Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 211 of 311
Found at i:72615732 original size:20 final size:19
Alignment explanation
Indices: 72615703--72615749 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
72615693 CAAACTTTTC
72615703 AAAAATTAAAAA-AAAGTTA
1 AAAAATTAAAAAGAAA-TTA
72615722 AAAAATGTAAAAAGAAATTA
1 AAAAAT-TAAAAAGAAATTA
72615742 AAGAAATT
1 AA-AAATT
72615750 GTATTTACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.24
20 12 0.48
21 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (19 bp):
AAAAATTAAAAAGAAATTA
Found at i:72615820 original size:14 final size:14
Alignment explanation
Indices: 72615801--72615827 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
72615791 AAAAATATGG
72615801 TTAATATTTAAAAA
1 TTAATATTTAAAAA
72615815 TTAATATTTAAAA
1 TTAATATTTAAAA
72615828 TTTTAAAAAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATATTTAAAAA
Found at i:72615842 original size:37 final size:37
Alignment explanation
Indices: 72615806--72615923 Score: 104
Period size: 37 Copynumber: 3.3 Consensus size: 37
72615796 TATGGTTAAT
*
72615806 ATTT-AAAAATTA-ATATTTAAAAT-TTTAAAAAATTA
1 ATTTGAAAAA-TACATATTTAAAATATATAAAAAATTA
*
72615841 ATTTGAAAAATACATTTTTAAAATATATAAAAAATTA
1 ATTTGAAAAATACATATTTAAAATATATAAAAAATTA
* * * * *
72615878 ATTTCACAAATATATATCTAAAGT-TA-AAAAAA-TA
1 ATTTGAAAAATACATATTTAAAATATATAAAAAATTA
* *
72615912 TTTTTAAAAATA
1 ATTTGAAAAATA
72615924 ATAATTTTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
34 11 0.16
35 12 0.17
36 17 0.25
37 29 0.42
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (37 bp):
ATTTGAAAAATACATATTTAAAATATATAAAAAATTA
Found at i:72615926 original size:15 final size:14
Alignment explanation
Indices: 72615901--72615937 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
72615891 ATATCTAAAG
*
72615901 TTAAAAAAATATTT
1 TTAAAAAAATAATT
72615915 TTAAAAATAATAATT
1 TTAAAAA-AATAATT
72615930 TTAAAAAA
1 TTAAAAAA
72615938 GTATTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTAAAAAAATAATT
Found at i:72616011 original size:22 final size:19
Alignment explanation
Indices: 72615986--72616041 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 19
72615976 TAAAGTTAAT
72615986 AATAAAAAATAAAACAAAATGA
1 AATAAAAAA-AAAACAAAA--A
*
72616008 AATAAGAAAAAAAATAAAAA
1 AATAA-AAAAAAAACAAAAA
72616028 AAGTAAAAAAAAAA
1 AA-TAAAAAAAAAA
72616042 AGATACAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 11 0.35
21 3 0.10
22 13 0.42
23 4 0.13
ACGTcount: A:0.82, C:0.02, G:0.05, T:0.11
Consensus pattern (19 bp):
AATAAAAAAAAAACAAAAA
Found at i:72616035 original size:17 final size:17
Alignment explanation
Indices: 72615989--72616039 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
72615979 AGTTAATAAT
* *
72615989 AAAAAATAAAACAAAATG
1 AAAAAAGAAAA-AAAATA
*
72616007 AAATAAGAAAAAAAATA
1 AAAAAAGAAAAAAAATA
72616024 AAAAAAGTAAAAAAAA
1 AAAAAAG-AAAAAAAA
72616040 AAAGATACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.82, C:0.02, G:0.06, T:0.10
Consensus pattern (17 bp):
AAAAAAGAAAAAAAATA
Found at i:72616085 original size:17 final size:17
Alignment explanation
Indices: 72616063--72616116 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
72616053 ATTAAGGAAC
72616063 AAAAGAAAAAAGTAAAA-
1 AAAAGAAAAAAG-AAAAT
* *
72616080 AAAAGAAATATGAAAAT
1 AAAAGAAAAAAGAAAAT
*
72616097 AAAAG-AAAAAGAAAAC
1 AAAAGAAAAAAGAAAAT
72616113 AAAA
1 AAAA
72616117 AGGTGTCAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 16 0.52
17 15 0.48
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAT
Found at i:72616117 original size:17 final size:16
Alignment explanation
Indices: 72616063--72616118 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 16
72616053 ATTAAGGAAC
*
72616063 AAAAGAAAAAAGTAAAA
1 AAAAG-AAAAAGAAAAA
* *
72616080 AAAAGAAATATGAAAAT
1 AAAAGAAA-AAGAAAAA
72616097 AAAAGAAAAAGAAAACA
1 AAAAGAAAAAGAAAA-A
72616114 AAAAG
1 AAAAG
72616119 GTGTCAGAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
16 9 0.28
17 23 0.72
ACGTcount: A:0.79, C:0.02, G:0.12, T:0.07
Consensus pattern (16 bp):
AAAAGAAAAAGAAAAA
Found at i:72617847 original size:208 final size:208
Alignment explanation
Indices: 72617482--72618150 Score: 1126
Period size: 212 Copynumber: 3.2 Consensus size: 208
72617472 GTCCAATTAG
**
72617482 ATATTACTGAATCTGCTAATACATACTTCATTTGGATAAAGTATGCATTATTAAAATTAAATTAA
1 ATATTACTGAATCTGCTAATACATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAA
*
72617547 AATATTGAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAAATAATAATTATTGTAATG
66 AATATTAAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAAATAATAATTATTGTAATG
* *
72617612 AGATACATGTTTTATTAGGTATAAGTATTTAAAATTTTGTTTCTGTAATGTGATATATGCGTAAA
131 AGATACATGTTTTATTAGGTATAAGTATTTAAAATTTTGTTTTTGTAATGTGATACATGCGTAAA
72617677 TATATATATAATC
196 TATATATATAATC
* * *
72617690 ATATTAGTGAATCTGCTAATGCGTACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAA
1 ATATTACTGAATCTGCTAATACATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAA
*
72617755 AATATTAAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAAATAACAATTATTGTAATG
66 AATATTAAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAAATAATAATTATTGTAATG
*
72617820 AGATACATGTTTTATTAGGTATAAGTATTTAAAATTTTATTTTTGTAATGTGATACATGCGTAAA
131 AGATACATGTTTTATTAGGTATAAGTATTTAAAATTTTGTTTTTGTAATGTGATACATGCGT--A
72617885 TATATATATATATAATC
194 -A-ATATATATATAATC
72617902 ATATTACTGAATCTGCTAATACATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAA
1 ATATTACTGAATCTGCTAATACATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAA
* *
72617967 AATATTAAATAAGAAATAAAATTATAAAATAATATGTTATTTGGAAAATAATTATTATTGTAATG
66 AATATTAAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAAATAATAATTATTGTAATG
*
72618032 AGATACATGTTTTATTAAGTATAAGTATTTAAAATTTTGTTTTTGTAATGTGATACATGCGT--A
131 AGATACATGTTTTATTAGGTATAAGTATTTAAAATTTTGTTTTTGTAATGTGATACATGCGTAAA
72618095 TATATATATAATC
196 TATATATATAATC
* * * * *
72618108 ATATTAGTGAATCTGTTAATACATACTTCGTCCGAATGAAGTA
1 ATATTACTGAATCTGCTAATACATACTTCATCCGGATAAAGTA
72618151 CGTATTAGCA
Statistics
Matches: 434, Mismatches: 23, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
206 52 0.12
208 182 0.42
210 1 0.00
211 1 0.00
212 198 0.46
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.39
Consensus pattern (208 bp):
ATATTACTGAATCTGCTAATACATACTTCATCCGGATAAAGTATGCATTATTAAAATTAAATTAA
AATATTAAATAAGAAATAAAATTATAAAACAATATGTTATTTGGAAAATAATAATTATTGTAATG
AGATACATGTTTTATTAGGTATAAGTATTTAAAATTTTGTTTTTGTAATGTGATACATGCGTAAA
TATATATATAATC
Found at i:72618324 original size:31 final size:29
Alignment explanation
Indices: 72618255--72618328 Score: 103
Period size: 29 Copynumber: 2.5 Consensus size: 29
72618245 ACAAAATAAT
**
72618255 AACATAAGTGACTAAAATGTAACATTTCA
1 AACATAAGTGACTAAAATGTAACATGGCA
72618284 AACATAAGTGACTAAAATGTAACATGAGGCA
1 AACATAAGTGACTAAAATGTAACAT--GGCA
*
72618315 AACAAAAGTGACTA
1 AACATAAGTGACTA
72618329 TTTTTGTAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 25 0.62
31 15 0.38
ACGTcount: A:0.50, C:0.14, G:0.15, T:0.22
Consensus pattern (29 bp):
AACATAAGTGACTAAAATGTAACATGGCA
Found at i:72630047 original size:12 final size:12
Alignment explanation
Indices: 72630030--72630060 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
72630020 GTTACAGCAG
72630030 CAGCAGCTGCAT
1 CAGCAGCTGCAT
72630042 CAGCAGCTGCAT
1 CAGCAGCTGCAT
72630054 CAGCAGC
1 CAGCAGC
72630061 CGTTGCCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.35, G:0.26, T:0.13
Consensus pattern (12 bp):
CAGCAGCTGCAT
Found at i:72630357 original size:3 final size:3
Alignment explanation
Indices: 72630349--72630380 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
72630339 AAGCATCCAG
72630349 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
72630381 AAGCTTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:72636206 original size:22 final size:21
Alignment explanation
Indices: 72636181--72636229 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
72636171 ATAGAATTTA
*
72636181 TAATATTTTTTTATGATAAATT
1 TAATATATTTTTA-GATAAATT
* *
72636203 TAATAATATTTTTAGTTTAATT
1 TAAT-ATATTTTTAGATAAATT
72636225 TAATA
1 TAATA
72636230 AATTAATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 14 0.61
23 8 0.35
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (21 bp):
TAATATATTTTTAGATAAATT
Found at i:72636992 original size:76 final size:75
Alignment explanation
Indices: 72636857--72636996 Score: 219
Period size: 76 Copynumber: 1.9 Consensus size: 75
72636847 AGTAATGTTG
*
72636857 TTTTCAAAATTCGAACTTAAGTTTTCTTTTAAAAATGCTATTTAATATTGGTTATTACTGCAATT
1 TTTTCAAAATTCGAACTTAAGTTTTCTTTTAAAAATGCTATTTAATATTGGTTACTACTGCAATT
72636922 TGGATGTGCA
66 TGGATGTGCA
* * *
72636932 TTTTTAAAATTTCGAACTTGAGCTTTTC-TTTAAAAATGTTATTTAATATTGGTTACTACTGCAA
1 TTTTCAAAA-TTCGAACTTAAG-TTTTCTTTTAAAAATGCTATTTAATATTGGTTACTACTGCAA
72636996 T
64 T
72636997 CCTTGGATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
75 8 0.14
76 46 0.78
77 5 0.08
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.46
Consensus pattern (75 bp):
TTTTCAAAATTCGAACTTAAGTTTTCTTTTAAAAATGCTATTTAATATTGGTTACTACTGCAATT
TGGATGTGCA
Found at i:72642019 original size:20 final size:22
Alignment explanation
Indices: 72641988--72642034 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
72641978 AACTATATAA
72641988 ATTTTGGAATTTTT-AAAAATT
1 ATTTTGGAATTTTTGAAAAATT
72642009 ATTTT-GAATTTTTGAAAAATT
1 ATTTTGGAATTTTTGAAAAATT
72642030 ATTTT
1 ATTTT
72642035 TTGATTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (22 bp):
ATTTTGGAATTTTTGAAAAATT
Found at i:72644088 original size:31 final size:30
Alignment explanation
Indices: 72644041--72644110 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
72644031 GGTTTGAAAT
*
72644041 TTTTAAAAATTTTGAAA-AATCTAATTAAAAA
1 TTTTAAAAACTTTGAAAGAAT-TAATT-AAAA
* *
72644072 TTTTGAAAACTTTGAAAGGATTAATTAAAA
1 TTTTAAAAACTTTGAAAGAATTAATTAAAA
*
72644102 TTTTTAAAA
1 TTTTAAAAA
72644111 TTGAAGGGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.35
31 20 0.59
32 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTTAAAAACTTTGAAAGAATTAATTAAAA
Found at i:72644432 original size:18 final size:19
Alignment explanation
Indices: 72644395--72644436 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
72644385 CATAATGTTC
*
72644395 TTAAATTATTACTCAAATT
1 TTAAATTACTACTCAAATT
*
72644414 TTAAATTACTCCT-AAATT
1 TTAAATTACTACTCAAATT
72644432 TTAAA
1 TTAAA
72644437 ATTTTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAATTACTACTCAAATT
Found at i:72647060 original size:3 final size:3
Alignment explanation
Indices: 72647054--72647082 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
72647044 CTCAAATATA
72647054 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
72647083 ATGATTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:72649411 original size:26 final size:27
Alignment explanation
Indices: 72649371--72649428 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 27
72649361 GTTGGATCGG
*
72649371 TTTATGAAATTTTTTAAAATTT-ATTGTT
1 TTTATGAAA-TTTTT-AAATTTAATTATT
72649399 TTTATGAAATTTTT-AATTTAATTATT
1 TTTATGAAATTTTTAAATTTAATTATT
72649425 TTTA
1 TTTA
72649429 GACTTACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 5 0.18
26 9 0.32
27 5 0.18
28 9 0.32
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (27 bp):
TTTATGAAATTTTTAAATTTAATTATT
Found at i:72656074 original size:42 final size:42
Alignment explanation
Indices: 72656025--72656107 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
72656015 TATTTTTTAG
72656025 TGGAGCCAATTCATTTGGGCCACCAGCCGTACTTTTTTTTTT
1 TGGAGCCAATTCATTTGGGCCACCAGCCGTACTTTTTTTTTT
72656067 TGGAGCCAATTCATTTGGGCCACCAGCCGTACTTTTTTTTT
1 TGGAGCCAATTCATTTGGGCCACCAGCCGTACTTTTTTTTT
72656108 ACTTTTGTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (42 bp):
TGGAGCCAATTCATTTGGGCCACCAGCCGTACTTTTTTTTTT
Found at i:72656112 original size:11 final size:11
Alignment explanation
Indices: 72656096--72656150 Score: 53
Period size: 11 Copynumber: 5.2 Consensus size: 11
72656086 CCACCAGCCG
72656096 TACTTTTTTTT
1 TACTTTTTTTT
**
72656107 TACTTTTGTCCT
1 TACTTTT-TTTT
*
72656119 T-CTTTTTTTC
1 TACTTTTTTTT
72656129 T--TTTTTTTT
1 TACTTTTTTTT
72656138 TACTTTTTTTT
1 TACTTTTTTTT
72656149 TA
1 TA
72656151 AAGTTTTATC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
9 8 0.23
10 2 0.06
11 22 0.63
12 3 0.09
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (11 bp):
TACTTTTTTTT
Found at i:72656136 original size:12 final size:12
Alignment explanation
Indices: 72656121--72656149 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
72656111 TTTGTCCTTC
72656121 TTTTTTT-CTTT
1 TTTTTTTACTTT
72656132 TTTTTTTACTTT
1 TTTTTTTACTTT
72656144 TTTTTT
1 TTTTTT
72656150 AAAGTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTACTTT
Found at i:72656253 original size:21 final size:23
Alignment explanation
Indices: 72656223--72656268 Score: 78
Period size: 21 Copynumber: 2.1 Consensus size: 23
72656213 ATTTGAAGTG
72656223 TTTTATAATATATATTTTT-AAA
1 TTTTATAATATATATTTTTGAAA
72656245 TTTTA-AATATATATTTTTGAAA
1 TTTTATAATATATATTTTTGAAA
72656267 TT
1 TT
72656269 ATTTTTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTATAATATATATTTTTGAAA
Found at i:72656262 original size:22 final size:22
Alignment explanation
Indices: 72656223--72656268 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
72656213 ATTTGAAGTG
*
72656223 TTTTATAATATATATTTTTAAA
1 TTTTATAATATATATTTTGAAA
72656245 TTTTA-AATATATATTTTTGAAA
1 TTTTATAATATATA-TTTTGAAA
72656267 TT
1 TT
72656269 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTATAATATATATTTTGAAA
Found at i:72656277 original size:34 final size:33
Alignment explanation
Indices: 72656223--72656300 Score: 104
Period size: 35 Copynumber: 2.2 Consensus size: 33
72656213 ATTTGAAGTG
72656223 TTTTATAATATATATTTTT-AAATTTTAAATATATAT
1 TTTTA-AAT-TAT-TTTTTAAAATTTTAAATAT-TAT
72656259 TTTTGAAATTATTTTTTAAAATTTTAAATATTAT
1 TTTT-AAATTATTTTTTAAAATTTTAAATATTAT
72656293 TTTTAAAT
1 TTTTAAAT
72656301 ATTAAATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
33 4 0.10
34 12 0.30
35 16 0.40
36 7 0.17
37 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (33 bp):
TTTTAAATTATTTTTTAAAATTTTAAATATTAT
Found at i:72656296 original size:13 final size:13
Alignment explanation
Indices: 72656245--72656304 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
72656235 TATTTTTAAA
72656245 TTTTAAATATATAT
1 TTTTAAATAT-TAT
*
72656259 TTTTGAA-ATTAT
1 TTTTAAATATTAT
*
72656271 TTTTTAA-A--A-
1 TTTTAAATATTAT
72656280 TTTTAAATATTAT
1 TTTTAAATATTAT
72656293 TTTTAAATATTA
1 TTTTAAATATTA
72656305 AATATATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
9 6 0.15
10 2 0.05
12 11 0.28
13 14 0.36
14 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
TTTTAAATATTAT
Found at i:72656315 original size:20 final size:20
Alignment explanation
Indices: 72656264--72656321 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
72656254 TATATTTTTG
*
72656264 AAAT-TATTTTTTAAAATTTT
1 AAATATATTTTTT-AAATATT
72656284 AAATAT-TATTTTTAAATATT
1 AAATATAT-TTTTTAAATATT
*
72656304 AAATATATTTTTTTAATA
1 AAATATATTTTTTAAATA
72656322 ATATAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 26 0.79
21 7 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AAATATATTTTTTAAATATT
Found at i:72656328 original size:22 final size:20
Alignment explanation
Indices: 72656270--72656328 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
72656260 TTTGAAATTA
*
72656270 TTTTTTAAAATTTTAAATATT
1 TTTTTTAAAA-TATAAATATT
*
72656291 ATTTTT-AAATATTAAATATAT
1 TTTTTTAAAATA-TAAATAT-T
72656312 TTTTTTAATAATATAAA
1 TTTTTTAA-AATATAAA
72656329 AAATTTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.03
20 10 0.32
21 11 0.35
22 5 0.16
23 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTTTAAAATATAAATATT
Found at i:72656449 original size:22 final size:21
Alignment explanation
Indices: 72656424--72656487 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 21
72656414 TTTAAATTTG
72656424 TTTTATAATATTTTAAATATA-
1 TTTTATAA-ATTTTAAATATAT
72656445 TTTT-T-AATTTTAAATATAAT
1 TTTTATAAATTTTAAATAT-AT
*
72656465 TTTTATAAATTATAAATATAT
1 TTTTATAAATTTTAAATATAT
72656486 TT
1 TT
72656488 AATATTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
18 11 0.29
19 2 0.05
20 5 0.13
21 9 0.24
22 11 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTATAAATTTTAAATATAT
Found at i:72656504 original size:40 final size:40
Alignment explanation
Indices: 72656424--72656504 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
72656414 TTTAAATTTG
* *
72656424 TTTTATAATATTTTAAATATATTTTTAATTTTAAATATAAT
1 TTTTATAATATTATAAATATA-TTTTAATTTTAAAAATAAT
72656465 TTTTATAA-ATTATAAATATA-TTTAATATTTAAAAAATAAT
1 TTTTATAATATTATAAATATATTTTAAT-TTT-AAAAATAAT
72656505 ATATTTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
38 6 0.17
39 3 0.08
40 19 0.53
41 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (40 bp):
TTTTATAATATTATAAATATATTTTAATTTTAAAAATAAT
Found at i:72663998 original size:19 final size:20
Alignment explanation
Indices: 72663960--72664000 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
72663950 CAGATCTTAT
72663960 TATATTATCAATCTTTAAAA
1 TATATTATCAATCTTTAAAA
72663980 TATATTATCCAA-C-TTAAAA
1 TATATTAT-CAATCTTTAAAA
72663999 TA
1 TA
72664001 AATCTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 9 0.45
21 3 0.15
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATTATCAATCTTTAAAA
Found at i:72666684 original size:80 final size:80
Alignment explanation
Indices: 72666282--72666681 Score: 782
Period size: 80 Copynumber: 5.0 Consensus size: 80
72666272 TTTTAACAAC
72666282 AAAAACTAGTGATGTTATCAATTTGGACGAGGTTAACTCCATTCCATTACTTTTTCATCCATTAA
1 AAAAACTAGTGATGTTATCAATTTGGACGAGGTTAACTCCATTCCATTACTTTTTCATCCATTAA
72666347 TACCTAATTCATGTT
66 TACCTAATTCATGTT
72666362 AAAAACTAGTGATGTTATCAATTTGGACGAGGTTAACTCCATTCCATTACTTTTTCATCCATTAA
1 AAAAACTAGTGATGTTATCAATTTGGACGAGGTTAACTCCATTCCATTACTTTTTCATCCATTAA
72666427 TACCTAATTCATGTT
66 TACCTAATTCATGTT
72666442 AAAAACTAGTGATGTTATCAATTTGGACGAGGTTAACTCCATTCCATTACTTTTTCATCCATTAA
1 AAAAACTAGTGATGTTATCAATTTGGACGAGGTTAACTCCATTCCATTACTTTTTCATCCATTAA
72666507 TACCTAATTCATGTT
66 TACCTAATTCATGTT
72666522 AAAAACTAGTGATGTTATCAATTTGGACGAGGTTAACTCCATTCCATTACTTTTTCATCCATTAA
1 AAAAACTAGTGATGTTATCAATTTGGACGAGGTTAACTCCATTCCATTACTTTTTCATCCATTAA
72666587 TACCTAATTCATGTT
66 TACCTAATTCATGTT
* *
72666602 TAAAACTAGTGATGTTATCAATTTGGACGAGATTAACTCCATTCCATTACTTTTTCATCCATTAA
1 AAAAACTAGTGATGTTATCAATTTGGACGAGGTTAACTCCATTCCATTACTTTTTCATCCATTAA
72666667 TACCTAATTCATGTT
66 TACCTAATTCATGTT
72666682 TAATCACCAT
Statistics
Matches: 318, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 318 1.00
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (80 bp):
AAAAACTAGTGATGTTATCAATTTGGACGAGGTTAACTCCATTCCATTACTTTTTCATCCATTAA
TACCTAATTCATGTT
Found at i:72667233 original size:13 final size:14
Alignment explanation
Indices: 72667215--72667249 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
72667205 GAGTTGATTT
72667215 TTTGAAAAA-AAAA
1 TTTGAAAAACAAAA
*
72667228 TTTGAAAAACAGAA
1 TTTGAAAAACAAAA
72667242 TTTGAAAA
1 TTTGAAAA
72667250 TGCCTCAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.60, C:0.03, G:0.11, T:0.26
Consensus pattern (14 bp):
TTTGAAAAACAAAA
Found at i:72667465 original size:76 final size:73
Alignment explanation
Indices: 72667320--72667556 Score: 291
Period size: 73 Copynumber: 3.2 Consensus size: 73
72667310 AACACAGAAA
* * * *
72667320 TTGAAGAACAAAAATGGAAAACACCTC-AGTGTCTTGAGGTTCAACTCACCTCTCGCAATATGAG
1 TTGAA-AACAGAAATTGAAAATACCTCAAGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAG
*
72667384 CTGATTTTTT
65 TTGA-TTTTT
*
72667394 TTTAAAGACAGAAATTGAAAATACCTCAATGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAA-ACAGAAATTGAAAATACCTCAA-GTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
72667459 GTTGA--TTT
64 GTTGATTTTT
* * * * *
72667467 TTGACAAACAAAAATTGAAATTACCTTAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGA-AAACAGAAATTGAAAATACCTCA-AGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGA
72667532 GTTGATTTTT
64 GTTGATTTTT
72667542 TTGAAAAACAGAAAT
1 TTG-AAAACAGAAAT
72667557 AAAAACATCA
Statistics
Matches: 142, Mismatches: 13, Indels: 15
0.84 0.08 0.09
Matches are distributed among these distances:
73 64 0.45
74 23 0.16
75 16 0.11
76 39 0.27
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (73 bp):
TTGAAAACAGAAATTGAAAATACCTCAAGTGTCTTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTTT
Found at i:72678028 original size:8 final size:8
Alignment explanation
Indices: 72677994--72678045 Score: 52
Period size: 8 Copynumber: 6.5 Consensus size: 8
72677984 TAGTGATGTG
*
72677994 AATAATAA
1 AATATTAA
*
72678002 AGTATATAA
1 AATAT-TAA
72678011 AATATT-A
1 AATATTAA
72678018 AATATTAA
1 AATATTAA
*
72678026 AATATCAA
1 AATATTAA
*
72678034 AATATTAG
1 AATATTAA
72678042 AATA
1 AATA
72678046 ATAATTAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 7 0.19
8 22 0.61
9 7 0.19
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (8 bp):
AATATTAA
Found at i:72678213 original size:20 final size:20
Alignment explanation
Indices: 72678156--72678215 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
72678146 AATACTACAT
72678156 AAATATGTACAT-ATATAAA
1 AAATATGTACATAATATAAA
** *
72678175 AAATAAATACGTGATAATATTAA
1 AAATATGTAC---ATAATATAAA
72678198 AAATATGTACATAATATA
1 AAATATGTACATAATATA
72678216 GTGTAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
19 8 0.26
20 7 0.23
22 2 0.06
23 14 0.45
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
AAATATGTACATAATATAAA
Found at i:72678256 original size:47 final size:48
Alignment explanation
Indices: 72678171--72678318 Score: 129
Period size: 48 Copynumber: 3.0 Consensus size: 48
72678161 TGTACATATA
* * * *
72678171 TAAAAAATAAATACGTGATA-ATATTAAAAATATGTACATAATATAGTG
1 TAAAAAATAAATACATAATATATATT-AAAATATATACATAAAATAGTG
* * *
72678219 TAAAAAATACATACATAATATA-ATTAAAATATATACATAAGATAACATG
1 TAAAAAATAAATACATAATATATATTAAAATATATACATAAAAT-A-GTG
* * *
72678268 TAAAATATATATATAAATAATATAGTATTAAAGATATATATATAAAATAGT
1 TAAAA-A-ATAAATACATAATATA-TATTAAA-ATATATACATAAAATAGT
72678319 ATAATATATA
Statistics
Matches: 81, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
47 16 0.20
48 21 0.26
49 8 0.10
50 1 0.01
51 14 0.17
52 1 0.01
53 7 0.09
54 13 0.16
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.32
Consensus pattern (48 bp):
TAAAAAATAAATACATAATATATATTAAAATATATACATAAAATAGTG
Found at i:72678287 original size:29 final size:29
Alignment explanation
Indices: 72678247--72678313 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
72678237 TATAATTAAA
*
72678247 ATATATACATAAGATAACATGTAAA-ATAT
1 ATATATAAATAAGATAACAT-TAAAGATAT
* **
72678276 ATATATAAATAATATAGTATTAAAGATAT
1 ATATATAAATAAGATAACATTAAAGATAT
72678305 ATATATAAA
1 ATATATAAA
72678314 ATAGTATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (29 bp):
ATATATAAATAAGATAACATTAAAGATAT
Found at i:72678329 original size:25 final size:26
Alignment explanation
Indices: 72678274--72678330 Score: 59
Period size: 25 Copynumber: 2.3 Consensus size: 26
72678264 CATGTAAAAT
*
72678274 ATATATATA--AATAATATAGTATTA
1 ATATATATATAAATAAAATAGTATTA
* *
72678298 A-AGATATATATATAAAATAGTA-TA
1 ATATATATATAAATAAAATAGTATTA
72678322 ATATATATA
1 ATATATATA
72678331 CGTAATACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
23 6 0.23
24 4 0.15
25 16 0.62
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (26 bp):
ATATATATATAAATAAAATAGTATTA
Found at i:72678403 original size:23 final size:25
Alignment explanation
Indices: 72678360--72678405 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
72678350 TATACCTAAT
72678360 ATATTAAAAGAATATATATAATATA
1 ATATTAAAAGAATATATATAATATA
*
72678385 ATATTAAGA-AATATA-ATAATA
1 ATATTAAAAGAATATATATAATA
72678406 ACAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
ATATTAAAAGAATATATATAATATA
Found at i:72678718 original size:16 final size:16
Alignment explanation
Indices: 72678680--72678718 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
72678670 CCAAAAAAAA
*
72678680 AAAAACTAGCCTCTCC
1 AAAAACTAGCCTCTAC
*
72678696 AAAAACTAGCCTTTAC
1 AAAAACTAGCCTCTAC
*
72678712 AATAACT
1 AAAAACT
72678719 TTCTCTCCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.28, G:0.05, T:0.23
Consensus pattern (16 bp):
AAAAACTAGCCTCTAC
Found at i:72678887 original size:30 final size:30
Alignment explanation
Indices: 72678846--72678944 Score: 162
Period size: 30 Copynumber: 3.3 Consensus size: 30
72678836 TAAGTACAAG
72678846 TGGTGGTGGAGCAAGTGTGGCTATTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTATTGGAGT
* *
72678876 AGGTAGTGGAGCAAGTGTGGCTATTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTATTGGAGT
* *
72678906 TGGTGGTGGAGCAAGTGTGGTTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTATTGGAGT
72678936 TGGTGGTGG
1 TGGTGGTGG
72678945 CAAATGCTAG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.17, C:0.05, G:0.48, T:0.29
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTATTGGAGT
Found at i:72679282 original size:7 final size:7
Alignment explanation
Indices: 72679220--72679282 Score: 62
Period size: 7 Copynumber: 9.4 Consensus size: 7
72679210 TATATTAACT
*
72679220 TAATATT
1 TAATATA
72679227 TAAGTAT-
1 TAA-TATA
72679234 TAATATA
1 TAATATA
72679241 TAATATA
1 TAATATA
72679248 TAATAT-
1 TAATATA
*
72679254 TATTATA
1 TAATATA
*
72679261 TTATATA
1 TAATATA
72679268 T-A-ATA
1 TAATATA
72679273 TAATATA
1 TAATATA
72679280 TAA
1 TAA
72679283 AACATAAAGT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
5 4 0.08
6 10 0.21
7 31 0.65
8 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (7 bp):
TAATATA
Found at i:72680495 original size:22 final size:22
Alignment explanation
Indices: 72680455--72680522 Score: 93
Period size: 22 Copynumber: 3.0 Consensus size: 22
72680445 CGTTCTATTA
*
72680455 TTAGCACGTTAAGTGCTCTCTGT
1 TTAGCAC-TTTAGTGCTCTCTGT
72680478 TTAGCACATTT-GTGCTCTCTGT
1 TTAGCAC-TTTAGTGCTCTCTGT
*
72680500 ATAGCACTTTAGTGCTCTCTGT
1 TTAGCACTTTAGTGCTCTCTGT
72680522 T
1 T
72680523 CTTTTGTGCA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
21 3 0.08
22 28 0.70
23 9 0.22
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (22 bp):
TTAGCACTTTAGTGCTCTCTGT
Found at i:72681147 original size:9 final size:9
Alignment explanation
Indices: 72681133--72681158 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
72681123 CAGAAATTTA
72681133 AAAAAAAAC
1 AAAAAAAAC
72681142 AAAAAAAAC
1 AAAAAAAAC
72681151 AAAAAAAA
1 AAAAAAAA
72681159 ATTCGTTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:72683180 original size:23 final size:23
Alignment explanation
Indices: 72683162--72683205 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
72683152 CGGAAACAAG
*
72683162 AGAAAAAACAAG-AAAGAAAAAA
1 AGAAAAAAAAAGAAAAGAAAAAA
*
72683184 ATAAAAAAAAAGAAAAGAAAAA
1 AGAAAAAAAAAGAAAAGAAAAA
72683206 CCCGTGTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.02
Consensus pattern (23 bp):
AGAAAAAAAAAGAAAAGAAAAAA
Found at i:72694862 original size:31 final size:33
Alignment explanation
Indices: 72694825--72694891 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
72694815 ATAGTTTATA
* *
72694825 TTTTTAT-AATTTTTAAAGAATTAAA-TAAAAT
1 TTTTTATCAATTTTTAAAAAATCAAAGTAAAAT
*
72694856 TTTTTATCAATTTTTAAAAAATCAAAGTATAAT
1 TTTTTATCAATTTTTAAAAAATCAAAGTAAAAT
72694889 TTT
1 TTT
72694892 ATCATTAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 7 0.23
32 16 0.52
33 8 0.26
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (33 bp):
TTTTTATCAATTTTTAAAAAATCAAAGTAAAAT
Found at i:72694892 original size:31 final size:30
Alignment explanation
Indices: 72694821--72694895 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 30
72694811 TTTAATAGTT
* * *
72694821 TATATTTTTAT-AATTTTTAAAGAATTAAA
1 TATAATTTTATCAATTTTTAAAAAATCAAA
*
72694850 TAAAATTTTTTATCAATTTTTAAAAAATCAAA
1 TATAA--TTTTATCAATTTTTAAAAAATCAAA
72694882 GTATAATTTTATCA
1 -TATAATTTTATCA
72694896 TTAGTAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
29 3 0.08
31 14 0.38
32 16 0.43
33 4 0.11
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (30 bp):
TATAATTTTATCAATTTTTAAAAAATCAAA
Found at i:72697357 original size:6 final size:6
Alignment explanation
Indices: 72697346--72697370 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
72697336 TTATGATGAT
72697346 TAATTA TAATTA TAATTA TAATTA T
1 TAATTA TAATTA TAATTA TAATTA T
72697371 TTGAATATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:72698481 original size:23 final size:24
Alignment explanation
Indices: 72698450--72698495 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
72698440 TTGCAGATGT
*
72698450 CACTCTGCATCGAAGTGCCACTAA
1 CACTCTGCATCGAAGTGCAACTAA
*
72698474 CACT-TGCATCGTAGTGCAACTA
1 CACTCTGCATCGAAGTGCAACTA
72698496 TCATTTGCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (24 bp):
CACTCTGCATCGAAGTGCAACTAA
Found at i:72699520 original size:18 final size:21
Alignment explanation
Indices: 72699478--72699520 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
72699468 CAAACTGAAA
*
72699478 AAATGATATACTTTAAGAGCT
1 AAATGATATACTTTAAGACCT
72699499 AAATGAT-T-CTTTAAG-CCT
1 AAATGATATACTTTAAGACCT
72699517 AAAT
1 AAAT
72699521 AAAGCAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 7 0.33
20 1 0.05
21 7 0.33
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (21 bp):
AAATGATATACTTTAAGACCT
Found at i:72701673 original size:30 final size:27
Alignment explanation
Indices: 72701639--72701696 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 27
72701629 AAAATTATGG
72701639 AAGTACTATAAAATTAGATATATTTAATTT
1 AAGTACTATAAAATT---TATATTTAATTT
* *
72701669 AAGTAGTTTAAAATTTATATTTAATTT
1 AAGTACTATAAAATTTATATTTAATTT
72701696 A
1 A
72701697 TTTATATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 13 0.50
30 13 0.50
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (27 bp):
AAGTACTATAAAATTTATATTTAATTT
Found at i:72707837 original size:16 final size:17
Alignment explanation
Indices: 72707813--72707852 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
72707803 TTTTTAGTGT
72707813 ATTATATTTT-AAGAAAA
1 ATTA-ATTTTAAAGAAAA
*
72707830 ATTAATTTTAAATAAAA
1 ATTAATTTTAAAGAAAA
72707847 ATTAAT
1 ATTAAT
72707853 CTAAAAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
ATTAATTTTAAAGAAAA
Found at i:72714931 original size:9 final size:9
Alignment explanation
Indices: 72714917--72714949 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
72714907 TTTATTTTTA
72714917 AAAATAATT
1 AAAATAATT
72714926 AAAATAATT
1 AAAATAATT
72714935 AAAAT-ATT
1 AAAATAATT
*
72714943 AATATAA
1 AAAATAA
72714950 AATATTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAATAATT
Found at i:72714956 original size:21 final size:19
Alignment explanation
Indices: 72714914--72714953 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
72714904 TATTTTATTT
72714914 TTAAAAATAATTAAAATAA
1 TTAAAAATAATTAAAATAA
72714933 TTAAAATATTAATATAAAATA
1 TTAAAA-A-TAAT-TAAAATA
72714954 TTATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 4 0.22
22 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TTAAAAATAATTAAAATAA
Found at i:72715082 original size:16 final size:16
Alignment explanation
Indices: 72715060--72715096 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
72715050 CAATTTTATT
72715060 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
72715077 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
72715092 TAATA
1 TAATA
72715097 TTCATCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:72729744 original size:24 final size:25
Alignment explanation
Indices: 72729716--72729764 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
72729706 CTTTTTTTAT
*
72729716 TAAATAAAAAAC-TTTAAAATATAA
1 TAAATAAAAAACATTTAAAACATAA
* *
72729740 TAAATCAAATACATTTAAAACATAA
1 TAAATAAAAAACATTTAAAACATAA
72729765 AAACAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAATAAAAAACATTTAAAACATAA
Found at i:72729757 original size:25 final size:23
Alignment explanation
Indices: 72729728--72729792 Score: 66
Period size: 25 Copynumber: 2.9 Consensus size: 23
72729718 AATAAAAAAC
*
72729728 TTTAAAATATAATAAATCAAATACA
1 TTTAAAACATAA-AAA-CAAATACA
72729753 TTTAAAACATAAAAACAAAT--A
1 TTTAAAACATAAAAACAAATACA
*
72729774 -TTAAAACA-AAAAATAAATA
1 TTTAAAACATAAAAACAAATA
72729793 AATAATGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 1 0.03
23 5 0.14
24 3 0.08
25 11 0.30
ACGTcount: A:0.66, C:0.08, G:0.00, T:0.26
Consensus pattern (23 bp):
TTTAAAACATAAAAACAAATACA
Found at i:72729791 original size:19 final size:20
Alignment explanation
Indices: 72729754--72729792 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
72729744 TCAAATACAT
72729754 TTAAAACATAAAAACAAATA
1 TTAAAACATAAAAACAAATA
*
72729774 TTAAAACA-AAAAATAAATA
1 TTAAAACATAAAAACAAATA
72729793 AATAATGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
TTAAAACATAAAAACAAATA
Found at i:72738958 original size:42 final size:42
Alignment explanation
Indices: 72738896--72738987 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
72738886 TAGATACCCG
*
72738896 CCACCACCAAATCAAGATCCATATCCACCTACGTCGTATCAA
1 CCACCACCAAATCAACATCCATATCCACCTACGTCGTATCAA
* * * *
72738938 CCGCCACCAAATCAACATCCATATCCATCTATGTTGTATCAA
1 CCACCACCAAATCAACATCCATATCCACCTACGTCGTATCAA
72738980 CCACCACC
1 CCACCACC
72738988 TCAATACGCT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.34, C:0.39, G:0.07, T:0.21
Consensus pattern (42 bp):
CCACCACCAAATCAACATCCATATCCACCTACGTCGTATCAA
Found at i:72743467 original size:24 final size:23
Alignment explanation
Indices: 72743440--72743494 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
72743430 TAGTTTGTAC
*
72743440 ATTATTCATATATTTTAAAAAAAT
1 ATTATTCAGAT-TTTTAAAAAAAT
* *
72743464 ATTATTCAGGTTTTTAAAATAAT
1 ATTATTCAGATTTTTAAAAAAAT
72743487 ATTATTCA
1 ATTATTCA
72743495 AGTTTTTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 19 0.68
24 9 0.32
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (23 bp):
ATTATTCAGATTTTTAAAAAAAT
Found at i:72743482 original size:23 final size:23
Alignment explanation
Indices: 72743452--72743501 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
72743442 TATTCATATA
*
72743452 TTTTAAAAAAATATTATTCAGGT
1 TTTTAAAAAAATATTATTCAAGT
*
72743475 TTTTAAAATAATATTATTCAAGT
1 TTTTAAAAAAATATTATTCAAGT
72743498 TTTT
1 TTTT
72743502 CATTGCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (23 bp):
TTTTAAAAAAATATTATTCAAGT
Found at i:72745826 original size:16 final size:16
Alignment explanation
Indices: 72745805--72745835 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
72745795 TATTTTAACA
72745805 AAAAAAAAAGAAAAAG
1 AAAAAAAAAGAAAAAG
*
72745821 AAAAAAATAGAAAAA
1 AAAAAAAAAGAAAAA
72745836 TCATACTCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAGAAAAAG
Found at i:72746449 original size:28 final size:28
Alignment explanation
Indices: 72746409--72746467 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
72746399 GTATTTCAGA
72746409 CAAATACGTGTAACAATTCATAAATATG
1 CAAATACGTGTAACAATTCATAAATATG
*
72746437 CAAATACTTGTAACAATTCATAAATATG
1 CAAATACGTGTAACAATTCATAAATATG
72746465 CAA
1 CAA
72746468 TTCACTAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.29
Consensus pattern (28 bp):
CAAATACGTGTAACAATTCATAAATATG
Found at i:72747131 original size:31 final size:31
Alignment explanation
Indices: 72747096--72747165 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
72747086 CTTGTCATTT
*
72747096 GTAGCCGAAGCTACCACTATTCACTAATCAG
1 GTAGCCGAAGCTACCACTATTCACTAATCAA
* * * * *
72747127 GTAGCCGGAGCTACCATTTTTCATTGATCAA
1 GTAGCCGAAGCTACCACTATTCACTAATCAA
72747158 GTAGCCGA
1 GTAGCCGA
72747166 TGATCAGGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTATTCACTAATCAA
Found at i:72747175 original size:46 final size:46
Alignment explanation
Indices: 72747122--72747211 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
72747112 CTATTCACTA
* * * *
72747122 ATCAGGTAGCCGGAGCTACCATTTTTCATTGATCAAGTAGCCGATG
1 ATCAGGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAACCGATG
*
72747168 ATCAGGTAGTCGAAGCTACCACTTTTCACTGATCAAGTAACCGA
1 ATCAGGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAACCGA
72747212 AGCTACCGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (46 bp):
ATCAGGTAGCCGAAGCTACCACTTTTCACTGATCAAGTAACCGATG
Found at i:72747289 original size:50 final size:50
Alignment explanation
Indices: 72747226--72747380 Score: 265
Period size: 50 Copynumber: 3.1 Consensus size: 50
72747216 ACCGCTTTTT
72747226 ACTTGTCATTTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATC
1 ACTT-TCATTTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATC
*
72747277 ACTTTCATTTGTCCTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATC
1 ACTTTCATTTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATC
* * *
72747327 ACTTTCACTTATCCTTGATCAGATAAGTGTAGCCAAAACTATCACTTATC
1 ACTTTCATTTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATC
72747377 ACTT
1 ACTT
72747381 GTTGCCATGG
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
50 95 0.96
51 4 0.04
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (50 bp):
ACTTTCATTTGTCCTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATC
Found at i:72751174 original size:2 final size:2
Alignment explanation
Indices: 72751167--72751205 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
72751157 GAAAATAATA
72751167 AG AG AG AG AG AG 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 AG AG AG AG AG AG A
72751206 TCTTGTTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:72753783 original size:92 final size:92
Alignment explanation
Indices: 72753633--72753812 Score: 263
Period size: 92 Copynumber: 2.0 Consensus size: 92
72753623 AAGTATTTTT
* * * * *
72753633 AAGTTTCATAAGACCTCAAGAATGTACGGGAAAATAGCACCGTGCTAAATGTTTGGGACTTATGA
1 AAGTTGCATAAGACCTCAAGAATGTACGGGAAAATAACACCATACTAAATGTATGGGACTTATGA
72753698 AA-CATTCATTTACAAGCATATATTTGC
66 AATC-TTCATTTACAAGCATATATTTGC
* **
72753725 AAGTTGCATAAGACCTCAAGAATGTATGGGAAAATAACATTATACTAAATGTATGGGACTTATGA
1 AAGTTGCATAAGACCTCAAGAATGTACGGGAAAATAACACCATACTAAATGTATGGGACTTATGA
*
72753790 AATCTTCATTTACACGCATATAT
66 AATCTTCATTTACAAGCATATAT
72753813 AGAAGCAAGC
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
92 77 0.99
93 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (92 bp):
AAGTTGCATAAGACCTCAAGAATGTACGGGAAAATAACACCATACTAAATGTATGGGACTTATGA
AATCTTCATTTACAAGCATATATTTGC
Found at i:72754019 original size:155 final size:155
Alignment explanation
Indices: 72753718--72754020 Score: 387
Period size: 155 Copynumber: 1.9 Consensus size: 155
72753708 TACAAGCATA
*
72753718 TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGGAAAATAACATTATACTAAATGTATGGGA
1 TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGGAAAACAACATTATACTAAATGTATGGGA
* * * * * * * * * *
72753783 CTTATGAAATCTTCATTTACACGCATATATAGAAGCAAGCATGCATGCATGCATGTATACATACA
66 CCTATGAAACCTTCATTTACACACACACACAGAACCAAGCATGCAAGCATGCATGCATACACACA
** *
72753848 TACATATGTATTTATGTATGTACAAG
131 TA-ATACATATGTATGTATGTACAAG
*
72753874 TATTTGCAAGTTGCATAAGACCTCAAGAATGTAT-GGAAAACAACATTATACTAAATGTATTGGA
1 TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGGAAAACAACATTATACTAAATGTATGGGA
* * *
72753938 CCTATGAAGCCTTCATTTACATACACACACAGACATCCATA-CATGCAAGCATGCATGCATTCAC
66 CCTATGAAACCTTCATTTACACACACACACAGA-A-CCA-AGCATGCAAGCATGCATGCATACAC
72754002 ACAT-ATACATATGTATGTA
128 ACATAATACATATGTATGTA
72754021 CGTATATACA
Statistics
Matches: 126, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
155 65 0.52
156 35 0.28
157 25 0.20
158 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (155 bp):
TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGGAAAACAACATTATACTAAATGTATGGGA
CCTATGAAACCTTCATTTACACACACACACAGAACCAAGCATGCAAGCATGCATGCATACACACA
TAATACATATGTATGTATGTACAAG
Found at i:72754181 original size:94 final size:94
Alignment explanation
Indices: 72754059--72754245 Score: 270
Period size: 94 Copynumber: 2.0 Consensus size: 94
72754049 TATCTAGAAG
* * *
72754059 TATTTGTAAGTTGCATAAGACCTCAAGAATGTATGGGAA-AACAGCATTATACTGAATGTATTG-
1 TATTTGCAAGTTGCATAAGACCTCAAGAATGTAT-GGAACAACAACATTATACTAAATGTA-TGA
*
72754122 GACCTATGAAACCTTCAATTACATACATACA
64 GACCTATGAAACCTGCAATTACATACATACA
*
72754153 TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGAACAACAACATTATGCTAAATGTATGAGA
1 TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGAACAACAACATTATACTAAATGTATGAGA
* * *
72754218 TCTATGGAACCTGCATTTACATACATAC
66 CCTATGAAACCTGCAATTACATACATAC
72754246 TTACATATGT
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
93 6 0.07
94 77 0.93
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (94 bp):
TATTTGCAAGTTGCATAAGACCTCAAGAATGTATGGAACAACAACATTATACTAAATGTATGAGA
CCTATGAAACCTGCAATTACATACATACA
Found at i:72756799 original size:8 final size:8
Alignment explanation
Indices: 72756786--72756825 Score: 62
Period size: 8 Copynumber: 4.8 Consensus size: 8
72756776 AACTCAAAAT
72756786 AAAAAAGA
1 AAAAAAGA
72756794 AAAAAATGA
1 AAAAAA-GA
72756803 AGAAAAAGA
1 A-AAAAAGA
72756812 AAAAAAGA
1 AAAAAAGA
72756820 AAAAAA
1 AAAAAA
72756826 CCTAACCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 19 0.63
9 6 0.20
10 5 0.17
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (8 bp):
AAAAAAGA
Found at i:72756810 original size:18 final size:16
Alignment explanation
Indices: 72756786--72756825 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 16
72756776 AACTCAAAAT
72756786 AAAAAAGAAAAAAATGA
1 AAAAAAGAAAAAAA-GA
72756803 AGAAAAAGAAAAAAAGA
1 A-AAAAAGAAAAAAAGA
72756820 AAAAAA
1 AAAAAA
72756826 CCTAACCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 4 0.18
18 13 0.59
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (16 bp):
AAAAAAGAAAAAAAGA
Found at i:72756817 original size:9 final size:9
Alignment explanation
Indices: 72756786--72756825 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
72756776 AACTCAAAAT
72756786 AAAAAAGAA
1 AAAAAAGAA
*
72756795 AAAAATGAA
1 AAAAAAGAA
*
72756804 GAAAAAG-A
1 AAAAAAGAA
72756812 AAAAAAGAA
1 AAAAAAGAA
72756821 AAAAA
1 AAAAA
72756826 CCTAACCTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:72758021 original size:19 final size:19
Alignment explanation
Indices: 72757997--72758034 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
72757987 TTGAGATTGC
*
72757997 CAACCTATTTGCTTGAAAT
1 CAACCTATTTGCCTGAAAT
72758016 CAACCTATTTGCCTGAAAT
1 CAACCTATTTGCCTGAAAT
72758035 TATTCATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (19 bp):
CAACCTATTTGCCTGAAAT
Found at i:72759695 original size:27 final size:27
Alignment explanation
Indices: 72759665--72759718 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
72759655 AATCAACACA
72759665 ATGTATAAACATTAAAAATTAAAATTG
1 ATGTATAAACATTAAAAATTAAAATTG
72759692 ATGTATAAACATTAAAAATTAAAATTG
1 ATGTATAAACATTAAAAATTAAAATTG
72759719 TTATTATACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (27 bp):
ATGTATAAACATTAAAAATTAAAATTG
Found at i:72764005 original size:25 final size:25
Alignment explanation
Indices: 72763958--72764005 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
72763948 TAGTCCCTAA
*
72763958 ACTTGAGAATGATTCCCATATTAAG
1 ACTTGAGAATGATTCCCACATTAAG
* * *
72763983 ACTTGATAATTATTCTCACATTA
1 ACTTGAGAATGATTCCCACATTA
72764006 GAGCTAGATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (25 bp):
ACTTGAGAATGATTCCCACATTAAG
Found at i:72772491 original size:33 final size:32
Alignment explanation
Indices: 72772448--72772512 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
72772438 ACTAAATATC
* *
72772448 TTCGACTTAAATTGAACTTCAAATTTCAAAATG
1 TTCGAATTAAATTG-ACTTCAAACTTCAAAATG
*
72772481 TTCGAATTAAATTGACTTTAAACTTCAAAATG
1 TTCGAATTAAATTGACTTCAAACTTCAAAATG
72772513 GTTTAATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (32 bp):
TTCGAATTAAATTGACTTCAAACTTCAAAATG
Found at i:72775187 original size:3 final size:3
Alignment explanation
Indices: 72775179--72775577 Score: 182
Period size: 3 Copynumber: 136.0 Consensus size: 3
72775169 TTTTAGCTAC
* * * * *
72775179 ATT ATT ATT A-A ATT AATT AATT -TT ACT ATC ATT ATT ATT CTT ACT
1 ATT ATT ATT ATT ATT -ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
* ** * *
72775224 ATT ATT ATT ATT ACT ACA ACT ATT ATT ATT ATG ATAT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
* * * * * *
72775269 TTT A-T ACTT ATT -TG CTT ATT ATT ACT ATT A-C ATT ATT A-T ATC
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
72775311 ATT AATT -TT A-T ATT ATT ACT ATT ATT ATT ATT ATT ATT ATA ATA
1 ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
72775355 ATT ATT ATT ACT ATT ATT ATT A-T GTT GTT TTT CTCT GTT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
* * * * *
72775399 ATT ATT ATT ATT ATT ACT ATT ATT TTT ATT TTT ATT TTT ATT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * * * * *
72775447 ACC ATT ATT ATT ACT ACT ATT ATT TTT ATT TTT ACT ATT ATT ATT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * * *
72775495 CCTT ATC ATT ATA ATA ATT GTT ATT ACT ATT ATT -TT TTT ACT ATT
1 -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
72775540 ATT ATT ATT GTC ATT -TT ATT A-T ATT -TT -TT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
72775578 TACTTATTTA
Statistics
Matches: 296, Mismatches: 79, Indels: 42
0.71 0.19 0.10
Matches are distributed among these distances:
2 28 0.09
3 250 0.84
4 18 0.06
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:72775572 original size:17 final size:16
Alignment explanation
Indices: 72775522--72775573 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
72775512 TTGTTATTAC
*
72775522 TATTATTTTTTTACTAT
1 TATTATTTTTTTA-TTT
* *
72775539 TATTATTATTGTCATTT
1 TATTATT-TTTTTATTT
72775556 TATTATATTTTTTATTT
1 TATTAT-TTTTTTATTT
72775573 T
1 T
72775574 TATTTACTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 23 0.82
18 5 0.18
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (16 bp):
TATTATTTTTTTATTT
Found at i:72775576 original size:18 final size:18
Alignment explanation
Indices: 72775553--72775590 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
72775543 ATTATTGTCA
*
72775553 TTTTATTATA-TTTTTTAT
1 TTTTATT-TACTTATTTAT
72775571 TTTTATTTACTTATTTAT
1 TTTTATTTACTTATTTAT
72775589 TT
1 TT
72775591 GCTTATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATTTACTTATTTAT
Found at i:72775620 original size:8 final size:8
Alignment explanation
Indices: 72775554--72775620 Score: 50
Period size: 8 Copynumber: 8.5 Consensus size: 8
72775544 TTATTGTCAT
72775554 TTTATTATA
1 TTTATT-TA
72775563 TTT-TTTA
1 TTTATTTA
72775570 -TT-TTTA
1 TTTATTTA
*
72775576 TTTACTTA
1 TTTATTTA
*
72775584 TTTATTTG
1 TTTATTTA
*
72775592 CTTATTTCA
1 TTTATTT-A
*
72775601 TTTTTTTA
1 TTTATTTA
*
72775609 TTTATTTG
1 TTTATTTA
72775617 TTTA
1 TTTA
72775621 AACTTTTAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
6 6 0.13
7 4 0.09
8 28 0.61
9 8 0.17
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.73
Consensus pattern (8 bp):
TTTATTTA
Found at i:72775620 original size:12 final size:12
Alignment explanation
Indices: 72775554--72775620 Score: 55
Period size: 12 Copynumber: 5.3 Consensus size: 12
72775544 TTATTGTCAT
72775554 TTTATTATATTT-
1 TTTATT-TATTTG
*
72775566 TTTATTTTTATTTA
1 TTTA--TTTATTTG
*
72775580 CTTATTTATTTG
1 TTTATTTATTTG
* *
72775592 CTTATTTCATTTT
1 TTTATTT-ATTTG
72775605 TTTATTTATTTG
1 TTTATTTATTTG
72775617 TTTA
1 TTTA
72775621 AACTTTTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
12 26 0.57
13 15 0.33
14 5 0.11
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.73
Consensus pattern (12 bp):
TTTATTTATTTG
Found at i:72786199 original size:31 final size:29
Alignment explanation
Indices: 72786137--72786229 Score: 100
Period size: 30 Copynumber: 3.1 Consensus size: 29
72786127 AGTTCTTCTC
* * *
72786137 ATATTATTTTTTAATTTTTTTAAAATATTT
1 ATATTATTTTTT-ATTTATTTAAATTTTTT
72786167 ATATTATTTTATT-TTAATATTTAAATTTTTT
1 ATATTATTTT-TTATT--TATTTAAATTTTTT
*
72786198 ATA-TATTTTTTATTTATTGAAATTTTTT
1 ATATTATTTTTTATTTATTTAAATTTTTT
72786226 ATAT
1 ATAT
72786230 AGTCATCTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
28 16 0.30
29 4 0.07
30 18 0.33
31 16 0.30
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (29 bp):
ATATTATTTTTTATTTATTTAAATTTTTT
Found at i:72786205 original size:30 final size:28
Alignment explanation
Indices: 72786141--72786230 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 28
72786131 CTTCTCATAT
* * *
72786141 TATTTTTTAATTTTTTTAAAATATTTATA
1 TATTTTTT-ATTTATTTAAATTTTTTATA
72786170 TTATTTTATT-TTAATATTTAAATTTTTTATA
1 -TATTTT-TTATT--TATTTAAATTTTTTATA
*
72786201 TATTTTTTATTTATTGAAATTTTTTATA
1 TATTTTTTATTTATTTAAATTTTTTATA
72786229 TA
1 TA
72786231 GTCATCTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
28 18 0.35
29 4 0.08
30 14 0.27
31 16 0.31
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (28 bp):
TATTTTTTATTTATTTAAATTTTTTATA
Found at i:72787006 original size:33 final size:32
Alignment explanation
Indices: 72786963--72787027 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
72786953 ACTAAATATC
* *
72786963 TTCGACTTAAATTGAACTTCAAATTTCAAAATG
1 TTCGAATTAAATTG-ACTTCAAACTTCAAAATG
*
72786996 TTCGAATTAAATTGACTTTAAACTTCAAAATG
1 TTCGAATTAAATTGACTTCAAACTTCAAAATG
72787028 GTTTAATTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (32 bp):
TTCGAATTAAATTGACTTCAAACTTCAAAATG
Found at i:72789702 original size:3 final size:3
Alignment explanation
Indices: 72789694--72790096 Score: 183
Period size: 3 Copynumber: 138.0 Consensus size: 3
72789684 TTTTAGCTAC
* * * * *
72789694 ATT ATT ATT A-A ATT AATT AATT -TT ACT ATC ATT ATT ATT CTT ACT
1 ATT ATT ATT ATT ATT -ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
* ** * *
72789739 ATT ATT ATT ATT ACT ACA ACT ATT ATT ATT ATG ATT A-T ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
72789785 TTT A-T ACTT ATT -TG CTT ATT ATT ACT ATT A-C ATT ATT A-T ATC
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
72789827 ATT AATT -TT A-T ATT ATT ACT ATT ATT ATT ATT ATT ATA ATA ATA
1 ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * *
72789871 ATT ATT ATT ACT ATT ATT ATT A-T GTT GTT TTT CTCT GTT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
* * * * *
72789915 ATT ATT ATT ATT ATT ACT ATT ATT TTT ATT TTT ATT TTT ATT ACT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
** * * * * *
72789963 ACC ATT ATT ATT ATT ACT ACT ATT ATT TTT ATT TTT ACT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * * * *
72790011 TTT CCTT ATC ATT ATA ATA ATT GTT ATT ACT ATT ATT -TT TTT ACT
1 ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
72790056 ATT ATT ATT ATT GTC ATT -TT ATT A-T ATT -TT -TT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
72790097 TACTTATTTA
Statistics
Matches: 300, Mismatches: 79, Indels: 42
0.71 0.19 0.10
Matches are distributed among these distances:
2 30 0.10
3 254 0.85
4 16 0.05
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:72790091 original size:17 final size:16
Alignment explanation
Indices: 72790041--72790092 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
72790031 TTGTTATTAC
*
72790041 TATTATTTTTTTACTAT
1 TATTATTTTTTTA-TTT
* *
72790058 TATTATTATTGTCATTT
1 TATTATT-TTTTTATTT
72790075 TATTATATTTTTTATTT
1 TATTAT-TTTTTTATTT
72790092 T
1 T
72790093 TATTTACTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
17 23 0.82
18 5 0.18
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (16 bp):
TATTATTTTTTTATTT
Found at i:72790095 original size:18 final size:18
Alignment explanation
Indices: 72790072--72790109 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
72790062 ATTATTGTCA
*
72790072 TTTTATTATA-TTTTTTAT
1 TTTTATT-TACTTATTTAT
72790090 TTTTATTTACTTATTTAT
1 TTTTATTTACTTATTTAT
72790108 TT
1 TT
72790110 GCTTATTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTATTTACTTATTTAT
Found at i:72790139 original size:8 final size:8
Alignment explanation
Indices: 72790073--72790139 Score: 50
Period size: 8 Copynumber: 8.5 Consensus size: 8
72790063 TTATTGTCAT
72790073 TTTATTATA
1 TTTATT-TA
72790082 TTT-TTTA
1 TTTATTTA
72790089 -TT-TTTA
1 TTTATTTA
*
72790095 TTTACTTA
1 TTTATTTA
*
72790103 TTTATTTG
1 TTTATTTA
*
72790111 CTTATTTCA
1 TTTATTT-A
*
72790120 TTTTTTTA
1 TTTATTTA
*
72790128 TTTATTTG
1 TTTATTTA
72790136 TTTA
1 TTTA
72790140 AACTTTTAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
6 6 0.13
7 4 0.09
8 28 0.61
9 8 0.17
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.73
Consensus pattern (8 bp):
TTTATTTA
Found at i:72790139 original size:12 final size:12
Alignment explanation
Indices: 72790073--72790139 Score: 55
Period size: 12 Copynumber: 5.3 Consensus size: 12
72790063 TTATTGTCAT
72790073 TTTATTATATTT-
1 TTTATT-TATTTG
*
72790085 TTTATTTTTATTTA
1 TTTA--TTTATTTG
*
72790099 CTTATTTATTTG
1 TTTATTTATTTG
* *
72790111 CTTATTTCATTTT
1 TTTATTT-ATTTG
72790124 TTTATTTATTTG
1 TTTATTTATTTG
72790136 TTTA
1 TTTA
72790140 AACTTTTAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
12 26 0.57
13 15 0.33
14 5 0.11
ACGTcount: A:0.19, C:0.04, G:0.03, T:0.73
Consensus pattern (12 bp):
TTTATTTATTTG
Found at i:72795852 original size:48 final size:48
Alignment explanation
Indices: 72795781--72795886 Score: 176
Period size: 48 Copynumber: 2.2 Consensus size: 48
72795771 CAAGATAAAT
* * *
72795781 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
72795829 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
*
72795877 ATGTGTATAT
1 ATATGTATAT
72795887 ATTGTGGCCG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 54 1.00
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
Found at i:72799689 original size:55 final size:55
Alignment explanation
Indices: 72799608--72799711 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 55
72799598 TACTTCACCT
* * *
72799608 AAAAAAGGGAGAGGCCAATGTGAAAACCCACAAAGGACGTTTTGAGACCTTCAAA
1 AAAAAAGGGAAAGGCCAATGTAAAAACCCACAAAGGACGCTTTGAGACCTTCAAA
* *
72799663 AAAAAATGGAAAGGCCAA-GTCAAAAACCCACAAAGGGCGCTTTGAGACC
1 AAAAAAGGGAAAGGCCAATGT-AAAAACCCACAAAGGACGCTTTGAGACC
72799712 AAAAGGGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
54 2 0.05
55 41 0.95
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (55 bp):
AAAAAAGGGAAAGGCCAATGTAAAAACCCACAAAGGACGCTTTGAGACCTTCAAA
Found at i:72800514 original size:44 final size:43
Alignment explanation
Indices: 72800464--72800672 Score: 163
Period size: 44 Copynumber: 4.8 Consensus size: 43
72800454 GGTAAATTCA
*
72800464 CAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGGATGAAAATTG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCA-GATGAAAATTG
* * * *
72800508 TAGATCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT-GAAAATTG
* * * **
72800552 CAAATCTTATCTTCCTAAGCATTAGTGGAGCAGAT-TTAA--G
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATGAAAATTG
* * * ** * *
72800592 CCACCATCCTATCTCCCTAAGCAGTAGTGAAATAGGCTGAAGATTG
1 -CA-GATCTTATCTCCCTAAGCAGTAGTGGAGCA-GATGAAAATTG
* * **
72800638 TAGATCTTATCTCCCTGAGCAACAGTGGAGCAGAT
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
72800673 CGAAGACGGC
Statistics
Matches: 124, Mismatches: 34, Indels: 15
0.72 0.20 0.09
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 24 0.19
43 7 0.06
44 88 0.71
45 1 0.01
46 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (43 bp):
CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATGAAAATTG
Found at i:72800735 original size:44 final size:44
Alignment explanation
Indices: 72800687--72800831 Score: 202
Period size: 44 Copynumber: 3.3 Consensus size: 44
72800677 GACGGCGAAT
* * **
72800687 CTTATATCCCT-ATGGTAGCAAGGGAGCAGATTTTAGCCACTAGC
1 CTTATCTCCCTGA-GGTAGCAAGGGAGCAGACTGAAGCCACTAGC
* *
72800731 CTTATCTCCCTGAGGTAGCAAGGAAGCATACTGAAGCCACTAGC
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGCCACTAGC
*
72800775 CTTATCTCCCTGAGGTAGCAAGGGAGCAGGCTGAAGCCACTAGC
1 CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGCCACTAGC
*
72800819 CTTGTCTCCCTGA
1 CTTATCTCCCTGA
72800832 ACAGTAGTGG
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
44 89 0.99
45 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.24, T:0.23
Consensus pattern (44 bp):
CTTATCTCCCTGAGGTAGCAAGGGAGCAGACTGAAGCCACTAGC
Found at i:72801406 original size:44 final size:42
Alignment explanation
Indices: 72801279--72801424 Score: 125
Period size: 44 Copynumber: 3.3 Consensus size: 42
72801269 GTCTTATGTC
* * * *
72801279 CCTGAAGATACAGTGGAGCAGACTGAAG-ATACCAATCTTATCTT
1 CCTGAAGTTGCAGTGGAGCAGATTGAAGCA-A-CAATCCTATC-T
* * * *
72801323 CCTGAAGTTGCAGCGGAGTAAATTGAAGCTACTAATCCTATCT
1 CCTGAAGTTGCAGTGGAGCAGATTGAAGCAAC-AATCCTATCT
*
72801366 CCATGAAGTTGCAGTGGAGCAGATTAAAGCAACAAGTCCTATGC-
1 CC-TGAAGTTGCAGTGGAGCAGATTGAAGCAACAA-TCCTAT-CT
72801410 CTCTGAAGTTGCAGT
1 C-CTGAAGTTGCAGT
72801425 AGGTCGGATT
Statistics
Matches: 83, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
43 6 0.07
44 75 0.90
45 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (42 bp):
CCTGAAGTTGCAGTGGAGCAGATTGAAGCAACAATCCTATCT
Found at i:72803000 original size:18 final size:18
Alignment explanation
Indices: 72802977--72803011 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
72802967 TTAATTAATT
72802977 TTGCTATCATTACTATTC
1 TTGCTATCATTACTATTC
* *
72802995 TTGCTATTATTATTATT
1 TTGCTATCATTACTATT
72803012 ACTACAACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.57
Consensus pattern (18 bp):
TTGCTATCATTACTATTC
Found at i:72813805 original size:3 final size:3
Alignment explanation
Indices: 72813758--72813906 Score: 95
Period size: 3 Copynumber: 50.0 Consensus size: 3
72813748 GGATGTTACA
* * * * * **
72813758 ATT ACT ATT ATT TTT ATT TTT ATT TTT ATT ACT ATT ACC ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * * * *
72813806 ATT ACT ACT ACT ATT ATT ATT ATT TTT ACT ATT ATT ATT TTT CTTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
* * * * * *
72813852 ATT ATT ATA ATA ATT GTT ATT ACT ATT ATT -TT -TT ACT ATT AAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
72813898 ATT ATT ATT
1 ATT ATT ATT
72813907 GTCATTTTGT
Statistics
Matches: 112, Mismatches: 32, Indels: 4
0.76 0.22 0.03
Matches are distributed among these distances:
2 4 0.04
3 105 0.94
4 3 0.03
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:72813898 original size:40 final size:40
Alignment explanation
Indices: 72813831--72813908 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
72813821 ATTATTATTT
* *
72813831 TTACTATTATTATTTTTCTTTATTATTATAATAATTGTTA
1 TTACTATTATTATTTTACTTTAATATTATAATAATTGTTA
* *
72813871 TTACTATTATT-TTTTACTATTAATATTATTATTATTGT
1 TTACTATTATTATTTTACT-TTAATATTATAATAATTGT
72813909 CATTTTGTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 6 0.18
40 27 0.82
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (40 bp):
TTACTATTATTATTTTACTTTAATATTATAATAATTGTTA
Found at i:72813949 original size:12 final size:12
Alignment explanation
Indices: 72813932--72813975 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
72813922 TTTATATTTT
72813932 TTTATTTACTTA
1 TTTATTTACTTA
*
72813944 TTTATTTGCTTA
1 TTTATTTACTTA
**
72813956 TTTCATTTTTTTA
1 TTT-ATTTACTTA
72813969 TTTATTT
1 TTTATTT
72813976 GTTTAAACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 18 0.64
13 10 0.36
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.73
Consensus pattern (12 bp):
TTTATTTACTTA
Found at i:72813969 original size:13 final size:12
Alignment explanation
Indices: 72813941--72813980 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
72813931 TTTTATTTAC
*
72813941 TTATTTATTTGC
1 TTATTTATTTGT
*
72813953 TTATTTCATTTTT
1 TTATTT-ATTTGT
72813966 TTATTTATTTGT
1 TTATTTATTTGT
72813978 TTA
1 TTA
72813981 AACTTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.72
Consensus pattern (12 bp):
TTATTTATTTGT
Found at i:72814761 original size:36 final size:36
Alignment explanation
Indices: 72814720--72814792 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
72814710 TAAAATGACT
* *
72814720 GAATTACCAGGTGATCTGATCGCACCTAAATAAAAA
1 GAATTACCAGGCGATCTGATCACACCTAAATAAAAA
*
72814756 GAATTACTAGGCGATCTGATCACACCTAAATAAAAA
1 GAATTACCAGGCGATCTGATCACACCTAAATAAAAA
72814792 G
1 G
72814793 GATTGGTGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.22
Consensus pattern (36 bp):
GAATTACCAGGCGATCTGATCACACCTAAATAAAAA
Found at i:72814914 original size:15 final size:16
Alignment explanation
Indices: 72814891--72814924 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
72814881 CTAAAATAAA
*
72814891 TTTATATATTATT-AT
1 TTTACATATTATTAAT
72814906 TTTACATATTATTAAT
1 TTTACATATTATTAAT
72814922 TTT
1 TTT
72814925 TGATTTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTACATATTATTAAT
Found at i:72816623 original size:11 final size:11
Alignment explanation
Indices: 72816609--72816637 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
72816599 TATATCTATT
72816609 ATATATTTTAA
1 ATATATTTTAA
72816620 ATATATTTTAA
1 ATATATTTTAA
72816631 ATA-ATTT
1 ATATATTT
72816638 AAAAATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATATTTTAA
Found at i:72822496 original size:16 final size:18
Alignment explanation
Indices: 72822475--72822512 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
72822465 TTAATGATAA
72822475 ATATG-TAAATA-TATAT
1 ATATGTTAAATATTATAT
*
72822491 ATATGTTAACTATTATAT
1 ATATGTTAAATATTATAT
72822509 ATAT
1 ATAT
72822513 ATGCTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 5 0.26
18 9 0.47
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (18 bp):
ATATGTTAAATATTATAT
Found at i:72823707 original size:19 final size:19
Alignment explanation
Indices: 72823685--72823739 Score: 92
Period size: 19 Copynumber: 2.9 Consensus size: 19
72823675 TACCATCTCC
72823685 AAAAACCTTAGTTTTTAGG
1 AAAAACCTTAGTTTTTAGG
* *
72823704 AAAAATCTTAGTTTGTAGG
1 AAAAACCTTAGTTTTTAGG
72823723 AAAAACCTTAGTTTTTA
1 AAAAACCTTAGTTTTTA
72823740 TCATGCTTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (19 bp):
AAAAACCTTAGTTTTTAGG
Found at i:72824933 original size:35 final size:35
Alignment explanation
Indices: 72824887--72824957 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
72824877 CAAGGCCCGA
*
72824887 AAACCTAATAAAGAATCATGCAACACCAATTTAGC
1 AAACCTAATAAAGAATCATGCAACACCAAATTAGC
72824922 AAACCTAATAAAGAATCATGCAACACCAAATTAGC
1 AAACCTAATAAAGAATCATGCAACACCAAATTAGC
72824957 A
1 A
72824958 GTCTTATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.51, C:0.23, G:0.08, T:0.18
Consensus pattern (35 bp):
AAACCTAATAAAGAATCATGCAACACCAAATTAGC
Found at i:72834180 original size:21 final size:22
Alignment explanation
Indices: 72834146--72834186 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
72834136 CATGTACTTC
72834146 ATTTTGACATAATTTCATCCTT
1 ATTTTGACATAATTTCATCCTT
*
72834168 ATTTTGA-ATAATTTGATCC
1 ATTTTGACATAATTTCATCC
72834187 ATGTCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.29, C:0.15, G:0.07, T:0.49
Consensus pattern (22 bp):
ATTTTGACATAATTTCATCCTT
Found at i:72836181 original size:33 final size:34
Alignment explanation
Indices: 72836142--72836207 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
72836132 TAAATTTAAT
* *
72836142 TTTTTATGAGAGCTAAAAT-ACAA-TTTATCATTG
1 TTTTTATAAGAACT-AAATCACAATTTTATCATTG
72836175 TTTTTATAAGAACTAAATCACAATTTTATCATT
1 TTTTTATAAGAACTAAATCACAATTTTATCATT
72836208 CTTGAGGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 4 0.14
33 16 0.55
34 9 0.31
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.44
Consensus pattern (34 bp):
TTTTTATAAGAACTAAATCACAATTTTATCATTG
Found at i:72838054 original size:2 final size:2
Alignment explanation
Indices: 72838049--72838095 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
72838039 AACAGAGCAA
72838049 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
72838091 GG AG A
1 AG AG A
72838096 AGAAGAAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:72840581 original size:21 final size:21
Alignment explanation
Indices: 72840555--72840704 Score: 106
Period size: 21 Copynumber: 7.1 Consensus size: 21
72840545 CGTGTTTACT
*
72840555 TTCTGTTTAGCTCTCACGAGC
1 TTCTGTTTAGCTCTTACGAGC
* * *
72840576 TTCTGTTTAAC-CTTTATGAGT
1 TTCTGTTTAGCTC-TTACGAGC
*
72840597 TTCTGTTCAGCTCTTACGAGC
1 TTCTGTTTAGCTCTTACGAGC
* * * *
72840618 TTCTGTTTAACCCTTATG-GG
1 TTCTGTTTAGCTCTTACGAGC
* *
72840638 TTCCTATTAAGCTCTTACGAGC
1 TT-CTGTTTAGCTCTTACGAGC
* * * * *
72840660 TTCTGTTTAACCCTTATGGGT
1 TTCTGTTTAGCTCTTACGAGC
* *
72840681 TTCTGTTTAGCTTTTACAAGC
1 TTCTGTTTAGCTCTTACGAGC
72840702 TTC
1 TTC
72840705 CATTCAACCC
Statistics
Matches: 92, Mismatches: 33, Indels: 8
0.69 0.25 0.06
Matches are distributed among these distances:
20 4 0.04
21 84 0.91
22 4 0.04
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.44
Consensus pattern (21 bp):
TTCTGTTTAGCTCTTACGAGC
Found at i:72840616 original size:42 final size:42
Alignment explanation
Indices: 72840554--72840731 Score: 248
Period size: 42 Copynumber: 4.2 Consensus size: 42
72840544 TCGTGTTTAC
* * *
72840554 TTTCTGTTTAGCTCTCACGAGCTTCTGTTTAACCTTTATGAG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
*
72840596 TTTCTGTTCAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
* * *
72840638 TTCCTATTAAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
* * ** *
72840680 TTTCTGTTTAGCTTTTACAAGCTTCCATTCAACCCTTATGGG
1 TTTCTGTTTAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
72840722 TTTCTGTTTA
1 TTTCTGTTTA
72840732 CCATTTATGT
Statistics
Matches: 121, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 121 1.00
ACGTcount: A:0.17, C:0.22, G:0.16, T:0.44
Consensus pattern (42 bp):
TTTCTGTTTAGCTCTTACGAGCTTCTGTTTAACCCTTATGGG
Found at i:72845813 original size:15 final size:16
Alignment explanation
Indices: 72845788--72845821 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
72845778 GAAATGTAAT
72845788 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
72845804 TTTA-TATTTTAATAA
1 TTTATTATTTTAATAA
72845819 TTT
1 TTT
72845822 TTTTAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:72845907 original size:16 final size:15
Alignment explanation
Indices: 72845886--72845929 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
72845876 TTCATATACT
72845886 AATTTAAAATTTTATA
1 AATTTAAAATTTTA-A
*
72845902 AATTTAAAAATGTTAA
1 AATTT-AAAATTTTAA
72845918 AATTT-AAATTTT
1 AATTTAAAATTTT
72845930 TTATTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 6 0.24
16 11 0.44
17 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
AATTTAAAATTTTAA
Found at i:72846047 original size:35 final size:32
Alignment explanation
Indices: 72845981--72846043 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
72845971 TCAAGACAAG
72845981 ATTGTTTCACTTTGATGTAATTATTATTATTT
1 ATTGTTTCACTTTGATGTAATTATTATTATTT
72846013 ATTGTTTCACTTTGATGTAATTATTATTATT
1 ATTGTTTCACTTTGATGTAATTATTATTATT
72846044 ATTTTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.06, G:0.10, T:0.59
Consensus pattern (32 bp):
ATTGTTTCACTTTGATGTAATTATTATTATTT
Found at i:72846766 original size:3 final size:3
Alignment explanation
Indices: 72846758--72846812 Score: 74
Period size: 3 Copynumber: 18.3 Consensus size: 3
72846748 ATGCTGCCAA
* * * *
72846758 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATC ATC ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
72846806 ATT ATT A
1 ATT ATT A
72846813 AATTTTCATG
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:72846884 original size:6 final size:6
Alignment explanation
Indices: 72846873--72846930 Score: 107
Period size: 6 Copynumber: 9.7 Consensus size: 6
72846863 GTGAAAAATT
72846873 GAAACA GAAACA GAAACA GAAACA GAAACA GAAACA GAAACA GAAACA
1 GAAACA GAAACA GAAACA GAAACA GAAACA GAAACA GAAACA GAAACA
*
72846921 GAAATA GAAA
1 GAAACA GAAA
72846931 ATGAAACGGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.67, C:0.14, G:0.17, T:0.02
Consensus pattern (6 bp):
GAAACA
Found at i:72847361 original size:22 final size:22
Alignment explanation
Indices: 72847322--72847383 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
72847312 AGTAGGCACT
* * *
72847322 GAAGTGCTAAGCAATAGGAAAC
1 GAAGTGCAAATCAGTAGGAAAC
* *
72847344 GAAGTGCAAATCAGTAGGCACC
1 GAAGTGCAAATCAGTAGGAAAC
72847366 GTAA-TGCAAATCAGTAGG
1 G-AAGTGCAAATCAGTAGG
72847384 CATTGTACTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 32 0.94
23 2 0.06
ACGTcount: A:0.40, C:0.16, G:0.27, T:0.16
Consensus pattern (22 bp):
GAAGTGCAAATCAGTAGGAAAC
Found at i:72848281 original size:3 final size:3
Alignment explanation
Indices: 72848273--72848303 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
72848263 ATGTTTTAAC
72848273 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
72848304 TTAACATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:72854050 original size:20 final size:19
Alignment explanation
Indices: 72854025--72854080 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
72854015 CTTGAAGAAT
72854025 TAAAATAATTAAAATAAAAA
1 TAAAATAA-TAAAATAAAAA
* *
72854045 TAAAATAATAAACTAAAAC
1 TAAAATAATAAAATAAAAA
*
72854064 TAAATAGAATAAAATAA
1 TAAA-ATAATAAAATAA
72854081 GTAGAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (19 bp):
TAAAATAATAAAATAAAAA
Done.