAAGCTAGCACTAGTCTTTAAT
Found at i:8803644 original size:6 final size:6
Alignment explanation
Indices: 8803633--8803661 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
8803623 AAGTGAGAAA
8803633 GAAGCG GAAGCG GAAGCG GAAGCG GAAGC
1 GAAGCG GAAGCG GAAGCG GAAGCG GAAGC
8803662 TTTAGTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.48, T:0.00
Consensus pattern (6 bp):
GAAGCG
Found at i:8840013 original size:8 final size:8
Alignment explanation
Indices: 8840002--8840042 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
8839992 ATTAATCTTT
8840002 TAAAATTA
1 TAAAATTA
8840010 TAAAA-TA
1 TAAAATTA
8840017 T-AAATTA
1 TAAAATTA
*
8840024 TTAAAATAA
1 -TAAAATTA
8840033 TAAAATTA
1 TAAAATTA
8840041 TA
1 TA
8840043 TTTTTTACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
6 3 0.11
7 5 0.18
8 15 0.54
9 5 0.18
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
TAAAATTA
Found at i:8840072 original size:23 final size:23
Alignment explanation
Indices: 8840029--8840072 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
8840019 AATTATTAAA
* **
8840029 ATAATAAAATTATATTTTTTACT
1 ATAATAAAAATATATAATTTACT
8840052 ATAATAAAAATATATAATTTA
1 ATAATAAAAATATATAATTTA
8840073 ATTCCGATCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (23 bp):
ATAATAAAAATATATAATTTACT
Found at i:8858616 original size:29 final size:27
Alignment explanation
Indices: 8858584--8858639 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
8858574 TTTTTGTGGT
* *
8858584 TTTTTTTTAATTTTAATACTATAAAAATA
1 TTTTATTTAAATTTAA-A-TATAAAAATA
8858613 TTTTATTTAAATTTAAATATAAAAATA
1 TTTTATTTAAATTTAAATATAAAAATA
8858640 ATATTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.40
28 1 0.04
29 14 0.56
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTTATTTAAATTTAAATATAAAAATA
Found at i:8858643 original size:30 final size:30
Alignment explanation
Indices: 8858583--8858650 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
8858573 TTTTTTGTGG
* * * *
8858583 TTTTTTTTTAATTTTAATACTATAAAAATA
1 TTTTATTTAAATTTAAATACTAAAAAAATA
8858613 TTTTATTTAAATTTAAATA-TAAAAATAATA
1 TTTTATTTAAATTTAAATACTAAAAA-AATA
8858643 TTTTATTT
1 TTTTATTT
8858651 GATGGAATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (30 bp):
TTTTATTTAAATTTAAATACTAAAAAAATA
Found at i:8859155 original size:29 final size:30
Alignment explanation
Indices: 8859082--8859159 Score: 97
Period size: 29 Copynumber: 2.6 Consensus size: 30
8859072 TTAGCAAAAG
* *
8859082 AGTGACTAAAATATTAAATTTTGATAACGTT
1 AGTGACTAAAATA-AAAATTTTGATAACATT
8859113 AGTGACTAAAATAAAAACTTTT-A-AACATT
1 AGTGACTAAAATAAAAA-TTTTGATAACATT
*
8859142 GGTGACTAAAATAAAAAT
1 AGTGACTAAAATAAAAAT
8859160 ATGCTAATAG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 1 0.02
29 21 0.49
30 4 0.09
31 17 0.40
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.32
Consensus pattern (30 bp):
AGTGACTAAAATAAAAATTTTGATAACATT
Found at i:8861850 original size:25 final size:24
Alignment explanation
Indices: 8861824--8861877 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
8861814 TATTTATCTT
*
8861824 AATTTTTTTAATTGTTAATATTTTTA
1 AATTTTTTT-ATTATTAAT-TTTTTA
*
8861850 AATTTTTTTATTATTAATTTTTAA
1 AATTTTTTTATTATTAATTTTTTA
8861874 AATT
1 AATT
8861878 GAATGAATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 9 0.35
25 8 0.31
26 9 0.35
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (24 bp):
AATTTTTTTATTATTAATTTTTTA
Found at i:8862659 original size:31 final size:30
Alignment explanation
Indices: 8862598--8862673 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
8862588 TATACAGAAA
* *
8862598 ATTAAATTAATTTATATTTTATATACATTAT
1 ATTAAATT-ATTTAAATCTTATATACATTAT
* *
8862629 ATTAAATTATTTAAATCTTATTTATTATTAT
1 ATTAAATTATTTAAATCTTATATA-CATTAT
*
8862660 ATTTAATT-TTTAAA
1 ATTAAATTATTTAAA
8862674 ATATTTTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
30 19 0.49
31 20 0.51
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (30 bp):
ATTAAATTATTTAAATCTTATATACATTAT
Found at i:8877547 original size:16 final size:15
Alignment explanation
Indices: 8877523--8877556 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
8877513 AGTTTTACTT
*
8877523 TTTAAAAATTAAAAC
1 TTTAAAAAATAAAAC
*
8877538 TTTAAAAAATAAAAT
1 TTTAAAAAATAAAAC
8877553 TTTA
1 TTTA
8877557 TTTAAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTAAAAAATAAAAC
Found at i:8886384 original size:20 final size:21
Alignment explanation
Indices: 8886346--8886385 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
8886336 TCTTCAGTAT
* *
8886346 CCATGATGGTAAAGCATAGGC
1 CCATGAAGGTAAAGAATAGGC
8886367 CCATGAAGG-AAAGAATAGG
1 CCATGAAGGTAAAGAATAGG
8886386 AGGTCTCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.40, C:0.15, G:0.30, T:0.15
Consensus pattern (21 bp):
CCATGAAGGTAAAGAATAGGC
Found at i:8889789 original size:3 final size:3
Alignment explanation
Indices: 8889783--8889814 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
8889773 TGTTAATTTG
8889783 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
8889815 TTGGTGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:8894015 original size:20 final size:19
Alignment explanation
Indices: 8893964--8894017 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
8893954 ATAGTTTAAT
8893964 AATTTATATATTTTCATATA
1 AATTT-TATATTTTCATATA
* * *
8893984 AATTTTGGTATTTTTAGTTTA
1 AATTTT-ATATTTTCA-TATA
8894005 AATTTTATATTTT
1 AATTTTATATTTT
8894018 AATTTAGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 18 0.64
21 9 0.32
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (19 bp):
AATTTTATATTTTCATATA
Found at i:8895313 original size:20 final size:21
Alignment explanation
Indices: 8895278--8895317 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
8895268 TTTGAGTTAG
8895278 TATTTGTTTCATTCCACAATA
1 TATTTGTTTCATTCCACAATA
*
8895299 TATTT-TTTTATTCCACAAT
1 TATTTGTTTCATTCCACAAT
8895318 CAATCTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.28, C:0.17, G:0.03, T:0.53
Consensus pattern (21 bp):
TATTTGTTTCATTCCACAATA
Found at i:8903827 original size:17 final size:18
Alignment explanation
Indices: 8903805--8903838 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
8903795 TTTTATGATG
8903805 TTTTTATATTT-TTTTAA
1 TTTTTATATTTATTTTAA
*
8903822 TTTTTATTTTTATTTTA
1 TTTTTATATTTATTTTA
8903839 TAATTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTATATTTATTTTAA
Found at i:8911091 original size:26 final size:28
Alignment explanation
Indices: 8911051--8911106 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
8911041 CCCAACAAAA
* *
8911051 AATAACATAACAAAAAGGGAGA-ATTTT
1 AATAACATAAAAAAAAGAGAGAGATTTT
8911078 AATAA-ATAAAAAAAAGAGAGAGATTTT
1 AATAACATAAAAAAAAGAGAGAGATTTT
8911105 AA
1 AA
8911107 AATTTTGGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.61, C:0.04, G:0.14, T:0.21
Consensus pattern (28 bp):
AATAACATAAAAAAAAGAGAGAGATTTT
Found at i:8911412 original size:15 final size:16
Alignment explanation
Indices: 8911378--8911415 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
8911368 TAATAAAATT
*
8911378 ATAATTTTATCATTTTA
1 ATAA-TTTATCATCTTA
8911395 ATAATTTAT-ATCTTA
1 ATAATTTATCATCTTA
8911410 ATAATT
1 ATAATT
8911416 ATTAAAGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 5 0.25
17 4 0.20
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (16 bp):
ATAATTTATCATCTTA
Found at i:8911447 original size:32 final size:33
Alignment explanation
Indices: 8911411--8911477 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
8911401 TATATCTTAA
*
8911411 TAATTATTAAAGGGTTAAA-TCAAATTTT-TTAT
1 TAATTATTAAA-GGTTAAAGTAAAATTTTATTAT
* *
8911443 TAATTTTTAGAGGTTAAAGTAAAATTTTATTAT
1 TAATTATTAAAGGTTAAAGTAAAATTTTATTAT
8911476 TA
1 TA
8911478 TTAATATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 7 0.23
32 17 0.57
33 6 0.20
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.48
Consensus pattern (33 bp):
TAATTATTAAAGGTTAAAGTAAAATTTTATTAT
Found at i:8914552 original size:33 final size:33
Alignment explanation
Indices: 8914515--8914584 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
8914505 TGTTTCTTTG
8914515 TACTATGTTTCATTCAATCACACATAATTCTCA
1 TACTATGTTTCATTCAATCACACATAATTCTCA
8914548 TACTATGTTTCATTCAATCACACATAATTCTCA
1 TACTATGTTTCATTCAATCACACATAATTCTCA
8914581 TACT
1 TACT
8914585 TTTGATTACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (33 bp):
TACTATGTTTCATTCAATCACACATAATTCTCA
Found at i:8920140 original size:17 final size:17
Alignment explanation
Indices: 8920120--8920153 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8920110 TGTTATTGTT
* *
8920120 TAATTTTATATATTAAA
1 TAATTTAATAAATTAAA
8920137 TAATTTAATAAATTAAA
1 TAATTTAATAAATTAAA
8920154 AAAATCGTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTTAATAAATTAAA
Found at i:8925325 original size:31 final size:31
Alignment explanation
Indices: 8925290--8925349 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
8925280 TTCTCATTGG
*
8925290 AATTCCAAATTATATGCTTAACATTTTGTGA
1 AATTCCAAATTACATGCTTAACATTTTGTGA
*
8925321 AATTCCAAGTTACATGCTTAACATTTTGT
1 AATTCCAAATTACATGCTTAACATTTTGT
8925350 AGGAATGGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (31 bp):
AATTCCAAATTACATGCTTAACATTTTGTGA
Found at i:8928094 original size:6 final size:6
Alignment explanation
Indices: 8928083--8928121 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
8928073 CCCATAAAAC
8928083 TTGTCA TTGTCA TTGTCA TTGTCA TTGTCA TTGTCA TTG
1 TTGTCA TTGTCA TTGTCA TTGTCA TTGTCA TTGTCA TTG
8928122 CAGCCTTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (6 bp):
TTGTCA
Found at i:8930663 original size:21 final size:23
Alignment explanation
Indices: 8930630--8930674 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
8930620 TTTACTTGTT
8930630 TATTTTTTAATTCAT-TAAATAA
1 TATTTTTTAATTCATGTAAATAA
*
8930652 TATTTTTT-ATTCATGTAATTAA
1 TATTTTTTAATTCATGTAAATAA
8930674 T
1 T
8930675 GTAAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (23 bp):
TATTTTTTAATTCATGTAAATAA
Found at i:8930827 original size:7 final size:7
Alignment explanation
Indices: 8930815--8930839 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
8930805 ATGAAAATAC
8930815 TTAAATG
1 TTAAATG
8930822 TTAAATG
1 TTAAATG
8930829 TTAAATG
1 TTAAATG
8930836 TTAA
1 TTAA
8930840 TGCATTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (7 bp):
TTAAATG
Found at i:8943823 original size:2 final size:2
Alignment explanation
Indices: 8943816--8943846 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8943806 ATAAATAGCT
8943816 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8943847 GGATATTACT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8951171 original size:27 final size:27
Alignment explanation
Indices: 8951135--8951189 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
8951125 TATTAAGGCG
8951135 ATATATAAATTGATGTTTTAAATACTT
1 ATATATAAATTGATGTTTTAAATACTT
8951162 ATATATAAATTGATGTTTTAAATACTT
1 ATATATAAATTGATGTTTTAAATACTT
8951189 A
1 A
8951190 CCATCATGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.42, C:0.04, G:0.07, T:0.47
Consensus pattern (27 bp):
ATATATAAATTGATGTTTTAAATACTT
Found at i:8953830 original size:17 final size:17
Alignment explanation
Indices: 8953790--8953865 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
8953780 CCCAATGAGA
8953790 TAAATTTAGTTTTAAA-T
1 TAAATTTA-TTTTAAATT
* *
8953807 TAGATTTATTTTGAATT
1 TAAATTTATTTTAAATT
*** *
8953824 TAAATTTGCATAAAATT
1 TAAATTTATTTTAAATT
*
8953841 TAAATTTATTATAAATT
1 TAAATTTATTTTAAATT
8953858 TAAATTTA
1 TAAATTTA
8953866 AAATTAAATT
Statistics
Matches: 45, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
16 6 0.13
17 39 0.87
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.51
Consensus pattern (17 bp):
TAAATTTATTTTAAATT
Found at i:8955912 original size:30 final size:30
Alignment explanation
Indices: 8955865--8955974 Score: 136
Period size: 30 Copynumber: 3.7 Consensus size: 30
8955855 CTCTATAGGT
*
8955865 CCCT-AAACTATCCAAAAATTATATTTTGA
1 CCCTCAAACTTTCCAAAAATTATATTTTGA
*
8955894 CCC-CAAAACTTTCTAAAAATTATATTTTGA
1 CCCTC-AAACTTTCCAAAAATTATATTTTGA
* * *
8955924 CCCTCAAACTTTTCTAAAATTACCATTTT-A
1 CCCTCAAACTTTCCAAAAATTA-TATTTTGA
8955954 CCCTCAAACTTTCCAAAAATT
1 CCCTCAAACTTTCCAAAAATT
8955975 CCTTTTTAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.04
30 60 0.87
31 6 0.09
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (30 bp):
CCCTCAAACTTTCCAAAAATTATATTTTGA
Found at i:8956086 original size:29 final size:29
Alignment explanation
Indices: 8955934--8956112 Score: 142
Period size: 29 Copynumber: 6.2 Consensus size: 29
8955924 CCCTCAAACT
* *
8955934 TTTCTAAAATTACCATTTT-ACCCTCAAAC
1 TTTCCAAAATTACCATTTTAACCC-CGAAC
*
8955963 TTTCCAAAAATT-CCTTTTTAACCCCG-A-
1 TTTCC-AAAATTACCATTTTAACCCCGAAC
*
8955990 TTTCACCAAAATTACCATTTTACCCCCTGAAC
1 TTT--CCAAAATTACCATTTTAACCCC-GAAC
*
8956022 TTTCCAAAATT-TCATTTTTAACCCCG-A-
1 TTTCCAAAATTACCA-TTTTAACCCCGAAC
*
8956049 TTTCACCAAAATTACCATTTTACCCCCGAAC
1 TTT--CCAAAATTACCATTTTAACCCCGAAC
* *
8956080 CTTCCAAAA-TCCCATTTTTAACCCCGAA-
1 TTTCCAAAATTACCA-TTTTAACCCCGAAC
8956108 TTTCC
1 TTTCC
8956113 CCGAAATTTC
Statistics
Matches: 122, Mismatches: 13, Indels: 31
0.73 0.08 0.19
Matches are distributed among these distances:
27 6 0.05
28 16 0.13
29 63 0.52
30 31 0.25
31 3 0.02
32 3 0.02
ACGTcount: A:0.31, C:0.32, G:0.03, T:0.35
Consensus pattern (29 bp):
TTTCCAAAATTACCATTTTAACCCCGAAC
Found at i:8956127 original size:58 final size:58
Alignment explanation
Indices: 8955939--8956120 Score: 267
Period size: 59 Copynumber: 3.1 Consensus size: 58
8955929 AAACTTTTCT
* *
8955939 AAAATTACCATTTTACCCTCAAACTTTCCAAAAATTCC-TTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCGAACTTTCC-AAAATTCCATTTTTAACCCCGATTTCACC
*
8955997 AAAATTACCATTTTACCCCCTGAACTTTCCAAAATTTCATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
* * *
8956056 AAAATTACCATTTTACCCCCGAACCTTCCAAAATCCCATTTTTAACCCCGAATTTCCCC
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCG-ATTTCACC
*
8956115 GAAATT
1 AAAATT
8956121 TCATTTTTGC
Statistics
Matches: 113, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
58 53 0.47
59 60 0.53
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.33
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:8958665 original size:13 final size:13
Alignment explanation
Indices: 8958647--8958675 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
8958637 AATACAGTTG
8958647 CCATGTTCAAATA
1 CCATGTTCAAATA
8958660 CCATGTTCAAATA
1 CCATGTTCAAATA
8958673 CCA
1 CCA
8958676 AAATTAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.28
Consensus pattern (13 bp):
CCATGTTCAAATA
Found at i:8959470 original size:2 final size:2
Alignment explanation
Indices: 8959463--8959497 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
8959453 AAATATGGTG
* *
8959463 TA TA TA TA TA TA CA CA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8959498 TTACAACCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:8960099 original size:41 final size:38
Alignment explanation
Indices: 8959999--8960102 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
8959989 TTCGAAGCAA
* *
8959999 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
8960036 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
8960074 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
8960103 CTCAAGGTGG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:8965420 original size:30 final size:30
Alignment explanation
Indices: 8965374--8965457 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
8965364 TACAATTTGA
8965374 TCATTGAACTATTTAAAATTTTTTATTTAAG
1 TCATTGAACTA-TTAAAATTTTTTATTTAAG
*
8965405 TCATTGAACTATTAAAAGTTTTTATTTAAG
1 TCATTGAACTATTAAAATTTTTTATTTAAG
* * *
8965435 TCATTGAGCTGTTAAGATTTTTT
1 TCATTGAACTATTAAAATTTTTT
8965458 TTAAAGTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 37 0.77
31 11 0.23
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (30 bp):
TCATTGAACTATTAAAATTTTTTATTTAAG
Found at i:8976241 original size:21 final size:20
Alignment explanation
Indices: 8976200--8976242 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
8976190 TTGAAATATG
* * *
8976200 AAAAGTAAAATTAAATTATT
1 AAAAATAAAAATAAATAATT
8976220 AAAAATAAAAATAAATAAATT
1 AAAAATAAAAATAAAT-AATT
8976241 AA
1 AA
8976243 TCGATTGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAAATAAAAATAAATAATT
Found at i:8988928 original size:30 final size:30
Alignment explanation
Indices: 8988892--8988951 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
8988882 AAAGTAAAAT
**
8988892 AATTCATAAATTAAAAAATAGGTAAATGTA
1 AATTCATAAATTAAAAAATAAATAAATGTA
8988922 AATTCATAAATTAAAAAATAAATAAATGTA
1 AATTCATAAATTAAAAAATAAATAAATGTA
8988952 TTATGCATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.60, C:0.03, G:0.07, T:0.30
Consensus pattern (30 bp):
AATTCATAAATTAAAAAATAAATAAATGTA
Found at i:8989068 original size:15 final size:14
Alignment explanation
Indices: 8989030--8989059 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8989020 GTTATTCATC
*
8989030 TTAAAAATCTCGAG
1 TTAAAAAACTCGAG
8989044 TTAAAAAACTCGAG
1 TTAAAAAACTCGAG
8989058 TT
1 TT
8989060 CAAACAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (14 bp):
TTAAAAAACTCGAG
Found at i:8999300 original size:2 final size:2
Alignment explanation
Indices: 8999293--8999320 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8999283 GATTAAGAAG
8999293 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
8999321 GTGTGTGTGT
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:9007967 original size:18 final size:19
Alignment explanation
Indices: 9007933--9007979 Score: 78
Period size: 18 Copynumber: 2.5 Consensus size: 19
9007923 TAATGAGGTA
9007933 TAATAATTTTTTGTAATAAT
1 TAAT-ATTTTTTGTAATAAT
9007953 TAATATTTTTT-TAATAAT
1 TAATATTTTTTGTAATAAT
9007971 TAATATTTT
1 TAATATTTT
9007980 AAAAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 16 0.59
19 7 0.26
20 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TAATATTTTTTGTAATAAT
Found at i:9012148 original size:16 final size:16
Alignment explanation
Indices: 9012129--9012159 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9012119 ACACTATAAC
9012129 TTTATTATATTACAAG
1 TTTATTATATTACAAG
*
9012145 TTTATTCTATTACAA
1 TTTATTATATTACAA
9012160 CGAACCAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.52
Consensus pattern (16 bp):
TTTATTATATTACAAG
Found at i:9021710 original size:24 final size:27
Alignment explanation
Indices: 9021660--9021715 Score: 82
Period size: 24 Copynumber: 2.2 Consensus size: 27
9021650 TTGTTATTAA
*
9021660 TAAATATAAAAATATATTTTTTATATT
1 TAAATATAAAAATATATTTATTATATT
9021687 TAAAT-TAAAAATAT-TTTATT-TATT
1 TAAATATAAAAATATATTTATTATATT
9021711 TAAAT
1 TAAAT
9021716 GAAATTCAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 9 0.32
25 5 0.18
26 9 0.32
27 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TAAATATAAAAATATATTTATTATATT
Found at i:9026591 original size:16 final size:14
Alignment explanation
Indices: 9026559--9026615 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
9026549 TTTTATTTAC
9026559 TTAAAAAATTAATTTT
1 TTAAAAAA-T-ATTTT
9026575 TTAAAAAATATTGTT
1 TTAAAAAATATT-TT
* *
9026590 TTAAATAATA-TTA
1 TTAAAAAATATTTT
*
9026603 TTGAAAAATATTT
1 TTAAAAAATATTT
9026616 CGAGATTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 9 0.26
14 6 0.17
15 12 0.34
16 8 0.23
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (14 bp):
TTAAAAAATATTTT
Found at i:9026891 original size:54 final size:53
Alignment explanation
Indices: 9026822--9026924 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 53
9026812 CCTCTTCTAG
* * *
9026822 TTTTTATATAAAATAGTAAAAATAACTTAAAA-TTTCTGTATAAAAAATAAATA
1 TTTTTATATAAAATAGTAAAAACAACTTAAAAGTCT-TATATAAAAAATAAATA
* * *
9026875 TTTTATATTTAAAATAGTGAAAACAATTTAAAAGTCTTATATAAAAAATA
1 TTTT-TATATAAAATAGTAAAAACAACTTAAAAGTCTTATATAAAAAATA
9026925 TCATATAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
53 4 0.10
54 36 0.86
55 2 0.05
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (53 bp):
TTTTTATATAAAATAGTAAAAACAACTTAAAAGTCTTATATAAAAAATAAATA
Found at i:9026917 original size:398 final size:389
Alignment explanation
Indices: 9026185--9026984 Score: 1244
Period size: 398 Copynumber: 2.0 Consensus size: 389
9026175 TTGTATTTAC
* *
9026185 TTAAAAAAATATTGTTTTAAATAATATTATTGAAAAATATTTCGAGATTTGGGTAAATTACATCT
1 TTAAAAAAATATTGTTTTAAATAATATTATTGAAAAATATTTCGAGATTTGGGTAAACTACACCT
* *
9026250 AAGGTGACTATAAGTTTATGTTTTGGTCACTCAACTTTTAAAAATTATAAAATTGTCATTGAATT
66 AAGCTGACTATAAGTTTACGTTTTGGTCACTCAACTTTTAAAAATTATAAAATTGTCATTGAATT
* * *
9026315 ATTCAAAAATTTCATTTAAGTCATTAGACTATTAAAATATTTGTTGTACGGCTTTCTCTGTTTGC
131 ATTCAAAAATTTCATTTAAGTCACTAAACTATTAAAATATTTGTTGTACGACTTTCTCTGTTTGC
* **
9026380 ACTGCCTGTACCAAACGAAAACTTTTTTTCTCATTTTCTTCTAGTTTTTATATAAAATAGTAAAA
196 ACTGCCTGTACCAAACGAAAACTTTTCTTCTCATCCTCTTCTAGTTTTTATATAAAATAGTAAAA
*
9026445 ATAACTTAAAATTTCTATATAAAAAATAAATATTTTATATCTAAAATAGAAAAAATAATTTAAAA
261 ATAACTTAAAATTTCTATATAAAAAATAAATATTTTATATCTAAAATAGAAAAAACAATTTAAAA
* *
9026510 GTTTTATATAAAAAACGTCATATAAAAGTTATGGTTATTTTTTATTTACTTAAAAAATTAATTT
326 GTCTTATATAAAAAACATCATATAAAAGTTATGGTTATTTTTTATTTACTTAAAAAATTAATTT
* *
9026574 TTTAAAAAATATTGTTTTAAATAATATTATTGAAAAATATTTCGAGATTTGTGTAAACTACACCT
1 TTAAAAAAATATTGTTTTAAATAATATTATTGAAAAATATTTCGAGATTTGGGTAAACTACACCT
* *
9026639 GAAATGACTATACTATTGGTAAGTTTACGTTTTGGTCGCTCAACTTTTAAAAATTATAAAA-TGA
66 --AA-G-CT-GACTA----TAAGTTTACGTTTTGGTCACTCAACTTTTAAAAATTATAAAATTG-
*
9026703 TCATTGAATTATTCAAAAATTTCATTTAAGTCACTAAACTATTAAAATATTTGTTGTATGACTTT
121 TCATTGAATTATTCAAAAATTTCATTTAAGTCACTAAACTATTAAAATATTTGTTGTACGACTTT
* * *
9026768 CTCTGTTTGTACTGTCTGTATCAAACGAAAACTTTTCTTCTTC-TCCTCTTCTAGTTTTTATATA
186 CTCTGTTTGCACTGCCTGTACCAAACGAAAACTTTTCTTC-TCATCCTCTTCTAGTTTTTATATA
* * **
9026832 AAATAGTAAAAATAACTTAAAATTTCTGTATAAAAAATAAATATTTTATATTTAAAATAGTGAAA
250 AAATAGTAAAAATAACTTAAAATTTCTATATAAAAAATAAATATTTTATATCTAAAATAGAAAAA
*
9026897 ACAATTTAAAAGTCTTATATAAAAAATATCATATAAAAGTTATGGTTATTTTTTATTTACTTAAA
315 ACAATTTAAAAGTCTTATATAAAAAACATCATATAAAAGTTATGGTTATTTTTTATTTACTTAAA
*
9026962 AGATTAATTT
380 AAATTAATTT
9026972 TTAAAAAAATATT
1 TTAAAAAAATATT
9026985 TATGAAAAAT
Statistics
Matches: 372, Mismatches: 28, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
389 61 0.16
391 2 0.01
392 1 0.00
393 1 0.00
394 4 0.01
397 2 0.01
398 299 0.80
399 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (389 bp):
TTAAAAAAATATTGTTTTAAATAATATTATTGAAAAATATTTCGAGATTTGGGTAAACTACACCT
AAGCTGACTATAAGTTTACGTTTTGGTCACTCAACTTTTAAAAATTATAAAATTGTCATTGAATT
ATTCAAAAATTTCATTTAAGTCACTAAACTATTAAAATATTTGTTGTACGACTTTCTCTGTTTGC
ACTGCCTGTACCAAACGAAAACTTTTCTTCTCATCCTCTTCTAGTTTTTATATAAAATAGTAAAA
ATAACTTAAAATTTCTATATAAAAAATAAATATTTTATATCTAAAATAGAAAAAACAATTTAAAA
GTCTTATATAAAAAACATCATATAAAAGTTATGGTTATTTTTTATTTACTTAAAAAATTAATTT
Found at i:9027813 original size:6 final size:7
Alignment explanation
Indices: 9027795--9027822 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
9027785 GGCCAAAGAT
9027795 TAAAAAA
1 TAAAAAA
9027802 TAAAAAA
1 TAAAAAA
9027809 TAAAAAA
1 TAAAAAA
9027816 TAAAAAA
1 TAAAAAA
9027823 AACAACATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
TAAAAAA
Found at i:9029535 original size:8 final size:8
Alignment explanation
Indices: 9029515--9029549 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
9029505 TAATTGAATC
9029515 ATTTTAAA
1 ATTTTAAA
* *
9029523 TTTTTATA
1 ATTTTAAA
9029531 ATTTTAAA
1 ATTTTAAA
9029539 ATTTTAAA
1 ATTTTAAA
9029547 ATT
1 ATT
9029550 CTAATATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
ATTTTAAA
Found at i:9034977 original size:3 final size:3
Alignment explanation
Indices: 9034969--9035008 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
9034959 CGACCACCCG
9034969 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCGT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT
9035009 CTCGGTGTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:9047387 original size:17 final size:18
Alignment explanation
Indices: 9047365--9047402 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
9047355 AGCTCAAAAG
9047365 TTTA-TTTAACAA-TGTTT
1 TTTATTTTAA-AAGTGTTT
9047382 TTTATTTTAAAAGTGTTT
1 TTTATTTTAAAAGTGTTT
9047400 TTT
1 TTT
9047403 TGTTCCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.63
Consensus pattern (18 bp):
TTTATTTTAAAAGTGTTT
Found at i:9047403 original size:19 final size:19
Alignment explanation
Indices: 9047379--9047418 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9047369 TTTAACAATG
**
9047379 TTTTTTATTTTAAAAGTGT
1 TTTTTTATTCCAAAAGTGT
*
9047398 TTTTTTGTTCCAAAAGTGT
1 TTTTTTATTCCAAAAGTGT
9047417 TT
1 TT
9047419 CTTAGAAGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.12, T:0.60
Consensus pattern (19 bp):
TTTTTTATTCCAAAAGTGT
Found at i:9051696 original size:17 final size:16
Alignment explanation
Indices: 9051674--9051725 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
9051664 AATAAACATT
9051674 TTTTGAGATAAAAAATA
1 TTTTGAGAT-AAAAATA
*
9051691 TTTTGAGATTAAAATA
1 TTTTGAGATAAAAATA
*
9051707 TTATT-AAAT-AAAATA
1 TT-TTGAGATAAAAATA
9051722 TTTT
1 TTTT
9051726 TAAGTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 2 0.06
15 8 0.25
16 11 0.34
17 11 0.34
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (16 bp):
TTTTGAGATAAAAATA
Found at i:9051704 original size:16 final size:16
Alignment explanation
Indices: 9051674--9051725 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
9051664 AATAAACATT
*
9051674 TTTTGAGATAAAAAATA
1 TTTTGAGAT-TAAAATA
9051691 TTTTGAGATTAAAATA
1 TTTTGAGATTAAAATA
*
9051707 TTATT-A-AATAAAATA
1 TT-TTGAGATTAAAATA
9051722 TTTT
1 TTTT
9051726 TAAGTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 2 0.06
15 10 0.31
16 9 0.28
17 11 0.34
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (16 bp):
TTTTGAGATTAAAATA
Found at i:9058010 original size:76 final size:76
Alignment explanation
Indices: 9057930--9058077 Score: 226
Period size: 76 Copynumber: 2.0 Consensus size: 76
9057920 AGATTTAAGT
* * * *
9057930 TTTTTTTATCAAATTAATATTTAGATGCTATTTT-GTATTAGTTTGTCAAATTAAACTAAAAATA
1 TTTTTTTACCAAATTAATATTTAGATACTATTTTAGTATTAATTTATCAAATTAAACTAAAAATA
*
9057994 TTGCCAAAATA
66 TTACCAAAATA
* *
9058005 TTTTTTTACCAAATTAATATTTAGATACTATTTTAGTATTAATTTATTAAATTAAACTAAAAATG
1 TTTTTTTACCAAATTAATATTTAGATACTATTTTAGTATTAATTTATCAAATTAAACTAAAAATA
9058070 TTACCAAA
66 TTACCAAA
9058078 TTTAATATAA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
75 32 0.49
76 33 0.51
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (76 bp):
TTTTTTTACCAAATTAATATTTAGATACTATTTTAGTATTAATTTATCAAATTAAACTAAAAATA
TTACCAAAATA
Found at i:9062324 original size:22 final size:24
Alignment explanation
Indices: 9062276--9062324 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
9062266 ATTTTAATAT
* *
9062276 TTAATATTTTTTTATATAGTTATC
1 TTAATATTTTTCTATATAGTTACC
*
9062300 TTAATA-TTTTCTA-ATATTTACC
1 TTAATATTTTTCTATATAGTTACC
9062322 TTA
1 TTA
9062325 GAGTAATATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 6 0.27
24 6 0.27
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (24 bp):
TTAATATTTTTCTATATAGTTACC
Found at i:9064005 original size:2 final size:2
Alignment explanation
Indices: 9063998--9064029 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9063988 CTCTTTAAGG
9063998 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
9064030 GTAATATCTT
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:9076886 original size:21 final size:21
Alignment explanation
Indices: 9076862--9076914 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
9076852 GGCTTCTTTT
*
9076862 GGTAGAAGTCTCACATGTATC
1 GGTAGAAGTCTCACAGGTATC
* * *
9076883 GGTAGAACTGTCATAGGTATC
1 GGTAGAAGTCTCACAGGTATC
9076904 GGTAGAAGTCT
1 GGTAGAAGTCT
9076915 GCACTGTTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.28
Consensus pattern (21 bp):
GGTAGAAGTCTCACAGGTATC
Found at i:9100139 original size:2 final size:2
Alignment explanation
Indices: 9100134--9100168 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
9100124 ATATATATAA
*
9100134 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
9100169 ATAATATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9121605 original size:21 final size:21
Alignment explanation
Indices: 9121564--9121605 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9121554 CTTCCTCCAT
*
9121564 CTCCTCTTCATCAATTTCTTC
1 CTCCTCTTCATCAATTACTTC
9121585 CTCCTCTTCATC-ATATACTTC
1 CTCCTCTTCATCAAT-TACTTC
9121606 TTCTTCCAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.17, C:0.38, G:0.00, T:0.45
Consensus pattern (21 bp):
CTCCTCTTCATCAATTACTTC
Found at i:9123169 original size:18 final size:18
Alignment explanation
Indices: 9123130--9123169 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
9123120 AGCTATAAAT
*
9123130 TATACACACACACATATA
1 TATACACACACACACATA
* *
9123148 TATACACACGCACACATG
1 TATACACACACACACATA
9123166 TATA
1 TATA
9123170 TGTATGTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.28, G:0.05, T:0.23
Consensus pattern (18 bp):
TATACACACACACACATA
Found at i:9139039 original size:57 final size:57
Alignment explanation
Indices: 9138892--9139040 Score: 244
Period size: 57 Copynumber: 2.6 Consensus size: 57
9138882 TCCTCGCATT
* * *
9138892 ATTTTTCCAACATTTTTGGCAAATTGTTCATAAAGAGGTTCTTGATTTCAGCTTGGG
1 ATTTTTCCAACATTTTTGGCCAATTGTTCGTAAAGAGGTTATTGATTTCAGCTTGGG
*
9138949 ATTTTCCCAACATTTTTGGCCAATTGTTCGTAAAGAGGTTATTGATTTCAGCTTGGG
1 ATTTTTCCAACATTTTTGGCCAATTGTTCGTAAAGAGGTTATTGATTTCAGCTTGGG
* *
9139006 ATTTTTCCAACGTTTTTGGCCAATTGTTTGTAAAG
1 ATTTTTCCAACATTTTTGGCCAATTGTTCGTAAAG
9139041 TGTCTAGTGA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 85 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42
Consensus pattern (57 bp):
ATTTTTCCAACATTTTTGGCCAATTGTTCGTAAAGAGGTTATTGATTTCAGCTTGGG
Found at i:9140625 original size:23 final size:25
Alignment explanation
Indices: 9140581--9140626 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
9140571 AGCATATATT
* *
9140581 TATTCTTATATTATATTTGTAAATG
1 TATTCTTATATTATAATAGTAAATG
9140606 TATTC-TAT-TTATAATAGTAAA
1 TATTCTTATATTATAATAGTAAA
9140627 AAAATTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 3 0.16
25 5 0.26
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (25 bp):
TATTCTTATATTATAATAGTAAATG
Found at i:9142377 original size:28 final size:29
Alignment explanation
Indices: 9142336--9142405 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
9142326 GTAAAACAAT
* * *
9142336 AAAATAAAATTTTAGGTTACTTAAAAGTT-G
1 AAAA-AAAA-TTTAGATCACTTAAAAATTGG
*
9142366 AAAAAAAATTTAGATCCCTTAAAAATTGG
1 AAAAAAAATTTAGATCACTTAAAAATTGG
*
9142395 TAAAAAAATTT
1 AAAAAAAATTT
9142406 TGGACCCTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 15 0.44
29 15 0.44
30 4 0.12
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (29 bp):
AAAAAAAATTTAGATCACTTAAAAATTGG
Found at i:9142445 original size:28 final size:26
Alignment explanation
Indices: 9142403--9142489 Score: 75
Period size: 28 Copynumber: 3.2 Consensus size: 26
9142393 GGTAAAAAAA
* *
9142403 TTTTGGACCCTTAAAAGTTAAAATTT
1 TTTTTGACCTTTAAAAGTTAAAATTT
***
9142429 TTTTTGACCCCTTTAAAAGTTGACAAAAAA
1 TTTTTGA--CCTTTAAAAGTT-A-AAATTT
* *
9142459 ATTTTGACCTTTAAAAGTTAAATTTT
1 TTTTTGACCTTTAAAAGTTAAAATTT
9142485 TTTTT
1 TTTTT
9142490 TTTTTGAACT
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
26 12 0.26
27 1 0.02
28 23 0.50
29 1 0.02
30 9 0.20
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (26 bp):
TTTTTGACCTTTAAAAGTTAAAATTT
Found at i:9146277 original size:13 final size:13
Alignment explanation
Indices: 9146259--9146284 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9146249 TGAATATACC
9146259 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
9146272 TTCTTTTTTTTTT
1 TTCTTTTTTTTTT
9146285 ATTGGAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTCTTTTTTTTTT
Found at i:9147097 original size:34 final size:34
Alignment explanation
Indices: 9147059--9147130 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
9147049 TGCTTTATTT
* *
9147059 TTTATTTTATTTTTCATATAAGGAAA-GTGCTCT-A
1 TTTATTTTAATTTT-ATAGAA-GAAAGGTGCTCTAA
9147093 TTTATTTTAATTTTATAGAAGAAAGGTGCTCTAA
1 TTTATTTTAATTTTATAGAAGAAAGGTGCTCTAA
9147127 TTTA
1 TTTA
9147131 GTGAGTTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 4 0.12
33 12 0.35
34 18 0.53
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (34 bp):
TTTATTTTAATTTTATAGAAGAAAGGTGCTCTAA
Found at i:9153001 original size:5 final size:5
Alignment explanation
Indices: 9152991--9153019 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
9152981 TACCTTAATT
9152991 ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAA
9153020 TATATATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAA
Found at i:9153474 original size:18 final size:19
Alignment explanation
Indices: 9153445--9153495 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
9153435 GATACTTTTT
* *
9153445 AAAAGTAATTTTGAATC-A
1 AAAAGTACTTTTGAAGCGA
*
9153463 AAAATTACTTTTG-AGCGA
1 AAAAGTACTTTTGAAGCGA
9153481 AAAAGTACTTTTGAA
1 AAAAGTACTTTTGAA
9153496 AAAGAAGCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 2 0.07
18 24 0.89
19 1 0.04
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (19 bp):
AAAAGTACTTTTGAAGCGA
Found at i:9153629 original size:18 final size:18
Alignment explanation
Indices: 9153602--9153645 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
9153592 TTTATTTGAT
9153602 AATA-TTTTTATCTTAAA
1 AATACTTTTTATCTTAAA
9153619 AATACTTTTTATCTTAAA
1 AATACTTTTTATCTTAAA
*
9153637 AGTACTTTT
1 AATACTTTT
9153646 GAGAAGCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.52
Consensus pattern (18 bp):
AATACTTTTTATCTTAAA
Found at i:9154894 original size:2 final size:2
Alignment explanation
Indices: 9154882--9154921 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
9154872 ACAAACAGCA
*
9154882 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
9154922 ATGCTTGTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:9158811 original size:5 final size:5
Alignment explanation
Indices: 9158801--9158837 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
9158791 TAGTCATGAC
9158801 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TT
9158838 CCTTCATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
TTTTG
Found at i:9164232 original size:18 final size:19
Alignment explanation
Indices: 9164199--9164244 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
9164189 ATAAAGAATA
9164199 ATTTAAAATGATAATTTTAT
1 ATTT-AAATGATAATTTTAT
* *
9164219 CTTTAAAT-ATAATTTTCT
1 ATTTAAATGATAATTTTAT
9164237 ATTTAAAT
1 ATTTAAAT
9164245 TATTAACATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 16 0.70
19 4 0.17
20 3 0.13
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTTAAATGATAATTTTAT
Found at i:9173346 original size:3 final size:3
Alignment explanation
Indices: 9173338--9173367 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9173328 AACGGATTGC
9173338 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
9173368 AACAGTAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:9182077 original size:31 final size:31
Alignment explanation
Indices: 9182040--9182098 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
9182030 TTTTTGACCC
*
9182040 AATTTGATACTTGAATTTGACATTTTTTCTT
1 AATTTGATACTTGAATATGACATTTTTTCTT
*
9182071 AATTTGATATTTGAATATGACATTTTTT
1 AATTTGATACTTGAATATGACATTTTTT
9182099 TTCCTAATTT
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:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (31 bp):
AATTTGATACTTGAATATGACATTTTTTCTT
Found at i:9182099 original size:33 final size:31
Alignment explanation
Indices: 9182040--9182109 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
9182030 TTTTTGACCC
* *
9182040 AATTTGATACTTGAATTTGACATTTTTTCTT
1 AATTTGATACTTGAATATGACATTTTTTCCT
*
9182071 AATTTGATATTTGAATATGACATTTTTTTTCCT
1 AATTTGATACTTGAATATGACA--TTTTTTCCT
9182104 AATTTG
1 AATTTG
9182110 GTATCTAAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 20 0.59
33 14 0.41
ACGTcount: A:0.27, C:0.09, G:0.10, T:0.54
Consensus pattern (31 bp):
AATTTGATACTTGAATATGACATTTTTTCCT
Found at i:9183751 original size:17 final size:19
Alignment explanation
Indices: 9183731--9183766 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9183721 TTAAAATAGT
9183731 AACAAA-ATTA-ACAATAA
1 AACAAATATTATACAATAA
9183748 AACAAATATTATACAATAA
1 AACAAATATTATACAATAA
9183767 CTAAATATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 4 0.24
19 7 0.41
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (19 bp):
AACAAATATTATACAATAA
Found at i:9185343 original size:24 final size:25
Alignment explanation
Indices: 9185299--9185350 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
9185289 GTTCCATTTC
*
9185299 ATTTTTATCATTTTAATAAATATAT
1 ATTTTTATAATTTTAATAAATATAT
9185324 ATTTTTATAATTTT--TAAA-ATAT
1 ATTTTTATAATTTTAATAAATATAT
9185346 ATTTT
1 ATTTT
9185351 AAAAATCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 9 0.35
23 4 0.15
25 13 0.50
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTTTATAATTTTAATAAATATAT
Found at i:9185429 original size:22 final size:24
Alignment explanation
Indices: 9185390--9185433 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
9185380 CAAACCTTTT
9185390 ACATCAATATTTTATTTCACATGA
1 ACATCAATATTTTATTTCACATGA
*
9185414 ACATC-AT-TTTTTTTTCACAT
1 ACATCAATATTTTATTTCACAT
9185434 TAATTATCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 2 0.11
24 5 0.26
ACGTcount: A:0.32, C:0.18, G:0.02, T:0.48
Consensus pattern (24 bp):
ACATCAATATTTTATTTCACATGA
Found at i:9194231 original size:25 final size:23
Alignment explanation
Indices: 9194186--9194238 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
9194176 ACACTAGCGC
9194186 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
9194209 GCTCTCTGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
9194232 GCTCTCT
1 GCTCTCT
9194239 TTGTGTACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 1 0.03
23 28 0.97
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:9194251 original size:36 final size:36
Alignment explanation
Indices: 9194204--9194274 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
9194194 ATTAGCACTG
* *
9194204 TGTGTGCTCTCTGATTAGCACTTCGTGTGCTCTCTT
1 TGTGTACTCTCTGATTAGCACTTCGTGTGCCCTCTT
* *
9194240 TGTGTACTCTCTGTTTAGCACTTTGTGTGCCCTCT
1 TGTGTACTCTCTGATTAGCACTTCGTGTGCCCTCT
9194275 GTTACCCAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.08, C:0.25, G:0.21, T:0.45
Consensus pattern (36 bp):
TGTGTACTCTCTGATTAGCACTTCGTGTGCCCTCTT
Found at i:9195757 original size:23 final size:23
Alignment explanation
Indices: 9195658--9195807 Score: 139
Period size: 23 Copynumber: 6.4 Consensus size: 23
9195648 CGAAGTACTT
9195658 AACAGTAAGCACACA-AGTGCTGGGGA
1 AACAGTAAGCACACACAGTGC----GA
9195684 AACAGTAAGCACACACAGTGC-A
1 AACAGTAAGCACACACAGTGCGA
* * * * *
9195706 ATCAGTAGGCGCACATAGCGC-A
1 AACAGTAAGCACACACAGTGCGA
*
9195728 AATCAGTAGGCACACGA-AGTGCGA
1 AA-CAGTAAGCACAC-ACAGTGCGA
*
9195752 AACAGTAAGCACACAAAGTGCGA
1 AACAGTAAGCACACACAGTGCGA
9195775 AACAGTAAGCACACACAGTGCTG-
1 AACAGTAAGCACACACAGTGC-GA
9195798 AACAGTAAGC
1 AACAGTAAGC
9195808 GCGCTAGCGT
Statistics
Matches: 108, Mismatches: 10, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
22 20 0.19
23 63 0.58
24 5 0.05
26 15 0.14
27 5 0.05
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACACAGTGCGA
Found at i:9199926 original size:2 final size:2
Alignment explanation
Indices: 9199919--9199959 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
9199909 GATGTAGATA
9199919 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
9199960 AGCAAGTTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9210172 original size:10 final size:9
Alignment explanation
Indices: 9210142--9210218 Score: 57
Period size: 9 Copynumber: 8.4 Consensus size: 9
9210132 ATTTTAATTT
*
9210142 TTTTTTCAA
1 TTTTTTAAA
*
9210151 TTTTTTATA
1 TTTTTTAAA
9210160 TTTTTTAAA
1 TTTTTTAAA
*
9210169 ATTTTTAAA
1 TTTTTTAAA
**
9210178 -TCATTAATA
1 TTTTTTAA-A
*
9210187 TTTTTTATA
1 TTTTTTAAA
* *
9210196 TTTTATAAT
1 TTTTTTAAA
9210205 TTTTTTATAA
1 TTTTTTA-AA
9210215 TTTT
1 TTTT
9210219 GAATTTATGT
Statistics
Matches: 51, Mismatches: 14, Indels: 5
0.73 0.20 0.07
Matches are distributed among these distances:
8 5 0.10
9 37 0.73
10 9 0.18
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:9211456 original size:42 final size:40
Alignment explanation
Indices: 9211391--9211477 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 40
9211381 CGACACCCCC
9211391 TATTTCAAAAAAAATTATATTTTTGGGTGTCGACCATGCA
1 TATTTCAAAAAAAATTATATTTTTGGGTGTCGACCATGCA
* * *
9211431 TATTTCAAAAAAAAATTGTAATTTTTGGGTGTCGGCTATGCA
1 TATTTC-AAAAAAAATTAT-ATTTTTGGGTGTCGACCATGCA
9211473 TATTT
1 TATTT
9211478 TTTGAGAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
40 6 0.14
41 11 0.26
42 25 0.60
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.40
Consensus pattern (40 bp):
TATTTCAAAAAAAATTATATTTTTGGGTGTCGACCATGCA
Found at i:9212478 original size:30 final size:30
Alignment explanation
Indices: 9212435--9212494 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
9212425 TAAATTTTAA
* * * *
9212435 AAAAATAATAATTAGAATATACATGAAATT
1 AAAAAGAAAAATTAAAATATACAAGAAATT
9212465 AAAAAGAAAAATTAAAATATACAAGAAATT
1 AAAAAGAAAAATTAAAATATACAAGAAATT
9212495 CGAAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (30 bp):
AAAAAGAAAAATTAAAATATACAAGAAATT
Found at i:9212510 original size:30 final size:30
Alignment explanation
Indices: 9212476--9212541 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
9212466 AAAAGAAAAA
*
9212476 TTAAAATATACAA-GAAATT-CGAAATTAAAT
1 TTAAAATA-AAAACGAAATTAC-AAATTAAAT
9212506 TTAAAATAAAAACGAAATTACAAATTAAAT
1 TTAAAATAAAAACGAAATTACAAATTAAAT
9212536 TTAAAA
1 TTAAAA
9212542 AGTAAAAGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 3 0.09
30 29 0.88
31 1 0.03
ACGTcount: A:0.61, C:0.06, G:0.05, T:0.29
Consensus pattern (30 bp):
TTAAAATAAAAACGAAATTACAAATTAAAT
Found at i:9214701 original size:20 final size:20
Alignment explanation
Indices: 9214670--9214727 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
9214660 ATGATGGATG
*
9214670 AAAGTCGATCAACGGCGGAC
1 AAAGTCGGTCAACGGCGGAC
* *
9214690 AAAGTTGGTCAACGGCGAAC
1 AAAGTCGGTCAACGGCGGAC
9214710 AAAGTCGGTCAACGGCGG
1 AAAGTCGGTCAACGGCGG
9214728 TCAACGGCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.33, C:0.22, G:0.33, T:0.12
Consensus pattern (20 bp):
AAAGTCGGTCAACGGCGGAC
Found at i:9215028 original size:83 final size:82
Alignment explanation
Indices: 9214890--9215658 Score: 1220
Period size: 83 Copynumber: 9.3 Consensus size: 82
9214880 TAAATATAAA
9214890 ATATGATAAAAATTGTAATATAATAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTAT
1 ATATGATAAAAATTGTAATATAATAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTAT
*
9214955 TGTCAAATCAACATATT
66 TGTCAAATCAACACATT
*
9214972 ATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAAT-AAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
*
9215037 TTGTCAAATTAACACATT
65 TTGTCAAATCAACACATT
*
9215055 ATTTGATAAAAATTGTAATATAA-AAAAA-TTTATTTAAAGATATAAAATTAATAAATATTGTAT
1 ATATGATAAAAATTGTAATATAATAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTAT
*
9215118 TGTCAAATTAACACATT
66 TGTCAAATCAACACATT
*
9215135 ATATGATAAAAATTGTAATATAATAAAATTTTTTATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAA-ATTTTATTTAAAGATATAAAATTAATAAATATTGTA
9215200 TTGTCAAATCAACACATT
65 TTGTCAAATCAACACATT
*
9215218 ATATGATAAAAATTGTAATATAATAAAATTTTTATTTAAAGATATAAAATTAATAAATATTGTAT
1 ATATGATAAAAATTGTAATATAATAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTAT
9215283 TGTCAAATCAACACATT
66 TGTCAAATCAACACATT
*
9215300 ATATGATAAAAATTGTAATATAATAAAAAATTATATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAAT-AAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTA
*
9215365 TTGTCAAATCAACATATT
65 TTGTCAAATCAACACATT
* * *
9215383 ATATTATAAAAATTGTAATATAATAAAAACTTTTATTTAAAAATATAAAATTAATAAATATTGAA
1 ATATGATAAAAATTGTAATATAATAAAAA-TTTTATTTAAAGATATAAAATTAATAAATATTGTA
*
9215448 TTATCAAATCAACACATT
65 TTGTCAAATCAACACATT
*
9215466 ATATGATAAAAATTGTACTATAATAAAAATTTTAATTTAAAGATATAAAATTAATAAATATTGTA
1 ATATGATAAAAATTGTAATATAATAAAAATTTT-ATTTAAAGATATAAAATTAATAAATATTGTA
*
9215531 TTGTCAAATCAATACATT
65 TTGTCAAATCAACACATT
* * * * *
9215549 ATATGATAAAAATTATAATATAATAATAATTTGTACTTTAAATATA-AAAATTTGATAAATAATG
1 ATATGATAAAAATTGTAATATAATAAAAATTT-TA-TTTAAAGATATAAAA-TTAATAAATATTG
* * *
9215613 TATTGTCAAATTAATACAAT
63 TATTGTCAAATCAACACATT
* *
9215633 ATTTGATATAAATTGTAATATAATAA
1 ATATGATAAAAATTGTAATATAATAA
9215659 CTATCTTTTT
Statistics
Matches: 644, Mismatches: 33, Indels: 18
0.93 0.05 0.03
Matches are distributed among these distances:
80 74 0.11
81 9 0.01
82 111 0.17
83 388 0.60
84 62 0.10
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (82 bp):
ATATGATAAAAATTGTAATATAATAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTAT
TGTCAAATCAACACATT
Found at i:9215339 original size:165 final size:165
Alignment explanation
Indices: 9214890--9215658 Score: 1213
Period size: 165 Copynumber: 4.7 Consensus size: 165
9214880 TAAATATAAA
*
9214890 ATATGATAAAAATTGTAATATAATAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTAT
1 ATATGATAAAAATTGTAATATAATAAAATTTTTATTTAAAGATATAAAATTAATAAATATTGTAT
* *
9214955 TGTCAAATCAACATATTATATGATAAAAATTGTAATATAATAAAAAAATTTATTTAAAGATATAA
66 TGTCAAATCAACACATTATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAA
*
9215020 AATTAATAAATATTGTATTGTCAAATTAACACATT
131 AATTAATAAATATTGTATTGTCAAATCAACACATT
* *
9215055 ATTTGATAAAAATTGTAATATAA-AAAA-ATTTATTTAAAGATATAAAATTAATAAATATTGTAT
1 ATATGATAAAAATTGTAATATAATAAAATTTTTATTTAAAGATATAAAATTAATAAATATTGTAT
* **
9215118 TGTCAAATTAACACATTATATGATAAAAATTGTAATATAATAAAATTTTTTATTTAAAGATATAA
66 TGTCAAATCAACACATTATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAA
9215183 AATTAATAAATATTGTATTGTCAAATCAACACATT
131 AATTAATAAATATTGTATTGTCAAATCAACACATT
9215218 ATATGATAAAAATTGTAATATAATAAAATTTTTATTTAAAGATATAAAATTAATAAATATTGTAT
1 ATATGATAAAAATTGTAATATAATAAAATTTTTATTTAAAGATATAAAATTAATAAATATTGTAT
*
9215283 TGTCAAATCAACACATTATATGATAAAAATTGTAATATAATAAAAAATTATATTTAAAGATATAA
66 TGTCAAATCAACACATTATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAA
*
9215348 AATTAATAAATATTGTATTGTCAAATCAACATATT
131 AATTAATAAATATTGTATTGTCAAATCAACACATT
* * * *
9215383 ATATTATAAAAATTGTAATATAATAAAAACTTTTATTTAAAAATATAAAATTAATAAATATTGAA
1 ATATGATAAAAATTGTAATATAAT-AAAATTTTTATTTAAAGATATAAAATTAATAAATATTGTA
* *
9215448 TTATCAAATCAACACATTATATGATAAAAATTGTACTATAAT-AAAAATTTTAATTTAAAGATAT
65 TTGTCAAATCAACACATTATATGATAAAAATTGTAATATAATAAAAAATTTT-ATTTAAAGATAT
*
9215512 AAAATTAATAAATATTGTATTGTCAAATCAATACATT
129 AAAATTAATAAATATTGTATTGTCAAATCAACACATT
* * * * *
9215549 ATATGATAAAAATTATAATATAATAATAATTTGTACTTTAAATATA-AAAATTTGATAAATAATG
1 ATATGATAAAAATTGTAATATAATAA-AATTTTTA-TTTAAAGATATAAAA-TTAATAAATATTG
* * * * *
9215613 TATTGTCAAATTAATACAATATTTGATATAAATTGTAATATAATAA
63 TATTGTCAAATCAACACATTATATGATAAAAATTGTAATATAATAA
9215659 CTATCTTTTT
Statistics
Matches: 557, Mismatches: 39, Indels: 13
0.91 0.06 0.02
Matches are distributed among these distances:
163 151 0.27
164 8 0.01
165 185 0.33
166 156 0.28
167 56 0.10
168 1 0.00
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (165 bp):
ATATGATAAAAATTGTAATATAATAAAATTTTTATTTAAAGATATAAAATTAATAAATATTGTAT
TGTCAAATCAACACATTATATGATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAA
AATTAATAAATATTGTATTGTCAAATCAACACATT
Found at i:9215806 original size:12 final size:12
Alignment explanation
Indices: 9215789--9215836 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
9215779 AAACATGTTC
9215789 ATTAATTTCCAA
1 ATTAATTTCCAA
9215801 ATTAATTTCAACTTAA
1 ATTAATTTC--C--AA
*
9215817 ATTAATTTTCAA
1 ATTAATTTCCAA
9215829 ATTAATTT
1 ATTAATTT
9215837 TTACACAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTAATTTCCAA
Found at i:9215835 original size:16 final size:16
Alignment explanation
Indices: 9215799--9215833 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
9215789 ATTAATTTCC
*
9215799 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
9215815 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
9215832 AA
1 AA
9215834 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:9215846 original size:28 final size:28
Alignment explanation
Indices: 9215789--9215846 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
9215779 AAACATGTTC
**
9215789 ATTAATTTCCAAATTAATTTCAACTTAA
1 ATTAATTTCCAAATTAATTTCAACACAA
* **
9215817 ATTAATTTTCAAATTAATTTTTACACAA
1 ATTAATTTCCAAATTAATTTCAACACAA
9215845 AT
1 AT
9215847 ATACTTCGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTAATTTCCAAATTAATTTCAACACAA
Found at i:9219638 original size:61 final size:60
Alignment explanation
Indices: 9219570--9220059 Score: 484
Period size: 61 Copynumber: 8.2 Consensus size: 60
9219560 AGGAGAAGTT
*
9219570 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGGAATTTTTTTATTCGAGAAAA-GG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTT-GAATTTTTTT-CTCGAGAAAAGGG
* * *
9219631 GGTGTCGGCCATTTGATGACCAACACCCAAAAAATTTTGAATTTTTTTCTCGAGAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACA-CCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGG
* * *
9219692 GGTGTCGGCCATTTGATGGCCAATATCAAAAAAATTTAAATTTTTTTCTCGAGAACAAGGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAA-AAGGG
* *
9219753 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTTGAAAAAAAGGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCG-AGAAAAGGG
* *
9219814 GGTATCGGCCA-TTGCAAGG-CAACACCAAAAAAATTTGAAATTTTTTTCTCGAGAAATAGGG
1 GGTGTCGGCCATTTG-ATGGCCAACACCAAAAAAATTTG-AATTTTTTTCTCGAGAAA-AGGG
*** * * ** * *
9219875 GGTGTCGGCCATGCAATGACCAACACCCAAAAAA-TACAATTTTTTT-TTGA-AATAGGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGG
* *** ** * * *
9219932 GGTGTCGACCATGCAATGGATAACACC-CAAAAATGT-AA-TTTTTT-T-GA-AATAGGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGG
** * *
9219986 GGTGTCGGCCATTTGATGGCCAACACCCCAAAATTTTGAAATTTTTTTC-CTGACAAAAGGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTG-AATTTTTTTCTC-GAGAAAAGGG
* *
9220047 AGTGTCGACCATT
1 GGTGTCGGCCATT
9220060 GCATGACTAA
Statistics
Matches: 363, Mismatches: 48, Indels: 36
0.81 0.11 0.08
Matches are distributed among these distances:
54 30 0.08
55 14 0.04
56 7 0.02
57 29 0.08
58 8 0.02
59 3 0.01
60 71 0.20
61 174 0.48
62 27 0.07
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (60 bp):
GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTTGAATTTTTTTCTCGAGAAAAGGG
Found at i:9219944 original size:57 final size:54
Alignment explanation
Indices: 9219866--9219997 Score: 185
Period size: 57 Copynumber: 2.4 Consensus size: 54
9219856 TTTTTCTCGA
9219866 GAAATAGGGGGTGTCGGCCATGCAAT-GACCAACACCCAAAAAATACAATTTTTTTTT
1 GAAATAGGGGGTGTCGGCCATGCAATGGA-CAACACCC-AAAAATACAA--TTTTTTT
* * **
9219923 GAAATAGGGGGTGTCGACCATGCAATGGATAACACCCAAAAATGTAATTTTTTT
1 GAAATAGGGGGTGTCGGCCATGCAATGGACAACACCCAAAAATACAATTTTTTT
9219977 GAAATAGGGGGTGTCGGCCAT
1 GAAATAGGGGGTGTCGGCCAT
9219998 TTGATGGCCA
Statistics
Matches: 69, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
54 27 0.39
56 8 0.12
57 32 0.46
58 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (54 bp):
GAAATAGGGGGTGTCGGCCATGCAATGGACAACACCCAAAAATACAATTTTTTT
Found at i:9221955 original size:23 final size:23
Alignment explanation
Indices: 9221929--9222010 Score: 94
Period size: 23 Copynumber: 3.5 Consensus size: 23
9221919 TTAATGTTCA
*
9221929 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-TAAACATTAAT
* *
9221952 CGAACATGTTCACAAACATTAAA
1 CGAACATGTTCATAAACATTAAT
*
9221975 CGAACATGTTCATGAACATATAAT
1 CGAACATGTTCATAAACAT-TAAT
*
9221999 TGAACATGTTCA
1 CGAACATGTTCA
9222011 CGAACAATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
22 3 0.06
23 33 0.66
24 14 0.28
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.30
Consensus pattern (23 bp):
CGAACATGTTCATAAACATTAAT
Found at i:9222050 original size:19 final size:19
Alignment explanation
Indices: 9222026--9222063 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9222016 AATGTTAATG
9222026 AATAATAAACAAACAAATA
1 AATAATAAACAAACAAATA
* *
9222045 AATAATAAATAAATAAATA
1 AATAATAAACAAACAAATA
9222064 CACATAGGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (19 bp):
AATAATAAACAAACAAATA
Found at i:9228860 original size:21 final size:21
Alignment explanation
Indices: 9228834--9228876 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9228824 GCGGTTTATA
* *
9228834 CAGATCCAATTACTTTCCTAC
1 CAGATCCAATGACCTTCCTAC
9228855 CAGATCCAATGACCTTCCTAC
1 CAGATCCAATGACCTTCCTAC
9228876 C
1 C
9228877 GGTTGCATCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.37, G:0.07, T:0.28
Consensus pattern (21 bp):
CAGATCCAATGACCTTCCTAC
Found at i:9230049 original size:2 final size:2
Alignment explanation
Indices: 9230044--9230080 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9230034 ACACAATAGG
9230044 AC AC AC AC AC AC AC AC AC AC AC AC 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
9230081 GAGAAATACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:9234793 original size:21 final size:21
Alignment explanation
Indices: 9234752--9234805 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
9234742 TTTGTGCTTT
9234752 AATATAAAT-TTAGAATAAAA
1 AATATAAATATTAGAATAAAA
* *
9234772 AATATAAATATTTGATTAAAA
1 AATATAAATATTAGAATAAAA
9234793 AAT-TCAAATATTA
1 AATAT-AAATATTA
9234806 AAGTGACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (21 bp):
AATATAAATATTAGAATAAAA
Done.