Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2039
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: 245426
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
File 2 of 2
Found at i:115815 original size:28 final size:27
Alignment explanation
Indices: 115760--115830 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
115750 GCCACCCATT
115760 TATTTGTCAAAAATGGTGGTTATTTTG
1 TATTTGTCAAAAATGGTGGTTATTTTG
*
115787 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TATTTGTCAAAAATGGTGGTTAT--TTTG
*
115815 TATTTGTCAAATATGG
1 TATTTGTCAAAAATGG
115831 AGGCTTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (27 bp):
TATTTGTCAAAAATGGTGGTTATTTTG
Found at i:117148 original size:16 final size:16
Alignment explanation
Indices: 117136--117166 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
117126 GTTTTTTGAG
117136 TTCGGGTTCTTTTGGT
1 TTCGGGTTCTTTTGGT
*
117152 TTTGGGTTCTTTTGG
1 TTCGGGTTCTTTTGG
117167 GTTGACCATT
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:0.00, C:0.10, G:0.32, T:0.58
Consensus pattern (16 bp):
TTCGGGTTCTTTTGGT
Found at i:118238 original size:25 final size:28
Alignment explanation
Indices: 118192--118252 Score: 83
Period size: 25 Copynumber: 2.3 Consensus size: 28
118182 AATATTGTCT
* *
118192 TTTTCAATATATATTTAATAGTT-GA-A
1 TTTTCAATATAAAATTAATAGTTAGACA
118218 TTTTCAA-ATAAAATTAATAGTTAGACA
1 TTTTCAATATAAAATTAATAGTTAGACA
118245 TTTTCAAT
1 TTTTCAAT
118253 TTACTTGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 13 0.43
26 9 0.30
27 8 0.27
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (28 bp):
TTTTCAATATAAAATTAATAGTTAGACA
Found at i:120923 original size:25 final size:26
Alignment explanation
Indices: 120893--120951 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
120883 AATCTATATA
* * *
120893 ATATAAATTTTTAATAT-ATCAAAAT
1 ATATAAATCTTAAACATAATCAAAAT
*
120918 ATATAATATCTTAAACATAATTAAAAT
1 ATATAA-ATCTTAAACATAATCAAAAT
120945 ATATAAA
1 ATATAAA
120952 AACGATATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
25 6 0.21
26 9 0.32
27 13 0.46
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (26 bp):
ATATAAATCTTAAACATAATCAAAAT
Found at i:123301 original size:160 final size:158
Alignment explanation
Indices: 123121--123463 Score: 411
Period size: 160 Copynumber: 2.2 Consensus size: 158
123111 TCAATGGGTA
** *
123121 AATGATAAAAGAGAATAAAGTGCAAAGTGATTTATGTCTTCT-AAA-CTAAAAAGAAAAAATAAA
1 AATGATAAAAGAGAATAAAGTAAAAAGTGATTTATGTCTTCTAAAATCTAAAAA-AAAAAAGAAA
* * * * * * *
123184 ATAAAAAGAAGATTGATAACATTTGAATGGTAAGATATGCTTCTATTTGATAACATTTTCGTGAT
65 AGAAAAAAAAGATTAATAACATTTGAAT-GAAAAATATGCTTATATTTGATAACATTTTCATGA-
*
123249 CCATTGCTTGTTAGTAGGGAATGCTTTAGAGC
128 CCATT-CTTGTTAGTAGGGAATGCTTTAGAAC
* * * * * * *
123281 AATGGTAAAAGAGAATAAAGTAAAAAGTTATTTATGTCTTTTAAAATTTTAAAAAACAAAGGAAA
1 AATGATAAAAGAGAATAAAGTAAAAAGTGATTTATGTCTTCTAAAATCTAAAAAAAAAAAGAAAA
* *
123346 GAAAAAAAATATTAATAACATTTGAATGAAAAATATGCTTATATTTGATATCATTTTCATGACCA
66 GAAAAAAAAGATTAATAACATTTGAATGAAAAATATGCTTATATTTGATAACATTTTCATGACCA
* * *
123411 TTCTTGTTGGTAGGGAATTCTTTATAAC
131 TTCTTGTTAGTAGGGAATGCTTTAGAAC
* *
123439 AATAATAAAAGAGAATAAATTAAAA
1 AATGATAAAAGAGAATAAAGTAAAA
123464 TGCTTTAGAT
Statistics
Matches: 155, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
158 44 0.28
159 5 0.03
160 67 0.43
161 34 0.22
162 5 0.03
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.32
Consensus pattern (158 bp):
AATGATAAAAGAGAATAAAGTAAAAAGTGATTTATGTCTTCTAAAATCTAAAAAAAAAAAGAAAA
GAAAAAAAAGATTAATAACATTTGAATGAAAAATATGCTTATATTTGATAACATTTTCATGACCA
TTCTTGTTAGTAGGGAATGCTTTAGAAC
Found at i:124065 original size:30 final size:29
Alignment explanation
Indices: 124005--124065 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 29
123995 ATGTTTTGCT
* *
124005 TATAAATAAAATGTATATATAATTTTTTTA
1 TATAAATAAAA-GTATATAAAATTTATTTA
124035 TATAAATTAAAA-TATATAAAATATTATTTA
1 TATAAA-TAAAAGTATATAAAAT-TTATTTA
124065 T
1 T
124066 TTGATATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 9 0.33
30 13 0.48
31 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
TATAAATAAAAGTATATAAAATTTATTTA
Found at i:124751 original size:3 final size:3
Alignment explanation
Indices: 124745--124775 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
124735 AAAAAAACCC
124745 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
124776 TATGAACTTA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:125305 original size:158 final size:161
Alignment explanation
Indices: 125130--125422 Score: 416
Period size: 158 Copynumber: 1.8 Consensus size: 161
125120 CTCAATGGAT
* * ** *
125130 AAATGATAGAAGAGAATAAAATAAAAAGTAATTTATGTCCACTAAAA-TAAAGGGAAAAAATAAA
1 AAATGATAAAAGAGAATAAAATAAAAAATAATTTATGTCCACTAAAATTAAAAAGAAAAAAGAAA
**
125194 ATA-AAAAG-AAGATTGATAACATTTGAAT-GGAAATATGCATT-TATTTGATAACATTTTCATG
66 A-AGAAAAGAAAGATTGATAACATTTGAATAAAAAATATGC-TTCTATTTGATAACATTTTCATG
125255 ATCCATTACTTATTAGTAGGGAATGCTTTAGAG
129 ATCCATTACTTATTAGTAGGGAATGCTTTAGAG
* * * *
125288 AAATGGTAAAAGAGAATAAAGTAAAAAATTATTTATGTCCTCTAAAATTAAAAAGAAAAAAGAAA
1 AAATGATAAAAGAGAATAAAATAAAAAATAATTTATGTCCACTAAAATTAAAAAGAAAAAAGAAA
* *
125353 AAGAAAAGAAAGATTGATGACATTTGAATAAAAAATATGCTTCTATTTGATATCATTTTCATGAT
66 AAGAAAAGAAAGATTGATAACATTTGAATAAAAAATATGCTTCTATTTGATAACATTTTCATGAT
125418 CCATT
131 CCATT
125423 GCTTTCTGGT
Statistics
Matches: 117, Mismatches: 13, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
158 42 0.36
159 20 0.17
160 21 0.18
161 34 0.29
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.30
Consensus pattern (161 bp):
AAATGATAAAAGAGAATAAAATAAAAAATAATTTATGTCCACTAAAATTAAAAAGAAAAAAGAAA
AAGAAAAGAAAGATTGATAACATTTGAATAAAAAATATGCTTCTATTTGATAACATTTTCATGAT
CCATTACTTATTAGTAGGGAATGCTTTAGAG
Found at i:125743 original size:21 final size:21
Alignment explanation
Indices: 125702--125744 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
125692 AGAACTTAAC
* *
125702 ACTAGAACTATGGAATATAAA
1 ACTAGAACAATGGAAGATAAA
125723 ACTA-AACAATGGAAGAGTAAA
1 ACTAGAACAATGGAAGA-TAAA
125744 A
1 A
125745 AAAAAAGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.19
Consensus pattern (21 bp):
ACTAGAACAATGGAAGATAAA
Found at i:125893 original size:3 final size:3
Alignment explanation
Indices: 125887--125934 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
125877 CTAAAAAAAT
*
125887 TAA TAA TAA TAA TAA TAA TCA TAA TAA TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
125933 TA
1 TA
125935 TTGTCCTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:126027 original size:18 final size:18
Alignment explanation
Indices: 126001--126036 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
125991 GAAATATGGC
126001 TTATCTTTTCTTAATTTT
1 TTATCTTTTCTTAATTTT
* *
126019 TTATTTTTTCTTTATTTT
1 TTATCTTTTCTTAATTTT
126037 CTCTATTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (18 bp):
TTATCTTTTCTTAATTTT
Found at i:126942 original size:15 final size:17
Alignment explanation
Indices: 126908--126942 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
126898 TGAAGAATTC
126908 TATTTTACTTTTACATA
1 TATTTTACTTTTACATA
126925 TATTTT-CTTTTA-ATA
1 TATTTTACTTTTACATA
126940 TAT
1 TAT
126943 GAAATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 6 0.33
17 6 0.33
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTTACTTTTACATA
Found at i:128039 original size:132 final size:135
Alignment explanation
Indices: 127799--128039 Score: 321
Period size: 132 Copynumber: 1.8 Consensus size: 135
127789 GACAATAAAC
127799 AATAAAGTAAAAAGTTATATATGTTGTCTAAAATAAAAAGAAAAAAAAAAGAAGAAGAATAATCT
1 AATAAAGTAAAAAGTTATATATGTTGTCTAAAATAAAAAGAAAAAAAAAAGAAGAAGAATAATCT
* * * *
127864 TTGAATGAAAATATGCTTCTCTTTGGTAATATTTTCATGATCCAATGTTTGTTAGGCAATAATAA
66 TTGAATGAAAATATGCTTATATTTGATAACATTTTCATGATCCAATGTTTGTTAGGCAATAATAA
127929 AAAAG
131 AAAAG
* * * * **
127934 AATAAAGTAAAAAGTTATTTATGTCT-TCTAAAAT-AAAA-TAAAAGAAAA-AATATTAATAA-C
1 AATAAAGTAAAAAGTTATATATGT-TGTCTAAAATAAAAAGAAAAAAAAAAGAAGAAGAATAATC
* *
127994 ATTTGAATGAAAATATGGTTATATTTGATACCATTTTCATGATCCA
65 -TTTGAATGAAAATATGCTTATATTTGATAACATTTTCATGATCCA
128040 TTGCTTGTAG
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
131 1 0.01
132 47 0.51
133 8 0.09
134 4 0.04
135 31 0.34
136 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (135 bp):
AATAAAGTAAAAAGTTATATATGTTGTCTAAAATAAAAAGAAAAAAAAAAGAAGAAGAATAATCT
TTGAATGAAAATATGCTTATATTTGATAACATTTTCATGATCCAATGTTTGTTAGGCAATAATAA
AAAAG
Found at i:130099 original size:22 final size:23
Alignment explanation
Indices: 130071--130124 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
130061 AAATTTGACA
*
130071 TATTTTATATTTATGTTGTAT-T
1 TATTTTATATTTATGTCGTATCT
*
130093 TATTTTATTTTTATGTCGTATCT
1 TATTTTATATTTATGTCGTATCT
*
130116 CATTTTATA
1 TATTTTATA
130125 CTATGTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.22, C:0.06, G:0.07, T:0.65
Consensus pattern (23 bp):
TATTTTATATTTATGTCGTATCT
Found at i:134722 original size:22 final size:22
Alignment explanation
Indices: 134696--134738 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
134686 AAATTTTATT
134696 TAAAT-TGAATTATAAAAATATA
1 TAAATATGAA-TATAAAAATATA
*
134718 TAAATATTAATATAAAAATAT
1 TAAATATGAATATAAAAATAT
134739 TATTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TAAATATGAATATAAAAATATA
Found at i:135933 original size:31 final size:30
Alignment explanation
Indices: 135884--135942 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
135874 AATTAAATAA
* *
135884 ATTTTTAATAATTATTATTATTATATTTTT
1 ATTTTAAATAAATATTATTATTATATTTTT
135914 ATTTTAAATAAATATTTATTATTATATTT
1 ATTTTAAATAAATA-TTATTATTATATTT
135943 CATTACACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (30 bp):
ATTTTAAATAAATATTATTATTATATTTTT
Found at i:136128 original size:2 final size:2
Alignment explanation
Indices: 136123--136153 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
136113 ACACACACAC
136123 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 A
136154 AATGGATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:137633 original size:148 final size:146
Alignment explanation
Indices: 137364--137683 Score: 412
Period size: 148 Copynumber: 2.2 Consensus size: 146
137354 CCAATGCTTG
* * * * *
137364 TTGAGCAATGATAAAAGAGAATAAAGTACAACATAATTTATGTCCTCTAAAATAGAAGGAAAAAA
1 TTGAGCAATGATAAAAGAGAATAAAGCAAAAAATAATTTATATCCTCTAAAATAGAAGAAAAAAA
*
137429 AAAGATTCATAACATTTGAATGGAAATATGTTTTCATTTGATAACATTTTCATGATCCATTGCTT
66 AAAGATTCATAACATTTGAATGAAAATATGTTTTCATTTGATAACATTTTCATGATCCATTGCTT
*
137494 GTTAGTAGGGAATACT
131 GTTAGTAGGAAATACT
* * * *
137510 TTAGAGCAATGGTAAAAGAGAATAAAGCAAAAAAGTTATTTATATCCTTTAAAATAGGAGAAAAA
1 TT-GAGCAATGATAAAAGAGAATAAAGCAAAAAA-TAATTTATATCCTCTAAAATAGAAGAAAAA
* * *
137575 AAAAAGATTGATAACATTTGAATTAAAATAT-TCTTAT-ATTTTAT-ACTATTTTCATGATCCAT
64 AAAAAGATTCATAACATTTGAATGAAAATATGT-TT-TCATTTGATAAC-ATTTTCATGATCCAT
* *
137637 TGCTTGTTGGTAGGAAATTCT
126 TGCTTGTTAGTAGGAAATACT
*
137658 TTGTAACAATGATAAAAGAGAATAAA
1 TTG-AGCAATGATAAAAGAGAATAAA
137684 TTAAAATGCT
Statistics
Matches: 150, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
146 2 0.01
147 31 0.21
148 116 0.77
149 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (146 bp):
TTGAGCAATGATAAAAGAGAATAAAGCAAAAAATAATTTATATCCTCTAAAATAGAAGAAAAAAA
AAAGATTCATAACATTTGAATGAAAATATGTTTTCATTTGATAACATTTTCATGATCCATTGCTT
GTTAGTAGGAAATACT
Found at i:138622 original size:22 final size:22
Alignment explanation
Indices: 138596--138638 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
138586 AAATTTTATT
*
138596 TAAAT-TTAATTATAAACATATA
1 TAAATATTAA-TATAAAAATATA
138618 TAAATATTAATATAAAAATAT
1 TAAATATTAATATAAAAATAT
138639 TATTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:139594 original size:2 final size:2
Alignment explanation
Indices: 139587--139619 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
139577 TTACTAGGTG
*
139587 TA TA TA TA TA CA 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 TA TA T
139620 TAATTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:140024 original size:2 final size:2
Alignment explanation
Indices: 140017--140059 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
140007 ATGGATATTA
140017 AT AT AT 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 AT AT AT
140059 A
1 A
140060 AACGGATTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:141526 original size:147 final size:150
Alignment explanation
Indices: 141329--141731 Score: 494
Period size: 147 Copynumber: 2.7 Consensus size: 150
141319 ATAAAAAGGA
** * * *
141329 AACATTTGAACGGAAATATGCCTCTATTTGATAATATTTTCATGATCCATTGCTTGTTACTAGGG
1 AACATTTGAATAGAAATATGCTTCTATTTGATAACATTTTCATGATCCATTGCTTGTTAGTAGGG
* * *
141394 GATGCTTTAGAGCAATGGTAAAAGAGAATAAAGTAAAAAAATTATTCATGTCCTCTAAAATT-AA
66 AATGCTTTAGAGCAATGGTAAAAGAGAATAAAATAAAAAAATTATTCATGTCCCCTAAAATTAAA
*
141458 AAAA-ACAA-AAAGATTCAT
131 AAAAGAAAAGAAAGATTCAT
*
141476 AACATTTGAATAGAAATATACTTCTATTTGATAACATTTTCATGATCCATTGCTTGTTAGTAGGG
1 AACATTTGAATAGAAATATGCTTCTATTTGATAACATTTTCATGATCCATTGCTTGTTAGTAGGG
* *
141541 AATGCTTTAGAGCAATGGTAAAAGAGAATAAAAT-AAAAAGTTATTTATGTCCCCTAAAATTAAA
66 AATGCTTTAGAGCAATGGTAAAAGAGAATAAAATAAAAAAATTATTCATGTCCCCTAAAATT---
*
141605 AACAAAAAAGAAAAGAAAGATTGAT
128 -A-AAAAAAGAAAAGAAAGATTCAT
* * * * *
141630 AACATTTGAATGAAAAATATGCTTATATTTGATATCATTTTCGTGA-CCATT-CTTGTTGGTAGG
1 AACATTTGAAT-AGAAATATGCTTCTATTTGATAACATTTTCATGATCCATTGCTTGTTAGTAGG
* * * ** *
141693 GAATTCTTTATAACAATAATAAAAGAGAATAAATTAAAA
65 GAATGCTTTAGAGCAATGGTAAAAGAGAATAAAATAAAA
141732 TGCTTTAGAT
Statistics
Matches: 221, Mismatches: 25, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
146 24 0.11
147 91 0.41
152 6 0.03
153 43 0.19
154 28 0.13
155 29 0.13
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (150 bp):
AACATTTGAATAGAAATATGCTTCTATTTGATAACATTTTCATGATCCATTGCTTGTTAGTAGGG
AATGCTTTAGAGCAATGGTAAAAGAGAATAAAATAAAAAAATTATTCATGTCCCCTAAAATTAAA
AAAAGAAAAGAAAGATTCAT
Found at i:144184 original size:18 final size:19
Alignment explanation
Indices: 144161--144199 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
144151 ATCAGTAATT
144161 ATCTTTAAAAG-ATTAAAA
1 ATCTTTAAAAGTATTAAAA
*
144179 ATCTTTAAAAGTTTTAAAA
1 ATCTTTAAAAGTATTAAAA
144198 AT
1 AT
144200 GAAAAATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (19 bp):
ATCTTTAAAAGTATTAAAA
Found at i:145082 original size:156 final size:156
Alignment explanation
Indices: 144789--145090 Score: 383
Period size: 156 Copynumber: 1.9 Consensus size: 156
144779 TAAATGATAG
* * *
144789 AAGAGAATAAAATACAAAGTAATTTATATCCTCTAAAATAAAGGGAAAAAATAAAATAAAAAGAA
1 AAGAGAATAAAATAAAAAGTAATTTATATCCTCTAAAATAAA--GAAAAAAGAAAAGAAAAAGAA
* * * *
144854 GATTGACAACATTTGAATGGAAATATGCATCTATTTGATAACATTTTCATGATCAATTGCTTATT
64 GATTAACAACATTTGAATGAAAAAATACATCTATTTGATAACATTTTCATGATCAATTGCTTATT
144919 AGTAGGGAATGCTTTACGGCAATGGTAA
129 AGTAGGGAATGCTTTACGGCAATGGTAA
* * * **
144947 AAGAGAATAAAGTAAAAAGTTATTTATGTCCTCTAAAATTTA-AAAAAAGAAAAG-AAAAGAAAG
1 AAGAGAATAAAATAAAAAGTAATTTATATCCTCTAAAATAAAGAAAAAAGAAAAGAAAAAG-AAG
* * * * *
145010 ATTAATAACATTTGAATGAAAAAAATACTTCTATTTGATATCATTTTCATGATCTATTGCTTGTT
65 ATTAACAACATTTGAATG-AAAAAATACATCTATTTGATAACATTTTCATGATCAATTGCTTATT
* *
145075 GGTAGGGAATTCTTTA
129 AGTAGGGAATGCTTTA
145091 TAACAATGAG
Statistics
Matches: 123, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
154 5 0.04
155 29 0.24
156 53 0.43
158 36 0.29
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (156 bp):
AAGAGAATAAAATAAAAAGTAATTTATATCCTCTAAAATAAAGAAAAAAGAAAAGAAAAAGAAGA
TTAACAACATTTGAATGAAAAAATACATCTATTTGATAACATTTTCATGATCAATTGCTTATTAG
TAGGGAATGCTTTACGGCAATGGTAA
Found at i:145385 original size:21 final size:20
Alignment explanation
Indices: 145348--145386 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
145338 CTTGACACTA
* *
145348 AAACCATGGAATATAAAACT
1 AAACAATGGAAGATAAAACT
145368 AAACAATGGAAGAGTAAAA
1 AAACAATGGAAGA-TAAAA
145387 AAAAAAGCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.59, C:0.10, G:0.15, T:0.15
Consensus pattern (20 bp):
AAACAATGGAAGATAAAACT
Found at i:145535 original size:3 final size:3
Alignment explanation
Indices: 145527--145565 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
145517 TCTAAAAAAT
*
145527 TAA TAA TAA TAA AAA TAA TAA TAA TAA TAA TATA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA
145566 CTGTCCTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:145659 original size:17 final size:18
Alignment explanation
Indices: 145632--145666 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
145622 GAAATATAGC
145632 TTATCTTTTCTTAATTTT
1 TTATCTTTTCTTAATTTT
*
145650 TTAT-TTTTCTTTATTTT
1 TTATCTTTTCTTAATTTT
145667 CTCTATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (18 bp):
TTATCTTTTCTTAATTTT
Found at i:149133 original size:24 final size:24
Alignment explanation
Indices: 149106--149156 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
149096 TTCTTGTGTC
149106 ATGAATCTTTGGTTGATTCTATAT
1 ATGAATCTTTGGTTGATTCTATAT
149130 ATGAATCTTTGGTTGATTCTATAT
1 ATGAATCTTTGGTTGATTCTATAT
149154 ATG
1 ATG
149157 TTCCTTCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.08, G:0.18, T:0.49
Consensus pattern (24 bp):
ATGAATCTTTGGTTGATTCTATAT
Found at i:150333 original size:24 final size:24
Alignment explanation
Indices: 150306--150375 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
150296 AATAAAAATT
*
150306 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAAAA
*
150330 AGCCA-TAATTTTTGACAAACAAAA
1 AGCCACCAA-TTTTGACAAACAAAA
*
150354 AGGAACCACCATTTTTGACAAA
1 A-G--CCACCAATTTTGACAAA
150376 TACAAAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 20 0.54
25 1 0.03
27 13 0.35
28 1 0.03
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAAAA
Found at i:150375 original size:27 final size:27
Alignment explanation
Indices: 150308--150404 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
150298 TAAAAATTAG
* *
150308 CCACCAATTTTGACAAACAACAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
**
150332 CCATAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * *
150359 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
150386 CCACCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
150405 CATGGTGGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
24 19 0.32
25 1 0.02
27 39 0.66
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:150423 original size:24 final size:25
Alignment explanation
Indices: 150392--150449 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
150382 GTAACCACCA
*
150392 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
*
150416 TTGTTGACAAACACAAAGGGTGGTTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
150442 TTGTTGAC
1 TTGTTGAC
150450 TAGCCACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.47
26 16 0.53
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:154930 original size:24 final size:24
Alignment explanation
Indices: 154903--154972 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
154893 AATAAAAATT
*
154903 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAAAA
*
154927 AGCCA-TAATTTTTGACAAACAAAA
1 AGCCACCAA-TTTTGACAAACAAAA
*
154951 AGGAACCACCATTTTTGACAAA
1 A-G--CCACCAATTTTGACAAA
154973 TACAAAGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 20 0.54
25 1 0.03
27 13 0.35
28 1 0.03
ACGTcount: A:0.46, C:0.23, G:0.10, T:0.21
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAAAA
Found at i:154972 original size:27 final size:27
Alignment explanation
Indices: 154905--155001 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
154895 TAAAAATTAG
* *
154905 CCACCAATTTTGACAAACAACAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
**
154929 CCATAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * *
154956 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
154983 CCACCATTGTTGACAAACA
1 CCACCATTTTTGACAAACA
155002 CATGGTGGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
24 19 0.32
25 1 0.02
27 39 0.66
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:155020 original size:24 final size:25
Alignment explanation
Indices: 154989--155046 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 25
154979 GTAACCACCA
*
154989 TTGTTGACAAACAC-ATGGTGGCTT
1 TTGTTGACAAACACAAGGGTGGCTT
*
155013 TTGTTGACAAACACAAAGGGTGGTTT
1 TTGTTGACAAACAC-AAGGGTGGCTT
155039 TTGTTGAC
1 TTGTTGAC
155047 TAGCCACCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 14 0.47
26 16 0.53
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (25 bp):
TTGTTGACAAACACAAGGGTGGCTT
Found at i:156614 original size:17 final size:18
Alignment explanation
Indices: 156592--156626 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
156582 AAAGTAAAGT
*
156592 AAAGCAAAGCAA-AAACA
1 AAAGCAAAACAATAAACA
156609 AAAGCAAAACAATAAACA
1 AAAGCAAAACAATAAACA
156627 TAATAAAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.17, G:0.09, T:0.03
Consensus pattern (18 bp):
AAAGCAAAACAATAAACA
Found at i:156852 original size:22 final size:22
Alignment explanation
Indices: 156826--156868 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
156816 AAATTTTATT
156826 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
156848 TAAATATTAATATAAAAATAT
1 TAAATATTAATATAAAAATAT
156869 TATTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:158260 original size:2 final size:2
Alignment explanation
Indices: 158255--158279 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
158245 ACACACATAC
158255 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
158280 AATGGATTTG
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:159603 original size:140 final size:137
Alignment explanation
Indices: 159384--159641 Score: 356
Period size: 140 Copynumber: 1.9 Consensus size: 137
159374 GAATAAAGAT
* * * * *
159384 TAAAGTAAAAAGTTATTTGTCTCTTCTAAAATAAATGGAAAAAAAAAAGAAAAGAGTGATAACAT
1 TAAAGTAAAAAGTAATTTATCTCCTCTAAAATAAAAGGAAAAAAAAAAAAAAAGAGTGATAACAT
* *
159449 ATGAATGGAAATATGCTTCTCTTTTG-TAACATTTTCATAATCCAATGCTTGTTCAGCAATGATA
66 ATGAATAGAAATATGCTTCT-ATTTGATAACATTTTCATAATCCAATGCTTGTTCAGCAATGATA
159513 AAAGAGAA
130 AAAGAGAA
* * *
159521 TAAAGTACAAAGTAATTTATGTCCTCTAAAATAAAAGGAAAAAAAATAAAAAAAAAGATTGATAA
1 TAAAGTAAAAAGTAATTTATCTCCTCTAAAATAAAAGG--AAAAAA-AAAAAAAAAGAGTGATAA
* * *
159586 CATTTGAATAGAAATATGCTTCTATTTGATAACATTTTCATGATCCATTGCTTGTT
63 CATATGAATAGAAATATGCTTCTATTTGATAACATTTTCATAATCCAATGCTTGTT
159642 AGTAGGGAAT
Statistics
Matches: 104, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
137 32 0.31
139 10 0.10
140 62 0.60
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (137 bp):
TAAAGTAAAAAGTAATTTATCTCCTCTAAAATAAAAGGAAAAAAAAAAAAAAAGAGTGATAACAT
ATGAATAGAAATATGCTTCTATTTGATAACATTTTCATAATCCAATGCTTGTTCAGCAATGATAA
AAGAGAA
Found at i:159950 original size:153 final size:153
Alignment explanation
Indices: 159504--159989 Score: 635
Period size: 150 Copynumber: 3.2 Consensus size: 153
159494 TGCTTGTTCA
* * * * ***
159504 GCAATGATAAAAGAGAATAAAGTACAAAGTAATTTATGTCCTCTAAAATAAAAGGAAAAAAAATA
1 GCAATGATAAAAGAGAATAAAGTAAAAAGTTATTTATGTCTTCTAAAATTAAA--AAAATTTA-A
*
159569 AAAAAAAAGATTGATAACATTTGAATAGAAATATGCTTCTATTTGATAACATTTTCATGATCCAT
63 AAAAAAAAGATTGATAACATTTGAATGGAAATATGCTTCTATTTGATAACATTTTCATGATCCAT
159634 TGCTTGTTAGTAGGGAATGCTTTAGG
128 TGCTTGTTAGTAGGGAATGCTTTAGG
* * ***
159660 GCAATGGTAAAAGAAAATAAAGTAAAAAGTTATTTATGTCTTCT-AAATT----TTTTTTAAAAA
1 GCAATGATAAAAGAGAATAAAGTAAAAAGTTATTTATGTCTTCTAAAATTAAAAAAATTT-AAAA
* *
159720 AAAGAAAGATTGATGAA-ATTTGAATGAAAATATGCTTCCATTTGATAACATTTTCATGATCCAT
65 AAA-AAAGATTGAT-AACATTTGAATGGAAATATGCTTCTATTTGATAACATTTTCATGATCCAT
*
159784 TGCTTGTTAGTAGGAAATGCTTTAGG
128 TGCTTGTTAGTAGGGAATGCTTTAGG
* *
159810 GCAATGGTAAAAGAGAATAAAGTAAAAAGTTATTTATGTCTTTTAAAATTAAAAAAATTTAAAAA
1 GCAATGATAAAAGAGAATAAAGTAAAAAGTTATTTATGTCTTCTAAAATTAAAAAAATTTAAAAA
* *
159875 AAAAAGATTGATAACATTTGAATGGAAATATGCTTATATTTGATACCATTTTCATGATCCATTGC
66 AAAAAGATTGATAACATTTGAATGGAAATATGCTTCTATTTGATAACATTTTCATGATCCATTGC
* * *
159940 TTGTTGGTAGGGAATTCTTT-GTA
131 TTGTTAGTAGGGAATGCTTTAG-G
* *
159963 ACAATGATAAAAGAGAATAAATTAAAA
1 GCAATGATAAAAGAGAATAAAGTAAAA
159990 TGCTTTAGAT
Statistics
Matches: 288, Mismatches: 32, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
149 6 0.02
150 122 0.42
151 7 0.02
152 3 0.01
153 97 0.34
154 7 0.02
155 7 0.02
156 39 0.14
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.33
Consensus pattern (153 bp):
GCAATGATAAAAGAGAATAAAGTAAAAAGTTATTTATGTCTTCTAAAATTAAAAAAATTTAAAAA
AAAAAGATTGATAACATTTGAATGGAAATATGCTTCTATTTGATAACATTTTCATGATCCATTGC
TTGTTAGTAGGGAATGCTTTAGG
Found at i:160174 original size:2 final size:2
Alignment explanation
Indices: 160167--160210 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
160157 AATAATAAAT
160167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
160209 TA
1 TA
160211 AAGACTGTCC
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:162921 original size:14 final size:14
Alignment explanation
Indices: 162880--162921 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
162870 TATTAGTAAA
162880 AAATAAAAATATTT
1 AAATAAAAATATTT
* *
162894 ATATAATTAA-ATTT
1 AAATAA-AAATATTT
162908 AAATAAAAATATTT
1 AAATAAAAATATTT
162922 TTATTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
13 2 0.09
14 18 0.82
15 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATAAAAATATTT
Found at i:168800 original size:22 final size:22
Alignment explanation
Indices: 168774--168816 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
168764 AAATTTTATT
168774 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
168796 TAAATATTAATATAAAAATAT
1 TAAATATTAATATAAAAATAT
168817 TATTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:170203 original size:2 final size:2
Alignment explanation
Indices: 170198--170226 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
170188 ACACACACAC
170198 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 A
170227 AATGGATTTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:170405 original size:15 final size:16
Alignment explanation
Indices: 170373--170415 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
170363 CAAATTATAT
*
170373 CTAAAATAATTCAAAA
1 CTAAAATAACTCAAAA
170389 CTAAAATAACT-AAAA
1 CTAAAATAACTCAAAA
*
170404 CTCAAATAACTC
1 CTAAAATAACTC
170416 GAATCAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (16 bp):
CTAAAATAACTCAAAA
Found at i:170900 original size:2 final size:2
Alignment explanation
Indices: 170893--170922 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
170883 ATTGGCTCAA
170893 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
170923 CTTAATGTAA
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:171573 original size:132 final size:132
Alignment explanation
Indices: 171332--171582 Score: 314
Period size: 132 Copynumber: 1.9 Consensus size: 132
171322 AACAGAGAAT
* * * * *
171332 AAAGATTAAAGTAAAAAATTATTTATCTCTTCTAAAATAAATGGAAAAAAAAAAGAGTTATAACC
1 AAAGAATAAAGTAAAAAATAATTTATCTCCTCTAAAATAAATAGAAAAAAAAAAGAGTTATAACA
171397 TATTAATGGAAATATGCTTCTCTTTAGTAACATTTTCATAATCCAATGCTTGTTGAGCAATGATA
66 TATTAATGGAAATATGCTTCTCTTTAGTAACATTTTCATAATCCAATGCTTGTTGAGCAATGATA
171462 AA
131 AA
* * * *
171464 AAAGAATAAAGTACAACATAATTTATGTCCTCTAAAATAAA-AGAAACAAAAGAAGA-TTCATAA
1 AAAGAATAAAGTAAAAAATAATTTATCTCCTCTAAAATAAATAGAAA-AAAAAAAGAGTT-ATAA
* * *
171527 CAT-TTGAATGGAAATATGTTTC-CATTT-GATAACATTTTCATGATCCATTGCTTGTT
64 CATATT-AATGGAAATATGCTTCTC-TTTAG-TAACATTTTCATAATCCAATGCTTGTT
171583 AGTAGGGAAT
Statistics
Matches: 102, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
131 10 0.10
132 92 0.90
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (132 bp):
AAAGAATAAAGTAAAAAATAATTTATCTCCTCTAAAATAAATAGAAAAAAAAAAGAGTTATAACA
TATTAATGGAAATATGCTTCTCTTTAGTAACATTTTCATAATCCAATGCTTGTTGAGCAATGATA
AA
Found at i:171713 original size:142 final size:143
Alignment explanation
Indices: 171511--171769 Score: 369
Period size: 142 Copynumber: 1.8 Consensus size: 143
171501 TAAAAGAAAC
* *
171511 AAAAGAAGATTCATAACATTTGAATGGAAATATGTTTCCATTTGATAACATTTTCATGATCCATT
1 AAAAGAAGATTCATAACATTTGAATGAAAATATGTTTACATTTGATAACATTTTCATGATCCATT
* * *
171576 GCTTGTTAGTAGGGAATACTTTAG-AGCAATGGTAAAAGAGAATAAAGTAAAAAAGTTATTTATG
66 GCTTGTTAGTAGAGAATACTTT-GTAACAATGATAAAAGAGAATAAAGTAAAAAAGTTATTTATG
171640 TCCTTTAAAATAGG
130 TCCTTTAAAATAGG
* * * * * *
171654 AAAA-AAGATTGATAACATTTGAATTAAAATATTTTTATATTTTATACCATTTTCATGATCCATT
1 AAAAGAAGATTCATAACATTTGAATGAAAATATGTTTACATTTGATAACATTTTCATGATCCATT
* * *
171718 GCTTGTTGGTAGAGAATTCTTTGTAACAATGATAAAAGAGAATAAATTAAAA
66 GCTTGTTAGTAGAGAATACTTTGTAACAATGATAAAAGAGAATAAAGTAAAA
171770 TGCTTTAGAT
Statistics
Matches: 101, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
141 1 0.01
142 96 0.95
143 4 0.04
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (143 bp):
AAAAGAAGATTCATAACATTTGAATGAAAATATGTTTACATTTGATAACATTTTCATGATCCATT
GCTTGTTAGTAGAGAATACTTTGTAACAATGATAAAAGAGAATAAAGTAAAAAAGTTATTTATGT
CCTTTAAAATAGG
Found at i:171946 original size:2 final size:2
Alignment explanation
Indices: 171939--171993 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
171929 TGTGTCAAAA
171939 AT AT AT 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 AT AT AT
171981 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
171994 AAGAGAGAGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:172722 original size:22 final size:22
Alignment explanation
Indices: 172697--172739 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
172687 AATTTTTATT
172697 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
172719 TAAATATTAATATAAAAATAT
1 TAAATATTAATATAAAAATAT
172740 TATTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:172867 original size:14 final size:14
Alignment explanation
Indices: 172833--172867 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
172823 AGCTTGCCTT
* *
172833 AAATATAAATATAT
1 AAATATTAATATAA
172847 AAATATTAATATAA
1 AAATATTAATATAA
172861 AAATATT
1 AAATATT
172868 TTTTTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATATTAATATAA
Found at i:173204 original size:32 final size:32
Alignment explanation
Indices: 173163--173393 Score: 327
Period size: 32 Copynumber: 7.2 Consensus size: 32
173153 TTTTAATTTT
173163 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
173195 TTTCAAAGCCCACACAAGTCAGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
*
173227 TTTCAAAGCCCACACAAGTCAGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
173259 TTCCAAAGCCCACATAAGTCGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* * *
173291 TTTCAAAGCCCACACAAATCGGTGGCGACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
173323 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
* ** * * * *
173355 TTTAAAAGCCCATGCAAATCAGTGGCGACCCT
1 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
173387 TTTCAAA
1 TTTCAAA
173394 TCACCATTTT
Statistics
Matches: 177, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 177 1.00
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.18
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
Found at i:174656 original size:17 final size:15
Alignment explanation
Indices: 174636--174685 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
174626 TTAGGTAAAA
174636 AAGAAAGAAAGAAGATG
1 AAGAAAGAAAGAA-A-G
174653 AAG-AAGAAAGAAAG
1 AAGAAAGAAAGAAAG
*
174667 AA-AAAGAAA-AAAA
1 AAGAAAGAAAGAAAG
174680 AAGAAA
1 AAGAAA
174686 AAAATATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.17
14 12 0.40
15 1 0.03
16 9 0.30
17 3 0.10
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
AAGAAAGAAAGAAAG
Found at i:174674 original size:10 final size:10
Alignment explanation
Indices: 174633--174689 Score: 62
Period size: 10 Copynumber: 5.4 Consensus size: 10
174623 AATTTAGGTA
174633 AAAAAGAAAG
1 AAAAAGAAAG
174643 AAAGAAGATGAAG
1 AAA-AAGA--AAG
174656 AAGAAAGAAAG
1 AA-AAAGAAAG
*
174667 AAAAAGAAAA
1 AAAAAGAAAG
174677 AAAAAGAAA-
1 AAAAAGAAAG
174686 AAAA
1 AAAA
174690 TATGAAATGG
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
9 4 0.10
10 19 0.45
11 9 0.21
13 9 0.21
14 1 0.02
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:183590 original size:145 final size:146
Alignment explanation
Indices: 183381--183645 Score: 374
Period size: 145 Copynumber: 1.8 Consensus size: 146
183371 AAAACGGAAA
* *
183381 AAAAAAAGAAGATTCATAACATTTGAATGGAAATATGTTTCCATTTGATAACATTTTCATGATCC
1 AAAAAAAGAAGATTCATAACATTTGAATGAAAATATGTTTACATTTGATAACATTTTCATGATCC
* *
183446 ATTGCTTGTTAGTAGGGAATACTTTAG-AGCAATGGTAAAAAAGAATAAAGTAAAAAAGTTATTT
66 ATTGCTTGTTAGTAGGGAATACTTT-GTAACAATGATAAAAAAGAATAAAGTAAAAAAGTTATTT
183510 ATGTCTTTTAAAATAGG
130 ATGTCTTTTAAAATAGG
* * * * *
183527 AAAAAAA-AAGATTGATAACATTTGAATTAAAATAT-TCTTATATTTTATACCATTTTCATGATC
1 AAAAAAAGAAGATTCATAACATTTGAATGAAAATATGT-TTACATTTGATAACATTTTCATGATC
* * * *
183590 CATTGCTTGTTGGTAGGGAATTCTTTGTAACAATGATAAAAGAGAATAAATTAAAA
65 CATTGCTTGTTAGTAGGGAATACTTTGTAACAATGATAAAAAAGAATAAAGTAAAA
183646 TGCTTTAGAT
Statistics
Matches: 104, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
144 2 0.02
145 95 0.91
146 7 0.07
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (146 bp):
AAAAAAAGAAGATTCATAACATTTGAATGAAAATATGTTTACATTTGATAACATTTTCATGATCC
ATTGCTTGTTAGTAGGGAATACTTTGTAACAATGATAAAAAAGAATAAAGTAAAAAAGTTATTTA
TGTCTTTTAAAATAGG
Found at i:184570 original size:22 final size:22
Alignment explanation
Indices: 184545--184587 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
184535 AATTTTTATT
184545 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
184567 TAAATATTAATATAAAAATAT
1 TAAATATTAATATAAAAATAT
184588 TATTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:184699 original size:14 final size:14
Alignment explanation
Indices: 184680--184713 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
184670 GAGCTTGCCT
184680 TAAATATAAATATA
1 TAAATATAAATATA
*
184694 TAAATATTAATATA
1 TAAATATAAATATA
*
184708 AAAATA
1 TAAATA
184714 ATTTTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAATATAAATATA
Found at i:184753 original size:13 final size:13
Alignment explanation
Indices: 184735--184759 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
184725 TTTTAGTAAT
184735 TATAAATAATAAA
1 TATAAATAATAAA
184748 TATAAATAATAA
1 TATAAATAATAA
184760 GAGTAGGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TATAAATAATAAA
Found at i:185235 original size:14 final size:14
Alignment explanation
Indices: 185216--185242 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
185206 TATTGTATGT
185216 TTAAAAATAAAAAA
1 TTAAAAATAAAAAA
185230 TTAAAAATAAAAA
1 TTAAAAATAAAAA
185243 TAAAACGTGT
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
TTAAAAATAAAAAA
Found at i:186178 original size:20 final size:20
Alignment explanation
Indices: 186140--186180 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
186130 ATAATACTTA
* *
186140 TTTATTTTTCAATATAATTT
1 TTTATTTTTCAACAAAATTT
*
186160 TTTATTTTTTAACAAAATTT
1 TTTATTTTTCAACAAAATTT
186180 T
1 T
186181 AATTAATCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTATTTTTCAACAAAATTT
Found at i:187628 original size:158 final size:154
Alignment explanation
Indices: 187324--187657 Score: 366
Period size: 158 Copynumber: 2.1 Consensus size: 154
187314 GTTGAGCGAA
* *
187324 GATAAAAGAGAATAAAGTACAAAGTAATTTATGTCCTCTAAAATAAAAAGAAAAAAAATAAAAAG
1 GATAAAAGAGAATAAAGTAAAAAGTAATTTATGTCCTCTAAAATAAAAAGAAAAAAAATAAAAAA
* * *
187389 AAGATCATAACGATTGAATGGAAATATGCTTCTATTCGATAACATTTTCATAATCCATTGCTTAT
66 AAGATCATAACGATTGAATGAAAATATGCTTATATTCGATAACATTTCCATAATCCATTGCTTAT
* * *
187454 TATTAGGGAATGCTTTAGAGCAAT
131 TAGTAGGCAATGCTTTAGAACAAT
* * * *
187478 GGTAAAAGAGAATAAAGTAAAGAAGTTATTTATGTCTTCTAAAATTAAAAATTAAAAAAAGA-AA
1 GATAAAAGAGAATAAAGTAAA-AAGTAATTTATGTCCTCTAAAA-TAAAAA-GAAAAAAA-ATAA
* * * * ** *
187542 AAAAAAGATTGATAA-TATTTGAATTAAAATATGCTTATATTTGATGCCATTTCCATGATCCATT
62 AAAAAAGA-TCATAACGA-TTGAATGAAAATATGCTTATATTCGATAACATTTCCATAATCCATT
* * * * *
187606 GCTTGTTGGTAGGCAATTCTTTATAATAAT
125 GCTTATTAGTAGGCAATGCTTTAGAACAAT
* *
187636 GATAGAAGAGAATAAATTAAAA
1 GATAAAAGAGAATAAAGTAAAA
187658 TGCTTTAGAT
Statistics
Matches: 147, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
154 19 0.13
155 20 0.14
156 6 0.04
157 18 0.12
158 84 0.57
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.31
Consensus pattern (154 bp):
GATAAAAGAGAATAAAGTAAAAAGTAATTTATGTCCTCTAAAATAAAAAGAAAAAAAATAAAAAA
AAGATCATAACGATTGAATGAAAATATGCTTATATTCGATAACATTTCCATAATCCATTGCTTAT
TAGTAGGCAATGCTTTAGAACAAT
Found at i:188108 original size:16 final size:16
Alignment explanation
Indices: 188083--188116 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
188073 GAAATATGGC
188083 TTATTCTTTCTTAATT
1 TTATTCTTTCTTAATT
* *
188099 TTATTTTTTCTTTATT
1 TTATTCTTTCTTAATT
188115 TT
1 TT
188117 TCTCTATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTCTTTCTTAATT
Found at i:191773 original size:22 final size:23
Alignment explanation
Indices: 191745--191798 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
191735 AAATTTGACA
* *
191745 TATTTTATATTTATGTTGTAT-T
1 TATTTTATATTTATATCGTATCT
*
191767 TATTTTATTTTTATATCGTATCT
1 TATTTTATATTTATATCGTATCT
191790 TATTTTATA
1 TATTTTATA
191799 AAATATATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.67
Consensus pattern (23 bp):
TATTTTATATTTATATCGTATCT
Found at i:212733 original size:3 final size:3
Alignment explanation
Indices: 212682--212717 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
212672 AAAAACCCCA
*
212682 AAG ACAG AAG AAG AAG AAG AAG AAT AAG AAG AAG AA
1 AAG A-AG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
212718 CCTGAGTCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.03, G:0.28, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:213381 original size:28 final size:28
Alignment explanation
Indices: 213346--213418 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 28
213336 TAATTTTATA
213346 ATTT-TATTTAAATAATTTTTATATTTTT
1 ATTTATATTTAAATAATTTTTAT-TTTTT
213374 A-TTATATTTAAATATATTTTTATTTTTT
1 ATTTATATTTAAATA-ATTTTTATTTTTT
213402 ATTTTATATTTAAATAA
1 A-TTTATATTTAAATAA
213419 ACTCTTTAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
27 2 0.05
28 17 0.41
29 9 0.22
30 13 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
ATTTATATTTAAATAATTTTTATTTTTT
Found at i:213440 original size:27 final size:26
Alignment explanation
Indices: 213410--213466 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
213400 TTATTTTATA
*
213410 TTTAAATAAACTCTTTAA-TCTTTGATT
1 TTTAAATAAACT-TTTAACT-TTTAATT
**
213437 TTTACGTAAACTTTTAACTTTTAATT
1 TTTAAATAAACTTTTAACTTTTAATT
213463 TTTA
1 TTTA
213467 CTTAAACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 15 0.58
27 11 0.42
ACGTcount: A:0.32, C:0.11, G:0.04, T:0.54
Consensus pattern (26 bp):
TTTAAATAAACTTTTAACTTTTAATT
Found at i:213463 original size:26 final size:27
Alignment explanation
Indices: 213416--213473 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
213406 TATATTTAAA
*
213416 TAAACTCTTTAATCTTTGATTTTTACG
1 TAAACTCTTTAATCTTTAATTTTTACG
*
213443 TAAACT-TTTAA-CTTTTAATTTTTACT
1 TAAACTCTTTAATC-TTTAATTTTTACG
213469 TAAAC
1 TAAAC
213474 AAACTCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 1 0.04
26 21 0.75
27 6 0.21
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.52
Consensus pattern (27 bp):
TAAACTCTTTAATCTTTAATTTTTACG
Found at i:215326 original size:16 final size:16
Alignment explanation
Indices: 215305--215337 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
215295 TGAGAAAACT
*
215305 TTTTTGTCAATTACCA
1 TTTTTGCCAATTACCA
215321 TTTTTGCCAATTACCA
1 TTTTTGCCAATTACCA
215337 T
1 T
215338 GGTAAAGTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTTTGCCAATTACCA
Found at i:218634 original size:2 final size:2
Alignment explanation
Indices: 218627--218661 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
218617 CTTGAATTTC
*
218627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
218662 CCTTTTGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:223436 original size:7 final size:7
Alignment explanation
Indices: 223412--223459 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
223402 TCATAATAGG
223412 TAAATTT
1 TAAATTT
*
223419 ATAAATAT
1 -TAAATTT
223427 TAAATTT
1 TAAATTT
223434 TAAATTT
1 TAAATTT
223441 TAAATATAT
1 TAAAT-T-T
*
223450 TAAATGT
1 TAAATTT
223457 TAA
1 TAA
223460 TTAATTGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
7 22 0.63
8 7 0.20
9 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (7 bp):
TAAATTT
Found at i:223442 original size:23 final size:22
Alignment explanation
Indices: 223412--223459 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
223402 TCATAATAGG
*
223412 TAAATTTATAA-ATATTAAATTT
1 TAAATTTA-AATATATTAAATGT
223434 TAAATTTTAAATATATTAAATGT
1 TAAA-TTTAAATATATTAAATGT
223457 TAA
1 TAA
223460 TTAATTGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TAAATTTAAATATATTAAATGT
Found at i:225031 original size:22 final size:21
Alignment explanation
Indices: 224976--225035 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 21
224966 TCATTAATTA
*
224976 ATTAATAAAAAAATATTTAAT
1 ATTAATATAAAAATATTTAAT
*
224997 TTTAAT-TATAAAAT-TTATAAAT
1 ATTAATATA-AAAATATT-T-AAT
225019 ATTAATATAAAAA-ATTT
1 ATTAATATAAAAATATTT
225036 TAATTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
20 3 0.10
21 12 0.39
22 14 0.45
23 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTAATATAAAAATATTTAAT
Found at i:231761 original size:20 final size:20
Alignment explanation
Indices: 231714--231788 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
231704 AAAAAGACAT
*
231714 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
231733 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
231754 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
231774 AATGTATCGATACAT
1 AATGTATCGATACAT
231789 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:231782 original size:40 final size:39
Alignment explanation
Indices: 231711--231788 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
231701 GGTAAAAAGA
* *
231711 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
231750 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
231789 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:232365 original size:32 final size:32
Alignment explanation
Indices: 232316--234008 Score: 2461
Period size: 32 Copynumber: 54.2 Consensus size: 32
232306 AATATGGTGA
* * **
232316 TTTGAAAAGGGTTGCCACTGACTTGCATGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
232348 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
232380 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
232412 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
232444 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
232476 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
232508 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
232540 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
232572 TTTGAAATGGGTTGCCACCGACTTGTGTGGGG
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
232604 TTTGGAATGGGTTGCCACCGACTTGTGTGGGG
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
232636 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
232668 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
232700 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
232732 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
232764 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
232796 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
232828 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
232860 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
232892 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
232924 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
232956 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
232988 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
233020 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
233052 TTTGGAATGGGTTGCCACCGACTTGTGTGGGA
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
233084 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
233116 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
233148 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
233180 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
233212 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
233244 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
233276 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
233308 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
233340 TTTGAAATGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
233372 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
233404 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
233436 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
233468 TTTGGAATGGGTTGCCACCGACTTGTGTGGGA
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
233500 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
233532 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
233564 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
233596 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
233628 TTTGAAATGGGTTGCCACCGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* **
233658 TCTGAAA-GGG-TGCCACTAAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * * * *
233686 TCTGAAAAGAG-TGCCACTGGC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
233715 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
* ** *
233744 TTTGAAA--GGATGCCAATGA-GT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
233772 TTTGAAA-GGG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
233800 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
* * * *
233829 TTTAAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * ** *
233858 TTTGAAAAGAG-TGCCACTAAC-T-TGTAGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
233887 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGT
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
*
233916 TTTGAAA-GGG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
233944 TTTGAAAAGAG-TGCCACTGA-TT-TGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
233973 TTTGAAA-GGAG-TGCCACTGAC-T-TGTGGGC
1 TTTGAAATGG-GTTGCCACCGACTTGTGTGGGC
234002 TTTGAAA
1 TTTGAAA
234009 GGGATGAACA
Statistics
Matches: 1585, Mismatches: 61, Indels: 33
0.94 0.04 0.02
Matches are distributed among these distances:
27 1 0.00
28 100 0.06
29 205 0.13
30 14 0.01
31 1 0.00
32 1264 0.80
ACGTcount: A:0.16, C:0.18, G:0.35, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:235244 original size:1 final size:1
Alignment explanation
Indices: 235240--235294 Score: 56
Period size: 1 Copynumber: 55.0 Consensus size: 1
235230 TTTTTTGCTA
* * * ** *
235240 TTTTTTCTTTTTTTTTTTGTTTTTTTGTTTTGGTTTTTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
235295 GGGTGTAAAG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (1 bp):
T
Found at i:235263 original size:13 final size:13
Alignment explanation
Indices: 235247--235294 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
235237 CTATTTTTTC
235247 TTTTTTTTTTTGT
1 TTTTTTTTTTTGT
* *
235260 TTTTTTGTTTTGG
1 TTTTTTTTTTTGT
235273 TTTTTTTTTTTGT
1 TTTTTTTTTTTGT
235286 TTTTTTTTT
1 TTTTTTTTT
235295 GGGTGTAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (13 bp):
TTTTTTTTTTTGT
Done.