Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 13 of 259
Found at i:3721558 original size:13 final size:13
Alignment explanation
Indices: 3721540--3721582 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
3721530 TTAATTTTTT
3721540 CTAAATATTATCA
1 CTAAATATTATCA
3721553 CTAAATA--ATC-
1 CTAAATATTATCA
*
3721563 CTAGATATTATCA
1 CTAAATATTATCA
3721576 CTAAATA
1 CTAAATA
3721583 ATTCAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.24
11 3 0.12
12 3 0.12
13 13 0.52
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:3722138 original size:17 final size:18
Alignment explanation
Indices: 3722118--3722151 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3722108 GAGCAGAAGC
3722118 AAGAAACAAGCA-AAAAG
1 AAGAAACAAGCATAAAAG
*
3722135 AAGAAAGAAGCATAAAA
1 AAGAAACAAGCATAAAA
3722152 AAAATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.71, C:0.09, G:0.18, T:0.03
Consensus pattern (18 bp):
AAGAAACAAGCATAAAAG
Found at i:3724253 original size:23 final size:23
Alignment explanation
Indices: 3724210--3724254 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3724200 TTATTGGCTC
* *
3724210 AAATGTCAAAAAAGTCCTTAAGA
1 AAATGTCAAAAAAATCATTAAGA
3724233 AAATG-CAAAAAAATCAATTAAG
1 AAATGTCAAAAAAATC-ATTAAG
3724255 CCCTTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (23 bp):
AAATGTCAAAAAAATCATTAAGA
Found at i:3725231 original size:9 final size:9
Alignment explanation
Indices: 3725217--3725249 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
3725207 GCTTGCTGGC
3725217 GAGAAATAA
1 GAGAAATAA
3725226 GAGAAATAA
1 GAGAAATAA
3725235 GAGAAATAA
1 GAGAAATAA
3725244 GAGAAA
1 GAGAAA
3725250 ATGATGCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (9 bp):
GAGAAATAA
Found at i:3733044 original size:17 final size:16
Alignment explanation
Indices: 3733022--3733064 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
3733012 ATATTTTTCC
3733022 ATAAAAATAATTAGAAA
1 ATAAAAA-AATTAGAAA
*
3733039 ATAAAAAAATTATAAA
1 ATAAAAAAATTAGAAA
3733055 ATATAAAAAA
1 ATA-AAAAAA
3733065 AATAAAATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (16 bp):
ATAAAAAAATTAGAAA
Found at i:3733059 original size:7 final size:8
Alignment explanation
Indices: 3733030--3733152 Score: 59
Period size: 8 Copynumber: 14.2 Consensus size: 8
3733020 CCATAAAAAT
*
3733030 AATTAGAA
1 AATTATAA
* *
3733038 AATAAAAA
1 AATTATAA
3733046 AATTATAA
1 AATTATAA
3733054 AA-TATAAA
1 AATTAT-AA
**
3733062 AAAAATAA
1 AATTATAA
3733070 AATTGATATA
1 AATT-ATA-A
3733080 AACTTATGAA
1 AA-TTAT-AA
*
3733090 AATAATTAA
1 AATTA-TAA
*
3733099 AAGTAATAA
1 AA-TTATAA
*
3733108 AATTGTAA
1 AATTATAA
*
3733116 ATATTAAAA
1 A-ATTATAA
*
3733125 AATATAAAA
1 AAT-TATAA
3733134 AATTATAA
1 AATTATAA
3733142 AATTAATAA
1 AATT-ATAA
3733151 AA
1 AA
3733153 CATGTTTAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
7 3 0.03
8 37 0.41
9 36 0.40
10 12 0.13
11 3 0.03
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (8 bp):
AATTATAA
Found at i:3733060 original size:18 final size:16
Alignment explanation
Indices: 3733022--3733071 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
3733012 ATATTTTTCC
*
3733022 ATAAAAATAATTAGAAA
1 ATAAAAA-AATTAAAAA
3733039 ATAAAAAAATTATAAAA
1 ATAAAAAAATTA-AAAA
*
3733056 TATAAAAAAAATAAAA
1 -ATAAAAAAATTAAAA
3733072 TTGATATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 5 0.17
17 13 0.45
18 11 0.38
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (16 bp):
ATAAAAAAATTAAAAA
Found at i:3733142 original size:19 final size:19
Alignment explanation
Indices: 3733120--3733323 Score: 73
Period size: 19 Copynumber: 10.7 Consensus size: 19
3733110 TTGTAAATAT
3733120 TAAAAAATATAAAAAATTA
1 TAAAAAATATAAAAAATTA
* * *
3733139 T-AAAATTAATAAAACATGTT
1 TAAAAAAT-ATAAAAAAT-TA
* * * **
3733159 TAAAATATTTTAAATTTTA
1 TAAAAAATATAAAAAATTA
* * *
3733178 T-AAAAATGTATAAAATTCT
1 TAAAAAATATAAAAAATT-A
* *
3733197 TAAAAACCTAT-AAAAATCA
1 TAAAAA-ATATAAAAAATTA
*
3733216 TAAAAAAATATTAAAAA-TA
1 T-AAAAAATATAAAAAATTA
* *
3733235 T-AAAAATGTATTAAAATTGA
1 TAAAAAATATA-AAAAATT-A
* * *
3733255 TATAAACT-TATAAAATTA
1 TAAAAAATATAAAAAATTA
*
3733273 TAAATAATCATAAAAAA-TA
1 TAAAAAAT-ATAAAAAATTA
*
3733292 TAAAAAATA-AAATATATTA
1 TAAAAAATATAAA-AAATTA
*
3733311 TAAAAATTATAAA
1 TAAAAAATATAAA
3733324 TTATAAATTA
Statistics
Matches: 132, Mismatches: 36, Indels: 33
0.66 0.18 0.16
Matches are distributed among these distances:
17 10 0.08
18 28 0.21
19 45 0.34
20 39 0.30
21 10 0.08
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (19 bp):
TAAAAAATATAAAAAATTA
Found at i:3733181 original size:30 final size:29
Alignment explanation
Indices: 3733127--3733251 Score: 80
Period size: 30 Copynumber: 4.3 Consensus size: 29
3733117 TATTAAAAAA
*
3733127 TATAAAAAATTATAAAATTAATAAAACATG
1 TATAAAATATTATAAAATTAATAAAA-ATG
* * * *
3733157 TTTAAAATATTTTAAATTTTATAAAAATG
1 TATAAAATATTATAAAATTAATAAAAATG
* * *
3733186 TATAAAATTCTTA-AAAACCT-ATAAAAATCA
1 TATAAAA-TATTATAAAA-TTAATAAAAAT-G
*
3733216 TAAAAAAATATTA-AAAA-T-ATAAAAATG
1 T-ATAAAATATTATAAAATTAATAAAAATG
3733243 TATTAAAAT
1 TA-TAAAAT
3733252 TGATATAAAC
Statistics
Matches: 75, Mismatches: 15, Indels: 13
0.73 0.15 0.13
Matches are distributed among these distances:
26 1 0.01
27 6 0.08
28 9 0.12
29 20 0.27
30 34 0.45
31 5 0.07
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.34
Consensus pattern (29 bp):
TATAAAATATTATAAAATTAATAAAAATG
Found at i:3733270 original size:57 final size:57
Alignment explanation
Indices: 3733176--3733297 Score: 149
Period size: 57 Copynumber: 2.1 Consensus size: 57
3733166 TTTTAAATTT
* *
3733176 TATAAAAATGTATAAAATTCTTAAAAACCTATAAAAATCATAAAAAAAT-ATTAAAAA
1 TATAAAAATGTATAAAATTCATAAAAACCTATAAAAATCAT-AAAAAATCATAAAAAA
* * * * *
3733233 TATAAAAATGTATTAAAATTGATATAAACTTAT-AAAATTATAAATAATCATAAAAAA
1 TATAAAAATGTA-TAAAATTCATAAAAACCTATAAAAATCATAAAAAATCATAAAAAA
3733290 TATAAAAA
1 TATAAAAA
3733298 ATAAAATATA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
56 6 0.11
57 34 0.61
58 16 0.29
ACGTcount: A:0.62, C:0.05, G:0.02, T:0.30
Consensus pattern (57 bp):
TATAAAAATGTATAAAATTCATAAAAACCTATAAAAATCATAAAAAATCATAAAAAA
Found at i:3733319 original size:9 final size:9
Alignment explanation
Indices: 3733043--3733339 Score: 120
Period size: 9 Copynumber: 32.6 Consensus size: 9
3733033 TAGAAAATAA
3733043 AAAAATTAT
1 AAAAATTAT
3733052 -AAAA-TAT
1 AAAAATTAT
**
3733059 AAAAAAAAT
1 AAAAATTAT
3733068 -AAAATTGAT
1 AAAAATT-AT
*
3733077 ATAAACTTAT
1 A-AAAATTAT
* *
3733087 GAAAATAAT
1 AAAAATTAT
* *
3733096 TAAAAGTA-
1 AAAAATTAT
*
3733104 ATAAAATTGT
1 A-AAAATTAT
*
3733114 AAATATTA-
1 AAAAATTAT
3733122 AAAAA-TAT
1 AAAAATTAT
3733130 AAAAAATTAT
1 -AAAAATTAT
3733140 -AAAATTAAT
1 AAAAATT-AT
*
3733149 AAAACATGTTT
1 AAAA-AT-TAT
*
3733160 AAAATATTTT
1 AAAA-ATTAT
**
3733170 AAATTTTAT
1 AAAAATTAT
3733179 AAAAATGTAT
1 AAAAAT-TAT
*
3733189 -AAAATTCTT
1 AAAAATT-AT
*
3733198 AAAAACCTAT
1 AAAAA-TTAT
*
3733208 AAAAATCAT
1 AAAAATTAT
*
3733217 AAAAAAATATT
1 -AAAAATTA-T
3733228 AAAAA-TAT
1 AAAAATTAT
3733236 AAAAATGTAT
1 AAAAAT-TAT
*
3733246 TAAAATTGAT
1 AAAAATT-AT
*
3733256 ATAAACTTAT
1 A-AAAATTAT
3733266 -AAAATTAT
1 AAAAATTAT
*
3733274 AAATAATCAT
1 AAA-AATTAT
*
3733284 AAAAAATAT
1 AAAAATTAT
*
3733293 AAAAAATA-
1 AAAAATTAT
3733301 AAATATATTAT
1 AAA-A-ATTAT
3733312 AAAAATTAT
1 AAAAATTAT
3733321 --AAATTAT
1 AAAAATTAT
3733328 --AAATTAT
1 AAAAATTAT
3733335 AAAAA
1 AAAAA
3733340 AAAGTCATTT
Statistics
Matches: 219, Mismatches: 38, Indels: 62
0.69 0.12 0.19
Matches are distributed among these distances:
7 19 0.09
8 39 0.18
9 73 0.33
10 63 0.29
11 24 0.11
12 1 0.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:3733329 original size:28 final size:28
Alignment explanation
Indices: 3733262--3733335 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
3733252 TGATATAAAC
3733262 TTATAAAATTAT-AAATA-ATCATAAAAA
1 TTAT-AAATTATAAAATATATCATAAAAA
* ** *
3733289 ATATAAAAAATAAAATATATTATAAAAA
1 TTATAAATTATAAAATATATCATAAAAA
*
3733317 TTATAAATTATAAATTATA
1 TTATAAATTATAAAATATA
3733336 AAAAAAAGTC
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
26 5 0.14
27 8 0.22
28 24 0.65
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (28 bp):
TTATAAATTATAAAATATATCATAAAAA
Found at i:3734476 original size:18 final size:19
Alignment explanation
Indices: 3734439--3734478 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3734429 ATAAAATCAA
*
3734439 ATAATAAATATGTAATTAT
1 ATAATAAAAATGTAATTAT
*
3734458 ATAATAAAAAT-TTATTAT
1 ATAATAAAAATGTAATTAT
3734476 ATA
1 ATA
3734479 TATCATTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
ATAATAAAAATGTAATTAT
Found at i:3739621 original size:97 final size:97
Alignment explanation
Indices: 3739413--3739761 Score: 283
Period size: 97 Copynumber: 3.5 Consensus size: 97
3739403 AAACAGATTC
* * *
3739413 CATTGATTCATAAAGGGGTGTGATTG-GACCAAAGGTAAGAATAGTGCCATTCGGTTCATTGCCA
1 CATTGATTCATAAAGGGGTGTGTTTGAG-CCAAAGGTAAGAATAGT---A-TCTGTTCATTG-AA
* * ** * * *
3739477 ATGCGAACTCCATTATGAATCCACCATTACAAGGATTT
60 ATGTGGACTCCATTACAAATCCACCATTACGAGCAATT
*
3739515 CATTGATTCATAAAGGGGTGTGTTTGAGCCAAAGGCAAGAATAGTA-CTGTTCATTGAATATGTG
1 CATTGATTCATAAAGGGGTGTGTTTGAGCCAAAGGTAAGAATAGTATCTGTTCATTGAA-ATGTG
*
3739579 GACTCCATTACAAATCCACCATAACGAGCAATT
65 GACTCCATTACAAATCCACCATTACGAGCAATT
* * * * * * *
3739612 CATTCATTCAGAAA-GGG-GTGTTTGGGCCAAAGGTAATAATATTACCGATTGGTTTCATTATCA
1 CATTGATTCATAAAGGGGTGTGTTTGAGCCAAAGGTAAGAATAGTATC---T-G-TTCA-T-TGA
* *
3739675 AATGGTGGACCCCATTACAAATCCACCATTACGAGCACTT
59 AAT-GTGGACTCCATTACAAATCCACCATTACGAGCAATT
* * ** * *
3739715 GATTTGATTCACAAAGTAGTGTGTTTGAGCCAAGGGTAAGAACAGTA
1 CA-TTGATTCATAAAGGGGTGTGTTTGAGCCAAAGGTAAGAATAGTA
3739762 CCATCACATG
Statistics
Matches: 201, Mismatches: 32, Indels: 24
0.78 0.12 0.09
Matches are distributed among these distances:
95 23 0.11
96 5 0.02
97 51 0.25
99 2 0.01
100 1 0.00
101 4 0.02
102 44 0.22
103 38 0.19
104 10 0.05
105 1 0.00
106 22 0.11
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (97 bp):
CATTGATTCATAAAGGGGTGTGTTTGAGCCAAAGGTAAGAATAGTATCTGTTCATTGAAATGTGG
ACTCCATTACAAATCCACCATTACGAGCAATT
Found at i:3744426 original size:3 final size:3
Alignment explanation
Indices: 3744418--3744445 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3744408 GAATTATTTC
3744418 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3744446 AGAAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3745791 original size:89 final size:84
Alignment explanation
Indices: 3745682--3745938 Score: 247
Period size: 89 Copynumber: 3.0 Consensus size: 84
3745672 TTTTGTTTTC
* * * ** *** * *
3745682 AAAATTAAAAGTAAATAAAATTCGTTTTGGGATTTATTCTCGTTGTTTAACGGGTTTTATTCCAT
1 AAAATTAAAGGTAAATAAAATCCGTTTCGAAATTTATTCTCGCCATTCAACGGATTTTATTCCAT
3745747 TATTTTAATTT-TATTTCCAAA
66 TATTTT-ATTTCTATTTCC--A
3745768 CAGGAAATTAAAGGTAAATAAAATCCGTTTCGAAATTTATTCTCGCCATTCAACGGATTTTATTC
1 -A--AAATTAAAGGTAAATAAAATCCGTTTCGAAATTTATTCTCGCCATTCAACGGATTTTATTC
* *
3745833 TATTATTTTGTTTCTATTTCCA
63 CATTATTTTATTTCTATTTCCA
* * * *
3745855 AAAATTAAAGGTAAATAAAAACCATTTC-AAGATTGATTCCCGCCATTCAAC-GATTTTATTCCA
1 AAAATTAAAGGTAAATAAAATCCGTTTCGAA-ATTTATTCTCGCCATTCAACGGATTTTATTCCA
* *
3745918 -AATTTT-TTTTTA-TTCCA
65 TTATTTTATTTCTATTTCCA
3745935 AAAA
1 AAAA
3745939 CGAGTAAAAT
Statistics
Matches: 147, Mismatches: 19, Indels: 15
0.81 0.10 0.08
Matches are distributed among these distances:
80 9 0.06
81 5 0.03
82 5 0.03
83 13 0.09
84 43 0.29
86 1 0.01
87 2 0.01
88 3 0.02
89 66 0.45
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (84 bp):
AAAATTAAAGGTAAATAAAATCCGTTTCGAAATTTATTCTCGCCATTCAACGGATTTTATTCCAT
TATTTTATTTCTATTTCCA
Found at i:3745961 original size:78 final size:79
Alignment explanation
Indices: 3745783--3746038 Score: 277
Period size: 78 Copynumber: 3.2 Consensus size: 79
3745773 AATTAAAGGT
* * * * *
3745783 AAATAAAATCCGTTTCGAA-ATTTATTCTCGCCATTCAACGGATTTTATTCTATTATTTTGTTTC
1 AAATAAAATCCGTTTC-AAGATTGATTCCCGCCATTCAAC-GATTTTATTCCA-AATTTT-TTTT
**
3745847 TATTTCCAAAAATTAAAGGT-
62 TATTTCCAAAAA--CGA-GTA
* *
3745867 AAATAAAAACCATTTCAAGATTGATTCCCGCCATTCAACGATTTTATTCCAAATTTTTTTTTA-T
1 AAATAAAATCCGTTTCAAGATTGATTCCCGCCATTCAACGATTTTATTCCAAATTTTTTTTTATT
3745931 TCCAAAAACGAGTA
66 TCCAAAAACGAGTA
* * * * *
3745945 AAATAAAATCTGTTTC-AGAATTGATTCCCTCCGTTCAATGATTTTATTCCAAATTTTGTTTTAT
1 AAATAAAATCCGTTTCAAG-ATTGATTCCCGCCATTCAACGATTTTATTCCAAATTTTTTTTTAT
*
3746009 TTTCAAAAACGAGTA
65 TTCCAAAAACGAGTA
3746024 AAATAAAATCCGTTT
1 AAATAAAATCCGTTT
3746039 TGGGATTGAG
Statistics
Matches: 150, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
77 4 0.03
78 54 0.36
79 28 0.19
80 9 0.06
81 5 0.03
82 5 0.03
83 13 0.09
84 32 0.21
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (79 bp):
AAATAAAATCCGTTTCAAGATTGATTCCCGCCATTCAACGATTTTATTCCAAATTTTTTTTTATT
TCCAAAAACGAGTA
Found at i:3746058 original size:79 final size:78
Alignment explanation
Indices: 3745783--3746107 Score: 232
Period size: 78 Copynumber: 4.1 Consensus size: 78
3745773 AATTAAAGGT
* * * * * * *
3745783 AAATAAAATCCGTTTC-GAAATTTATTCTCGCCATTCAACGGATTTTATTCTATTATTTTGTTTC
1 AAATAAAATCCGTTTCAG-AATTGAGTCCCTCCGTTCAAC-GATTTTATTCCA-AATTTTGTTT-
**
3745847 TATTTCCAAAAATTAAAGGT-
62 TA-TTCCAAAAA--CGA-GTA
* * * * * *
3745867 AAATAAAAACCATTTCA-AGATTGATTCCCGCCATTCAACGATTTTATTCCAAATTTTTTTTTAT
1 AAATAAAATCCGTTTCAGA-ATTGAGTCCCTCCGTTCAACGATTTTATTCCAAATTTTGTTTTAT
3745931 TCCAAAAACGAGTA
65 TCCAAAAACGAGTA
* * *
3745945 AAATAAAATCTGTTTCAGAATTGATTCCCTCCGTTCAATGATTTTATTCCAAATTTTGTTTTATT
1 AAATAAAATCCGTTTCAGAATTGAGTCCCTCCGTTCAACGATTTTATTCCAAATTTTGTTTTA-T
*
3746010 TTCAAAAACGAGTA
65 TCCAAAAACGAGTA
** * * ** * *
3746024 AAATAAAATCCGTTTTGGGATTGAGT-CTTGCCGTTCAACGGGTTTATT--ACATTTTGATTTTG
1 AAATAAAATCCGTTTCAGAATTGAGTCCCT-CCGTTCAACGATTTTATTCCAAATTTTG-TTTTA
3746086 TTGCCAAAAACGAG-A
64 TT-CCAAAAACGAGTA
*
3746101 AATTAAA
1 AAATAAA
3746108 TTAAATAAAA
Statistics
Matches: 203, Mismatches: 30, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
77 18 0.09
78 71 0.35
79 51 0.25
80 9 0.04
81 2 0.01
82 8 0.04
83 12 0.06
84 32 0.16
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.39
Consensus pattern (78 bp):
AAATAAAATCCGTTTCAGAATTGAGTCCCTCCGTTCAACGATTTTATTCCAAATTTTGTTTTATT
CCAAAAACGAGTA
Found at i:3748671 original size:49 final size:48
Alignment explanation
Indices: 3748433--3748689 Score: 222
Period size: 49 Copynumber: 5.4 Consensus size: 48
3748423 TTTAGGTGAT
* * *
3748433 GTGTGTGCTAGTGTAAGACCTGTCTAGGACATGGCATCGACACT-GATAA
1 GTGTGAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGAC-TTAGAT-A
* * * * * *
3748482 ATATGAGCCACTGTAAGACCTGTCTGAGACATGGCATCGGCTTCAAGATA
1 GTGTGAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACTT--AGATA
** * * * *
3748532 -TGCAAGCTAGTGTAAGACCTGTCTCGGACATGGCATTGGCTTA-A-G
1 GTGTGAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGATA
* **
3748577 GTGTG-TC-AGTGTAAGACCTGTCTGGGACATGGCATCGACACAGATGA
1 GTGTGAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGAT-A
* *
3748624 GTGGGAGCTAGTGTAAGACCTATCTGGGACATGGCATCGACTTAGAT-
1 GTGTGAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGATA
* *
3748671 GTGAGAGCCAGTGTAAGAC
1 GTGTGAGCTAGTGTAAGAC
3748690 TATGTTTGGA
Statistics
Matches: 165, Mismatches: 34, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
44 30 0.18
45 2 0.01
46 3 0.02
47 22 0.13
48 2 0.01
49 102 0.62
50 1 0.01
51 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.25
Consensus pattern (48 bp):
GTGTGAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGACTTAGATA
Found at i:3755968 original size:49 final size:49
Alignment explanation
Indices: 3755726--3755998 Score: 161
Period size: 49 Copynumber: 5.7 Consensus size: 49
3755716 TGTGTGTCCT
* * ** * * *
3755726 AGTGTCAGACCTGTCTGGGACATGGCATCGGCACCAATAAATGAGA-TCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTCGATATATGAAAGT-C
* * ** * * *
3755775 AGTGTAAGACCTATCT-GGACATGACATCGGTTTCAAGATATGCAAG-C
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTCGATATATGAAAGTC
* * * ** * *
3755822 TAGTGTAAAACCTGTTTGGGACATGGCATCGGCTT-G--AGGTG--TGTT
1 -AGTGTAAGACCTGTCTGGGACATGGCATCGACTTCGATATATGAAAGTC
* * * * *
3755867 AGTGTAAGACCTGTCTGGGACATGGCATCAAC-ACAGATGA-GTGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTC-GAT-ATATGAAAGTC
3755916 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTCGATATATGAAAGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACTTCGATATATGAAAGTC
* * * * *
3755965 AGTGTAAGACTTGTCTAGAACATGACATTGACTT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACTT
3755999 AGATGTGAGA
Statistics
Matches: 173, Mismatches: 38, Indels: 26
0.73 0.16 0.11
Matches are distributed among these distances:
44 29 0.17
45 1 0.01
46 3 0.02
47 4 0.02
48 36 0.21
49 99 0.57
50 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACTTCGATATATGAAAGTC
Found at i:3767304 original size:3 final size:3
Alignment explanation
Indices: 3767296--3767347 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
3767286 AAAATGGTGC
3767296 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3767344 TTA T
1 TTA T
3767348 CGTAATATTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3767583 original size:11 final size:11
Alignment explanation
Indices: 3767563--3767610 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
3767553 AATACATTTC
*
3767563 AAAAATAAAAAT
1 AAAAA-AAAAAG
3767575 AAAAAAAAAAG
1 AAAAAAAAAAG
3767586 AAAAAAAAAAG
1 AAAAAAAAAAG
*
3767597 -AAAAAGAAAG
1 AAAAAAAAAAG
3767607 AAAA
1 AAAA
3767611 CTCTTGTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 9 0.27
11 19 0.58
12 5 0.15
ACGTcount: A:0.88, C:0.00, G:0.08, T:0.04
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:3767589 original size:10 final size:10
Alignment explanation
Indices: 3767576--3767610 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
3767566 AATAAAAATA
3767576 AAAAAAAAAG
1 AAAAAAAAAG
3767586 AAAAAAAAAAG
1 -AAAAAAAAAG
*
3767597 AAAAAGAAAG
1 AAAAAAAAAG
3767607 AAAA
1 AAAA
3767611 CTCTTGTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:3767589 original size:17 final size:17
Alignment explanation
Indices: 3767563--3767610 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
3767553 AATACATTTC
*
3767563 AAAAATAAAAATAAAAA-
1 AAAAAGAAAAA-AAAAAG
3767580 AAAAAGAAAAAAAAAAG
1 AAAAAGAAAAAAAAAAG
3767597 AAAAAGAAAGAAAA
1 AAAAAGAAA-AAAA
3767611 CTCTTGTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 5 0.18
17 19 0.68
18 4 0.14
ACGTcount: A:0.88, C:0.00, G:0.08, T:0.04
Consensus pattern (17 bp):
AAAAAGAAAAAAAAAAG
Found at i:3767602 original size:6 final size:6
Alignment explanation
Indices: 3767563--3767605 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
3767553 AATACATTTC
* *
3767563 AAAAAT AAAAAT AAAAA- AAAAAG AAAAA- AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA
3767606 GAAAACTCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 10 0.29
6 25 0.71
ACGTcount: A:0.88, C:0.00, G:0.07, T:0.05
Consensus pattern (6 bp):
AAAAAG
Found at i:3768375 original size:30 final size:30
Alignment explanation
Indices: 3768339--3768397 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3768329 ATTTTATTGC
3768339 TAATTTT-TTTATTATTTTTA-AGGCATTTGT
1 TAATTTTGTTT-TTA-TTTTAGAGGCATTTGT
3768369 TAATTTTGTTTTTATTTTAGAGGCATTTG
1 TAATTTTGTTTTTATTTTAGAGGCATTTG
3768398 CTTGTTAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 5 0.19
30 19 0.70
31 3 0.11
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.61
Consensus pattern (30 bp):
TAATTTTGTTTTTATTTTAGAGGCATTTGT
Found at i:3771547 original size:34 final size:32
Alignment explanation
Indices: 3771509--3771615 Score: 115
Period size: 34 Copynumber: 3.2 Consensus size: 32
3771499 AGCACATTGT
* *
3771509 ATGCTCAAGTGAGCCATTCCAACCAGTACACCAA
1 ATGCTCAA--GAGCCAATCCAACCAGCACACCAA
*
3771543 ATGCTCTCAAGAGCCAATCCATCCAGCACACCAA
1 ATG--CTCAAGAGCCAATCCAACCAGCACACCAA
* *
3771577 ATGCTCGTAAGAGCAAATCCATCCAGCACACCAA
1 ATGCTC--AAGAGCCAATCCAACCAGCACACCAA
3771611 ATGCT
1 ATGCT
3771616 TTATATCGGT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
32 3 0.05
34 57 0.88
36 5 0.08
ACGTcount: A:0.36, C:0.34, G:0.14, T:0.17
Consensus pattern (32 bp):
ATGCTCAAGAGCCAATCCAACCAGCACACCAA
Found at i:3775077 original size:28 final size:28
Alignment explanation
Indices: 3775037--3775092 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
3775027 TCATAGGTTC
*
3775037 TTTTGGAAAGCTATATGGAAGCTTGACA
1 TTTTGGAAAGCTATATGGAAGCTCGACA
3775065 TTTTGGAAAGCTATATGGAAGCTCGACA
1 TTTTGGAAAGCTATATGGAAGCTCGACA
3775093 CTATCCCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.30
Consensus pattern (28 bp):
TTTTGGAAAGCTATATGGAAGCTCGACA
Found at i:3789249 original size:5 final size:5
Alignment explanation
Indices: 3789234--3789286 Score: 58
Period size: 5 Copynumber: 11.2 Consensus size: 5
3789224 ACCCATCGCT
* *
3789234 TCATA TTATA TCATA TCATA TCATA TCATA T-ATA T-ATA T-ATA TAATA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
*
3789281 TAATA T
1 TCATA T
3789287 AACAAGATAC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
4 12 0.27
5 33 0.73
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (5 bp):
TCATA
Found at i:3789415 original size:17 final size:17
Alignment explanation
Indices: 3789367--3789424 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 17
3789357 ATGTATCAAA
*
3789367 TAAAATTTAAATAATTT
1 TAAAAATTAAATAATTT
*
3789384 AAGTAAAATTAAATAAATTT
1 TA--AAAATTAAAT-AATTT
*
3789404 TAAAAATT-AATATTTT
1 TAAAAATTAAATAATTT
3789420 TAAAA
1 TAAAA
3789425 TATTCAGTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
16 9 0.26
17 4 0.12
18 6 0.18
19 9 0.26
20 6 0.18
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
TAAAAATTAAATAATTT
Found at i:3789757 original size:31 final size:32
Alignment explanation
Indices: 3789669--3789757 Score: 76
Period size: 31 Copynumber: 2.8 Consensus size: 32
3789659 ATGATTTTAA
* *
3789669 ATAATATATTAACTTTCCTATAATTAGAATAG
1 ATAATATATTAAGTTTCCTATAATTAAAATAG
* * ****
3789701 TTAA-ATATCACAGTAAAATAT-ATTAAAAT-G
1 ATAATATATTA-AGTTTCCTATAATTAAAATAG
3789731 ATAATATATTAAGTTTCCTATAATTAA
1 ATAATATATTAAGTTTCCTATAATTAA
3789758 TATTTATTAT
Statistics
Matches: 40, Mismatches: 14, Indels: 7
0.66 0.23 0.11
Matches are distributed among these distances:
30 10 0.25
31 22 0.55
32 8 0.20
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (32 bp):
ATAATATATTAAGTTTCCTATAATTAAAATAG
Found at i:3793046 original size:3 final size:3
Alignment explanation
Indices: 3793034--3793085 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
3793024 TTCTTCTTCT
* * * * * *
3793034 TCC TCT TCC TCC TCC TCC TCT TTC TCC TCC TCC TTC TCT TCT TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
3793082 TCC T
1 TCC T
3793086 ATTCTTCCTC
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (3 bp):
TCC
Found at i:3793052 original size:15 final size:15
Alignment explanation
Indices: 3793034--3793095 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
3793024 TTCTTCTTCT
3793034 TCCTCTTCCTCCTCC
1 TCCTCTTCCTCCTCC
3793049 TCCTCTTTCTCCTCCTCC
1 TCCTC--T-TCCTCCTCC
* *
3793067 TTCTCTTCTTCCTCC
1 TCCTCTTCCTCCTCC
* *
3793082 TCCTATTCTTCCTC
1 TCCTCTTCCTCCTC
3793096 ATTTGCTCCC
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 25 0.62
16 1 0.03
17 1 0.03
18 13 0.32
ACGTcount: A:0.02, C:0.52, G:0.00, T:0.47
Consensus pattern (15 bp):
TCCTCTTCCTCCTCC
Found at i:3793063 original size:18 final size:18
Alignment explanation
Indices: 3793037--3793085 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
3793027 TTCTTCTTCC
3793037 TCTTCCTCCTCCTCCTCT
1 TCTTCCTCCTCCTCCTCT
*
3793055 T-TCTCCTCCTCCTTCTCT
1 TCT-TCCTCCTCCTCCTCT
3793073 TCTTCCTCCTCCT
1 TCTTCCTCCTCCT
3793086 ATTCTTCCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 1 0.04
18 26 0.93
19 1 0.04
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (18 bp):
TCTTCCTCCTCCTCCTCT
Found at i:3793091 original size:18 final size:17
Alignment explanation
Indices: 3793037--3793092 Score: 62
Period size: 18 Copynumber: 3.3 Consensus size: 17
3793027 TTCTTCTTCC
* *
3793037 TCTTCCTCCTCCTCCTC
1 TCTTCTTCCTCCTCCTT
3793054 T-TTC-TCCTCCTCCTT
1 TCTTCTTCCTCCTCCTT
3793069 CTCTTCTTCCTCCTCCTAT
1 -TCTTCTTCCTCCTCCT-T
3793088 TCTTC
1 TCTTC
3793093 CTCATTTGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
15 10 0.29
16 4 0.12
17 4 0.12
18 15 0.44
19 1 0.03
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (17 bp):
TCTTCTTCCTCCTCCTT
Found at i:3808415 original size:15 final size:15
Alignment explanation
Indices: 3808395--3808425 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3808385 TTATGATTAA
3808395 AGTTTATACGAGCTT
1 AGTTTATACGAGCTT
*
3808410 AGTTTATATGAGCTT
1 AGTTTATACGAGCTT
3808425 A
1 A
3808426 CTAAGTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (15 bp):
AGTTTATACGAGCTT
Found at i:3809978 original size:6 final size:6
Alignment explanation
Indices: 3809967--3809999 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
3809957 ATTATTTTTA
3809967 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATT
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATT
3810000 TTCTATTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTAAT
Found at i:3809981 original size:19 final size:18
Alignment explanation
Indices: 3809948--3810020 Score: 78
Period size: 19 Copynumber: 3.9 Consensus size: 18
3809938 TTTTATTAAA
3809948 ATTAATA-TAATTATTTTT
1 ATTAATATTAA-TATTTTT
**
3809966 AATTAATATTAATATTAAT
1 -ATTAATATTAATATTTTT
3809985 ATTAATATTAATATTTTCT
1 ATTAATATTAATATTTT-T
3810004 ATTAA-ATTTAATATTTT
1 ATTAATA-TTAATATTTT
3810021 CCATTTTTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
18 16 0.34
19 28 0.60
20 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTAATATTAATATTTTT
Found at i:3809983 original size:37 final size:37
Alignment explanation
Indices: 3809941--3810018 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 37
3809931 GAAAATATTT
3809941 TATTAAAATTAATA-TAATTATTTT-TAATT-AATATTAA
1 TATTAAAATTAATATTAA-TATTTTCT-ATTAAAT-TTAA
*
3809978 TATTAATATTAATATTAATATTTTCTATTAAATTTAA
1 TATTAAAATTAATATTAATATTTTCTATTAAATTTAA
3810015 TATT
1 TATT
3810019 TTCCATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
37 30 0.81
38 7 0.19
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (37 bp):
TATTAAAATTAATATTAATATTTTCTATTAAATTTAA
Found at i:3809987 original size:25 final size:23
Alignment explanation
Indices: 3809934--3809987 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
3809924 CCGAGAGGAA
3809934 AATA-TTTTATTAAAATTAATAT
1 AATATTTTTATTAAAATTAATAT
*
3809956 AATTATTTTTAATTAATATTAATATT
1 AA-TATTTTT-ATTAAAATTAATA-T
3809982 AATATT
1 AATATT
3809988 AATATTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 2 0.07
23 2 0.07
24 4 0.15
25 16 0.59
26 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATTTTTATTAAAATTAATAT
Found at i:3810308 original size:21 final size:21
Alignment explanation
Indices: 3810284--3810335 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
3810274 TTATTTTTTG
3810284 AATTTTTAATCTAAAAATTGT-
1 AATTTTTAATCTAAAAATT-TC
3810305 AATTTTTAATCTAAAAATTTC
1 AATTTTTAATCTAAAAATTTC
3810326 AATTTTTAAT
1 AATTTTTAAT
3810336 ATTTATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 1 0.03
21 29 0.97
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (21 bp):
AATTTTTAATCTAAAAATTTC
Found at i:3810587 original size:11 final size:10
Alignment explanation
Indices: 3810553--3810634 Score: 51
Period size: 11 Copynumber: 7.8 Consensus size: 10
3810543 ATATTTTATG
*
3810553 TATTATTTTA
1 TATTATTTAA
3810563 TCATTATATT-A
1 T-ATTAT-TTAA
3810574 TATTATTTAAA
1 TATTATTT-AA
* *
3810585 TATTCATGTAT
1 TATT-ATTTAA
3810596 TATTATATT-A
1 TATTAT-TTAA
3810606 TATTATTTAAA
1 TATTATTT-AA
* *
3810617 TATAATTTAT
1 TATTATTTAA
3810627 TATTATTT
1 TATTATTT
3810635 TTAAAATTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
9 4 0.07
10 22 0.39
11 26 0.46
12 5 0.09
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (10 bp):
TATTATTTAA
Found at i:3810587 original size:16 final size:16
Alignment explanation
Indices: 3810568--3810619 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
3810558 TTTTATCATT
3810568 ATATTATATTATTTAA
1 ATATTATATTATTTAA
3810584 ATATTCATGTATTA-TT--
1 ATATT-A--TATTATTTAA
3810600 ATATTATATTATTTAA
1 ATATTATATTATTTAA
3810616 ATAT
1 ATAT
3810620 AATTTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
13 5 0.17
14 2 0.07
15 1 0.03
16 14 0.47
17 1 0.03
18 2 0.07
19 5 0.17
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (16 bp):
ATATTATATTATTTAA
Found at i:3810605 original size:32 final size:31
Alignment explanation
Indices: 3810565--3810632 Score: 109
Period size: 32 Copynumber: 2.2 Consensus size: 31
3810555 TTATTTTATC
*
3810565 ATTATATTATATTATTTAAATATTCATGTATT
1 ATTATATTATATTATTTAAATA-TAATGTATT
*
3810597 ATTATATTATATTATTTAAATATAATTTATT
1 ATTATATTATATTATTTAAATATAATGTATT
3810628 ATTAT
1 ATTAT
3810633 TTTTAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 12 0.35
32 22 0.65
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (31 bp):
ATTATATTATATTATTTAAATATAATGTATT
Found at i:3810703 original size:9 final size:9
Alignment explanation
Indices: 3810633--3810709 Score: 52
Period size: 9 Copynumber: 8.2 Consensus size: 9
3810623 TTATTATTAT
3810633 TTTTAAA-A
1 TTTTAAATA
3810641 TTTTAAAATA
1 TTTT-AAATA
* *
3810651 TGTTATATA
1 TTTTAAATA
3810660 TTATTAAAT-
1 TT-TTAAATA
*
3810669 TTATAAATAA
1 TTTTAAAT-A
3810679 TTTACTAAA-A
1 TTT--TAAATA
3810689 TATTTAAATA
1 T-TTTAAATA
3810699 TTTTAAATA
1 TTTTAAATA
3810708 TT
1 TT
3810710 GTCTAAAATG
Statistics
Matches: 54, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
8 9 0.17
9 24 0.44
10 15 0.28
11 2 0.04
12 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (9 bp):
TTTTAAATA
Found at i:3812235 original size:51 final size:51
Alignment explanation
Indices: 3812176--3812283 Score: 162
Period size: 51 Copynumber: 2.1 Consensus size: 51
3812166 ATCCTTAAAG
* * *
3812176 TTTACACATTCTATTAATTTGGTCTTAATTTAATAAATTTAACCTACAATA
1 TTTACACATTCTATCAATTTAGTCTTAATTTAACAAATTTAACCTACAATA
* * *
3812227 TTTACACATTCTGTCAATTTAGTCTTAATTTAACAAATTTAGCTTACAATA
1 TTTACACATTCTATCAATTTAGTCTTAATTTAACAAATTTAACCTACAATA
3812278 TTTACA
1 TTTACA
3812284 TAGAATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (51 bp):
TTTACACATTCTATCAATTTAGTCTTAATTTAACAAATTTAACCTACAATA
Found at i:3812955 original size:13 final size:12
Alignment explanation
Indices: 3812935--3812976 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
3812925 TAATTAAATG
3812935 TTTT-AATTTTT
1 TTTTAAATTTTT
3812946 TTTGTAAATTTTT
1 TTT-TAAATTTTT
*
3812959 TTTTATATTTTT
1 TTTTAAATTTTT
*
3812971 TGTTAA
1 TTTTAA
3812977 TGTGGTATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
11 3 0.12
12 13 0.50
13 10 0.38
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (12 bp):
TTTTAAATTTTT
Found at i:3813914 original size:17 final size:15
Alignment explanation
Indices: 3813864--3813915 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
3813854 AAATACTATT
3813864 TTTTATTTTTATAGAAA
1 TTTTATTTTT-TA-AAA
*
3813881 TTTTA-TTTTTAATA
1 TTTTATTTTTTAAAA
3813895 TTTATATTTTTTATAAA
1 TTT-TATTTTTTA-AAA
3813912 TTTT
1 TTTT
3813916 GTTGATGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 11 0.37
17 10 0.33
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTTATTTTTTAAAA
Found at i:3814254 original size:9 final size:9
Alignment explanation
Indices: 3814183--3814257 Score: 50
Period size: 9 Copynumber: 8.1 Consensus size: 9
3814173 TATTATTATA
3814183 TTTAAA-AT
1 TTTAAATAT
3814191 TTTCAAATAT
1 TTT-AAATAT
*
3814201 TTTATATAT
1 TTTAAATAT
3814210 TATT--ATAT
1 T-TTAAATAT
3814218 TTATAAATAATT
1 TT-TAAAT-A-T
3814230 TATTAAA-AT
1 T-TTAAATAT
*
3814239 ATTAAATAT
1 TTTAAATAT
3814248 TTTAAATAT
1 TTTAAATAT
3814257 T
1 T
3814258 GTCTAAATTA
Statistics
Matches: 54, Mismatches: 3, Indels: 19
0.71 0.04 0.25
Matches are distributed among these distances:
7 1 0.02
8 14 0.26
9 21 0.39
10 10 0.19
11 1 0.02
12 6 0.11
13 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTAAATAT
Found at i:3814275 original size:57 final size:58
Alignment explanation
Indices: 3814157--3814276 Score: 129
Period size: 57 Copynumber: 2.1 Consensus size: 58
3814147 TATATTAAAT
** * * *
3814157 TATTTAAATAATAAATTATTATTATATTTAAAATTTTCAAATATTTTATATATTATTA
1 TATTTAAATAATAAATTATTAAAATATTTAAAATTTTCAAATATTGTATAAATTATAA
* * *
3814215 TATTTATA-AATAATTTATTAAAATA-TTAAATATTTT-AAATATTGTCTAAATTAATAA
1 TATTTAAATAATAAATTATTAAAATATTTAAA-ATTTTCAAATATTGTATAAATT-ATAA
3814272 TATTT
1 TATTT
3814277 TTTTGGTTTC
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
56 18 0.35
57 27 0.52
58 7 0.13
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.52
Consensus pattern (58 bp):
TATTTAAATAATAAATTATTAAAATATTTAAAATTTTCAAATATTGTATAAATTATAA
Found at i:3814871 original size:16 final size:18
Alignment explanation
Indices: 3814852--3814884 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3814842 GTAAAAATTA
3814852 AATT-TTAAAAA-AAAAG
1 AATTGTTAAAAATAAAAG
3814868 AATTGTTAAAAATAAAA
1 AATTGTTAAAAATAAAA
3814885 ATTGTTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (18 bp):
AATTGTTAAAAATAAAAG
Found at i:3814887 original size:16 final size:16
Alignment explanation
Indices: 3814851--3814890 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3814841 GGTAAAAATT
3814851 AAATT-TTAAAAAAAA
1 AAATTGTTAAAAAAAA
*
3814866 AGAATTGTTAAAAATAA
1 A-AATTGTTAAAAAAAA
3814883 AAATTGTT
1 AAATTGTT
3814891 TCAGTTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 11 0.50
17 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (16 bp):
AAATTGTTAAAAAAAA
Found at i:3823097 original size:86 final size:85
Alignment explanation
Indices: 3823005--3823304 Score: 298
Period size: 87 Copynumber: 3.5 Consensus size: 85
3822995 TTAAACGGTA
* * * *
3823005 GGAATAAATCTCGAAACAAATTTTATTTAATTTTAATTTCTCGTTTTGGCAACAAAATTAAAATG
1 GGAATAAATCCCGAAACAAATTTTATTTAATTTTAATTTCTCGTTTTGGAAATAAAATCAAAATG
*
3823070 TAATAAATTCGTTGAACGGCT
66 -AATAAATTCGTTGAACGGCG
* * *
3823091 GGAATAAATCCCGAAACAGATTTTATTTTAATTTTAA-TACTCATTTTGGAAATAAAATCAAAAT
1 GGAATAAATCCCGAAACAAATTTTA-TTTAATTTTAATTTCTCGTTTTGGAAATAAAATCAAAA-
* * *
3823155 TGGAATAAAATCAATTGAACGACG
64 T-GAATAAATTC-GTTGAACGGCG
* * * * * * *
3823179 GGAATAAAACCCGAAGCGAATTTTATTTAACTTTAATTCCCCG-TTTGGAAATAAAATAGAAAAT
1 GGAATAAATCCCGAAACAAATTTTATTTAATTTTAATTTCTCGTTTTGGAAATAAAAT-CAAAAT
*
3823243 AGAATAAAATCCGTTGAACGGCG
65 -GAAT-AAATTCGTTGAACGGCG
* ** * *
3823266 GGAATAAATACCGAAACGGATTTTATTTACTTTTGATTT
1 GGAATAAATCCCGAAACAAATTTTATTTAATTTTAATTT
3823305 GGAAACAAAA
Statistics
Matches: 174, Mismatches: 33, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
86 44 0.25
87 89 0.51
88 41 0.24
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (85 bp):
GGAATAAATCCCGAAACAAATTTTATTTAATTTTAATTTCTCGTTTTGGAAATAAAATCAAAATG
AATAAATTCGTTGAACGGCG
Found at i:3823202 original size:88 final size:84
Alignment explanation
Indices: 3822971--3823299 Score: 293
Period size: 87 Copynumber: 3.8 Consensus size: 84
3822961 ACTTGAAAAC
** * ** * * *
3822971 AAAATAAAATCAAATAAAATCTTGTTAAACGGTAGGAATAAATCTCGAAACAAATTTTATTTAAT
1 AAAATAAAATGGAATAAAATC--GTTGAACGGCGGGAATAAAACCCGAAACGAATTTTATTTAAT
* * *
3823036 TTTAATTTCTCGTTTTGGCAAC
64 TTTAA-TTCTCATTTTGGAAAT
* * * *
3823058 AAAATTAAAATGTAATAAATTCGTTGAACGGCTGGAATAAATCCCGAAAC-AGATTTTATTTTAA
1 AAAA-TAAAATGGAATAAAATCGTTGAACGGCGGGAATAAAACCCGAAACGA-ATTTTA-TTTAA
*
3823122 TTTTAATACTCATTTTGGAAAT
63 TTTTAATTCTCATTTTGGAAAT
* * *
3823144 AAAATCAAAATTGGAATAAAATCAATTGAACGACGGGAATAAAACCCGAAGCGAATTTTATTTAA
1 AAAAT-AAAA-TGGAATAAAATC-GTTGAACGGCGGGAATAAAACCCGAAACGAATTTTATTTAA
* * **
3823209 CTTTAATTCCCCGTTTGGAAAT
63 TTTTAATTCTCATTTTGGAAAT
* *
3823231 AAAATAGAAAATAGAATAAAATCCGTTGAACGGCGGGAATAAATA-CCGAAACGGATTTTATTTA
1 AAAAT--AAAATGGAATAAAAT-CGTTGAACGGCGGGAATAAA-ACCCGAAACGAATTTTATTTA
*
3823295 CTTTT
62 ATTTT
3823300 GATTTGGAAA
Statistics
Matches: 201, Mismatches: 31, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
85 2 0.01
86 50 0.25
87 99 0.49
88 49 0.24
89 1 0.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (84 bp):
AAAATAAAATGGAATAAAATCGTTGAACGGCGGGAATAAAACCCGAAACGAATTTTATTTAATTT
TAATTCTCATTTTGGAAAT
Found at i:3826330 original size:13 final size:13
Alignment explanation
Indices: 3826312--3826342 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
3826302 AAAAAAGAAG
3826312 TTTTTTTTTT-CT
1 TTTTTTTTTTCCT
3826324 TTTTTTTTTTCCT
1 TTTTTTTTTTCCT
3826337 TTTTTT
1 TTTTTT
3826343 GACCAGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTTCCT
Found at i:3826384 original size:3 final size:3
Alignment explanation
Indices: 3826376--3826401 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3826366 TAAAGAATCT
3826376 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
3826402 GAGAGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3827199 original size:20 final size:20
Alignment explanation
Indices: 3827148--3827200 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
3827138 TTTGAAACAG
*
3827148 AAAATTTTAATTATTTATATAA
1 AAAATTTT-A-TATTCATATAA
** *
3827170 AAAACGTTATATTCATATAT
1 AAAATTTTATATTCATATAA
3827190 AAAATTTTATA
1 AAAATTTTATA
3827201 ATAATACATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 18 0.72
21 1 0.04
22 6 0.24
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (20 bp):
AAAATTTTATATTCATATAA
Found at i:3828223 original size:27 final size:27
Alignment explanation
Indices: 3828154--3828208 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
3828144 CAGTCCCAAA
3828154 AGTCCAAAATAATTAATTACGAAAACT
1 AGTCCAAAATAATTAATTACGAAAACT
3828181 AGTCCAAAATAATTAATTACGAAAACT
1 AGTCCAAAATAATTAATTACGAAAACT
3828208 A
1 A
3828209 TCTTATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (27 bp):
AGTCCAAAATAATTAATTACGAAAACT
Found at i:3830780 original size:41 final size:41
Alignment explanation
Indices: 3830718--3830893 Score: 280
Period size: 41 Copynumber: 4.3 Consensus size: 41
3830708 GTTTGGAATT
* *
3830718 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
3830759 GGTGATCTAAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* *
3830800 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
3830841 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
3830882 GGTGATCCGAAT
1 GGTGATCTGAAT
3830894 ATGATGAATT
Statistics
Matches: 123, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 123 1.00
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
Found at i:3830855 original size:82 final size:82
Alignment explanation
Indices: 3830718--3830887 Score: 331
Period size: 82 Copynumber: 2.1 Consensus size: 82
3830708 GTTTGGAATT
3830718 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
3830783 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
*
3830800 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
3830865 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
3830882 GGTGAT
1 GGTGAT
3830888 CCGAATATGA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 87 1.00
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (82 bp):
GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTATAAGC
CTAGCAGGCTAAGTGCC
Found at i:3864054 original size:44 final size:44
Alignment explanation
Indices: 3863993--3864587 Score: 744
Period size: 44 Copynumber: 13.5 Consensus size: 44
3863983 GAGACAATGT
*
3863993 AGATCGAAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * * * *
3864037 AAATCGAAGAGAACAGATTTGGTGTCTCTATATTGTTAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * *
3864081 AGATCGAACATAGCAGATTTGACGTCTCTGTATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * * * * * * **
3864125 AAATCGAAGAGAACATATTTGGTGTCTCTATATTGTCAAACAAT
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * *
3864169 AGATCGAACATAGCAGATTTGACGTCTCTGTATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * * *
3864213 AAATCGAAGATAGCAGATTTGGCATCTCTATATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* *
3864257 AGATCGAAGAGAACAGATTTGGCGTCTCTATATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* **
3864301 AGATCGAAGATAGCAGATTTGGCACCTCTGTATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
*
3864345 AGATCGAAAATAGA-AGATTTGGCGTCTCTGTATTGTCAGAGAGC
1 AGATCGAAGATA-ACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* **
3864389 AGATCGAAGATAGCAGATTTGGCACCTCTGTATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* * *
3864433 ATATCGAAGATAGC-GAATTTGGCGTCTCTGTATTGTCAGAAAGC
1 AGATCGAAGATAACAG-ATTTGGCGTCTCTGTATTGTCAGAGAGC
**
3864477 AGATCGAAGATAACAGATTTGGTATCTCTGTATTGTCAGAGAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* ** * *
3864521 AGATCAAAGATAACAGATTCAGCGTCTCTGTATTGTCAAAAAGC
1 AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
* *
3864565 AGGTCGGAGATAACAGATTTGGC
1 AGATCGAAGATAACAGATTTGGC
3864588 ATTCTTAAGT
Statistics
Matches: 466, Mismatches: 81, Indels: 8
0.84 0.15 0.01
Matches are distributed among these distances:
43 1 0.00
44 464 1.00
45 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (44 bp):
AGATCGAAGATAACAGATTTGGCGTCTCTGTATTGTCAGAGAGC
Found at i:3866228 original size:24 final size:23
Alignment explanation
Indices: 3866196--3866278 Score: 62
Period size: 25 Copynumber: 3.4 Consensus size: 23
3866186 TATAAAATAA
*
3866196 TATATATTATTTTTATTTATATAT
1 TATACATTATTTTTATTTAT-TAT
*
3866220 TATTCATTATATTATT-TTTATTAT
1 TATACATTAT-TT-TTATTTATTAT
* *
3866244 TATACATT-TTATTTATAAATCTTAT
1 TATACATTATT-TTTAT--TTATTAT
3866269 TATACATTAT
1 TATACATTAT
3866279 ATGTTTTACT
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
22 3 0.06
23 3 0.06
24 18 0.38
25 20 0.43
26 3 0.06
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (23 bp):
TATACATTATTTTTATTTATTAT
Found at i:3866454 original size:21 final size:21
Alignment explanation
Indices: 3866430--3866469 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3866420 TATATGATAG
3866430 TTATCATATTA-TTATATTTCA
1 TTAT-ATATTATTTATATTTCA
*
3866451 TTATATTTTATTTATATTT
1 TTATATATTATTTATATTT
3866470 TTTATTACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATATATTATTTATATTTCA
Found at i:3866498 original size:10 final size:10
Alignment explanation
Indices: 3866430--3866502 Score: 53
Period size: 10 Copynumber: 7.2 Consensus size: 10
3866420 TATATGATAG
3866430 TTATCATATTA
1 TTAT-ATATTA
3866441 TTATAT-TTCA
1 TTATATATT-A
*
3866451 TTATATTTTA
1 TTATATATTA
3866461 TT-TATATT-
1 TTATATATTA
* *
3866469 TTTTATTACATA
1 TTATA-TA-TTA
*
3866481 TCATATATTA
1 TTATATATTA
3866491 TTATATATTA
1 TTATATATTA
3866501 TT
1 TT
3866503 CCCTATTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
8 2 0.04
9 9 0.18
10 27 0.54
11 9 0.18
12 3 0.06
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATATATTA
Found at i:3866533 original size:7 final size:7
Alignment explanation
Indices: 3866519--3866554 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
3866509 TTATCTTCCT
3866519 TTTATTA
1 TTTATTA
*
3866526 TATATTA
1 TTTATTA
3866533 TTTCATTA
1 TTT-ATTA
3866541 TTTATTA
1 TTTATTA
3866548 TTTATTA
1 TTTATTA
3866555 GTATAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (7 bp):
TTTATTA
Found at i:3866540 original size:15 final size:14
Alignment explanation
Indices: 3866519--3866559 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
3866509 TTATCTTCCT
3866519 TTTATTATATATTA
1 TTTATTATATATTA
*
3866533 TTTCATTATTTATTA
1 TTT-ATTATATATTA
3866548 TTTATTAGTATA
1 TTTATTA-TATA
3866560 AAAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (14 bp):
TTTATTATATATTA
Found at i:3868377 original size:16 final size:16
Alignment explanation
Indices: 3868356--3868389 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3868346 TCCCAAAAAA
3868356 GTTAATTTTTGATAAT
1 GTTAATTTTTGATAAT
3868372 GTTAATTTTTGATAAT
1 GTTAATTTTTGATAAT
3868388 GT
1 GT
3868390 GCTACTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (16 bp):
GTTAATTTTTGATAAT
Found at i:3871190 original size:21 final size:21
Alignment explanation
Indices: 3871143--3871192 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3871133 TATGAGCTCC
* *
3871143 TTTATGTTTTGTTTTTCCAAA
1 TTTATTTTTTGTTTATCCAAA
3871164 TTTATTTTTTGTATTAT-CAAA
1 TTTATTTTTTGT-TTATCCAAA
3871185 TTTATTTT
1 TTTATTTT
3871193 AATAAAACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.66
Consensus pattern (21 bp):
TTTATTTTTTGTTTATCCAAA
Found at i:3871281 original size:27 final size:27
Alignment explanation
Indices: 3871250--3871324 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
3871240 AAAAAGTTAT
* * *
3871250 ACCCTAAATCATAAGTCTTAAGTTTTA
1 ACCCTAAATCATAAATCTTAAATCTTA
*
3871277 ACCCTAAATCCTAAATCTTAAATCTTA
1 ACCCTAAATCATAAATCTTAAATCTTA
* *
3871304 ACACTAAA-CTTTAAATCTTAA
1 ACCCTAAATC-ATAAATCTTAA
3871325 CCTTTAAGCC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.02
27 40 0.98
ACGTcount: A:0.41, C:0.21, G:0.03, T:0.35
Consensus pattern (27 bp):
ACCCTAAATCATAAATCTTAAATCTTA
Found at i:3873070 original size:64 final size:64
Alignment explanation
Indices: 3872915--3873173 Score: 225
Period size: 68 Copynumber: 3.9 Consensus size: 64
3872905 TGGATGATAC
* ** * ** * *
3872915 AGATAGTATGTAGCTAGGTCACATGTATGGTGCTGGGTGCACATCATGT-GTACAAGAGAGCTAC
1 AGATA-TATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGCTAC
3872979 AAG
64 --G
* *
3872982 ACATTATTATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTAC
1 AGA-TA-TATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTAC
3873047 G
64 G
* * * * * *
3873048 GGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTA
1 AGATATATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTA
3873113 CG
63 CG
* * * * * *
3873115 AGATAAAT-TGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGTATACAAGAGAGC
1 AGATATATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGC
3873174 CGAACTATAT
Statistics
Matches: 156, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
63 20 0.13
64 26 0.17
65 2 0.01
66 24 0.15
67 34 0.22
68 49 0.31
69 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (64 bp):
AGATATATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACG
Found at i:3875003 original size:7 final size:7
Alignment explanation
Indices: 3874993--3875065 Score: 51
Period size: 7 Copynumber: 10.6 Consensus size: 7
3874983 CATTGAGCCC
3874993 TAAACCT
1 TAAACCT
*
3875000 TAAACCA
1 TAAACCT
*
3875007 TAAATCT
1 TAAACCT
*
3875014 TAAATCT
1 TAAACCT
3875021 TAAA-CT
1 TAAACCT
*
3875027 TAAACCC
1 TAAACCT
* *
3875034 TAAGCCA
1 TAAACCT
3875041 TAAACC-
1 TAAACCT
**
3875047 TAAAATT
1 TAAACCT
3875054 CTAAACCT
1 -TAAACCT
3875062 TAAA
1 TAAA
3875066 TCATAGACCC
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
6 10 0.19
7 37 0.71
8 5 0.10
ACGTcount: A:0.48, C:0.23, G:0.01, T:0.27
Consensus pattern (7 bp):
TAAACCT
Found at i:3875010 original size:14 final size:13
Alignment explanation
Indices: 3874991--3875197 Score: 53
Period size: 14 Copynumber: 15.2 Consensus size: 13
3874981 AACATTGAGC
3874991 CCTAAACCTTAAA
1 CCTAAACCTTAAA
*
3875004 CCATAAATCTTAAA
1 CC-TAAACCTTAAA
*
3875018 TCTTAAA-CTTAAA
1 -CCTAAACCTTAAA
* *
3875031 CCCTAAGCCATAAA
1 -CCTAAACCTTAAA
**
3875045 CCTAAAATTCTAAA
1 CCTAAACCT-TAAA
* * *
3875059 CCTTAAATCATAGAC
1 CC-TAAACCTTA-AA
* *
3875074 CCTAAATCTTAAG
1 CCTAAACCTTAAA
3875087 CTCTAAACC-TAAA
1 C-CTAAACCTTAAA
* *
3875100 CCCTACACCTTACAC
1 -CCTAAACCTTA-AA
*
3875115 CCTCAACCTT-AA
1 CCTAAACCTTAAA
* *
3875127 CTCGAACCCTCTAAA
1 C-CTAAACCT-TAAA
*
3875142 CCTTAAGCAC-TAAA
1 CC-TAAAC-CTTAAA
* * *
3875156 CTTACACCTTAAG
1 CCTAAACCTTAAA
* * *
3875169 CCATCAAGCTTAAC
1 CC-TAAACCTTAAA
3875183 CCTAAACCTTAAA
1 CCTAAACCTTAAA
3875196 CC
1 CC
3875198 ATATTCTCTA
Statistics
Matches: 137, Mismatches: 40, Indels: 34
0.65 0.19 0.16
Matches are distributed among these distances:
12 3 0.02
13 50 0.36
14 68 0.50
15 15 0.11
16 1 0.01
ACGTcount: A:0.40, C:0.32, G:0.03, T:0.25
Consensus pattern (13 bp):
CCTAAACCTTAAA
Found at i:3878618 original size:16 final size:16
Alignment explanation
Indices: 3878594--3878631 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3878584 TGGATTTAAT
3878594 TTAGAACTCTAAACGA
1 TTAGAACTCTAAACGA
* *
3878610 TTAGGACTCTAAATGA
1 TTAGAACTCTAAACGA
3878626 TTAGAA
1 TTAGAA
3878632 TGGAACTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
TTAGAACTCTAAACGA
Found at i:3879015 original size:26 final size:26
Alignment explanation
Indices: 3878986--3879035 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3878976 AAAAATTGTT
3878986 AAAACTCTT-ATAAAAAAAACTCAATA
1 AAAACTCTTGA-AAAAAAAACTCAATA
* *
3879012 AAAATTCTTGAAAAGAAAACTCAA
1 AAAACTCTTGAAAAAAAAACTCAA
3879036 AGAGAATCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 20 0.95
27 1 0.05
ACGTcount: A:0.60, C:0.14, G:0.04, T:0.22
Consensus pattern (26 bp):
AAAACTCTTGAAAAAAAAACTCAATA
Found at i:3880923 original size:7 final size:7
Alignment explanation
Indices: 3880915--3880989 Score: 64
Period size: 7 Copynumber: 10.9 Consensus size: 7
3880905 GTCATATTTG
*
3880915 GGGTTTG
1 GGGTTTT
3880922 GGGTTTT
1 GGGTTTT
*
3880929 AGGTTTT
1 GGGTTTT
3880936 GGGTTTT
1 GGGTTTT
3880943 GGGTTTAT
1 GGGTTT-T
*
3880951 -GGTTAT
1 GGGTTTT
3880957 -GGTTTT
1 GGGTTTT
*
3880963 GAGTTTT
1 GGGTTTT
*
3880970 GAGTTTT
1 GGGTTTT
*
3880977 AGGTTTT
1 GGGTTTT
*
3880984 GAGTTT
1 GGGTTT
3880990 GAGGTTGGGT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
6 6 0.11
7 49 0.88
8 1 0.02
ACGTcount: A:0.09, C:0.00, G:0.36, T:0.55
Consensus pattern (7 bp):
GGGTTTT
Found at i:3880939 original size:14 final size:14
Alignment explanation
Indices: 3880923--3881025 Score: 63
Period size: 14 Copynumber: 7.5 Consensus size: 14
3880913 TGGGGTTTGG
* *
3880923 GGTTTTAGGTTTTG
1 GGTTTTGGGTTTTA
3880937 GGTTTTGGG-TTTA
1 GGTTTTGGGTTTTA
*
3880950 TGGTTAT-GGTTTT-
1 -GGTTTTGGGTTTTA
*
3880963 GAGTTTTGAGTTTTA
1 G-GTTTTGGGTTTTA
* *
3880978 GGTTTTGAGTTTGA
1 GGTTTTGGGTTTTA
*
3880992 GG--TTGGGTTTAA
1 GGTTTTGGGTTTTA
* *
3881004 TGTTTTAGGGTTTAA
1 GGTTTT-GGGTTTTA
3881019 GGTTTTG
1 GGTTTTG
3881026 TATTTCAAGT
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
12 10 0.14
13 9 0.13
14 38 0.54
15 14 0.20
ACGTcount: A:0.13, C:0.00, G:0.34, T:0.53
Consensus pattern (14 bp):
GGTTTTGGGTTTTA
Found at i:3880954 original size:21 final size:20
Alignment explanation
Indices: 3880924--3880989 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
3880914 GGGGTTTGGG
*
3880924 GTTTTAGGTTTTGGGTTTTGG
1 GTTTT-GGTTTTGGGTTTTGA
*
3880945 GTTTATGGTTAT-GGTTTTGA
1 GTTT-TGGTTTTGGGTTTTGA
*
3880965 GTTTTGAGTTTTAGGTTTTGA
1 GTTTTG-GTTTTGGGTTTTGA
3880986 GTTT
1 GTTT
3880990 GAGGTTGGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.05
20 15 0.38
21 21 0.54
22 1 0.03
ACGTcount: A:0.11, C:0.00, G:0.32, T:0.58
Consensus pattern (20 bp):
GTTTTGGTTTTGGGTTTTGA
Found at i:3881101 original size:21 final size:21
Alignment explanation
Indices: 3881054--3881128 Score: 57
Period size: 21 Copynumber: 3.6 Consensus size: 21
3881044 TTGGATTTTG
*
3881054 AGTTTTGAGTTTAGGGTTTAC
1 AGTTTAGAGTTTAGGGTTTAC
* *
3881075 AATTTAGAGTTTAGTGTTTA-
1 AGTTTAGAGTTTAGGGTTTAC
*
3881095 AGGTTTAG-GATTTTGGGTTT-C
1 A-GTTTAGAG-TTTAGGGTTTAC
*
3881116 GAGTTTCGAGTTT
1 -AGTTTAGAGTTT
3881129 TGTGTTTCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.20, C:0.04, G:0.28, T:0.48
Consensus pattern (21 bp):
AGTTTAGAGTTTAGGGTTTAC
Found at i:3881129 original size:21 final size:21
Alignment explanation
Indices: 3881105--3881170 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
3881095 AGGTTTAGGA
* *
3881105 TTTTGGGTTTCGAGTTTCGAG
1 TTTTGAGTTTCAAGTTTCGAG
* *
3881126 TTTTGTGTTTCAAGTTTCAAG
1 TTTTGAGTTTCAAGTTTCGAG
* * *
3881147 CTTTGAGTTTTAGGTTTCGAG
1 TTTTGAGTTTCAAGTTTCGAG
3881168 TTT
1 TTT
3881171 ATTTTTAGAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.14, C:0.09, G:0.26, T:0.52
Consensus pattern (21 bp):
TTTTGAGTTTCAAGTTTCGAG
Found at i:3881836 original size:35 final size:35
Alignment explanation
Indices: 3881797--3881881 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 35
3881787 TAAGAATTAG
* *
3881797 AGTTTAAGGTTCAAGGTTCAGGGTTCATGATTAAA
1 AGTTTAAGGTTCAAGGTTAAGGGTTCAAGATTAAA
* * *
3881832 AGTTTAGGGCTT-AAGGTTAAGGGTTCAAGGTTTAA
1 AGTTTAAGG-TTCAAGGTTAAGGGTTCAAGATTAAA
*
3881867 AGTTTAGTGGTTCAA
1 AGTTTA-AGGTTCAA
3881882 CAACCACTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
35 35 0.85
36 6 0.15
ACGTcount: A:0.29, C:0.07, G:0.28, T:0.35
Consensus pattern (35 bp):
AGTTTAAGGTTCAAGGTTAAGGGTTCAAGATTAAA
Found at i:3882604 original size:5 final size:5
Alignment explanation
Indices: 3882594--3882623 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
3882584 AAATGAAGTG
3882594 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT CTTTT
3882624 TCCCTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:3883742 original size:30 final size:31
Alignment explanation
Indices: 3883706--3883765 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
3883696 CCCCACCTAT
3883706 ATTTTTAA-AA-TATATATTATTTTTAATTTA
1 ATTTTTAATAATTATAT-TTATTTTTAATTTA
* *
3883736 ATTTTTAATAATTTTATTTATTTTTTATTT
1 ATTTTTAATAATTATATTTATTTTTAATTT
3883766 TTAAAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 14 0.54
32 4 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (31 bp):
ATTTTTAATAATTATATTTATTTTTAATTTA
Found at i:3883774 original size:26 final size:26
Alignment explanation
Indices: 3883705--3883783 Score: 79
Period size: 26 Copynumber: 2.9 Consensus size: 26
3883695 GCCCCACCTA
3883705 TATTTTTAAAATATATATTATTTTTAATTT
1 TATTTTTAAAA-AT-T-TTATTTTT-ATTT
* *
3883735 AATTTTTAATAATTTTATTTATT-TTT
1 TATTTTTAAAAATTTTATTT-TTATTT
*
3883761 TATTTTTAAAAATTTTATATTTA
1 TATTTTTAAAAATTTTATTTTTA
3883784 GTTATCTTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
25 2 0.05
26 20 0.48
27 6 0.14
28 3 0.07
29 2 0.05
30 9 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TATTTTTAAAAATTTTATTTTTATTT
Found at i:3884241 original size:14 final size:14
Alignment explanation
Indices: 3884208--3884234 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3884198 TTAGAATTTT
3884208 TATTTTTTAAAATA
1 TATTTTTTAAAATA
3884222 TATTTTTTAAAAT
1 TATTTTTTAAAAT
3884235 CTTTTTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTTTTAAAATA
Found at i:3884266 original size:18 final size:19
Alignment explanation
Indices: 3884204--3884292 Score: 59
Period size: 18 Copynumber: 4.9 Consensus size: 19
3884194 AATTTTAGAA
3884204 TTTTTATTTTTTAAAATA-
1 TTTTTATTTTTTAAAATAT
*
3884222 ----TATTTTTTAAAATCT
1 TTTTTATTTTTTAAAATAT
*
3884237 TTTTTGA-ATTTT-AAATAT
1 TTTTT-ATTTTTTAAAATAT
3884255 TTTTTATTTTTTCAAAAT-T
1 TTTTTATTTTTT-AAAATAT
*
3884274 TTTATTTTATTTTTAAAAT
1 TTT-TTAT-TTTTTAAAAT
3884293 TATAATTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
14 13 0.24
17 1 0.02
18 14 0.25
19 9 0.16
20 13 0.24
21 5 0.09
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (19 bp):
TTTTTATTTTTTAAAATAT
Found at i:3884291 original size:20 final size:19
Alignment explanation
Indices: 3884225--3884293 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 19
3884215 TAAAATATAT
* *
3884225 TTTTTAAAATCTTTTTTGA
1 TTTTTAAAATTTTTTTTTA
* *
3884244 ATTTTAAATATTTTTTATT-
1 TTTTTAAA-ATTTTTTTTTA
*
3884263 TTTTCAAAATTTTTATTTTA
1 TTTTTAAAATTTTT-TTTTA
3884283 TTTTTAAAATT
1 TTTTTAAAATT
3884294 ATAATTTTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
18 6 0.15
19 16 0.41
20 17 0.44
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.65
Consensus pattern (19 bp):
TTTTTAAAATTTTTTTTTA
Found at i:3884300 original size:20 final size:22
Alignment explanation
Indices: 3884256--3884301 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
3884246 TTTAAATATT
* *
3884256 TTTTATTTTTTCAAAATTTTTA
1 TTTTATTTTTTCAAAATTATAA
3884278 TTTTA-TTTTT-AAAATTATAA
1 TTTTATTTTTTCAAAATTATAA
3884298 TTTT
1 TTTT
3884302 TAAATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 5 0.23
22 5 0.23
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTATTTTTTCAAAATTATAA
Found at i:3884753 original size:5 final size:5
Alignment explanation
Indices: 3884743--3884775 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
3884733 GTTTAATCAT
3884743 TTTAA TTTAA TTTAA TTTAA TTTAA TTT-A TTTA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTA
3884776 TTAAAATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:3884861 original size:27 final size:27
Alignment explanation
Indices: 3884826--3884880 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
3884816 TTTTTTTATA
*
3884826 ATTTTTATTTTAAAATGAAAAAAATTT
1 ATTTTTATTTAAAAATGAAAAAAATTT
3884853 ATTTTTATTTAAAAATGAAAAAAATTT
1 ATTTTTATTTAAAAATGAAAAAAATTT
3884880 A
1 A
3884881 AAAATTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (27 bp):
ATTTTTATTTAAAAATGAAAAAAATTT
Found at i:3888286 original size:47 final size:47
Alignment explanation
Indices: 3888211--3888334 Score: 126
Period size: 47 Copynumber: 2.6 Consensus size: 47
3888201 TTCGACCTCG
* ** * *
3888211 AGTCAATGAGGCACTATAAGTGTCGTACTGTTACTG-TTACTTTGGTTTA
1 AGTCGATGAGGCAC--TAAGTACCGTACTGTTACTGTTTACTTCGG-CTA
* *
3888260 A-TCTGATGAGGTACTGAGTACCGTACTGTTACTGTTTACTTCGGCTA
1 AGTC-GATGAGGCACTAAGTACCGTACTGTTACTGTTTACTTCGGCTA
*
3888307 AGTCGATGAGGCACTAAGTGCCGTACTG
1 AGTCGATGAGGCACTAAGTACCGTACTG
3888335 GTGTGTTGGT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
47 41 0.66
48 12 0.19
49 9 0.15
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (47 bp):
AGTCGATGAGGCACTAAGTACCGTACTGTTACTGTTTACTTCGGCTA
Found at i:3890817 original size:17 final size:17
Alignment explanation
Indices: 3890787--3890819 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3890777 AACCCAGCAG
3890787 ACCCGTTACTACCCAAA
1 ACCCGTTACTACCCAAA
3890804 ACCCGGTTAC-ACCCAA
1 ACCC-GTTACTACCCAA
3890820 GCTCGAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.33, C:0.42, G:0.09, T:0.15
Consensus pattern (17 bp):
ACCCGTTACTACCCAAA
Found at i:3891997 original size:18 final size:17
Alignment explanation
Indices: 3891974--3892007 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3891964 TTTTGAATTT
3891974 TATTATGTATTTAATATA
1 TATTAT-TATTTAATATA
*
3891992 TATTATTATTTTATAT
1 TATTATTATTTAATAT
3892008 TAAAATTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
TATTATTATTTAATATA
Found at i:3892304 original size:17 final size:17
Alignment explanation
Indices: 3892282--3892333 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
3892272 GTTTTCATAT
3892282 TATTTTATTACATATTA
1 TATTTTATTACATATTA
* * *
3892299 TATTTTACTCCATATGA
1 TATTTTATTACATATTA
*
3892316 TA-TTT-TTATATATTA
1 TATTTTATTACATATTA
3892331 TAT
1 TAT
3892334 ACATTTTATC
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
15 8 0.30
16 3 0.11
17 16 0.59
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (17 bp):
TATTTTATTACATATTA
Found at i:3892333 original size:15 final size:15
Alignment explanation
Indices: 3892239--3892333 Score: 54
Period size: 15 Copynumber: 6.0 Consensus size: 15
3892229 CTTATATACA
3892239 TTTTATATATTTCACTAT
1 TTTTATATA-TT-A-TAT
*
3892257 ATTTATATATTAT-T
1 TTTTATATATTATAT
3892271 TGTTT-TCATATTAT-T
1 T-TTTAT-ATATTATAT
*
3892286 TTATTACATATTATA-
1 TT-TTATATATTATAT
*
3892301 TTTTACTCCATATGATAT
1 TTTTA-T--ATATTATAT
3892319 TTTTATATATTATAT
1 TTTTATATATTATAT
3892334 ACATTTTATC
Statistics
Matches: 62, Mismatches: 6, Indels: 21
0.70 0.07 0.24
Matches are distributed among these distances:
14 6 0.10
15 32 0.52
16 1 0.02
17 10 0.16
18 13 0.21
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (15 bp):
TTTTATATATTATAT
Found at i:3895218 original size:22 final size:22
Alignment explanation
Indices: 3895188--3895232 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3895178 TTACTTTTAC
*
3895188 TATTGAATTTGAATAGA-AATAA
1 TATTGAATTT-AATAAATAATAA
*
3895210 TATTTAATTTAATAAATAATAA
1 TATTGAATTTAATAAATAATAA
3895232 T
1 T
3895233 CTATCCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (22 bp):
TATTGAATTTAATAAATAATAA
Found at i:3896597 original size:16 final size:15
Alignment explanation
Indices: 3896551--3896597 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
3896541 CAAAAAATTT
*
3896551 TAATTATTTATATAA
1 TAATAATTTATATAA
*
3896566 AAATAATGTT-TATAA
1 TAATAAT-TTATATAA
3896581 TAATACATTTATATAA
1 TAATA-ATTTATATAA
3896597 T
1 T
3896598 CTAATATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
TAATAATTTATATAA
Found at i:3897962 original size:98 final size:98
Alignment explanation
Indices: 3897838--3898022 Score: 327
Period size: 98 Copynumber: 1.9 Consensus size: 98
3897828 CGGTCACAAG
*
3897838 GCCCAAATTGGTCTTACTCGTGTGGATCACACGGCCTGGCTCAAATTCCCATACGCCC-GTGTGG
1 GCCCAAATTGGTCTTACTCGTGTGGATCACACGGCCTGGCTCAAATTCCCACACGCCCTGTG-GG
*
3897902 CCCACACGGCTTATTTGCTTGAGGCACGCACATA
65 CCCACACGGCCTATTTGCTTGAGGCACGCACATA
*
3897936 GCCCAAATTGGTCTTACTCGTGTGGATCACACGGCTTGGCTCAAATTCCCACACGCCCTGTGGGC
1 GCCCAAATTGGTCTTACTCGTGTGGATCACACGGCCTGGCTCAAATTCCCACACGCCCTGTGGGC
3898001 CCACACGGCCTATTTGCTTGAG
66 CCACACGGCCTATTTGCTTGAG
3898023 TCTGTGCCTC
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
98 80 0.96
99 3 0.04
ACGTcount: A:0.19, C:0.32, G:0.24, T:0.25
Consensus pattern (98 bp):
GCCCAAATTGGTCTTACTCGTGTGGATCACACGGCCTGGCTCAAATTCCCACACGCCCTGTGGGC
CCACACGGCCTATTTGCTTGAGGCACGCACATA
Found at i:3899618 original size:2 final size:2
Alignment explanation
Indices: 3899611--3899637 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3899601 TAATTGGTGT
3899611 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
3899638 CCCTTTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3900266 original size:34 final size:35
Alignment explanation
Indices: 3900222--3900288 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3900212 CTGTAAAATG
3900222 TTTTCCGTAAAATGAATT-CTGGAAAATATTTTAC
1 TTTTCCGTAAAATGAATTACTGGAAAATATTTTAC
* *
3900256 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGAATTACTGGAAAATATTTT
3900289 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.43
Consensus pattern (35 bp):
TTTTCCGTAAAATGAATTACTGGAAAATATTTTAC
Found at i:3901662 original size:27 final size:27
Alignment explanation
Indices: 3901632--3901701 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
3901622 AATAATCAAT
*
3901632 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
3901659 TCAATATCTAACCAATTCAAGACATATA
1 TCAATATCCAA-CAATTCAAAACATATA
*
3901687 TCAAAATCCAACAAT
1 TCAATATCCAACAAT
3901702 CTAAAATTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.50, C:0.21, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:3907541 original size:16 final size:15
Alignment explanation
Indices: 3907519--3907556 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
3907509 TAATTTGATC
*
3907519 AATTTTAATTTTTAA
1 AATTTTAAATTTTAA
3907534 ATATTTTAAATTTTAA
1 A-ATTTTAAATTTTAA
3907550 AATTTTA
1 AATTTTA
3907557 GTCTTAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AATTTTAAATTTTAA
Found at i:3913993 original size:22 final size:22
Alignment explanation
Indices: 3913968--3914032 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
3913958 GTTAAGGGTT
3913968 AAATTTACTATTATGTCATTAG
1 AAATTTACTATTATGTCATTAG
* * * *
3913990 AAA--TCCAATT-T-T-ACTAT
1 AAATTTACTATTATGTCATTAG
3914007 AAATTTACTATTATGTCATTAG
1 AAATTTACTATTATGTCATTAG
3914029 AAAT
1 AAAT
3914033 CCAATTTTAC
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 6 0.20
18 1 0.03
19 6 0.20
20 6 0.20
21 1 0.03
22 10 0.33
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (22 bp):
AAATTTACTATTATGTCATTAG
Found at i:3914021 original size:39 final size:39
Alignment explanation
Indices: 3913967--3914045 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
3913957 TGTTAAGGGT
3913967 TAAATTTACTATTATGTCATTAGAAATCCAATTTTACTA
1 TAAATTTACTATTATGTCATTAGAAATCCAATTTTACTA
3914006 TAAATTTACTATTATGTCATTAGAAATCCAATTTTACTA
1 TAAATTTACTATTATGTCATTAGAAATCCAATTTTACTA
3914045 T
1 T
3914046 TGGTAAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (39 bp):
TAAATTTACTATTATGTCATTAGAAATCCAATTTTACTA
Found at i:3922199 original size:18 final size:18
Alignment explanation
Indices: 3922162--3922215 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
3922152 ATAATAAAAT
*
3922162 AATTCAAAATAATTTTTAA
1 AATTCAAAAT-ATTTATAA
3922181 AATTCAAAATATTTATAA
1 AATTCAAAATATTTATAA
*
3922199 AAGTTCCAAA-ATTTATA
1 AA-TTCAAAATATTTATA
3922216 TATTTTTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (18 bp):
AATTCAAAATATTTATAA
Found at i:3923159 original size:17 final size:17
Alignment explanation
Indices: 3923137--3923170 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3923127 CAAAACTTCA
*
3923137 AAAAAAAATTAAGAAAT
1 AAAAAAAATTAAAAAAT
*
3923154 AAAAAAATTTAAAAAAT
1 AAAAAAAATTAAAAAAT
3923171 TGTTTGGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (17 bp):
AAAAAAAATTAAAAAAT
Found at i:3923237 original size:21 final size:19
Alignment explanation
Indices: 3923196--3923240 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 19
3923186 GTTTTTTTTA
3923196 TTTA-GAAAATTTTAGAAT
1 TTTATGAAAATTTTAGAAT
*
3923214 TTTATGAAAACTTTTAATAAT
1 TTTATGAAAA-TTTT-AGAAT
3923235 TTTATG
1 TTTATG
3923241 GTATTTTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 5 0.22
20 4 0.17
21 10 0.43
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (19 bp):
TTTATGAAAATTTTAGAAT
Found at i:3924896 original size:14 final size:15
Alignment explanation
Indices: 3924877--3924917 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
3924867 ATTTTCATAA
3924877 CTATTATTTA-TACT
1 CTATTATTTATTACT
3924891 CTATTA-TTATTACT
1 CTATTATTTATTACT
3924905 -TATTATTTTATTA
1 CTATTA-TTTATTA
3924918 TTGTTATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.33
14 10 0.42
15 6 0.25
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (15 bp):
CTATTATTTATTACT
Found at i:3924896 original size:45 final size:44
Alignment explanation
Indices: 3924847--3924958 Score: 115
Period size: 42 Copynumber: 2.6 Consensus size: 44
3924837 TCACTGTTAT
*
3924847 TATTATTATCACTCGTTATTATTTTCATAACTATTAT-TTATACT-C
1 TATTATTATCACTC-TTATTATTTT-ATAACTATTATCTAATA-TAC
* * * *
3924892 TATTATTATTA--CTTATTATTTTATTATTGTTATCTAATATAC
1 TATTATTATCACTCTTATTATTTTATAACTATTATCTAATATAC
*
3924934 TATTATTATCACTATTATTATTTTA
1 TATTATTATCACTCTTATTATTTTA
3924959 CTATTGTAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
41 9 0.16
42 25 0.45
43 1 0.02
44 11 0.20
45 10 0.18
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (44 bp):
TATTATTATCACTCTTATTATTTTATAACTATTATCTAATATAC
Found at i:3924898 original size:3 final size:3
Alignment explanation
Indices: 3924892--3925010 Score: 91
Period size: 3 Copynumber: 39.7 Consensus size: 3
3924882 ATTTATACTC
* * *
3924892 TAT TAT TAT TACT TAT TAT T-T TAT TAT TGT TAT CTAA TA- TAC TAT
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * * * * * * *
3924937 TAT TAT CAC TAT TAT TAT T-T TAC TAT TGT AACT TAA TAT TTT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT
3924982 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3925011 AACTAATTAA
Statistics
Matches: 91, Mismatches: 19, Indels: 12
0.75 0.16 0.10
Matches are distributed among these distances:
2 6 0.07
3 78 0.86
4 7 0.08
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:3924955 original size:18 final size:18
Alignment explanation
Indices: 3924832--3924955 Score: 73
Period size: 18 Copynumber: 7.1 Consensus size: 18
3924822 TTATTACTAC
* *
3924832 TATTGTCACTGTTATTAT
1 TATTATCACTATTATTAT
*
3924850 TATTATCACTCGTTATTAT
1 TATTATCACT-ATTATTAT
*
3924869 T-TTCATAACTATTA-T-T
1 TATT-ATCACTATTATTAT
*
3924885 TA-TA-CTCTATTATTAT
1 TATTATCACTATTATTAT
* *
3924901 TACTTATTA-TTTTATTAT
1 TA-TTATCACTATTATTAT
* * *
3924919 TGTTATCTAATA-TACTAT
1 TATTATC-ACTATTATTAT
3924937 TATTATCACTATTATTAT
1 TATTATCACTATTATTAT
3924955 T
1 T
3924956 TTACTATTGT
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
14 6 0.08
15 2 0.03
16 6 0.08
17 8 0.10
18 43 0.54
19 15 0.19
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTATCACTATTATTAT
Found at i:3925036 original size:54 final size:54
Alignment explanation
Indices: 3924934--3925041 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
3924924 TCTAATATAC
** * *
3924934 TATTATTATCACTATTATTATTTTACTATTGTAACTTAATATTTTTGTTATTAT
1 TATTATTATCACTATTATTATTAAACTAATGTAACTTAATATTATTGTTATTAT
* * * *
3924988 TATTATTATTATTATTATTATTAAACTAAT-TAATTTCATATTAATTGTTATTAT
1 TATTATTATCACTATTATTATTAAACTAATGTAACTTAATATT-ATTGTTATTAT
3925042 ACTATATACT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
53 10 0.22
54 35 0.78
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (54 bp):
TATTATTATCACTATTATTATTAAACTAATGTAACTTAATATTATTGTTATTAT
Found at i:3925262 original size:3 final size:3
Alignment explanation
Indices: 3925173--3925252 Score: 65
Period size: 3 Copynumber: 26.3 Consensus size: 3
3925163 ATTCCAAATG
* * *
3925173 TTA TTC TTA TT- TTCA TTA TTA TTA TTA TT- TCTA TTA TTCT TTA TTG
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA T-TA TTA TT-A TTA TTA
* * *
3925219 TCA TTA TTG TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3925253 AGCTATTATT
Statistics
Matches: 60, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
2 3 0.05
3 52 0.87
4 5 0.08
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3926763 original size:18 final size:18
Alignment explanation
Indices: 3926742--3926783 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
3926732 TTTTTTATTT
3926742 TTTTTATAATTTTCTAAG-
1 TTTTTAT-ATTTTCTAAGA
*
3926760 TTTTAATATTTTCTAAGA
1 TTTTTATATTTTCTAAGA
3926778 TTTTTA
1 TTTTTA
3926784 AGGAATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTTTATATTTTCTAAGA
Found at i:3931243 original size:33 final size:33
Alignment explanation
Indices: 3931201--3931266 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
3931191 TGATGATTCG
*
3931201 TTGCTCTCTAAATAATCTGATTCAAGGTGGAGT
1 TTGCTCTCTAAATAATCTAATTCAAGGTGGAGT
*
3931234 TTGCTCTCTACATAATCTAATTCAAGGTGGAGT
1 TTGCTCTCTAAATAATCTAATTCAAGGTGGAGT
3931267 AGTGTTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (33 bp):
TTGCTCTCTAAATAATCTAATTCAAGGTGGAGT
Found at i:3936534 original size:34 final size:34
Alignment explanation
Indices: 3936492--3936571 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
3936482 TTGTTTGCAT
*
3936492 ACTG-TACTGAAGA-GGGCTCAGGCCCAGACTGTC-
1 ACTGTTACTGAA-ATGGGCTCAGGCCAAGACTG-CG
3936525 ACTGTTACTGAAATGGGCTCAGGCCAAGACTGCG
1 ACTGTTACTGAAATGGGCTCAGGCCAAGACTGCG
*
3936559 ACTATTACTGAAA
1 ACTGTTACTGAAA
3936572 AAGGGGCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
33 6 0.14
34 36 0.86
ACGTcount: A:0.29, C:0.24, G:0.26, T:0.21
Consensus pattern (34 bp):
ACTGTTACTGAAATGGGCTCAGGCCAAGACTGCG
Found at i:3941782 original size:40 final size:39
Alignment explanation
Indices: 3941725--3941955 Score: 340
Period size: 40 Copynumber: 5.8 Consensus size: 39
3941715 TGGGATTTAA
*
3941725 CCGGATATAGCTACTCGCTCAAATGCCTTCGGGACTTAGC
1 CCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGC
3941765 CCGGATATAGTAGCTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTA-CTCGCACAAATGCCTTCGGGACTTAGC
*
3941805 CCGGATATAATAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGC
3941845 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGC
*
3941885 CCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGT-ACTCGCACAAATGCCTTCGGGACTTAGC
*
3941925 CCGGA-ATTAGTCACTAGCACAAATGCCTTCG
1 CCGGATA-TAGT-ACTCGCACAAATGCCTTCG
3941956 TTATCATCCG
Statistics
Matches: 183, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
39 3 0.02
40 179 0.98
41 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (39 bp):
CCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:3948602 original size:9 final size:9
Alignment explanation
Indices: 3948562--3948670 Score: 62
Period size: 9 Copynumber: 11.4 Consensus size: 9
3948552 TCTTTTTCCC
3948562 TTTTTATTTA
1 TTTTTA-TTA
3948572 TTTATTTATTA
1 -TT-TTTATTA
*
3948583 TTCTTATTTA
1 TTTTTA-TTA
3948593 TTTTTATTA
1 TTTTTATTA
*
3948602 TATTTATTA
1 TTTTTATTA
3948611 TCCTTTT-TT-
1 T--TTTTATTA
*
3948620 TTGTATTTTTA
1 TT-T-TTATTA
3948631 TTTTT-TTA
1 TTTTTATTA
*
3948639 TTCTTATTA
1 TTTTTATTA
*
3948648 TGTTTATTA
1 TTTTTATTA
*
3948657 TTTATTCTTA
1 TTT-TTATTA
3948667 TTTT
1 TTTT
3948671 AGCTATCGTA
Statistics
Matches: 79, Mismatches: 9, Indels: 22
0.72 0.08 0.20
Matches are distributed among these distances:
7 1 0.01
8 8 0.10
9 33 0.42
10 23 0.29
11 10 0.13
12 4 0.05
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTTATTA
Found at i:3948605 original size:21 final size:21
Alignment explanation
Indices: 3948565--3948602 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
3948555 TTTTCCCTTT
3948565 TTATTTATTTATTTATTATTC
1 TTATTTATTTATTTATTATTC
3948586 TTATTTA-TT-TTTATTAT
1 TTATTTATTTATTTATTAT
3948603 ATTTATTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.47
20 2 0.12
21 7 0.41
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATTTATTTATTTATTATTC
Found at i:3951010 original size:34 final size:34
Alignment explanation
Indices: 3950937--3951014 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
3950927 AGTGACAGTC
*
3950937 CAGTATCAGTGTGGGCCTTAGCCCATATCAGTAG
1 CAGTATCAGTGTGGGCCTTAGCCCATATCAGTAA
* * * *
3950971 TAGTATTATTGTGGGCCTTAGCTCAT-TACAGTAA
1 CAGTATCAGTGTGGGCCTTAGCCCATAT-CAGTAA
3951005 CAGTATCAGT
1 CAGTATCAGT
3951015 AATGCAACAG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
33 1 0.03
34 34 0.97
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (34 bp):
CAGTATCAGTGTGGGCCTTAGCCCATATCAGTAA
Found at i:3951074 original size:22 final size:23
Alignment explanation
Indices: 3951034--3951076 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
3951024 GAAGTCCTAC
3951034 CCGTCCATCCTCTACACTCCACT
1 CCGTCCATCCTCTACACTCCACT
3951057 CCGTCCATCCT-TACACTCCA
1 CCGTCCATCCTCTACACTCCA
3951077 TGTAGGGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.19, C:0.51, G:0.05, T:0.26
Consensus pattern (23 bp):
CCGTCCATCCTCTACACTCCACT
Done.