Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014911.1 Kokia drynarioides strain JFW-HI SEQ_129954, 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: 378737
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 301 characters in sequence are not A, C, G, or T
Found at i:8319 original size:18 final size:16
Alignment explanation
Indices: 8290--8325 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
8280 TTTTGAGCTA
8290 TTTAATTTTTTTTCTT
1 TTTAATTTTTTTTCTT
8306 TTTAACTTTCTTTTTCTT
1 TTTAA-TTT-TTTTTCTT
8324 TT
1 TT
8326 CCTTCTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 3 0.17
18 10 0.56
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTAATTTTTTTTCTT
Found at i:9172 original size:11 final size:11
Alignment explanation
Indices: 9156--9180 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9146 AATTATGAAT
9156 TTTCATTTATA
1 TTTCATTTATA
9167 TTTCATTTATA
1 TTTCATTTATA
9178 TTT
1 TTT
9181 TTAATATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTCATTTATA
Found at i:20154 original size:160 final size:160
Alignment explanation
Indices: 19983--20304 Score: 644
Period size: 160 Copynumber: 2.0 Consensus size: 160
19973 AGACAAACAA
19983 AAAAAATCAATGGTGACATTCAAGCAATGCTAAAGATATTGAATTTCCTTCTCCATAAAATAGAA
1 AAAAAATCAATGGTGACATTCAAGCAATGCTAAAGATATTGAATTTCCTTCTCCATAAAATAGAA
20048 GCAATTTACATGAATGTCAAGCACTTTATGGCATGAATTTGAAGCATATTTTCTCGTCTTAGACA
66 GCAATTTACATGAATGTCAAGCACTTTATGGCATGAATTTGAAGCATATTTTCTCGTCTTAGACA
20113 CAAATATAAGCAAAATTGGCTACAGGAAAC
131 CAAATATAAGCAAAATTGGCTACAGGAAAC
20143 AAAAAATCAATGGTGACATTCAAGCAATGCTAAAGATATTGAATTTCCTTCTCCATAAAATAGAA
1 AAAAAATCAATGGTGACATTCAAGCAATGCTAAAGATATTGAATTTCCTTCTCCATAAAATAGAA
20208 GCAATTTACATGAATGTCAAGCACTTTATGGCATGAATTTGAAGCATATTTTCTCGTCTTAGACA
66 GCAATTTACATGAATGTCAAGCACTTTATGGCATGAATTTGAAGCATATTTTCTCGTCTTAGACA
20273 CAAATATAAGCAAAATTGGCTACAGGAAAC
131 CAAATATAAGCAAAATTGGCTACAGGAAAC
20303 AA
1 AA
20305 CCAAAAAGCA
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 162 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (160 bp):
AAAAAATCAATGGTGACATTCAAGCAATGCTAAAGATATTGAATTTCCTTCTCCATAAAATAGAA
GCAATTTACATGAATGTCAAGCACTTTATGGCATGAATTTGAAGCATATTTTCTCGTCTTAGACA
CAAATATAAGCAAAATTGGCTACAGGAAAC
Found at i:23217 original size:158 final size:158
Alignment explanation
Indices: 22940--23242 Score: 536
Period size: 158 Copynumber: 1.9 Consensus size: 158
22930 TTTTAGGTGT
22940 CAATTTAAATTTTCAAATGGGATGAGAATATAGTTTTAATTAAATAAATTTAATTAATTAAAATT
1 CAATTTAAATTTTCAAATGGGATGAGAATATAGTTTTAATTAAATAAATTTAATTAATTAAAATT
*
23005 TTAAAGGCTAAACTTTAAATAAAAATCCTAAACCCATTTCCACAAGCTTCTCTTCTTCATCTTAA
66 TTAAAGCCTAAACTTTAAATAAAAATCCTAAACCCATTTCCACAAGCTTCTCTTCTTCATCTTAA
*
23070 TCTTAATCTTAATCTAGATTTTAAGCGC
131 TCTTAATCTCAATCTAGATTTTAAGCGC
* *
23098 CAATTTGAATTTTCAAATGGGATGAGAATATATTTTTAATTAAATAAATTTAATTAATTAAAATT
1 CAATTTAAATTTTCAAATGGGATGAGAATATAGTTTTAATTAAATAAATTTAATTAATTAAAATT
* *
23163 TTAAAGCCTAAACTTTAAATAAAAA-CCTTAAACCCATTTCCGCAAGCTTCTCTTCTTCATCTTT
66 TTAAAGCCTAAACTTTAAATAAAAATCC-TAAACCCATTTCCACAAGCTTCTCTTCTTCATCTTA
23227 ATCTTAATCTCAATCT
130 ATCTTAATCTCAATCT
23243 TCATCTTCTT
Statistics
Matches: 138, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
157 2 0.01
158 136 0.99
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (158 bp):
CAATTTAAATTTTCAAATGGGATGAGAATATAGTTTTAATTAAATAAATTTAATTAATTAAAATT
TTAAAGCCTAAACTTTAAATAAAAATCCTAAACCCATTTCCACAAGCTTCTCTTCTTCATCTTAA
TCTTAATCTCAATCTAGATTTTAAGCGC
Found at i:25984 original size:19 final size:19
Alignment explanation
Indices: 25944--25985 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
25934 AATTGAATCA
*
25944 TGAT-TTTTTTAAAAAAAT
1 TGATGTTTTTTAAAAAAAC
**
25962 TGATGTTTTTTAATCAAAC
1 TGATGTTTTTTAAAAAAAC
25981 TGATG
1 TGATG
25986 AGACTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.48
Consensus pattern (19 bp):
TGATGTTTTTTAAAAAAAC
Found at i:42010 original size:3 final size:3
Alignment explanation
Indices: 42004--42033 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41994 ATAATTAGAT
42004 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42034 ATATAATATA
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:59587 original size:23 final size:24
Alignment explanation
Indices: 59552--59604 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
59542 AAATTAAACC
59552 TCAAAATCCTAAAATA-AAAAACTT
1 TCAAAATCCT-AAATACAAAAACTT
* **
59576 TCAAAAT-GTAAATACAAAATTTT
1 TCAAAATCCTAAATACAAAAACTT
59599 TCAAAA
1 TCAAAA
59605 GTATTATGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 5 0.20
23 13 0.52
24 7 0.28
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
TCAAAATCCTAAATACAAAAACTT
Found at i:68898 original size:17 final size:18
Alignment explanation
Indices: 68873--68906 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
68863 TAAAATATGC
*
68873 ATAATAAAATTAAAATGA
1 ATAATAAAATCAAAATGA
68891 ATAA-AAAATCAAAATG
1 ATAATAAAATCAAAATG
68907 CCAATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.68, C:0.03, G:0.06, T:0.24
Consensus pattern (18 bp):
ATAATAAAATCAAAATGA
Found at i:83424 original size:64 final size:66
Alignment explanation
Indices: 83356--83482 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 66
83346 TACCTAAATA
* *
83356 ATATATAATTTAGT-AAGAAATTAAAAATTAAACTATAAATA-TATATGTG-AAAATATTTAAAT
1 ATATATAATTTA-TCAAGAAACTAAAAATTAAAATATAAATAGTATATGTGAAAAATATTTAAAT
83418 GT
65 GT
* *
83420 ATATATAATTTATCAAGACACTAAAAATTAAAATATAAATATGTATGTGTGAAAAATATTTAA
1 ATATATAATTTATCAAGAAACTAAAAATTAAAATATAAATA-GTATATGTGAAAAATATTTAA
83483 GATCATTGAT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
63 1 0.02
64 36 0.65
66 7 0.13
67 11 0.20
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (66 bp):
ATATATAATTTATCAAGAAACTAAAAATTAAAATATAAATAGTATATGTGAAAAATATTTAAATG
T
Found at i:85344 original size:17 final size:17
Alignment explanation
Indices: 85322--85357 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
85312 GAATCAAGGT
85322 TTTTAA-AATATTTTTAA
1 TTTTAATAAT-TTTTTAA
85339 TTTTAATAATTTTTTAA
1 TTTTAATAATTTTTTAA
85356 TT
1 TT
85358 GAACCAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTAATAATTTTTTAA
Found at i:86069 original size:18 final size:20
Alignment explanation
Indices: 86041--86077 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
86031 TAATATATAT
86041 AATTCAAAATTA-AAAAAAA
1 AATTCAAAATTACAAAAAAA
86060 AATT-AAAATTACAAAAAA
1 AATTCAAAATTACAAAAAA
86078 GTTACAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.22
Consensus pattern (20 bp):
AATTCAAAATTACAAAAAAA
Found at i:86082 original size:11 final size:10
Alignment explanation
Indices: 86064--86096 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 10
86054 AAAAAAAATT
86064 AAAATTACAA
1 AAAATTACAA
86074 AAAAGTTACAA
1 AAAA-TTACAA
86085 AAAATTA-AA
1 AAAATTACAA
86094 AAA
1 AAA
86097 TGAAAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 5 0.23
10 7 0.32
11 10 0.45
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (10 bp):
AAAATTACAA
Found at i:87476 original size:31 final size:29
Alignment explanation
Indices: 87441--87512 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
87431 ATCTCAAAAT
*
87441 TATACATAAAATATGATTTAATGTGCAATTG
1 TATACATGAAATATGATTT--TGTGCAATTG
* * *
87472 TATACATGAACTTTGATTTTGTGCAATTT
1 TATACATGAAATATGATTTTGTGCAATTG
87501 TATACATGAAAT
1 TATACATGAAAT
87513 TTTGATTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 20 0.56
31 16 0.44
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (29 bp):
TATACATGAAATATGATTTTGTGCAATTG
Found at i:87495 original size:29 final size:30
Alignment explanation
Indices: 87462--87520 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
87452 TATGATTTAA
87462 TGTGCAATTGTATACATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* *
87491 TGTGCAATTTTATACATGAAATTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
87521 GATCAAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.47
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:92277 original size:2 final size:2
Alignment explanation
Indices: 92270--92295 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
92260 TATAAATAAA
92270 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
92296 GTTATTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:98191 original size:22 final size:22
Alignment explanation
Indices: 98137--98191 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
98127 TAAATATTAA
* * *
98137 GATAAATAATTTTTTATTTTTAT
1 GATAAAT-ATTATTTATCTCTAT
98160 GAT-AATATTATTTATCTCTAT
1 GATAAATATTATTTATCTCTAT
98181 GATAAATATTA
1 GATAAATATTA
98192 AATTTAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.54
22 10 0.36
23 3 0.11
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (22 bp):
GATAAATATTATTTATCTCTAT
Found at i:99149 original size:6 final size:6
Alignment explanation
Indices: 99138--99164 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
99128 AAACACATCC
99138 CCCATG CCCATG CCCATG CCCATG CCC
1 CCCATG CCCATG CCCATG CCCATG CCC
99165 CCTCTCCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.56, G:0.15, T:0.15
Consensus pattern (6 bp):
CCCATG
Found at i:103932 original size:22 final size:22
Alignment explanation
Indices: 103901--103944 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
103891 ATAAATATTT
*
103901 TTATAGAACTTTTACAAAAAAA
1 TTATACAACTTTTACAAAAAAA
**
103923 TTATACAACTTTTTTAAAAAAA
1 TTATACAACTTTTACAAAAAAA
103945 ATACTAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.36
Consensus pattern (22 bp):
TTATACAACTTTTACAAAAAAA
Found at i:103986 original size:16 final size:18
Alignment explanation
Indices: 103949--104001 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 18
103939 AAAAAAATAC
103949 TAAAATTA-TGTAATT-TA
1 TAAAATTACT-TAATTATA
*
103966 -AAAAATACTTAA-TATA
1 TAAAATTACTTAATTATA
*
103982 TAAAATTATTTAATTATA
1 TAAAATTACTTAATTATA
104000 TA
1 TA
104002 TATATATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 1 0.03
16 11 0.38
17 11 0.38
18 6 0.21
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (18 bp):
TAAAATTACTTAATTATA
Found at i:131523 original size:109 final size:109
Alignment explanation
Indices: 131332--131549 Score: 436
Period size: 109 Copynumber: 2.0 Consensus size: 109
131322 CTCGAACAAA
131332 AACAAATTCTTGTTCTTGATCCACTAAGTTTGCGTAAAATTCTCAAACCAGAGTAGGGGAGTAAC
1 AACAAATTCTTGTTCTTGATCCACTAAGTTTGCGTAAAATTCTCAAACCAGAGTAGGGGAGTAAC
131397 CAGAAGGGTGGTCACAAAAAGACTCCCACGCGACTAATAGTGTG
66 CAGAAGGGTGGTCACAAAAAGACTCCCACGCGACTAATAGTGTG
131441 AACAAATTCTTGTTCTTGATCCACTAAGTTTGCGTAAAATTCTCAAACCAGAGTAGGGGAGTAAC
1 AACAAATTCTTGTTCTTGATCCACTAAGTTTGCGTAAAATTCTCAAACCAGAGTAGGGGAGTAAC
131506 CAGAAGGGTGGTCACAAAAAGACTCCCACGCGACTAATAGTGTG
66 CAGAAGGGTGGTCACAAAAAGACTCCCACGCGACTAATAGTGTG
131550 GTGGACTTGT
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 109 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (109 bp):
AACAAATTCTTGTTCTTGATCCACTAAGTTTGCGTAAAATTCTCAAACCAGAGTAGGGGAGTAAC
CAGAAGGGTGGTCACAAAAAGACTCCCACGCGACTAATAGTGTG
Found at i:136191 original size:15 final size:15
Alignment explanation
Indices: 136171--136199 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
136161 TTGACTATTG
136171 CTATAACCTCCTTGC
1 CTATAACCTCCTTGC
136186 CTATAACCTCCTTG
1 CTATAACCTCCTTG
136200 GTTCAAAGAA
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:0.21, C:0.38, G:0.07, T:0.34
Consensus pattern (15 bp):
CTATAACCTCCTTGC
Found at i:141368 original size:11 final size:10
Alignment explanation
Indices: 141337--141406 Score: 59
Period size: 11 Copynumber: 6.5 Consensus size: 10
141327 TAGAAGTTTG
141337 AAAAATAAAAT
1 AAAAA-AAAAT
*
141348 AAAAACAAAT
1 AAAAAAAAAT
141358 AACAAAAAAAT
1 AA-AAAAAAAT
*
141369 AAAAGTACAAAT
1 AAAA--AAAAAT
*
141381 AAAAGAAAAAG
1 AAAA-AAAAAT
*
141392 AAAAATAAAT
1 AAAAAAAAAT
141402 AAAAA
1 AAAAA
141407 CATAAAACTA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
10 17 0.35
11 22 0.46
12 9 0.19
ACGTcount: A:0.80, C:0.04, G:0.04, T:0.11
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:141378 original size:23 final size:21
Alignment explanation
Indices: 141343--141405 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 21
141333 TTTGAAAAAT
141343 AAAATAAAAACAAATAACAA-A
1 AAAATAAAAACAAATAA-AAGA
141364 AAAATAAAAGTACAAATAAAAGA
1 AAAATAAAA--ACAAATAAAAGA
* *
141387 AAAAGAAAAATAAATAAAA
1 AAAATAAAAACAAATAAAA
141406 ACATAAAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
21 18 0.49
22 2 0.05
23 17 0.46
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.11
Consensus pattern (21 bp):
AAAATAAAAACAAATAAAAGA
Found at i:141406 original size:17 final size:18
Alignment explanation
Indices: 141336--141422 Score: 54
Period size: 18 Copynumber: 4.8 Consensus size: 18
141326 ATAGAAGTTT
141336 GAAAAATAAAATAAAAACA
1 GAAAAAT-AAATAAAAACA
* * * *
141355 -AATAACAAAAAAATAAAA
1 GAAAAATAAATAAA-AACA
*
141373 GTACAAATAAA-AGAAAA-A
1 G-AAAAATAAATA-AAAACA
141391 GAAAAATAAATAAAAACA
1 GAAAAATAAATAAAAACA
* *
141409 TAAAACTAAATAAA
1 GAAAAATAAATAAA
141423 TTCACTAATC
Statistics
Matches: 52, Mismatches: 10, Indels: 13
0.69 0.13 0.17
Matches are distributed among these distances:
17 18 0.35
18 23 0.44
19 3 0.06
20 8 0.15
ACGTcount: A:0.77, C:0.06, G:0.05, T:0.13
Consensus pattern (18 bp):
GAAAAATAAATAAAAACA
Found at i:143921 original size:62 final size:60
Alignment explanation
Indices: 143767--143942 Score: 185
Period size: 62 Copynumber: 2.8 Consensus size: 60
143757 TCCAAAAAAA
* **
143767 TATTATTTTAATA-ATTTAATAATAAATTTAATTTAATATTTATCTTTATAGTATTTTATT
1 TATTATTTTAATATATTTAATATTAAATTTAATTTAATATTTATC-TTATAGTATAATATT
* * *
143827 AATTTAATATTAAAGTGATATTTTAATATTAAATTTAATTTAATGTTTATCTTATAG-ATAAATA
1 TA-TT-AT-TTTAA-T-ATA-TTTAATATTAAATTTAATTTAATATTTATCTTATAGTAT-AATA
143891 TT
59 TT
*
143893 CTATTATTTTAATAATATTTAATATTAAATTTAATCTAATATTTATCTTA
1 -TATTATTTTAAT-ATATTTAATATTAAATTTAATTTAATATTTATCTTA
143943 AAAAATTATA
Statistics
Matches: 96, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
60 1 0.01
61 2 0.02
62 33 0.34
63 8 0.08
64 5 0.05
65 5 0.05
66 13 0.14
67 29 0.30
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (60 bp):
TATTATTTTAATATATTTAATATTAAATTTAATTTAATATTTATCTTATAGTATAATATT
Found at i:143961 original size:57 final size:62
Alignment explanation
Indices: 143766--143962 Score: 178
Period size: 67 Copynumber: 3.2 Consensus size: 62
143756 TTCCAAAAAA
* * * **
143766 ATATTATTTTAAT-A-ATTTAATAATAAATTTAATTTAATATTTATCTTTATAG-TATTTTATT
1 ATATTAATTTAATAATATTTAATATTAAATTTAATCTAATATTTATC-TTATAGATA-AATATT
* * *
143827 A-ATTTAATATTAAAGTGATATTTTAATATTAAATTTAATTTAATGTTTATCTTATAGATAAATA
1 ATA-TTAAT-TT-AA-TAATA-TTTAATATTAAATTTAATCTAATATTTATCTTATAGATAAATA
143891 TT
61 TT
* *
143893 CTATTATTTTAATAATATTTAATATTAAATTTAATCTAATATTTATC-T-TA-A-AAA-ATT
1 ATATTAATTTAATAATATTTAATATTAAATTTAATCTAATATTTATCTTATAGATAAATATT
143950 ATATTAATTTAAT
1 ATATTAATTTAAT
143963 GTTAAAGTTA
Statistics
Matches: 115, Mismatches: 12, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
57 14 0.12
58 3 0.03
59 1 0.01
60 3 0.03
61 6 0.05
62 30 0.26
63 6 0.05
64 3 0.03
65 3 0.03
66 15 0.13
67 31 0.27
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (62 bp):
ATATTAATTTAATAATATTTAATATTAAATTTAATCTAATATTTATCTTATAGATAAATATT
Found at i:148478 original size:20 final size:20
Alignment explanation
Indices: 148455--148602 Score: 131
Period size: 20 Copynumber: 7.4 Consensus size: 20
148445 CTTTCAAGGA
148455 CATCGAAGTGCAAACAGGGG
1 CATCGAAGTGCAAACAGGGG
* *
148475 CATCGGAGTGCAAATAGGGG
1 CATCGAAGTGCAAACAGGGG
* * *
148495 CATCAAAGTGTAAACAAGGG
1 CATCGAAGTGCAAACAGGGG
* *
148515 CA-C-AATTGTGCAAATAGAGG
1 CATCGAA--GTGCAAACAGGGG
* * *
148535 CATCGAAGTGTAAATAGCGG
1 CATCGAAGTGCAAACAGGGG
* *
148555 TA-CCAGAGTGCAAACAGGGG
1 CATCGA-AGTGCAAACAGGGG
148575 CATCGAAGTGCAAACAGGGG
1 CATCGAAGTGCAAACAGGGG
*
148595 CACCGAAG
1 CATCGAAG
148603 ATCAATCAGG
Statistics
Matches: 101, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
18 2 0.02
19 3 0.03
20 91 0.90
21 3 0.03
22 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.32, T:0.14
Consensus pattern (20 bp):
CATCGAAGTGCAAACAGGGG
Found at i:148513 original size:60 final size:60
Alignment explanation
Indices: 148449--148627 Score: 179
Period size: 60 Copynumber: 3.0 Consensus size: 60
148439 AGTGTGCTTT
* * * * *
148449 CAAGGACATCGAAGTGCAAACAGGGGCATCGGAGTGCAAATAGGGGCATCAAAGTGTAAA
1 CAAGGGCATCGAAGTGCAAACAGGGGCATCGAAGTGCAAATAGCGGCACCAAAGTGCAAA
* * * * *
148509 CAAGGGCA-C-AATTGTGCAAATAGAGGCATCGAAGTGTAAATAGCGGTACCAGAGTGCAAA
1 CAAGGGCATCGAA--GTGCAAACAGGGGCATCGAAGTGCAAATAGCGGCACCAAAGTGCAAA
* *
148569 CAGGGGCATCGAAGTGCAAACAGGGGCACCGAAGAT-C-AATCAG-GGCACCAAAGTGCAAA
1 CAAGGGCATCGAAGTGCAAACAGGGGCATCGAAG-TGCAAAT-AGCGGCACCAAAGTGCAAA
148628 TAAAGGCACT
Statistics
Matches: 96, Mismatches: 17, Indels: 13
0.76 0.13 0.10
Matches are distributed among these distances:
58 2 0.02
59 18 0.19
60 72 0.75
61 2 0.02
62 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.30, T:0.13
Consensus pattern (60 bp):
CAAGGGCATCGAAGTGCAAACAGGGGCATCGAAGTGCAAATAGCGGCACCAAAGTGCAAA
Found at i:148525 original size:80 final size:80
Alignment explanation
Indices: 148421--148597 Score: 196
Period size: 80 Copynumber: 2.2 Consensus size: 80
148411 GGGGCACTGG
* ** * * *
148421 AGTGCATACAAGGGCACAAGTGTGC-TTTCA-AGGACATCGAAGTGCAAACAGGGGCATCGGAGT
1 AGTGCAAACAAGGGCACAAGTGTGCAAAT-AGAGG-CATCGAAGTGCAAACAGCGGCACCAGAGT
*
148484 GCAAATAGGGGCATCAA
64 GCAAACAGGGGCATCAA
* * * * *
148501 AGTGTAAACAAGGGCACAATTGTGCAAATAGAGGCATCGAAGTGTAAATAGCGGTACCAGAGTGC
1 AGTGCAAACAAGGGCACAAGTGTGCAAATAGAGGCATCGAAGTGCAAACAGCGGCACCAGAGTGC
*
148566 AAACAGGGGCATCGA
66 AAACAGGGGCATCAA
*
148581 AGTGCAAACAGGGGCAC
1 AGTGCAAACAAGGGCAC
148598 CGAAGATCAA
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
80 76 0.95
81 4 0.05
ACGTcount: A:0.36, C:0.18, G:0.31, T:0.15
Consensus pattern (80 bp):
AGTGCAAACAAGGGCACAAGTGTGCAAATAGAGGCATCGAAGTGCAAACAGCGGCACCAGAGTGC
AAACAGGGGCATCAA
Found at i:148612 original size:20 final size:20
Alignment explanation
Indices: 148458--148627 Score: 116
Period size: 20 Copynumber: 8.6 Consensus size: 20
148448 TCAAGGACAT
*
148458 CGAAGTGCAAACAGGGGCAT
1 CGAAGTGCAAACAGGGGCAC
* * *
148478 CGGAGTGCAAATAGGGGCAT
1 CGAAGTGCAAACAGGGGCAC
* * *
148498 CAAAGTGTAAACAAGGGCA-
1 CGAAGTGCAAACAGGGGCAC
* * *
148517 C-AATTGTGCAAATAGAGGCAT
1 CGAA--GTGCAAACAGGGGCAC
* * * *
148538 CGAAGTGTAAATAGCGGTAC
1 CGAAGTGCAAACAGGGGCAC
*
148558 C-AGAGTGCAAACAGGGGCAT
1 CGA-AGTGCAAACAGGGGCAC
148578 CGAAGTGCAAACAGGGGCAC
1 CGAAGTGCAAACAGGGGCAC
*
148598 CGAAGAT-CAATCA-GGGCAC
1 CGAAG-TGCAAACAGGGGCAC
*
148617 CAAAGTGCAAA
1 CGAAGTGCAAA
148628 TAAAGGCACT
Statistics
Matches: 118, Mismatches: 24, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
18 3 0.03
19 15 0.13
20 95 0.81
21 3 0.03
22 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.31, T:0.13
Consensus pattern (20 bp):
CGAAGTGCAAACAGGGGCAC
Found at i:148613 original size:40 final size:39
Alignment explanation
Indices: 148455--148598 Score: 146
Period size: 40 Copynumber: 3.6 Consensus size: 39
148445 CTTTCAAGGA
**
148455 CATCGAAGTGCAAACAGGGGCATCGGAGTGCAAATAGGGG
1 CATCGAAGTGCAAACAGGGGCA-CCAAGTGCAAATAGGGG
* * * *
148495 CATCAAAGTGTAAACAAGGGCA-CAATTGTGCAAATAGAGG
1 CATCGAAGTGCAAACAGGGGCACCAA--GTGCAAATAGGGG
* * * * *
148535 CATCGAAGTGTAAATAGCGGTACCAGAGTGCAAACAGGGG
1 CATCGAAGTGCAAACAGGGGCACCA-AGTGCAAATAGGGG
148575 CATCGAAGTGCAAACAGGGGCACC
1 CATCGAAGTGCAAACAGGGGCACC
148599 GAAGATCAAT
Statistics
Matches: 83, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
38 1 0.01
40 79 0.95
41 2 0.02
42 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.31, T:0.14
Consensus pattern (39 bp):
CATCGAAGTGCAAACAGGGGCACCAAGTGCAAATAGGGG
Found at i:170908 original size:18 final size:17
Alignment explanation
Indices: 170885--170931 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 17
170875 CATTTAATAA
170885 TTTTAATAATTTTTGAAT
1 TTTTAA-AATTTTTGAAT
170903 TTTTAAATATTTTTGAAT
1 TTTTAAA-ATTTTTGAAT
170921 TTTTAAAATTT
1 TTTTAAAATTT
170932 CAATTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
TTTTAAAATTTTTGAAT
Found at i:174417 original size:18 final size:18
Alignment explanation
Indices: 174394--174431 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
174384 TAATATAGTT
174394 TTATTCG-GTTTATTCGAA
1 TTATTCGAG-TTATTCGAA
174412 TTATTCGAGTTATTCGAA
1 TTATTCGAGTTATTCGAA
174430 TT
1 TT
174432 TGAAAATCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.24, C:0.11, G:0.16, T:0.50
Consensus pattern (18 bp):
TTATTCGAGTTATTCGAA
Found at i:174721 original size:25 final size:25
Alignment explanation
Indices: 174674--174724 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
174664 AAAATGCAAA
* *
174674 AAAGGAAGAAGAAAAAACCAGAAGG
1 AAAGGAAAAAGAAAAAACAAGAAGG
* *
174699 AAAGGAAAAAGAAAGAAGAAGAAGG
1 AAAGGAAAAAGAAAAAACAAGAAGG
174724 A
1 A
174725 TACAGGGCGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.67, C:0.04, G:0.29, T:0.00
Consensus pattern (25 bp):
AAAGGAAAAAGAAAAAACAAGAAGG
Found at i:184411 original size:21 final size:21
Alignment explanation
Indices: 184387--184497 Score: 63
Period size: 21 Copynumber: 5.3 Consensus size: 21
184377 AAAGATACTA
184387 GGTGGGTTCGGAACTATTCCG
1 GGTGGGTTCGGAACTATTCCG
** *
184408 GGTGGGCCCGGAAATATAAT-C-
1 GGTGGGTTCGGAACTAT--TCCG
* *
184429 GGCGGGTTTGGAACTATTCCG
1 GGTGGGTTCGGAACTATTCCG
*
184450 GGTGGG-CCTGGCAA-TATAAT-C-
1 GGTGGGTTC-GG-AACTAT--TCCG
*
184471 GGCGGGTTCGGAACTATTCCG
1 GGTGGGTTCGGAACTATTCCG
184492 GGTGGG
1 GGTGGG
184498 CCAAGAGGAG
Statistics
Matches: 64, Mismatches: 14, Indels: 24
0.63 0.14 0.24
Matches are distributed among these distances:
19 2 0.03
20 4 0.06
21 51 0.80
22 5 0.08
23 2 0.03
ACGTcount: A:0.18, C:0.19, G:0.39, T:0.24
Consensus pattern (21 bp):
GGTGGGTTCGGAACTATTCCG
Found at i:184442 original size:42 final size:42
Alignment explanation
Indices: 184390--184499 Score: 193
Period size: 42 Copynumber: 2.6 Consensus size: 42
184380 GATACTAGGT
184390 GGGTTCGGAACTATTCCGGGTGGGCCCGGAAATATAATCGGC
1 GGGTTCGGAACTATTCCGGGTGGGCCCGGAAATATAATCGGC
* * *
184432 GGGTTTGGAACTATTCCGGGTGGGCCTGGCAATATAATCGGC
1 GGGTTCGGAACTATTCCGGGTGGGCCCGGAAATATAATCGGC
184474 GGGTTCGGAACTATTCCGGGTGGGCC
1 GGGTTCGGAACTATTCCGGGTGGGCC
184500 AAGAGGAGGA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.18, C:0.21, G:0.37, T:0.24
Consensus pattern (42 bp):
GGGTTCGGAACTATTCCGGGTGGGCCCGGAAATATAATCGGC
Found at i:192296 original size:8 final size:8
Alignment explanation
Indices: 192285--192327 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
192275 AATAATAAAA
192285 TTATAATT
1 TTATAATT
*
192293 TTATTATT
1 TTATAATT
192301 TTAATAA-T
1 TT-ATAATT
*
192309 TTATATTT
1 TTATAATT
192317 TTATAATT
1 TTATAATT
192325 TTA
1 TTA
192328 AAGAAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 3 0.10
8 23 0.79
9 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTATAATT
Found at i:192317 original size:15 final size:16
Alignment explanation
Indices: 192287--192325 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
192277 TAATAAAATT
192287 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
192304 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
192319 ATAATTT
1 ATAATTT
192326 TAAAGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:192325 original size:24 final size:23
Alignment explanation
Indices: 192258--192329 Score: 83
Period size: 24 Copynumber: 3.1 Consensus size: 23
192248 GATTGAAATT
**
192258 AAATTATATATTTTTATAATAATA
1 AAATT-TATATTTTTATAATTTTA
* *
192282 AAA-TTATAATTTTATTATTTTA
1 AAATTTATATTTTTATAATTTTA
192304 ATAATTTATATTTTTATAATTTTA
1 A-AATTTATATTTTTATAATTTTA
192328 AA
1 AA
192330 GAAAATATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 15 0.38
23 4 0.10
24 21 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATTTATATTTTTATAATTTTA
Found at i:193889 original size:20 final size:19
Alignment explanation
Indices: 193823--193889 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 19
193813 AGAAATTTAC
193823 AAATTGTTAAAAAATATAGA
1 AAATT-TTAAAAAATATAGA
***
193843 AAATTTTTAAATGTTATA-A
1 AAA-TTTTAAAAAATATAGA
193862 AAATTTTAGAAAAATATAGA
1 AAATTTTA-AAAAATATAGA
193882 AAATTTTA
1 AAATTTTA
193890 TTTAAAATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 5 0.13
19 10 0.26
20 21 0.55
21 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.37
Consensus pattern (19 bp):
AAATTTTAAAAAATATAGA
Found at i:195391 original size:17 final size:16
Alignment explanation
Indices: 195364--195402 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 16
195354 ATTTAGTCTT
195364 TTTTATTTTTAATTTAA
1 TTTT-TTTTTAATTTAA
195381 TATTTTTTTTAATTTAA
1 T-TTTTTTTTAATTTAA
195398 TTTTT
1 TTTTT
195403 ATATTCTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 14 0.67
18 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTTTTAATTTAA
Found at i:196362 original size:17 final size:17
Alignment explanation
Indices: 196340--196373 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
196330 GATGCAATGT
196340 GATGCGAATGGAGCAGG
1 GATGCGAATGGAGCAGG
196357 GATGCGAATGGAGCAGG
1 GATGCGAATGGAGCAGG
196374 AATATTCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.47, T:0.12
Consensus pattern (17 bp):
GATGCGAATGGAGCAGG
Found at i:198180 original size:17 final size:17
Alignment explanation
Indices: 198140--198180 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
198130 TCATGTTATT
198140 TTAAAAAAATAAAAAAA
1 TTAAAAAAATAAAAAAA
*
198157 TTCAAAAAAT--AAAAA
1 TTAAAAAAATAAAAAAA
198172 TTAAAAAAA
1 TTAAAAAAA
198181 GTACATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.59
17 9 0.41
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (17 bp):
TTAAAAAAATAAAAAAA
Found at i:198261 original size:22 final size:22
Alignment explanation
Indices: 198231--198274 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
198221 AACTGATTTT
198231 TTTGAAAAAAAATGAAAATATAA
1 TTTGAAAAAAAATGAAAA-ATAA
*
198254 TTTG-AAAAAATTGAAAAATAA
1 TTTGAAAAAAAATGAAAAATAA
198275 AAAAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (22 bp):
TTTGAAAAAAAATGAAAAATAA
Found at i:198781 original size:19 final size:19
Alignment explanation
Indices: 198750--198819 Score: 51
Period size: 20 Copynumber: 3.8 Consensus size: 19
198740 ACCAAAGTGA
*
198750 TTTA-ATTTAGTTTTATAT
1 TTTATATTTTGTTTTATAT
*
198768 TTTATATTTTGTTTTTGTAT
1 TTTATATTTTG-TTTTATAT
198788 TTGTAT-TTGTT-TTTTAT-T
1 TT-TATATT-TTGTTTTATAT
*
198806 TTTGTA-TTTGTTTT
1 TTTATATTTTGTTTT
198820 TGTTTTGCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
16 2 0.05
17 7 0.17
18 7 0.17
19 10 0.24
20 11 0.26
21 5 0.12
ACGTcount: A:0.16, C:0.00, G:0.10, T:0.74
Consensus pattern (19 bp):
TTTATATTTTGTTTTATAT
Found at i:198783 original size:6 final size:6
Alignment explanation
Indices: 198774--198825 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
198764 ATATTTTATA
* * * *
198774 TTTTGT TTTTGT ATTTGT ATTTGTT TTTTAT TTTTGT ATTTGT TTTTGT
1 TTTTGT TTTTGT TTTTGT TTTTG-T TTTTGT TTTTGT TTTTGT TTTTGT
198823 TTT
1 TTT
198826 GCATTACATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
6 35 0.90
7 4 0.10
ACGTcount: A:0.08, C:0.00, G:0.13, T:0.79
Consensus pattern (6 bp):
TTTTGT
Found at i:198807 original size:25 final size:25
Alignment explanation
Indices: 198774--198825 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
198764 ATATTTTATA
*
198774 TTTTGTTTTTGTATTTGTATTTGTT
1 TTTTATTTTTGTATTTGTATTTGTT
*
198799 TTTTATTTTTGTATTTGTTTTTGTT
1 TTTTATTTTTGTATTTGTATTTGTT
198824 TT
1 TT
198826 GCATTACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.08, C:0.00, G:0.13, T:0.79
Consensus pattern (25 bp):
TTTTATTTTTGTATTTGTATTTGTT
Found at i:198820 original size:19 final size:19
Alignment explanation
Indices: 198760--198820 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
198750 TTTAATTTAG
*
198760 TTTTATATTTTATATTTTGTT
1 TTTTAT-TTTTGTA-TTTGTT
198781 TTTGTA--TTTGTATTTGTT
1 TTT-TATTTTTGTATTTGTT
198799 TTTTATTTTTGTATTTGTT
1 TTTTATTTTTGTATTTGTT
198818 TTT
1 TTT
198821 GTTTTGCATT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 2 0.06
18 9 0.25
19 20 0.56
21 3 0.08
22 2 0.06
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (19 bp):
TTTTATTTTTGTATTTGTT
Found at i:202239 original size:22 final size:22
Alignment explanation
Indices: 202193--202239 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
202183 TTTTCTATAT
* *
202193 TTTTCAAAAAAAATATATAATA
1 TTTTCAAAAAAAAAATATAACA
*
202215 TTTTCAAAAAAAAAATATAGCA
1 TTTTCAAAAAAAAAATATAACA
202237 TTT
1 TTT
202240 AATTATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (22 bp):
TTTTCAAAAAAAAAATATAACA
Found at i:202260 original size:9 final size:9
Alignment explanation
Indices: 202248--202301 Score: 51
Period size: 9 Copynumber: 6.1 Consensus size: 9
202238 TTAATTATTT
*
202248 TAATTTCTA
1 TAATTTATA
202257 TAATTTATA
1 TAATTTATA
202266 -AATTTATA
1 TAATTTATA
*
202274 -ATATTTTTA
1 TA-ATTTATA
202283 TGAATTT-TA
1 T-AATTTATA
202292 TAATTTATA
1 TAATTTATA
202301 T
1 T
202302 TTTAAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 14 0.36
9 20 0.51
10 4 0.10
11 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (9 bp):
TAATTTATA
Found at i:202288 original size:27 final size:26
Alignment explanation
Indices: 202250--202300 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
202240 AATTATTTTA
202250 ATTTCTATAA-TTTATAAATTTATAAT
1 ATTTCTATAATTTTAT-AATTTATAAT
*
202276 ATTTTTATGAATTTTATAATTTATA
1 ATTTCTAT-AATTTTATAATTTATA
202301 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 10 0.45
28 5 0.23
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (26 bp):
ATTTCTATAATTTTATAATTTATAAT
Found at i:203452 original size:25 final size:25
Alignment explanation
Indices: 203436--203482 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
203426 TTAAAACTGG
203436 TTTAT-TA-AATAATTTTTTAAAAT
1 TTTATGTATAATAATTTTTTAAAAT
*
203459 TTTATGTATAATAA-TTATTAAAAT
1 TTTATGTATAATAATTTTTTAAAAT
203483 ATAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 5 0.24
24 11 0.52
25 5 0.24
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TTTATGTATAATAATTTTTTAAAAT
Found at i:203943 original size:27 final size:28
Alignment explanation
Indices: 203907--203965 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
203897 AAACATGCAG
203907 TTTTGAAAAATTAGATTAA-AAA-AAATA
1 TTTTGAAAAATTAGATTAATAAATAAA-A
* *
203934 TTTTTAAAAATTATATTAATAAATAAAA
1 TTTTGAAAAATTAGATTAATAAATAAAA
203962 TTTT
1 TTTT
203966 AATAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 17 0.61
28 8 0.29
29 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (28 bp):
TTTTGAAAAATTAGATTAATAAATAAAA
Found at i:203963 original size:18 final size:18
Alignment explanation
Indices: 203940--203974 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
203930 AATATTTTTA
*
203940 AAAATTATATTAATAAAT
1 AAAATTATAATAATAAAT
*
203958 AAAATTTTAATAATAAA
1 AAAATTATAATAATAAA
203975 ATTTTAAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTATAATAATAAAT
Found at i:203974 original size:14 final size:15
Alignment explanation
Indices: 203949--203981 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
203939 AAAAATTATA
203949 TTAATAAATAAAATT
1 TTAATAAATAAAATT
203964 TTAAT-AATAAAATT
1 TTAATAAATAAAATT
203978 TTAA
1 TTAA
203982 ATAACTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAATAAATAAAATT
Found at i:211549 original size:24 final size:24
Alignment explanation
Indices: 211503--211821 Score: 305
Period size: 24 Copynumber: 13.3 Consensus size: 24
211493 GAAATAAATC
* *
211503 AAACGTATTCATGTTGACGAGCGT
1 AAACGTACTCATGCTGACGAGCGT
* *
211527 AAATGTACTAATGCTGACGAGCGT
1 AAACGTACTCATGCTGACGAGCGT
* * * *
211551 AAACGTATTCATACTGATGAGCAT
1 AAACGTACTCATGCTGACGAGCGT
* * *
211575 AAACGTACTCATTCTAACGAGCAT
1 AAACGTACTCATGCTGACGAGCGT
* * * *
211599 AAACGTATTCATGCTAACAAGTGT
1 AAACGTACTCATGCTGACGAGCGT
*
211623 AAACGTACTCATGCTGACGAGCTT
1 AAACGTACTCATGCTGACGAGCGT
* *
211647 AAACGTATTCATGCTAACGAGCGT
1 AAACGTACTCATGCTGACGAGCGT
* * * *
211671 AAATGTATTCATGTTGACGAGCAT
1 AAACGTACTCATGCTGACGAGCGT
* *
211695 AAACGTGCTCATGCTAACGAGCGT
1 AAACGTACTCATGCTGACGAGCGT
* **
211719 AAACGTACTCATGCTGATGAGCAA
1 AAACGTACTCATGCTGACGAGCGT
* * * *
211743 AAACGTATTCATGTTGACGAGTGA
1 AAACGTACTCATGCTGACGAGCGT
* *
211767 AAACGTATTCATGCTGACGAGTGT
1 AAACGTACTCATGCTGACGAGCGT
* * **
211791 AAACGTATTCATGTTGACGAGTAT
1 AAACGTACTCATGCTGACGAGCGT
211815 AAACGTA
1 AAACGTA
211822 AAGAAGTTCT
Statistics
Matches: 244, Mismatches: 51, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 244 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (24 bp):
AAACGTACTCATGCTGACGAGCGT
Found at i:211583 original size:48 final size:48
Alignment explanation
Indices: 211503--211821 Score: 359
Period size: 48 Copynumber: 6.6 Consensus size: 48
211493 GAAATAAATC
* * * *
211503 AAACGTATTCATGTTGACGAGCGTAAATGTACTAATGCTGACGAGCGT
1 AAACGTATTCATGCTGACGAGCGTAAACGTACTCATGCTGACGAGCAT
* * * * *
211551 AAACGTATTCATACTGATGAGCATAAACGTACTCATTCTAACGAGCAT
1 AAACGTATTCATGCTGACGAGCGTAAACGTACTCATGCTGACGAGCAT
* * * *
211599 AAACGTATTCATGCTAACAAGTGTAAACGTACTCATGCTGACGAGCTT
1 AAACGTATTCATGCTGACGAGCGTAAACGTACTCATGCTGACGAGCAT
* * * *
211647 AAACGTATTCATGCTAACGAGCGTAAATGTATTCATGTTGACGAGCAT
1 AAACGTATTCATGCTGACGAGCGTAAACGTACTCATGCTGACGAGCAT
** * * *
211695 AAACGTGCTCATGCTAACGAGCGTAAACGTACTCATGCTGATGAGCAA
1 AAACGTATTCATGCTGACGAGCGTAAACGTACTCATGCTGACGAGCAT
* * * * **
211743 AAACGTATTCATGTTGACGAGTGAAAACGTATTCATGCTGACGAGTGT
1 AAACGTATTCATGCTGACGAGCGTAAACGTACTCATGCTGACGAGCAT
* **
211791 AAACGTATTCATGTTGACGAGTATAAACGTA
1 AAACGTATTCATGCTGACGAGCGTAAACGTA
211822 AAGAAGTTCT
Statistics
Matches: 227, Mismatches: 44, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 227 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (48 bp):
AAACGTATTCATGCTGACGAGCGTAAACGTACTCATGCTGACGAGCAT
Found at i:213233 original size:26 final size:27
Alignment explanation
Indices: 213204--213300 Score: 110
Period size: 27 Copynumber: 3.7 Consensus size: 27
213194 AACACGTCAG
* * *
213204 GAAAGGAA-GCCTTTGTGACGTAATAC
1 GAAAGAAATGCCTTTGTGACATGATAC
* *
213230 GAAAGAAATTCCTTTGTGACATGATAT
1 GAAAGAAATGCCTTTGTGACATGATAC
*
213257 GAAAGAAATGCCTTTGTGGCATGATATC
1 GAAAGAAATGCCTTTGTGACATGATA-C
213285 -AAAGAAA-GCCTTTGTG
1 GAAAGAAATGCCTTTGTG
213301 GTAAAATATG
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
26 16 0.26
27 45 0.74
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (27 bp):
GAAAGAAATGCCTTTGTGACATGATAC
Found at i:213243 original size:27 final size:27
Alignment explanation
Indices: 213204--213330 Score: 107
Period size: 27 Copynumber: 4.8 Consensus size: 27
213194 AACACGTCAG
* *
213204 GAAAGGAA-GCCTTTGTGACGTAATAC
1 GAAAGAAATGCCTTTGTGACATAATAC
* * *
213230 GAAAGAAATTCCTTTGTGACATGATAT
1 GAAAGAAATGCCTTTGTGACATAATAC
* *
213257 GAAAGAAATGCCTTTGTGGCATGATATC
1 GAAAGAAATGCCTTTGTGACATAATA-C
** * *
213285 -AAAGAAA-GCCTTTGTGGTAAAATAT
1 GAAAGAAATGCCTTTGTGACATAATAC
* *
213310 GACAGAAATGCTTTTGTGACA
1 GAAAGAAATGCCTTTGTGACA
213331 AGAGTTAAAT
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
26 27 0.33
27 54 0.67
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (27 bp):
GAAAGAAATGCCTTTGTGACATAATAC
Found at i:215544 original size:3 final size:3
Alignment explanation
Indices: 215536--215562 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
215526 ACAGGCTTTA
215536 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
215563 AGATATAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:221861 original size:17 final size:17
Alignment explanation
Indices: 221839--221886 Score: 80
Period size: 17 Copynumber: 2.8 Consensus size: 17
221829 TAATACTAAG
221839 ATGCAATGACAAT-GGAA
1 ATGCAATGACAATAGG-A
221856 ATGCAATGACAATAGGA
1 ATGCAATGACAATAGGA
221873 ATGCAATGACAATA
1 ATGCAATGACAATA
221887 TTTACTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 28 0.93
18 2 0.07
ACGTcount: A:0.48, C:0.12, G:0.21, T:0.19
Consensus pattern (17 bp):
ATGCAATGACAATAGGA
Found at i:233376 original size:106 final size:106
Alignment explanation
Indices: 233186--233399 Score: 401
Period size: 106 Copynumber: 2.0 Consensus size: 106
233176 TCTATAGTAG
233186 GTAATGGTTGGTCTAGCAATACTCCCTTGAGTTAAATCTATAGTAGGTAAAGAGTACTCCCTTAT
1 GTAATGGTTGGTCTAGCAATACTCCCTTGAGTTAAATCTATAGTAGGTAAAGAGTACTCCCTTAT
* *
233251 AGTTCTTTGTTCCTTTGCCATTGGTTCGTTTGTAGGCAGTT
66 AGTTCTTTGTTCCTCTGCCATTCGTTCGTTTGTAGGCAGTT
*
233292 GTAATGGTTGGTCTAGCAATACTCCCTTGAGTTAAATCTATAGTAGGTAACGAGTACTCCCTTAT
1 GTAATGGTTGGTCTAGCAATACTCCCTTGAGTTAAATCTATAGTAGGTAAAGAGTACTCCCTTAT
233357 AGTTCTTTGTTCCTCTGCCATTCGTTCGTTTGTAGGCAGTT
66 AGTTCTTTGTTCCTCTGCCATTCGTTCGTTTGTAGGCAGTT
233398 GT
1 GT
233400 GAAGGTATGT
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 105 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (106 bp):
GTAATGGTTGGTCTAGCAATACTCCCTTGAGTTAAATCTATAGTAGGTAAAGAGTACTCCCTTAT
AGTTCTTTGTTCCTCTGCCATTCGTTCGTTTGTAGGCAGTT
Found at i:235609 original size:13 final size:13
Alignment explanation
Indices: 235580--235608 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
235570 GATATGCGTG
235580 AAAACTAAAACTA
1 AAAACTAAAACTA
235593 AAAACTAAAA-TA
1 AAAACTAAAACTA
235605 AAAA
1 AAAA
235609 ATAACTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAACTAAAACTA
Found at i:247931 original size:24 final size:24
Alignment explanation
Indices: 247899--247946 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
247889 ACAGGCTTTG
*
247899 TTTCTTCCTTATCATTCTCATCTT
1 TTTCCTCCTTATCATTCTCATCTT
* * *
247923 TTTCCTCCTTCTCTTTTTCATCTT
1 TTTCCTCCTTATCATTCTCATCTT
247947 CTTGATTGAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTCCTCCTTATCATTCTCATCTT
Found at i:253660 original size:11 final size:11
Alignment explanation
Indices: 253644--253668 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
253634 CAGATGGTTA
253644 TATCAACAAAT
1 TATCAACAAAT
253655 TATCAACAAAT
1 TATCAACAAAT
253666 TAT
1 TAT
253669 AACCTCTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (11 bp):
TATCAACAAAT
Found at i:260218 original size:20 final size:20
Alignment explanation
Indices: 260189--260259 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
260179 GGTTGGTAAA
* *
260189 AAAGTTAACGGTCAACCGCC
1 AAAGTCAACGGTCAACCGTC
*
260209 AAAGTCAACGGTCTAA-AGTC
1 AAAGTCAACGGTC-AACCGTC
** *
260229 AAAGTCAACTATCAACCATC
1 AAAGTCAACGGTCAACCGTC
260249 AAAGTCAACGG
1 AAAGTCAACGG
260260 GTCAGTCAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.05
20 36 0.90
21 2 0.05
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.17
Consensus pattern (20 bp):
AAAGTCAACGGTCAACCGTC
Found at i:261115 original size:30 final size:30
Alignment explanation
Indices: 261066--261147 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
261056 CCATAATTTT
*
261066 TTTATTAAAA--CCCAATTAGTCCCTAA-A
1 TTTATTAAAATTCCAAATTAGTCCCTAAGA
261093 TATTATTAAAATTCCAAATTAGTCCCTAAGA
1 T-TTATTAAAATTCCAAATTAGTCCCTAAGA
** * *
261124 TTCGTAAAAATTCCAATTTAGTCC
1 TTTATTAAAATTCCAAATTAGTCC
261148 TTGAAAACAC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.02
28 9 0.20
30 34 0.74
31 2 0.04
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (30 bp):
TTTATTAAAATTCCAAATTAGTCCCTAAGA
Found at i:262310 original size:3 final size:3
Alignment explanation
Indices: 262302--262327 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
262292 ACCCACAAGT
262302 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
262328 TCCCACTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:264454 original size:20 final size:20
Alignment explanation
Indices: 264431--264478 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
264421 AAAGTCAAGG
264431 GTCAACGGTCAA-TAATCAAA
1 GTCAACGGTCAACT-ATCAAA
** *
264451 GTCAAATGTCAACTGTCAAA
1 GTCAACGGTCAACTATCAAA
264471 GTCAACGG
1 GTCAACGG
264479 GTTCATGTCG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
GTCAACGGTCAACTATCAAA
Found at i:267060 original size:17 final size:18
Alignment explanation
Indices: 267038--267071 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
267028 GAATTCTTTG
267038 TCTTTA-GTATTTATTTA
1 TCTTTAGGTATTTATTTA
*
267055 TCTTTAGGTTTTTATTT
1 TCTTTAGGTATTTATTT
267072 TTATTTCTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.68
Consensus pattern (18 bp):
TCTTTAGGTATTTATTTA
Found at i:289190 original size:52 final size:51
Alignment explanation
Indices: 289125--289365 Score: 167
Period size: 52 Copynumber: 4.7 Consensus size: 51
289115 TAAAAATATG
** *
289125 TTTTTTAGTTATTTTAAAGAAAAGTTTAAATTTTTAAACAAAGTTTTGATTT
1 TTTTTTAACTATTTTAAAGAAAAGTTTAAATTTTTAAACAAAATTTTGA-TT
* * **
289177 TTTTTTAACTATTTTGAAATAAAAGTTTGAATTTTTAAGTAAAATATTT-ATT
1 TTTTTTAACTATTTT-AAAGAAAAGTTTAAATTTTTAAACAAAAT-TTTGATT
* ** ****
289229 TTCTTTAA--A----AAAGAGAAAGTTTACTTTTTTAAA-AAAATAAAAATCT
1 TTTTTTAACTATTTTAAAGA-AAAGTTTAAATTTTTAAACAAAATTTTGAT-T
* * *
289275 GCTTTTTTAATTATTTTAAAGAAAAATTTTAAATTTTTAAACAAAATTTTGATA
1 --TTTTTTAACTATTTTAAAG-AAAAGTTTAAATTTTTAAACAAAATTTTGATT
* *
289329 TTTTTT-ACTATTTCGAAATAAAAGTTTAAATTTTTAA
1 TTTTTTAACTATTT-TAAAGAAAAGTTTAAATTTTTAA
289366 GTAAATTAAT
Statistics
Matches: 144, Mismatches: 29, Indels: 33
0.70 0.14 0.16
Matches are distributed among these distances:
45 11 0.08
46 15 0.10
48 7 0.05
50 2 0.01
51 23 0.16
52 31 0.22
53 25 0.17
54 22 0.15
55 8 0.06
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (51 bp):
TTTTTTAACTATTTTAAAGAAAAGTTTAAATTTTTAAACAAAATTTTGATT
Found at i:289332 original size:20 final size:20
Alignment explanation
Indices: 289286--289332 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
289276 CTTTTTTAAT
289286 TATTTTAAAGAAAAATTTTA
1 TATTTTAAAGAAAAATTTTA
* *
289306 AATTTTTAAA-CAAAATTTTGA
1 TA-TTTTAAAGAAAAATTTT-A
289327 TATTTT
1 TATTTT
289333 TTACTATTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (20 bp):
TATTTTAAAGAAAAATTTTA
Found at i:289350 original size:151 final size:148
Alignment explanation
Indices: 289027--289532 Score: 578
Period size: 151 Copynumber: 3.4 Consensus size: 148
289017 AAGTTTTGGT
* * * *
289027 TTTTTTTAAACAATTTCGAAATAAAAGCTTCGATTTTTAAGTAAAATAGTGATTTTGTTTAAAAA
1 TTTTTTT-AACTATTTCGAAATAAAAGCTTTGATTTTTAAGTAAAATAATGATTTTCTTTAAAAA
* *
289092 AGAGATTTAGATTT-TTTTTT---AAATAAAAATATGTTTTTTAGTTATTTTAAAG-AAAAGTTT
65 AGAGA--AAG-TTTATTTTTTAAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAAGTTT
*
289152 AAATTTTTAAACAAAGTTTTGA
127 AAATTTTTAAACAAAATTTTGA
* * *
289174 TTTTTTTTTAACTATTTTGAAATAAAAG-TTTGAATTTTTAAGTAAAATATTTATTTTCTTTAAA
1 --TTTTTTTAACTATTTCGAAATAAAAGCTTTG-ATTTTTAAGTAAAATAATGATTTTCTTTAAA
* *
289238 AAAGAGAAAGTTTACTTTTTTAAAAAAATAAAAATCTGCTTTTTTAATTATTTTAAAGAAAAATT
63 AAAGAGAAAGTTTA-TTTTTT-AAAAAATAAAAATCTG-TTTTTTAGTTATTTTAAAGAAAAAGT
289303 TTAAATTTTTAAACAAAATTTTGA
125 TTAAATTTTTAAACAAAATTTTGA
* * * *
289327 TATTTTTT-ACTATTTCGAAATAAAAG-TTTAAATTTTTAAGTAAATTAATGATTTTCATCAACA
1 T-TTTTTTAACTATTTCGAAATAAAAGCTTT-GATTTTTAAGTAAAATAATGATTTTCTTTAA-A
* * * * **
289390 AAAAAAAAAGGTTTATATTTTTAAAAAATAAAAAACTGTTTTTTAGTGATTTTAAAGAAAAAGAC
63 AAAGAGAAA-GTTTAT-TTTTTAAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAAGTT
289455 TAAATTTTTAAACAAAATTTTGA
126 TAAATTTTTAAACAAAATTTTGA
* * * * *
289478 TTTTTTTAACTATTTCAAAATAAAAGTTTTGATTTTGAAGTAAAGTAATAATTTT
1 TTTTTTTAACTATTTCGAAATAAAAGCTTTGATTTTTAAGTAAAATAATGATTTT
289533 GTTTTAGTTA
Statistics
Matches: 310, Mismatches: 31, Indels: 30
0.84 0.08 0.08
Matches are distributed among these distances:
145 3 0.01
146 2 0.01
147 9 0.03
148 52 0.17
149 7 0.02
150 6 0.02
151 142 0.46
152 51 0.16
153 38 0.12
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.45
Consensus pattern (148 bp):
TTTTTTTAACTATTTCGAAATAAAAGCTTTGATTTTTAAGTAAAATAATGATTTTCTTTAAAAAA
GAGAAAGTTTATTTTTTAAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAAGTTTAAAT
TTTTAAACAAAATTTTGA
Found at i:290996 original size:238 final size:238
Alignment explanation
Indices: 290566--291033 Score: 751
Period size: 238 Copynumber: 2.0 Consensus size: 238
290556 AAAATAATAA
*
290566 TAATGATAAAAGATCGAATAAATTGTAGATGAATTTTAAGATTTCTCTTAATTCATTAGTAATTT
1 TAATAATAAAAGATCGAATAAATTGTAGATGAATTTTAAGATTTCTCTTAATTCATTAGTAATTT
* * *
290631 TTTAGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTAAAGGTATCTTACTAGAATT
66 TTTAGGTTTTTTCAAGATTCTAAAATAGAATTAATTTTAAGAATTAAAAGTATCTTACTAGAATT
* * *
290696 ATTTAGGTATCGTTTAGGATTCTCGTCAGAAGTAAAAATTTCTAATTTAAGTTTTGAATTAGATA
131 ATTTAGGTATCGTTTAGGATTATCGTCAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
290761 AGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTACATCGGAG
196 AGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTACATCGGAG
* *
290804 TAATAATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAATTT
1 TAATAATAAAAGATCGAATAAATTGTAGATGAATTTTAAGATTTCTCTTAATTCATTAGTAA-TT
* * *
290869 TTTTGGGTTTTTTCAAGATTCTAAAATAG-GTTAATTTTAAGAA-TAGAAAGTATTTTACTAGAA
65 TTTTAGGTTTTTTCAAGATTCTAAAATAGAATTAATTTTAAGAATTA-AAAGTATCTTACTAGAA
* * * *
290932 TTATTTAGGTATCTTTTAGGGTTATTGTTAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGA
129 TTATTTAGGTATCGTTTAGGATTATCGTCAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGA
*
290997 TAAGTTTGGTGAACACGTTTTAGTCAAGTTACAAGTA
194 TAAGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTA
291034 AATTGGAGGC
Statistics
Matches: 211, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
237 2 0.01
238 181 0.86
239 28 0.13
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (238 bp):
TAATAATAAAAGATCGAATAAATTGTAGATGAATTTTAAGATTTCTCTTAATTCATTAGTAATTT
TTTAGGTTTTTTCAAGATTCTAAAATAGAATTAATTTTAAGAATTAAAAGTATCTTACTAGAATT
ATTTAGGTATCGTTTAGGATTATCGTCAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
AGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTACATCGGAG
Found at i:294350 original size:4 final size:4
Alignment explanation
Indices: 294341--294380 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
294331 ACCTGAATTT
* *
294341 ATTC ATTC ATTC ACTC ATTC ATTC ATTC ATTC ACTC ATTC
1 ATTC ATTC ATTC ATTC ATTC ATTC ATTC ATTC ATTC ATTC
294381 GCTCATTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (4 bp):
ATTC
Found at i:298422 original size:58 final size:58
Alignment explanation
Indices: 298357--298472 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
298347 CTAGTCACTT
*
298357 TTATTCATTTAATCGTTTTCATTCATTTACCAATATGCATACTCATAATTATTTCAGG
1 TTATTCATTTAATCGTTTTCATTCATATACCAATATGCATACTCATAATTATTTCAGG
298415 TTATTCATTTAATCGTTTTCATTCATATACCAATATGCATACTCATAATTATTTCAGG
1 TTATTCATTTAATCGTTTTCATTCATATACCAATATGCATACTCATAATTATTTCAGG
298473 GATGTACATC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.30, C:0.17, G:0.07, T:0.46
Consensus pattern (58 bp):
TTATTCATTTAATCGTTTTCATTCATATACCAATATGCATACTCATAATTATTTCAGG
Found at i:303145 original size:20 final size:21
Alignment explanation
Indices: 303111--303151 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
303101 TTAAATCAAG
*
303111 GAAAAAAT-ACAAAAATAGAA
1 GAAAAAATAAAAAAAATAGAA
303131 GAAAAAATAAAAAAAATAGAA
1 GAAAAAATAAAAAAAATAGAA
303152 AGAGAGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (21 bp):
GAAAAAATAAAAAAAATAGAA
Found at i:303648 original size:42 final size:42
Alignment explanation
Indices: 303555--303990 Score: 499
Period size: 42 Copynumber: 10.5 Consensus size: 42
303545 AAGGAAAGCA
303555 TTCATTGCATTTAGAGGCCCAGGTGTGGAGG-TCCATTTAC-T
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCT-CATTTACTT
* * * * * *
303596 TTCATCGCATTCAGAAGTCCAGATGTGAAGGCTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCTCATTTACTT
303638 TTCATTGCATTTAGAGGCCCAGGTGTGGAGG-TCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCT-CATTTACTT
* * ** *
303680 TTCATCGCATTCAGAGGCCCAGGTGTAAAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCTCATTTACTT
** *
303722 TTCATTGCATTTAGAGGATCAGGTGTGGAGTC-CATTTAC-T
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCTCATTTACTT
* * *
303762 TTCATTGCATTTAAAGGCTCAGGTGTGGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCTCATTTACTT
* *
303804 TTCATTGCATTTAGAGGCCGAAGTGTGGAGG-TCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCT-CATTTACTT
* * *
303846 TTCATTGCATTTAGATGCCTAGGTGTGAAGGCTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCTCATTTACTT
* * * * *
303888 TTCGTTACATTTAGAGGCCCAAGTGTAGAGGTTCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCTCATTTACTT
* * * *
303930 TTTATTGCATTTGGAGGCCCAGGTGTGGA-GATCTACTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCTC-ATTTACTT
*
303972 TTCATTGCAATTAGAGGCC
1 TTCATTGCATTTAGAGGCC
303991 TAAACATAGA
Statistics
Matches: 331, Mismatches: 55, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
40 29 0.09
41 51 0.15
42 250 0.76
43 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCTCATTTACTT
Found at i:303734 original size:84 final size:84
Alignment explanation
Indices: 303555--303990 Score: 565
Period size: 84 Copynumber: 5.2 Consensus size: 84
303545 AAGGAAAGCA
* * * * *
303555 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTAC-TTTCATCGCATTCAGAAGTCCAGA
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
303619 TGTGAAGGCTCATTTACTT
66 TGTGAAGGCTCATTTACTT
* *
303638 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATCGCATTCAGAGGCCCAGG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* *
303703 TGTAAAGGCCCATTTACTT
66 TGTGAAGGCTCATTTACTT
** * *
303722 TTCATTGCATTTAGAGGATCAGGTGTGGA-GTCCATTTAC-TTTCATTGCATTTAAAGGCTCAGG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* *
303785 TGTGGAGGTTCATTTACTT
66 TGTGAAGGCTCATTTACTT
* * * *
303804 TTCATTGCATTTAGAGGCCGAAGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGATGCCTAGG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
303869 TGTGAAGGCTCATTTACTT
66 TGTGAAGGCTCATTTACTT
* * * * * * *
303888 TTCGTTACATTTAGAGGCCCAAGTGTAGAGGTTCATTTACTTTTTATTGCATTTGGAGGCCCAGG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
* * *
303953 TGTGGA-GATCTACTTACTT
66 TGTGAAGGCTC-ATTTACTT
*
303972 TTCATTGCAATTAGAGGCC
1 TTCATTGCATTTAGAGGCC
303991 TAAACATAGA
Statistics
Matches: 309, Mismatches: 40, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
82 60 0.19
83 63 0.20
84 186 0.60
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (84 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCATTGCATTTAGAGGCCCAGG
TGTGAAGGCTCATTTACTT
Found at i:303832 original size:166 final size:166
Alignment explanation
Indices: 303555--303990 Score: 570
Period size: 166 Copynumber: 2.6 Consensus size: 166
303545 AAGGAAAGCA
* * * *
303555 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTCATCGCATTCAGAAGTCCAGAT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTCATTGCATTTA-AAGGCCAGGT
* * *
303620 GTGAAGGCTCATTTACTTTTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTTCAT
65 GTGGAGGATCATTTACTTTTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCAT
303685 CGCATTCAGAGGCCCAGGTGTAAAGGCCCATTTACTT
130 CGCATTCAGAGGCCCAGGTGTAAAGGCCCATTTACTT
**
303722 TTCATTGCATTTAGAGGATCAGGTGTGGA-GTCCATTTACTTTCATTGCATTTAAAGGCTCAGGT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTCATTGCATTTAAAGGC-CAGGT
* *
303786 GTGGAGGTTCATTTACTTTTCATTGCATTTAGAGGCCGAAGTGTGGAGGTCCATTTACTTTTCAT
65 GTGGAGGATCATTTACTTTTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCAT
* * * * * *
303851 TGCATTTAGATGCCTAGGTGTGAAGGCTCATTTACTT
130 CGCATTCAGAGGCCCAGGTGTAAAGGCCCATTTACTT
* * * * * * **
303888 TTCGTTACATTTAGAGGCCCAAGTGTAGAGGTTCATTTACTTTTTATTGCATTTGGAGGCCCAGG
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTAC-TTTCATTGCATTTAAAGG-CCAGG
* *
303953 TGTGGA-GATCTACTTACTTTTCATTGCAATTAGAGGCC
64 TGTGGAGGATC-ATTTACTTTTCATTGCATTTAGAGGCC
303991 TAAACATAGA
Statistics
Matches: 235, Mismatches: 29, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
165 4 0.02
166 141 0.60
167 39 0.17
168 50 0.21
169 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (166 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTTTCATTGCATTTAAAGGCCAGGTG
TGGAGGATCATTTACTTTTCATTGCATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTTTTCATC
GCATTCAGAGGCCCAGGTGTAAAGGCCCATTTACTT
Found at i:304347 original size:11 final size:11
Alignment explanation
Indices: 304317--304341 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
304307 AAATAGAGGT
304317 TTTTATTTTTC
1 TTTTATTTTTC
304328 TTTTATTTTTC
1 TTTTATTTTTC
304339 TTT
1 TTT
304342 CTTTTTGGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTTC
Found at i:304392 original size:3 final size:3
Alignment explanation
Indices: 304386--304432 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
304376 ATTATTATTA
*
304386 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTT TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
304433 TTTAAGATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.30, T:0.70
Consensus pattern (3 bp):
TTG
Found at i:304820 original size:5 final size:5
Alignment explanation
Indices: 304810--304839 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
304800 AAAATCCGAT
304810 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC
304840 ATTTGTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTCC
Found at i:305351 original size:51 final size:50
Alignment explanation
Indices: 305127--305352 Score: 123
Period size: 51 Copynumber: 4.5 Consensus size: 50
305117 AATTTATTTT
* ** *
305127 TTTTTAAATAAAAATTTG-TTTTTTTAGTTATTTTAAAGAAAAATTTTAAA
1 TTTTTAAACAAAGTTTTGATTTTTTTAG-TATTTTAAAGAAAAAGTTTAAA
* * * * *
305177 TTTTTAAACAAAGTTTTCATTTTTTTAACTATTTCGAAATAAAAA-TTTAGA
1 TTTTTAAACAAAGTTTTGATTTTTTT-AGTATTT-TAAAGAAAAAGTTTAAA
** ** * * *
305228 TTTTTAAGTAAAGTAATGATTTTCATTA--A---AAAAGAAAAAAAGTTTAGATTTT
1 TTTTTAAACAAAGTTTTGATTTT-TTTAGTATTTTAAAG--AAAAAGTTTA-A---A
*
305280 TTTTTAAA-AAA-ATTT-A-TTTTTTAGTGATTTTAAAGAAAAAGTTTAAA
1 TTTTTAAACAAAGTTTTGATTTTTTTAGT-ATTTTAAAGAAAAAGTTTAAA
305327 TTTTTAAACAAAGTTTTGATTTTTTT
1 TTTTTAAACAAAGTTTTGATTTTTTT
305353 TAACTATTTC
Statistics
Matches: 129, Mismatches: 26, Indels: 41
0.66 0.13 0.21
Matches are distributed among these distances:
45 3 0.02
47 16 0.12
48 10 0.08
49 5 0.04
50 18 0.14
51 55 0.43
52 18 0.14
53 4 0.03
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.48
Consensus pattern (50 bp):
TTTTTAAACAAAGTTTTGATTTTTTTAGTATTTTAAAGAAAAAGTTTAAA
Found at i:305431 original size:150 final size:148
Alignment explanation
Indices: 304893--305443 Score: 664
Period size: 150 Copynumber: 3.7 Consensus size: 148
304883 TTGAGAAAAA
* * *
304893 TTTTGGTTTTTTTAAACAATTTCGAAATAAAAGCTTTT-ATTTTTAAGTAAAATAGTTATTTTCT
1 TTTTGATTTTTTT-AACTATTTCGAAATAAAAG-TTTTGATTTTTAAGTAAAATAGTGATTTTCT
* * *
304957 TTAAAAAAAAG-AAAGTTTAGA-TTTTTAAAAATAAAAATCAGTTTTTTAGTTATTTTAAAG-AA
64 TTAAAAAAAAGAAAAGTTTAGATTTTTTTAAAA-AAAATTTA-TTTTTTAGTTATTTTAAAGAAA
* *
305019 AAGTTTACATTTTTAAACGAAG
127 AAGTTTAAATTTTTAAACAAAG
*
305041 TTTTGA-TTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTTAAGTAAAATAGTGATTTTCTT
1 TTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGA-TTTTTAAGTAAAATAGTGATTTTCTT
* * ** *
305105 TCAAAAAGAGAAAA-TTTATTTTTTTTTAAATAAAAATTTGTTTTTTTAGTTATTTTAAAGAAAA
65 TAAAAAAAAGAAAAGTTTAGATTTTTTTAAA-AAAAATTT-ATTTTTTAGTTATTTTAAAGAAAA
*
305169 ATTTTAAATTTTTAAACAAAG
128 AGTTTAAATTTTTAAACAAAG
* * * * * *
305190 TTTTCATTTTTTTAACTATTTCGAAATAAAAATTTAGATTTTTAAGTAAAGTAATGATTTTCATT
1 TTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCTTT
* * *
305255 AAAAAAGAAAAAAAGTTTAGATTTTTTTTTAAAAAAATTTATTTTTTAGTGATTTTAAAGAAAAA
66 AAAAAA-AAGAAAAGTTTAGA-TTTTTTTAAAAAAAATTTATTTTTTAGTTATTTTAAAGAAAAA
305320 GTTTAAATTTTTAAACAAAG
129 GTTTAAATTTTTAAACAAAG
* * *
305340 TTTTGATTTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTGAAGTAAAATAGTAATTTTGTT
1 TTTTGA-TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTT-CT
** * ** *
305405 TTAATTAAAAGAAAATTTTTTATTTTTTTGAAAAAAATT
64 TTAAAAAAAAGAAAAGTTTAGATTTTTTTAAAAAAAATT
305444 CGATCACCGT
Statistics
Matches: 344, Mismatches: 46, Indels: 24
0.83 0.11 0.06
Matches are distributed among these distances:
145 3 0.01
146 19 0.06
147 43 0.12
148 40 0.12
149 56 0.16
150 97 0.28
151 71 0.21
152 15 0.04
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.47
Consensus pattern (148 bp):
TTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAGTGATTTTCTTT
AAAAAAAAGAAAAGTTTAGATTTTTTTAAAAAAAATTTATTTTTTAGTTATTTTAAAGAAAAAGT
TTAAATTTTTAAACAAAG
Found at i:306025 original size:22 final size:22
Alignment explanation
Indices: 306000--306045 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
305990 TTTGTTTACT
306000 TTCATGTCTATTTATATTTATA
1 TTCATGTCTATTTATATTTATA
306022 TTCATGTCTATTTATATTTATA
1 TTCATGTCTATTTATATTTATA
306044 TT
1 TT
306046 TTTTTTTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.04, T:0.61
Consensus pattern (22 bp):
TTCATGTCTATTTATATTTATA
Found at i:306860 original size:240 final size:236
Alignment explanation
Indices: 306440--306915 Score: 727
Period size: 240 Copynumber: 2.0 Consensus size: 236
306430 AAAATAATAA
* *
306440 TAATGATAAAAAATCAAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTACTTT
1 TAATAATAAAAAATCAAATAAGTAGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTACTTT
*
306505 TTAGGTTTTTTTAGGATTCTAAAATATAATTAATTTTAAGAATTAAAGGTATCTTACTAGAATTA
66 TTAGGTTTTTTTAGGATTCTAAAATAAAATTAATTTTAAGAATTAAAGGTATCTTACTAGAATTA
* * *
306570 TTTAGGTATCCCTTAGGGTTCTCGTCAGAAATAAAAATTTCTAATTTAAGTTTTAAATTAGATAA
131 TTTAGGTATCCCTTAGGGTTATCATCAGAAATAAAAATCTCTAATTTAAG-TTTAAATTAGATAA
* *
306635 ATTTGGTGAACACGTCTTAGTCAAGTTAGATGTAAATCGGAG
195 ATTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAATCGGAG
* * *
306677 TAATAATAAAAGATCAAATAAGTAGTAGATGAATTTTAATATTTCTCTTTATTCATTAGTAATTT
1 TAATAATAAAAAATCAAATAAGTAGTAGATGAATTTTAATATTTCTCTTAATTCATTAGT-A-CT
* * *
306742 TTTTAGGTTTTTTTTAGGATTCTAAAATAAAATTAATTTTAAGAATTGAAGGTATTTTACTTGAA
64 TTTTAGG-TTTTTTTAGGATTCTAAAATAAAATTAATTTTAAGAATTAAAGGTATCTTACTAGAA
* * * * *
306807 TTATTTAGGTATCCTTTGGGGTTATTATTAGAAGTAAAAATCTCTAATTTAAGTTTAAATTAGAT
128 TTATTTAGGTATCCCTTAGGGTTATCATCAGAAATAAAAATCTCTAATTTAAGTTTAAATTAGAT
* *
306872 AAGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAATTGGAG
193 AAATTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAATCGGAG
306916 ACATTTTTAG
Statistics
Matches: 215, Mismatches: 21, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
237 56 0.26
238 1 0.00
239 60 0.28
240 98 0.46
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (236 bp):
TAATAATAAAAAATCAAATAAGTAGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTACTTT
TTAGGTTTTTTTAGGATTCTAAAATAAAATTAATTTTAAGAATTAAAGGTATCTTACTAGAATTA
TTTAGGTATCCCTTAGGGTTATCATCAGAAATAAAAATCTCTAATTTAAGTTTAAATTAGATAAA
TTTGGTGAACACGTCTTAGTCAAGTTACAAGTAAATCGGAG
Found at i:308173 original size:30 final size:30
Alignment explanation
Indices: 308112--308192 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
308102 TATCATAATT
*
308112 AAATAATTATTTAATAATTAT-TATTTCAAAA
1 AAATAA-T-TTTAATAATTTTATATTTCAAAA
*
308143 AAATAATTTTAATAATTTTATATTTTAAAA
1 AAATAATTTTAATAATTTTATATTTCAAAA
308173 AAATAATTTTAATAATTTTA
1 AAATAATTTTAATAATTTTA
308193 AAATCATTTG
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 11 0.23
30 30 0.64
31 6 0.13
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (30 bp):
AAATAATTTTAATAATTTTATATTTCAAAA
Found at i:308177 original size:21 final size:23
Alignment explanation
Indices: 308153--308195 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
308143 AAATAATTTT
308153 AATAATTTT-AT-ATTTTAAAAA
1 AATAATTTTAATAATTTTAAAAA
308174 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
308196 TCATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 2 0.10
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATAATTTTAATAATTTTAAAAA
Found at i:311306 original size:27 final size:27
Alignment explanation
Indices: 311273--311375 Score: 102
Period size: 27 Copynumber: 3.9 Consensus size: 27
311263 TTCATAGCAT
311273 AATATGAAAGAAATGCTTTTGTGGCAA
1 AATATGAAAGAAATGCTTTTGTGGCAA
* * * *
311300 AATATGAAAGGAATGCCTTTGTTGCAT
1 AATATGAAAGAAATGCTTTTGTGGCAA
* * **
311327 GATAAGAAAGAAA-GCTTTTGTGGTGA
1 AATATGAAAGAAATGCTTTTGTGGCAA
*
311353 AATATGACATG-AATGCTTTTGTG
1 AATATGA-AAGAAATGCTTTTGTG
311376 AAAAGGGTTA
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
26 15 0.25
27 44 0.75
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (27 bp):
AATATGAAAGAAATGCTTTTGTGGCAA
Found at i:311356 original size:53 final size:54
Alignment explanation
Indices: 311269--311374 Score: 142
Period size: 53 Copynumber: 2.0 Consensus size: 54
311259 AGCCTTCATA
*
311269 GCATAATATGAAAGAAATGCTTTTGTGGCAAAATATGAAAGGAATGCCTTTGTT
1 GCATAATAAGAAAGAAATGCTTTTGTGGCAAAATATGAAAGGAATGCCTTTGTT
* ** * * *
311323 GCATGATAAGAAAGAAA-GCTTTTGTGGTGAAATATGACATGAATGCTTTTGT
1 GCATAATAAGAAAGAAATGCTTTTGTGGCAAAATATGAAAGGAATGCCTTTGT
311375 GAAAAGGGTT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
53 30 0.67
54 15 0.33
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (54 bp):
GCATAATAAGAAAGAAATGCTTTTGTGGCAAAATATGAAAGGAATGCCTTTGTT
Found at i:314280 original size:20 final size:20
Alignment explanation
Indices: 314251--314336 Score: 75
Period size: 20 Copynumber: 4.3 Consensus size: 20
314241 AAATTGAGTT
*
314251 AAAATGATTTTAAACAAGTC
1 AAAATAATTTTAAACAAGTC
* *
314271 AAAATAATTTGAACCAAGTC
1 AAAATAATTTTAAACAAGTC
* * * **
314291 AAAGTCATTTT-AGCACTTC
1 AAAATAATTTTAAACAAGTC
*
314310 AAAATATTTTTCAAACAAGTC
1 AAAATAATTTT-AAACAAGTC
314331 AAAATA
1 AAAATA
314337 GCTTCAGGCC
Statistics
Matches: 49, Mismatches: 15, Indels: 3
0.73 0.22 0.04
Matches are distributed among these distances:
19 13 0.27
20 25 0.51
21 11 0.22
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.30
Consensus pattern (20 bp):
AAAATAATTTTAAACAAGTC
Found at i:316657 original size:49 final size:49
Alignment explanation
Indices: 316595--316690 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 49
316585 TATGAAGTAA
* *
316595 GTATATAGTAGTATATCTGCAATT-TCTGGTGGCTTGACCACAATATTCT
1 GTATATAGAAGTATATCTG-AATTATCTGGTGGCTCGACCACAATATTCT
* * *
316644 GTATCTAGAAGTATATTTGTATTATCTGGTGGCTCGACCACAATATT
1 GTATATAGAAGTATATCTGAATTATCTGGTGGCTCGACCACAATATT
316691 TTGTTTCTGG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
48 3 0.07
49 38 0.93
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.39
Consensus pattern (49 bp):
GTATATAGAAGTATATCTGAATTATCTGGTGGCTCGACCACAATATTCT
Found at i:318564 original size:15 final size:15
Alignment explanation
Indices: 318517--318579 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 15
318507 GTTTGGATTC
**
318517 AAAGGAAAAGAAAAT
1 AAAGGAAAAGAAAGG
* *
318532 AAAGCAAAAGAAAAG
1 AAAGGAAAAGAAAGG
* * *
318547 AAAAGAAAGGATAGG
1 AAAGGAAAAGAAAGG
*
318562 AAAGGAAATGAAAGG
1 AAAGGAAAAGAAAGG
318577 AAA
1 AAA
318580 ATAAATTATA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.68, C:0.02, G:0.25, T:0.05
Consensus pattern (15 bp):
AAAGGAAAAGAAAGG
Found at i:318564 original size:20 final size:20
Alignment explanation
Indices: 318517--318579 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
318507 GTTTGGATTC
* *
318517 AAAGGAAAAGAAAATAAAGC
1 AAAGGAAAAGAAAAGAAAGG
*
318537 AAAAGAAAAGAAAAGAAAGG
1 AAAGGAAAAGAAAAGAAAGG
* * *
318557 ATAGGAAAGGAAATGAAAGG
1 AAAGGAAAAGAAAAGAAAGG
318577 AAA
1 AAA
318580 ATAAATTATA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.68, C:0.02, G:0.25, T:0.05
Consensus pattern (20 bp):
AAAGGAAAAGAAAAGAAAGG
Found at i:320607 original size:11 final size:11
Alignment explanation
Indices: 320591--320677 Score: 54
Period size: 11 Copynumber: 7.2 Consensus size: 11
320581 CCTATATTGT
320591 TTTAATTTTTA
1 TTTAATTTTTA
320602 TTTAATTTGGTTTCA
1 TTTAA-TT--TTT-A
320617 TTTATATTTTTA
1 TTTA-ATTTTTA
320629 TATT-ATTTTCACTA
1 T-TTAATTTT---TA
320643 TTT-ATTTTGTA
1 TTTAATTTT-TA
320654 TTTAATTTTTA
1 TTTAATTTTTA
320665 TTT-ATTTGTTA
1 TTTAATTT-TTA
320676 TT
1 TT
320678 CATTTTCTTT
Statistics
Matches: 64, Mismatches: 1, Indels: 22
0.74 0.01 0.25
Matches are distributed among these distances:
10 4 0.06
11 25 0.39
12 9 0.14
13 12 0.19
14 6 0.09
15 7 0.11
16 1 0.02
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (11 bp):
TTTAATTTTTA
Found at i:326653 original size:95 final size:95
Alignment explanation
Indices: 326490--326774 Score: 507
Period size: 95 Copynumber: 3.0 Consensus size: 95
326480 AAAAAAATAG
326490 TTTCGACAGCTTGGCGACTCCACTGGGGATCGAACCCAGAATCTCTGATTCAGGTACCCTTAATC
1 TTTCGACAGCTTGGCGACTCCACTGGGGATCGAACCCAGAATCTCTGATTCAGGTACCCTTAATC
326555 TAGAACTCAAACTACGTATACTAAACCCTA
66 TAGAACTCAAACTACGTATACTAAACCCTA
* * * *
326585 TTTCGACAACTTGGCGACTCCATTGGGGATCGAACCCAGAATCTCTGATTCAAGTACCTTTAATC
1 TTTCGACAGCTTGGCGACTCCACTGGGGATCGAACCCAGAATCTCTGATTCAGGTACCCTTAATC
326650 TAGAACTCAAACTACGTATACTAAACCCTA
66 TAGAACTCAAACTACGTATACTAAACCCTA
* *
326680 TTTCGATAGCTTGGCGACTCCACTGGGGATCGAACTCAGAATCTCTGATTCAGGTACCCTTAATC
1 TTTCGACAGCTTGGCGACTCCACTGGGGATCGAACCCAGAATCTCTGATTCAGGTACCCTTAATC
*
326745 TAGAACTCAAACTACATATACTAAACCCTA
66 TAGAACTCAAACTACGTATACTAAACCCTA
326775 AGTGCTTATC
Statistics
Matches: 179, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
95 179 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.27
Consensus pattern (95 bp):
TTTCGACAGCTTGGCGACTCCACTGGGGATCGAACCCAGAATCTCTGATTCAGGTACCCTTAATC
TAGAACTCAAACTACGTATACTAAACCCTA
Found at i:332098 original size:52 final size:52
Alignment explanation
Indices: 332020--332121 Score: 159
Period size: 52 Copynumber: 2.0 Consensus size: 52
332010 AAATAGGTCC
* * * * *
332020 GATGACTATGTGTCATCATGAGTATATGAATCCTTTATGGATTATGAGGTTT
1 GATGACAATGTGCCATCATAAGTATATGAATCCTTTACGAATTATGAGGTTT
332072 GATGACAATGTGCCATCATAAGTATATGAATCCTTTACGAATTATGAGGT
1 GATGACAATGTGCCATCATAAGTATATGAATCCTTTACGAATTATGAGGT
332122 CAAATGACTA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (52 bp):
GATGACAATGTGCCATCATAAGTATATGAATCCTTTACGAATTATGAGGTTT
Found at i:332129 original size:52 final size:52
Alignment explanation
Indices: 332021--332134 Score: 156
Period size: 52 Copynumber: 2.2 Consensus size: 52
332011 AATAGGTCCG
* * * * ***
332021 ATGACTATGTGTCATCATGAGTATATGAATCCTTTATGGATTATGAGGTTTG
1 ATGACTATGTGCCATCATAAGTATATGAATCCTTTACGAATTATGAGGTCAA
*
332073 ATGACAATGTGCCATCATAAGTATATGAATCCTTTACGAATTATGAGGTCAA
1 ATGACTATGTGCCATCATAAGTATATGAATCCTTTACGAATTATGAGGTCAA
332125 ATGACTATGT
1 ATGACTATGT
332135 TTCATGTGAG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (52 bp):
ATGACTATGTGCCATCATAAGTATATGAATCCTTTACGAATTATGAGGTCAA
Found at i:332895 original size:116 final size:115
Alignment explanation
Indices: 332691--332911 Score: 293
Period size: 116 Copynumber: 1.9 Consensus size: 115
332681 TATCCATGAG
* * * * *
332691 TGTATCGGTAGAAGTATAGGGGAGGAGAGAGGTTGTTCTCTAACTTGGGTTGTATCGGTAGTTGA
1 TGTATCGATAGAAGTATAGGAGAGGAGAGAGGTTG-TCTCTAACTTAGGTTGTATCGATAGATGA
* *
332756 ATAACAAGTATCGGTAGTTATGTATTTAGAAGTATCGGTATTTTACGTGTT
65 ATAACAAGTATCGGTAGTCATGTATTTAGAAATATCGGTATTTTACGTGTT
* *
332807 TGTATCGATAGAAGTACT-GGAGAGGAGAGAGGTTG-CATACTGACTTATGTTGTATCGATAGAT
1 TGTATCGATAGAAGTA-TAGGAGAGGAGAGAGGTTGTC-T-CTAACTTAGGTTGTATCGATAGAT
* *
332870 GAATATCAAGTGTCGGTAGTCATGTATTTAGAAATATCGGTA
63 GAATAACAAGTATCGGTAGTCATGTATTTAGAAATATCGGTA
332912 GTTCCTATAC
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
114 1 0.01
115 1 0.01
116 88 0.97
117 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.34
Consensus pattern (115 bp):
TGTATCGATAGAAGTATAGGAGAGGAGAGAGGTTGTCTCTAACTTAGGTTGTATCGATAGATGAA
TAACAAGTATCGGTAGTCATGTATTTAGAAATATCGGTATTTTACGTGTT
Found at i:332926 original size:116 final size:114
Alignment explanation
Indices: 332691--332938 Score: 277
Period size: 116 Copynumber: 2.1 Consensus size: 114
332681 TATCCATGAG
* * * * *
332691 TGTATCGGTAGAAGTATAGGGGAGGAGAGAGGTTGTTCTCTAACTTGGGTTGTATCGGTAGTTGA
1 TGTATCGATAGAAGTATAGGAGAGGAGAGAGGTTG-TCTCTAACTTAGGTTGTATCGATAGATGA
* * * **
332756 ATAACAAGTATCGGTAGTTATGTATTTAGAAGTATCGGTATTTTACGTGTT
65 ATAACAAGTATCGGTAGTCATGTATTTAGAAATATCGGTATTCTAC-TACT
* *
332807 TGTATCGATAGAAGTACT-GGAGAGGAGAGAGGTTG-CATACTGACTTATGTTGTATCGATAGAT
1 TGTATCGATAGAAGTA-TAGGAGAGGAGAGAGGTTGTC-T-CTAACTTAGGTTGTATCGATAGAT
* *
332870 GAATATCAAGTGTCGGTAGTCATGTATTTAGAAATATCGGTAGTTCCTA-TACT
63 GAATAACAAGTATCGGTAGTCATGTATTTAGAAATATCGGTA-TT-CTACTACT
*
332923 TGTATCGTTAGAAGTA
1 TGTATCGATAGAAGTA
332939 GCAGGGTAAG
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
114 1 0.01
115 1 0.01
116 105 0.94
117 3 0.03
118 2 0.02
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (114 bp):
TGTATCGATAGAAGTATAGGAGAGGAGAGAGGTTGTCTCTAACTTAGGTTGTATCGATAGATGAA
TAACAAGTATCGGTAGTCATGTATTTAGAAATATCGGTATTCTACTACT
Found at i:336879 original size:52 final size:52
Alignment explanation
Indices: 336795--336981 Score: 182
Period size: 52 Copynumber: 3.6 Consensus size: 52
336785 TGAATGAAAT
* * * * *
336795 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTTCGATGACTATGTGTCATCATAAGTATATGAATCCTTTACGAATTATG
*
336847 AGGTTTGATGACTATGTGTCATCATAAGTATATGAATCCTTTACGAATTATG
1 AGGTTCGATGACTATGTGTCATCATAAGTATATGAATCCTTTACGAATTATG
* * * * ** *
336899 AGGTTCAATAACTATGTGTCA--AGTGAGTATATGATTCCCAATACGAATTA-A
1 AGGTTCGATGACTATGTGTCATCA-TAAGTATATGAAT-CCTTTACGAATTATG
* * * *
336950 AGGTCCGATGACTCTGTGTCATCGTGAGTATA
1 AGGTTCGATGACTATGTGTCATCATAAGTATA
336982 AAAAATGTAT
Statistics
Matches: 112, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
50 1 0.01
51 28 0.25
52 83 0.74
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (52 bp):
AGGTTCGATGACTATGTGTCATCATAAGTATATGAATCCTTTACGAATTATG
Found at i:341545 original size:101 final size:101
Alignment explanation
Indices: 341348--341531 Score: 246
Period size: 101 Copynumber: 1.8 Consensus size: 101
341338 GTAACATATC
* ** *
341348 TCAATCTCCACTGAAGTTACAGTGGAATAGAGTGAAGTCATACTTAAATCTTATATCCTTGAAGA
1 TCAATCTCCACTGAAGTCACAGTGGAATAGAGTGAAGTCATACCCAAATCCTATATCCTTGAAGA
*
341413 TGCAATGGATCGGATTAAAACTCACAATAGCAGACT
66 TGCAATGGATCGAATTAAAACTCACAATAGCAGACT
* * *
341449 TCAATCTCCACTGAAGTCGCAGTGGAATGGAGTGAAGTTACA-AGCCCGAATCCTATATCCTTGA
1 TCAATCTCCACTGAAGTCACAGTGGAATAGAGTGAAG-T-CATA-CCCAAATCCTATATCCTTGA
*
341513 AGTTGCAA-GGATCGAATTA
63 AGATGCAATGGATCGAATTA
341532 GAGATACGGT
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
101 34 0.48
102 12 0.17
103 25 0.35
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (101 bp):
TCAATCTCCACTGAAGTCACAGTGGAATAGAGTGAAGTCATACCCAAATCCTATATCCTTGAAGA
TGCAATGGATCGAATTAAAACTCACAATAGCAGACT
Found at i:345372 original size:113 final size:114
Alignment explanation
Indices: 345172--345403 Score: 376
Period size: 113 Copynumber: 2.0 Consensus size: 114
345162 AAGACTTAAT
*
345172 AAATACATTATTAGATTTATATATAATCAAATTTAAGTCTTAGAGTTGAATTCAATATGATTTAA
1 AAATACATTATTAGATTTATATATAATCAAATTTAAGTCTTA-AGTTGAACTCAATATGATTTAA
*
345237 AAGCCAAATAAAGTCTAAAACTCGTTATTCTCGCTTTAATCACATCTAGA
65 AAGCCAAATAAAGTCTAAAACTCGTTATTCTCGCTTTAATCACATCTAAA
* *
345287 AAATACATTATTTGGTTTATATATAATCAAATTTAAGTCTT-AGTTGAACTCAATATGATTTAAA
1 AAATACATTATTAGATTTATATATAATCAAATTTAAGTCTTAAGTTGAACTCAATATGATTTAAA
* * * *
345351 AGCCAAATAAAGTTTAAAACTCGTTATTTTCGTTTTAATCACCTCTAAA
66 AGCCAAATAAAGTCTAAAACTCGTTATTCTCGCTTTAATCACATCTAAA
345400 AAAT
1 AAAT
345404 TCTACTCACA
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
113 70 0.64
115 39 0.36
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (114 bp):
AAATACATTATTAGATTTATATATAATCAAATTTAAGTCTTAAGTTGAACTCAATATGATTTAAA
AGCCAAATAAAGTCTAAAACTCGTTATTCTCGCTTTAATCACATCTAAA
Found at i:352144 original size:18 final size:18
Alignment explanation
Indices: 352117--352154 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
352107 AATATTTATA
*
352117 TTATATTATTTCA-ATATT
1 TTATAATATTT-ATATATT
352135 TTATAATATTTATATATT
1 TTATAATATTTATATATT
352153 TT
1 TT
352155 TTTATTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATAATATTTATATATT
Found at i:355695 original size:25 final size:26
Alignment explanation
Indices: 355666--355716 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
355656 ATCTAACATT
355666 TAATTAAT-ATTATTTT-TATTTTTTA
1 TAATTAATGA-TATTTTATATTTTTTA
*
355691 TAATTATTGATATTTTATATTTTTTA
1 TAATTAATGATATTTTATATTTTTTA
355717 AAGTTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (26 bp):
TAATTAATGATATTTTATATTTTTTA
Found at i:355907 original size:16 final size:16
Alignment explanation
Indices: 355888--355940 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
355878 AAATAAGATT
355888 GTAATGGAATAGAGTC
1 GTAATGGAATAGAGTC
*
355904 GTAATGGAATAAAG-C
1 GTAATGGAATAGAGTC
* *
355919 TGTAATTGAATAGAGTT
1 -GTAATGGAATAGAGTC
355936 GTAAT
1 GTAAT
355941 CAGTAATTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 30 0.97
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30
Consensus pattern (16 bp):
GTAATGGAATAGAGTC
Found at i:360590 original size:12 final size:12
Alignment explanation
Indices: 360573--360602 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
360563 GGTACTGTGT
360573 CTGTTCATATAA
1 CTGTTCATATAA
360585 CTGTTCATATAA
1 CTGTTCATATAA
360597 CTGTTC
1 CTGTTC
360603 CTTAACGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (12 bp):
CTGTTCATATAA
Found at i:375015 original size:40 final size:40
Alignment explanation
Indices: 374763--375022 Score: 172
Period size: 40 Copynumber: 6.5 Consensus size: 40
374753 ATATAGTTCT
* * * *
374763 GGCTACGGCCTAGGAAGCTTTGAGCCAGTGATG-TGATTTA
1 GGCTACGACCTAGTAGGCTTTGAGCCAGTGA-GATGATTCA
* * * * * *
374803 GGCTACGGCCTAGCAGGCTTTAATCC-GTTGATATGATTTA
1 GGCTACGACCTAGTAGGCTTTGAGCCAG-TGAGATGATTCA
* * * *
374843 GCCTATGATCGAGTA-GCTTTGAGCC-GTTGATG-TGATTCA
1 GGCTACGACCTAGTAGGCTTTGAGCCAG-TGA-GATGATTCA
* * * * * ***
374882 GGATATGGCCTAATAGACTTTGAGTTTGTGAGATGATTCA
1 GGCTACGACCTAGTAGGCTTTGAGCCAGTGAGATGATTCA
* * * * *
374922 GGCTACGATCTAGCAGGATTTGAGTCGGTGATG-TGATTCA
1 GGCTACGACCTAGTAGGCTTTGAGCCAGTGA-GATGATTCA
374962 GGCTACGACCTAGTAGGCTTTGAGCCAGTGAGATGATTCA
1 GGCTACGACCTAGTAGGCTTTGAGCCAGTGAGATGATTCA
* *
375002 GGTTACAACCTAGTAGGCTTT
1 GGCTACGACCTAGTAGGCTTT
375023 TAGCTGGTGT
Statistics
Matches: 171, Mismatches: 41, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
39 31 0.18
40 138 0.81
41 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (40 bp):
GGCTACGACCTAGTAGGCTTTGAGCCAGTGAGATGATTCA
Found at i:378528 original size:18 final size:18
Alignment explanation
Indices: 378505--378541 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
378495 ACAATTCATA
378505 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
378523 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
378541 T
1 T
378542 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Done.