Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004891.1 Hibiscus syriacus cultivar Beakdansim tig00011010_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: 87039
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:3055 original size:36 final size:36
Alignment explanation
Indices: 3015--3201 Score: 112
Period size: 38 Copynumber: 5.1 Consensus size: 36
3005 TGAGATAAAA
3015 TTTCAAGGGAAATATCTC-AGTGAGATGCAATTTTTG
1 TTTCAAGGGAAATATCTCAAGTGAGATG-AATTTTTG
* * * *
3051 TTTCAA-GGAGATTGTCTCAAGTGAGGA-GAA-ATTTA
1 TTTCAAGGGA-AATATCTCAAGTGA-GATGAATTTTTG
* ** * *
3086 TTTCAAGAGAAAATATCTTTAGTGAGATAAAATTTTG
1 TTTCAAG-GGAAATATCTCAAGTGAGATGAATTTTTG
* * * * *
3123 TTTCGAGAGAAACTATCTCGAGTGATATGAAATTTTTT
1 TTTCAAGGGAAA-TATCTCAAGTGAGATG-AATTTTTG
** * *
3161 TTTTGAGGAAAACTATCTCAAGTGAGATAGAATTATTG
1 TTTCAAGGGAAA-TATCTCAAGTGAGAT-GAATTTTTG
3199 TTT
1 TTT
3202 TGAGAGAAAC
Statistics
Matches: 113, Mismatches: 28, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
35 14 0.12
36 29 0.26
37 29 0.26
38 40 0.35
39 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (36 bp):
TTTCAAGGGAAATATCTCAAGTGAGATGAATTTTTG
Found at i:3068 original size:67 final size:69
Alignment explanation
Indices: 2927--3147 Score: 195
Period size: 67 Copynumber: 3.2 Consensus size: 69
2917 CATGTAGGAA
* * *
2927 TGTCTCGAGTGAGACTAAATTTTTCAAGAGAAATATCTCAAGTTAGATGAAATTTGTTTCAGGGG
1 TGTCTCGAGTGAGACTAAATATTTCAAGAGAAATATCTCAAGTGAGATGAAATTTGTTTCAGGAG
2992 AATC
66 AATC
* * *
2996 CGTCTCGAGTGAGA-TAAA-ATTTCAAGGGAAATATCTC-AGTGAGATGCAATTTTTGTTTCAAG
1 TGTCTCGAGTGAGACTAAATATTTCAAGAGAAATATCTCAAGTGAGATG-AA-ATTTGTTTC-AG
3058 GAG-AT-
63 GAGAATC
* * ** *
3063 TGTCTCAAGTGAGGA-GAAATTTATTTCAAGAGAAAATATCTTTAGTGAGATAAAATTTTGTTTC
1 TGTCTCGAGTGA-GACTAAA--TATTTCAAGAG-AAATATCTCAAGTGAGATGAAA-TTTGTTTC
*
3127 -GAGAGAAAC
61 AG-GAGAATC
*
3136 TATCTCGAGTGA
1 TGTCTCGAGTGA
3148 TATGAAATTT
Statistics
Matches: 123, Mismatches: 16, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
66 8 0.07
67 29 0.24
68 19 0.15
69 17 0.14
70 1 0.01
71 12 0.10
72 19 0.15
73 18 0.15
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (69 bp):
TGTCTCGAGTGAGACTAAATATTTCAAGAGAAATATCTCAAGTGAGATGAAATTTGTTTCAGGAG
AATC
Found at i:3140 original size:37 final size:37
Alignment explanation
Indices: 3091--3266 Score: 149
Period size: 38 Copynumber: 4.7 Consensus size: 37
3081 ATTTATTTCA
* ** *
3091 AGAGAAAATATCTTTAGTGAGATAAAATTTTGTTTCG
1 AGAGAAACTATCTCAAGTGAGATAAAATTTTGTTTTG
* * * *
3128 AGAGAAACTATCTCGAGTGATATGAAATTTTTTTTTTG
1 AGAGAAACTATCTCAAGTGAGAT-AAAATTTTGTTTTG
*
3166 AG-GAAAACTATCTCAAGTGAGATAGAATTATTGTTTTG
1 AGAG-AAACTATCTCAAGTGAGATAAAATT-TTGTTTTG
* * ** * *
3204 AGAGAAACTGTCTCGAGTGAGACGAAA-CTTGTTTTA
1 AGAGAAACTATCTCAAGTGAGATAAAATTTTGTTTTG
* * *
3240 AGAAAAACTATCTTAAGTGAGACAAAA
1 AGAGAAACTATCTCAAGTGAGATAAAA
3267 AAAATTTTAG
Statistics
Matches: 111, Mismatches: 24, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
36 29 0.26
37 24 0.22
38 57 0.51
39 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.33
Consensus pattern (37 bp):
AGAGAAACTATCTCAAGTGAGATAAAATTTTGTTTTG
Found at i:3424 original size:60 final size:61
Alignment explanation
Indices: 3337--3469 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 61
3327 AAACATCCTC
* * *
3337 AAGAGAGAGAAAATAGTCATGAAAAAGACAAGATTATTTGAA-AATTTTAAAGATGGCCTT
1 AAGAGAGGGAAAATAGTCATGAAAAAGACAAGATTATTTGAAGAATTTTAAAGATGCCCTA
* * * * * * *
3397 AAGAGAGGGAAAAT-GATCTTGAGAAAGACAATATTTTTTTAAGGATTTTACAGATGCCCTA
1 AAGAGAGGGAAAATAG-TCATGAAAAAGACAAGATTATTTGAAGAATTTTAAAGATGCCCTA
3458 AAGAGAGGGAAA
1 AAGAGAGGGAAA
3470 GTATAGTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.02
60 34 0.56
61 26 0.43
ACGTcount: A:0.45, C:0.08, G:0.23, T:0.25
Consensus pattern (61 bp):
AAGAGAGGGAAAATAGTCATGAAAAAGACAAGATTATTTGAAGAATTTTAAAGATGCCCTA
Found at i:3738 original size:21 final size:21
Alignment explanation
Indices: 3712--3757 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
3702 AATAAAGGGG
3712 ATAATAATAAGAATGAAAGAA
1 ATAATAATAAGAATGAAAGAA
* *
3733 ATAATAATAAGAATGATATAA
1 ATAATAATAAGAATGAAAGAA
3754 ATAA
1 ATAA
3758 GAAAGGATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (21 bp):
ATAATAATAAGAATGAAAGAA
Found at i:4168 original size:19 final size:21
Alignment explanation
Indices: 4125--4176 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
4115 GAAACCCCTT
4125 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
4146 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
4165 TGAAGATACATG
1 TGAAAATACATG
4177 CTCTTCGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:5096 original size:30 final size:31
Alignment explanation
Indices: 5055--5114 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
5045 ACATGTTGCC
**
5055 ATGATATCTAAATGATATACAAACATAATAA
1 ATGATATCTAAAACATATACAAACATAATAA
**
5086 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATACAAACATAATA
5115 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATACAAACATAATAA
Found at i:7865 original size:22 final size:22
Alignment explanation
Indices: 7837--7885 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
7827 TAAAGGGGAT
7837 AATAAT-ATAAGTAATGAAAAGA
1 AATAATAATAAG-AATGAAAAGA
* *
7859 AATAATAATAAGAATGATATGA
1 AATAATAATAAGAATGAAAAGA
7881 AATAA
1 AATAA
7886 AGAAAGGATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.24
Consensus pattern (22 bp):
AATAATAATAAGAATGAAAAGA
Found at i:8341 original size:19 final size:21
Alignment explanation
Indices: 8298--8348 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
8288 GAAACCCCTT
8298 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
8319 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
8338 TGAAGATACAT
1 TGAAAATACAT
8349 CCTCTTCGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:9277 original size:30 final size:31
Alignment explanation
Indices: 9236--9295 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
9226 ACATGTTGCC
**
9236 ATGATATCTAAATGATATGAAAACATAATAA
1 ATGATATCTAAAACATATGAAAACATAATAA
*
9267 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGAAAACATAATA
9296 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGAAAACATAATAA
Found at i:11299 original size:194 final size:193
Alignment explanation
Indices: 10986--11385 Score: 464
Period size: 194 Copynumber: 2.1 Consensus size: 193
10976 ATACGTGATG
* * * *
10986 AAAAGA-AAATTGTCACATTGTTAGTAACATAGTATATCGTCACCTAATAGTAGCATGGATGACA
1 AAAAGAGATATTGTCACATTGTTAGTAACATAATATATCGTCACCTAATAATAGCATGAATGACA
* ** **
11050 TTTATATATAACGTCACTATATAATTAATATTCAATGACAACTAATTATGTCACTAAATTATGTA
66 TTTATACATAACACCACTATATAATTAATATTCAATGACAACTAATTATGTCACTAAATTAAATA
* ***
11115 AAATTTCATTATTGATGATTTATATCGTCACCGCTAATACATTAAAATCAACCTATATGTGAC
131 AAATTTCATTATTGATAATTTATATCGTCACAAATAATACATTAAAATCAACCTATATGTGAC
* * * * **
11178 GAAAGAGATATTGTCACATTTTTAGTGACATAATATAAAT-GTTACCTAATAATATTATGAATGA
1 AAAAGAGATATTGTCACATTGTTAGTAACATAATAT--ATCGTCACCTAATAATAGCATGAATGA
* * * * * **
11242 CATTTATGCATAACACCACTTTATAATTTATATTCTATGA-AAGTTGGTTATGTCACTAAATTAA
64 CATTTATACATAACACCACTATATAATTAATATTCAATGACAA-CTAATTATGTCACTAAATTAA
* * * * * *
11306 ATAAGATTTCGTTATTGATAATTTATATTGTCATAAATAATGCATTAAAATCAACTTATATGTGA
128 ATAAAATTTCATTATTGATAATTTATATCGTCACAAATAATACATTAAAATCAACCTATATGTGA
11371 C
193 C
11372 AAAAGAGATATTGT
1 AAAAGAGATATTGT
11386 AGCAAATCAC
Statistics
Matches: 171, Mismatches: 33, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
192 5 0.03
193 27 0.16
194 137 0.80
195 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (193 bp):
AAAAGAGATATTGTCACATTGTTAGTAACATAATATATCGTCACCTAATAATAGCATGAATGACA
TTTATACATAACACCACTATATAATTAATATTCAATGACAACTAATTATGTCACTAAATTAAATA
AAATTTCATTATTGATAATTTATATCGTCACAAATAATACATTAAAATCAACCTATATGTGAC
Found at i:12668 original size:20 final size:20
Alignment explanation
Indices: 12626--12675 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
12616 TAATTATTAA
*
12626 AAATTAGAAAAAAATATAGAT
1 AAATTA-AAAAAAATATAAAT
* *
12647 AAATTAAAAATAATTTAAAT
1 AAATTAAAAAAAATATAAAT
*
12667 AATTTAAAA
1 AAATTAAAA
12676 TACTAAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (20 bp):
AAATTAAAAAAAATATAAAT
Found at i:13532 original size:22 final size:22
Alignment explanation
Indices: 13506--13551 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
13496 GTGAATTTTA
13506 TTACTTTGGACTTCAATTTCAT
1 TTACTTTGGACTTCAATTTCAT
13528 TTACTTTGGACTTCAATTTCAT
1 TTACTTTGGACTTCAATTTCAT
13550 TT
1 TT
13552 GAGTATTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.17, G:0.09, T:0.52
Consensus pattern (22 bp):
TTACTTTGGACTTCAATTTCAT
Found at i:18452 original size:2 final size:2
Alignment explanation
Indices: 18447--18478 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
18437 TTTTGTATTG
18447 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18479 CCGCCAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22071 original size:22 final size:22
Alignment explanation
Indices: 22041--22107 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
22031 ATATGATTAC
*
22041 ATGAAAATGTGATACAAGCTAT
1 ATGACAATGTGATACAAGCTAT
* * * *
22063 ATGACAATGAGCTACATGATTAT
1 ATGACAATGTGATACAAG-CTAT
* *
22086 ATGTCTATGTGATACAAGCTAT
1 ATGACAATGTGATACAAGCTAT
22108 GTGAAATATG
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
22 17 0.52
23 16 0.48
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (22 bp):
ATGACAATGTGATACAAGCTAT
Found at i:22082 original size:45 final size:45
Alignment explanation
Indices: 21989--22107 Score: 139
Period size: 45 Copynumber: 2.6 Consensus size: 45
21979 TTGATCTATG
* * * * * *
21989 TGATTACATGAAAATGTGATATAAGGTATGTGGCATTGACCTATA
1 TGATTACATGAAAATGTGATACAAGCTATATGACAATGACCTACA
*
22034 TGATTACATGAAAATGTGATACAAGCTATATGACAATGAGCTACA
1 TGATTACATGAAAATGTGATACAAGCTATATGACAATGACCTACA
* ***
22079 TGATTATATGTCTATGTGATACAAGCTAT
1 TGATTACATGAAAATGTGATACAAGCTAT
22108 GTGAAATATG
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (45 bp):
TGATTACATGAAAATGTGATACAAGCTATATGACAATGACCTACA
Found at i:22255 original size:23 final size:23
Alignment explanation
Indices: 22187--22273 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 23
22177 GAGTCGAGGG
* * * *
22187 TTCTATGTGGTCCTTTGGGATAA
1 TTCTACGTGGTCCTTCGGGACAT
22210 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
*
22233 TTCTACGTGGTCCTTCAGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
* *
22256 ATCTATGTGG-CACTTCGG
1 TTCTACGTGGTC-CTTCGG
22274 TGCATATTCT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 1 0.02
23 54 0.98
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:23726 original size:24 final size:24
Alignment explanation
Indices: 23699--23744 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
23689 TGAGCTTTGG
23699 GAAGCTCAGCAATATAAAACTATC
1 GAAGCTCAGCAATATAAAACTATC
23723 GAAGCTCAGCAATATAAAACTA
1 GAAGCTCAGCAATATAAAACTA
23745 CCAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.20
Consensus pattern (24 bp):
GAAGCTCAGCAATATAAAACTATC
Found at i:31188 original size:22 final size:22
Alignment explanation
Indices: 31141--31234 Score: 129
Period size: 22 Copynumber: 4.3 Consensus size: 22
31131 TCGAGGGTTC
31141 TATGTGGTCCTTCGGGACAAAAT
1 TATGTGGTCCTTCGGGAC-AAAT
*
31164 TATGTGGTCCTTTGGGACAAAT
1 TATGTGGTCCTTCGGGACAAAT
31186 TATGTGGTCCTTCGGGAC-AAT
1 TATGTGGTCCTTCGGGACAAAT
* *
31207 TATGTGG-CACTTCGGTAAAAAT
1 TATGTGGTC-CTTCGGGACAAAT
31229 TATGTG
1 TATGTG
31235 AGCTGTGGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
20 1 0.02
21 17 0.26
22 30 0.46
23 17 0.26
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (22 bp):
TATGTGGTCCTTCGGGACAAAT
Found at i:31229 original size:43 final size:44
Alignment explanation
Indices: 31141--31234 Score: 129
Period size: 43 Copynumber: 2.1 Consensus size: 44
31131 TCGAGGGTTC
* *
31141 TATGTGGTCCTTCGGGACAAAATTATGTGGTCCTTTGGGACAAAT
1 TATGTGGTCCTTCGGGAC-AAATTATGTGGTCCTTCGGGAAAAAT
*
31186 TATGTGGTCCTTCGGGAC-AATTATGTGG-CACTTCGGTAAAAAT
1 TATGTGGTCCTTCGGGACAAATTATGTGGTC-CTTCGGGAAAAAT
31229 TATGTG
1 TATGTG
31235 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
42 1 0.02
43 26 0.58
45 18 0.40
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (44 bp):
TATGTGGTCCTTCGGGACAAATTATGTGGTCCTTCGGGAAAAAT
Found at i:32226 original size:16 final size:16
Alignment explanation
Indices: 32205--32237 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
32195 ACAAAGAAAA
32205 AAATAAGTAACAATTT
1 AAATAAGTAACAATTT
*
32221 AAATAAGTAATAATTT
1 AAATAAGTAACAATTT
32237 A
1 A
32238 TTTTAGAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (16 bp):
AAATAAGTAACAATTT
Found at i:32360 original size:32 final size:32
Alignment explanation
Indices: 32324--32387 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
32314 CAGTTGTTTC
32324 AAATTCATGAATTCTAAGAAAGACATCAAGAT
1 AAATTCATGAATTCTAAGAAAGACATCAAGAT
32356 AAATTCATGAATTCTAAGAAAGACATCAAGAT
1 AAATTCATGAATTCTAAGAAAGACATCAAGAT
32388 TTATAATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.25
Consensus pattern (32 bp):
AAATTCATGAATTCTAAGAAAGACATCAAGAT
Found at i:33344 original size:27 final size:27
Alignment explanation
Indices: 33314--33377 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
33304 AGGTGCTTAA
33314 AATGTTTTTAGATCAATCTAGATATCT
1 AATGTTTTTAGATCAATCTAGATATCT
33341 AATGTTTTTAGATCAATCTAGATATCT
1 AATGTTTTTAGATCAATCTAGATATCT
33368 AATGTTTTTA
1 AATGTTTTTA
33378 ATATTACACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (27 bp):
AATGTTTTTAGATCAATCTAGATATCT
Found at i:34279 original size:20 final size:20
Alignment explanation
Indices: 34256--34304 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
34246 GCGAATTTAG
34256 AATTCGCAACACAGAAGTCA
1 AATTCGCAACACAGAAGTCA
* *
34276 AATTCGCAACACATAAGTTA
1 AATTCGCAACACAGAAGTCA
34296 AATTCGCAA
1 AATTCGCAA
34305 AGTACGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.20
Consensus pattern (20 bp):
AATTCGCAACACAGAAGTCA
Found at i:34355 original size:26 final size:26
Alignment explanation
Indices: 34317--34366 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
34307 TACGTTTATT
* * * *
34317 TTTGCAACGCGAATTTTATTTTCGAA
1 TTTGAAACACGAATATTAATTTCGAA
34343 TTTGAAACACGAATATTAATTTCG
1 TTTGAAACACGAATATTAATTTCG
34367 TAACACAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (26 bp):
TTTGAAACACGAATATTAATTTCGAA
Found at i:38996 original size:40 final size:40
Alignment explanation
Indices: 38906--39084 Score: 130
Period size: 40 Copynumber: 4.5 Consensus size: 40
38896 AAATAAAAGT
** * *
38906 TGTTGCGAAATTAAAATTCGTGCTGCGAATTCGAAAATCG
1 TGTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCG
* * * *
38946 AGTTGTGAAAACAGAATTCGTGTTGCGAATTAGAAAATCT
1 TGTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCG
* *
38986 TGTTGCGAAAAGAAAACTT-GTGTTGCGAATTTA-AAAATCA
1 TGTTGCGAAAACAAAA-TTCGTGTTGCGAA-TTAGAAAATCG
* ** * * * *
39026 CGTTGCGAATTCAGAAA-TCGAGTTGCAAATTTGAAATTTCG
1 TGTTGCGAAAACA-AAATTCGTGTTGCGAATTAGAAA-ATCG
* *
39067 TGTTGCGAATACCAAATT
1 TGTTGCGAAAACAAAATT
39085 TGCAACACGA
Statistics
Matches: 107, Mismatches: 25, Indels: 13
0.74 0.17 0.09
Matches are distributed among these distances:
39 3 0.03
40 83 0.78
41 21 0.20
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (40 bp):
TGTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCG
Found at i:39041 original size:80 final size:81
Alignment explanation
Indices: 38905--39075 Score: 177
Period size: 80 Copynumber: 2.1 Consensus size: 81
38895 AAAATAAAAG
** * * * *
38905 TTGTTGCGAAATTAAAATTCGTGCTGCGAATTCGAAAATCGAGTTGTGAAAACAGAATTCGTGTT
1 TTGTTGCGAAAAGAAAATTCGTGCTGCGAATTCAAAAATCGAGTTGCGAAAACAGAAATCGAGTT
*
38970 GCGAATTAGAAA-ATC
66 GCAAATTAGAAATATC
* * **
38985 TTGTTGCGAAAAGAAAACTT-GTGTTGCGAATTTAAAAATC-ACGTTGCGAATTCAGAAATCGAG
1 TTGTTGCGAAAAGAAAA-TTCGTGCTGCGAATTCAAAAATCGA-GTTGCGAAAACAGAAATCGAG
* *
39048 TTGCAAATTTGAAATTTC
64 TTGCAAATTAGAAATATC
*
39066 GTGTTGCGAA
1 TTGTTGCGAA
39076 TACCAAATTT
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
79 1 0.01
80 60 0.81
81 13 0.18
ACGTcount: A:0.35, C:0.12, G:0.22, T:0.31
Consensus pattern (81 bp):
TTGTTGCGAAAAGAAAATTCGTGCTGCGAATTCAAAAATCGAGTTGCGAAAACAGAAATCGAGTT
GCAAATTAGAAATATC
Found at i:39050 original size:20 final size:21
Alignment explanation
Indices: 38929--39056 Score: 74
Period size: 20 Copynumber: 6.4 Consensus size: 21
38919 AAATTCGTGC
38929 TGCGAATTC-GAAAATCGAGT
1 TGCGAATTCAGAAAATCGAGT
* ** * *
38949 TGTGAAAACAG-AATTCGTGT
1 TGCGAATTCAGAAAATCGAGT
**
38969 TGCGAATT-AGAAAATCTTGT
1 TGCGAATTCAGAAAATCGAGT
* * *
38989 TGCGAA--AAGAAAACTTGTGT
1 TGCGAATTCAGAAAA-TCGAGT
*
39009 TGCGAATTTA-AAAATC-ACGT
1 TGCGAATTCAGAAAATCGA-GT
39029 TGCGAATTCAG-AAATCGAGT
1 TGCGAATTCAGAAAATCGAGT
*
39049 TGCAAATT
1 TGCGAATT
39057 TGAAATTTCG
Statistics
Matches: 82, Mismatches: 17, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
19 8 0.10
20 67 0.82
21 6 0.07
22 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (21 bp):
TGCGAATTCAGAAAATCGAGT
Found at i:39190 original size:20 final size:20
Alignment explanation
Indices: 39167--39212 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
39157 AAGAAATTCT
*
39167 AGTTGCGAATTTTAAAACTG
1 AGTTGCGAATTTGAAAACTG
39187 AGTTGCGAATTTGAAAACTG
1 AGTTGCGAATTTGAAAACTG
*
39207 TGTTGC
1 AGTTGC
39213 AAAATTAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (20 bp):
AGTTGCGAATTTGAAAACTG
Found at i:39330 original size:2 final size:2
Alignment explanation
Indices: 39323--39369 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
39313 TATTTTCTCT
39323 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39365 TA TA T
1 TA TA T
39370 TTGAAAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45314 original size:16 final size:16
Alignment explanation
Indices: 45301--45333 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
45291 TGATCTGATC
45301 TGACATTTACCTGACT
1 TGACATTTACCTGACT
45317 TGACATTTACCTGACT
1 TGACATTTACCTGACT
45333 T
1 T
45334 ATATATCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (16 bp):
TGACATTTACCTGACT
Found at i:45494 original size:29 final size:30
Alignment explanation
Indices: 45404--45499 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 30
45394 TAAATCATAC
* * *
45404 TAATTAATATGATTAATT-T-TTAAATATTA
1 TAATAAATAT-ATTAATTATATTAATTATAA
*
45433 TAATAAA-ATATTAATTATAATAATTA-AA
1 TAATAAATATATTAATTATATTAATTATAA
* *
45461 TTAATAAATATTTTAA-TATATTAATTATGA
1 -TAATAAATATATTAATTATATTAATTATAA
*
45491 TAATTAATA
1 TAATAAATA
45500 CACTTTATAA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
27 7 0.13
28 4 0.07
29 36 0.67
30 7 0.13
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (30 bp):
TAATAAATATATTAATTATATTAATTATAA
Found at i:45537 original size:22 final size:20
Alignment explanation
Indices: 45513--45592 Score: 83
Period size: 22 Copynumber: 3.9 Consensus size: 20
45503 TTTATAATTA
45513 ATACTTATATTTATATACTTT
1 ATACTTATATTTA-ATACTTT
45534 AATACTTTATATTTAATAC-TT
1 -ATAC-TTATATTTAATACTTT
*
45555 ATATTATATAGTTTAATACTTT
1 ATACT-TATA-TTTAATACTTT
*
45577 ATA-TTATATGTAATAC
1 ATACTTATATTTAATAC
45593 CCCAATTTAG
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
19 8 0.15
20 11 0.21
21 11 0.21
22 13 0.25
23 9 0.17
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (20 bp):
ATACTTATATTTAATACTTT
Found at i:45570 original size:35 final size:36
Alignment explanation
Indices: 45501--45581 Score: 137
Period size: 35 Copynumber: 2.3 Consensus size: 36
45491 TAATTAATAC
*
45501 ACTTTATAATTAATACTTATATTTATATACTTTAAT
1 ACTTTATATTTAATACTTATATTTATATACTTTAAT
*
45537 ACTTTATATTTAATACTTATA-TTATATAGTTTAAT
1 ACTTTATATTTAATACTTATATTTATATACTTTAAT
45572 ACTTTATATT
1 ACTTTATATT
45582 ATATGTAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
35 23 0.53
36 20 0.47
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.54
Consensus pattern (36 bp):
ACTTTATATTTAATACTTATATTTATATACTTTAAT
Found at i:46363 original size:17 final size:17
Alignment explanation
Indices: 46341--46374 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46331 TTACAACCCG
46341 ACCCGACCCGACCCGTT
1 ACCCGACCCGACCCGTT
*
46358 ACCCGACCTGACCCGTT
1 ACCCGACCCGACCCGTT
46375 GACTCGACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.50, G:0.18, T:0.15
Consensus pattern (17 bp):
ACCCGACCCGACCCGTT
Found at i:48920 original size:24 final size:24
Alignment explanation
Indices: 48788--48906 Score: 193
Period size: 24 Copynumber: 5.0 Consensus size: 24
48778 TTCGATTCGA
48788 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
48812 ATTCTGATCTGATATTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
48836 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
48860 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
48884 ATTTTGATATGATACTTGACATG
1 ATTCTGATCTGATACTTGACATG
48907 AATTATGTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 88 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:49720 original size:16 final size:15
Alignment explanation
Indices: 49699--49785 Score: 60
Period size: 14 Copynumber: 5.9 Consensus size: 15
49689 GGGGGTTACA
49699 TTATATACTTTAGTAC
1 TTATATACTTTA-TAC
*
49715 TTATATACTTTATAT
1 TTATATACTTTATAC
49730 TTA-ATAC-TTATA-
1 TTATATACTTTATAC
* *
49742 TTCAAACACTTTATTAC
1 TT-ATATACTTTA-TAC
49759 TT-TATA-TTCTATA-
1 TTATATACTT-TATAC
*
49772 TTTTATACTTTATA
1 TTATATACTTTATA
49786 TATAAAGTAC
Statistics
Matches: 59, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
12 2 0.03
13 8 0.14
14 19 0.32
15 14 0.24
16 14 0.24
17 2 0.03
ACGTcount: A:0.33, C:0.11, G:0.01, T:0.54
Consensus pattern (15 bp):
TTATATACTTTATAC
Found at i:49783 original size:7 final size:7
Alignment explanation
Indices: 49702--49785 Score: 50
Period size: 7 Copynumber: 11.6 Consensus size: 7
49692 GGTTACATTA
49702 TATACTT
1 TATACTT
49709 TAGTACTT
1 TA-TACTT
49717 ATATACTT
1 -TATACTT
49725 TATA-TT
1 TATACTT
49731 TAATAC-T
1 T-ATACTT
49738 TATA-TT
1 TATACTT
* *
49744 CAAACACTT
1 --TATACTT
49753 TATTACTT
1 TA-TACTT
49761 TATA-TT
1 TATACTT
*
49767 CTATATTT
1 -TATACTT
49775 TATACTT
1 TATACTT
49782 TATA
1 TATA
49786 TATAAAGTAC
Statistics
Matches: 61, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
6 9 0.15
7 28 0.46
8 20 0.33
9 4 0.07
ACGTcount: A:0.33, C:0.12, G:0.01, T:0.54
Consensus pattern (7 bp):
TATACTT
Found at i:49831 original size:13 final size:13
Alignment explanation
Indices: 49813--49844 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
49803 AACAAACATG
49813 AAATTGGAAATAA
1 AAATTGGAAATAA
49826 AAATTGGAAATAA
1 AAATTGGAAATAA
49839 AAATTG
1 AAATTG
49845 AATAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (13 bp):
AAATTGGAAATAA
Found at i:51558 original size:22 final size:22
Alignment explanation
Indices: 51527--51568 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
51517 CTTAAAATTT
51527 TAATACATGCATCAT-ACATACA
1 TAATACATGCAT-ATAACATACA
*
51549 TAATATATGCATATAACATA
1 TAATACATGCATATAACATA
51569 TGTATCATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.48, C:0.17, G:0.05, T:0.31
Consensus pattern (22 bp):
TAATACATGCATATAACATACA
Found at i:51696 original size:2 final size:2
Alignment explanation
Indices: 51689--51856 Score: 170
Period size: 2 Copynumber: 87.5 Consensus size: 2
51679 ATACATACAT
* * * *
51689 AC AC AC AC GC AC GC AC GC GC AC AC AC AC AC AC AC A- 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
* * * * * *
51730 AC AC GC AC GC AC GC AC GC AC GC AC AC AC AT A- 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
* * *
51771 AC AC A- AC AC AC GC AC GC AC AC AC AT 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
51811 AC AC AC AC AC -C AC AC AC AC AC AC AC AC -C AC AC AC -C AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
51850 AC AC AC A
1 AC AC AC A
51857 TAAAAGCTTA
Statistics
Matches: 137, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
1 7 0.05
2 130 0.95
ACGTcount: A:0.44, C:0.48, G:0.07, T:0.01
Consensus pattern (2 bp):
AC
Found at i:51730 original size:17 final size:17
Alignment explanation
Indices: 51708--51856 Score: 148
Period size: 17 Copynumber: 8.9 Consensus size: 17
51698 CACGCACGCG
51708 CACACACACACACACAA
1 CACACACACACACACAA
* * *
51725 CACACACACGCACGCACG
1 CACACACACACACACA-A
* *
51743 CACGCACGCACACACATA
1 CACACACACACACACA-A
51761 -ACACACACACACACAA
1 CACACACACACACACAA
* *
51777 CACACGCACGCACAC-A
1 CACACACACACACACAA
*
51793 CATA-ACACACACAC-A
1 CACACACACACACACAA
51808 CACACACACACAC-C-A
1 CACACACACACACACAA
*
51823 CACACACACACACACCA
1 CACACACACACACACAA
51840 CACACCACACACACACA
1 CACA-CACACACACACA
51857 TAAAAGCTTA
Statistics
Matches: 108, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
15 27 0.25
16 14 0.13
17 44 0.41
18 23 0.21
ACGTcount: A:0.46, C:0.48, G:0.05, T:0.01
Consensus pattern (17 bp):
CACACACACACACACAA
Found at i:51898 original size:22 final size:22
Alignment explanation
Indices: 51873--51914 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
51863 CTTAAAATTT
51873 TAATACATGCATCAT-ACATACA
1 TAATACATGCAT-ATAACATACA
*
51895 TAATATATGCATATAACATA
1 TAATACATGCATATAACATA
51915 TGTATCATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.48, C:0.17, G:0.05, T:0.31
Consensus pattern (22 bp):
TAATACATGCATATAACATACA
Found at i:52142 original size:17 final size:16
Alignment explanation
Indices: 52107--52146 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
52097 AATACACACA
52107 ACAT-TATGCATATAT
1 ACATATATGCATATAT
*
52122 ACATATATGCATGTAAT
1 ACATATATGCATAT-AT
52139 ACATATAT
1 ACATATAT
52147 TAGAGTTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 8 0.36
17 10 0.45
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (16 bp):
ACATATATGCATATAT
Found at i:52161 original size:7 final size:7
Alignment explanation
Indices: 52146--52231 Score: 64
Period size: 7 Copynumber: 12.3 Consensus size: 7
52136 AATACATATA
*
52146 TTAGAGT
1 TTAGGGT
52153 TTAGGGT
1 TTAGGGT
**
52160 TTAATGT
1 TTAGGGT
*
52167 TTAGTGT
1 TTAGGGT
*
52174 TTATGGT
1 TTAGGGT
*
52181 TTAGGAT
1 TTAGGGT
**
52188 TTATTGT
1 TTAGGGT
**
52195 TTATAGT
1 TTAGGGT
**
52202 TTAAAGT
1 TTAGGGT
52209 TTAGGGT
1 TTAGGGT
52216 TTAGGGT
1 TTAGGGT
52223 TTAGGGT
1 TTAGGGT
52230 TT
1 TT
52232 CTATAAACTA
Statistics
Matches: 64, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 64 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (7 bp):
TTAGGGT
Found at i:52170 original size:14 final size:14
Alignment explanation
Indices: 52151--52231 Score: 74
Period size: 14 Copynumber: 5.8 Consensus size: 14
52141 ATATATTAGA
52151 GTTTAGGGTTTAAT
1 GTTTAGGGTTTAAT
*
52165 GTTTAGTGTTT-AT
1 GTTTAGGGTTTAAT
* *
52178 GGTTTAGGATTTATT
1 -GTTTAGGGTTTAAT
** *
52193 GTTTATAGTTTAAA
1 GTTTAGGGTTTAAT
**
52207 GTTTAGGGTTTAGG
1 GTTTAGGGTTTAAT
52221 GTTTAGGGTTT
1 GTTTAGGGTTT
52232 CTATAAACTA
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
13 2 0.04
14 49 0.94
15 1 0.02
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (14 bp):
GTTTAGGGTTTAAT
Found at i:52231 original size:21 final size:21
Alignment explanation
Indices: 52146--52231 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 21
52136 AATACATATA
* *
52146 TTAGAGTTTAGGGTTTAATGT
1 TTAGTGTTTAGGGTTTAAGGT
*
52167 TTAGTGTTTATGGTTT-AGGAT
1 TTAGTGTTTAGGGTTTAAGG-T
* ** *
52188 TTATTGTTTATAGTTTAAAGT
1 TTAGTGTTTAGGGTTTAAGGT
* *
52209 TTAGGGTTTAGGGTTTAGGGT
1 TTAGTGTTTAGGGTTTAAGGT
52230 TT
1 TT
52232 CTATAAACTA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
20 2 0.04
21 47 0.92
22 2 0.04
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (21 bp):
TTAGTGTTTAGGGTTTAAGGT
Found at i:52330 original size:13 final size:11
Alignment explanation
Indices: 52305--52351 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
52295 TAATTTACTT
52305 TATATAGTTTA
1 TATATAGTTTA
*
52316 TATATAGGTTA
1 TATATAGTTTA
52327 TATATA---TA
1 TATATAGTTTA
52335 TATATAGTTTA
1 TATATAGTTTA
52346 TATATA
1 TATATA
52352 CTATACGTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 8 0.25
11 24 0.75
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:52336 original size:17 final size:17
Alignment explanation
Indices: 52314--52356 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
52304 TTATATAGTT
52314 TATATATAGGTTATATATA
1 TATATATA-GTT-TATATA
52333 TATATATAGTTTATATA
1 TATATATAGTTTATATA
52350 TACTATA
1 TA-TATA
52357 CGTGGTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.35
18 7 0.30
19 8 0.35
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (17 bp):
TATATATAGTTTATATA
Found at i:52740 original size:21 final size:21
Alignment explanation
Indices: 52716--52769 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
52706 TCTATTTATA
*
52716 TTATGGTTTATGGTTTAGTAT
1 TTATGGTTTATGGTTTAGGAT
**
52737 TTATGGTTTAAAGTTTAGGAT
1 TTATGGTTTATGGTTTAGGAT
* *
52758 TTAGGGGTTATG
1 TTATGGTTTATG
52770 AATTAGAGTT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (21 bp):
TTATGGTTTATGGTTTAGGAT
Found at i:52877 original size:2 final size:2
Alignment explanation
Indices: 52872--52941 Score: 90
Period size: 2 Copynumber: 36.0 Consensus size: 2
52862 TTATATAGTT
* * *
52872 TA TA TA TA TA TA TA TA TA TG T- TA TC TA TA TA TG T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
52912 TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
52942 CACTATACAT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
1 2 0.03
2 58 0.97
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53124 original size:2 final size:2
Alignment explanation
Indices: 53113--53156 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
53103 ATAGTATTTC
53113 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
53154 TA T
1 TA T
53157 CTAATCTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53392 original size:19 final size:21
Alignment explanation
Indices: 53366--53421 Score: 91
Period size: 19 Copynumber: 2.8 Consensus size: 21
53356 TCTCAATTCT
53366 TAATTTCCCTCTAAATTTTTC
1 TAATTTCCCTCTAAATTTTTC
53387 T-A-TTCCCTCTAAA-TTTTC
1 TAATTTCCCTCTAAATTTTTC
53405 TAATTTCCCTCTAAATT
1 TAATTTCCCTCTAAATT
53422 CTCAATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.19
19 12 0.38
20 12 0.38
21 2 0.06
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATTTCCCTCTAAATTTTTC
Found at i:53414 original size:20 final size:20
Alignment explanation
Indices: 53366--53421 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
53356 TCTCAATTCT
53366 TAATTTCCCTCTAAATTTTTC
1 TAATTTCCCTCTAAA-TTTTC
53387 T-A-TTCCCTCTAAATTTTC
1 TAATTTCCCTCTAAATTTTC
53405 TAATTTCCCTCTAAATT
1 TAATTTCCCTCTAAATT
53422 CTCAATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.18
19 12 0.36
20 14 0.42
21 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATTTCCCTCTAAATTTTC
Found at i:53549 original size:2 final size:2
Alignment explanation
Indices: 53542--53791 Score: 64
Period size: 2 Copynumber: 126.0 Consensus size: 2
53532 ACTTTGAATA
* *
53542 AT AT AT AT AT AT AT AT AT AT AC ACT AT AT -T A- AT AT AA AT -T
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * * * * *
53582 AT AGT TT AT AA ACT AT AT AT -T TT TT AT AT -T TT AT AC AT AT AT
1 AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
53624 AGT TT AC AT AT AT AT AGT TT AC AT AT AT AGT TT AT AT AT AT AGT
1 A-T AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT A-T
* * *
53668 -T CAT AT AA AC AT A- AT TT AT AT AT AT A- ACT -T AT A- AT A- AT
1 AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * *
53706 -T AT AT AGT TT AT A- AT AT AA AT AT AGT TT AT AT AT AT AGT TT
1 AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT
* *
53747 AT AT AT AT AGT TT AT AT AT AA ACT -T AT AT -T AT AT AT AT AT -T
1 AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
53788 AT AT
1 AT AT
53792 TTTTTTCAAT
Statistics
Matches: 179, Mismatches: 39, Indels: 60
0.64 0.14 0.22
Matches are distributed among these distances:
1 16 0.09
2 151 0.84
3 12 0.07
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:53660 original size:103 final size:102
Alignment explanation
Indices: 53544--53791 Score: 249
Period size: 103 Copynumber: 2.4 Consensus size: 102
53534 TTTGAATAAT
* * * *
53544 ATATATA-TATATATATATACACTATATTAATATAAATTATAGTTTATAAAC-TAT-ATATTTTT
1 ATATATAGTTTATATATATA-ACTATATTAATATAAATTATA-TATAT-AACTTATAATA-ATTA
*
53606 TATA-TTT-T-ATACATATATAGTTTACATATATATAGTTTAC
62 TATAGTTTATAATACAAATATAGTTT--ATATATATAGTTTAC
** * * *
53646 ATATATAGTTTATATATATAGTTCATATAAACATAATTTATATATATAACTTATAATAATTATAT
1 ATATATAGTTTATATATATAACT-ATATTAATATAAATTATATATATAACTTATAATAATTATAT
* *
53711 AGTTTATAATATAAATATAGTTTATATATATAGTTTAT
65 AGTTTATAATACAAATATAGTTTATATATATAGTTTAC
*
53749 ATATATAGTTTATATATA-AACTTATATTATATATATATTATAT
1 ATATATAGTTTATATATATAAC-TATATTA-ATATAAATTATAT
53792 TTTTTTCAAT
Statistics
Matches: 119, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
101 3 0.03
102 27 0.23
103 75 0.63
104 1 0.01
105 13 0.11
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (102 bp):
ATATATAGTTTATATATATAACTATATTAATATAAATTATATATATAACTTATAATAATTATATA
GTTTATAATACAAATATAGTTTATATATATAGTTTAC
Found at i:53736 original size:49 final size:42
Alignment explanation
Indices: 53618--53786 Score: 157
Period size: 41 Copynumber: 3.8 Consensus size: 42
53608 TATTTTATAC
* * *
53618 ATATATAGTTTACATAT--ATATAGTTTACATATATAGTTTAT
1 ATATATAGTTTATATATAAATATA-TTTATATATATACTTTAT
*
53659 ATATATAGTTCATATA-AACATA-ATTTATATATATAACTTATAAT
1 ATATATAGTTTATATATAA-ATATATTTATATATAT-ACTT-T-AT
*
53703 AATTATATAGTTTATAATATAAATATAGTTTATATATATAGTTTAT
1 -A-TATATAGTTTAT-ATATAAATATA-TTTATATATATACTTTAT
53749 ATATATAGTTTATATATAAACTTATATTATATATATAT
1 ATATATAGTTTATATATAAA--TATATT-TATATATAT
53787 TATATTTTTT
Statistics
Matches: 107, Mismatches: 6, Indels: 26
0.77 0.04 0.19
Matches are distributed among these distances:
41 24 0.22
42 4 0.04
43 11 0.10
44 16 0.15
45 15 0.14
46 13 0.12
47 7 0.07
48 6 0.06
49 11 0.10
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.48
Consensus pattern (42 bp):
ATATATAGTTTATATATAAATATATTTATATATATACTTTAT
Found at i:53741 original size:13 final size:13
Alignment explanation
Indices: 53618--53766 Score: 128
Period size: 13 Copynumber: 11.4 Consensus size: 13
53608 TATTTTATAC
53618 ATATATAGTTTACAT
1 ATATATAGTTT--AT
*
53633 ATATATAGTTTAC
1 ATATATAGTTTAT
53646 ATATATAGTTTAT
1 ATATATAGTTTAT
53659 ATATATAGTTCATAT
1 ATATATAGTT--TAT
* * *
53674 AAACATAATTTAT
1 ATATATAGTTTAT
**
53687 ATATATAACTTAT
1 ATATATAGTTTAT
53700 A-ATA-A--TTAT
1 ATATATAGTTTAT
* *
53709 ATAGTTTA-TAATAT
1 ATA-TATAGT-TTAT
*
53723 AAATATAGTTTAT
1 ATATATAGTTTAT
53736 ATATATAGTTTAT
1 ATATATAGTTTAT
53749 ATATATAGTTTAT
1 ATATATAGTTTAT
53762 ATATA
1 ATATA
53767 AACTTATATT
Statistics
Matches: 112, Mismatches: 14, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
9 5 0.04
10 1 0.01
11 2 0.02
12 4 0.04
13 73 0.65
14 6 0.05
15 21 0.19
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (13 bp):
ATATATAGTTTAT
Found at i:53778 original size:17 final size:16
Alignment explanation
Indices: 53758--53792 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
53748 TATATATAGT
53758 TTATATATAAACTTATA
1 TTATATATAAA-TTATA
*
53775 TTATATATATATTATA
1 TTATATATAAATTATA
53791 TT
1 TT
53793 TTTTTCAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATATAAATTATA
Found at i:53781 original size:26 final size:26
Alignment explanation
Indices: 53618--53766 Score: 73
Period size: 28 Copynumber: 5.2 Consensus size: 26
53608 TATTTTATAC
* * *
53618 ATATATAGTTTACATATATATAGTTTAC
1 ATATATAGTTT--ATATATAAACTTTAT
* *
53646 ATATATAGTTTATATATATAGTTCATAT
1 ATATATAGTTTATATATAAACTT--TAT
* * *
53674 AAACATAATTTATATATATAACTTATAAT
1 ATATATAGTTTATATATA-AACTT-T-AT
*
53703 AATTATATAGTTTATAATATAAATATAGTTTAT
1 -A-TATATAGTTTAT-ATAT--A-A-ACTTTAT
* *
53736 ATATATAGTTTATATATATAGTTTAT
1 ATATATAGTTTATATATAAACTTTAT
53762 ATATA
1 ATATA
53767 AACTTATATT
Statistics
Matches: 100, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
26 24 0.24
28 31 0.31
29 5 0.05
30 5 0.05
31 21 0.21
32 5 0.05
33 2 0.02
34 4 0.04
35 3 0.03
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (26 bp):
ATATATAGTTTATATATAAACTTTAT
Found at i:53785 original size:11 final size:11
Alignment explanation
Indices: 53683--53791 Score: 52
Period size: 13 Copynumber: 9.5 Consensus size: 11
53673 TAAACATAAT
53683 TTATATATATAA
1 TTATATATAT-A
53695 CTTATA-ATA-A
1 -TTATATATATA
53705 TTATATAGTTTATA
1 TTATATA---TATA
* *
53719 ATATAAATATA
1 TTATATATATA
53730 GTTTATATATATA
1 --TTATATATATA
53743 GTTTATATATATA
1 --TTATATATATA
53756 GTT-TATATATA
1 -TTATATATATA
53767 --A-ACT-TATA
1 TTATA-TATATA
53775 TTATATATATA
1 TTATATATATA
53786 TTATAT
1 TTATAT
53792 TTTTTTCAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
8 5 0.06
9 6 0.08
10 4 0.05
11 23 0.29
12 5 0.06
13 29 0.37
14 6 0.08
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (11 bp):
TTATATATATA
Found at i:57741 original size:30 final size:31
Alignment explanation
Indices: 57696--57755 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
57686 GTTTAATTTT
*
57696 TAATATAACCTTTAAATTTTAGATAAAATAC
1 TAATATAACCTTTAAACTTTAGATAAAATAC
*
57727 TAATTTAA-CTTTAAACTTTAGATAAAATA
1 TAATATAACCTTTAAACTTTAGATAAAATA
57756 TCAATTTGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.40
Consensus pattern (31 bp):
TAATATAACCTTTAAACTTTAGATAAAATAC
Found at i:68264 original size:868 final size:868
Alignment explanation
Indices: 66589--68324 Score: 3472
Period size: 868 Copynumber: 2.0 Consensus size: 868
66579 TAAGCCCTAT
66589 GGACGTACGGGCCTAAGGATACATGCCCAAACCTATCCTTAGGTGGCTTCCTTTTTGCTGTGTGC
1 GGACGTACGGGCCTAAGGATACATGCCCAAACCTATCCTTAGGTGGCTTCCTTTTTGCTGTGTGC
66654 TTAAGGTATGCCCTGCGGACGTAGTTCTGAGGAACTGCGGATGCTGTACATGAAAAGGATTTAAA
66 TTAAGGTATGCCCTGCGGACGTAGTTCTGAGGAACTGCGGATGCTGTACATGAAAAGGATTTAAA
66719 CTACGAGTTACAAAAGTGAAACTTCATTATGATTTTATGATGATTTACTGAACTATTACTCATTT
131 CTACGAGTTACAAAAGTGAAACTTCATTATGATTTTATGATGATTTACTGAACTATTACTCATTT
66784 ATTGTACCTACTATGATTTTATCGTACTGTTGGAACACACTAGACATCCTATTCGATCTCATGAA
196 ATTGTACCTACTATGATTTTATCGTACTGTTGGAACACACTAGACATCCTATTCGATCTCATGAA
66849 AACGTGATACTATGAATGATTCCTATGAACTGTGATCTTCATGGTTTCTACTAATGGAATCCCAG
261 AACGTGATACTATGAATGATTCCTATGAACTGTGATCTTCATGGTTTCTACTAATGGAATCCCAG
66914 ATTATCTTGCAAACTGGTATACGTTTGATTCAATAAGGAAATTATGACTTCACATTTATCTGCAT
326 ATTATCTTGCAAACTGGTATACGTTTGATTCAATAAGGAAATTATGACTTCACATTTATCTGCAT
66979 GTCCTTTAGCATCACTCGGTAGTTCTGTATTACTGAGCTTTCCGAAGCTCACTCTATTACTCACC
391 GTCCTTTAGCATCACTCGGTAGTTCTGTATTACTGAGCTTTCCGAAGCTCACTCTATTACTCACC
67044 ATTGCAGGTTAAAAGAATTGTATCAGTGCAACTATCGACTTCAGTAAGGGAGTTCTTCCAGCGTT
456 ATTGCAGGTTAAAAGAATTGTATCAGTGCAACTATCGACTTCAGTAAGGGAGTTCTTCCAGCGTT
67109 GTTTGCAGAGTATGGTACATGTGATTAGGGGGCATGTAATTGTATTTTGTTTTATATAGGAGTCT
521 GTTTGCAGAGTATGGTACATGTGATTAGGGGGCATGTAATTGTATTTTGTTTTATATAGGAGTCT
67174 GAAAATCTGTTTTATTTCTTCATATTGATAAATTATTTTATAATTTATATGTTTTAATAAAAGAT
586 GAAAATCTGTTTTATTTCTTCATATTGATAAATTATTTTATAATTTATATGTTTTAATAAAAGAT
67239 TTAAATTTTCCGCTATTTTTATGGTGGGTCACTTTGGTGGCCTTAATGTGACACTCCAGATCGGA
651 TTAAATTTTCCGCTATTTTTATGGTGGGTCACTTTGGTGGCCTTAATGTGACACTCCAGATCGGA
67304 TCGGGTTATCCGTATCGGTCTGAGGGGGTTACATTTAGTTGTATCAGAGTTATGGTTTGAGTCAA
716 TCGGGTTATCCGTATCGGTCTGAGGGGGTTACATTTAGTTGTATCAGAGTTATGGTTTGAGTCAA
67369 AATTTTTGAAAAAAAAATGGTTTTTGTACGAATAATCTTTGAAAAAACTTTATAAAATGGGACCT
781 AATTTTTGAAAAAAAAATGGTTTTTGTACGAATAATCTTTGAAAAAACTTTATAAAATGGGACCT
67434 TTTAGTACGAAATGAGGCTTTTC
846 TTTAGTACGAAATGAGGCTTTTC
67457 GGACGTACGGGCCTAAGGATACATGCCCAAACCTATCCTTAGGTGGCTTCCTTTTTGCTGTGTGC
1 GGACGTACGGGCCTAAGGATACATGCCCAAACCTATCCTTAGGTGGCTTCCTTTTTGCTGTGTGC
67522 TTAAGGTATGCCCTGCGGACGTAGTTCTGAGGAACTGCGGATGCTGTACATGAAAAGGATTTAAA
66 TTAAGGTATGCCCTGCGGACGTAGTTCTGAGGAACTGCGGATGCTGTACATGAAAAGGATTTAAA
67587 CTACGAGTTACAAAAGTGAAACTTCATTATGATTTTATGATGATTTACTGAACTATTACTCATTT
131 CTACGAGTTACAAAAGTGAAACTTCATTATGATTTTATGATGATTTACTGAACTATTACTCATTT
67652 ATTGTACCTACTATGATTTTATCGTACTGTTGGAACACACTAGACATCCTATTCGATCTCATGAA
196 ATTGTACCTACTATGATTTTATCGTACTGTTGGAACACACTAGACATCCTATTCGATCTCATGAA
67717 AACGTGATACTATGAATGATTCCTATGAACTGTGATCTTCATGGTTTCTACTAATGGAATCCCAG
261 AACGTGATACTATGAATGATTCCTATGAACTGTGATCTTCATGGTTTCTACTAATGGAATCCCAG
67782 ATTATCTTGCAAACTGGTATACGTTTGATTCAATAAGGAAATTATGACTTCACATTTATCTGCAT
326 ATTATCTTGCAAACTGGTATACGTTTGATTCAATAAGGAAATTATGACTTCACATTTATCTGCAT
67847 GTCCTTTAGCATCACTCGGTAGTTCTGTATTACTGAGCTTTCCGAAGCTCACTCTATTACTCACC
391 GTCCTTTAGCATCACTCGGTAGTTCTGTATTACTGAGCTTTCCGAAGCTCACTCTATTACTCACC
67912 ATTGCAGGTTAAAAGAATTGTATCAGTGCAACTATCGACTTCAGTAAGGGAGTTCTTCCAGCGTT
456 ATTGCAGGTTAAAAGAATTGTATCAGTGCAACTATCGACTTCAGTAAGGGAGTTCTTCCAGCGTT
67977 GTTTGCAGAGTATGGTACATGTGATTAGGGGGCATGTAATTGTATTTTGTTTTATATAGGAGTCT
521 GTTTGCAGAGTATGGTACATGTGATTAGGGGGCATGTAATTGTATTTTGTTTTATATAGGAGTCT
68042 GAAAATCTGTTTTATTTCTTCATATTGATAAATTATTTTATAATTTATATGTTTTAATAAAAGAT
586 GAAAATCTGTTTTATTTCTTCATATTGATAAATTATTTTATAATTTATATGTTTTAATAAAAGAT
68107 TTAAATTTTCCGCTATTTTTATGGTGGGTCACTTTGGTGGCCTTAATGTGACACTCCAGATCGGA
651 TTAAATTTTCCGCTATTTTTATGGTGGGTCACTTTGGTGGCCTTAATGTGACACTCCAGATCGGA
68172 TCGGGTTATCCGTATCGGTCTGAGGGGGTTACATTTAGTTGTATCAGAGTTATGGTTTGAGTCAA
716 TCGGGTTATCCGTATCGGTCTGAGGGGGTTACATTTAGTTGTATCAGAGTTATGGTTTGAGTCAA
68237 AATTTTTGAAAAAAAAATGGTTTTTGTACGAATAATCTTTGAAAAAACTTTATAAAATGGGACCT
781 AATTTTTGAAAAAAAAATGGTTTTTGTACGAATAATCTTTGAAAAAACTTTATAAAATGGGACCT
68302 TTTAGTACGAAATGAGGCTTTTC
846 TTTAGTACGAAATGAGGCTTTTC
68325 TATAGATTTC
Statistics
Matches: 868, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
868 868 1.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (868 bp):
GGACGTACGGGCCTAAGGATACATGCCCAAACCTATCCTTAGGTGGCTTCCTTTTTGCTGTGTGC
TTAAGGTATGCCCTGCGGACGTAGTTCTGAGGAACTGCGGATGCTGTACATGAAAAGGATTTAAA
CTACGAGTTACAAAAGTGAAACTTCATTATGATTTTATGATGATTTACTGAACTATTACTCATTT
ATTGTACCTACTATGATTTTATCGTACTGTTGGAACACACTAGACATCCTATTCGATCTCATGAA
AACGTGATACTATGAATGATTCCTATGAACTGTGATCTTCATGGTTTCTACTAATGGAATCCCAG
ATTATCTTGCAAACTGGTATACGTTTGATTCAATAAGGAAATTATGACTTCACATTTATCTGCAT
GTCCTTTAGCATCACTCGGTAGTTCTGTATTACTGAGCTTTCCGAAGCTCACTCTATTACTCACC
ATTGCAGGTTAAAAGAATTGTATCAGTGCAACTATCGACTTCAGTAAGGGAGTTCTTCCAGCGTT
GTTTGCAGAGTATGGTACATGTGATTAGGGGGCATGTAATTGTATTTTGTTTTATATAGGAGTCT
GAAAATCTGTTTTATTTCTTCATATTGATAAATTATTTTATAATTTATATGTTTTAATAAAAGAT
TTAAATTTTCCGCTATTTTTATGGTGGGTCACTTTGGTGGCCTTAATGTGACACTCCAGATCGGA
TCGGGTTATCCGTATCGGTCTGAGGGGGTTACATTTAGTTGTATCAGAGTTATGGTTTGAGTCAA
AATTTTTGAAAAAAAAATGGTTTTTGTACGAATAATCTTTGAAAAAACTTTATAAAATGGGACCT
TTTAGTACGAAATGAGGCTTTTC
Found at i:70385 original size:31 final size:31
Alignment explanation
Indices: 70349--70453 Score: 119
Period size: 31 Copynumber: 3.5 Consensus size: 31
70339 TAAATTAAAA
70349 GTTTAGTGG-CTAAAGTATAAACTTAGGAAAG
1 GTTTAG-GGACTAAAGTATAAACTTAGGAAAG
* * ** *
70380 GTTTAGGGACTAAATTGTAATTTTA--AAAA
1 GTTTAGGGACTAAAGTATAAACTTAGGAAAG
70409 GTTTAGTGG-CTAAAGTATAAACTTAGGAAAG
1 GTTTAG-GGACTAAAGTATAAACTTAGGAAAG
70440 GTTTAGGGACTAAA
1 GTTTAGGGACTAAA
70454 TTGTAATTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
29 21 0.36
30 6 0.10
31 32 0.54
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (31 bp):
GTTTAGGGACTAAAGTATAAACTTAGGAAAG
Found at i:70435 original size:60 final size:60
Alignment explanation
Indices: 70345--70471 Score: 254
Period size: 60 Copynumber: 2.1 Consensus size: 60
70335 TGAATAAATT
70345 AAAAGTTTAGTGGCTAAAGTATAAACTTAGGAAAGGTTTAGGGACTAAATTGTAATTTTA
1 AAAAGTTTAGTGGCTAAAGTATAAACTTAGGAAAGGTTTAGGGACTAAATTGTAATTTTA
70405 AAAAGTTTAGTGGCTAAAGTATAAACTTAGGAAAGGTTTAGGGACTAAATTGTAATTTTA
1 AAAAGTTTAGTGGCTAAAGTATAAACTTAGGAAAGGTTTAGGGACTAAATTGTAATTTTA
70465 AAAAGTT
1 AAAAGTT
70472 ATGTGGAAAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 67 1.00
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (60 bp):
AAAAGTTTAGTGGCTAAAGTATAAACTTAGGAAAGGTTTAGGGACTAAATTGTAATTTTA
Found at i:74200 original size:54 final size:55
Alignment explanation
Indices: 74013--74216 Score: 302
Period size: 55 Copynumber: 3.7 Consensus size: 55
74003 CAAATGGCAC
*
74013 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAAGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* * * * *
74068 TGTGTTCAAAACTAAGAAATTCAAAATAAGTTTATGAATTTTCTTATGGGCATTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* *
74123 TGCGTGTAAAACTAAGAAATTCATAATAAGTTTATG-ATTTCCGTATGGGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
* * *
74177 TGTGTGCAAAATTAAAAAATTCATAATAATTTTATGAATT
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATT
74217 AGAGTAGGCA
Statistics
Matches: 130, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
54 46 0.35
55 84 0.65
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.35
Consensus pattern (55 bp):
TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
Found at i:74338 original size:81 final size:82
Alignment explanation
Indices: 74242--74525 Score: 468
Period size: 79 Copynumber: 3.5 Consensus size: 82
74232 CTAAAATAAT
* * *
74242 AGATTTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAATGGTT
1 AGATTTAATGGCCTAGCTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATTAAAGGTT
74307 AAATACCTTTGAGTAAA
66 AAATACCTTTGAGTAAA
* *
74324 AGA-TTAATGACCTAGCTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAAATTAAAGGTT
1 AGATTTAATGGCCTAGCTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATTAAAGGTT
74388 AAATACCTTTGAGTAAA
66 AAATACCTTTGAGTAAA
*
74405 AGATTTAATGGCCTAGC---GCATTTGACAGAAAAGTGTCAATTATGCCAGTTAGATTAAAGGTT
1 AGATTTAATGGCCTAGCTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATTAAAGGTT
*
74467 AAATACCTTTAAGTAAA
66 AAATACCTTTGAGTAAA
*
74484 AGATTTAATGGCCTAGCTATGCATTTGACAGAAAGGTGTCAA
1 AGATTTAATGGCCTAGCTATGCATTTGACAGAAATGTGTCAA
74526 CTATCAATAG
Statistics
Matches: 188, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
79 76 0.40
81 76 0.40
82 36 0.19
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (82 bp):
AGATTTAATGGCCTAGCTATGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATTAAAGGTT
AAATACCTTTGAGTAAA
Found at i:74710 original size:13 final size:13
Alignment explanation
Indices: 74656--74704 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
74646 TGCGTCATAA
74656 ATTTATGACGCAC
1 ATTTATGACGCAC
**
74669 ATTTATGACATAC
1 ATTTATGACGCAC
*
74682 ATTTATGACGCGC
1 ATTTATGACGCAC
74695 ATTTATGACG
1 ATTTATGACG
74705 TTCATTGAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:74710 original size:26 final size:26
Alignment explanation
Indices: 74651--74703 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
74641 AACTGTGCGT
*
74651 CATAAATTTATGACGCACATTTATGA
1 CATACATTTATGACGCACATTTATGA
*
74677 CATACATTTATGACGCGCATTTATGA
1 CATACATTTATGACGCACATTTATGA
74703 C
1 C
74704 GTTCATTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (26 bp):
CATACATTTATGACGCACATTTATGA
Found at i:78997 original size:19 final size:20
Alignment explanation
Indices: 78973--79011 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
78963 GGGCGCCACC
* *
78973 GATGAGGAGTAGAAA-TGTT
1 GATGAGAAGGAGAAAGTGTT
78992 GATGAGAAGGAGAAAGTGTT
1 GATGAGAAGGAGAAAGTGTT
79012 TGGTCTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (20 bp):
GATGAGAAGGAGAAAGTGTT
Found at i:79489 original size:82 final size:81
Alignment explanation
Indices: 79345--79807 Score: 624
Period size: 82 Copynumber: 5.7 Consensus size: 81
79335 TCTTGTAGTG
* ** * *
79345 TATGTCAGTTAGATGAAATATTAAATACTTTTGAGTAAAAGATTTAATGGCCTAGCTCTGCATTT
1 TATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTTAATGGCCTAGCTATGCATTT
*
79410 GATAGAAAGATGTCAAT
66 GACAGAAAG-TGTCAAT
* * *
79427 TATGCCAGTTAGATGGAAGGTTAAATACATTTGAGTAAAAGATTTAATGGCCTAGTTGTGCATTT
1 TATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTTAATGGCCTAGCTATGCATTT
79492 GACAGAAAGGTGTCAAT
66 GACAGAAA-GTGTCAAT
** * * *
79509 TATGGTAGTTAGATGAATGGTTAAATACCTTTGAGTAAAATATTTAATGGCCTAGCTATGCATTT
1 TATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTTAATGGCCTAGCTATGCATTT
* * *
79574 AAAAGAAATGTGTTAAT
66 GACAGAAA-GTGTCAAT
* * * *
79591 TTTGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAATATTTAATGGCCTAGCTACGCATTT
1 TATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTTAATGGCCTAGCTATGCATTT
*
79656 GATAGAAAAGTGTCAAT
66 GACAG-AAAGTGTCAAT
* * *
79673 TATGCCAGTTAGATGAAAGGTTAAATAGATTTGAGTAAAAGA-TTAATGGCCAAGCTATGTATTT
1 TATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTTAATGGCCTAGCTATGCATTT
79737 GACAGAAATGTGTCAAT
66 GACAGAAA-GTGTCAAT
*
79754 TATGCCAGTTAGATGAAAAGTTAAATA-ACTTTGAGTAAAAGATTTAATGGCCTA
1 TATGCCAGTTAGATGAAAGGTTAAATACA-TTTGAGTAAAAGATTTAATGGCCTA
79808 ACTTATGATT
Statistics
Matches: 338, Mismatches: 38, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
80 4 0.01
81 70 0.21
82 260 0.77
83 4 0.01
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.33
Consensus pattern (81 bp):
TATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTTAATGGCCTAGCTATGCATTT
GACAGAAAGTGTCAAT
Found at i:82737 original size:55 final size:55
Alignment explanation
Indices: 82675--83041 Score: 540
Period size: 55 Copynumber: 6.7 Consensus size: 55
82665 TACCAAATGA
*
82675 CACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
1 CACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
* * *
82730 CATTGTGTGTGCAAAACTAAGAAATTCATAATAACTTTATGAA-TTTCTGTAAGGG
1 CACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATGGG
* * *
82785 CACTGTGTGTGCAAAACTAAGAAAATCATAATAAGTATATGAATTTCCGTATGGG
1 CACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
* *
82840 CACTATGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGG
1 CACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
* * * * *
82895 CACAGTGCGTGCAATACTAATAAATTCATAATAAGTTTATGAATTTTTGTATGGG
1 CACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
* *
82950 CACTGTGTGTGTAAAACTAAGAAATTCATAAAAAGTTTATGAA-TTTCTGTATGGG
1 CACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTC-GTATGGG
* *
83005 CACTGTGTGTGCAAAACTAAGAAATTTATAGTAAGTT
1 CACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTT
83042 GTGGATTACC
Statistics
Matches: 278, Mismatches: 31, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
54 7 0.03
55 268 0.96
56 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (55 bp):
CACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGG
Found at i:83258 original size:82 final size:82
Alignment explanation
Indices: 83148--84052 Score: 1192
Period size: 82 Copynumber: 11.1 Consensus size: 82
83138 TGTTGTAAAA
* * ** *
83148 TAAAAGATTTAATGGCTTAGTTACGCATTTGACAGAAAGGTGTTAATTATGCCAGTTAGATGAAA
1 TAAAAGATTTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
*
83213 GGTTAAATACCTTTAAG
66 GGTTAAATACCTTTGAG
* * * * * *
83230 TAAAAGATTTAATGGCCAAGTTGTGCATTGGACAGAAAGGAGTCAATTATGCTAGTTAAATGAAA
1 TAAAAGATTTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
*
83295 GGTTAAATACCTGTGAG
66 GGTTAAATACCTTTGAG
* * * * *
83312 TAAAAGATTTAATGGCCTAGCTGTGTATTTGACATAAAGTTGGCAATTATGCTAGTTAGATGAAA
1 TAAAAGATTTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* *
83377 TGTTAAATACCTTTAAG
66 GGTTAAATACCTTTGAG
* * * *
83394 TAAAAGATTTAATGGCCTAGGTGTGCATTTGACATAAAGGTGTAAATTATGCCAGTTTGATGAAA
1 TAAAAGATTTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
83459 GGTTAAATACCTTTGAG
66 GGTTAAATACCTTTGAG
* * * * * * *
83476 TGAAAGATTTAAAGGCCTAGCTATGCATTTGACAAAAAAGTTTCAATTATGCCAGTTTGATGAAA
1 TAAAAGATTTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
83541 GGTTAAATACCTTTGAG
66 GGTTAAATACCTTTGAG
* * * *
83558 TAAAAGATTTAATGGCCTA-CTTGTGCATGTGACAAAAAAGTGTCAATTATTCCAGTTAGATGAA
1 TAAAAGATTTAATGGCCTAGC-TGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAA
83622 AGGTTAAATACCTTTGAG
65 AGGTTAAATACCTTTGAG
* * * *
83640 TAAAAGA-TTAATGGCCTAGCTATGCATTTGAGAGAAATGTGTCAATTATGCCACTTAGATGAAA
1 TAAAAGATTTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
*
83704 GGTTAAATACTTTTGAG
66 GGTTAAATACCTTTGAG
* * * *
83721 TAAAAGATTTAATGGCCTAGTTGTGCATTTGACAGAAAGGTGCCAATTATGCCAGTTAAATAAAA
1 TAAAAGATTTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
83786 GGTTTAAATACCTTTGAG
66 GG-TTAAATACCTTTGAG
* * * *
83804 TAAAAGA-TTAATGGCCTAGCTGTGCATTTGGCAAAAAAGTGTCAATT-TACCAGTTAGATGAAA
1 TAAAAGATTTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
83867 GGTTAAATACCTTTGAG
66 GGTTAAATACCTTTGAG
* * *
83884 TAAAAGATTTAATGGCCTAGCTGTGCATTTGAAAGAAAGGTGTCAATCATGCCAGTTAGATAAAA
1 TAAAAGATTTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
* *
83949 GGCTAAATGCCTTTGAG
66 GGTTAAATACCTTTGAG
* * * * *
83966 TTAAAGATTTAAT-GCCTAGATGTGCATTTGGCAGAAACGTGTCAATTATGCAAGTTAGATGAAA
1 TAAAAGATTTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
** * *
84030 GACTAAATGCC-TTGGG
66 GGTTAAATACCTTTGAG
84046 TAAAAGA
1 TAAAAGA
84053 CTAAATGATT
Statistics
Matches: 725, Mismatches: 92, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
80 32 0.04
81 176 0.24
82 496 0.68
83 21 0.03
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (82 bp):
TAAAAGATTTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
GGTTAAATACCTTTGAG
Done.