Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003702.1 Hibiscus syriacus cultivar Beakdansim tig00007916_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: 110464
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3422 original size:20 final size:18
Alignment explanation
Indices: 3397--3439 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
3387 AATTTTACAT
3397 TTATAATAGTAGGATATATA
1 TTATAATA-TA-GATATATA
*
3417 TTATAATATATATATATA
1 TTATAATATAGATATATA
3435 TTATA
1 TTATA
3440 TTCAATACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.55
19 2 0.09
20 8 0.36
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (18 bp):
TTATAATATAGATATATA
Found at i:4775 original size:42 final size:42
Alignment explanation
Indices: 4729--4829 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
4719 AGGTCAGGGA
*
4729 CCGCGCCTGACCTTTATAATTATATATAGCGTAGATTAAAGG
1 CCGCGCCTGACCTTTATAATTATATATAGCGCAGATTAAAGG
* * *
4771 CCGCGTCTGACCTTTATAATTATATATAGCGCAGGTTAAGGG
1 CCGCGCCTGACCTTTATAATTATATATAGCGCAGATTAAAGG
*
4813 TCGCGCCTGACCTTTAT
1 CCGCGCCTGACCTTTAT
4830 TAGGTTAAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (42 bp):
CCGCGCCTGACCTTTATAATTATATATAGCGCAGATTAAAGG
Found at i:5258 original size:15 final size:14
Alignment explanation
Indices: 5217--5266 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
5207 ATTTTTTTTA
5217 AATTTAATTACT-T
1 AATTTAATTACTCT
5230 AACTTTCAAATTACTCCT
1 AA-TTT--AATTACT-CT
5248 AATTTAATTACTCT
1 AATTTAATTACTCT
5262 AATTT
1 AATTT
5267 TCAATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
13 2 0.06
14 10 0.31
15 7 0.22
16 7 0.22
17 3 0.09
18 3 0.09
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTTAATTACTCT
Found at i:5286 original size:32 final size:31
Alignment explanation
Indices: 5206--5283 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
5196 ACTAAAGTTT
5206 AATTTTTTTTAAATTTAATTACTTAACTTTCA
1 AATTTTTTTT-AATTTAATTACTTAACTTTCA
** ** *
5238 AATTACTCCTAATTTAATTACTCTAATTTTC-
1 AATTTTTTTTAATTTAATTACT-TAACTTTCA
5269 AATTTTTTTTAATTT
1 AATTTTTTTTAATTT
5284 TAAATTATAT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (31 bp):
AATTTTTTTTAATTTAATTACTTAACTTTCA
Found at i:6068 original size:2 final size:2
Alignment explanation
Indices: 6061--6096 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6051 GATAGTTTTA
6061 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
6097 TCAAATTATA
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:9984 original size:24 final size:25
Alignment explanation
Indices: 9957--10005 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
9947 ATTTATTTTA
*
9957 TGAATTTAATATTAAT-AAAATATT
1 TGAATATAATATTAATCAAAATATT
* *
9981 TGAATATCATTTTAATCAAAATATT
1 TGAATATAATATTAATCAAAATATT
10006 AATTATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (25 bp):
TGAATATAATATTAATCAAAATATT
Found at i:10078 original size:24 final size:27
Alignment explanation
Indices: 10021--10112 Score: 86
Period size: 27 Copynumber: 3.6 Consensus size: 27
10011 TTAAAATATT
10021 TAAAATATATTTATTAATATTTCATAA
1 TAAAATATATTTATTAATATTTCATAA
*
10048 TATAATATATTT-TTAATA-TT-ATAA
1 TAAAATATATTTATTAATATTTCATAA
** *
10072 TAAAATA-ATCAATT-ATATTATAATAA
1 TAAAATATATTTATTAATATT-TCATAA
* *
10098 TATAAGATATTTATT
1 TAAAATATATTTATT
10113 TTTATTTTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
23 5 0.10
24 13 0.25
25 3 0.06
26 15 0.29
27 16 0.31
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (27 bp):
TAAAATATATTTATTAATATTTCATAA
Found at i:10078 original size:29 final size:27
Alignment explanation
Indices: 10024--10129 Score: 96
Period size: 26 Copynumber: 4.0 Consensus size: 27
10014 AAATATTTAA
*
10024 AATATATTTATTAATATTTCATAATAT
1 AATATATTTATTAATATTTAATAATAT
*
10051 AATATATTT-TTAATA-TT-ATAATAA
1 AATATATTTATTAATATTTAATAATAT
**
10075 AATA-ATCAATT-ATATTATAATAATAT
1 AATATATTTATTAATATT-TAATAATAT
* **
10101 AAGATATTTATTTTTATTTTAATAATAT
1 AATATATTTATTAATA-TTTAATAATAT
10129 A
1 A
10130 TAATAAATTA
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
23 5 0.08
24 13 0.20
25 3 0.05
26 15 0.23
27 14 0.22
28 12 0.19
29 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (27 bp):
AATATATTTATTAATATTTAATAATAT
Found at i:17450 original size:3 final size:3
Alignment explanation
Indices: 17442--17479 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
17432 TCTACAAAAA
17442 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
17480 ATTTTATCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:17963 original size:24 final size:23
Alignment explanation
Indices: 17936--17983 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
17926 CAGAGGAAGA
17936 AGAAAGAAAAAGAAAAAGATAGAG
1 AGAAAGAAAAAGAAAAAG-TAGAG
* * *
17960 AGAAAGAGAACGAAATAGTAGAG
1 AGAAAGAAAAAGAAAAAGTAGAG
17983 A
1 A
17984 AAACAAAGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.65, C:0.02, G:0.27, T:0.06
Consensus pattern (23 bp):
AGAAAGAAAAAGAAAAAGTAGAG
Found at i:18933 original size:30 final size:30
Alignment explanation
Indices: 18890--19118 Score: 354
Period size: 30 Copynumber: 7.7 Consensus size: 30
18880 GATTATTTTA
*
18890 TTTGCTA-TTTAGTCCTTTAAGTTTTTATT
1 TTTGCTATTTTAGTCCTTTAAGTTTCTATT
* *
18919 TTTGTTATTTTAGTCCCTTAAGTTTCTATT
1 TTTGCTATTTTAGTCCTTTAAGTTTCTATT
*
18949 TTTGCTATTTTAGTCCCTTAAGTTTCTATT
1 TTTGCTATTTTAGTCCTTTAAGTTTCTATT
* *
18979 TTTGCTATTTTAATCCCTTAAGTTTCTATT
1 TTTGCTATTTTAGTCCTTTAAGTTTCTATT
19009 TTTGCTATTTTAGTCCTTTAAGTTTCTATT
1 TTTGCTATTTTAGTCCTTTAAGTTTCTATT
* * *
19039 TTTTCTATTTTAGTCCTTTAAATTT-TGTT
1 TTTGCTATTTTAGTCCTTTAAGTTTCTATT
19068 TTTGCTATTTTAGTCCTTTAAGTTTCTATT
1 TTTGCTATTTTAGTCCTTTAAGTTTCTATT
*
19098 TTTGCTATTTTGGTCCTTTAA
1 TTTGCTATTTTAGTCCTTTAA
19119 ATCGAATATG
Statistics
Matches: 184, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
29 32 0.17
30 152 0.83
ACGTcount: A:0.17, C:0.14, G:0.10, T:0.60
Consensus pattern (30 bp):
TTTGCTATTTTAGTCCTTTAAGTTTCTATT
Found at i:23915 original size:37 final size:37
Alignment explanation
Indices: 23872--23993 Score: 151
Period size: 37 Copynumber: 3.3 Consensus size: 37
23862 GTCTTGCTAA
23872 AGACAATTTTTCCTAAAAACAAATTTTGTCTCGCTTG
1 AGACAATTTTTCCTAAAAACAAATTTTGTCTCGCTTG
*
23909 AGACAA-TTTTCTCTAAAAACAAATTTTGTCTCACTTG
1 AGACAATTTTTC-CTAAAAACAAATTTTGTCTCGCTTG
* * * * *
23946 AGAAAATTTCT-ATCAAAAC-AATTTTATCTCGCTTG
1 AGACAATTTTTCCTAAAAACAAATTTTGTCTCGCTTG
23981 AGACAATTGTTTC
1 AGACAATT-TTTC
23994 TTTAAAAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
35 21 0.29
36 13 0.18
37 35 0.49
38 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (37 bp):
AGACAATTTTTCCTAAAAACAAATTTTGTCTCGCTTG
Found at i:24167 original size:36 final size:35
Alignment explanation
Indices: 24127--24238 Score: 90
Period size: 36 Copynumber: 3.2 Consensus size: 35
24117 TTTGTTTCCT
*
24127 TTGAAACAAATTTTTTCTCCCTTGAGACACTTTCTC
1 TTGAAACAAATTTTATCT-CCTTGAGACACTTTCTC
*** *
24163 TTGAAACAAA-ACCATCT--TTGAGATC-GTTTCTC
1 TTGAAACAAATTTTATCTCCTTGAGA-CACTTTCTC
* *
24195 TTGAAACAAATTTTGTCTCTCATGAGACAAC-TTCTC
1 TTGAAACAAATTTTATCTC-CTTGAGAC-ACTTTCTC
24231 TTGAAACA
1 TTGAAACA
24239 TCATCTTTGA
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
32 22 0.38
33 4 0.07
35 4 0.07
36 28 0.48
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.37
Consensus pattern (35 bp):
TTGAAACAAATTTTATCTCCTTGAGACACTTTCTC
Found at i:24203 original size:68 final size:67
Alignment explanation
Indices: 24042--24266 Score: 223
Period size: 66 Copynumber: 3.4 Consensus size: 67
24032 AAAATTTATA
* * * * *
24042 ATCTTTGAGTTTGTTTCTCTTGAAACAAATATTATCTCCCTTTAGAC-CGTTTCTCATAAAACAA
1 ATCTTTGAGATTGTTTCTCTTGAAACAAATTTTATCTCCCTTGAGACAC-TTTCTCTTGAAACAA
24106 CAAC
65 -AAC
* *
24110 --CTTTGAGTTTGTTTC-CTTTGAAACAAATTTTTTCTCCCTTGAGACACTTTCTCTTGAAACAA
1 ATCTTTGAGATTGTTTCTC-TTGAAACAAATTTTATCTCCCTTGAGACACTTTCTCTTGAAACAA
24172 AACC
65 AA-C
* * * *
24176 ATCTTTGAGATCGTTTCTCTTGAAACAAATTTTGTCTCTCATGAGACAAC-TTCTCTTGAAAC--
1 ATCTTTGAGATTGTTTCTCTTGAAACAAATTTTATCTCCCTTGAGAC-ACTTTCTCTTGAAACAA
*
24238 ATC
65 AAC
*
24241 ATCTTTGA-ACTGGTTTCTCTTGAAAC
1 ATCTTTGAGA-TTGTTTCTCTTGAAAC
24267 CATTATCCCT
Statistics
Matches: 137, Mismatches: 12, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
64 1 0.01
65 27 0.20
66 55 0.40
67 1 0.01
68 50 0.36
69 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.40
Consensus pattern (67 bp):
ATCTTTGAGATTGTTTCTCTTGAAACAAATTTTATCTCCCTTGAGACACTTTCTCTTGAAACAAA
AC
Found at i:24341 original size:43 final size:43
Alignment explanation
Indices: 24292--24472 Score: 126
Period size: 43 Copynumber: 4.2 Consensus size: 43
24282 TGGTCTGCTA
*
24292 TCCTCATCGCGTAAGAACCGAGTCATCCCTAGATAACCAGCCG
1 TCCTCATCACGTAAGAACCGAGTCATCCCTAGATAACCAGCCG
** *
24335 TCCTCATCACGTAAGAACC-ATGTTATCATCCCTAAAGATGGCCTA-CCA
1 TCCTCATCACGTAAGAACCGA-G---TCATCCCT--AGATAACC-AGCCG
*
24383 TCCTCATCACGTAAGAACCGTGTCATCCACT-G---ACCAGACC-
1 TCCTCATCACGTAAGAACCGAGTCATCC-CTAGATAACCAG-CCG
* * * * *
24423 TTCTCATCACGT-AGAAGTCGTGTCACCCCTAGATAACCAGTCG
1 TCCTCATCACGTAAGAA-CCGAGTCATCCCTAGATAACCAGCCG
24466 TCCTCAT
1 TCCTCAT
24473 TGCGTAGGAA
Statistics
Matches: 110, Mismatches: 11, Indels: 34
0.71 0.07 0.22
Matches are distributed among these distances:
39 7 0.06
40 23 0.21
41 2 0.02
42 2 0.02
43 31 0.28
45 6 0.05
46 10 0.09
48 28 0.25
49 1 0.01
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.23
Consensus pattern (43 bp):
TCCTCATCACGTAAGAACCGAGTCATCCCTAGATAACCAGCCG
Found at i:24563 original size:134 final size:131
Alignment explanation
Indices: 24313--24589 Score: 338
Period size: 134 Copynumber: 2.1 Consensus size: 131
24303 TAAGAACCGA
* *
24313 GTCATCCCTAGATAACCAGCCGTCCTCATCACGTAAGAACCATGTTATCATCCCTAAAGATGGCC
1 GTCACCCCTAGATAACCAGCCGTCCTCATCACGTAAGAACCATGTTATCATCCCTAAAGATGGCA
** * *
24378 TACCATCCTCATCACGTAAGAACCGTGTCATCCACTGACCAGACCTTCTCATCACGTAGAAGTCG
66 TACCATCCTCATCACGTAAGAACCGTGTCATCCACCAACCAGACCTCCTCATCACATAGAAGTCG
24443 T
131 T
* ** * * *
24444 GTCACCCCTAGATAACCAGTCGTCCTCATTGCGTAGGAACCGTGTTATCACCCTCTCTAAAGATG
1 GTCACCCCTAGATAACCAGCCGTCCTCATCACGTAAGAACCATGTTATCA---TCCCTAAAGATG
* ** * * * * *
24509 GTATGTCGTCCTCATCGCGTAGGAACCGTGTCATCCACCAACCAGATCTCCTCATCACATAGGAG
63 GCATACCATCCTCATCACGTAAGAACCGTGTCATCCACCAACCAGACCTCCTCATCACATAGAAG
24574 TCGT
128 TCGT
*
24578 GTCACCCTTAGA
1 GTCACCCCTAGA
24590 CGACCATAAC
Statistics
Matches: 122, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
131 44 0.36
134 78 0.64
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (131 bp):
GTCACCCCTAGATAACCAGCCGTCCTCATCACGTAAGAACCATGTTATCATCCCTAAAGATGGCA
TACCATCCTCATCACGTAAGAACCGTGTCATCCACCAACCAGACCTCCTCATCACATAGAAGTCG
T
Found at i:24786 original size:3 final size:3
Alignment explanation
Indices: 24778--24825 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
24768 TCCACAAAAA
24778 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
24824 TA
1 TA
24826 ATACAAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:25354 original size:23 final size:25
Alignment explanation
Indices: 25327--25373 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
25317 AGAAAACCAT
*
25327 AAAGAAAA-GAAA-AAGATAGAAAG
1 AAAGAAAACGAAATAAGAGAGAAAG
25350 AAAGAAAACGAAATAAGAGAGAAA
1 AAAGAAAACGAAATAAGAGAGAAA
25374 ACAAAGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 4 0.19
25 9 0.43
ACGTcount: A:0.72, C:0.02, G:0.21, T:0.04
Consensus pattern (25 bp):
AAAGAAAACGAAATAAGAGAGAAAG
Found at i:26353 original size:30 final size:30
Alignment explanation
Indices: 26302--26471 Score: 209
Period size: 30 Copynumber: 5.7 Consensus size: 30
26292 GATTATTTTA
*
26302 TTTT-CTA-TTTAGTCTCTTAAGTTTCTAT
1 TTTTGCTATTTTAGTCCCTTAAGTTTCTAT
* *
26330 TTTTTCTATTTTACTCCCTTAAGTTTCTAT
1 TTTTGCTATTTTAGTCCCTTAAGTTTCTAT
26360 TTTTGCTATTTTAGTCCCTTAAGTTTCTAT
1 TTTTGCTATTTTAGTCCCTTAAGTTTCTAT
* ** * *
26390 TTTTGATATTTTAGTCATTTAAATTCCTAT
1 TTTTGCTATTTTAGTCCCTTAAGTTTCTAT
* * *
26420 TTTTTCTATTTTAGTCCTTTATGTTTCTAT
1 TTTTGCTATTTTAGTCCCTTAAGTTTCTAT
* *
26450 TTTTGCTATTTTGGTCCTTTAA
1 TTTTGCTATTTTAGTCCCTTAA
26472 ATCGAATATG
Statistics
Matches: 122, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
28 4 0.03
29 3 0.02
30 115 0.94
ACGTcount: A:0.18, C:0.15, G:0.08, T:0.60
Consensus pattern (30 bp):
TTTTGCTATTTTAGTCCCTTAAGTTTCTAT
Found at i:30685 original size:17 final size:20
Alignment explanation
Indices: 30647--30685 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
30637 GAGTGAACCT
30647 AAACAAGAACACAATTTAGC
1 AAACAAGAACACAATTTAGC
30667 AAACAA-AACA-AATTT-GC
1 AAACAAGAACACAATTTAGC
30684 AA
1 AA
30686 CTGCAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 5 0.26
19 4 0.21
20 6 0.32
ACGTcount: A:0.59, C:0.18, G:0.08, T:0.15
Consensus pattern (20 bp):
AAACAAGAACACAATTTAGC
Found at i:31538 original size:32 final size:32
Alignment explanation
Indices: 31502--31581 Score: 151
Period size: 32 Copynumber: 2.5 Consensus size: 32
31492 TGGATGTTAC
31502 GGGTACCCGATAATCGAGTATTCGAATTTTGT
1 GGGTACCCGATAATCGAGTATTCGAATTTTGT
31534 GGGTACCCGATAATCGAGTATTCGAATTTTGT
1 GGGTACCCGATAATCGAGTATTCGAATTTTGT
*
31566 GGGTACCCGGTAATCG
1 GGGTACCCGATAATCG
31582 GATACCCGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (32 bp):
GGGTACCCGATAATCGAGTATTCGAATTTTGT
Found at i:35924 original size:18 final size:18
Alignment explanation
Indices: 35901--35971 Score: 108
Period size: 18 Copynumber: 4.0 Consensus size: 18
35891 TGACCGGTCA
*
35901 CGACCCGACCTGTTGACC
1 CGACCCGACCCGTTGACC
*
35919 CGACCCGACCCGTTGGCC
1 CGACCCGACCCGTTGACC
35937 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
35955 CGACCCGA-TCGTTGACC
1 CGACCCGACCCGTTGACC
35972 GTTGATCGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
17 8 0.16
18 41 0.84
ACGTcount: A:0.15, C:0.46, G:0.24, T:0.14
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:36059 original size:29 final size:29
Alignment explanation
Indices: 35981--36060 Score: 115
Period size: 29 Copynumber: 2.8 Consensus size: 29
35971 CGTTGATCGG
* * *
35981 TGCTATTCTGGTAAATAATTCGGTTTTGG
1 TGCTATTCTGGTAAATAATTTGGGTTTGA
*
36010 TGCTAATCTGGTAAATAATTTGGGTTTGA
1 TGCTATTCTGGTAAATAATTTGGGTTTGA
*
36039 TGCTATTCTGGTAATTAATTTG
1 TGCTATTCTGGTAAATAATTTG
36061 AAATGGGTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.45
Consensus pattern (29 bp):
TGCTATTCTGGTAAATAATTTGGGTTTGA
Found at i:36071 original size:29 final size:29
Alignment explanation
Indices: 35979--36081 Score: 89
Period size: 29 Copynumber: 3.6 Consensus size: 29
35969 ACCGTTGATC
* *** *
35979 GGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTTGAAATG
* *** *
36008 GGTGCTAATCTGGTAAATAATTTGGGTTT
1 GGTGCTATTCTGGTAAATAATTTGAAATG
* *
36037 GATGCTATTCTGGTAATTAATTTGAAATG
1 GGTGCTATTCTGGTAAATAATTTGAAATG
*
36066 GGTGCTATTTTGGTAA
1 GGTGCTATTCTGGTAA
36082 TTATTTTAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.24, C:0.08, G:0.25, T:0.43
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTTGAAATG
Found at i:36082 original size:29 final size:29
Alignment explanation
Indices: 36039--36104 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
36029 TTGGGTTTGA
* * *
36039 TGCTATTCTGGTAATTAATTTGAAATGGG
1 TGCTATTTTGGTAATTAATTTAAAAAGGG
* *
36068 TGCTATTTTGGTAATTATTTTAAAAAGTG
1 TGCTATTTTGGTAATTAATTTAAAAAGGG
36097 TGCTATTT
1 TGCTATTT
36105 GTGTAAAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.27, C:0.06, G:0.20, T:0.47
Consensus pattern (29 bp):
TGCTATTTTGGTAATTAATTTAAAAAGGG
Found at i:49667 original size:21 final size:21
Alignment explanation
Indices: 49641--49680 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
49631 CAGAACCCGA
*
49641 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
49662 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
49681 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:53560 original size:22 final size:21
Alignment explanation
Indices: 53518--53557 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
53508 GAGTTTGTTT
*
53518 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
53539 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
53558 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:54615 original size:4 final size:4
Alignment explanation
Indices: 54592--54694 Score: 77
Period size: 4 Copynumber: 25.0 Consensus size: 4
54582 CATGTTAGAT
* ** * *
54592 ATAA A-AA ATAA AGAAA ATAA ATAA ATAA ATTTAA CCAA AAAA AGAA ATAAA
1 ATAA ATAA ATAA A-TAA ATAA ATAA ATAA A--TAA ATAA ATAA ATAA AT-AA
*
54643 ATAAA ATAA A-ATA ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-G ATAA
1 AT-AA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
54691 ATAA
1 ATAA
54695 GAATGATAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
3 6 0.07
4 59 0.73
5 13 0.16
6 3 0.04
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:54661 original size:12 final size:12
Alignment explanation
Indices: 54592--54717 Score: 60
Period size: 12 Copynumber: 11.2 Consensus size: 12
54582 CATGTTAGAT
54592 ATAAAA-AATAA
1 ATAAAATAATAA
*
54603 AGAAAATAAATAA
1 ATAAAAT-AATAA
*
54616 AT-AAAT-TTAA
1 ATAAAATAATAA
** * *
54626 CCAAAAAAAGAA
1 ATAAAATAATAA
54638 ATAAAAT-A-AA
1 ATAAAATAATAA
54648 ATAAAATAATAA
1 ATAAAATAATAA
54660 AT---A-AATAA
1 ATAAAATAATAA
54668 AT-AAATAAATAA
1 ATAAAAT-AATAA
*
54680 AT-AAATGATAA
1 ATAAAATAATAA
*
54691 ATAAGAATGAT-A
1 ATAA-AATAATAA
54703 ATAATAATAATAA
1 ATAA-AATAATAA
54716 AT
1 AT
54718 GATATTAAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 24
0.70 0.11 0.19
Matches are distributed among these distances:
8 7 0.08
9 1 0.01
10 13 0.15
11 16 0.18
12 36 0.41
13 15 0.17
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (12 bp):
ATAAAATAATAA
Found at i:54709 original size:19 final size:20
Alignment explanation
Indices: 54651--54734 Score: 74
Period size: 19 Copynumber: 4.5 Consensus size: 20
54641 AAATAAAATA
54651 AAATAATAAAT-A-AATAAAT
1 AAATAATAAATGATAAT-AAT
*
54670 AAATAAATAAAT-A-AATGAT
1 AAAT-AATAAATGATAATAAT
*
54689 AAATAA-GAATGATAATAAT
1 AAATAATAAATGATAATAAT
*
54708 -AATAATAAATGATATTAA-
1 AAATAATAAATGATAATAAT
54726 AAATAATAA
1 AAATAATAA
54735 GTAATAGGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.05
18 8 0.15
19 33 0.60
20 11 0.20
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (20 bp):
AAATAATAAATGATAATAAT
Found at i:56773 original size:105 final size:105
Alignment explanation
Indices: 56457--57233 Score: 1250
Period size: 105 Copynumber: 7.4 Consensus size: 105
56447 GTATTGTTCC
* * * * * * *
56457 GAGTCCAATATCCTCCGCTGTGAAGTTGAAACTGGTTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
* * * *
56522 CTAACGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCCG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * **
56563 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTTGAAATTGAGAAGCTGTCGGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAA-ATGTTTGTTGACA
** *** *
56628 GTCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTT
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
56670 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
56735 CGGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
56775 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
56840 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
56880 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
56945 CAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
56985 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAATGTTTGTTAACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
57050 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
57090 GAGTCC-ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
57154 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
57194 GAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
57234 GGTAAAACCT
Statistics
Matches: 623, Mismatches: 45, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
104 100 0.16
105 388 0.62
106 45 0.07
107 90 0.14
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:58080 original size:14 final size:13
Alignment explanation
Indices: 58063--58102 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 13
58053 CTCTTTTTGG
58063 TTTTTTGTTTTGTT
1 TTTTTTGTTTT-TT
58077 TTTTTTGTTTTTT
1 TTTTTTGTTTTTT
58090 TTTGTTT-TTTTTT
1 TTT-TTTGTTTTTT
58103 CCAACTTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (13 bp):
TTTTTTGTTTTTT
Found at i:58082 original size:9 final size:9
Alignment explanation
Indices: 58065--58101 Score: 56
Period size: 9 Copynumber: 3.9 Consensus size: 9
58055 CTTTTTGGTT
58065 TTTTGTTTTG
1 TTTT-TTTTG
58075 TTTTTTTTG
1 TTTTTTTTG
58084 TTTTTTTTTG
1 -TTTTTTTTG
58094 TTTTTTTT
1 TTTTTTTT
58102 TCCAACTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 13 0.50
10 13 0.50
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:58087 original size:19 final size:19
Alignment explanation
Indices: 58065--58101 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
58055 CTTTTTGGTT
58065 TTTTGTTTTGTTTTTTTTG
1 TTTTGTTTTGTTTTTTTTG
*
58084 TTTTTTTTTGTTTTTTTT
1 TTTTGTTTTGTTTTTTTT
58102 TCCAACTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (19 bp):
TTTTGTTTTGTTTTTTTTG
Found at i:58088 original size:10 final size:10
Alignment explanation
Indices: 58064--58102 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
58054 TCTTTTTGGT
58064 TTTTTGTTTTG
1 TTTTT-TTTTG
58075 -TTTTTTTTG
1 TTTTTTTTTG
58084 TTTTTTTTTG
1 TTTTTTTTTG
58094 TTTTTTTTT
1 TTTTTTTTT
58103 CCAACTTAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 5 0.19
10 22 0.81
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:64373 original size:793 final size:793
Alignment explanation
Indices: 62847--64435 Score: 3142
Period size: 793 Copynumber: 2.0 Consensus size: 793
62837 TCTCATCATC
*
62847 TGAAAACGAGATGAGATTATTAGCTTGAATATTGTTCACCAGTTGATCCATTTTGCTGACTGGTA
1 TGAAAACGAGATGAGATTATTAGCTTGAATATTGTTCACCAGTCGATCCATTTTGCTGACTGGTA
62912 TGTCTTGTGGCACGAACGTTTGATTAAGGACATTCAACAACGCTTCTCGGTGTGCTTCCGAGCTT
66 TGTCTTGTGGCACGAACGTTTGATTAAGGACATTCAACAACGCTTCTCGGTGTGCTTCCGAGCTT
*
62977 AAAAATAGTGCTAGCATTGAAGTACGTGTAGGTAAGTTGTGGAGCTGTTCTATAATGTTGTACTC
131 AAAAATAGTGCTAGCATTGAAGTACGTGTAGGTAAGTTGTGGAGCTGTTCTACAATGTTGTACTC
63042 GCTGTGCTTCAAGATCTTGAGGAACTCTTTAGCTTCTTCCTCCTTTATAGGTTCATTGACAACTA
196 GCTGTGCTTCAAGATCTTGAGGAACTCTTTAGCTTCTTCCTCCTTTATAGGTTCATTGACAACTA
63107 GTACATCTCCTTTGAACGGCTCCAGTGGTCTTTGCCCCACTTTACTATTACCTCCTCCGGAAGTA
261 GTACATCTCCTTTGAACGGCTCCAGTGGTCTTTGCCCCACTTTACTATTACCTCCTCCGGAAGTA
63172 CTCACCTGACACTCGTACTTCCATGGCACTTGCCGATTGTCCTTATATTGAAAAGGCCGAGGTGC
326 CTCACCTGACACTCGTACTTCCATGGCACTTGCCGATTGTCCTTATATTGAAAAGGCCGAGGTGC
63237 GGAGATTACCACCTTGGCTGGTGTTGTCACTGTCATGCTTGCCTTAGGGGTAATTATCAAAGGAC
391 GGAGATTACCACCTTGGCTGGTGTTGTCACTGTCATGCTTGCCTTAGGGGTAATTATCAAAGGAC
63302 TACCCCTACCAAATTTTCTATCTGATGATTCTCCGGTGGCACAAACATCTGCTTCCAAAGAATCT
456 TACCCCTACCAAATTTTCTATCTGATGATTCTCCGGTGGCACAAACATCTGCTTCCAAAGAATCT
63367 TAAATTTCTTCGTAAAACTCCAGCTCTTTCTGGTTCATCATGAGTTGAACTAACGATCTGAACTC
521 TAAATTTCTTCGTAAAACTCCAGCTCTTTCTGGTTCATCATGAGTTGAACTAACGATCTGAACTC
63432 TGGGCAATCTTTTACTTTATGTCATTCTTCGTTGTGGTAACAACAATGGTTACCACCATCATTTT
586 TGGGCAATCTTTTACTTTATGTCATTCTTCGTTGTGGTAACAACAATGGTTACCACCATCATTTT
63497 CTGTCGTACCTGGATATAGTGCAAGAAGCCCTGCCTTCACCATTTGGCTCCATACCCAAGCCAAA
651 CTGTCGTACCTGGATATAGTGCAAGAAGCCCTGCCTTCACCATTTGGCTCCATACCCAAGCCAAA
63562 GGAGATTTGACCTCTGAAACACTCAATTTAACTTTCCTGCCCCCTTCGGTAGTAACGGCATTGAT
716 GGAGATTTGACCTCTGAAACACTCAATTTAACTTTCCTGCCCCCTTCGGTAGTAACGGCATTGAT
63627 TCCTGTCTCCTGA
781 TCCTGTCTCCTGA
63640 TGAAAACGAGATGAGATTATTAGCTTGAATATTGTTCACCAGTCGATCCATTTTGCTGACTGGTA
1 TGAAAACGAGATGAGATTATTAGCTTGAATATTGTTCACCAGTCGATCCATTTTGCTGACTGGTA
63705 TGTCTTGTGGCACGAACGTTTGATTAAGGACATTCAACAACGCTTCTCGGTGTGCTTCCGAGCTT
66 TGTCTTGTGGCACGAACGTTTGATTAAGGACATTCAACAACGCTTCTCGGTGTGCTTCCGAGCTT
63770 AAAAATAGTGCTAGCATTGAAGTACGTGTAGGTAAGTTGTGGAGCTGTTCTACAATGTTGTACTC
131 AAAAATAGTGCTAGCATTGAAGTACGTGTAGGTAAGTTGTGGAGCTGTTCTACAATGTTGTACTC
63835 GCTGTGCTTCAAGATCTTGAGGAACTCTTTAGCTTCTTCCTCCTTTATAGGTTCATTGACAACTA
196 GCTGTGCTTCAAGATCTTGAGGAACTCTTTAGCTTCTTCCTCCTTTATAGGTTCATTGACAACTA
63900 GTACATCTCCTTTGAACGGCTCCAGTGGTCTTTGCCCCACTTTACTATTACCTCCTCCGGAAGTA
261 GTACATCTCCTTTGAACGGCTCCAGTGGTCTTTGCCCCACTTTACTATTACCTCCTCCGGAAGTA
63965 CTCACCTGACACTCGTACTTCCATGGCACTTGCCGATTGTCCTTATATTGAAAAGGCCGAGGTGC
326 CTCACCTGACACTCGTACTTCCATGGCACTTGCCGATTGTCCTTATATTGAAAAGGCCGAGGTGC
64030 GGAGATTACCACCTTGGCTGGTGTTGTCACTGTCATGCTTGCCTTAGGGGTAATTATCAAAGGAC
391 GGAGATTACCACCTTGGCTGGTGTTGTCACTGTCATGCTTGCCTTAGGGGTAATTATCAAAGGAC
64095 TACCCCTACCAAATTTTCTATCTGATGATTCTCCGGTGGCACAAACATCTGCTTCCAAAGAATCT
456 TACCCCTACCAAATTTTCTATCTGATGATTCTCCGGTGGCACAAACATCTGCTTCCAAAGAATCT
*
64160 TGAATTTCTTCGTAAAACTCCAGCTCTTTCTGGTTCATCATGAGTTGAACTAACGATCTGAACTC
521 TAAATTTCTTCGTAAAACTCCAGCTCTTTCTGGTTCATCATGAGTTGAACTAACGATCTGAACTC
64225 TGGGCAATCTTTTACTTTATGTCATTCTTCGTTGTGGTAACAACAATGGTTACCACCATCATTTT
586 TGGGCAATCTTTTACTTTATGTCATTCTTCGTTGTGGTAACAACAATGGTTACCACCATCATTTT
*
64290 CTGTCGTACCTGGATATGGTGCAAGAAGCCCTGCCTTCACCATTTGGCTCCATACCCAAGCCAAA
651 CTGTCGTACCTGGATATAGTGCAAGAAGCCCTGCCTTCACCATTTGGCTCCATACCCAAGCCAAA
64355 GGAGATTTGACCTCTGAAACACTCAATTTAACTTTCCTGCCCCCTTCGGTAGTAACGGCATTGAT
716 GGAGATTTGACCTCTGAAACACTCAATTTAACTTTCCTGCCCCCTTCGGTAGTAACGGCATTGAT
64420 TCCTGTCTCCTGA
781 TCCTGTCTCCTGA
64433 TGA
1 TGA
64436 TTAGGCAAGG
Statistics
Matches: 792, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
793 792 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (793 bp):
TGAAAACGAGATGAGATTATTAGCTTGAATATTGTTCACCAGTCGATCCATTTTGCTGACTGGTA
TGTCTTGTGGCACGAACGTTTGATTAAGGACATTCAACAACGCTTCTCGGTGTGCTTCCGAGCTT
AAAAATAGTGCTAGCATTGAAGTACGTGTAGGTAAGTTGTGGAGCTGTTCTACAATGTTGTACTC
GCTGTGCTTCAAGATCTTGAGGAACTCTTTAGCTTCTTCCTCCTTTATAGGTTCATTGACAACTA
GTACATCTCCTTTGAACGGCTCCAGTGGTCTTTGCCCCACTTTACTATTACCTCCTCCGGAAGTA
CTCACCTGACACTCGTACTTCCATGGCACTTGCCGATTGTCCTTATATTGAAAAGGCCGAGGTGC
GGAGATTACCACCTTGGCTGGTGTTGTCACTGTCATGCTTGCCTTAGGGGTAATTATCAAAGGAC
TACCCCTACCAAATTTTCTATCTGATGATTCTCCGGTGGCACAAACATCTGCTTCCAAAGAATCT
TAAATTTCTTCGTAAAACTCCAGCTCTTTCTGGTTCATCATGAGTTGAACTAACGATCTGAACTC
TGGGCAATCTTTTACTTTATGTCATTCTTCGTTGTGGTAACAACAATGGTTACCACCATCATTTT
CTGTCGTACCTGGATATAGTGCAAGAAGCCCTGCCTTCACCATTTGGCTCCATACCCAAGCCAAA
GGAGATTTGACCTCTGAAACACTCAATTTAACTTTCCTGCCCCCTTCGGTAGTAACGGCATTGAT
TCCTGTCTCCTGA
Found at i:68343 original size:10 final size:10
Alignment explanation
Indices: 68318--68351 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
68308 AAGGTTAGTA
*
68318 AAATAGAAAT
1 AAATAAAAAT
*
68328 AGATAAAAAT
1 AAATAAAAAT
68338 AAATAAAAAT
1 AAATAAAAAT
68348 AAAT
1 AAAT
68352 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:69212 original size:4 final size:4
Alignment explanation
Indices: 69189--69279 Score: 53
Period size: 4 Copynumber: 22.0 Consensus size: 4
69179 CATGTTAGAT
* ** * *
69189 ATAA A-AA ATAA AGAAA ATAA ATAA ATAA ATTTAA CCAA AAAA AGAA ATAAA
1 ATAA ATAA ATAA A-TAA ATAA ATAA ATAA A--TAA ATAA ATAA ATAA AT-AA
*
69240 ATAAA ATAA A-ATA ATAA ATAA ATAA ATAA AT-G ATAA ATAA
1 AT-AA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA
69280 GAATGATAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 16
0.73 0.11 0.17
Matches are distributed among these distances:
3 6 0.09
4 47 0.68
5 13 0.19
6 3 0.04
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:69282 original size:48 final size:48
Alignment explanation
Indices: 69193--69301 Score: 114
Period size: 48 Copynumber: 2.2 Consensus size: 48
69183 TTAGATATAA
*
69193 AAAATAAAGAAAATAAATAAATAAATTTAACCAAAAAAAGAAAT-AAAAT
1 AAAATAAA-AAAATAAATAAATAAATTAAACCAAAAAAAG-AATGAAAAT
* ** * *
69242 AAAATAAAATAATAAATAAATAAA-TAAATGATAAATAAGAATGATAAT
1 AAAATAAAAAAATAAATAAATAAATTAAACCA-AAAAAAGAATGAAAAT
69290 AATAATAAAAAA
1 AA-AATAAAAAA
69302 TGATATTAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
47 7 0.14
48 27 0.54
49 16 0.32
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (48 bp):
AAAATAAAAAAATAAATAAATAAATTAAACCAAAAAAAGAATGAAAAT
Found at i:69294 original size:19 final size:19
Alignment explanation
Indices: 69249--69316 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
69239 AATAAAATAA
69249 AATAATAAATAAATAA--AT
1 AATAATAAATAAA-AATGAT
* *
69267 AAATGATAAATAAGAATGAT
1 -AATAATAAATAAAAATGAT
69287 AATAAT-AATAAAAAATGAT
1 AATAATAAAT-AAAAATGAT
*
69306 ATTAA-AAATAA
1 AATAATAAATAA
69317 TAAGTAATAG
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
18 7 0.17
19 31 0.77
20 2 0.05
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (19 bp):
AATAATAAATAAAAATGAT
Found at i:76548 original size:26 final size:26
Alignment explanation
Indices: 76519--76576 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
76509 TTTATATTAC
* * * *
76519 ATAATACAAATTCAGAAACTAATGTA
1 ATAATAAAAACTCAAAAACCAATGTA
*
76545 ATAAAAAAAACTCAAAAACCAATGTA
1 ATAATAAAAACTCAAAAACCAATGTA
*
76571 AAAATA
1 ATAATA
76577 TAGTTAAATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.21
Consensus pattern (26 bp):
ATAATAAAAACTCAAAAACCAATGTA
Found at i:77220 original size:7 final size:7
Alignment explanation
Indices: 77205--77301 Score: 72
Period size: 7 Copynumber: 13.9 Consensus size: 7
77195 CTTTGCAATG
*
77205 AACCTTA
1 AACCCTA
77212 AACCCTA
1 AACCCTA
77219 AACCCTA
1 AACCCTA
77226 AACCAC-A
1 AACC-CTA
*
77233 AACTCTA
1 AACCCTA
77240 AA-CCTCA
1 AACCCT-A
* *
77247 AGCCTTA
1 AACCCTA
* *
77254 AGCCATA
1 AACCCTA
*
77261 AACCTTA
1 AACCCTA
77268 AACCCTA
1 AACCCTA
*
77275 AATCCTA
1 AACCCTA
**
77282 AACTTTA
1 AACCCTA
77289 AACCCTA
1 AACCCTA
77296 AACCCT
1 AACCCT
77302 TAATTTGATT
Statistics
Matches: 71, Mismatches: 15, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
6 3 0.04
7 65 0.92
8 3 0.04
ACGTcount: A:0.42, C:0.35, G:0.02, T:0.21
Consensus pattern (7 bp):
AACCCTA
Found at i:77229 original size:21 final size:21
Alignment explanation
Indices: 77210--77301 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
77200 CAATGAACCT
*
77210 TAAACCCTAAACCCTAAACCAC
1 TAAACCCTAAACCTTAAACC-C
* * * *
77232 -AAACTCTAAACCTCAAGCCT
1 TAAACCCTAAACCTTAAACCC
* *
77252 TAAGCCATAAACCTTAAACCC
1 TAAACCCTAAACCTTAAACCC
* *
77273 TAAATCCTAAACTTTAAACCC
1 TAAACCCTAAACCTTAAACCC
77294 TAAACCCT
1 TAAACCCT
77302 TAATTTGATT
Statistics
Matches: 53, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.42, C:0.35, G:0.02, T:0.21
Consensus pattern (21 bp):
TAAACCCTAAACCTTAAACCC
Found at i:78888 original size:23 final size:23
Alignment explanation
Indices: 78849--78915 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
78839 GTTTTTGAGA
* *
78849 TTGAATCGAGTTTAAAGTCGAGC
1 TTGAATCGAGCTCAAAGTCGAGC
* *
78872 TTGAATTGAGCTCAAAGTCAAGC
1 TTGAATCGAGCTCAAAGTCGAGC
*
78895 TTGAATCGAGCTCAAACTCGA
1 TTGAATCGAGCTCAAAGTCGA
78916 ATAGTGAGGC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (23 bp):
TTGAATCGAGCTCAAAGTCGAGC
Found at i:104653 original size:31 final size:31
Alignment explanation
Indices: 104592--104653 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
104582 AGTTAAATGT
* * * *
104592 TTATGTAAATTTTAATATATTGTTATATAAA
1 TTATGTAAAATTTAATATAATGTAAAATAAA
104623 TTATGTAAAATTTAATATTAAT-TAAAATAAA
1 TTATGTAAAATTTAATA-TAATGTAAAATAAA
104654 AATATATGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 23 0.88
32 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (31 bp):
TTATGTAAAATTTAATATAATGTAAAATAAA
Found at i:104716 original size:25 final size:25
Alignment explanation
Indices: 104686--104747 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
104676 TTATTCTACT
* *
104686 AATTTATCTTTAAATTTTATAAAAA
1 AATTTATATATAAATTTTATAAAAA
*
104711 AATTTATATATAAATTTTATTAAAA
1 AATTTATATATAAATTTTATAAAAA
* *
104736 AGTATATATATA
1 AATTTATATATA
104748 TTTATTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
AATTTATATATAAATTTTATAAAAA
Found at i:104741 original size:23 final size:24
Alignment explanation
Indices: 104696--104757 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 24
104686 AATTTATCTT
* *
104696 TAAATTTTATAAAAAAATTTATATA
1 TAAATTTTAT-TAAAAATGTATATA
104721 TAAATTTTATTAAAAA-GTATATA
1 TAAATTTTATTAAAAATGTATATA
*
104744 TATA-TTTATTAAAA
1 TAAATTTTATTAAAA
104758 TAATAAAGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 10 0.29
23 9 0.26
24 5 0.15
25 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (24 bp):
TAAATTTTATTAAAAATGTATATA
Done.