Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005905.1 Hibiscus syriacus cultivar Beakdansim tig00013871_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 131366
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:5642 original size:17 final size:16
Alignment explanation
Indices: 5616--5647 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5606 TTTCGATATG
5616 ATAAATTTAAATAAAA
1 ATAAATTTAAATAAAA
5632 ATAATATTTAAATAAA
1 ATAA-ATTTAAATAAA
5648 TCATCATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAAATTTAAATAAAA
Found at i:9013 original size:35 final size:37
Alignment explanation
Indices: 8956--9025 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
8946 CCGGTATTCA
* *
8956 TTTTTTATTTGTTTTATTATAATTA-ATCTTTATGTT
1 TTTTTTATTTATTTTATAATAATTATATCTTTATGTT
* *
8992 TTTTTTTTTTATTTT-TAATAATTATGTCTTTATG
1 TTTTTTATTTATTTTATAATAATTATATCTTTATG
9026 ACACGTCTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 8 0.28
36 21 0.72
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (37 bp):
TTTTTTATTTATTTTATAATAATTATATCTTTATGTT
Found at i:16134 original size:8 final size:8
Alignment explanation
Indices: 16121--16185 Score: 60
Period size: 8 Copynumber: 7.9 Consensus size: 8
16111 CAAAACAATT
16121 AATAAAAA
1 AATAAAAA
16129 AATAAAAA
1 AATAAAAA
*
16137 CAATAAATA
1 -AATAAAAA
16146 AATAAAAAGA
1 AAT-AAAA-A
*
16156 AACAAAAA
1 AATAAAAA
* *
16164 AATCATAA
1 AATAAAAA
16172 AAT-AAAA
1 AATAAAAA
16179 AATAAAA
1 AATAAAA
16186 TAAACCTGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
7 6 0.13
8 23 0.50
9 14 0.30
10 3 0.07
ACGTcount: A:0.80, C:0.05, G:0.02, T:0.14
Consensus pattern (8 bp):
AATAAAAA
Found at i:16138 original size:21 final size:21
Alignment explanation
Indices: 16112--16189 Score: 65
Period size: 21 Copynumber: 3.7 Consensus size: 21
16102 TGAAATAATC
*
16112 AAAACAATTAATAAA-AAAATA
1 AAAACAATAAATAAATAAAA-A
16133 AAAACAATAAATAAATAAAAA
1 AAAACAATAAATAAATAAAAA
* *
16154 GAAACAA-AAA-AATCATAAAAT
1 AAAACAATAAATAA--ATAAAAA
16175 AAAA-AATAAAATAAA
1 AAAACAAT-AAATAAA
16190 CCTGAGGACC
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
19 2 0.04
20 5 0.11
21 31 0.66
22 7 0.15
23 2 0.04
ACGTcount: A:0.78, C:0.05, G:0.01, T:0.15
Consensus pattern (21 bp):
AAAACAATAAATAAATAAAAA
Found at i:16284 original size:51 final size:50
Alignment explanation
Indices: 16215--16312 Score: 117
Period size: 51 Copynumber: 1.9 Consensus size: 50
16205 GCATAAAATA
* * * *
16215 AAATAATAGTTACTAAAATGCAAGAAAATAAAA-AATAGTAGTTAAATAGG
1 AAATAATAGTGACAAAAATGCAA-AAAATAAAATAACAGTAGCTAAATAGG
* *
16265 AAATAAATAGTGACAAAAATGTAAAAATTAAAATAACAGTAGCTAAAT
1 AAAT-AATAGTGACAAAAATGCAAAAAATAAAATAACAGTAGCTAAAT
16313 CAAAAACTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 12 0.30
51 28 0.70
ACGTcount: A:0.59, C:0.05, G:0.12, T:0.23
Consensus pattern (50 bp):
AAATAATAGTGACAAAAATGCAAAAAATAAAATAACAGTAGCTAAATAGG
Found at i:19281 original size:30 final size:30
Alignment explanation
Indices: 19245--19304 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
19235 TTTTTAAAAA
19245 GTAAATTTCAAAATTACCAAATTGTGACAC
1 GTAAATTTCAAAATTACCAAATTGTGACAC
* *
19275 GTAAATTTCAAAATTATCAACTTGTGACAC
1 GTAAATTTCAAAATTACCAAATTGTGACAC
19305 ATGTCAACGG
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:0.42, C:0.17, G:0.10, T:0.32
Consensus pattern (30 bp):
GTAAATTTCAAAATTACCAAATTGTGACAC
Found at i:21490 original size:21 final size:21
Alignment explanation
Indices: 21466--21509 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
21456 ATTCGTTGCA
21466 ATAGTCCAAGTTCACGTTACG
1 ATAGTCCAAGTTCACGTTACG
* *
21487 ATAGTCGAAGTTCACGTTGCG
1 ATAGTCCAAGTTCACGTTACG
21508 AT
1 AT
21510 TTTTTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (21 bp):
ATAGTCCAAGTTCACGTTACG
Found at i:21940 original size:19 final size:19
Alignment explanation
Indices: 21916--22003 Score: 77
Period size: 19 Copynumber: 4.3 Consensus size: 19
21906 TTATTTTGGA
*
21916 TTTTTCATTATCGCAACAC
1 TTTTTCACTATCGCAACAC
21935 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
*
21957 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* *
21979 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
21998 ATTTTT
1 -TTTTT
22004 TAAAATCGCG
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
19 24 0.43
20 4 0.07
21 4 0.07
22 12 0.21
23 6 0.11
25 6 0.11
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.38
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:28233 original size:3 final size:3
Alignment explanation
Indices: 28196--28253 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
28186 ACTTAAAAAA
* * *
28196 TAT TA- TAT TGT TAT TTT TAT TA- TAT AAT TACT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
*
28240 TAG TAT TAT TAT TA
1 TAT TAT TAT TAT TA
28254 ATTTATATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:30377 original size:4 final size:4
Alignment explanation
Indices: 30368--30403 Score: 54
Period size: 4 Copynumber: 8.8 Consensus size: 4
30358 AAATTAGTAT
*
30368 TTTA TTTA TTTA TTTA TTTA TATA TTTA TTATA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTT
30404 TTATTCACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 25 0.86
5 4 0.14
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:30781 original size:6 final size:7
Alignment explanation
Indices: 30756--30785 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
30746 AATTAAATAT
*
30756 ATTTTGA
1 ATTTTTA
30763 ATTTTTA
1 ATTTTTA
30770 ATTTTTA
1 ATTTTTA
30777 ATTTTTA
1 ATTTTTA
30784 AT
1 AT
30786 AATATAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (7 bp):
ATTTTTA
Found at i:31232 original size:18 final size:18
Alignment explanation
Indices: 31209--31249 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
31199 TTCTTTCAAA
31209 TTTTTTAT-TACTTATTAT
1 TTTTTTATATA-TTATTAT
31227 TTTTTTATATATTATTAT
1 TTTTTTATATATTATTAT
31245 TTTTT
1 TTTTT
31250 ATTTTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTATATATTATTAT
Found at i:31257 original size:18 final size:18
Alignment explanation
Indices: 31208--31257 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
31198 TTTCTTTCAA
31208 ATTTTTTA--TTACTTATT
1 ATTTTTTATTTTA-TTATT
*
31225 ATTTTTT-TATATATTATT
1 ATTTTTTAT-TTTATTATT
31243 ATTTTTTATTTTATT
1 ATTTTTTATTTTATT
31258 TATTTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 7 0.26
18 17 0.63
19 3 0.11
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTTTATTTTATTATT
Found at i:32872 original size:14 final size:14
Alignment explanation
Indices: 32834--32887 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
32824 ATTTTAAATA
*
32834 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
32848 TTTTACATTTGCAT
1 ATTTACATTTGCAT
32862 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
32877 CTTTGCATTTG
1 ATTTACATTTG
32888 TATTGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:35871 original size:2 final size:2
Alignment explanation
Indices: 35864--35899 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
35854 TTATCCTTTA
35864 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35900 CCTTTGTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38649 original size:114 final size:113
Alignment explanation
Indices: 38449--38672 Score: 360
Period size: 114 Copynumber: 2.0 Consensus size: 113
38439 TGCCAGGTGA
38449 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* * *
38514 TTTGGTATGAACCCCAAAACCAATCATTAGATTTAAA-AGATGAATTTGC
66 TTCGGTAGGAACCCCAAAACC-ATCATTAGAATTAAAGA-ATGAATTTGC
* *
38563 TCATAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTTTTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* *
38628 TTCGGTAGGAACCCCAGAACCATCATTGGAATTAAAGAATGAATT
66 TTCGGTAGGAACCCCAAAACCATCATTAGAATTAAAGAATGAATT
38673 GCATGACCGT
Statistics
Matches: 102, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
113 20 0.20
114 82 0.80
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (113 bp):
TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
TTCGGTAGGAACCCCAAAACCATCATTAGAATTAAAGAATGAATTTGC
Found at i:41164 original size:22 final size:22
Alignment explanation
Indices: 41135--41189 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
41125 ATCTACACTC
**
41135 TTCAAAGATGGTAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
41157 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
41179 TTCAAAGATGA
1 TTCAAAGATGA
41190 AAACTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:42157 original size:112 final size:113
Alignment explanation
Indices: 41589--42359 Score: 1088
Period size: 113 Copynumber: 6.8 Consensus size: 113
41579 TAGCAAAGAT
*
41589 TCAAATCCATCATATGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
41654 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
41702 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
41767 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
41815 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
41880 AGAATGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
41928 TCAAATCCATCAT-TCGATGGATCAGCATTTCCA-AAGAAAGTTCATAATGAGAAGAACTCATCT
1 TCAAATCCATCATCT-GATGGATCAGCTTTTCCAGAA-AAAGTTCATAATGAGAAGAACTCATCT
* * *
41991 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAATTGTTCAACTTTTTGC
64 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * * ** * *
42041 TTAAATTCATCATTTGATGGATCATCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATTTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
42106 AGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGC
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * ** * ** *
42153 TTAAATTCATCACCCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
42218 AG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-C
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * ** * *
42264 CCTGAATTCATCA-CTTGATGAATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCT
1 TC-AAATCCATCATC-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCT
*
42328 GAAG-AGGAAGAAGAAGTTCATAATGAGAAGAA
64 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAA
42360 CACATCTGAA
Statistics
Matches: 605, Mismatches: 46, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
111 3 0.00
112 218 0.36
113 383 0.63
114 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (113 bp):
TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:42356 original size:39 final size:40
Alignment explanation
Indices: 42302--42399 Score: 171
Period size: 39 Copynumber: 2.5 Consensus size: 40
42292 TTTCCAGAGA
**
42302 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAG
1 AAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAG
42341 AAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAG
1 AAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAG
42381 AAGTTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
42400 TTTGTTCAAC
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
39 28 0.50
40 28 0.50
ACGTcount: A:0.49, C:0.08, G:0.24, T:0.18
Consensus pattern (40 bp):
AAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAG
Found at i:42359 original size:20 final size:20
Alignment explanation
Indices: 42334--42399 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
42324 ATCTGAAGAG
42334 GAAGAAGAAGTTCATAATGA
1 GAAGAAGAAGTTCATAATGA
*
42354 GAAGAACACA--TC-TGAA-GAA
1 GAAGAAGA-AGTTCAT-AATG-A
42373 GGAAGAAGAAGTTCATAATGA
1 -GAAGAAGAAGTTCATAATGA
42394 GAAGAA
1 GAAGAA
42400 TTTGTTCAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 16
0.67 0.04 0.30
Matches are distributed among these distances:
18 2 0.06
19 6 0.17
20 20 0.56
21 6 0.17
22 2 0.06
ACGTcount: A:0.52, C:0.08, G:0.26, T:0.15
Consensus pattern (20 bp):
GAAGAAGAAGTTCATAATGA
Found at i:42392 original size:264 final size:264
Alignment explanation
Indices: 42079--42625 Score: 776
Period size: 264 Copynumber: 2.1 Consensus size: 264
42069 TACCAGTTAG
* *
42079 AGTTCATAATGAGAAGAACTCATTTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACACATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
* * * * ** *
42144 ACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAA
66 ACCTTTTGCTCAAATCCATCACCCGATGGATCAGCAGTGCCAGAAAAAGTTCATAATGAGAAGAA
* * *
42209 CTCATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTC
131 CTCATCTGAAGAAGGAAAAAGAAATTCATAATAAGAAGAACTTGTTCAACCTTTTCCCTGAATTC
* *** **
42273 ATCACTT-GATGAATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGA
196 ATCA-TTCGATGAATCAGCATTTCCAGA-AAAGTTCATAATGAGAAGAACACATCTGAAGAAGGA
42336 AGAAGA
259 AGAAGA
*
42342 AGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACACATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * ** *
42407 AACCTTTTGCTCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGA
65 AACCTTTTGCTCAAATCCATCACCCGATGGATCAGCAGTGCCAGAAAAAGTTCATAATGAGAAGA
* * * *
42472 ACTCATCTGAAGAATGAAAAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTTGAATT
130 ACTCATCTGAAGAAGGAAAAAGAAATTCATAATAAGAAGAACTTGTTCAACCTTTTCCCTGAATT
* *
42537 CATCATTCGATGGATCAGCATTTCCAGAAGAGTTCATAATGAGAAGAACACATCTGAAGAAGGAA
195 CATCATTCGATGAATCAGCATTTCCAGAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAA
42602 GAAGA
260 GAAGA
42607 AGTTCATAATGAGAAGAAC
1 AGTTCATAATGAGAAGAAC
42626 TTGTTTAACA
Statistics
Matches: 250, Mismatches: 30, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
263 29 0.12
264 127 0.51
265 94 0.38
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (264 bp):
AGTTCATAATGAGAAGAACACATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTTTGCTCAAATCCATCACCCGATGGATCAGCAGTGCCAGAAAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAAGGAAAAAGAAATTCATAATAAGAAGAACTTGTTCAACCTTTTCCCTGAATTC
ATCATTCGATGAATCAGCATTTCCAGAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAG
AAGA
Found at i:42466 original size:152 final size:152
Alignment explanation
Indices: 42191--42513 Score: 472
Period size: 152 Copynumber: 2.1 Consensus size: 152
42181 TGCCAGTTAG
*
42191 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAACACATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
* * * ** *
42256 ACCTTTTCCCTGAATTCATCACTTGATGAATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTCCCTAAATCCATCACTTGATGAATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAA
* *
42321 CTTATCTGAAG-AGGAAGAAGA
131 CTCATCTGAAGAAGGAAAAAGA
*
42342 AGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACACATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* *
42407 AACCTTTT-GCTCAAATCCATCA-TCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAA
65 AACCTTTTCCCT-AAATCCATCACT-TGATGAATCAGCTTTTCCAGAAAAAGTTCATAATGAGAA
*
42470 GAACTCATCTGAAGAATGAAAAAGA
128 GAACTCATCTGAAGAAGGAAAAAGA
*
42495 AGTTCATAATAAGAAGAAC
1 AGTTCATAATGAGAAGAAC
42514 TTGTTCAACC
Statistics
Matches: 154, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
151 31 0.20
152 97 0.63
153 26 0.17
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (152 bp):
AGTTCATAATGAGAAGAACACATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
ACCTTTTCCCTAAATCCATCACTTGATGAATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAAGGAAAAAGA
Found at i:42582 original size:225 final size:222
Alignment explanation
Indices: 42336--42754 Score: 644
Period size: 225 Copynumber: 1.9 Consensus size: 222
42326 CTGAAGAGGA
*
42336 AGAAGAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAAGAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* * *
42401 TTGTTCAACCTTTTGCTCAAATCCATCA-TCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAAT
66 TTGTTCAACATTTTGCTCAAATCCATCATTC-GATGGATCAGCATTGCCAGAAAAAGTTCATAAT
42465 GAGAAGAACTCATCTGAAGAATGAAAAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGC
130 GAGAAGAACTCATCTGAAG-A-GAAAAAG-AGTTCATAATAAGAAGAACTTGTTCAACC-TTTGC
42530 TTGAATTCATCATTCGATGGATCAGCATTTCC
191 TTGAATTCATCATTCGATGGATCAGCATTTCC
42562 AGAAG-AGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
1 AGAAGAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
* ** * ****
42626 TTGTTTAACATTTTGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGTTCGAGTTCATAATG
66 TTGTTCAACATTTTGCTCAAATCCATCATTCGATGGATCAGCATTGCCAGAAAAAGTTCATAATG
* * *
42691 AGAAGAACTCATCTGAAGAGGAGAAGAGTTCATAATGAGAAGAACTTGTTCAACCTTTGCTTGA
131 AGAAGAACTCATCTGAAGAGAAAAAGAGTTCATAATAAGAAGAACTTGTTCAACCTTTGCTTGA
42755 CTCTATCACA
Statistics
Matches: 177, Mismatches: 15, Indels: 7
0.89 0.08 0.04
Matches are distributed among these distances:
221 9 0.05
222 28 0.16
223 5 0.03
224 1 0.01
225 127 0.72
226 7 0.04
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (222 bp):
AGAAGAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACATTTTGCTCAAATCCATCATTCGATGGATCAGCATTGCCAGAAAAAGTTCATAATG
AGAAGAACTCATCTGAAGAGAAAAAGAGTTCATAATAAGAAGAACTTGTTCAACCTTTGCTTGAA
TTCATCATTCGATGGATCAGCATTTCC
Found at i:42605 original size:489 final size:487
Alignment explanation
Indices: 41847--42748 Score: 1495
Period size: 489 Copynumber: 1.8 Consensus size: 487
41837 CAGCTTTTCC
* *
41847 AGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAATGAAGAAGAAATTCATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
41912 TTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAAAGAAAGTTCATAATG
66 TTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAAAGAAAGTTCATAATG
* * *
41977 AGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAATTGTTCAACTTTTTGCT
131 AGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATAAGAAGAAATTGTTCAACCTTTTGCT
* * * * *
42042 TAAATTCATCATTTGATGGATCATCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAA
196 TAAATTCATCATTCGATGGATCAGCATTACCAGTAAGAGTTCATAATGAGAAGAACACATCTGAA
* *
42107 GAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACCCGGTG
261 GAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGCTTAAATTCATCACCCGATG
42172 GATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCAT
326 GATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGG-AGAAG-AATTCAT
*
42237 AATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCATCACTTGATGAATTATTTTTTCCAGAGA
389 AATGAGAAGAACTTGTTCAACCTTTTCCCTGAATTCATCACTTGATGAATTATTTTTTCCAGAGA
42302 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGA
454 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGA
* *
42336 AGAAGAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAT
1 AGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
*
42401 TTGTTCAACCTTTTGCTCAAATCCATCA-TCTGATGGATCAGCTTTTCCAGAA-AAAGTTCATAA
66 TTGTTCAACCTTTTGCTCAAATCCATCATTC-GATGGATCAGCATTTCCA-AAGAAAGTTCATAA
* *
42464 TGAGAAGAACTCATCTGAAGAATGAAAAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTG
129 TGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATAAGAAGAAATTGTTCAACCTTTTG
* *
42529 CTTGAATTCATCATTCGATGGATCAGCATTTCCAG-AAGAGTTCATAATGAGAAGAACACATCTG
194 CTTAAATTCATCATTCGATGGATCAGCATTACCAGTAAGAGTTCATAATGAGAAGAACACATCTG
* * **
42593 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACATTTTGCTTGAATTCATCATTCG
259 AAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGCTTAAATTCATCACCCG
* * *
42658 ATGGATCAGCATTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAGAAGAGTTCA
323 ATGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAGAAGAATTCA
42723 TAATGAGAAGAACTTGTTCAACCTTT
388 TAATGAGAAGAACTTGTTCAACCTTT
42749 GCTTGACTCT
Statistics
Matches: 383, Mismatches: 27, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
487 30 0.08
488 38 0.10
489 313 0.82
490 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (487 bp):
AGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
TTGTTCAACCTTTTGCTCAAATCCATCATTCGATGGATCAGCATTTCCAAAGAAAGTTCATAATG
AGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATAAGAAGAAATTGTTCAACCTTTTGCT
TAAATTCATCATTCGATGGATCAGCATTACCAGTAAGAGTTCATAATGAGAAGAACACATCTGAA
GAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACATTTTGCTTAAATTCATCACCCGATG
GATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAGAAGAATTCATAA
TGAGAAGAACTTGTTCAACCTTTTCCCTGAATTCATCACTTGATGAATTATTTTTTCCAGAGAAA
GTTCATAATGAGAAGAACTTATCTGAAGAGGA
Found at i:42623 original size:112 final size:113
Alignment explanation
Indices: 42342--42754 Score: 622
Period size: 113 Copynumber: 3.7 Consensus size: 113
42332 AGGAAGAAGA
*
42342 AGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
** * * *
42407 AACCTTTTGCTCAAATCCATCA-TCTGATGGATCAGCTTTTCCAGAAAA
66 AACCTTTTGCTTGAATTCATCATTC-GATGGATCAGCATTTCCAGAAAG
* * * *
42455 AGTTCATAATGAGAAGAACTCATCTGAAGAATGAAAAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
42520 AACCTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAG-AAG
66 AACCTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAAG
*
42567 AGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
1 AGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * ***
42632 AACATTTTGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGTTCG
66 AACCTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAAG
*
42680 AGTTCATAATGAGAAGAACTCATCTGAAG-AGG-AGAAG-AGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
42742 AACC-TTTGCTTGA
66 AACCTTTTGCTTGA
42755 CTCTATCACA
Statistics
Matches: 276, Mismatches: 22, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
109 9 0.03
110 27 0.10
111 5 0.02
112 107 0.39
113 126 0.46
114 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTTGAATTCATCATTCGATGGATCAGCATTTCCAGAAAG
Found at i:44045 original size:27 final size:29
Alignment explanation
Indices: 44004--44060 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 29
43994 AATTAGTATT
44004 TTATTTATTTATTTATTCA-T-ATATTTA
1 TTATTTATTTATTTATTCACTAATATTTA
44031 TTATTTATATT-TTTATTCACTAATATTTA
1 TTATTTAT-TTATTTATTCACTAATATTTA
44060 T
1 T
44061 ATGAAATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 16 0.59
28 3 0.11
29 8 0.30
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (29 bp):
TTATTTATTTATTTATTCACTAATATTTA
Found at i:44919 original size:16 final size:16
Alignment explanation
Indices: 44893--44934 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
44883 TAGACCAGTT
44893 TTTTGTCTTAAAAATGA
1 TTTT-TCTTAAAAATGA
*
44910 TTTTTCTT-AAAATTA
1 TTTTTCTTAAAAATGA
44925 TTTTT-TTAAA
1 TTTTTCTTAAA
44935 GACGTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 13 0.57
16 4 0.17
17 4 0.17
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (16 bp):
TTTTTCTTAAAAATGA
Found at i:48562 original size:64 final size:64
Alignment explanation
Indices: 48461--48885 Score: 645
Period size: 64 Copynumber: 6.6 Consensus size: 64
48451 TGCAGCTTTT
*
48461 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACACCTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* *
48525 AGAGTCAATTTCAACTTCACAGTGAAGGATATTGGACTCAACAAACAACTTTCCAATTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * ** * *
48589 AGAGTCAATTTCAAATTCATAATGAAGGATATTAGACTCAACAAACAATTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * * *
48653 AGAGTCTATTTCAACTTCACAACGAAGGATATTGGACTCAAAAAACAACTTTCTAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
48717 AGAGTCAATTTCAACTTCACAGTGAATGATATTGGACTCAACAAACAACTTTCTAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* *
48781 AGAGTCAGTTTCAACTTCACAGCGAATGATATTGGACTCAACAAACAACTTTCCAGCTTT-ATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAG-TTTCATTC
* * *
48845 AGAGTCAATTTCAACTTCACAACAAATGATATTGGACTCAA
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAA
48886 AACAATGCAA
Statistics
Matches: 332, Mismatches: 28, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
64 329 0.99
65 3 0.01
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
Found at i:49001 original size:66 final size:66
Alignment explanation
Indices: 48911--49123 Score: 182
Period size: 66 Copynumber: 3.4 Consensus size: 66
48901 ACAAGCTTAT
* * * *
48911 ATTTCAAATTCAAGACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
1 ATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCTC
48976 A
66 A
* * * * * *
48977 ATTTCAACTTCACGACGAAGGATAT-C--GT----GC-CCAC--AAGCAGC-AATGTAACC--CT
1 ATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCA-CAACGAATG-AGCCATCC
**
49029 TGG
64 TCA
*
49032 ATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATACTC
1 ATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCTC
49097 A
66 A
* *
49098 ATTTCAACTTCACGATGAATGATATC
1 ATTTCAACTTCACGACGAAGGATATC
49124 GTGCCTAACG
Statistics
Matches: 109, Mismatches: 23, Indels: 30
0.67 0.14 0.19
Matches are distributed among these distances:
55 26 0.24
56 6 0.06
57 6 0.06
58 4 0.04
59 2 0.02
62 2 0.02
63 4 0.04
64 6 0.06
65 6 0.06
66 47 0.43
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (66 bp):
ATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCTC
A
Found at i:49068 original size:121 final size:121
Alignment explanation
Indices: 48911--49128 Score: 373
Period size: 121 Copynumber: 1.8 Consensus size: 121
48901 ACAAGCTTAT
*
48911 ATTTCAAATTCAAGACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCAC
1 ATTTCAAATTCAAGACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATACAC
48976 AATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGTAACCCTTGG
66 AATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGTAACCCTTGG
* * * *
49032 ATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATACTC
1 ATTTCAAATTCAAGACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATACAC
* *
49097 AATTTCAACTTCACGATGAATGATATCGTGCC
66 AATTTCAACTTCACGACGAAGGATATCGTGCC
49129 TAACGGATCG
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
121 90 1.00
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.23
Consensus pattern (121 bp):
ATTTCAAATTCAAGACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATACAC
AATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGTAACCCTTGG
Found at i:49342 original size:85 final size:85
Alignment explanation
Indices: 49187--49420 Score: 294
Period size: 85 Copynumber: 2.8 Consensus size: 85
49177 CCCAGTGCAA
* * * *
49187 CATAACTCAAGGCGAGAAGGGTTATCTGTC-ATCAAATACCTTCGAGTTCGATTACATTTAGCTC
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAA-ACCTTCGAGTTCGATTATATTCAGCTC
*
49251 AAAGGCATATCAAATTTACAT
65 AAAGGCATATCAAATTTACAG
* * *
49272 CATAGCTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTATATTCATCT-A
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTATATTCAGCTCA
* *
49336 AGAGGCATATTAAATTTATAG
66 A-AGGCATATCAAATTTACAG
* * * *
49357 CATAGCTCAAGGCGAGAAGGGTTATCTGT-AAACAAAAACTGACGAGTTCGATTCTATTCAGCTC
1 CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAAACCT-TCGAGTTCGATTATATTCAGCTC
49421 GATGACACAT
Statistics
Matches: 128, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
84 10 0.08
85 114 0.89
86 4 0.03
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (85 bp):
CATAGCTCAAGGCGAGAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTATATTCAGCTCA
AAGGCATATCAAATTTACAG
Found at i:50173 original size:3 final size:3
Alignment explanation
Indices: 50155--50237 Score: 132
Period size: 3 Copynumber: 27.7 Consensus size: 3
50145 ACTTAAAAAA
*
50155 TAT TA- TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
50202 TAT TACT TAT TAT TAT TAT TAG TAT TAT TAT TAT TA
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
50238 ATTTATATAT
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.03
3 69 0.93
4 3 0.04
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:53287 original size:19 final size:20
Alignment explanation
Indices: 53248--53287 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
53238 TAAGTGTTAA
*
53248 TGAATTTTAAGATTTTATAT
1 TGAATTTTAAGATTATATAT
53268 TGAATTTTAA-ATTATATAT
1 TGAATTTTAAGATTATATAT
53287 T
1 T
53288 CGATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (20 bp):
TGAATTTTAAGATTATATAT
Found at i:53539 original size:35 final size:36
Alignment explanation
Indices: 53480--53549 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
53470 ATTACCCAGA
53480 GGGAACAGATTCCCCCCCAAGGGGTACCAATTCCCT
1 GGGAACAGATTCCCCCCCAAGGGGTACCAATTCCCT
* *
53516 GGGAACAGATTTCCCCCC-AGGGGTACCGATTCCC
1 GGGAACAGATTCCCCCCCAAGGGGTACCAATTCCC
53550 CCCAGGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 15 0.47
36 17 0.53
ACGTcount: A:0.23, C:0.36, G:0.24, T:0.17
Consensus pattern (36 bp):
GGGAACAGATTCCCCCCCAAGGGGTACCAATTCCCT
Found at i:56758 original size:19 final size:20
Alignment explanation
Indices: 56721--56758 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
56711 AGTGTTAATG
*
56721 AATTTTAATATTTTATATTA
1 AATTTTAATATTATATATTA
56741 AATTTTAA-ATTATATATT
1 AATTTTAATATTATATATT
56759 CGATTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATTTTAATATTATATATTA
Found at i:59961 original size:21 final size:22
Alignment explanation
Indices: 59920--59961 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
59910 TTTAATGTCG
* *
59920 ATATTATTTTTAATCAAAATCT
1 ATATAATTATTAATCAAAATCT
59942 ATATAATTATTAAT-AAAATC
1 ATATAATTATTAATCAAAATC
59962 CAAGATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATAATTATTAATCAAAATCT
Found at i:62352 original size:15 final size:15
Alignment explanation
Indices: 62329--62360 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
62319 TAATTTCCCC
*
62329 TTTTGTAAATACAAA
1 TTTTATAAATACAAA
62344 TTTTATAAATACAAA
1 TTTTATAAATACAAA
62359 TT
1 TT
62361 AACATATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (15 bp):
TTTTATAAATACAAA
Found at i:64123 original size:38 final size:38
Alignment explanation
Indices: 64048--64124 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 38
64038 CTTGGAAAAT
* *
64048 ATTTATATATTTTCTTTAAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTGAAAATCATAAA
* * *
64086 ATTTATATACTTTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATATA-TTTTCTTTAAAAAAATTGAAAATCATAAA
64124 A
1 A
64125 AATGTTTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 15 0.45
39 18 0.55
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (38 bp):
ATTTATATATTTTCTTTAAAAAAATTGAAAATCATAAA
Found at i:73967 original size:44 final size:44
Alignment explanation
Indices: 73912--73995 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
73902 GTTCGTGAAT
*
73912 GTTAAACGAACATGGTGGCGAACATATAATCAAATATGTTTGTG
1 GTTAAACGAACATGGTGACGAACATATAATCAAATATGTTTGTG
* * *
73956 GTTAAATGAACATGTTGACGAACATATAATCGAATATGTT
1 GTTAAACGAACATGGTGACGAACATATAATCAAATATGTT
73996 CCTGAACGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (44 bp):
GTTAAACGAACATGGTGACGAACATATAATCAAATATGTTTGTG
Found at i:74032 original size:23 final size:24
Alignment explanation
Indices: 74006--74060 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
73996 CCTGAACGTT
* *
74006 TAAACGAACA-AGTTTACAAAT-AC
1 TAAACGAACATA-TTTAAAAATAAA
74029 TAAACGAACATATTTAAAAATAAA
1 TAAACGAACATATTTAAAAATAAA
74053 TAAACGAA
1 TAAACGAA
74061 TATGAATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.58, C:0.13, G:0.07, T:0.22
Consensus pattern (24 bp):
TAAACGAACATATTTAAAAATAAA
Found at i:76559 original size:88 final size:87
Alignment explanation
Indices: 76406--76569 Score: 204
Period size: 88 Copynumber: 1.9 Consensus size: 87
76396 AGTCGAAAAG
* * *
76406 CGAGTCAATAAACTAACTATTCGTGAACATAAATGAATCATGCACACATTTATTGGAGTTTGTAT
1 CGAGTCAATAAACTAACTATTCGTGAACATAAACGAATCAT-CACACATTTATTCGAGTTCGTAT
76471 ATTTATTAAATGAAGTAAGTAAA
65 ATTTATTAAATGAAGTAAGTAAA
* * * * * * *
76494 CGAGTCAATAAATTGACTTGTTCGTGAATATCAACGAATCAT-ATACATTTTATTCGTGTTCGTA
1 CGAGTCAATAAACTAAC-TATTCGTGAACATAAACGAATCATCACACA-TTTATTCGAGTTCGTA
76558 TATTTATTAAAT
64 TATTTATTAAAT
76570 AATATAAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
87 4 0.06
88 40 0.62
89 20 0.31
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (87 bp):
CGAGTCAATAAACTAACTATTCGTGAACATAAACGAATCATCACACATTTATTCGAGTTCGTATA
TTTATTAAATGAAGTAAGTAAA
Found at i:82454 original size:3 final size:3
Alignment explanation
Indices: 82446--82517 Score: 117
Period size: 3 Copynumber: 24.0 Consensus size: 3
82436 CAATTTTGAC
82446 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
82494 ATT ATT ATC ATC ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
82518 TCATTCCTCT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:84528 original size:16 final size:16
Alignment explanation
Indices: 84507--84539 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
84497 CTAATAGTGG
84507 ATTTTTGGAGTATATT
1 ATTTTTGGAGTATATT
84523 ATTTTTGGAGTATATT
1 ATTTTTGGAGTATATT
84539 A
1 A
84540 GCCCTCTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (16 bp):
ATTTTTGGAGTATATT
Found at i:87523 original size:9 final size:9
Alignment explanation
Indices: 87509--87533 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
87499 ATTGAATCCC
87509 GGATTTTCG
1 GGATTTTCG
87518 GGATTTTCG
1 GGATTTTCG
87527 GGATTTT
1 GGATTTT
87534 TTATTTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.08, G:0.32, T:0.48
Consensus pattern (9 bp):
GGATTTTCG
Found at i:88016 original size:3 final size:3
Alignment explanation
Indices: 88008--88066 Score: 82
Period size: 3 Copynumber: 18.7 Consensus size: 3
87998 TTGTAAGTTA
88008 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT ATAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT -AAT
*
88056 GAT AAT AAT AA
1 AAT AAT AAT AA
88067 AAAAGACCCG
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
3 43 0.84
4 7 0.14
5 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:88322 original size:43 final size:43
Alignment explanation
Indices: 88268--88497 Score: 161
Period size: 43 Copynumber: 5.4 Consensus size: 43
88258 ATAACTTGGT
* *
88268 TCCTACTTGATGAGGACG-GCTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAAGA-GAGCTGGTTATCTATGGTTGACACGGC
* ** *
88311 TCCTACGTGATGAAGAGATCTGG---TCGGTGGGTGACACGGC
1 TCCTACGTGATGAAGAGAGCTGGTTATCTATGGTTGACACGGC
* ** ** * * *
88351 TCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGT
1 TCCTACGTGATGAAGAGAGCTGGTTATCT-ATGGT--TGACACGGC
*
88397 TCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTGACACGGC
1 TCCTACGTGATGAAGA-GAGCTGGTTATCTATGGTTGACACGGC
* * ** *
88440 TCATACGTGATGAAGAGATCTGG---TCTGGGGAATGACACGGC
1 TCCTACGTGATGAAGAGAGCTGGTTATCTATGG-TTGACACGGC
*
88481 TCATACGTGATGAAGAG
1 TCCTACGTGATGAAGAG
88498 TTCTGGCCAT
Statistics
Matches: 149, Mismatches: 28, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
40 40 0.27
41 26 0.17
42 2 0.01
43 45 0.30
44 2 0.01
45 4 0.03
46 29 0.19
47 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.26
Consensus pattern (43 bp):
TCCTACGTGATGAAGAGAGCTGGTTATCTATGGTTGACACGGC
Found at i:88447 original size:129 final size:130
Alignment explanation
Indices: 88214--88549 Score: 568
Period size: 129 Copynumber: 2.6 Consensus size: 130
88204 TGGTGGGGAC
* * * * ** *
88214 GACACTGCTCATACGTGATGAAGAGTTCTGGTCGTCTAAGGGTGATAACTTGGTTCCTACTTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
* *
88279 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTC-GGTGG-G
66 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGG-GGAA
88342 T
130 T
88343 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
88408 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAAT
66 GAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAAT
88473 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
1 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
88538 GAGGACGGCTGG
66 GAGGACGGCTGG
88550 CCATCTTTAG
Statistics
Matches: 196, Mismatches: 9, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
129 116 0.59
130 80 0.41
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (130 bp):
GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGAT
GAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGAAT
Found at i:88555 original size:46 final size:45
Alignment explanation
Indices: 88215--88539 Score: 189
Period size: 46 Copynumber: 7.4 Consensus size: 45
88205 GGTGGGGACG
* * *
88215 ACACTGCTCATACGTGATGAAGAGTTCTGGTCGTCTAAGGGTGATA
1 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAA-GGTGATA
** * * * * * ** * *
88261 ACTTGGTTCCTACTTGATGAGGACG-GCTGGTTATCTATGGT--TG
1 ACACGGCTCATACGTGATGAAGA-GTTCTGGCCATCTAAGGTGATA
* * * *
88304 ACACGGCTCCTACGTGATGAAGAGATCTGG---TC---GGTGGGTG
1 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAGGT-GATA
88344 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCT-AAGGTGATA
* * * * ** * *
88390 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT--TG
1 ACACGGCTCATACGTGATGAAGA-GTTCTGGCCATCTAAGGTGATA
* * *
88433 ACACGGCTCATACGTGATGAAGAGATCTGG---TCT--GGGGAATG
1 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAGGTG-ATA
88474 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCT-AAGGTGATA
* *
88520 ACACGGTTCCTACGTGATGA
1 ACACGGCTCATACGTGATGA
88540 GGACGGCTGG
Statistics
Matches: 216, Mismatches: 40, Indels: 46
0.72 0.13 0.15
Matches are distributed among these distances:
37 3 0.01
38 2 0.01
40 35 0.16
41 31 0.14
42 2 0.01
43 50 0.23
44 3 0.01
45 7 0.03
46 75 0.35
47 8 0.04
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (45 bp):
ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAGGTGATA
Found at i:89363 original size:63 final size:62
Alignment explanation
Indices: 89018--89375 Score: 202
Period size: 63 Copynumber: 5.6 Consensus size: 62
89008 GTATCTTAGT
* * *
89018 GAGACAAAATTTTGTTTCCAAA-GAAACAGACTC--AGATTTTCTTCAAAAGAAACTGTTTTAA
1 GAGACAAAATTTTGTTT-CAAAGGAAACAGACTCAAAGATTTT-TTCAAAAGAAATTGTCTCAA
* * ** * * * * * *
89079 GGGAGAAAACCTTGTTTC-CAGAGAAACAAACTCAAAGATGATCTTGTTTTAAGAGAAAATGTTT
1 GAGACAAAATTTTGTTTCAAAG-GAAACAGACTC-AA-A-GAT-TT-TTTCAAAAGAAATTGTCT
89143 CAA
60 CAA
*** * *
89146 GAGACAAAA-TTTGTTT-AAAGGGAAAC-GACTCAAAGATGACATTGAAAGGAAATTGTCTCATG
1 GAGACAAAATTTTGTTTCAAA-GGAAACAGACTCAAAGAT-TTTTTCAAAAGAAATTGTCTCA--
*
89208 C
62 A
* * *
89209 GAGACAAAA-TTTGTTTTAATA-GAAAC-GATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCT
1 GAGACAAAATTTTGTTTCAA-AGGAAACAGA-CTCAAAGAT---T-TTTTCAAAAGAAATTGTCT
*
89271 CGA
60 CAA
*
89274 GAGACAAAATTTTGTTTCAAAGGAAACCA-ACTCAAAGATTTTTTCAAAAGAAATTGTCTTTAA
1 GAGACAAAATTTTGTTTCAAAGGAAA-CAGACTCAAAGATTTTTTCAAAAGAAATTGTC-TCAA
*
89337 GAGATAAAATTTTGTTTTTC-AA-GAAACAGACTCAAAGAT
1 GAGACAAAATTTTG--TTTCAAAGGAAACAGACTCAAAGAT
89376 GAATCACATC
Statistics
Matches: 230, Mismatches: 40, Indels: 52
0.71 0.12 0.16
Matches are distributed among these distances:
59 1 0.00
60 1 0.00
61 37 0.16
62 22 0.10
63 54 0.23
64 14 0.06
65 20 0.09
66 37 0.16
67 43 0.19
68 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.29
Consensus pattern (62 bp):
GAGACAAAATTTTGTTTCAAAGGAAACAGACTCAAAGATTTTTTCAAAAGAAATTGTCTCAA
Found at i:89733 original size:67 final size:68
Alignment explanation
Indices: 89597--89753 Score: 273
Period size: 68 Copynumber: 2.3 Consensus size: 68
89587 TCATTTTAAG
* *
89597 AGAAACAGATTCAAAGATTTTTTTTTCAAAAGCAAATATCTTAAGAGAGACAAAAATTTTGTTTC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGCAAATATCTTAAGAGAGACAAAAATTTTGTTTC
89662 CAA
66 CAA
89665 AGAAACAGACTCAAAGATTTTTGTTTCAAAAG-AAATTATCTTAAGAGAGAC-AAAATTTTGTTT
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGCAAA-TATCTTAAGAGAGACAAAAATTTTGTTT
89728 CCAA
65 CCAA
89732 AGAAACAGACTCAAAGATTTTT
1 AGAAACAGACTCAAAGATTTTT
89754 TCAAAAGAAA
Statistics
Matches: 86, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
67 41 0.48
68 45 0.52
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (68 bp):
AGAAACAGACTCAAAGATTTTTGTTTCAAAAGCAAATATCTTAAGAGAGACAAAAATTTTGTTTC
CAA
Found at i:89758 original size:26 final size:27
Alignment explanation
Indices: 89725--89781 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
89715 CAAAATTTTG
*
89725 TTTCCAAAGAAACAGA-CTCAAAGATTT
1 TTTCAAAAGAAACA-ATCTCAAAGATTT
89752 TTTCAAAAGAAACAATCTCAAAGATTT
1 TTTCAAAAGAAACAATCTCAAAGATTT
89779 TTT
1 TTT
89782 TTTTCACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.32
Consensus pattern (27 bp):
TTTCAAAAGAAACAATCTCAAAGATTT
Found at i:89946 original size:29 final size:29
Alignment explanation
Indices: 89866--89954 Score: 128
Period size: 29 Copynumber: 3.1 Consensus size: 29
89856 GAGACAAAAC
*
89866 TTTGTTTCAAAAGAAATAGACTCAAAGAT
1 TTTGTTTCAAAAGAAACAGACTCAAAGAT
89895 ATTTGTTTCAAAAGAAACA-ACTCAAAGAT
1 -TTTGTTTCAAAAGAAACAGACTCAAAGAT
*
89924 TTT-TATTCAAAAGGAACAGACTCAAAGAT
1 TTTGT-TTCAAAAGAAACAGACTCAAAGAT
89953 TT
1 TT
89955 ATCTCAAGAG
Statistics
Matches: 55, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
27 1 0.02
28 15 0.27
29 22 0.40
30 17 0.31
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (29 bp):
TTTGTTTCAAAAGAAACAGACTCAAAGAT
Found at i:89961 original size:28 final size:27
Alignment explanation
Indices: 89871--89968 Score: 99
Period size: 28 Copynumber: 3.4 Consensus size: 27
89861 AAAACTTTGT
* *
89871 TTCAAAAGAAATAGACTCAAAGATATTTGT
1 TTCAAAAGAAACAGACTCAAAG--ATTT-A
89901 TTCAAAAGAAACA-ACTCAAAGATTTTTA
1 TTCAAAAGAAACAGACTCAAAGA--TTTA
*
89929 TTCAAAAGGAACAGACTCAAAGATTTA
1 TTCAAAAGAAACAGACTCAAAGATTTA
*
89956 TCTCAAGAGAAAC
1 T-TCAAAAGAAAC
89969 TGTCTCCAGA
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
27 6 0.10
28 21 0.36
29 20 0.34
30 12 0.20
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (27 bp):
TTCAAAAGAAACAGACTCAAAGATTTA
Found at i:90610 original size:156 final size:157
Alignment explanation
Indices: 90345--90636 Score: 426
Period size: 156 Copynumber: 1.9 Consensus size: 157
90335 TCTCAAAGGG
** * *
90345 AAAAGGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAGGTGAGATTAATTTT
1 AAAAGGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAAATGAGATCAACTTT
* * * *
90410 GTTTTTAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGCAATT
66 GTTTATAGTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAACGAGACGAAATT
90475 TGTTTTAAAATTCTCAAAATTTGTGGA
131 TGTTTTAAAATTCTCAAAATTTGTGGA
* * * *
90502 AAAATGTCTCAAGCGAGACGAAATTTGTTTTGAAATAAA-TACGATCTAAAATGAGATCAACTTT
1 AAAAGGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAAATGAGATCAACTTT
* * *
90566 GTTTA-ATGTGAAACAAATTCAAATTTTGTATCTTAAAGGAAAAATGTCTCAAATGAGACGAAAT
66 GTTTATA-GTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAACGAGACGAAAT
90630 TTGTTTT
130 TTGTTTT
90637 GAAAGAAATT
Statistics
Matches: 119, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
155 1 0.01
156 81 0.68
157 37 0.31
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.33
Consensus pattern (157 bp):
AAAAGGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCTAAAATGAGATCAACTTT
GTTTATAGTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAACGAGACGAAATT
TGTTTTAAAATTCTCAAAATTTGTGGA
Found at i:91045 original size:14 final size:14
Alignment explanation
Indices: 91026--91053 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
91016 TTTATGTATC
91026 ATGTATGTATGTGT
1 ATGTATGTATGTGT
91040 ATGTATGTATGTGT
1 ATGTATGTATGTGT
91054 TCTCAATCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (14 bp):
ATGTATGTATGTGT
Found at i:92253 original size:12 final size:11
Alignment explanation
Indices: 92225--92262 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
92215 TCCTCTTTTG
*
92225 TTCTTTGCTTT
1 TTCTTTGATTT
92236 TTCTTTGATTT
1 TTCTTTGATTT
92247 TTGCTTTGATTT
1 TT-CTTTGATTT
92259 TTCT
1 TTCT
92263 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:92971 original size:46 final size:45
Alignment explanation
Indices: 92879--92972 Score: 116
Period size: 46 Copynumber: 2.1 Consensus size: 45
92869 ATAAATGCAG
* * * *
92879 TGTTTCAAGGTGGAAAGAATGTTTCAAGGCCTTAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
* * *
92924 TGTTTCCAGGTTGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGG-TGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
92970 TGT
1 TGT
92973 CAAAAATTGG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
45 9 0.22
46 32 0.78
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.28
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
Found at i:95460 original size:31 final size:32
Alignment explanation
Indices: 95404--95465 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
95394 TGACAAAATG
95404 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
95436 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
95466 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:98834 original size:9 final size:9
Alignment explanation
Indices: 98820--98844 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
98810 GATTGAATCC
98820 GGATTTTCG
1 GGATTTTCG
98829 GGATTTTCG
1 GGATTTTCG
98838 GGATTTT
1 GGATTTT
98845 TTATTTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.08, G:0.32, T:0.48
Consensus pattern (9 bp):
GGATTTTCG
Found at i:99327 original size:3 final size:3
Alignment explanation
Indices: 99319--99371 Score: 70
Period size: 3 Copynumber: 16.7 Consensus size: 3
99309 TTGTAAGTTA
*
99319 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT ATAT AAAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT -AAT AAT AAT
99367 AAT AA
1 AAT AA
99372 AAAAGACCCG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 37 0.82
4 7 0.16
5 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:103584 original size:19 final size:19
Alignment explanation
Indices: 103531--103585 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
103521 CGATCAGACT
* *
103531 AGTCAACAGGTCAGGTTAA
1 AGTCAACAGGTCGGGTCAA
* *
103550 AGTCAACGGGTTGGGTCAA
1 AGTCAACAGGTCGGGTCAA
*
103569 AGTCAACAAGTCGGGTC
1 AGTCAACAGGTCGGGTC
103586 GGGTTGACTC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.31, T:0.20
Consensus pattern (19 bp):
AGTCAACAGGTCGGGTCAA
Found at i:104815 original size:21 final size:22
Alignment explanation
Indices: 104780--104824 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 22
104770 ACTTGACATG
104780 AAATAAGAAATTAAA-ATTTTAAT
1 AAATAAG-AATTAAATA-TTTAAT
104803 AAATAAG-ATTAAATATTTAAT
1 AAATAAGAATTAAATATTTAAT
104824 A
1 A
104825 TAAATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 13 0.62
22 1 0.05
23 7 0.33
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (22 bp):
AAATAAGAATTAAATATTTAAT
Found at i:104827 original size:23 final size:22
Alignment explanation
Indices: 104780--104851 Score: 58
Period size: 23 Copynumber: 3.1 Consensus size: 22
104770 ACTTGACATG
*
104780 AAATAAGAAATTAAAATTTTA-AT
1 AAATAAG--ATTAAAATTTAATAT
104803 AAATAAGATTAAATATTTAATAT
1 AAATAAGATTAAA-ATTTAATAT
* *
104826 AAATTA-TTTAAAAATATTAATAT
1 AAATAAGATT-AAAAT-TTAATAT
104849 AAA
1 AAA
104852 ATTTTATTTG
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
21 6 0.14
22 9 0.21
23 27 0.64
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (22 bp):
AAATAAGATTAAAATTTAATAT
Found at i:112446 original size:31 final size:31
Alignment explanation
Indices: 112409--112486 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
112399 TAAAAAAACA
* *
112409 TAAGTTTTAGTCACTTACGTTATTGTTTTAT
1 TAAGTTTTAGTCACTTACATTATCGTTTTAT
112440 TAAGTTTTGATGT-A-TTACATTATCGTTTTAT
1 TAAGTTTT-A-GTCACTTACATTATCGTTTTAT
*
112471 TAAGTTTTGGTCACTT
1 TAAGTTTTAGTCACTT
112487 GGACATTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 2 0.05
30 1 0.03
31 33 0.82
32 2 0.05
33 2 0.05
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.54
Consensus pattern (31 bp):
TAAGTTTTAGTCACTTACATTATCGTTTTAT
Found at i:121286 original size:24 final size:24
Alignment explanation
Indices: 121247--121293 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
121237 TTTTTATATA
*
121247 TAATAATATTACATATTTAATTAT
1 TAATAATATTACATATTAAATTAT
* *
121271 TAATAATTTTATATATTAAATTA
1 TAATAATATTACATATTAAATTA
121294 AACTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATAATATTACATATTAAATTAT
Found at i:123025 original size:30 final size:30
Alignment explanation
Indices: 122989--123045 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
122979 AAATAGATTT
*
122989 CGATTATAAGACGA-TGTTTTGTTGAGTCCC
1 CGATTATAAGAC-ATTGTTCTGTTGAGTCCC
*
123019 CGATTATAGGACATTGTTCTGTTGAGT
1 CGATTATAAGACATTGTTCTGTTGAGT
123046 TTATCGACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.23, C:0.14, G:0.25, T:0.39
Consensus pattern (30 bp):
CGATTATAAGACATTGTTCTGTTGAGTCCC
Found at i:128805 original size:24 final size:24
Alignment explanation
Indices: 128760--128809 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
128750 TGGTGGTTGG
*
128760 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
128784 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
128808 TT
1 TT
128810 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Done.