Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000062.1 Hibiscus syriacus cultivar Beakdansim tig00000101_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: 175151
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2189 original size:16 final size:17
Alignment explanation
Indices: 2157--2189 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2147 CTTATTGCCT
*
2157 CAACATTAAACCATCTA
1 CAACACTAAACCATCTA
2174 CAACACTAAA-CATCTA
1 CAACACTAAACCATCTA
2190 TTCTTGACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (17 bp):
CAACACTAAACCATCTA
Found at i:5013 original size:9 final size:9
Alignment explanation
Indices: 4981--5069 Score: 59
Period size: 9 Copynumber: 10.3 Consensus size: 9
4971 TAACATTACT
4981 TAATA-ATA
1 TAATATATA
4989 CTAATAT-TA
1 -TAATATATA
*
4998 TTA-ATATA
1 TAATATATA
5006 TAATATATAA
1 TAATATAT-A
* *
5016 TAAAACATA
1 TAATATATA
5025 TACA-AT-TAA
1 TA-ATATAT-A
5034 TAATATATA
1 TAATATATA
5043 TAAT-TA-A
1 TAATATATA
5050 TAATATATA
1 TAATATATA
5059 TAATA-ATA
1 TAATATATA
5067 TAA
1 TAA
5070 ACGGACAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 21
0.71 0.05 0.23
Matches are distributed among these distances:
7 7 0.11
8 18 0.28
9 31 0.48
10 9 0.14
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (9 bp):
TAATATATA
Found at i:5047 original size:16 final size:16
Alignment explanation
Indices: 4980--5066 Score: 90
Period size: 16 Copynumber: 5.4 Consensus size: 16
4970 GTAACATTAC
*
4980 TTAATAATACTAATATTA
1 TTAATAATA-T-ATATAA
4998 TTAATATATAATATATAA
1 TTAATA-AT-ATATATAA
* *
5016 -TAA-AACATATACAA
1 TTAATAATATATATAA
5030 TTAATAATATATATAA
1 TTAATAATATATATAA
5046 TTAATAATATATATAA
1 TTAATAATATATATAA
5062 -TAATA
1 TTAATA
5067 TAAACGGACA
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
14 7 0.12
15 9 0.15
16 26 0.43
17 3 0.05
18 11 0.18
19 3 0.05
20 1 0.02
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
TTAATAATATATATAA
Found at i:5055 original size:12 final size:13
Alignment explanation
Indices: 4981--5069 Score: 53
Period size: 14 Copynumber: 6.8 Consensus size: 13
4971 TAACATTACT
4981 TAATAATACTAATA
1 TAATAATA-TAATA
* *
4995 TTATTA-AT-ATA
1 TAATAATATAATA
5006 TAAT-ATATAATA
1 TAATAATATAATA
* * *
5018 AAACATATACAAT-
1 TAATA-ATATAATA
5031 TAATAATAT-ATA
1 TAATAATATAATA
5043 TAATTAATAATATATA
1 TAA-TAAT-ATA-ATA
5059 TAATAATATAA
1 TAATAATATAA
5070 ACGGACAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 19
0.67 0.11 0.22
Matches are distributed among these distances:
10 1 0.02
11 10 0.18
12 12 0.21
13 9 0.16
14 15 0.26
15 4 0.07
16 6 0.11
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATAATATAATA
Found at i:16871 original size:42 final size:41
Alignment explanation
Indices: 16812--16956 Score: 134
Period size: 42 Copynumber: 3.5 Consensus size: 41
16802 AAGAATCTGT
* *
16812 TTCACTACTCTTTCGTGAAGATCAGACTCATGGTTGGAATAC
1 TTCACTACTCTTCCGTGAAGATCAGATTCA-GGTTGGAATAC
* * * * * **
16854 TTCACTATTCTTCCGTGAAGGT-TGATTTAAG-AAGAAT-C
1 TTCACTACTCTTCCGTGAAGATCAGATTCAGGTTGGAATAC
16892 TGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGGTTGGAATAC
1 ---TTCACTACTCTTCCGTGAAGATCAGATTC-AGGTTGGAATAC
*
16937 TTCATTACTCTTCCGTGAAG
1 TTCACTACTCTTCCGTGAAG
16957 GTTGATTTAA
Statistics
Matches: 79, Mismatches: 17, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
38 1 0.01
39 4 0.05
40 1 0.01
41 24 0.30
42 42 0.53
43 2 0.03
44 4 0.05
45 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (41 bp):
TTCACTACTCTTCCGTGAAGATCAGATTCAGGTTGGAATAC
Found at i:16907 original size:41 final size:41
Alignment explanation
Indices: 16854--17038 Score: 221
Period size: 41 Copynumber: 4.5 Consensus size: 41
16844 GTTGGAATAC
* *
16854 TTCACTATTCTTCCGTGAAGGTTGATTTAAGAAGAATCTGT
1 TTCACTACTCTTCCGTGAAGGTTGATTTAAGAAGAACCTGT
* * * ** **
16895 TTCACTACTCTTCCGTGAAGATCAGATTCAAGGTTGGAA--TAC
1 TTCACTACTCTTCCGTGAAGGT-TGATTTAA-G-AAGAACCTGT
* *
16937 TTCATTACTCTTCCGTGAAGGTTGATTTAAGAAGAACCTAT
1 TTCACTACTCTTCCGTGAAGGTTGATTTAAGAAGAACCTGT
16978 TTCACTACTCTTCCGTGAAGGTTGATTTAAGAAGAACCTGT
1 TTCACTACTCTTCCGTGAAGGTTGATTTAAGAAGAACCTGT
*
17019 TTCACTACTCTTTCGTGAAG
1 TTCACTACTCTTCCGTGAAG
17039 ATCACATTTA
Statistics
Matches: 121, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
39 3 0.02
40 1 0.01
41 86 0.71
42 27 0.22
43 1 0.01
44 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (41 bp):
TTCACTACTCTTCCGTGAAGGTTGATTTAAGAAGAACCTGT
Found at i:16912 original size:83 final size:83
Alignment explanation
Indices: 16793--16997 Score: 338
Period size: 83 Copynumber: 2.5 Consensus size: 83
16783 AGGCTAATAA
* * *
16793 TGATTTGAGAAGAATCTGTTTCACTACTCTTTCGTGAAGATCAGACTCATGGTTGGAATACTTCA
1 TGATTTAAGAAGAATCTGTTTCACTACTCTTCCGTGAAGATCAGACTCAAGGTTGGAATACTTCA
*
16858 CTATTCTTCCGTGAAGGT
66 CTACTCTTCCGTGAAGGT
*
16876 TGATTTAAGAAGAATCTGTTTCACTACTCTTCCGTGAAGATCAGATTCAAGGTTGGAATACTTCA
1 TGATTTAAGAAGAATCTGTTTCACTACTCTTCCGTGAAGATCAGACTCAAGGTTGGAATACTTCA
*
16941 TTACTCTTCCGTGAAGGT
66 CTACTCTTCCGTGAAGGT
* *
16959 TGATTTAAGAAGAACCTATTTCACTACTCTTCCGTGAAG
1 TGATTTAAGAAGAATCTGTTTCACTACTCTTCCGTGAAG
16998 GTTGATTTAA
Statistics
Matches: 114, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 114 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (83 bp):
TGATTTAAGAAGAATCTGTTTCACTACTCTTCCGTGAAGATCAGACTCAAGGTTGGAATACTTCA
CTACTCTTCCGTGAAGGT
Found at i:17157 original size:20 final size:20
Alignment explanation
Indices: 17132--17253 Score: 154
Period size: 20 Copynumber: 6.1 Consensus size: 20
17122 AGACTGACAG
*
17132 ATGACCCAAAGGATTTACAA
1 ATGACCCGAAGGATTTACAA
* * * *
17152 ATGACCAGGATGATTTACCA
1 ATGACCCGAAGGATTTACAA
*
17172 ATGACCCGGAGGATTTACAA
1 ATGACCCGAAGGATTTACAA
*
17192 ATGACCCGAATGATTTACAA
1 ATGACCCGAAGGATTTACAA
*
17212 ATGACCTGAAGGATTTACAA
1 ATGACCCGAAGGATTTACAA
* *
17232 ATGACCCGAAGGTTTTATAA
1 ATGACCCGAAGGATTTACAA
17252 AT
1 AT
17254 TCGTGGAAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (20 bp):
ATGACCCGAAGGATTTACAA
Found at i:23064 original size:18 final size:18
Alignment explanation
Indices: 23036--23085 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
23026 AAATATTAAA
* *
23036 ACTATATATATTAAATTAT
1 ACTA-ATATATAAAAGTAT
*
23055 CCTAATATATAAAAGTAT
1 ACTAATATATAAAAGTAT
23073 ACTAATATTATAA
1 ACTAATA-TATAA
23086 TTAATCTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 18 0.69
19 8 0.31
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (18 bp):
ACTAATATATAAAAGTAT
Found at i:32402 original size:45 final size:45
Alignment explanation
Indices: 32341--32522 Score: 199
Period size: 43 Copynumber: 3.9 Consensus size: 45
32331 ATATATGTAA
*
32341 TATATAGTTTTAAAAACATATACGTATAATTTTGAAAAACATATATG
1 TATATAGTTTTGAAAACATATA--TATAATTTTGAAAAACATATATG
*
32388 TATA-A-TTTTGAAAACATATATATAGTTTTGAAAAACATATATG
1 TATATAGTTTTGAAAACATATATATAATTTTGAAAAACATATATG
* * *
32431 ATATATAGTTTTGAAAAATATATATAATATAGTTTTGAATACATATATAATG
1 -TATATAGTTTTG-AAAACATATAT-ATA-A-TTTTGAA-AAACATAT-ATG
* *
32483 TATATAGTTTTGAAAATATATATATAGTTTTG-AAAACATA
1 TATATAGTTTTGAAAACATATATATAATTTTGAAAAACATA
32523 GTTTTAAAAA
Statistics
Matches: 117, Mismatches: 9, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
43 22 0.19
44 4 0.03
45 20 0.17
46 7 0.06
47 19 0.16
48 3 0.03
49 3 0.03
50 18 0.15
51 18 0.15
52 3 0.03
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (45 bp):
TATATAGTTTTGAAAACATATATATAATTTTGAAAAACATATATG
Found at i:32480 original size:23 final size:22
Alignment explanation
Indices: 32312--32522 Score: 169
Period size: 23 Copynumber: 9.1 Consensus size: 22
32302 ATTATAATAG
* *
32312 TATATATACAGTTTTGAAAATA
1 TATATATATAGTTTTGAAAACA
*
32334 TATGTAATATATAGTTTTAAAAACA
1 TA--T-ATATATAGTTTTGAAAACA
** *
32359 TATACGTATAATTTTGAAAAACA
1 TATATATATAGTTTTG-AAAACA
* *
32382 TATATGTATAATTTTGAAAAC-
1 TATATATATAGTTTTGAAAACA
32403 -ATATATATAGTTTTGAAAAACATA
1 TATATATATAGTTTTG-AAAAC--A
*
32427 TATGATATATAGTTTTGAAAAATA
1 TAT-ATATATAGTTTTG-AAAACA
*
32451 TATATAATATAGTTTTGAATACATA
1 TATAT-ATATAGTTTTGAA-A-ACA
32476 TATAATGTATATAGTTTTG-AAA-A
1 TAT-A--TATATAGTTTTGAAAACA
32499 TATATATATAGTTTTGAAAACA
1 TATATATATAGTTTTGAAAACA
32521 TA
1 TA
32523 GTTTTAAAAA
Statistics
Matches: 160, Mismatches: 11, Indels: 36
0.77 0.05 0.17
Matches are distributed among these distances:
20 25 0.16
21 8 0.05
22 20 0.12
23 30 0.19
24 18 0.11
25 27 0.17
26 20 0.12
27 11 0.07
28 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (22 bp):
TATATATATAGTTTTGAAAACA
Found at i:32524 original size:61 final size:61
Alignment explanation
Indices: 32459--32574 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
32449 TATATATAAT
* * * *
32459 ATAGTTTTGAATACATATATAATGTA-TATAGTTTTGAAAATATATATATAGTTTTGAAAAC
1 ATAGTTTTAAAAACATATATAATATACTATAGGTTTGAAAA-ATATATATAGTTTTGAAAAC
*
32520 ATAGTTTTAAAAACATATATAATATACTATAGGTTTGTAAAATATATATAGTTTT
1 ATAGTTTTAAAAACATATATAATATACTATAGGTTTGAAAAATATATATAGTTTT
32575 TTAAAAATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
61 37 0.76
62 12 0.24
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.43
Consensus pattern (61 bp):
ATAGTTTTAAAAACATATATAATATACTATAGGTTTGAAAAATATATATAGTTTTGAAAAC
Found at i:32525 original size:14 final size:14
Alignment explanation
Indices: 32506--32536 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
32496 AAATATATAT
*
32506 ATAGTTTTGAAAAC
1 ATAGTTTTAAAAAC
32520 ATAGTTTTAAAAAC
1 ATAGTTTTAAAAAC
32534 ATA
1 ATA
32537 TATAATATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (14 bp):
ATAGTTTTAAAAAC
Found at i:32579 original size:19 final size:19
Alignment explanation
Indices: 32540--32584 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
32530 AAACATATAT
32540 AATATACTATAGGTTTGTAA
1 AATATA-TATAGGTTTGTAA
* *
32560 AATATATATAGTTTTTTAA
1 AATATATATAGGTTTGTAA
32579 AA-ATAT
1 AATATAT
32585 CTTATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 13 0.57
20 6 0.26
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (19 bp):
AATATATATAGGTTTGTAA
Found at i:34066 original size:111 final size:113
Alignment explanation
Indices: 33856--34067 Score: 302
Period size: 113 Copynumber: 1.9 Consensus size: 113
33846 CCTATATGAG
* * * * * * *
33856 AGCTTGTTCAACCTCAACATGGTCTTTATGGGATAATATAGAACTTATATAGGAGAGTTTGTCTA
1 AGCTTATTCAACCTCAACATGGCCTTTAAGGGAGAATAGAGAACTTATATAGGAGAGTCTGCCTA
33921 CTCATTCCATATAGGAGGAAGCAATCAAGGAAGAAGTTAATATAGGAA
66 CTCATTCCATATAGGAGGAAGCAATCAAGGAAGAAGTTAATATAGGAA
* * *
33969 AGCTTATTCGACCTCAACATGGCCTTTAAGGGAGAATAGGGAGCTTATATAGGAGAG-CT-CCTA
1 AGCTTATTCAACCTCAACATGGCCTTTAAGGGAGAATAGAGAACTTATATAGGAGAGTCTGCCTA
* *
34032 CTCGTTCCATATAGGAGGAAGCGATCAAGGAAGAAG
66 CTCATTCCATATAGGAGGAAGCAATCAAGGAAGAAG
34068 AAGTTCATAT
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
111 37 0.43
112 1 0.01
113 49 0.56
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (113 bp):
AGCTTATTCAACCTCAACATGGCCTTTAAGGGAGAATAGAGAACTTATATAGGAGAGTCTGCCTA
CTCATTCCATATAGGAGGAAGCAATCAAGGAAGAAGTTAATATAGGAA
Found at i:34397 original size:15 final size:16
Alignment explanation
Indices: 34377--34419 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
34367 TAGAAAATTG
*
34377 AGAAAAAATGGA-AAA
1 AGAAAAAATAGACAAA
34392 AGAAAAAGA-AGACAAA
1 AGAAAAA-ATAGACAAA
34408 AGAAAAAATAGA
1 AGAAAAAATAGA
34420 GAGAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (16 bp):
AGAAAAAATAGACAAA
Found at i:36995 original size:104 final size:104
Alignment explanation
Indices: 36921--37138 Score: 361
Period size: 104 Copynumber: 2.1 Consensus size: 104
36911 CTTTTTTTTA
36921 TTTACATCC-TTTAATTTCCAGCATTTCAATTCTAGTCCATTAATTTTCAATATTTAATTTTTCT
1 TTTA-ATCCTTTTAATTTCCAGCATTTCAATTCTAGTCCATTAATTTTCAATATTTAATTTTTCT
*
36985 ACATTTTTT-AATTTTTCCTTACTTTCTTCTTTCTTTCAT
65 ACATTTTTTAAATTATTCCTTACTTTCTTCTTTCTTTCAT
*
37024 TTTAGTCCTTTTTAATTTCCAGCATTTCAATTCTAGTCCATTAATTTTCAATATTTAATTTTTCT
1 TTTAATCC-TTTTAATTTCCAGCATTTCAATTCTAGTCCATTAATTTTCAATATTTAATTTTTCT
*
37089 ACATTTTTT-AATTTTTCCTTACTTTCTTCTTTCTTTCAT
65 ACATTTTTTAAATTATTCCTTACTTTCTTCTTTCTTTCAT
*
37128 TTTAGTCCTTT
1 TTTAATCCTTT
37139 ATTTGATGCA
Statistics
Matches: 112, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
102 3 0.03
103 7 0.06
104 102 0.91
ACGTcount: A:0.21, C:0.19, G:0.03, T:0.57
Consensus pattern (104 bp):
TTTAATCCTTTTAATTTCCAGCATTTCAATTCTAGTCCATTAATTTTCAATATTTAATTTTTCTA
CATTTTTTAAATTATTCCTTACTTTCTTCTTTCTTTCAT
Found at i:43173 original size:19 final size:19
Alignment explanation
Indices: 43149--43185 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
43139 TTAAAAATTA
43149 TGCATTGTTTTTTCTGCAT
1 TGCATTGTTTTTTCTGCAT
* *
43168 TGCATTTTTTTTTTTGCA
1 TGCATTGTTTTTTCTGCA
43186 CTATTTAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.14, G:0.14, T:0.62
Consensus pattern (19 bp):
TGCATTGTTTTTTCTGCAT
Found at i:45873 original size:31 final size:30
Alignment explanation
Indices: 45800--45885 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 30
45790 CCATGAATGG
* * * *
45800 ATTTGGAAAAGTTAAGTGACCAAAATGTAA
1 ATTTGGAAAAGTTTAGTGACTAAAGTATAA
* *
45830 ATTT-TAAAAGTTTAGTGGCTAAAGTATAA
1 ATTTGGAAAAGTTTAGTGACTAAAGTATAA
*
45859 ACTTTGGAAAAGTTTAGAGACTAAAGT
1 A-TTTGGAAAAGTTTAGTGACTAAAGT
45886 GTAATCTTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 20 0.44
30 7 0.16
31 18 0.40
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (30 bp):
ATTTGGAAAAGTTTAGTGACTAAAGTATAA
Found at i:46835 original size:11 final size:11
Alignment explanation
Indices: 46819--46852 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
46809 TTCATGCTTG
46819 AATCGAATCAA
1 AATCGAATCAA
*
46830 AATCG-AGCAA
1 AATCGAATCAA
46840 AATCGAATCAA
1 AATCGAATCAA
46851 AA
1 AA
46853 GGATGAGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.15
Consensus pattern (11 bp):
AATCGAATCAA
Found at i:49073 original size:16 final size:15
Alignment explanation
Indices: 49047--49077 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
49037 CTGAAATTTC
49047 TTAAAATAATTAATA
1 TTAAAATAATTAATA
49062 TTAAATATAATTAATA
1 TTAAA-ATAATTAATA
49078 GTATGAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAAATAATTAATA
Found at i:56924 original size:2 final size:2
Alignment explanation
Indices: 56912--56955 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
56902 TTAAAGTTAC
56912 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56955 A
1 A
56956 CTAAAATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:58774 original size:24 final size:24
Alignment explanation
Indices: 58747--58819 Score: 58
Period size: 24 Copynumber: 3.0 Consensus size: 24
58737 CGTTCATTTA
58747 CGTTC-GTGAACGTTCGGTTATGTT
1 CGTTCGGT-AACGTTCGGTTATGTT
* * * *
58771 CGTTTGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
* * * *
58795 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGGTTATGTT
58819 C
1 C
58820 ATTCATTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 40 0.95
25 2 0.05
ACGTcount: A:0.11, C:0.14, G:0.25, T:0.51
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGGTTATGTT
Found at i:58779 original size:14 final size:14
Alignment explanation
Indices: 58757--58813 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
58747 CGTTCGTGAA
*
58757 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
58771 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
58785 CG--T--TTATGTT
1 CGTTTGGTTATGTT
* *
58795 CGTTCGATTATGTT
1 CGTTTGGTTATGTT
58809 CGTTT
1 CGTTT
58814 ATGTTCATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 9 0.25
12 1 0.03
14 26 0.72
ACGTcount: A:0.09, C:0.12, G:0.25, T:0.54
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:58829 original size:24 final size:24
Alignment explanation
Indices: 58758--58832 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
58748 GTTCGTGAAC
* * * *
58758 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCATTCGATTAT
*
58782 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCATTCGATTAT
58806 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCATTCGA-TTAT
58830 GTT
1 GTT
58833 TAACCCAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.02
24 45 0.98
ACGTcount: A:0.12, C:0.11, G:0.21, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCATTCGATTAT
Found at i:59569 original size:16 final size:16
Alignment explanation
Indices: 59544--59616 Score: 105
Period size: 16 Copynumber: 4.7 Consensus size: 16
59534 CCAACGTTTA
* *
59544 TGTTCGTTTATTTTCG
1 TGTTCATTTATGTTCG
59560 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
59576 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
59592 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
59608 T-TT-ATTTAT
1 TGTTCATTTAT
59617 TAAATGACGA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
14 5 0.09
15 2 0.04
16 46 0.87
ACGTcount: A:0.11, C:0.11, G:0.18, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:59978 original size:39 final size:39
Alignment explanation
Indices: 59911--60049 Score: 163
Period size: 39 Copynumber: 3.6 Consensus size: 39
59901 ATATAGCATA
* *
59911 AGGA-CCTGCGGTAAGGACTTACCCTGAGCACAAGGCAG
1 AGGAGCCTGCGGTAAGGACTTACCTTGAGCACAAAGCAG
* * *
59949 AGGAGCCTACGGTAAGAACTTACTTTGAGCACAAAGCAG
1 AGGAGCCTGCGGTAAGGACTTACCTTGAGCACAAAGCAG
** ** *
59988 AGGAGTTTGCGACAAGGACTTACCTTGAGCACAAAGCAA
1 AGGAGCCTGCGGTAAGGACTTACCTTGAGCACAAAGCAG
* *
60027 AGGAGCTTGCGGTAAGGTCTTAC
1 AGGAGCCTGCGGTAAGGACTTAC
60050 AAGTCATAGA
Statistics
Matches: 83, Mismatches: 17, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
38 4 0.05
39 79 0.95
ACGTcount: A:0.32, C:0.22, G:0.29, T:0.18
Consensus pattern (39 bp):
AGGAGCCTGCGGTAAGGACTTACCTTGAGCACAAAGCAG
Found at i:60873 original size:28 final size:23
Alignment explanation
Indices: 60814--60871 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
60804 CCGGTTTGGT
*
60814 TCGGGTCAGGTCAGGTAGACGGG
1 TCGGGTCGGGTCAGGTAGACGGG
60837 TCGGGTCGGGTCAGGTAGACGGG
1 TCGGGTCGGGTCAGGTAGACGGG
*
60860 TCGGATCGGGTC
1 TCGGGTCGGGTC
60872 GGCCCAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.14, C:0.19, G:0.48, T:0.19
Consensus pattern (23 bp):
TCGGGTCGGGTCAGGTAGACGGG
Found at i:61502 original size:161 final size:163
Alignment explanation
Indices: 61235--61558 Score: 634
Period size: 161 Copynumber: 2.0 Consensus size: 163
61225 GAAAAAATAG
61235 GGTTAAAACTTTTCGGAAATATAAAGTTTTTTTAAATTTTTGGGGGTTTTAAAACCATACTTATG
1 GGTTAAAACTTTTCGGAAATATAAAGTTTTTTTAAATTTTTGGGGGTTTTAAAACCATACTTATG
61300 AAAAATGGTATAAGTACACTATAGGTCATCCGATTTTAATACTTTTCAAATTTAGATCTGAATTT
66 AAAAATGGTATAAGTACACTATAGGTCATCCGATTTTAATACTTTTCAAATTTAGATCTGAATTT
61365 AATCAAAATTTCTCTTTTGTCCTCAAATTTAAT
131 AATCAAAATTTCTCTTTTGTCCTCAAATTTAAT
61398 GGTTAAAACTTTTCGGAAATATAAAGTTTTTTTAAA-TTTT-GGGGTTTTAAAACCATACTTATG
1 GGTTAAAACTTTTCGGAAATATAAAGTTTTTTTAAATTTTTGGGGGTTTTAAAACCATACTTATG
61461 AAAAATGGTATAAGTACACTATAGGTCATCCGATTTTAATACTTTTCAAATTTAGATCTGAATTT
66 AAAAATGGTATAAGTACACTATAGGTCATCCGATTTTAATACTTTTCAAATTTAGATCTGAATTT
61526 AATCAAAATTTCTCTTTTGTCCTCAAATTTAAT
131 AATCAAAATTTCTCTTTTGTCCTCAAATTTAAT
61559 TAAAATTTCA
Statistics
Matches: 161, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
161 121 0.75
162 4 0.02
163 36 0.22
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (163 bp):
GGTTAAAACTTTTCGGAAATATAAAGTTTTTTTAAATTTTTGGGGGTTTTAAAACCATACTTATG
AAAAATGGTATAAGTACACTATAGGTCATCCGATTTTAATACTTTTCAAATTTAGATCTGAATTT
AATCAAAATTTCTCTTTTGTCCTCAAATTTAAT
Found at i:79742 original size:21 final size:21
Alignment explanation
Indices: 79711--79750 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
79701 TAAATTAAGG
79711 TTTTTATAAATAAATTTTTATT
1 TTTTTATAAAT-AATTTTTATT
79733 TTTTTA-AAATAATTTTTA
1 TTTTTATAAATAATTTTTA
79751 AAATTACTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTATAAATAATTTTTATT
Found at i:79944 original size:2 final size:2
Alignment explanation
Indices: 79937--79971 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
79927 TTAATATGTA
79937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
79972 ATTATTCCTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:80395 original size:2 final size:2
Alignment explanation
Indices: 80388--80420 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
80378 TTAATGTGTA
80388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
80421 ATTATTCCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:80635 original size:449 final size:451
Alignment explanation
Indices: 79750--80654 Score: 1616
Period size: 449 Copynumber: 2.0 Consensus size: 451
79740 AATAATTTTT
*
79750 AAAATTACTAGAATATGACACGTATCATTTAATGAAATTTACGTTCTGGACATCTAAAATGATAA
1 AAAATTACTAGAATATGACACGTATCATTTAATGAAATTTACGTTCTGGACATCTAAAATCATAA
79815 CGTTTGTAACATCATACATTTGTTTTTAACAAAAAATTCTTTAAACACATAATGTTAATTTTAAG
66 CGTTTGTAACATCATACATTTGTTTTTAACAAAAAATTCTTTAAACACATAATGTTAATTTTAAG
79880 TAAACTTTGAGCCTATGTATTTTTGTCAAAATTTATTTAAAAATAAATTAATATGTAATATATAT
131 TAAACTTTGAGCCTATGTATTTTTGTCAAAATTTATTTAAAAATAAATTAATATGTAATATATAT
79945 ATATATATATATATATATATATATATAATTATTCCTGATCAAAACAAACAGTTCTTAAAATCAAT
196 ATATATATATATATATATATATATATAATTATTCCTGATCAAAACAAACAGTTCTTAAAATCAAT
*
80010 TATGATTTAACCTAAATTTTATTTTATTTTTATCTAACCTAATTTAACCAGTGTTTTAAAAATCG
261 TATGATTTAACCTAAATTTTATTTTATTTTTATCTAACCTAATTTAACCAGTGTTTTAAAAATCA
*
80075 GACTGGACCGGCCGGTTCAACCGGGAACCGTTGCCTAGTCCGATTCAATCTACACCGGTTGAACC
326 GACAGGACCGGCCGGTTCAACCGGGAACCGTTGCCTAGTCCGATTCAATCTACACCGGTTGAACC
* * *
80140 GCTACTAGTAAACCGAACGGAACCGCTGAACCGTTCGAATCGAACCGACTGAAAACCGGAA
391 GCTACTAGTAAACCGAACGGAACCGCTGAACCGTCCGAACCGAACCGACTGAAAACCGAAA
*
80201 AAAATTACTAGAATATGACATGTATCATTTAATGAAATTTACGTTCTGGACATCTAAAATCATAA
1 AAAATTACTAGAATATGACACGTATCATTTAATGAAATTTACGTTCTGGACATCTAAAATCATAA
* *
80266 CGTTTGTAACATCATACATTTGTTTTTAACAAAAAATTCTTTAGACACCTAATGTTAATTTTAAG
66 CGTTTGTAACATCATACATTTGTTTTTAACAAAAAATTCTTTAAACACATAATGTTAATTTTAAG
* *
80331 TATACTTTGAGCCTATGTATTTTTGTCAAAATTTATTTAAAAATAAATTAATGTGT-A-ATATAT
131 TAAACTTTGAGCCTATGTATTTTTGTCAAAATTTATTTAAAAATAAATTAATATGTAATATATAT
*
80394 ATATATATATATATATATATATATATAATTATTCCTGATCAAAACAAGCAGTTCTTAAAATCAAT
196 ATATATATATATATATATATATATATAATTATTCCTGATCAAAACAAACAGTTCTTAAAATCAAT
*
80459 TATGATTTAACCTAAATTTTATTTTATTTTTATCTAACCTAATTTAACCAGTGTTTTGAAAATCA
261 TATGATTTAACCTAAATTTTATTTTATTTTTATCTAACCTAATTTAACCAGTGTTTTAAAAATCA
*
80524 GACAGGACCGGCCGGTTCAACCGGGAACCGTTGTCTAGTCCGATTCAATCTACACCGGTTGAACC
326 GACAGGACCGGCCGGTTCAACCGGGAACCGTTGCCTAGTCCGATTCAATCTACACCGGTTGAACC
* ** * **
80589 GCTACTAGTGAACCGGCCGGAACCGCTTAACCGTCCGAACCGAACCGGTTGAAAACCGAAA
391 GCTACTAGTAAACCGAACGGAACCGCTGAACCGTCCGAACCGAACCGACTGAAAACCGAAA
80650 AAAAT
1 AAAAT
80655 CGGAAAAAAC
Statistics
Matches: 434, Mismatches: 20, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
449 253 0.58
450 1 0.00
451 180 0.41
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (451 bp):
AAAATTACTAGAATATGACACGTATCATTTAATGAAATTTACGTTCTGGACATCTAAAATCATAA
CGTTTGTAACATCATACATTTGTTTTTAACAAAAAATTCTTTAAACACATAATGTTAATTTTAAG
TAAACTTTGAGCCTATGTATTTTTGTCAAAATTTATTTAAAAATAAATTAATATGTAATATATAT
ATATATATATATATATATATATATATAATTATTCCTGATCAAAACAAACAGTTCTTAAAATCAAT
TATGATTTAACCTAAATTTTATTTTATTTTTATCTAACCTAATTTAACCAGTGTTTTAAAAATCA
GACAGGACCGGCCGGTTCAACCGGGAACCGTTGCCTAGTCCGATTCAATCTACACCGGTTGAACC
GCTACTAGTAAACCGAACGGAACCGCTGAACCGTCCGAACCGAACCGACTGAAAACCGAAA
Found at i:82262 original size:19 final size:19
Alignment explanation
Indices: 82208--82262 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 19
82198 AATTAAATTA
*
82208 TTAATAATAT-TAATATAT
1 TTAAAAATATATAATATAT
* * *
82226 ATATATATATA-AAT-TAT
1 TTAAAAATATATAATATAT
82243 TTAAAAATATATAATATAT
1 TTAAAAATATATAATATAT
82262 T
1 T
82263 ATTTTTATAT
Statistics
Matches: 27, Mismatches: 7, Indels: 5
0.69 0.18 0.13
Matches are distributed among these distances:
17 11 0.41
18 12 0.44
19 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAAAATATATAATATAT
Found at i:82272 original size:39 final size:36
Alignment explanation
Indices: 82183--82273 Score: 98
Period size: 35 Copynumber: 2.5 Consensus size: 36
82173 AATATATGAA
* *
82183 AATATTATATTTTTAAAT-TAAATTATTAATAATATT
1 AATA-TATATTTTTATATATAAATTATTAAAAATATT
*
82219 AATATATA--TATATATATAAATTATTTAAAAATATAT
1 AATATATATTTTTATATATAAATTA-TTAAAAATAT-T
82255 AATATATTATTTTTATATA
1 AATATA-TATTTTTATATA
82274 CTTAAGGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
33 5 0.11
34 7 0.16
35 13 0.29
36 11 0.24
37 2 0.04
39 7 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
AATATATATTTTTATATATAAATTATTAAAAATATT
Found at i:82983 original size:37 final size:37
Alignment explanation
Indices: 82910--82984 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
82900 GTTGGAAAAT
*
82910 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTTAAAATCATAAA
* *
82947 ATTTATATAATTTT-TTTTACAAATTTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTT-AAAATCATAAA
82984 A
1 A
82985 AGATTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTTAAAATCATAAA
Found at i:85602 original size:24 final size:24
Alignment explanation
Indices: 85570--85631 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
85560 ATCGTGCCGC
* *
85570 AAGAGCAGAGAAAATTATTGTCAT
1 AAGAGCAGAGAAAATGATTGCCAT
85594 AAGAGCAGAGAAAATGATTGCCAT
1 AAGAGCAGAGAAAATGATTGCCAT
85618 AAGAGCAGAGAAAA
1 AAGAGCAGAGAAAA
85632 AGCGTTACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.50, C:0.10, G:0.24, T:0.16
Consensus pattern (24 bp):
AAGAGCAGAGAAAATGATTGCCAT
Found at i:86966 original size:64 final size:64
Alignment explanation
Indices: 86887--87015 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
86877 TTCATTGAAC
*
86887 TTTACAAGCATAATAGTGTATCAATAATCTAATGTATACATCATGAATCTTATAAACATAATCA
1 TTTACAAGCATAATAGTGTATCAATAATATAATGTATACATCATGAATCTTATAAACATAATCA
* *
86951 TTTACAAGCATAATAGTGTATCAATAATATATTGTATACATCATGAATCTTATAAACGTAATCA
1 TTTACAAGCATAATAGTGTATCAATAATATAATGTATACATCATGAATCTTATAAACATAATCA
87015 T
1 T
87016 GGTAGTAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.36
Consensus pattern (64 bp):
TTTACAAGCATAATAGTGTATCAATAATATAATGTATACATCATGAATCTTATAAACATAATCA
Found at i:87040 original size:64 final size:64
Alignment explanation
Indices: 86889--87041 Score: 157
Period size: 64 Copynumber: 2.4 Consensus size: 64
86879 CATTGAACTT
* * * * * *
86889 TACAAGCATAATAGTGTATCAATAATCTAATGTATACATCATGAATCTTATAAACATAATCATT
1 TACAAGAATAATAATGAAACAATAATATAATGTATACATCATGAATCTTATAAACATAATCATG
* * * * * *
86953 TACAAGCATAATAGTGTATCAATAATATATTGTATACATCATGAATCTTATAAACGTAATCATGG
1 TACAAGAATAATAATGAAACAATAATATAATGTATACATCATGAATCTTATAAACATAATCAT-G
*
87018 TAGTAA-AATAATAAT-AAACAATAA
1 TA-CAAGAATAATAATGAAACAATAA
87042 GTACATGCAT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
64 67 0.86
65 9 0.12
66 2 0.03
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (64 bp):
TACAAGAATAATAATGAAACAATAATATAATGTATACATCATGAATCTTATAAACATAATCATG
Found at i:88472 original size:35 final size:35
Alignment explanation
Indices: 88426--88564 Score: 170
Period size: 35 Copynumber: 3.9 Consensus size: 35
88416 AGATGAACAA
** * *
88426 TTGAATCGAAAGTGCTTATGCTTCATCCCGTTCAC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
* *
88461 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC-AC
* * * *
88497 TTGAGTTGAAAGTGTCGATGCTTCCTTCCGTTCAG
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
*
88532 TTGAATCGAAAGTGCCGATGCTTCCTTTCGTTC
1 TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
88565 TTCTTATTCA
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
35 57 0.66
36 30 0.34
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.37
Consensus pattern (35 bp):
TTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC
Found at i:88743 original size:15 final size:15
Alignment explanation
Indices: 88723--88752 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
88713 GTAATAAGGT
88723 GGTAACAAGGGGTCA
1 GGTAACAAGGGGTCA
88738 GGTAACAAGGGGTCA
1 GGTAACAAGGGGTCA
88753 TACGTACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.40, T:0.13
Consensus pattern (15 bp):
GGTAACAAGGGGTCA
Found at i:89231 original size:229 final size:230
Alignment explanation
Indices: 88829--89287 Score: 911
Period size: 229 Copynumber: 2.0 Consensus size: 230
88819 CGAATTAACG
88829 AGTACCTCATGGCCTCGAGGGTCAAATTCTCGCTCACATCCACCCTTTGCTTTGTTACCGTTTCA
1 AGTACCTCATGGCCTCGAGGGTCAAATTCTCGCTCACATCCACCCTTTGCTTTGTTACCGTTTCA
88894 ATAGAGTTGGAGGGAGCATGAACATATTGGATTGCTTTCTTGGACAATCTTGCAGGGCATCAGAG
66 ATAGAGTTGGAGGGAGCATGAACATATTGGATTGCTTTCTTGGACAATCTTGCAGGGCATCAGAG
88959 CTTAAAGATGGGGAATTCTCTGGTTGGTGAAGTTAAAGCAACACTAGCGGGTCTTGAAAACTTGG
131 CTTAAAGATGGGGAATTCTCTGGTTGGTGAAGTTAAAGCAACACTAGCGGGTCTTGAAAACTTGG
89024 TTTCTCCAGGAACAACAAACGAAGGTGGAGAAGAA
196 TTTCTCCAGGAACAACAAACGAAGGTGGAGAAGAA
89059 AGTACCTCATGGCCTCGAGGGTCAAATTCTCGCTCACATCCACCCTTTGCTTTGTTACCGTTTCA
1 AGTACCTCATGGCCTCGAGGGTCAAATTCTCGCTCACATCCACCCTTTGCTTTGTTACCGTTTCA
89124 ATAGAGTTGG-GGGAGCATGAACATATTGGATTGCTTTCTTGGACAATCTTGCAGGGCATCAGAG
66 ATAGAGTTGGAGGGAGCATGAACATATTGGATTGCTTTCTTGGACAATCTTGCAGGGCATCAGAG
89188 CTTAAAGATGGGGAATTCTCTGGTTGGTGAAGTTAAAGCAACACTAGCGGGTCTTGAAAACTTGG
131 CTTAAAGATGGGGAATTCTCTGGTTGGTGAAGTTAAAGCAACACTAGCGGGTCTTGAAAACTTGG
89253 TTTCTCCAGGAACAACAAACGAAGGTGGAGAAGAA
196 TTTCTCCAGGAACAACAAACGAAGGTGGAGAAGAA
89288 GCACTCAACA
Statistics
Matches: 229, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
229 154 0.67
230 75 0.33
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (230 bp):
AGTACCTCATGGCCTCGAGGGTCAAATTCTCGCTCACATCCACCCTTTGCTTTGTTACCGTTTCA
ATAGAGTTGGAGGGAGCATGAACATATTGGATTGCTTTCTTGGACAATCTTGCAGGGCATCAGAG
CTTAAAGATGGGGAATTCTCTGGTTGGTGAAGTTAAAGCAACACTAGCGGGTCTTGAAAACTTGG
TTTCTCCAGGAACAACAAACGAAGGTGGAGAAGAA
Found at i:91625 original size:2 final size:2
Alignment explanation
Indices: 91618--91644 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
91608 TACATTTTTC
91618 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
91645 TCCTAGTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:96120 original size:31 final size:31
Alignment explanation
Indices: 96082--96142 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
96072 CAAACGGTCA
96082 GGGACCATAATGCAAATAGACTAAATGTTGG
1 GGGACCATAATGCAAATAGACTAAATGTTGG
*
96113 GGGACCATATTGCAAATAGACTAAATGTTG
1 GGGACCATAATGCAAATAGACTAAATGTTG
96143 AGAGACTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (31 bp):
GGGACCATAATGCAAATAGACTAAATGTTGG
Found at i:96155 original size:31 final size:31
Alignment explanation
Indices: 96084--96157 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
96074 AACGGTCAGG
* * *
96084 GACCATAATGCAAATAGACTAAATGTTGGGG
1 GACCATATTGCAAATAGACTAAATGTTGAGA
96115 GACCATATTGCAAATAGACTAAATGTTGAGA
1 GACCATATTGCAAATAGACTAAATGTTGAGA
**
96146 GACTGTATTGCA
1 GACCATATTGCA
96158 TGTTTTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.26
Consensus pattern (31 bp):
GACCATATTGCAAATAGACTAAATGTTGAGA
Found at i:103947 original size:66 final size:67
Alignment explanation
Indices: 103866--104001 Score: 229
Period size: 67 Copynumber: 2.0 Consensus size: 67
103856 AAAATACATA
* * * *
103866 CATCATTCTTATTAATTTAATAATA-TTTTTATAAAGTAATCTTATAATAATTTGCATTTGGCAA
1 CATCATTCTTATTAATATAATAATATTTTTTATAAAGCAATCTTAGAATAATTTACATTTGGCAA
103930 CT
66 CT
103932 CATCATTCTTATTAATATAATAATATTTTTTATAAAGCAATCTTAGAATAATTTACATTTGGCAA
1 CATCATTCTTATTAATATAATAATATTTTTTATAAAGCAATCTTAGAATAATTTACATTTGGCAA
103997 CT
66 CT
103999 CAT
1 CAT
104002 TTTCTCTGGC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 24 0.37
67 41 0.63
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.45
Consensus pattern (67 bp):
CATCATTCTTATTAATATAATAATATTTTTTATAAAGCAATCTTAGAATAATTTACATTTGGCAA
CT
Found at i:106662 original size:39 final size:39
Alignment explanation
Indices: 106556--106675 Score: 120
Period size: 39 Copynumber: 3.1 Consensus size: 39
106546 GTTTAAAAAC
* *
106556 AATTTAGAATGTTTAATGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAATG-ATAAGGTGAAATAATTTAAGAAATTAAG
* * *
106596 AATTTAGAATGATATGGTGGTAA-AATTTAAGAAATTAGG
1 AATTTAGAATGATAAGGT-GAAATAATTTAAGAAATTAAG
* * *
106635 AATTTTGAAT-ATAAGAGTGAAATAATTTGAG-AATTATG
1 AATTTAGAATGATAAG-GTGAAATAATTTAAGAAATTAAG
106673 AAT
1 AAT
106676 ATAAATTTAA
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
38 16 0.24
39 37 0.55
40 14 0.21
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (39 bp):
AATTTAGAATGATAAGGTGAAATAATTTAAGAAATTAAG
Found at i:110630 original size:53 final size:53
Alignment explanation
Indices: 110549--110993 Score: 658
Period size: 53 Copynumber: 8.4 Consensus size: 53
110539 CTTTCAAAAA
* * *
110549 TATGTATGCATCCATGATATTCAAAATGAGTTTGTGAATTACCATTTCGACAC
1 TATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGACAC
** *
110602 TATGTGTGCATCCATGGTATTCATAATGAACTTGTGAATTATCATTTCGACAC
1 TATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGACAC
110655 TATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGACAC
1 TATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGACAC
*
110708 TATGTGTGAATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGACAC
1 TATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGACAC
* * *
110761 TATGTGTGCATCCATGGTATTCACACTGAGTTTGTGAATTACCATTTC-AGCAT
1 TATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGA-CAC
* * * *
110814 TATGTGTGCATCCATGGTATTCATAATGAGTTTGTAAATTACCATTTTGGCAG
1 TATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGACAC
* * * *
110867 TATATGTACATCCATGGTATTCGTAATGAGTTTGTGAATTACCATTTCAACAC
1 TATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGACAC
* * * *
110920 TATGTGTGCATCCATGGTATTCATAATAAGTTTATGAATTACTATTTCGGCAC
1 TATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGACAC
* *
110973 TATGTATGCATCCATGATATT
1 TATGTGTGCATCCATGGTATT
110994 TTATGATATG
Statistics
Matches: 352, Mismatches: 38, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
52 1 0.00
53 351 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (53 bp):
TATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTCGACAC
Found at i:113081 original size:22 final size:23
Alignment explanation
Indices: 113048--113091 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
113038 TATTTTTGGA
113048 ATGGATTGGTTG-TTTCCACAAC
1 ATGGATTGGTTGATTTCCACAAC
*
113070 ATGGA-TGAGTTGATTTTCACAA
1 ATGGATTG-GTTGATTTCCACAA
113092 GAAGTGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.11
22 9 0.47
23 8 0.42
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (23 bp):
ATGGATTGGTTGATTTCCACAAC
Found at i:113968 original size:76 final size:77
Alignment explanation
Indices: 113841--114048 Score: 296
Period size: 77 Copynumber: 2.7 Consensus size: 77
113831 GTTGTACAAG
* * *
113841 GGGGGAATCGGTACCCCCT-TGGGGGGG-ATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG-
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGC
**
113903 CAAAACTGTTTA
66 CAAAACCATTTA
* * *
113915 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGATTCCCTCCGAGCATTCTGGAAATCTCGGGGC
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGC
113980 CAAAACCATTTA
66 CAAAACCATTTA
* * *
113992 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCAATCTGTAATT
1 GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATT
114049 TTTGGCTTTG
Statistics
Matches: 118, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
74 17 0.14
75 8 0.07
76 31 0.26
77 62 0.53
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.25
Consensus pattern (77 bp):
GGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAATTCTCGGAGC
CAAAACCATTTA
Found at i:114661 original size:17 final size:17
Alignment explanation
Indices: 114639--114682 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
114629 TTCATAAATC
114639 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
114656 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
114673 -AAATATCCAA
1 CAAA-ATCCAA
114683 AAAGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:114674 original size:9 final size:8
Alignment explanation
Indices: 114634--114685 Score: 54
Period size: 9 Copynumber: 6.4 Consensus size: 8
114624 CACTATTCAT
114634 AAATCC-A
1 AAATCCAA
114641 AAATCCAA
1 AAATCCAA
*
114649 CAATCCACA
1 AAATCCA-A
114658 AAAT-CAA
1 AAATCCAA
114665 ACAATCCAA
1 A-AATCCAA
114674 AATATCCAA
1 AA-ATCCAA
114683 AAA
1 AAA
114686 GTTGAAACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
7 8 0.21
8 14 0.37
9 16 0.42
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (8 bp):
AAATCCAA
Found at i:116637 original size:21 final size:20
Alignment explanation
Indices: 116609--116670 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
116599 AACAGAACCC
*
116609 CAGGGGGGTATCGATTCCC-
1 CAGGGGGGGATCGATTCCCT
* *
116628 CTGTGGGGGGAATCGGTTCCCT
1 CAG-GGGGGG-ATCGATTCCCT
116650 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGGATCGATTCCCT
116670 C
1 C
116671 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.06
20 16 0.46
21 15 0.43
22 2 0.06
ACGTcount: A:0.13, C:0.26, G:0.39, T:0.23
Consensus pattern (20 bp):
CAGGGGGGGATCGATTCCCT
Found at i:122546 original size:75 final size:77
Alignment explanation
Indices: 122437--122636 Score: 280
Period size: 75 Copynumber: 2.6 Consensus size: 77
122427 CCGTTGTACA
* * * *
122437 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
* **
122501 -TAAAACTGTTT
66 CCAAAACCATTT
* *
122512 A-GGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGGG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
122576 CCAAAACCATTT
66 CCAAAACCATTT
*
122588 AGGGGGGAATCGGTTCCTCCTATGGGGGGGAATCGGTTCCCTCTGAGCA
1 AGGGGGGAATCGGTTCCTCCTAT-GGGGGGAATCGGTTCCCTCCGAGCA
122637 ATCTGTAATT
Statistics
Matches: 111, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
74 17 0.15
75 40 0.36
76 9 0.08
77 21 0.19
78 24 0.22
ACGTcount: A:0.20, C:0.23, G:0.34, T:0.23
Consensus pattern (77 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAAATCTCGGAG
CCAAAACCATTT
Found at i:127238 original size:53 final size:53
Alignment explanation
Indices: 127175--127677 Score: 641
Period size: 53 Copynumber: 9.5 Consensus size: 53
127165 GCGTACTTTT
* * * *
127175 GACACTATGTGTGCATCAATGGTATAT-GTAATGAGTTTTTGAATTGCCATTTC
1 GACACTATGTGTGCATCCATGGTAT-TCATAATGAGTTTGTGAATTACCATTTC
** * * *
127228 GACACTATGTGTGCATATATGGTATTCATAATGAGTTTGAGAATTACTATTTT
1 GACACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTC
* *
127281 GACACTATGTGTGCATCCATGGTATTTATAATGAGTTTGTTAATTACCATTTC
1 GACACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTC
* * * * **
127334 GGCACAATGTGTTCATCCATGGTATTCATAATGAGTTTGCGAATTAGTATTTC
1 GACACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTC
* * * * * *
127387 GTCACTATGTGTGCATCCATTGTATTCTTAATGAGTTTGTGAATTAGCTTTTT
1 GACACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTC
* *
127440 GGCACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCCTTTC
1 GACACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTC
* * *
127493 GGCATTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTATCATTTC
1 GACACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTC
* * *
127546 GGCACTATGTGTGCATCCATGGTATTCATAATGAGCTTGTGAATTACCATTTTG
1 GACACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCA-TTTC
* * * *
127600 GA-ATTATGTGTGCATCCATAGTATTCATAATAAGTTTATGAATTACCATTTC
1 GACACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTC
* *
127652 AACACTATGTGTGCATCCATGATATT
1 GACACTATGTGTGCATCCATGGTATT
127678 TTATGATATG
Statistics
Matches: 391, Mismatches: 56, Indels: 6
0.86 0.12 0.01
Matches are distributed among these distances:
52 5 0.01
53 382 0.98
54 4 0.01
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (53 bp):
GACACTATGTGTGCATCCATGGTATTCATAATGAGTTTGTGAATTACCATTTC
Found at i:137678 original size:273 final size:270
Alignment explanation
Indices: 137171--137713 Score: 1043
Period size: 273 Copynumber: 2.0 Consensus size: 270
137161 AATTTTCTCC
137171 ATTGAAATAAGGTGGCTTATTGACTGGTTGAGAGTCTTCAATGTAGTAAGAGCCGTCGGTCGAAG
1 ATTGAAATAAGGTGGCTTATTGACTGGTTGAGAGTCTTCAATGTAGTAAGAGCCGTCGGTCGAAG
137236 CCTTCTCGGTTGTGTCAGGAATTGATAGAGCTTCTTCAATAATTGTCTTAAGGTTGTTAGACCTT
66 CCTTCTCGGTTGTGTCAGGAATTGATAGAGCTTCTTCAATAATTGTCTTAAGGTTGTTAGACCTT
137301 CTATGACTCAGCTTTCATACCAATTGTGAGGATTTTTGAAGATCAAATTGATAACCAAAATTTTC
131 CTATGACTCAGCTTTCATACCAATTGTGAGGATTTTTGAAGATCAAATTGATAACCAAAATTTTC
137366 CAAGAGTGGGTGAATTGGCTTTTTTGAGAGTTTAGGGAGTAAGGAGTAAAAGGATAGGAAAATTT
196 CAAGAGTGGGTGAATTGGCTTTTTTGAGAGTTTAGGGAGTAAGGAGTAAAAGGATAGGAAAATTT
137431 GCACAATGAT
261 GCACAATGAT
137441 ATTGAAATAAGGTGGCTTATTGACTGGTTGAGAGTCTTCAATGTAGTAAGAGCCGTCGGTCGAAG
1 ATTGAAATAAGGTGGCTTATTGACTGGTTGAGAGTCTTCAATGTAGTAAGAGCCGTCGGTCGAAG
137506 CCATCTTCTCGGTTGTGTCAGGAATTGATAGAGCTTCTTCAATAATTGTCTTAAGGTTGTTAGAC
66 -C--CTTCTCGGTTGTGTCAGGAATTGATAGAGCTTCTTCAATAATTGTCTTAAGGTTGTTAGAC
137571 CTTCTAATGACTCAGCTTTCATACCAATTGTGAGGATTTTTGAAGATCAAATTGATAACCAAAAT
128 CTTCT-ATGACTCAGCTTTCATACCAATTGTGAGGATTTTTGAAGATCAAATTGATAACCAAAAT
137636 TTTCCAAGAGTGGGTGAATTGGC-TTTTTGAGAGTTTAGGGAGTAAGGAGTAAAAGGATAGGAAA
192 TTTCCAAGAGTGGGTGAATTGGCTTTTTTGAGAGTTTAGGGAGTAAGGAGTAAAAGGATAGGAAA
137700 ATTTGCACAATGAT
257 ATTTGCACAATGAT
137714 TTATAGTGGT
Statistics
Matches: 269, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
270 65 0.24
271 1 0.00
273 121 0.45
274 82 0.30
ACGTcount: A:0.30, C:0.13, G:0.25, T:0.33
Consensus pattern (270 bp):
ATTGAAATAAGGTGGCTTATTGACTGGTTGAGAGTCTTCAATGTAGTAAGAGCCGTCGGTCGAAG
CCTTCTCGGTTGTGTCAGGAATTGATAGAGCTTCTTCAATAATTGTCTTAAGGTTGTTAGACCTT
CTATGACTCAGCTTTCATACCAATTGTGAGGATTTTTGAAGATCAAATTGATAACCAAAATTTTC
CAAGAGTGGGTGAATTGGCTTTTTTGAGAGTTTAGGGAGTAAGGAGTAAAAGGATAGGAAAATTT
GCACAATGAT
Found at i:147105 original size:20 final size:20
Alignment explanation
Indices: 147082--147151 Score: 106
Period size: 20 Copynumber: 3.5 Consensus size: 20
147072 CTAAAAGAGG
147082 AGTTTTGAAACACTTGTGAA
1 AGTTTTGAAACACTTGTGAA
147102 AGTTTTGAAACACTTGTGAA
1 AGTTTTGAAACACTTGTGAA
**
147122 AGTTTTGAAACTTTTGTG-A
1 AGTTTTGAAACACTTGTGAA
*
147141 AGTTTCGAAAC
1 AGTTTTGAAAC
147152 TTCAAAGCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 11 0.23
20 36 0.77
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (20 bp):
AGTTTTGAAACACTTGTGAA
Found at i:147295 original size:6 final size:6
Alignment explanation
Indices: 147280--147494 Score: 205
Period size: 6 Copynumber: 35.8 Consensus size: 6
147270 GATATTTCTG
* * *
147280 ACACAA ACACAC ACACAC ACACAC ACACAC ACGCAC GCACAC ACACAC
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
* * * * * * *
147328 ACACAC ACGCAC ACGCAC ACACGC ACACGC ACACGC ACACGC ACACGC
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
** * * * * * * *
147376 ACATGC ACACGC ACACGC ACACGC ACACGC ACACGC ACACGC ACACGC
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
* * * * * *
147424 ACACAC ACACAC ACACAT ACATAC AGACAC ACACAC ACATAC ATACAG
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
147472 ACACAC ACACAC ACACAC ACACA
1 ACACAC ACACAC ACACAC ACACA
147495 AAACTTCAAA
Statistics
Matches: 186, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 186 1.00
ACGTcount: A:0.43, C:0.46, G:0.09, T:0.02
Consensus pattern (6 bp):
ACACAC
Found at i:147637 original size:2 final size:2
Alignment explanation
Indices: 147632--147775 Score: 233
Period size: 2 Copynumber: 74.0 Consensus size: 2
147622 TTCTCTCTCT
147632 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
147674 CA CA CA CA CA CA CA CA CA CA CA CA CA -A CA CA CA -A CA CA -A
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
* *
147713 CA CA -A CA CA CA CA CA CA CA CA CA CA CA CA CA CA TA CA TA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
*
147754 GA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA
147776 AAACTTCAAA
Statistics
Matches: 132, Mismatches: 6, Indels: 8
0.90 0.04 0.05
Matches are distributed among these distances:
1 4 0.03
2 128 0.97
ACGTcount: A:0.51, C:0.47, G:0.01, T:0.01
Consensus pattern (2 bp):
CA
Found at i:147854 original size:281 final size:274
Alignment explanation
Indices: 147351--147959 Score: 930
Period size: 281 Copynumber: 2.2 Consensus size: 274
147341 CGCACACACG
* * * * * * * * * *
147351 CACACGCACACGCACACGCACACGCACATGCACACGCACACGCACACGCACACGCACACGCACAC
1 CACACACACACACACACACACACACACA-ACACACACACACACACACACACACACACACACACAC
* * * * * *
147416 GCACACGCACACACACACACACACATACATACAGACACACACACACATACATACAGACACACACA
65 ACACACACACACACACACACACACACACACACACACACACACACACACACATACAGACACACACA
* *
147481 CACACACACACACAAAACTTCAAAGCCTATTGTTTTGGTAGAGTTTCGAAACTTTAGGTCAAGGC
130 CACACACACACACAAAACTTCAAAGCCTATTATTTTGGTAGAGTTTCGAAACTTTAGGTCAAAGC
147546 TTGTTTTAAAAGATAATTTTTGATATTTTGAGAAAGATAAGACTTTGAAAATTGTTCTAAAGATT
195 TTGTTTTAAAAGATAATTTTTGATATTTTGAGAAAGATAAGACTTTGAAAATTGTTCTAAAGATT
147611 TTTAATGATATTTCT
260 TTTAATGATATTTCT
* * *
147626 CTCTCTCACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
1 CACACACACACACACACACACACACACA-ACACACACACACACACACACACACACACACACACAC
*
147691 ACACACACAACACACAACACAACACAACACACACACACACACACACACACACACATACATACAGA
65 ACACACAC-ACACAC-ACAC-ACAC-ACACACACACACACACACACACACACACATACAGAC--A
*
147756 CACACACACACACACACACAAAACTTCAAAGCCTATTATTTTGGTAGAGTTTCGAAACTTTCGGT
124 CACACACACACACACACACAAAACTTCAAAGCCTATTATTTTGGTAGAGTTTCGAAACTTTAGGT
147821 CAAAGCTTGTTTTAAAAGATAATTTTTGATATTTTGAGAAAGATAAGACTTTGAAAATTGTTCTA
189 CAAAGCTTGTTTTAAAAGATAATTTTTGATATTTTGAGAAAGATAAGACTTTGAAAATTGTTCTA
147886 AAGATTTTTAATGATATTTCT
254 AAGATTTTTAATGATATTTCT
*
147907 GACACACACACACACACACACACACACAACACACACACACACACACACACACA
1 CACACACACACACACACACACACACACAACACACACACACACACACACACACA
147960 TTGAAACACT
Statistics
Matches: 301, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
275 58 0.19
276 6 0.02
277 4 0.01
278 4 0.01
279 31 0.10
280 25 0.08
281 173 0.57
ACGTcount: A:0.41, C:0.30, G:0.10, T:0.19
Consensus pattern (274 bp):
CACACACACACACACACACACACACACAACACACACACACACACACACACACACACACACACACA
CACACACACACACACACACACACACACACACACACACACACACACACACATACAGACACACACAC
ACACACACACACAAAACTTCAAAGCCTATTATTTTGGTAGAGTTTCGAAACTTTAGGTCAAAGCT
TGTTTTAAAAGATAATTTTTGATATTTTGAGAAAGATAAGACTTTGAAAATTGTTCTAAAGATTT
TTAATGATATTTCT
Found at i:147915 original size:2 final size:2
Alignment explanation
Indices: 147908--147959 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
147898 GATATTTCTG
147908 AC AC AC AC AC AC AC AC AC AC AC AC AC A- AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
147949 AC AC AC AC AC A
1 AC AC AC AC AC A
147960 TTGAAACACT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:147999 original size:19 final size:19
Alignment explanation
Indices: 147969--148026 Score: 98
Period size: 19 Copynumber: 3.0 Consensus size: 19
147959 ATTGAAACAC
*
147969 TTGTGAAAGTTTTGAAACTT
1 TTGTG-AAGTTTCGAAACTT
147989 TTGTGAAGTTTCGAAACTT
1 TTGTGAAGTTTCGAAACTT
148008 TTGTGAAGTTTCGAAACTT
1 TTGTGAAGTTTCGAAACTT
148027 CAAAGCCTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 32 0.86
20 5 0.14
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.43
Consensus pattern (19 bp):
TTGTGAAGTTTCGAAACTT
Found at i:148162 original size:4 final size:4
Alignment explanation
Indices: 148153--148183 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
148143 GATATTTCTG
148153 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
148184 CACACACACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:148372 original size:215 final size:214
Alignment explanation
Indices: 147980--148408 Score: 768
Period size: 215 Copynumber: 2.0 Consensus size: 214
147970 TGTGAAAGTT
** * *
147980 TTGAAACTTTTGTGAAGTTTCGAAACTTTTGTGAAGTTTCGAAACTTCAAAGCCTATTGTTTTGG
1 TTGAAACACTTGTGAAGTTTCGAAACTTTTGCGAAGTTTCAAAACTTCAAAGCCTATTGTTTTGG
*
148045 TAGAGTTTCGAAGCTTCCGGTCAAAGCTTGTTTTAAAAGATAATTTTTGATATTTTGAGAAAGAT
66 TAGAGTTTCGAAACTTCCGGTCAAAGCTTGTTTTAAAAGATAATTTTTGATATTTTGAGAAAGAT
* *
148110 AAGACTTTGAAATTTGTTCTAAAGATTTTTAATGATATTTCTGACATACATACATACATACATAC
131 AAGACTTTGAAAATTGTTCTAAAGATTTTTAATGATATTTCTGACATACATACATACATACAAAC
148175 ATACATACACACACACACA
196 ATACATACACACACACACA
*
148194 TTGAAACACTTGTGAAAGTTTTGAAACTTTTGCGAAGTTTCAAAACTTCAAAGCCTATTGTTTTG
1 TTGAAACACTTGTG-AAGTTTCGAAACTTTTGCGAAGTTTCAAAACTTCAAAGCCTATTGTTTTG
*
148259 GTAGAGTTTCGAAACTTTCGGTCAAAGCTTGTTTTAAAAGATAATTTTTGATATTTTGAGAAAGA
65 GTAGAGTTTCGAAACTTCCGGTCAAAGCTTGTTTTAAAAGATAATTTTTGATATTTTGAGAAAGA
148324 TAAGACTTTGAAAATTGTTCTAAAGATTTTTAATGATATTTCTGACATACATACATACATACAAA
130 TAAGACTTTGAAAATTGTTCTAAAGATTTTTAATGATATTTCTGACATACATACATACATACAAA
148389 CATACATACACACACACACA
195 CATACATACACACACACACA
148409 CACACACACA
Statistics
Matches: 205, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
214 12 0.06
215 193 0.94
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (214 bp):
TTGAAACACTTGTGAAGTTTCGAAACTTTTGCGAAGTTTCAAAACTTCAAAGCCTATTGTTTTGG
TAGAGTTTCGAAACTTCCGGTCAAAGCTTGTTTTAAAAGATAATTTTTGATATTTTGAGAAAGAT
AAGACTTTGAAAATTGTTCTAAAGATTTTTAATGATATTTCTGACATACATACATACATACAAAC
ATACATACACACACACACA
Found at i:148377 original size:4 final size:4
Alignment explanation
Indices: 148368--148398 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
148358 GATATTTCTG
*
148368 ACAT ACAT ACAT ACAT ACAA ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
148399 CACACACACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.55, C:0.26, G:0.00, T:0.19
Consensus pattern (4 bp):
ACAT
Found at i:148952 original size:159 final size:161
Alignment explanation
Indices: 148726--149030 Score: 401
Period size: 160 Copynumber: 1.9 Consensus size: 161
148716 CACACTTCAG
* *
148726 TTGTAGTTAGGAGATTTTTCCATGAATTCCCACTCAAAAAGGCATTGATTTGATTTTTATTTAAT
1 TTGTAGTTAGGAGACTTTTCCATGAATTCCCACACAAAAAGGCATTGATTTGATTTTTATTTAAT
* *
148791 ATTAAAAATAGTATAA-ATTATATTAAAATTATTAAG-AAAAACATTCAAATAAAAGGGTATTC-
66 ATTAAAAATAGTATAAGATTATATTAAAAATATTAAGAAAAAACATTCAAATAAAA-GG-ATACA
*
148853 TTTTGTATGGACAATCTTTGAAAACACGCTTTC
129 TTTTGTATGAACAATCTTTGAAAACACGCTTTC
* *
148886 TTGTAGTT-GAGAGACTTTTCCAT-AGATTCCC-CACAAATATGCATTGCA-TTGATTTTGT-TT
1 TTGTAGTTAG-GAGACTTTTCCATGA-ATTCCCACACAAAAAGGCATTG-ATTTGATTTT-TATT
* ** *
148946 TAATATTGAAAATAGTATAAGATTATATTAAAAATATTAAGAAAAAACATTTGAATAAAATGATA
62 TAATATTAAAAATAGTATAAGATTATATTAAAAATATTAAGAAAAAACATTCAAATAAAAGGATA
149011 CATTTTGTATGAACAATCTT
127 CATTTTGTATGAACAATCTT
149031 CAAAAATTCA
Statistics
Matches: 127, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
159 46 0.36
160 65 0.51
161 16 0.13
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (161 bp):
TTGTAGTTAGGAGACTTTTCCATGAATTCCCACACAAAAAGGCATTGATTTGATTTTTATTTAAT
ATTAAAAATAGTATAAGATTATATTAAAAATATTAAGAAAAAACATTCAAATAAAAGGATACATT
TTGTATGAACAATCTTTGAAAACACGCTTTC
Found at i:151021 original size:2 final size:2
Alignment explanation
Indices: 151014--151061 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
151004 AGATGGTACA
151014 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
151056 AT AT AT
1 AT AT AT
151062 TCATCTGTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:152208 original size:23 final size:24
Alignment explanation
Indices: 152163--152208 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
152153 ACCGATCAAA
*
152163 GTCAATGGTCAACAGGTTGACTCG
1 GTCAATGGTCAACAGGTTAACTCG
152187 GTCAAT-GTCAAC-GAGTTAACTC
1 GTCAATGGTCAACAG-GTTAACTC
152209 ATTGAGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 13 0.65
24 6 0.30
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (24 bp):
GTCAATGGTCAACAGGTTAACTCG
Found at i:152217 original size:13 final size:14
Alignment explanation
Indices: 152199--152230 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
152189 CAATGTCAAC
152199 GAGTTAACTCA-TT
1 GAGTTAACTCAGTT
152212 GAGTTAACTCAGTT
1 GAGTTAACTCAGTT
152226 GAGTT
1 GAGTT
152231 GACTTAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (14 bp):
GAGTTAACTCAGTT
Found at i:153946 original size:75 final size:75
Alignment explanation
Indices: 153814--154040 Score: 341
Period size: 74 Copynumber: 3.0 Consensus size: 75
153804 TAATATAACG
* * * *
153814 AAATGGTAATTCACATACTCATTATGAATACCATGGATGCACACAGAGTGTCGAAAGTACACAAA
1 AAATGGTAATTCACA-ACTCATTATGAATACCATGGATGCACATATAGTGCCAAAAGTACACAAA
153879 GTACTGATACA
65 GTACTGATACA
153890 AAATGGTAATTCACAACTCATTATGAATACCATGGATGCACATATAGTGCCAAAAGTACAC-AAG
1 AAATGGTAATTCACAACTCATTATGAATACCATGGATGCACATATAGTGCCAAAAGTACACAAAG
*
153954 TACTGATACG
66 TACTGATACA
* * *
153964 AAATGGTAATTCACAACTCATTATGAATACAATGGATGCACATATAGTACCGAAAA-TACAAAAA
1 AAATGGTAATTCACAACTCATTATGAATACCATGGATGCACATATAGTGCC-AAAAGTACACAAA
*
154028 GTACTTATACA
65 GTACTGATACA
154039 AA
1 AA
154041 TGCAACATAT
Statistics
Matches: 139, Mismatches: 10, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
74 65 0.47
75 59 0.42
76 15 0.11
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (75 bp):
AAATGGTAATTCACAACTCATTATGAATACCATGGATGCACATATAGTGCCAAAAGTACACAAAG
TACTGATACA
Found at i:154827 original size:20 final size:19
Alignment explanation
Indices: 154804--154845 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
154794 CTCAAACAAT
154804 AATT-TTCAATAATGTACATC
1 AATTATTCAATAAT-TACA-C
*
154824 AATTATTTAATAATTACAC
1 AATTATTCAATAATTACAC
154843 AAT
1 AAT
154846 CAGCCCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 8 0.40
21 8 0.40
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.40
Consensus pattern (19 bp):
AATTATTCAATAATTACAC
Found at i:155892 original size:51 final size:51
Alignment explanation
Indices: 155836--155935 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
155826 ATATCTACAC
* *
155836 TTATATATGAATT-TAATCAATTT-AAACTATAATAAATTTTAAAAAATAATA
1 TTATATATGAATTAT-ATC-ATTTGAAACTATAATAAAATATAAAAAATAATA
155887 TTATATATGAATTATATCATTTGAAACTATAATAAAATATAAAAAATAA
1 TTATATATGAATTATATCATTTGAAACTATAATAAAATATAAAAAATAA
155936 AAGTAAAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
50 4 0.09
51 40 0.89
52 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (51 bp):
TTATATATGAATTATATCATTTGAAACTATAATAAAATATAAAAAATAATA
Found at i:156861 original size:50 final size:50
Alignment explanation
Indices: 156807--156902 Score: 149
Period size: 50 Copynumber: 1.9 Consensus size: 50
156797 ATAGTTAGTG
156807 TGAATATGAAGGC-TCACTCTTAAAGATTCTGATGCGTGCGCCTTATAGGC
1 TGAATATGAA-GCTTCACTCTTAAAGATTCTGATGCGTGCGCCTTATAGGC
* * *
156857 TGAATATGAAGCTTCATTCTTAAAGATTCTTATGCGTGTGCCTTAT
1 TGAATATGAAGCTTCACTCTTAAAGATTCTGATGCGTGCGCCTTAT
156903 TATAACATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
49 2 0.05
50 40 0.95
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (50 bp):
TGAATATGAAGCTTCACTCTTAAAGATTCTGATGCGTGCGCCTTATAGGC
Found at i:158015 original size:16 final size:16
Alignment explanation
Indices: 157991--158043 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
157981 AAAACTTAAG
*
157991 AATTCGAGTCTAATTT
1 AATTTGAGTCTAATTT
158007 AATTTGAGTCTAATTT
1 AATTTGAGTCTAATTT
158023 AATTTGAGTCTAATTT
1 AATTTGAGTCTAATTT
158039 AATTT
1 AATTT
158044 AAGATCTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.49
Consensus pattern (16 bp):
AATTTGAGTCTAATTT
Found at i:158556 original size:129 final size:131
Alignment explanation
Indices: 158237--158600 Score: 549
Period size: 129 Copynumber: 2.8 Consensus size: 131
158227 ATAATTTTAT
*
158237 GAGAGAAAACGATAATATCTAATTATTTCCAATC-TGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* *
158301 GTCATTTATTACTCCAATCGAAATG-AGAGATATCACTATTTCTTCTTAAAATTCAATATTGATT
66 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTGCGTCTTAAAATTCAATATTGATT
158365 A
131 A
* * * *
158366 AAGTGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACATCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * *
158431 GTCATTTCTTACTCCAATCGAAATGAAGAGATATCACTATTGCGTCTTTATA-TCAATATTGATT
66 GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTGCGTCTTAAAATTCAATATTGATT
*
158495 C
131 A
158496 GAGAG-AAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
1 GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
* * * *
158560 GTAAGTTATTACTCC-ATCCGAAATGAAAAGATATTACTATT
66 GTCATTTATTACTCCAAT-CGAAATGAAGAGATATCACTATT
158601 TTCAATATTG
Statistics
Matches: 212, Mismatches: 20, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
128 2 0.01
129 121 0.57
130 67 0.32
131 22 0.10
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (131 bp):
GAGAGAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCA
GTCATTTATTACTCCAATCGAAATGAAGAGATATCACTATTGCGTCTTAAAATTCAATATTGATT
A
Found at i:159807 original size:6 final size:6
Alignment explanation
Indices: 159796--160861 Score: 1928
Period size: 6 Copynumber: 181.3 Consensus size: 6
159786 GAAGTGGCGA
159796 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
159844 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
159892 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
159940 ATAC-- ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
* *
159986 ATACAT ATACAT ATACAT ATACAT ATACAT ATATAC ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160034 ATACAT ATAC-- ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160080 ATACAT ATACAT ATAC-- ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160126 ACATACAT ATACAT ATACAT ATACAT ATACAT ATAC-- ATACAT ATACAT
1 --ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160174 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT AT--AT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160220 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160268 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160316 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160364 ATAC-- ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160410 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160458 ATACAT ATACAT ATACAT ATACAT ATACAT ATAC-- ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160504 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160552 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160600 ATACAT ATACAT ATACAT ATACAT ATAC-- ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160646 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160694 ATACAT ATACAT ATACAT ATACAT ATACAT ATAC-- ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160740 ATACAT ATACAT ATACAT ATAC-- ATACAT ATACAT ATAC-- ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160784 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATAC--
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
160830 ATACAT ATACAT ATACAT ATACAT ATACAT AT
1 ATACAT ATACAT ATACAT ATACAT ATACAT AT
160862 GTATATACAC
Statistics
Matches: 1030, Mismatches: 4, Indels: 52
0.95 0.00 0.05
Matches are distributed among these distances:
4 48 0.05
6 976 0.95
8 6 0.01
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:168172 original size:21 final size:21
Alignment explanation
Indices: 168148--168195 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
168138 CTAAATAGTG
168148 ACTAAAATAAATAAAAT-TAAA
1 ACTAAAAT-AATAAAATATAAA
* *
168169 ACTATAATACTAAAATATAAA
1 ACTAAAATAATAAAATATAAA
*
168190 ATTAAA
1 ACTAAA
168196 GTATTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (21 bp):
ACTAAAATAATAAAATATAAA
Found at i:169426 original size:3 final size:3
Alignment explanation
Indices: 169418--169535 Score: 167
Period size: 3 Copynumber: 41.0 Consensus size: 3
169408 TTTGGGCATG
169418 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
169466 TAA TAA TAA T-A GAA TAA TAA -AA TAA TAA -AA TAA TAA TAA TAG T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
169510 TAAA TAA -AA TAA T-A TAA TAA TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA
169536 AAGCTAAATG
Statistics
Matches: 104, Mismatches: 4, Indels: 14
0.85 0.03 0.11
Matches are distributed among these distances:
2 10 0.10
3 92 0.88
4 2 0.02
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:170021 original size:122 final size:122
Alignment explanation
Indices: 169722--170569 Score: 1096
Period size: 122 Copynumber: 6.9 Consensus size: 122
169712 GATGATAATT
* * *
169722 TATCTCCTTCTGTGAT-GTAATCTAGCAAAAAGG-TGAACAAATTCTTCTCATTATGAAATTCTT
1 TATCTCCTTCTGTGATAG-AATCGAGC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTT
* * * * **
169785 CTCCTTCTTCAGATGAGTTATTCTCATTATGAACTCTTTTTGGAAATGTTGATACTGATC
64 CTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTC-TTCTGAAAATGTTGATGTTGATC
* ** * *
169845 TATCTTCTTCTGTGATAGCGTCGAGCAAAAGGTCGAACAAATTCTTCTCATTATGAACTTCTTCT
1 TATCTCCTTCTGTGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
* * *
169910 TCATCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGATGCTGATA
66 TCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGATGTTGATC
* * * * * *
169967 TATCTTCTTCTGTGATAGAGTCTAGCAAAAGGTTAAACAAATTCTCCTCATTATGAACTTCTTCT
1 TATCTCCTTCTGTGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
* *
170032 TCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTG-GAATGTTGATGTTGATC
66 TCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGATGTTGATC
* * * *
170088 TATCTCCTTCTATGATAGAGTCTAGCAAAAGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCT
1 TATCTCCTTCTGTGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
* *
170153 TCATCTTCAGATAAGTTCTTCTCATTATGAACT-TTCTCAGGAAAA-G-TGTATGTTGATC
66 TCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCT---GAAAATGTTG-ATGTTGATC
* * * * *
170211 TATCTCCATCTGTGATAGAATCGAACAAAAAGTTAAACAAGTTCTTCTCATTATGAACTTCTCCT
1 TATCTCCTTCTGTGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
* * * *
170276 CCTTCTTCAGATGAGTTATTCTCATTATGAACACTTCTGGAAATGTTGATGTTGATC
66 TCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGATGTTGATC
* * * * *
170333 TATCTCCTTCTGTGATAGAATCGAACAAAAAGTAGAATATGTTCTTCTCATTATGAACTTCTTCT
1 TATCTCCTTCTGTGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
* * * * *
170398 CCTCCTTCAGATAAGTTCTTCTCATTATGAACACTTCTGGAAATGTTGATGTTGATC
66 TCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGATGTTGATC
* * *
170455 TATCTCCTTCTGTGATAGAATCGAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTAT
1 TATCTCCTTCTGTGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
* *
170520 CCTTCTTCATATGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGAT
66 TCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGAT
170570 CCATCGGGTG
Statistics
Matches: 651, Mismatches: 64, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
120 4 0.01
121 108 0.17
122 354 0.54
123 178 0.27
124 7 0.01
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (122 bp):
TATCTCCTTCTGTGATAGAATCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT
TCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGATGTTGATC
Found at i:171035 original size:22 final size:22
Alignment explanation
Indices: 170951--171035 Score: 116
Period size: 22 Copynumber: 3.9 Consensus size: 22
170941 AAATCCAATA
* * *
170951 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
* *
170973 AACCTATCATCTTTAAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
*
170995 AATCTATCATCTTTTAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
171017 AATCTATCATCTTTGAAGA
1 AATCTATCATCTTTGAAGA
171036 ATGTAAATGT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:171681 original size:18 final size:18
Alignment explanation
Indices: 171658--171713 Score: 103
Period size: 18 Copynumber: 3.1 Consensus size: 18
171648 TATATAAAAG
*
171658 AATAAATTGAATTTCGAA
1 AATAAATTGAATTTTGAA
171676 AATAAATTGAATTTTGAA
1 AATAAATTGAATTTTGAA
171694 AATAAATTGAATTTTGAA
1 AATAAATTGAATTTTGAA
171712 AA
1 AA
171714 GATAAACTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.36
Consensus pattern (18 bp):
AATAAATTGAATTTTGAA
Found at i:172100 original size:9 final size:8
Alignment explanation
Indices: 172073--172132 Score: 74
Period size: 8 Copynumber: 7.8 Consensus size: 8
172063 TTATATATAT
172073 ATTTTTTC
1 ATTTTTTC
172081 --TTTTTC
1 ATTTTTTC
172087 ATTTTTTC
1 ATTTTTTC
172095 ATTTTTTC
1 ATTTTTTC
172103 ATTTTTTTC
1 A-TTTTTTC
172112 ATTTTTT-
1 ATTTTTTC
172119 -TTCTTTTC
1 ATT-TTTTC
172127 ATTTTT
1 ATTTTT
172133 CTTCTTCAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
6 8 0.17
7 4 0.09
8 24 0.52
9 10 0.22
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (8 bp):
ATTTTTTC
Found at i:172125 original size:15 final size:15
Alignment explanation
Indices: 172090--172138 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
172080 CTTTTTCATT
*
172090 TTTTCATTTTTTCATTT
1 TTTTCATTTTTT--TTC
172107 TTTTCATTTTTTTTC
1 TTTTCATTTTTTTTC
*
172122 TTTTCATTTTTCTTC
1 TTTTCATTTTTTTTC
172137 TT
1 TT
172139 CAAGCATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 18 0.60
17 12 0.40
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTCATTTTTTTTC
Done.