Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold88
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: 1260485
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 2 of 8
Found at i:103985 original size:8 final size:8
Alignment explanation
Indices: 103925--104007 Score: 70
Period size: 8 Copynumber: 10.9 Consensus size: 8
103915 TAAAATATTT
*
103925 TTTATAAA
1 TTTATATA
103933 TTTATAT-
1 TTTATATA
103940 TTTA-ATAA
1 TTTATAT-A
103948 TTTATATA
1 TTTATATA
*
103956 -ATATATA
1 TTTATATA
*
103963 TTTAAATA
1 TTTATATA
103971 TTTATATA
1 TTTATATA
103979 TTTATAT-
1 TTTATATA
*
103986 TATAT-TA
1 TTTATATA
103993 TTTAT-TA
1 TTTATATA
104000 TGTTATAT
1 T-TTATAT
104008 TTAATTTTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
6 3 0.05
7 21 0.34
8 34 0.56
9 3 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (8 bp):
TTTATATA
Found at i:104020 original size:28 final size:28
Alignment explanation
Indices: 103969--104054 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
103959 TATATTTAAA
* *
103969 TATTTATATATTTATATTATATTATTTA-T
1 TATTTATAT-TTAATTTTA-ATTATTTATT
*
103998 TATGTTATATTTAATTTTAATTAATTATT
1 TAT-TTATATTTAATTTTAATTATTTATT
* *
104027 TATTTGTATTT-ATATT-ATTATTTATT
1 TATTTATATTTAATTTTAATTATTTATT
104053 TA
1 TA
104055 AAAGGGACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
26 11 0.22
27 4 0.08
28 14 0.29
29 14 0.29
30 6 0.12
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (28 bp):
TATTTATATTTAATTTTAATTATTTATT
Found at i:104640 original size:19 final size:19
Alignment explanation
Indices: 104598--104640 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
104588 TTATACATTC
* *
104598 TTAATTTTATTTTATATCT
1 TTAATTTTAATTTAAATCT
* *
104617 ATAATTTTAATTTAAATTT
1 TTAATTTTAATTTAAATCT
104636 TTAAT
1 TTAAT
104641 CATTTTTTAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTAATTTTAATTTAAATCT
Found at i:104753 original size:20 final size:19
Alignment explanation
Indices: 104693--104753 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
104683 AACTCAATTA
104693 AAAAT-TTTATATATATTTT
1 AAAATATTTATATAT-TTTT
* * *
104712 AAATATAATAAT-TATATTT
1 AAA-ATATTTATATATTTTT
104731 AAAATATTTATATATTTTAT
1 AAAATATTTATATATTTT-T
104751 AAA
1 AAA
104754 TAATATCAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
18 6 0.19
19 14 0.44
20 9 0.28
21 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AAAATATTTATATATTTTT
Found at i:111441 original size:16 final size:16
Alignment explanation
Indices: 111406--111442 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
111396 AAAATATTAA
111406 AAATATTTTTTATATT
1 AAATATTTTTTATATT
111422 -AATA-TTTTTATAATT
1 AAATATTTTTTAT-ATT
111437 AAATAT
1 AAATAT
111443 AGTAAAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 5
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.39
15 7 0.39
16 4 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AAATATTTTTTATATT
Found at i:113131 original size:14 final size:15
Alignment explanation
Indices: 113107--113139 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
113097 TTGATCTGAC
*
113107 TTTATTTTATTATTT
1 TTTATTTTATTATTA
113122 TTTA-TTTATTATTA
1 TTTATTTTATTATTA
113136 TTTA
1 TTTA
113140 AATAAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTTATTATTA
Found at i:114729 original size:170 final size:172
Alignment explanation
Indices: 114539--114945 Score: 423
Period size: 170 Copynumber: 2.4 Consensus size: 172
114529 AATTTAAGTA
* * * * *
114539 AAATCACTATTTAAAAGTATGACTTTTATATTTGGTATGTTAATAGTGACGAGCCCATCATATT-
1 AAATCACCATTTATAAGTATGACTTTCATAATTGGTATGTTGATAGTGACG-GCCCATCATATTA
* * *
114603 ATGTATTGGGTTCAAAAATGACATGCGTAT-TATAAC-GTATCAT-AGTAG-TTTCCATTCATCC
65 AGGTATTGGGTTCAAAAATGACATGCGTATACATAACAG-ATCATGA-TAGCCTT-CATTCATCC
* *
114664 AATCC-CACTCTATTATTT-TTTATCTATTATTATCAAATACAAATT
127 AA-CCACACTCTATTATTTCTCTATCTATCATTATCAAATACAAATT
* * * * * **
114709 AAATCACCATTCATAAGTATGAATTTCATAATTGGCATGTTGACAATGGTGGCCCATCATATTAA
1 AAATCACCATTTATAAGTATGACTTTCATAATTGGTATGTTGATAGTGACGGCCCATCATATTAA
* * * ** * **
114774 GGTATTTGGTTCAAAAATGGCATGCGTATACATAACAGATGATGATAGCCTTGGTTGATCTGACC
66 GGTATTGGGTTCAAAAATGACATGCGTATACATAACAGATCATGATAGCCTTCATTCATCCAACC
* * *
114839 ACACTCTATTATTTCTCTATCTATCATTCTCCAATACAAGTT
131 ACACTCTATTATTTCTCTATCTATCATTATCAAATACAAATT
* * * *
114881 AAATCACCATTTATAAGTATGACTTCCATAATTGGTATGTTGATAGCGATAGGCCTATCATATTA
1 AAATCACCATTTATAAGTATGACTTTCATAATTGGTATGTTGATAGTGA-CGGCCCATCATATTA
114946 GGGCATTTGT
Statistics
Matches: 191, Mismatches: 38, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
169 12 0.06
170 68 0.36
171 31 0.16
172 67 0.35
173 13 0.07
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.37
Consensus pattern (172 bp):
AAATCACCATTTATAAGTATGACTTTCATAATTGGTATGTTGATAGTGACGGCCCATCATATTAA
GGTATTGGGTTCAAAAATGACATGCGTATACATAACAGATCATGATAGCCTTCATTCATCCAACC
ACACTCTATTATTTCTCTATCTATCATTATCAAATACAAATT
Found at i:115067 original size:168 final size:166
Alignment explanation
Indices: 114868--115174 Score: 436
Period size: 168 Copynumber: 1.8 Consensus size: 166
114858 TCTATCATTC
* * * * * *
114868 TCCAATACAAGTTAAATCACCATTTATAAGTATGACTTCCATAATTGGTATGTTGATAGCGATAG
1 TCCAATACAAATTAAATCACCATTCATAAGTATGACTTCCACAATTAGTATGTTAACAGCGATAG
* *
114933 GCCTATCATATTAGGGCATTTGTTTAAAAAAAAAATG-CTAAATAGTGATTTAACTTGTATATGT
66 GCCTATCATATTAGAGCATTTGGTT---AAAAAAATGACTAAATAGTGATTTAACTTGTATATGT
114997 AACGTATGATAGTAATCTCTTCTCTCCATTATTTTCTTG
128 AACGTATGATAGTAATCTCTTCTCTCCATTATTTTCTTG
* * * *
115036 TCCAATACAAATTAAATCACCATTCATAAGTATGTCTTTCACAATTAGTATGTTAACAGTGATGG
1 TCCAATACAAATTAAATCACCATTCATAAGTATGACTTCCACAATTAGTATGTTAACAGCGATAG
* * *
115101 GCCTATCATATTATAGCATTTGGTTAAAAAAATGCACTATATAGTGATTTAATTTGTATATGTAA
66 GCCTATCATATTAGAGCATTTGGTTAAAAAAATG-ACTAAATAGTGATTTAACTTGTATATGTAA
115166 CGTATGATA
130 CGTATGATA
115175 ATAGTCTCGA
Statistics
Matches: 122, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
165 9 0.07
167 36 0.30
168 77 0.63
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (166 bp):
TCCAATACAAATTAAATCACCATTCATAAGTATGACTTCCACAATTAGTATGTTAACAGCGATAG
GCCTATCATATTAGAGCATTTGGTTAAAAAAATGACTAAATAGTGATTTAACTTGTATATGTAAC
GTATGATAGTAATCTCTTCTCTCCATTATTTTCTTG
Found at i:116211 original size:189 final size:187
Alignment explanation
Indices: 115960--116300 Score: 402
Period size: 188 Copynumber: 1.8 Consensus size: 187
115950 GCACTTAGTT
* * *
115960 AAAAAAAAACACTAAATGGTAATTTAACTTGTTTGCGTAGCGAATGTCAGTAGCCTCAATTGATC
1 AAAAAAAAACACTAAATGGTAATTTAACTTGTATACGTAACGAATGTCAGTA-CCTCAATTGAT-
* ** * * * *
116025 TGACTCCCTTCCATT-A-TTTATCAATCTATTATTGCCTAATATAAACTAAATCACTATTTATCA
64 TAAAGCCCTTCCATTAATTTTAT--ATCTATTATTGCCTAATACAAACTAAATCACCATTCATAA
* *
116088 GTATGACTTTCACAATTTGTATGTTAACAACAATGGGCCATCATATTAGAGCGTTTGGTTC
127 GTATAACTTTCACAATTAGTATGTTAACAACAATGGGCCATCATATTAGAGCGTTTGGTTC
* * * *
116149 AAAAAAAAACACTAAATGGTGATTTAGCTTGTATACGTAATGGATGATAACAGT-CC-CAATTGA
1 AAAAAAAAACACTAAATGGTAATTTAACTTGTATACGTAACGAATG-T--CAGTACCTCAATTGA
* * * * *
116212 TTAAAGCCCTTCTATTAATTTTATGTTTATTATTGTCTAATACAAATTAAATCACCATTCATAAG
63 TTAAAGCCCTTCCATTAATTTTATATCTATTATTGCCTAATACAAACTAAATCACCATTCATAAG
116277 TATAACTTTCACAATTAGTATGTT
128 TATAACTTTCACAATTAGTATGTT
116301 GACAGACTTT
Statistics
Matches: 126, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
188 66 0.52
189 48 0.38
190 8 0.06
192 4 0.03
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.36
Consensus pattern (187 bp):
AAAAAAAAACACTAAATGGTAATTTAACTTGTATACGTAACGAATGTCAGTACCTCAATTGATTA
AAGCCCTTCCATTAATTTTATATCTATTATTGCCTAATACAAACTAAATCACCATTCATAAGTAT
AACTTTCACAATTAGTATGTTAACAACAATGGGCCATCATATTAGAGCGTTTGGTTC
Found at i:119374 original size:2 final size:2
Alignment explanation
Indices: 119367--119407 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
119357 TACTTACCAG
* * *
119367 AC AC AC AC CC AC AC AC AC AC AC AC AC GC AC AC GC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
119408 GAAACCAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.44, C:0.51, G:0.05, T:0.00
Consensus pattern (2 bp):
AC
Found at i:119431 original size:6 final size:7
Alignment explanation
Indices: 119409--119433 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
119399 GCACACACAG
119409 AAACCAA
1 AAACCAA
119416 AAACCAA
1 AAACCAA
119423 AAACCAA
1 AAACCAA
119430 AAAC
1 AAAC
119434 ATGGGATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (7 bp):
AAACCAA
Found at i:126872 original size:12 final size:12
Alignment explanation
Indices: 126857--126886 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
126847 GCGTTTATAC
*
126857 ATATATACATAT
1 ATATATAAATAT
126869 ATATATAAATAT
1 ATATATAAATAT
126881 ATATAT
1 ATATAT
126887 CTATGCATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATATAAATAT
Found at i:127859 original size:49 final size:49
Alignment explanation
Indices: 127754--127866 Score: 115
Period size: 49 Copynumber: 2.3 Consensus size: 49
127744 TATTATTAAA
** * * *
127754 AATATTATTTTTATATTAATATTTTATATATTTTATAATTAAATTAAAAT
1 AATATTATTTTT-TATTAATAAATAATATATTTAATAATTAAAATAAAAT
*
127804 AA-ATTATTTTTTATTAATAAATAATA-ATTTAAATAAATTAAAAT-AATT
1 AATATTATTTTTTATTAATAAATAATATATTT-AAT-AATTAAAATAAAAT
*
127852 AATATTATATTTTAT
1 AATATTATTTTTTAT
127867 AAAAACAAAC
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
47 4 0.08
48 19 0.36
49 28 0.53
50 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (49 bp):
AATATTATTTTTTATTAATAAATAATATATTTAATAATTAAAATAAAAT
Found at i:128931 original size:23 final size:23
Alignment explanation
Indices: 128905--128984 Score: 63
Period size: 23 Copynumber: 3.4 Consensus size: 23
128895 CGTTTAGATT
*
128905 TATTTATTTATTATTTTTAAATA
1 TATTTATTTATTATTTATAAATA
* * *
128928 TATTCGA-TTATATATTTATGAACA
1 TATT-TATTTAT-TATTTATAAATA
* * *
128952 TATTCATTTAATATTTAGAAATA
1 TATTTATTTATTATTTATAAATA
*
128975 AATTTATTTA
1 TATTTATTTA
128985 AATTAAATAA
Statistics
Matches: 43, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
23 26 0.60
24 17 0.40
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
TATTTATTTATTATTTATAAATA
Found at i:129034 original size:20 final size:20
Alignment explanation
Indices: 128984--129080 Score: 67
Period size: 20 Copynumber: 4.9 Consensus size: 20
128974 AAATTTATTT
* * *
128984 AAATTAAATAAA-TAAAATT
1 AAATTAATTAAATTTAAATA
* *
129003 AAATATATTTAATTTTAAATA
1 AAAT-TAATTAAATTTAAATA
129024 AAATTAATTAAAATTT-AATA
1 AAATTAATT-AAATTTAAATA
* *
129044 AATTTAA-TAAATTTAAATT
1 AAATTAATTAAATTTAAATA
*
129063 AAATATAA-AAAATTTAAA
1 AAAT-TAATTAAATTTAAA
129081 AATAAACAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
18 6 0.10
19 11 0.18
20 31 0.50
21 14 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATTAATTAAATTTAAATA
Found at i:129048 original size:9 final size:9
Alignment explanation
Indices: 129020--129083 Score: 58
Period size: 9 Copynumber: 6.8 Consensus size: 9
129010 TTTAATTTTA
*
129020 AATAAAATT
1 AATAAATTT
129029 AATTAAAATTT
1 AA-T-AAATTT
129040 AATAAATTT
1 AATAAATTT
129049 AATAAATTT
1 AATAAATTT
*
129058 AAATTAAATAT
1 -AA-TAAATTT
*
129069 AAAAAATTT
1 AATAAATTT
129078 AA-AAAT
1 AATAAAT
129084 AAACAAATGA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
8 4 0.09
9 24 0.51
10 6 0.13
11 13 0.28
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
AATAAATTT
Found at i:135425 original size:17 final size:18
Alignment explanation
Indices: 135382--135426 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
135372 TAAAAAATAT
*
135382 AATTA-AAATATGATGAA
1 AATTATAAATATGATCAA
135399 AATATATAAATATG-TCAA
1 AAT-TATAAATATGATCAA
135417 AATTATAAAT
1 AATTATAAAT
135427 TATTAATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 8 0.32
19 7 0.28
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (18 bp):
AATTATAAATATGATCAA
Found at i:137648 original size:56 final size:57
Alignment explanation
Indices: 137571--137680 Score: 159
Period size: 56 Copynumber: 1.9 Consensus size: 57
137561 TGGTGTCACT
* * *
137571 GTTCCTTTTAGTCCTGATCACACATGCCATATG-TTCCTCCGGTTCTTTATTTTAAA
1 GTTCCTTTTAGTCCTGATCACACATACCAAATGTTTCCTCCAGTTCTTTATTTTAAA
* * *
137627 GTTCCTTTTAGTCCTGGTCACACATACCAAATGTTTGCTCCAGTTTTTTATTTT
1 GTTCCTTTTAGTCCTGATCACACATACCAAATGTTTCCTCCAGTTCTTTATTTT
137681 GCTTTAGTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
56 30 0.64
57 17 0.36
ACGTcount: A:0.19, C:0.24, G:0.13, T:0.45
Consensus pattern (57 bp):
GTTCCTTTTAGTCCTGATCACACATACCAAATGTTTCCTCCAGTTCTTTATTTTAAA
Found at i:140774 original size:21 final size:21
Alignment explanation
Indices: 140750--140789 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
140740 ATTTAACATT
140750 TATTTAATTCATATCATATTA
1 TATTTAATTCATATCATATTA
** *
140771 TATTTGTTTCATATTATAT
1 TATTTAATTCATATCATAT
140790 ATTATATTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (21 bp):
TATTTAATTCATATCATATTA
Found at i:146050 original size:19 final size:19
Alignment explanation
Indices: 146001--146050 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
145991 TATTTTGTAT
*
146001 TATTTA-AAATAATATTAA
1 TATTTATAATTAATATTAA
* **
146019 AATTTATTTTTAATATTAA
1 TATTTATAATTAATATTAA
146038 TATTTATAATTAA
1 TATTTATAATTAA
146051 ATTTGATATA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATTTATAATTAATATTAA
Found at i:149045 original size:3 final size:3
Alignment explanation
Indices: 149039--149080 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
149029 TATTATTTGG
149039 ATA ATA ATA ATA A-A A-A ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
149081 CACTTAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:154715 original size:13 final size:14
Alignment explanation
Indices: 154697--154732 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
154687 TTAAAAATAA
*
154697 TAAATTAGATT-AT
1 TAAATTAAATTAAT
154710 TAAATTAAATTAAT
1 TAAATTAAATTAAT
154724 TAAATTAAA
1 TAAATTAAA
154733 AATTAATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
TAAATTAAATTAAT
Found at i:154897 original size:18 final size:17
Alignment explanation
Indices: 154812--154893 Score: 55
Period size: 17 Copynumber: 4.6 Consensus size: 17
154802 TTAAAAATTT
154812 TAAAATT-TTTAATTTTA
1 TAAAATTATTT-ATTTTA
*
154829 TAATAA--ATTTATTATA
1 TAA-AATTATTTATTTTA
*
154845 TATAATGCTATTTAAGTTTTA
1 TAAAAT--TATTT-A-TTTTA
154866 TAAAATTATTTATTTTGA
1 TAAAATTATTTATTTT-A
154884 TAAAA-TATTT
1 TAAAATTATTT
154894 TATTATATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
15 2 0.04
16 7 0.13
17 15 0.29
18 9 0.17
19 9 0.17
20 1 0.02
21 9 0.17
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
TAAAATTATTTATTTTA
Found at i:156165 original size:2 final size:2
Alignment explanation
Indices: 156158--156186 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
156148 TAAATGTACC
156158 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
156187 CCTCCCAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:156335 original size:93 final size:93
Alignment explanation
Indices: 156176--156372 Score: 376
Period size: 93 Copynumber: 2.1 Consensus size: 93
156166 TATATATATA
156176 TATATATATATCCTCCCAACCAAGTCTTCCCTTTCACAATATATAAATGTCATTTTCAATTGTTC
1 TATATATATATCCTCCCAACCAAGTCTTCCCTTTCACAATATATAAATGTCATTTTCAATTGTTC
*
156241 TTTGTTTAGAATTTGTGTTCTATTCTTT
66 TTTGTTTAGAATTTGTGTTCTATTATTT
*
156269 TATATATATATCCTCCCAACCAAGTCTTCCCTTTCACAATATATAGATGTCATTTTCAATTGTTC
1 TATATATATATCCTCCCAACCAAGTCTTCCCTTTCACAATATATAAATGTCATTTTCAATTGTTC
156334 TTTGTTTAGAATTTGTGTTCTATTATTT
66 TTTGTTTAGAATTTGTGTTCTATTATTT
156362 TATATATATAT
1 TATATATATAT
156373 ATATAAATAA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 102 1.00
ACGTcount: A:0.27, C:0.18, G:0.08, T:0.48
Consensus pattern (93 bp):
TATATATATATCCTCCCAACCAAGTCTTCCCTTTCACAATATATAAATGTCATTTTCAATTGTTC
TTTGTTTAGAATTTGTGTTCTATTATTT
Found at i:156598 original size:24 final size:20
Alignment explanation
Indices: 156571--156636 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 20
156561 TTTTATTTGA
156571 TTAAATAATTAAATTTATATATAT
1 TTAAATAATT-AA-TT-TATA-AT
*
156595 TTAATTAATTAATTTATAAT
1 TTAAATAATTAATTTATAAT
156615 TTAAATAA-TATATTTA-AAT
1 TTAAATAATTA-ATTTATAAT
156634 TTA
1 TTA
156637 CACCGAAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 8 0.21
20 14 0.36
21 4 0.10
22 2 0.05
23 2 0.05
24 9 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTAAATAATTAATTTATAAT
Found at i:157671 original size:2 final size:2
Alignment explanation
Indices: 157664--157696 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
157654 AACTATATTA
157664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
157697 AATTCATGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:159699 original size:18 final size:18
Alignment explanation
Indices: 159678--159714 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
159668 TAAAACAATA
*
159678 ATATTAAAAATTATTTTT
1 ATATTAAAAATTATATTT
*
159696 ATATTAATAATTATATTT
1 ATATTAAAAATTATATTT
159714 A
1 A
159715 AATATAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTAAAAATTATATTT
Found at i:160751 original size:5 final size:5
Alignment explanation
Indices: 160733--160805 Score: 58
Period size: 5 Copynumber: 14.2 Consensus size: 5
160723 AATTTAAATG
* * * *
160733 TTAAA TTTAA TTAAC TTAAA TTAAA TTAAT TTAAA TGTTAAA CTT-GA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA --TTAAA -TTAAA
* *
160780 TTAAC TTAAA TTAAA TTAAT TTAAA T
1 TTAAA TTAAA TTAAA TTAAA TTAAA T
160806 GTAATTAATT
Statistics
Matches: 52, Mismatches: 13, Indels: 6
0.73 0.18 0.08
Matches are distributed among these distances:
4 2 0.04
5 43 0.83
6 2 0.04
7 5 0.10
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (5 bp):
TTAAA
Found at i:160764 original size:37 final size:37
Alignment explanation
Indices: 160723--160807 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
160713 AAATATGATA
*
160723 AATTTAAATGTTAAATTTAATTAACTTAAATTAAATT
1 AATTTAAATGTTAAACTTAATTAACTTAAATTAAATT
*
160760 AATTTAAATGTTAAACTTGATTAACTTAAATTAAATT
1 AATTTAAATGTTAAACTTAATTAACTTAAATTAAATT
160797 AATTTAAATGT
1 AATTTAAATGT
160808 AATTAATTCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (37 bp):
AATTTAAATGTTAAACTTAATTAACTTAAATTAAATT
Found at i:162307 original size:2 final size:2
Alignment explanation
Indices: 162300--162343 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
162290 TGGTGAATGA
162300 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
162342 AG
1 AG
162344 GCAGGACAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:164103 original size:275 final size:278
Alignment explanation
Indices: 163603--164120 Score: 848
Period size: 275 Copynumber: 1.9 Consensus size: 278
163593 CTTAGGAAGT
* * *
163603 CCCCAATCCCAAGCTTGTGTTGCTCAGAGCCAAAGCCATCCTCGTACTTGAGGGATTTGCAGACT
1 CCCCAATCCCAAGCTTGTGTTGCTCAAAGACAAAGCCATCCTCATACTTGAGGGATTTGCAGACT
* *
163668 CTGGGGGTTAAGAATAGCTGGGCAAAATCTCAGTTCAACTTTGATTGAGGGACAGGACTTGCTCA
66 CTGAGGGTTAAGAATAGCTGGGCAAAATCTCAATTCAACTTTGATT-AGGGACAGGACTTGCTCA
* *
163733 AAAAATTTTCATCGGAAAGGATGAAGCAAGGTAGGCTTAGGGGCAAATGATCACGCTGGCAGTGG
130 AAAAATTTTCATCGGAAAGGATGAAACAAGGTAGGCTGAGGGGCAAATGATCACGCTGGCAGTGG
* *
163798 TTATTCTAATTTTCTTCTTTAACTCCTTCAAAATTCACTATCTTAACTCAGTTTCCTCTATTTTC
195 TTATTCTAATTTTCTTATTTAACCCCTTCAAAATTCACTATCTTAACTCAGTTTCCTCTATTTTC
163863 TCAAGCTATCACAACTCAG
260 TCAAGCTATCACAACTCAG
163882 CCCCAATCCCAAGCTTGTGTTGCTCAAAGACAAAGCCATCCTCATACTTGAGGGATTTGCAG-CT
1 CCCCAATCCCAAGCTTGTGTTGCTCAAAGACAAAGCCATCCTCATACTTGAGGGATTTGCAGACT
*
163946 CCTGAGGGTTAAGAA-A-CTGGGCAAAATCTCAATTCAACTTTGATT-GGGACAGGATTTGCTCA
66 -CTGAGGGTTAAGAATAGCTGGGCAAAATCTCAATTCAACTTTGATTAGGGACAGGACTTGCTCA
* *
164008 AAAGATTTTCATGGGAAAGGATGAAACAAGGTAGGCTGAGGGGCAAATGATCATC-CTGGCAGTG
130 AAAAATTTTCATCGGAAAGGATGAAACAAGGTAGGCTGAGGGGCAAATGATCA-CGCTGGCAGTG
**
164072 GTTATTCTAATTTTCTTATTTAACCCCTTCAAAATTTGCTATCTTAACT
194 GTTATTCTAATTTTCTTATTTAACCCCTTCAAAATTCACTATCTTAACT
164121 AAGGCCCCTT
Statistics
Matches: 223, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
275 119 0.53
276 1 0.00
277 28 0.13
278 3 0.01
279 72 0.32
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (278 bp):
CCCCAATCCCAAGCTTGTGTTGCTCAAAGACAAAGCCATCCTCATACTTGAGGGATTTGCAGACT
CTGAGGGTTAAGAATAGCTGGGCAAAATCTCAATTCAACTTTGATTAGGGACAGGACTTGCTCAA
AAAATTTTCATCGGAAAGGATGAAACAAGGTAGGCTGAGGGGCAAATGATCACGCTGGCAGTGGT
TATTCTAATTTTCTTATTTAACCCCTTCAAAATTCACTATCTTAACTCAGTTTCCTCTATTTTCT
CAAGCTATCACAACTCAG
Found at i:167279 original size:18 final size:18
Alignment explanation
Indices: 167256--167293 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
167246 AAAGTGCTCA
167256 TCATCTTAACATCTAAGT
1 TCATCTTAACATCTAAGT
167274 TCATCTTAACATCTAAGT
1 TCATCTTAACATCTAAGT
167292 TC
1 TC
167294 GAGACCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (18 bp):
TCATCTTAACATCTAAGT
Found at i:167347 original size:43 final size:43
Alignment explanation
Indices: 167274--167357 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
167264 ACATCTAAGT
* * * **
167274 TCATCTTAACATCTAAGTTCGAGACCAATATCCGTTACAGATA
1 TCATCCTAACATCTAAGTTCAAAACCAATATCAATTACAGATA
*
167317 TCATCCTAACATCTAAGTTCAAAACGAATATCAATTACAGA
1 TCATCCTAACATCTAAGTTCAAAACCAATATCAATTACAGA
167358 CACTAATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.29
Consensus pattern (43 bp):
TCATCCTAACATCTAAGTTCAAAACCAATATCAATTACAGATA
Found at i:169342 original size:20 final size:19
Alignment explanation
Indices: 169316--169365 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
169306 TTTTATTTGA
*
169316 TTTAATTTAAATTATTATT
1 TTTAATTTAAATTAATATT
*
169335 TATTAA-TTAAAATAATATT
1 T-TTAATTTAAATTAATATT
169354 TTT-ATTTAAATT
1 TTTAATTTAAATT
169366 TAATCATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 1 0.04
18 8 0.31
19 13 0.50
20 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAATTTAAATTAATATT
Found at i:169398 original size:20 final size:21
Alignment explanation
Indices: 169360--169400 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
169350 TATTTTTATT
169360 TAAATTTAATCATAAAAATTA
1 TAAATTTAATCATAAAAATTA
169381 TAAATATTAAT-A-AAAAATTA
1 TAAAT-TTAATCATAAAAATTA
169401 ATATTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATTTAATCATAAAAATTA
Found at i:171584 original size:16 final size:16
Alignment explanation
Indices: 171563--171593 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
171553 TTATATTAAT
*
171563 AATAAAATTAAATTTA
1 AATAAAAATAAATTTA
171579 AATAAAAATAAATTT
1 AATAAAAATAAATTT
171594 TTATTACGTA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAAAAATAAATTTA
Found at i:171978 original size:8 final size:7
Alignment explanation
Indices: 171965--172005 Score: 55
Period size: 7 Copynumber: 5.6 Consensus size: 7
171955 ATGATGATCC
171965 AAAAAGA
1 AAAAAGA
171972 GAAAAAGA
1 -AAAAAGA
*
171980 AAAAAAA
1 AAAAAGA
171987 AAAAAGA
1 AAAAAGA
171994 AAGAAAGA
1 AA-AAAGA
172002 AAAA
1 AAAA
172006 TTAAAGGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:172279 original size:2 final size:2
Alignment explanation
Indices: 172274--172314 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
172264 TTTTTATTTG
172274 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
172315 GTGTGTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:177950 original size:4 final size:4
Alignment explanation
Indices: 177943--177972 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
177933 TATTTTTAAT
177943 TTTA TTTA TTTA TTTA TTTA -TTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
177973 TAAACAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:177974 original size:12 final size:12
Alignment explanation
Indices: 177943--177972 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
177933 TATTTTTAAT
177943 TTTATTTATTTA
1 TTTATTTATTTA
177955 TTTATTTA-TTA
1 TTTATTTATTTA
177966 TTTATTT
1 TTTATTT
177973 TAAACAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATTTATTTA
Found at i:178339 original size:35 final size:35
Alignment explanation
Indices: 178288--178358 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
178278 AAATTACAAA
*
178288 TGTTGAGTTTCGTACTAAATACAAATGTTTAGTTT
1 TGTTGAGTTTCATACTAAATACAAATGTTTAGTTT
178323 TGTTGAGTTTCATACTAAATACAAATGTTTAGTTT
1 TGTTGAGTTTCATACTAAATACAAATGTTTAGTTT
178358 T
1 T
178359 TTTGTATAAA
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:0.30, C:0.08, G:0.15, T:0.46
Consensus pattern (35 bp):
TGTTGAGTTTCATACTAAATACAAATGTTTAGTTT
Found at i:179492 original size:22 final size:22
Alignment explanation
Indices: 179450--179514 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
179440 TATTCAGATT
* *
179450 ATTATTTAAA--TAATAAAAAA
1 ATTATTTAAATTTAATTATAAA
179470 ATTATTTAAATTTAATTATAAA
1 ATTATTTAAATTTAATTATAAA
* *
179492 AATATATAAATATTAA-TATAAA
1 ATTATTTAAAT-TTAATTATAAA
179514 A
1 A
179515 ATAATTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.26
22 24 0.63
23 4 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTATTTAAATTTAATTATAAA
Found at i:179515 original size:22 final size:21
Alignment explanation
Indices: 179460--179517 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
179450 ATTATTTAAA
* *
179460 TAATAAAAAAATTATTTAAATT
1 TAATATAAAAA-TATATAAATT
179482 TAATTATAAAAATATATAAATAT
1 TAA-TATAAAAATATATAAAT-T
179505 TAATATAAAAATA
1 TAATATAAAAATA
179518 ATTTATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 21 0.66
23 11 0.34
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATATAAAAATATATAAATT
Found at i:182035 original size:5 final size:5
Alignment explanation
Indices: 182025--182052 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
182015 TTCCATTCTT
182025 TTAAA TTAAA TTAAA TTAAA TTAAA TTA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTA
182053 TCTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
TTAAA
Found at i:182676 original size:22 final size:22
Alignment explanation
Indices: 182651--182692 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
182641 AAAAATTACA
*
182651 AAAATTATATATATTTATTTTT
1 AAAATTATATATATATATTTTT
182673 AAAATTATATATATATATTT
1 AAAATTATATATATATATTT
182693 AAAAATAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AAAATTATATATATATATTTTT
Found at i:183035 original size:2 final size:2
Alignment explanation
Indices: 183028--183052 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
183018 AATTGTTTTA
183028 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
183053 AGTGAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:183565 original size:23 final size:24
Alignment explanation
Indices: 183539--183588 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
183529 ATATATATTT
*
183539 AATAATTGAAT-TTTTTACATAAA
1 AATAATTAAATATTTTTACATAAA
* *
183562 AATAATTAAATATTTTTCCATTAA
1 AATAATTAAATATTTTTACATAAA
183586 AAT
1 AAT
183589 TTAAGATGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (24 bp):
AATAATTAAATATTTTTACATAAA
Found at i:183917 original size:8 final size:9
Alignment explanation
Indices: 183904--183946 Score: 54
Period size: 8 Copynumber: 4.8 Consensus size: 9
183894 TGCATGAATA
183904 AATTTA-AT
1 AATTTATAT
183912 AATTTA-AT
1 AATTTATAT
183920 AATTTATATT
1 AATTTATA-T
183930 ATATTTATAT
1 A-ATTTATAT
183940 AATTTAT
1 AATTTAT
183947 CATGTTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 14 0.44
9 7 0.22
10 4 0.12
11 7 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATTTATAT
Found at i:183986 original size:15 final size:15
Alignment explanation
Indices: 183928--183986 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
183918 ATAATTTATA
183928 TTATATTTATATAAT
1 TTATATTTATATAAT
*
183943 TTATCATGT-TATAA-
1 TTAT-ATTTATATAAT
*
183957 TTATATTTAAAATAAT
1 TTATATTT-ATATAAT
183973 TTATATTTATATAA
1 TTATATTTATATAA
183987 AATTTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 3 0.08
14 4 0.11
15 18 0.50
16 11 0.31
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (15 bp):
TTATATTTATATAAT
Found at i:184007 original size:27 final size:30
Alignment explanation
Indices: 183961--184049 Score: 96
Period size: 32 Copynumber: 3.0 Consensus size: 30
183951 TTATAATTAT
*
183961 ATTTAAAATAATTTATATTT-A-TATA-AA
1 ATTTAAAATATTTTATATTTAATTATATAA
183988 ATTTAAAATATTATTA-ATTTAAATTATATAA
1 ATTTAAAATATT-TTATATTT-AATTATATAA
*
184019 ATTTTAAAATATTTATATATTTAATCATATA
1 A-TTTAAAATATTT-TATATTTAATTATATA
184050 TATTATTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
27 15 0.29
28 3 0.06
29 1 0.02
30 4 0.08
31 4 0.08
32 21 0.40
33 4 0.08
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTTAAAATATTTTATATTTAATTATATAA
Found at i:184008 original size:16 final size:16
Alignment explanation
Indices: 183986--184042 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
183976 TATTTATATA
183986 AAATTTAAAATATTAT
1 AAATTTAAAATATTAT
* *
184002 TAATTTAAATTA-TAT
1 AAATTTAAAATATTAT
184017 AAATTTTAAAATATTTAT
1 AAA-TTTAAAATA-TTAT
*
184035 ATATTTAA
1 AAATTTAA
184043 TCATATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
15 5 0.15
16 18 0.55
17 5 0.15
18 5 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATTTAAAATATTAT
Found at i:184018 original size:32 final size:33
Alignment explanation
Indices: 183969--184031 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
183959 ATATTTAAAA
*
183969 TAATTTATATTTATATAAAATTTAAAATATTAT
1 TAATTTATAATTATATAAAATTTAAAATATTAT
*
184002 TAATTTA-AATTATATAAATTTTAAAATATT
1 TAATTTATAATTATATAAAATTTAAAATATT
184032 TATATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 21 0.75
33 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TAATTTATAATTATATAAAATTTAAAATATTAT
Found at i:184021 original size:15 final size:15
Alignment explanation
Indices: 183979--184022 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
183969 TAATTTATAT
183979 TTATATAAAATTTAAA
1 TTATAT-AAATTTAAA
* *
183995 ATATTATTAATTTAAA
1 TTA-TATAAATTTAAA
184011 TTATATAAATTT
1 TTATATAAATTT
184023 TAAAATATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 8 0.35
16 12 0.52
17 3 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTATATAAATTTAAA
Found at i:184376 original size:27 final size:27
Alignment explanation
Indices: 184334--184388 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
184324 CATTCGTATT
*
184334 TAATATATATTTAAATATA-AATAAAA
1 TAATATATATTTAAATATATAAAAAAA
*
184360 TAATATAATTTTTAAATATATAAAAAAA
1 TAATAT-ATATTTAAATATATAAAAAAA
184388 T
1 T
184389 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.24
27 12 0.48
28 7 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
TAATATATATTTAAATATATAAAAAAA
Found at i:184801 original size:11 final size:11
Alignment explanation
Indices: 184787--184829 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
184777 AATTATTAAG
184787 ATATTTATATT
1 ATATTTATATT
*
184798 ATATTAATA-T
1 ATATTTATATT
184808 ATATTTATATT
1 ATATTTATATT
184819 AT-TATTATATT
1 ATAT-TTATATT
184830 TAAAATATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTTATATT
Found at i:184804 original size:19 final size:21
Alignment explanation
Indices: 184778--184827 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
184768 AACTTAATTA
184778 ATTATTA-AGATATTTATATT
1 ATTATTATAGATATTTATATT
*
184798 A-TATTAATATATATTTATATT
1 ATTATT-ATAGATATTTATATT
184819 ATTATTATA
1 ATTATTATA
184828 TTTAAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.15
20 2 0.08
21 16 0.62
22 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTATTATAGATATTTATATT
Found at i:184898 original size:13 final size:13
Alignment explanation
Indices: 184880--184915 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
184870 GTTTATTATG
184880 TTTATATTATATT
1 TTTATATTATATT
184893 TTTATATTATATT
1 TTTATATTATATT
*
184906 TTTAAATTAT
1 TTTATATTAT
184916 GTTAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTATATTATATT
Found at i:188551 original size:2 final size:2
Alignment explanation
Indices: 188544--188574 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
188534 ACCATTACAA
*
188544 AC AC AC AC AC GC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
188575 TTTATAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.48, G:0.03, T:0.00
Consensus pattern (2 bp):
AC
Found at i:192616 original size:22 final size:23
Alignment explanation
Indices: 192591--192646 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
192581 ACATACTTAA
192591 ATTATTTT-TAATTATATAATAT
1 ATTATTTTATAATTATATAATAT
* *
192613 ATTAATTTTATATTTATATATTAT
1 ATT-ATTTTATAATTATATAATAT
*
192637 ATAATTTTAT
1 ATTATTTTAT
192647 CATATAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.10
23 12 0.41
24 14 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTATTTTATAATTATATAATAT
Found at i:192637 original size:24 final size:23
Alignment explanation
Indices: 192594--192646 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
192584 TACTTAAATT
192594 ATTTT-TAATTATATAATATATTA
1 ATTTTATAATTATATAATATA-TA
* *
192617 ATTTTATATTTATATATTATATA
1 ATTTTATAATTATATAATATATA
192640 ATTTTAT
1 ATTTTAT
192647 CATATAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 14 0.52
24 13 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTTATAATTATATAATATATA
Found at i:192810 original size:22 final size:22
Alignment explanation
Indices: 192775--192822 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
192765 ATCTACTTAA
* *
192775 ATAAATTTAAATTTTTTAA-TT
1 ATAAATTGAAATTTTTAAATTT
192796 ATAAATATGAAATTTTTAAATTT
1 ATAAAT-TGAAATTTTTAAATTT
192819 ATAA
1 ATAA
192823 TTTATAACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 11 0.48
23 6 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATAAATTGAAATTTTTAAATTT
Found at i:192951 original size:18 final size:17
Alignment explanation
Indices: 192912--192954 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
192902 TATAATTTTT
*
192912 AAAATATATTAAAATTT
1 AAAATATATTAAAATTA
* *
192929 TAAATATATTTAATATTA
1 AAAATATA-TTAAAATTA
192947 AAAATATA
1 AAAATATA
192955 CTTATATCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATATATTAAAATTA
Found at i:198131 original size:2 final size:2
Alignment explanation
Indices: 198124--198153 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
198114 CTTAACATAC
198124 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
198154 GAGCAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:199037 original size:20 final size:20
Alignment explanation
Indices: 199001--199041 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
198991 TTTAGTTGAT
199001 ATAATTAAAATTATTATTTA
1 ATAATTAAAATTATTATTTA
*
199021 ATAA-TAAAATTTTTTATTTA
1 ATAATTAAAA-TTATTATTTA
199041 A
1 A
199042 ATTTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAATTAAAATTATTATTTA
Found at i:199098 original size:49 final size:47
Alignment explanation
Indices: 198974--199103 Score: 108
Period size: 49 Copynumber: 2.7 Consensus size: 47
198964 CGAATCTTAC
* **
198974 ATAAAAATATTAATAATTTTAGTTGATATAATTA-AAATTATTATTTAATA
1 ATAAAAATTTTAATAATTTTA----ATATAATTATAAATTATTAAATAATA
* * * *
199024 AT-AAAATTTT--TTATTTAAATTTAATTATAAATATATATAAATATTA
1 ATAAAAATTTTAATAATTTTAATATAATTATAAAT-TAT-TAAATAATA
199070 ATAAAAATTTTAATAATTTTAATATAATT-TAAAT
1 ATAAAAATTTTAATAATTTTAATATAATTATAAAT
199104 GATAAAAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
43 8 0.12
44 4 0.06
45 3 0.05
46 8 0.12
47 14 0.22
48 5 0.08
49 20 0.31
50 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (47 bp):
ATAAAAATTTTAATAATTTTAATATAATTATAAATTATTAAATAATA
Found at i:199138 original size:16 final size:16
Alignment explanation
Indices: 199117--199154 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
199107 AAAAAAATCA
*
199117 TTAAATTCACTTAAAT
1 TTAAATTAACTTAAAT
*
199133 TTAAATTAATTTAAAT
1 TTAAATTAACTTAAAT
199149 TTAAAT
1 TTAAAT
199155 AATTTTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATTAACTTAAAT
Found at i:204669 original size:49 final size:49
Alignment explanation
Indices: 204603--204697 Score: 163
Period size: 49 Copynumber: 1.9 Consensus size: 49
204593 TTACCACCTG
*
204603 AAAATGTATATATGAGCATATATTCTATGTATGTCCAAACCAATTACCA
1 AAAATGTATATATGAGCATATATTCTAAGTATGTCCAAACCAATTACCA
* *
204652 AAAATGTATATATGAGCATATGTTCTAAGTATGTCCAAACTAATTA
1 AAAATGTATATATGAGCATATATTCTAAGTATGTCCAAACCAATTA
204698 AAACAATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.34
Consensus pattern (49 bp):
AAAATGTATATATGAGCATATATTCTAAGTATGTCCAAACCAATTACCA
Found at i:205554 original size:24 final size:26
Alignment explanation
Indices: 205496--205554 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 26
205486 TAATAAAAAT
205496 TTAATAATTTTAATTGAATTTAATTTAA
1 TTAA-AATTTTAATTGAATTT-ATTTAA
205524 TTAAAATTTTAA-T-AATTT-TTTAAA
1 TTAAAATTTTAATTGAATTTATTT-AA
205548 TTAAAAT
1 TTAAAAT
205555 ATGATGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.10
24 9 0.30
25 5 0.17
26 1 0.03
27 8 0.27
28 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
TTAAAATTTTAATTGAATTTATTTAA
Found at i:215794 original size:22 final size:22
Alignment explanation
Indices: 215769--215810 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
215759 TTAAAAATCA
215769 TTTTATTATAAA-AATAATTTTT
1 TTTTATT-TAAATAATAATTTTT
215791 TTTTATTTAAATAATAATTT
1 TTTTATTTAAATAATAATTT
215811 ATACCGGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTATTTAAATAATAATTTTT
Found at i:217882 original size:3 final size:3
Alignment explanation
Indices: 217874--217903 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
217864 CAAGAAAGGG
217874 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
217904 CCTTTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:218100 original size:23 final size:23
Alignment explanation
Indices: 218069--218121 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
218059 GGAGAAAGAA
*
218069 ATATTTTTTCATAG-ATAAAAAAT
1 ATATATTTTCAT-GTATAAAAAAT
* *
218092 ATATATTTTTATGTATAAAAATT
1 ATATATTTTCATGTATAAAAAAT
218115 ATA-ATTT
1 ATATATTT
218122 AAAAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
ATATATTTTCATGTATAAAAAAT
Found at i:219417 original size:16 final size:15
Alignment explanation
Indices: 219398--219495 Score: 54
Period size: 12 Copynumber: 7.1 Consensus size: 15
219388 AAATTTTTTA
219398 TATTTATAATTAAATT
1 TATTTATAATTAAA-T
*
219414 TATTTAAAAATTAAAT
1 TATTT-ATAATTAAAT
*
219430 TATTTAT--TT-GAT
1 TATTTATAATTAAAT
*
219442 TATTTAT--TTTAAT
1 TATTTATAATTAAAT
*
219455 TTTTTAT-ATTAAA-
1 TATTTATAATTAAAT
*
219468 T-TTTA-AATAAAAT
1 TATTTATAATTAAAT
*
219481 T-TTTATATTTAAAT
1 TATTTATAATTAAAT
219495 T
1 T
219496 TATTGAATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
12 20 0.30
13 16 0.24
14 11 0.16
15 1 0.01
16 11 0.16
17 8 0.12
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (15 bp):
TATTTATAATTAAAT
Found at i:219472 original size:25 final size:24
Alignment explanation
Indices: 219444--219523 Score: 60
Period size: 25 Copynumber: 3.3 Consensus size: 24
219434 TATTTGATTA
219444 TTTATTTTAATTTTTTATATTAAAT
1 TTTATTTTAA-TTTTTATATTAAAT
* **
219469 TTTAAATAAAATTTTTATATTTAAA-
1 TTT-ATTTTAATTTTTATA-TTAAAT
*
219494 TTTA-TTGAA-TTTTAT-TTAAAT
1 TTTATTTTAATTTTTATATTAAAT
219515 TATTATTTT
1 T-TTATTTT
219524 TAAAAAATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
20 5 0.11
21 1 0.02
22 9 0.20
23 5 0.11
24 1 0.02
25 14 0.32
26 9 0.20
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (24 bp):
TTTATTTTAATTTTTATATTAAAT
Found at i:220238 original size:18 final size:19
Alignment explanation
Indices: 220202--220244 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
220192 ATATATAATA
220202 TTATATTTATTATGTAATTTT
1 TTATATTTATTA--TAATTTT
220223 TTATATTTATTA-AATTTT
1 TTATATTTATTATAATTTT
220241 TTAT
1 TTAT
220245 GTTTCAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.45
21 12 0.55
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATATTTATTATAATTTT
Found at i:220541 original size:29 final size:30
Alignment explanation
Indices: 220496--220563 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
220486 TGAATTGTAT
*
220496 TTAAATT-AATTTATTTTAT-TATTTAAAA
1 TTAAATTAAAATTATTTTATATATTTAAAA
* *
220524 TTATATTAAAATTATTTTATATTTTTAAAA
1 TTAAATTAAAATTATTTTATATATTTAAAA
220554 TTAAATTAAA
1 TTAAATTAAA
220564 TTAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 6 0.18
29 11 0.32
30 17 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
TTAAATTAAAATTATTTTATATATTTAAAA
Found at i:220543 original size:34 final size:30
Alignment explanation
Indices: 220488--220576 Score: 81
Period size: 34 Copynumber: 2.9 Consensus size: 30
220478 TTAGAGTTTG
* *
220488 AATTGTATTTAAATTAATTTATTTTATTATTTAA
1 AATTATATTAAAATTAATTTA---TATT-TTTAA
*
220522 AATTATATTAAAATTATTTTATATTTTTAA
1 AATTATATTAAAATTAATTTATATTTTTAA
* * *
220552 AATTAAATT-AAATTAAATTAAATTT
1 AATTATATTAAAATTAATTTATATTT
220577 AAATTTTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
29 13 0.27
30 13 0.27
31 4 0.08
34 18 0.38
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (30 bp):
AATTATATTAAAATTAATTTATATTTTTAA
Found at i:220564 original size:29 final size:28
Alignment explanation
Indices: 220496--220566 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 28
220486 TGAATTGTAT
*
220496 TTAAATTAATTTATTTTATTATTTAAAA
1 TTAAATTAAATTATTTTATTATTTAAAA
* *
220524 TTATATTAAAATTATTTTATATTTTTAAAA
1 TTAAATT-AAATTATTTTAT-TATTTAAAA
220554 TTAAATTAAATTA
1 TTAAATTAAATTA
220567 AATTAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 6 0.16
29 17 0.46
30 14 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TTAAATTAAATTATTTTATTATTTAAAA
Found at i:220582 original size:6 final size:5
Alignment explanation
Indices: 220551--220581 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
220541 TATATTTTTA
220551 AAATT AAATT AAATT AAATT AAATTT AAATT
1 AAATT AAATT AAATT AAATT AAA-TT AAATT
220582 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AAATT
Found at i:220583 original size:35 final size:35
Alignment explanation
Indices: 220521--220588 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
220511 TTATTATTTA
* * * *
220521 AAATTATATTAAAATTATTTTATATTTTTAAAATT
1 AAATTAAATTAAAATTAATTTAAATTTTAAAAATT
220556 AAATTAAATT-AAATTAAATTTAAATTTTAAAAA
1 AAATTAAATTAAAATT-AATTTAAATTTTAAAAA
220589 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 5 0.18
35 23 0.82
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (35 bp):
AAATTAAATTAAAATTAATTTAAATTTTAAAAATT
Found at i:220590 original size:21 final size:21
Alignment explanation
Indices: 220566--220606 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
220556 AAATTAAATT
*
220566 AAATTAAATTTAAATTTTAAA
1 AAATTAAATTTAAAATTTAAA
**
220587 AAATTTTATTTAAAATTTAA
1 AAATTAAATTTAAAATTTAA
220607 TTCGTATAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATTAAATTTAAAATTTAAA
Found at i:220769 original size:3 final size:3
Alignment explanation
Indices: 220761--220791 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
220751 CATAATTCTT
220761 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
220792 ATGGTAATTA
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):
TTA
Found at i:221721 original size:19 final size:19
Alignment explanation
Indices: 221699--221761 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 19
221689 AATTTAATTA
221699 ATATAAAATAAAAAATATT
1 ATATAAAATAAAAAATATT
* *
221718 ATATATAAT-ATAAATA-T
1 ATATAAAATAAAAAATATT
*
221735 ATA-AATATTAAAAAA-ATT
1 ATATAA-AATAAAAAATATT
221753 -TATAAAATA
1 ATATAAAATA
221762 TTTTAAATAA
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
16 1 0.03
17 12 0.35
18 13 0.38
19 8 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATAAAATAAAAAATATT
Found at i:221736 original size:20 final size:19
Alignment explanation
Indices: 221699--221814 Score: 65
Period size: 20 Copynumber: 5.9 Consensus size: 19
221689 AATTTAATTA
* *
221699 ATATAAAATAAAAAATATT
1 ATATATAATAAAATATATT
221718 ATATATAATATAAATATA-T
1 ATATATAATA-AAATATATT
* * * *
221737 AAATATTAAAAAAATTTATA
1 ATATA-TAATAAAATATATT
* * * *
221757 AAATAT-TTTAAATAAAATT
1 ATATATAATAAAAT-ATATT
221776 ATAATATAATAAAATATATAT
1 AT-ATATAATAAAATATAT-T
*
221797 AAATATAATATAAATATA
1 ATATATAATA-AAATATA
221815 CGAGTTATAA
Statistics
Matches: 72, Mismatches: 17, Indels: 14
0.70 0.17 0.14
Matches are distributed among these distances:
18 4 0.06
19 24 0.33
20 30 0.42
21 14 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATATAATAAAATATATT
Found at i:221788 original size:16 final size:14
Alignment explanation
Indices: 221717--221808 Score: 55
Period size: 15 Copynumber: 6.3 Consensus size: 14
221707 TAAAAAATAT
221717 TATATATAATATAAA
1 TATATATAATA-AAA
221732 TATATA-AATATTAAA
1 TATATATAATA--AAA
* * *
221747 AAAAT-TTATAAAA
1 TATATATAATAAAA
*
221760 TAT-TTTAAATAAAA
1 TATATAT-AATAAAA
221774 TTATAATATAATAAAA
1 -TAT-ATATAATAAAA
*
221790 TATATATAAATATAA
1 TATATAT-AATAAAA
221805 TATA
1 TATA
221809 AATATACGAG
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
12 1 0.02
13 5 0.08
14 14 0.23
15 32 0.52
16 7 0.11
17 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATATATAATAAAA
Found at i:221798 original size:11 final size:11
Alignment explanation
Indices: 221717--221814 Score: 50
Period size: 11 Copynumber: 9.4 Consensus size: 11
221707 TAAAAAATAT
*
221717 TATATATAATA
1 TATATATAAAA
*
221728 TAAATATATAAA
1 TATATATA-AAA
221740 TAT-TA-AAAA
1 TATATATAAAA
* *
221749 AATTTATAAAA
1 TATATATAAAA
*
221760 TAT-T-TTAAA
1 TATATATAAAA
* *
221769 TA-AAATTATAA
1 TATATA-TAAAA
221780 TATA-ATAAAA
1 TATATATAAAA
221790 TATATAT-AAA
1 TATATATAAAA
221800 TATA-ATATAAA
1 TATATATA-AAA
221811 TATA
1 TATA
221815 CGAGTTATAA
Statistics
Matches: 67, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
9 13 0.19
10 19 0.28
11 30 0.45
12 5 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TATATATAAAA
Found at i:222136 original size:31 final size:31
Alignment explanation
Indices: 222098--222158 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
222088 ATTTTTTTAA
* *
222098 TATTTAAATAAAATTTTTAATTTTTAATTTT
1 TATTTAAATAAAATTTTAAATATTTAATTTT
*
222129 TATTTAAATAATATTTTAAATATTTAATTT
1 TATTTAAATAAAATTTTAAATATTTAATTT
222159 ATATCCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TATTTAAATAAAATTTTAAATATTTAATTTT
Found at i:222415 original size:2 final size:2
Alignment explanation
Indices: 222410--222441 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
222400 AGAGAGTCTT
222410 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
222442 AAAGTAAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:222572 original size:42 final size:42
Alignment explanation
Indices: 222491--222578 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
222481 ATTTTACCAA
222491 TTTTCATAATTTTATATACGGTTAATATATTAATAAACTGAT
1 TTTTCATAATTTTATATACGGTTAATATATTAATAAACTGAT
*
222533 TTTTCATAATTTTATATACTGTTAATATATTAATAAACTGAT
1 TTTTCATAATTTTATATACGGTTAATATATTAATAAACTGAT
222575 TTTT
1 TTTT
222579 AGATTAAACA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (42 bp):
TTTTCATAATTTTATATACGGTTAATATATTAATAAACTGAT
Found at i:222881 original size:2 final size:2
Alignment explanation
Indices: 222868--222911 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
222858 TTAAATCTTT
* *
222868 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
222910 TA
1 TA
222912 ATAGTTAGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:223396 original size:20 final size:20
Alignment explanation
Indices: 223349--223389 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
223339 TAAGAGATCG
* *
223349 ATCTTTCTTTAAAAAATCGAT
1 ATCTTT-TTAAAAAAATCAAT
223370 ATCTTTTTAAAAAAATCAAT
1 ATCTTTTTAAAAAAATCAAT
223390 CACTTTTGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.41
Consensus pattern (20 bp):
ATCTTTTTAAAAAAATCAAT
Found at i:224112 original size:22 final size:22
Alignment explanation
Indices: 224073--224114 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
224063 AATTAAATTC
**
224073 AAATAAAAATTTTTATTAATAT
1 AAATAAAAATTTAAATTAATAT
*
224095 AAATAATAATTTAAATTAAT
1 AAATAAAAATTTAAATTAAT
224115 TCGAACCTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATAAAAATTTAAATTAATAT
Found at i:227118 original size:30 final size:30
Alignment explanation
Indices: 227083--227139 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
227073 AAAGATGGTA
227083 TTTTAAGAAAGTTAAACTTGCATATAATAT
1 TTTTAAGAAAGTTAAACTTGCATATAATAT
227113 TTTTAAGAAAGTTAAACTTGCATATAA
1 TTTTAAGAAAGTTAAACTTGCATATAA
227140 GAACCAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.39
Consensus pattern (30 bp):
TTTTAAGAAAGTTAAACTTGCATATAATAT
Found at i:231549 original size:22 final size:23
Alignment explanation
Indices: 231524--231570 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
231514 TTTTTTTTCG
231524 ATATGATTT-AATTTT-TATATTT
1 ATAT-ATTTAAATTTTATATATTT
231546 ATATATTTAAAATTTTATATATTT
1 ATATATTT-AAATTTTATATATTT
231570 A
1 A
231571 AAAAATAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 4 0.18
23 6 0.27
24 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
ATATATTTAAATTTTATATATTT
Found at i:231576 original size:18 final size:16
Alignment explanation
Indices: 231543--231573 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
231533 AATTTTTATA
231543 TTTATATATTTAAAAT
1 TTTATATATTTAAAAT
231559 TTTATATATTTAAAA
1 TTTATATATTTAAAA
231574 AATAATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTATATATTTAAAAT
Found at i:231645 original size:16 final size:17
Alignment explanation
Indices: 231561--231640 Score: 53
Period size: 18 Copynumber: 4.8 Consensus size: 17
231551 TTTAAAATTT
231561 TATATATTTAA--AAAA
1 TATATATTTAATTAAAA
231576 TA-AT-TTTAATATAAAA
1 TATATATTTAAT-TAAAA
* * * *
231592 TAAATA-TTAAATATGAT
1 TATATATTTAATTA-AAA
231609 TAATATATTTAATTACAAA
1 T-ATATATTTAATTA-AAA
231628 TATATATTTAATT
1 TATATATTTAATT
231641 TAATAAAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 13
0.70 0.11 0.19
Matches are distributed among these distances:
13 5 0.10
14 2 0.04
15 2 0.04
16 8 0.16
17 8 0.16
18 16 0.33
19 8 0.16
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (17 bp):
TATATATTTAATTAAAA
Found at i:232740 original size:33 final size:30
Alignment explanation
Indices: 232682--232741 Score: 84
Period size: 33 Copynumber: 1.9 Consensus size: 30
232672 ATTTTTTAAA
*
232682 ATCAAAATATTTAAAATTCTAATTTAAGTT
1 ATCAAAATATTTAAAATTATAATTTAAGTT
232712 ATCAAATATATCTTAAAATATATAATTTAA
1 ATCAAA-ATAT-TTAAAAT-TATAATTTAA
232742 AAATAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 6 0.23
31 4 0.15
32 7 0.27
33 9 0.35
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.42
Consensus pattern (30 bp):
ATCAAAATATTTAAAATTATAATTTAAGTT
Found at i:233273 original size:23 final size:22
Alignment explanation
Indices: 233225--233270 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
233215 AATATTATAC
*
233225 ATTTAATTATTTTTATTAATTAA
1 ATTTAATTATTTTAATT-ATTAA
233248 ATTTAATTATTTTAAATT-TTAA
1 ATTTAATTATTTT-AATTATTAA
233270 A
1 A
233271 ATTATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 13 0.62
24 3 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTAATTATTTTAATTATTAA
Found at i:233379 original size:13 final size:14
Alignment explanation
Indices: 233346--233414 Score: 53
Period size: 13 Copynumber: 5.4 Consensus size: 14
233336 TTTGAATTCA
*
233346 AATCAATCAAATTT
1 AATCAATTAAATTT
233360 AAT-AATTAAA-TT
1 AATCAATTAAATTT
**
233372 AATCAATT---TCG
1 AATCAATTAAATTT
233383 AATCAATTAAATTT
1 AATCAATTAAATTT
*
233397 AAT-ATTTAAATTT
1 AATCAATTAAATTT
233410 -ATCAA
1 AATCAA
233415 ATTTGATCAT
Statistics
Matches: 42, Mismatches: 7, Indels: 13
0.68 0.11 0.21
Matches are distributed among these distances:
11 8 0.19
12 7 0.17
13 20 0.48
14 7 0.17
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.41
Consensus pattern (14 bp):
AATCAATTAAATTT
Found at i:233468 original size:16 final size:16
Alignment explanation
Indices: 233425--233480 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
233415 ATTTGATCAT
*
233425 TTTAAATTAATTTAAA
1 TTTAAATTATTTTAAA
* * **
233441 TTTTAATAATTTTGTA
1 TTTAAATTATTTTAAA
233457 TTTAAATTATTTTAAA
1 TTTAAATTATTTTAAA
233473 TTTAAATT
1 TTTAAATT
233481 TATCATTGTG
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:233628 original size:21 final size:21
Alignment explanation
Indices: 233603--233646 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
233593 CGTATTTAAA
*
233603 ATATTTACATCAATAAATCAT
1 ATATTTACATCAATAAACCAT
*
233624 ATATTTACATCATTAAACCAT
1 ATATTTACATCAATAAACCAT
233645 AT
1 AT
233647 TTAATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (21 bp):
ATATTTACATCAATAAACCAT
Found at i:233935 original size:29 final size:29
Alignment explanation
Indices: 233903--233959 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
233893 AACTTATATA
233903 TAAAAATAATAATATTTT-A-TAATTAAAAT
1 TAAAAA-AAT-ATATTTTCATTAATTAAAAT
*
233932 TAAATAAATATATTTTCATTAATTAAAA
1 TAAAAAAATATATTTTCATTAATTAAAA
233960 ACAAGCTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 7 0.28
28 4 0.16
29 14 0.56
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
TAAAAAAATATATTTTCATTAATTAAAAT
Found at i:233944 original size:27 final size:29
Alignment explanation
Indices: 233906--233959 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
233896 TTATATATAA
233906 AAATAATAATATTTT-A-TAATTAAAATT
1 AAATAATAATATTTTCATTAATTAAAATT
233933 AAATAA-ATATATTTTCATTAATTAAAA
1 AAATAATA-ATATTTTCATTAATTAAAA
233960 ACAAGCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 1 0.04
27 13 0.54
28 1 0.04
29 9 0.38
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
AAATAATAATATTTTCATTAATTAAAATT
Found at i:234081 original size:21 final size:21
Alignment explanation
Indices: 234055--234094 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
234045 ATTAAAAAAT
234055 TATTTT-TAATTAATATTTATA
1 TATTTTATAATTAA-ATTTATA
234076 TATTTTATAATTAAATTTA
1 TATTTTATAATTAAATTTA
234095 AATAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTATAATTAAATTTATA
Found at i:234482 original size:3 final size:3
Alignment explanation
Indices: 234474--234513 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
234464 ATTCAAATGC
234474 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
234514 GATTGTTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:236281 original size:2 final size:2
Alignment explanation
Indices: 236274--236306 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
236264 TATTATCATT
236274 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 A
236307 AACAAAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:240538 original size:2 final size:2
Alignment explanation
Indices: 240531--240566 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
240521 TCCCTAATGA
240531 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
240567 TTCTTAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:243072 original size:19 final size:20
Alignment explanation
Indices: 243048--243089 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
243038 TTTGCATAGT
243048 CTCATTACTC-AGTCATGCA
1 CTCATTACTCAAGTCATGCA
243067 CTCATTACTCATAGTCATGCA
1 CTCATTACTCA-AGTCATGCA
243088 CT
1 CT
243090 GCTAAGACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.48
21 11 0.52
ACGTcount: A:0.26, C:0.31, G:0.10, T:0.33
Consensus pattern (20 bp):
CTCATTACTCAAGTCATGCA
Found at i:244759 original size:2 final size:2
Alignment explanation
Indices: 244752--244776 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
244742 CGTTCAAGGT
244752 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
244777 TGATAATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:245029 original size:19 final size:19
Alignment explanation
Indices: 244993--245031 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
244983 AATTTTAAAT
244993 TATAAAAAATTTAGATTTAA
1 TATAAAAAATTTA-ATTTAA
245013 TATAAAATAATTT-ATTTAA
1 TATAAAA-AATTTAATTTAA
245032 ATTTATTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
TATAAAAAATTTAATTTAA
Found at i:246004 original size:26 final size:25
Alignment explanation
Indices: 245969--246018 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
245959 ATAAATTATT
245969 AAAATAAATTATAAT-ATATTTATATA
1 AAAATAAATTAT--TCATATTTATATA
*
245995 AAAATCAATTATTCATATTTATAT
1 AAAATAAATTATTCATATTTATAT
246019 TATTTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 1 0.05
25 10 0.45
26 11 0.50
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (25 bp):
AAAATAAATTATTCATATTTATATA
Found at i:246514 original size:18 final size:18
Alignment explanation
Indices: 246491--246525 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
246481 TGAGTAATTC
*
246491 ATTTAAAATATGATTAAA
1 ATTTAAAATATAATTAAA
*
246509 ATTTAAGATATAATTAA
1 ATTTAAAATATAATTAA
246526 TTAATCGTAT
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:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
ATTTAAAATATAATTAAA
Found at i:246718 original size:19 final size:20
Alignment explanation
Indices: 246691--246729 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
246681 TATAGAAATT
* *
246691 ATAATTAAATATTATTTTAA
1 ATAATTAAACACTATTTTAA
246711 ATAA-TAAACACTATTTTAA
1 ATAATTAAACACTATTTTAA
246730 GCATTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
ATAATTAAACACTATTTTAA
Found at i:247339 original size:20 final size:20
Alignment explanation
Indices: 247314--247355 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
247304 TATACTTATA
*
247314 TAAGTTTTTAAATTTTAATT
1 TAAGTTTATAAATTTTAATT
*
247334 TAAGTTTATAATTTTTAATT
1 TAAGTTTATAAATTTTAATT
247354 TA
1 TA
247356 TACTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (20 bp):
TAAGTTTATAAATTTTAATT
Found at i:247756 original size:38 final size:40
Alignment explanation
Indices: 247666--247759 Score: 113
Period size: 38 Copynumber: 2.4 Consensus size: 40
247656 TAATATAATA
* *
247666 TATATGATGTAATATATTTAATAATTTATTATATTTATGTT
1 TATATTAT-TAATATATTTAATAATTTATTATATTTATATT
* *
247707 TAAAATT-TTAATATA-TTAATAATTT-TTTTATTTATATT
1 T-ATATTATTAATATATTTAATAATTTATTATATTTATATT
247745 TATATTATTAATATA
1 TATATTATTAATATA
247760 AAAATATAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
37 4 0.09
38 20 0.43
39 10 0.22
40 7 0.15
41 2 0.04
42 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (40 bp):
TATATTATTAATATATTTAATAATTTATTATATTTATATT
Found at i:247998 original size:20 final size:18
Alignment explanation
Indices: 247957--247999 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
247947 ATTATTCAAC
*
247957 ATTTTTAATTAATTAATT
1 ATTTTTAATTAATTAATA
*
247975 ATTTTTATTTAAATTTAATA
1 ATTTTTAATT-AA-TTAATA
247995 ATTTT
1 ATTTT
248000 AATATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 2 0.10
20 10 0.48
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTAATTAATTAATA
Found at i:248095 original size:22 final size:23
Alignment explanation
Indices: 248061--248105 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
248051 TTTTAATAAA
*
248061 TTAATAATTTTTAT-TATATAATT
1 TTAATAATATTTATAT-TATAATT
248084 TTAA-AATATTTATATTATAATT
1 TTAATAATATTTATATTATAATT
248106 ATATCATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TTAATAATATTTATATTATAATT
Found at i:250363 original size:2 final size:2
Alignment explanation
Indices: 250358--250400 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
250348 TGCGTGTATG
* *
250358 TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
250400 T
1 T
250401 GCGAACTGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:252274 original size:26 final size:26
Alignment explanation
Indices: 252238--252287 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
252228 TAGATGGATA
**
252238 AGTAATAGTCTAGGAAGAAAAAGATG
1 AGTAATAGTCTAAAAAGAAAAAGATG
252264 AGTAATAGTCTAAAAAGAAAAAGA
1 AGTAATAGTCTAAAAAGAAAAAGA
252288 GGAAAGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.18
Consensus pattern (26 bp):
AGTAATAGTCTAAAAAGAAAAAGATG
Found at i:252602 original size:2 final size:2
Alignment explanation
Indices: 252537--252589 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
252527 GCTACAATCT
252537 TA TA -A TA TA TA TA TA TA TA TA TA TA -A TA TA -A TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
252575 TA CA TA TA TA CA TA T
1 TA TA TA TA TA TA TA T
252590 GTGTGTGTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
1 4 0.09
2 39 0.91
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Done.