Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018173.1 Corchorus olitorius cultivar O-4 contig18206, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 175804
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:40 original size:24 final size:24
Alignment explanation
Indices: 13--125 Score: 91
Period size: 24 Copynumber: 4.5 Consensus size: 24
3 CCAGCACCGA
13 CACCACCACCAACACCTCCACCTG
1 CACCACCACCAACACCTCCACCTG
* * *
37 CACCACCTCCAACACCTCCTCCTCCTC
1 CACCACCACCAACA---CCTCCACCTG
* *
64 CACCTCTACCACCACCGCCTCCACCTG
1 CA-C-C-ACCACCAACACCTCCACCTG
* * **
91 CACCACCTCCAACACCTCCTCCAA
1 CACCACCACCAACACCTCCACCTG
115 CACCACCACCA
1 CACCACCACCA
126 GCACTTACTC
Statistics
Matches: 68, Mismatches: 15, Indels: 12
0.72 0.16 0.13
Matches are distributed among these distances:
24 37 0.54
25 1 0.01
26 1 0.01
27 20 0.29
28 1 0.01
29 1 0.01
30 7 0.10
ACGTcount: A:0.25, C:0.60, G:0.03, T:0.12
Consensus pattern (24 bp):
CACCACCACCAACACCTCCACCTG
Found at i:43 original size:15 final size:15
Alignment explanation
Indices: 15--101 Score: 66
Period size: 15 Copynumber: 5.8 Consensus size: 15
5 AGCACCGACA
**
15 CCACCACCAACACCT
1 CCACCACCTCCACCT
** *
30 CCACCTGCACCACCT
1 CCACCACCTCCACCT
* *
45 CCAACACCTCCTCCT
1 CCACCACCTCCACCT
* * *
60 CCTCCACCTCTACCA
1 CCACCACCTCCACCT
*
75 CCACCGCCTCCACCT
1 CCACCACCTCCACCT
*
90 GCACCACCTCCA
1 CCACCACCTCCA
102 ACACCTCCTC
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 53 1.00
ACGTcount: A:0.22, C:0.61, G:0.03, T:0.14
Consensus pattern (15 bp):
CCACCACCTCCACCT
Found at i:106 original size:12 final size:12
Alignment explanation
Indices: 91--121 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
81 CCTCCACCTG
91 CACCACCTCCAA
1 CACCACCTCCAA
*
103 CACCTCCTCCAA
1 CACCACCTCCAA
115 CACCACC
1 CACCACC
122 ACCAGCACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.29, C:0.61, G:0.00, T:0.10
Consensus pattern (12 bp):
CACCACCTCCAA
Found at i:106 original size:27 final size:27
Alignment explanation
Indices: 27--113 Score: 113
Period size: 27 Copynumber: 3.2 Consensus size: 27
17 ACCACCAACA
27 CCTCCACCTGCACCACCTCCAACACCT
1 CCTCCACCTGCACCACCTCCAACACCT
* * * * *
54 CCTCCTCCTCCACC-TCTACCACCACCG
1 CCTCCACCTGCACCACCT-CCAACACCT
81 CCTCCACCTGCACCACCTCCAACACCT
1 CCTCCACCTGCACCACCTCCAACACCT
108 CCTCCA
1 CCTCCA
114 ACACCACCAC
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
26 2 0.04
27 44 0.92
28 2 0.04
ACGTcount: A:0.20, C:0.61, G:0.03, T:0.16
Consensus pattern (27 bp):
CCTCCACCTGCACCACCTCCAACACCT
Found at i:121 original size:54 final size:54
Alignment explanation
Indices: 17--121 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
7 CACCGACACC
** *
17 ACCACCAACACCTCCACCTGCACCACCTCCAACACCTCCTCCTCCTCCACCTCT
1 ACCACCAACACCTCCACCTGCACCACCTCCAACACCTCCTCCAACACCACCTCT
* *
71 ACCACCACCGCCTCCACCTGCACCACCTCCAACACCTCCTCCAACACCACC
1 ACCACCAACACCTCCACCTGCACCACCTCCAACACCTCCTCCAACACCACC
122 ACCAGCACTT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.24, C:0.60, G:0.03, T:0.13
Consensus pattern (54 bp):
ACCACCAACACCTCCACCTGCACCACCTCCAACACCTCCTCCAACACCACCTCT
Found at i:136 original size:24 final size:24
Alignment explanation
Indices: 91--136 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
81 CCTCCACCTG
* *
91 CACCACCTCCAACACCTCCTCCAA
1 CACCACCACCAACACCTACTCCAA
* *
115 CACCACCACCAGCACTTACTCC
1 CACCACCACCAACACCTACTCC
137 TCCCCCAACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.28, C:0.57, G:0.02, T:0.13
Consensus pattern (24 bp):
CACCACCACCAACACCTACTCCAA
Found at i:204 original size:39 final size:36
Alignment explanation
Indices: 162--298 Score: 118
Period size: 36 Copynumber: 3.6 Consensus size: 36
152 TCCGACGCCG
*
162 CCACCAGCACCTACACCACCTCCTCCTCCAGCACCTA
1 CCACCACCACCTACACCACCTCCTCCTCCAGC-CCTA
* *
199 TGCCACCACCA-ATACCACCCCCTACTCCTCCTCCAGCGCCTA
1 --CCACCACCACCTA-CA-CCAC--CTCCTCCTCCAGC-CCTA
* *
241 -CACCACCACCAACACCTCCTCCTCCTCCA-CCTCTA
1 CCACCACCACCTACACCACCTCCTCCTCCAGCC-CTA
*
276 CCACCACCACCTCCACCACCTCC
1 CCACCACCACCTACACCACCTCC
299 GGCACCTCCT
Statistics
Matches: 81, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
34 1 0.01
35 4 0.05
36 30 0.37
38 5 0.06
39 20 0.25
40 4 0.05
42 17 0.21
ACGTcount: A:0.23, C:0.59, G:0.04, T:0.15
Consensus pattern (36 bp):
CCACCACCACCTACACCACCTCCTCCTCCAGCCCTA
Found at i:208 original size:42 final size:42
Alignment explanation
Indices: 162--257 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
152 TCCGACGCCG
* **
162 CCACCAGCACCTACACCAC-CTCCTCCTCCAGCACCTATGCCA
1 CCACCAACACCTAC-CCACACTCCTCCTCCAGCACCTACACCA
* * *
204 CCACCAATACC-ACCCCCTACTCCTCCTCCAGCGCCTACACCA
1 CCACCAACACCTACCCAC-ACTCCTCCTCCAGCACCTACACCA
246 CCACCAACACCT
1 CCACCAACACCT
258 CCTCCTCCTC
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
40 3 0.07
41 2 0.05
42 39 0.89
ACGTcount: A:0.25, C:0.56, G:0.05, T:0.14
Consensus pattern (42 bp):
CCACCAACACCTACCCACACTCCTCCTCCAGCACCTACACCA
Found at i:216 original size:36 final size:36
Alignment explanation
Indices: 163--432 Score: 105
Period size: 36 Copynumber: 7.2 Consensus size: 36
153 CCGACGCCGC
* *
163 CACCAGCACCTACACCACCTCCTCCTCCAGCACCTA
1 CACCACCACCAACACCACCTCCTCCTCCAGCACCTA
** * *
199 TGCCACCACCAATACCACCCCCTACTCCTCCTCCAGCGCCTA
1 CACCACCACC-A-A-CA-CCAC--CTCCTCCTCCAGCACCTA
*
241 CACCACCACCAACACCTCCTCCTCCTCCA-C-CTCTA
1 CACCACCACCAACACCACCTCCTCCTCCAGCAC-CTA
** ** * ** * *
276 CCACCACCACCTCCACCACCTCCGGCACCTCCTCCAA
1 -CACCACCACCAACACCACCTCCTCCTCCAGCACCTA
* * * * *
313 CACCACCACCAGCACCTA-CTCCACCCCCAACACCTC
1 CACCACCACCAACACC-ACCTCCTCCTCCAGCACCTA
* ** * * **
349 CTCCTGCACTACCACCGGCTCCTCCTCCAGCACCTA
1 CACCACCACCAACACCACCTCCTCCTCCAGCACCTA
** * * *
385 TGCCGCCACCAACACCTCCTCCTCCACCTCCACCACCTA
1 CACCACCACCAACACCACCTCCT---CCTCCAGCACCTA
*
424 CACCCCCAC
1 CACCACCAC
433 TTGCTCCACC
Statistics
Matches: 170, Mismatches: 49, Indels: 27
0.69 0.20 0.11
Matches are distributed among these distances:
34 1 0.01
35 4 0.02
36 104 0.61
37 4 0.02
38 5 0.03
39 22 0.13
40 4 0.02
41 1 0.01
42 25 0.15
ACGTcount: A:0.22, C:0.59, G:0.05, T:0.14
Consensus pattern (36 bp):
CACCACCACCAACACCACCTCCTCCTCCAGCACCTA
Found at i:271 original size:24 final size:24
Alignment explanation
Indices: 241--334 Score: 80
Period size: 24 Copynumber: 3.9 Consensus size: 24
231 CCAGCGCCTA
*
241 CACCACCACCAACACCTCCTCCTC
1 CACCACCACCAGCACCTCCTCCTC
* * * * * *
265 CTCCACCTCTACCACCACCACCTC
1 CACCACCACCAGCACCTCCTCCTC
* * **
289 CACCACCTCCGGCACCTCCTCCAA
1 CACCACCACCAGCACCTCCTCCTC
*
313 CACCACCACCAGCACCTACTCC
1 CACCACCACCAGCACCTCCTCC
335 ACCCCCAACA
Statistics
Matches: 53, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.23, C:0.61, G:0.03, T:0.13
Consensus pattern (24 bp):
CACCACCACCAGCACCTCCTCCTC
Found at i:346 original size:24 final size:24
Alignment explanation
Indices: 300--346 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
290 ACCACCTCCG
* *
300 GCACCTCCTCCAACACCACCACCA
1 GCACCTACTCCAACACCAACACCA
* *
324 GCACCTACTCCACCCCCAACACC
1 GCACCTACTCCAACACCAACACC
347 TCCTCCTGCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.60, G:0.04, T:0.09
Consensus pattern (24 bp):
GCACCTACTCCAACACCAACACCA
Found at i:363 original size:42 final size:42
Alignment explanation
Indices: 261--364 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 42
251 AACACCTCCT
* * * * **
261 CCTCCTCCACCTCTACCACCACCACCTCCACCACCTCCGGCA
1 CCTCCTCCAACACTACCACCACCACCTACACCACCCCCAACA
* * *
303 CCTCCTCCAACACCACCACCAGCACCTACTCCACCCCCAACA
1 CCTCCTCCAACACTACCACCACCACCTACACCACCCCCAACA
**
345 CCTCCTCCTGCACTACCACC
1 CCTCCTCCAACACTACCACC
365 GGCTCCTCCT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.22, C:0.61, G:0.04, T:0.13
Consensus pattern (42 bp):
CCTCCTCCAACACTACCACCACCACCTACACCACCCCCAACA
Found at i:411 original size:18 final size:18
Alignment explanation
Indices: 318--412 Score: 57
Period size: 18 Copynumber: 5.3 Consensus size: 18
308 TCCAACACCA
* * *
318 CCACCAGCACCTACTCCA
1 CCACCAACACCTCCTCCT
*
336 CCCCCAACACCTCCTCCT
1 CCACCAACACCTCCTCCT
* * * **
354 GCACTACCACCGGCTCCT
1 CCACCAACACCTCCTCCT
* * * *
372 CCTCCAGCACCT-ATGCCG
1 CCACCAACACCTCCT-CCT
390 CCACCAACACCTCCTCCT
1 CCACCAACACCTCCTCCT
408 CCACC
1 CCACC
413 TCCACCACCT
Statistics
Matches: 54, Mismatches: 21, Indels: 4
0.68 0.27 0.05
Matches are distributed among these distances:
17 1 0.02
18 52 0.96
19 1 0.02
ACGTcount: A:0.20, C:0.58, G:0.07, T:0.15
Consensus pattern (18 bp):
CCACCAACACCTCCTCCT
Found at i:457 original size:30 final size:30
Alignment explanation
Indices: 406--462 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
396 ACACCTCCTC
* *
406 CTCCACCTCCACCACCTACACCCCCACTTG
1 CTCCACCTCCACCACCGACACCACCACTTG
* *
436 CTCCACCTCCGCCTCCGACACCACCAC
1 CTCCACCTCCACCACCGACACCACCAC
463 CAACTTCGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.19, C:0.61, G:0.05, T:0.14
Consensus pattern (30 bp):
CTCCACCTCCACCACCGACACCACCACTTG
Found at i:1911 original size:14 final size:14
Alignment explanation
Indices: 1892--1919 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1882 TACCTAAAAT
1892 AAATATACTGAAAC
1 AAATATACTGAAAC
1906 AAATATACTGAAAC
1 AAATATACTGAAAC
1920 TAATCGTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
AAATATACTGAAAC
Found at i:21876 original size:87 final size:87
Alignment explanation
Indices: 21730--21888 Score: 318
Period size: 87 Copynumber: 1.8 Consensus size: 87
21720 ACAAGGTAGG
21730 TGGACATGGCCTTAAACATGTTCTTATAAACTATTCACAGCCATTACTGTTGGTAGGTTCAATGG
1 TGGACATGGCCTTAAACATGTTCTTATAAACTATTCACAGCCATTACTGTTGGTAGGTTCAATGG
21795 AACTATGAACAAGGTAGATTAC
66 AACTATGAACAAGGTAGATTAC
21817 TGGACATGGCCTTAAACATGTTCTTATAAACTATTCACAGCCATTACTGTTGGTAGGTTCAATGG
1 TGGACATGGCCTTAAACATGTTCTTATAAACTATTCACAGCCATTACTGTTGGTAGGTTCAATGG
21882 AACTATG
66 AACTATG
21889 TGAGCACTTG
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (87 bp):
TGGACATGGCCTTAAACATGTTCTTATAAACTATTCACAGCCATTACTGTTGGTAGGTTCAATGG
AACTATGAACAAGGTAGATTAC
Found at i:38276 original size:21 final size:21
Alignment explanation
Indices: 38252--38291 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
38242 AGCCCGAAAT
38252 CAACTCCACGCA-CACCTCTAC
1 CAACTCCAC-CACCACCTCTAC
38273 CAACTCCACCACCACCTCT
1 CAACTCCACCACCACCTCT
38292 TCCTCTCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.28, C:0.55, G:0.03, T:0.15
Consensus pattern (21 bp):
CAACTCCACCACCACCTCTAC
Found at i:42921 original size:13 final size:13
Alignment explanation
Indices: 42905--42930 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42895 GACATTTAAT
42905 TATAAAAAATTTA
1 TATAAAAAATTTA
42918 TATAAAAAATTTA
1 TATAAAAAATTTA
42931 AAAAATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATAAAAAATTTA
Found at i:48715 original size:23 final size:23
Alignment explanation
Indices: 48689--48733 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
48679 TGGCTTCCAA
*
48689 GGTTTTA-TATTAAACTTATTTTG
1 GGTTTTATTA-TAAACGTATTTTG
48712 GGTTTTATTATAAACGTATTTT
1 GGTTTTATTATAAACGTATTTT
48734 AAATGTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.27, C:0.04, G:0.13, T:0.56
Consensus pattern (23 bp):
GGTTTTATTATAAACGTATTTTG
Found at i:86242 original size:23 final size:22
Alignment explanation
Indices: 86211--86255 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
86201 TCAGCTACAC
*
86211 TTTTATTTATTTTTCAATCAACA
1 TTTTATTTA-ATTTCAATCAACA
* *
86234 TTTTTTTTAATTTCATTCAACA
1 TTTTATTTAATTTCAATCAACA
86256 CTTTGCTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATTTAATTTCAATCAACA
Found at i:87064 original size:14 final size:15
Alignment explanation
Indices: 87039--87067 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
87029 TGTTTAATCT
87039 CTCGAATCCAATCAC
1 CTCGAATCCAATCAC
87054 CTCGAAT-CAATCAC
1 CTCGAATCCAATCAC
87068 TTGTTGACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.38, G:0.07, T:0.21
Consensus pattern (15 bp):
CTCGAATCCAATCAC
Found at i:87282 original size:12 final size:12
Alignment explanation
Indices: 87265--87289 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
87255 CACAATTTCT
87265 ATCTAAGCATAA
1 ATCTAAGCATAA
87277 ATCTAAGCATAA
1 ATCTAAGCATAA
87289 A
1 A
87290 AAGGACAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (12 bp):
ATCTAAGCATAA
Found at i:110022 original size:63 final size:61
Alignment explanation
Indices: 109893--110043 Score: 175
Period size: 63 Copynumber: 2.5 Consensus size: 61
109883 TTGCAGAGAT
* *
109893 TAATGTTGAAATTGAGGCAATGTCCC---GAATAATTTGTGGTCCATTGGACTCGCAAAGA
1 TAATGTTGAAATTGATGCAATGTCCCGTAGAATAATTTGCGGTCCATTGGACTCGCAAAGA
* * *
109951 TTAATGTTGAAATTGATGCAATGTCCCGTAAGAATACTTTGCGGTCCATTGAGACTTGCAATGGA
1 -TAATGTTGAAATTGATGCAATGTCCCGT-AGAATAATTTGCGGTCCATTG-GACTCGCAA-AGA
* *
110016 -AATGTTGATATTGATGCATTGTCCCGTA
1 TAATGTTGAAATTGATGCAATGTCCCGTA
110044 CTATAAAGTT
Statistics
Matches: 79, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
59 25 0.32
62 1 0.01
63 43 0.54
64 8 0.10
65 2 0.03
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.32
Consensus pattern (61 bp):
TAATGTTGAAATTGATGCAATGTCCCGTAGAATAATTTGCGGTCCATTGGACTCGCAAAGA
Found at i:110355 original size:237 final size:234
Alignment explanation
Indices: 109928--110396 Score: 699
Period size: 237 Copynumber: 2.0 Consensus size: 234
109918 CGAATAATTT
* * *
109928 GTGGTCCATTGGACTCGCAAAGATTAATGTTGAAATTGATGCAATGTCCCGTAAGAATACTTTGC
1 GTGGTCCACTGGACTCGCAAAGATTAATGTTGAAATTGATGCAATGTCCCATAAGAACACTTTGC
* * * * *
109993 GGTCCATTGAGACTTGCAATGGAAATGTTGATATTGATGCATTGTCCCGTACTATAAAGTTTGGT
66 GGTCCACTGAGACTTGCAAAGGAAATGTTGATATCGATGCATTGTCCCATACTAGAAAGTTTGGT
* *
110058 ATTGACAGTTGCTTATAGATGGTGAGTTCTATATTTGAGAGGCTCAGTTTGATGAAAATATTAGT
131 ATTGACAGTTGCTTATAGATGGTGAGTTCTATATTTGAGAGGCTCAATTTGATCAAAATA-T-GT
* *
110123 GTCATTTGTACGGG-TGTTGGTTGCTCT-TCTTTGTATACTTA
194 GTCATATGT-CGGGATGTCGGTTGCTCTGT-TTTGTATACTTA
** *
110164 GTGGTCCACTGGACTCGCAAAGATTTTTGTTGAAATTGATGCAATGTCCCATATGAACACTTTGC
1 GTGGTCCACTGGACTCGCAAAGATTAATGTTGAAATTGATGCAATGTCCCATAAGAACACTTTGC
*
110229 GGTCCACTGAGACTTGCAAAGGTTAATGTTGATATCGATGCATTGTCCCATACTAGAAAGTTTGG
66 GGTCCACTGAGACTTGCAAAGG-AAATGTTGATATCGATGCATTGTCCCATACTAGAAAGTTTGG
* * *
110294 TATTGACAGTTGCTTATGGTTGGTGCGTTCTATATTTGAGAGGCTCAATTTGATCAAAATATGTG
130 TATTGACAGTTGCTTATAGATGGTGAGTTCTATATTTGAGAGGCTCAATTTGATCAAAATATGTG
*
110359 TCATATGTGGGGATGTCGGTTGCTCTGTTTTGTATACT
195 TCATATGTCGGGATGTCGGTTGCTCTGTTTTGTATACT
110397 GCTGAGCTTT
Statistics
Matches: 210, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
234 3 0.01
235 32 0.15
236 81 0.39
237 94 0.45
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.37
Consensus pattern (234 bp):
GTGGTCCACTGGACTCGCAAAGATTAATGTTGAAATTGATGCAATGTCCCATAAGAACACTTTGC
GGTCCACTGAGACTTGCAAAGGAAATGTTGATATCGATGCATTGTCCCATACTAGAAAGTTTGGT
ATTGACAGTTGCTTATAGATGGTGAGTTCTATATTTGAGAGGCTCAATTTGATCAAAATATGTGT
CATATGTCGGGATGTCGGTTGCTCTGTTTTGTATACTTA
Found at i:113520 original size:29 final size:29
Alignment explanation
Indices: 113478--113558 Score: 162
Period size: 29 Copynumber: 2.8 Consensus size: 29
113468 GCTCCCCTTT
113478 TGCTTTAATTGATTCCTCATATATGCAAG
1 TGCTTTAATTGATTCCTCATATATGCAAG
113507 TGCTTTAATTGATTCCTCATATATGCAAG
1 TGCTTTAATTGATTCCTCATATATGCAAG
113536 TGCTTTAATTGATTCCTCATATA
1 TGCTTTAATTGATTCCTCATATA
113559 GTCCATGTTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.43
Consensus pattern (29 bp):
TGCTTTAATTGATTCCTCATATATGCAAG
Found at i:116459 original size:30 final size:28
Alignment explanation
Indices: 116403--116456 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
116393 TTCTTCCCTT
* * *
116403 TCCATTTTGTCACATATAATGCTCTCCC
1 TCCATTTTGCCACACACAATGCTCTCCC
116431 TCCATTTTGCCACACACAATGCTCTC
1 TCCATTTTGCCACACACAATGCTCTC
116457 TCCTGATATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.22, C:0.35, G:0.07, T:0.35
Consensus pattern (28 bp):
TCCATTTTGCCACACACAATGCTCTCCC
Found at i:126537 original size:80 final size:80
Alignment explanation
Indices: 126446--126606 Score: 322
Period size: 80 Copynumber: 2.0 Consensus size: 80
126436 TTTCTTCTTT
126446 TTAATTACTATTTTTATTTAAATATTGATGCAGCTTGTGAAGGTGATACTTAAAGTAAAGATTTA
1 TTAATTACTATTTTTATTTAAATATTGATGCAGCTTGTGAAGGTGATACTTAAAGTAAAGATTTA
126511 TATCGCAATCTTCTA
66 TATCGCAATCTTCTA
126526 TTAATTACTATTTTTATTTAAATATTGATGCAGCTTGTGAAGGTGATACTTAAAGTAAAGATTTA
1 TTAATTACTATTTTTATTTAAATATTGATGCAGCTTGTGAAGGTGATACTTAAAGTAAAGATTTA
126591 TATCGCAATCTTCTA
66 TATCGCAATCTTCTA
126606 T
1 T
126607 ATTTAAACTA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.43
Consensus pattern (80 bp):
TTAATTACTATTTTTATTTAAATATTGATGCAGCTTGTGAAGGTGATACTTAAAGTAAAGATTTA
TATCGCAATCTTCTA
Found at i:139645 original size:13 final size:13
Alignment explanation
Indices: 139627--139651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
139617 GGTTGCCCAA
139627 CCAAAAAAAAAAC
1 CCAAAAAAAAAAC
139640 CCAAAAAAAAAA
1 CCAAAAAAAAAA
139652 AAAATCCTGT
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:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (13 bp):
CCAAAAAAAAAAC
Found at i:141060 original size:28 final size:29
Alignment explanation
Indices: 141015--141077 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
141005 TGTGGCGTGT
* *
141015 TTTTCCCCCTAAATTTCAATTTTG-GACA
1 TTTTGCCCCTAAACTTCAATTTTGAGACA
* *
141043 TTTTGCCCCTGAACTTCAATTTTGAGACG
1 TTTTGCCCCTAAACTTCAATTTTGAGACA
141072 TTTTGC
1 TTTTGC
141078 TTGTGCCGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.43
Consensus pattern (29 bp):
TTTTGCCCCTAAACTTCAATTTTGAGACA
Found at i:141158 original size:21 final size:20
Alignment explanation
Indices: 141129--141167 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
141119 CTGAGGGGGC
141129 AAAACGTCCCAAAATTGAAGT
1 AAAACGT-CCAAAATTGAAGT
*
141150 AAAATGTCCAAAATTGAA
1 AAAACGTCCAAAATTGAA
141168 ATTCAGGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (20 bp):
AAAACGTCCAAAATTGAAGT
Found at i:144157 original size:31 final size:31
Alignment explanation
Indices: 144115--144174 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
144105 TGTTTAGCAA
144115 CCAAAACAAAACTTCTCCCAAACAGATTTTG
1 CCAAAACAAAACTTCTCCCAAACAGATTTTG
*
144146 CCAAAATAAAACTTCTCCCAAACAGATTT
1 CCAAAACAAAACTTCTCCCAAACAGATTT
144175 CACTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.28, G:0.05, T:0.23
Consensus pattern (31 bp):
CCAAAACAAAACTTCTCCCAAACAGATTTTG
Found at i:144834 original size:2 final size:2
Alignment explanation
Indices: 144827--144863 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
144817 TAGCTAGATT
144827 TA TA TA TA 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 TA TA TA TA T
144864 TTTATGCATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:145159 original size:3 final size:3
Alignment explanation
Indices: 145153--145235 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
145143 CACAAACTAC
145153 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
145201 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
145236 AAAGTGAAAA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:145508 original size:17 final size:19
Alignment explanation
Indices: 145466--145510 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
145456 TTTATGAACT
145466 TATTATTATAATAATAATA
1 TATTATTATAATAATAATA
* *
145485 TAATATTAT-AT-ATTATA
1 TATTATTATAATAATAATA
145502 TATTATTAT
1 TATTATTAT
145511 TAAGTATACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 13 0.57
18 2 0.09
19 8 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTATTATAATAATAATA
Found at i:146087 original size:14 final size:15
Alignment explanation
Indices: 146056--146096 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
146046 ATTTCTTTTC
*
146056 AAAAA-AAATAAAGA
1 AAAAAGAAAGAAAGA
146070 AAAAAGAAAGAAAGA
1 AAAAAGAAAGAAAGA
*
146085 AAAGA-AAAGAAA
1 AAAAAGAAAGAAA
146097 CTTAATAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAGAAAGA
Found at i:159728 original size:4 final size:4
Alignment explanation
Indices: 159719--159755 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
159709 GTTCTTCTAA
159719 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
159756 ATTTTCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (4 bp):
CTTT
Found at i:162005 original size:12 final size:12
Alignment explanation
Indices: 161988--162034 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
161978 AGTGGGGGTA
161988 ATACTATACTAT
1 ATACTATACTAT
162000 ATACTATACTAT
1 ATACTATACTAT
162012 ATAC-ATAC-AT
1 ATACTATACTAT
162022 ATA-TATA-TAT
1 ATACTATACTAT
162032 ATA
1 ATA
162035 TCAAAGGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
10 13 0.39
11 4 0.12
12 16 0.48
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (12 bp):
ATACTATACTAT
Found at i:164881 original size:33 final size:33
Alignment explanation
Indices: 164839--164904 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
164829 CTTGAATAAA
*
164839 ATACTACTTAGGCACTATATTGTAATCTTCAAT
1 ATACTACTTAGGCACTATATCGTAATCTTCAAT
164872 ATACTACTTAGGCACTATATCGTAATCTTCAAT
1 ATACTACTTAGGCACTATATCGTAATCTTCAAT
164905 CCCCACGGTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (33 bp):
ATACTACTTAGGCACTATATCGTAATCTTCAAT
Found at i:169369 original size:16 final size:17
Alignment explanation
Indices: 169348--169380 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
169338 CATTCTGTTG
169348 AGTGAT-TATATGTCTC
1 AGTGATATATATGTCTC
*
169364 AGTGATATATTTGTCTC
1 AGTGATATATATGTCTC
169381 TGAGCCATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.45
Consensus pattern (17 bp):
AGTGATATATATGTCTC
Found at i:174378 original size:336 final size:333
Alignment explanation
Indices: 172593--175801 Score: 3791
Period size: 336 Copynumber: 9.7 Consensus size: 333
172583 ACAAGGTATT
* * ** * * *
172593 AGCTAAGTTTTGCATGATTTTTGGCGTCAAAGA--AGTTGAAATATCTATATTCATCTAACTAAA
1 AGCTCAGTTTTGCATGATTTTTGGCG-CCAAGACTTCTTGAAATATCTTTATTCTTCTAACCAAA
* * * * * *
172656 TCTCAGTCATATTGGATTTAAGGATTTGCTTTTACGAGCATTTGAATCATGTTTCCATTTAATCA
65 TCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCA
* * * * *
172721 GAAATTATTTCAGATAAAACTGGAAAAATGATATTAGAAGTGTGAAAA--AC-TCATTCTTTTTG
130 GAAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCTCTTCATTCTTTTTG
* * * * *
172783 TCGTTGAAATATATATATTTTTTATGAGTGTCGTGGCTAAAAATTTAGGAAAAATCTTTTGTGTC
195 GCGTTG-AAT-TATATA-TTTTTATGAGTAT-TTGGCTAAAAATTTAGGAAAAATCTTTCGGGTC
* * *
172848 AA-TTTTTTGAAAAATTTTAGCCG-AATCATGTACTAACCATCACAGTTTTTTTTGGGCT-AAAA
256 AATTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAG---TTTTT-GGCTAAAAA
**
172910 ACGCGTTCCGGG-TTCC
317 ACGCGTTCCGGGACCCC
* ** * * * * **
172926 AGCTCAGTTTTGCATAATTTTTGATGTCAAGACTCCTTGAAATATCTATACTCAACTAACCAAAT
1 AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAATATCTTTATTCTTCTAACCAAAT
* * * * *
172991 CTCAGCCACATTGGACTT-GGTGATTTGTTTTTATGAGCATCTGAATCATTTTTCGATTTAATCA
66 CTCAGCCACATTAGATTTAAG-GATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCA
* * * * * * *
173055 TG-AATAAATGCAGATAAAACTCGAAAATCGATATTACAAGTGTGAAAAAG-TCTTCATTCTTTT
130 -GAAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTG-AAAAGCTCTTCATTCTTTT
* * * * * *
173118 TAGCGATGAATTATATATTTTTATTAGTATTGTGGCAAAAAATTTAGGAAAAATATTACGGGTCA
193 TGGCGTTGAATTATATATTTTTATGAGTATT-TGGCTAAAAATTTAGGAAAAATCTTTCGGGTCA
* * * * ** *
173183 A-CTTTTCGAAAAATTTTAGCCGAAAT-ATGTA-T-ATTATCATAGTTTTTGGTTAAAAAACGCG
257 ATTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAAAACGCG
* * *
173244 TTCTGAGATCCC
322 TTCCGGGACCCC
* * * ** *** * *
173256 GGCCCAATTTTATATGATTTTTTTTGACAAGACTCCTTGAAATATC--TA------T-A-C---T
1 AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAATATCTTTATTCTTCTAACCAAAT
* * * * * * * *
173308 -T-AGCTACATTGGATTTAATGTTTTGTTTTCACGAGCATCTGAATCATGTTTCAATTTAGTCAT
66 CTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAG
** * *
173371 AAATTAATTTTGATAAAATTGGAAAAACGATATTAGAGGCGTGAAAAGCTTTTCATTCTTTTTGG
131 AAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCTCTTCATTCTTTTTGG
* * * *
173436 CGTTGAATTATACATTTTTAAGAGTATTATGGCTAAAAATTTAAGAAAAATCTTTCGGGTCAA-A
196 CGTTGAATTATATATTTTTATGAGTATT-TGGCTAAAAATTTAGGAAAAATCTTTCGGGTCAATT
* * * *
173500 TTTTTGCAAAATTTTAACCGAAATCCTGTACT-A-CATCACACTTTTTGGCTAAAAAACGCGTTC
260 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAAAACGCGTTC
173563 CGGGACCCC
325 CGGGACCCC
* * * *
173572 -GACACAGTTTTGCATGATTTTTGGCGCCAAGAC-TCCTGAAATATCTATATTCATCTAACCAAA
1 AG-CTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAATATCTTTATTCTTCTAACCAAA
* * *
173635 TCTCAGTCACATTGGATTTAAGGATTGGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCA
65 TCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCA
* * *
173700 GAAAATAATTCAGATAAAATTGGAAAAACGATATTAGAAGCATGAAAAGCTCTTAATTCTTTTT-
130 GAAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCTCTTCATTCTTTTTG
**
173764 TTGTTGAATTATATAATTTTTATGAGTATTGTGGCTAAAAATTTAGGAAAAATCTTTCGGGTCAA
195 GCGTTGAATTATAT-ATTTTTATGAGTATT-TGGCTAAAAATTTAGGAAAAATCTTTCGGGTCAA
* *
173829 TTTTTTTGCAAAATTATAGCCAAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAAAACGCGT
258 TTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAAAACGCGT
**
173894 T-CTAGACCCC
323 TCCGGGACCCC
** * * ** *
173904 AGCTCAGTTTTGCATGATTTTTATCGCCAAGACTCCTTCAAATATCTACATTCATCTAACCAAAT
1 AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAATATCTTTATTCTTCTAACCAAAT
* * * *
173969 CTCAGCCACATTGGATTTAAGGATTCGTTTTTACAAGCATGTGAATCATGTTTCGATTTAATCAG
66 CTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAG
* * * * * *
174034 ACATTAATTCAGATTAAATTAGAAAAACGATATTAAAAGCGTGAAAAGCTCTTCATTATTTCTGG
131 AAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCTCTTCATTCTTTTTGG
* * * *
174099 CGTTGAATTATATATTTTTATGAGTATTGTTGCTAAAAGTTTAGGAGAAATCTTCCGGGTCAA-T
196 CGTTGAATTATATATTTTTATGAGTATT-TGGCTAAAAATTTAGGAAAAATCTTTCGGGTCAATT
* * *
174163 TTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATCACAGTTTTTGGCTAAAAAACGCGTTT
260 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAAAACGCGTTC
174228 CGGGACCACGGC
325 CGGGACC-C--C
* ** * * * * *
174240 -GACTTAGTTTTGCATGATTTTTGGCGTGAAGACTCCTTAAAATATATATATTCATCTAACCAAA
1 AG-CTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAATATCTTTATTCTTCTAACCAAA
* *
174304 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTGAA-CA
65 TCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCA
* * *
174368 TGAAATTAATTCAGATAAAATTGGAAAAACGATAATAGAAGCGTGAAAAGCTCTTCATTCTATAT
130 -GAAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCTCTTCATTCTTTTT
* * * * * *
174433 GTCATTTAATTATATATGTTTTATAAGTTTTATGGCTAAGAATTTAGGAAAAATCTTTCGGGTCA
194 GGCGTTGAATTATATAT-TTTTATGAGTATT-TGGCTAAAAATTTAGGAAAAATCTTTCGGGTCA
*
174498 ATTTTTTTGCAAAATTTGAGCCGAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAAAACGCG
257 ATTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAAAACGCG
*
174563 TTCCGGGGCCCC
322 TTCCGGGACCCC
* * *
174575 AGCTTAGTTTTGCATGATTTTTGGCGTCAAGACTTCTTGAAATATATTTATTCTTCTAACCAAAT
1 AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAATATCTTTATTCTTCTAACCAAAT
* * *
174640 CTCAGCCACATTAGATTTAAGGATTTGTTTTTACAAGCATTTGAATCATGTTTCGATTTAATCAT
66 CTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAG
* * * * * * *
174705 AAATTACTTCAGAGATAATTGGAAAATCAATATTAGAAGCGTGAAAAACTCTTCATTCTTTTTGC
131 AAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCTCTTCATTCTTTTTGG
* * ** *
174770 CGTTGAATTATATATTTTTTATCATTATTTTTTTCTAAAAATTTAGGAAAAATCTTTCGGATCAA
196 CGTTGAATTATATA-TTTTTATGAGTA--TTTGGCTAAAAATTTAGGAAAAATCTTTCGGGTCAA
*
174835 TTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAACGCGT
258 TTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAAAACGCGT
174900 TCCCGGG-CCCC
323 T-CCGGGACCCC
* * *
174911 AGCTCAGCTTTGCATGATTTTTGGTGCCAAGACTTCTTGAAATATATTTATTCTTCTAACCAAAT
1 AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAATATCTTTATTCTTCTAACCAAAT
* * *
174976 CTCAGCCACATTAGATTTAAGGATTTGTTTTCACGAGCTTCTGAATCATGTTTGGATTTAATCAG
66 CTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAG
** * *
175041 AAATTAGCTCAGATAAAATTGGAAAAAC-AGTATTAGAAGCGTGAAAATCTCTTCAATCTTTTTG
131 AAATTAATTCAGATAAAATTGGAAAAACGA-TATTAGAAGCGTGAAAAGCTCTTCATTCTTTTTG
* *
175105 GAGTTTAATTATATATTTTTATGAGTATATTGGCTAAAAATTTAGGAAAAATCTTTCGGGTCAAT
195 GCGTTGAATTATATATTTTTATGAGTAT-TTGGCTAAAAATTTAGGAAAAATCTTTCGGGTCAA-
** *
175170 TTTTTTTGCAAAATTTTAGCCGAAATCAAGTATTAACCATCATAGTTTTTGGCTAAAAAACGCGT
258 TTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAAAACGCGT
175235 TCC-GGAGCCCC
323 TCCGGGA-CCCC
175246 AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAATATCTTTATTCTTCTAACCAAAA
1 AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAATATCTTTATTCTTCTAACC-AAA
*
175311 TCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGGGCATCTGAATCATGTTTCGATTTAATCA
65 TCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCA
* * *
175376 GAAATTAAATCAGATAAAATTGGAAAAAC-AGTATTAGAAGCATGAAAATCTCTTCAATT-TTTT
130 GAAATTAATTCAGATAAAATTGGAAAAACGA-TATTAGAAGCGTGAAAAGCTCTTC-ATTCTTTT
175439 TGGCGTTGAATTATATATTTTTTATGAGTATATTGGCTAAAAATTTAGGAAAAAAT-TTTCGGGT
193 TGGCGTTGAATTATATA-TTTTTATGAGTAT-TTGGCTAAAAATTTAGG-AAAAATCTTTCGGGT
* * *
175503 CAA-TTTTTTGC-AAATTTTAGCCGAAATCGTGTACTAACCATAATAGTTTTTTGCTAAAAATCG
255 CAATTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAAAACG
* * *
175566 CGCTCCGGGGCTCC
320 CGTTCCGGGACCCC
* * *
175580 AGCTCAATTTTGCATGATTTTTGGCGCCAAAACTTCTTGAAATATCTTTATTCTTCTAACAAAAT
1 AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAATATCTTTATTCTTCTAACCAAAT
* * * *
175645 CTCAGTCACATTAGATTTAAGGATTTGTTTTTATGAGCATCTGAATCATGTATAGATTTAATCAG
66 CTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAG
* * * * *
175710 AAATTAAATCAGATAAAATTGGAAAAA-AAGTATTAGAAGCGTGAAAATCTCTTCAATCTTCTTG
131 AAATTAATTCAGATAAAATTGGAAAAACGA-TATTAGAAGCGTGAAAAGCTCTTCATTCTTTTTG
*
175774 GCGTTGAATTATATATTTTTATAAGTAT
195 GCGTTGAATTATATATTTTTATGAGTAT
175802 ATT
Statistics
Matches: 2507, Mismatches: 304, Indels: 131
0.85 0.10 0.04
Matches are distributed among these distances:
314 5 0.00
315 182 0.07
316 60 0.02
317 5 0.00
320 1 0.00
321 1 0.00
322 1 0.00
323 1 0.00
324 1 0.00
325 1 0.00
328 6 0.00
329 31 0.01
330 196 0.08
331 28 0.01
332 122 0.05
333 384 0.15
334 337 0.13
335 353 0.14
336 611 0.24
337 107 0.04
338 74 0.03
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (333 bp):
AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAATATCTTTATTCTTCTAACCAAAT
CTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAG
AAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCTCTTCATTCTTTTTGG
CGTTGAATTATATATTTTTATGAGTATTTGGCTAAAAATTTAGGAAAAATCTTTCGGGTCAATTT
TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAAAACGCGTTCC
GGGACCCC
Found at i:174759 original size:671 final size:664
Alignment explanation
Indices: 172593--175801 Score: 3823
Period size: 671 Copynumber: 4.8 Consensus size: 664
172583 ACAAGGTATT
* * ** *
172593 AGCTAAGTTTTGCATGATTTTTGGCGTCAAAGA--AGTTGAAATATCTATATTCATCTAACTAAA
1 AGCTCAGTTTTGCATGATTTTTGGCG-CCAAGACTCCTTGAAATATCTATATTCATCTAACCAAA
* * * * *
172656 TCTCAGTCATATTGGATTTAAGGATTTGCTTTTACGAGCATTTGAATCATGTTTCCATTTAATCA
65 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCA
* * * *
172721 GAAATTATTTCAGATAAAACTGGAAAAATGATATTAGAAGTGTGAAAAA--C-TCATTCTTTTTG
130 GAAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAACTCTTCATT-TTTTTG
* * * * *
172783 TCGTTGAAATATATATATTTTTTATGAGTGTCGTGGCTAAAAATTTAGGAAAAATCTTTTGTGTC
194 GCGTTG-AAT-TATATATTTTTTATGAGTATTGTGGCTAAAAATTTAGGAAAAATCTTTCGGGTC
* *
172848 AATTTTTTGAAAAATTTTAGCCG-AATCATGTACTAACCATCACAGTTTTTTTTGGGCT-AAAAA
257 AATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAG---TTTTT-GGCTAAAAAA
** * ** *
172911 CGCGTTCCGGGTTCC-AGCTCAGTTTTGCATAATTTTTGATGTCAAGACTCCTTGAAATATCTAT
318 CGCGTTCCGGGCCCCGA-CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTAT
* * * * *
172975 ACTCAACTAACCAAATCTCAGCCACATTGGACTT-GGTGATTTGTTTTTATGAGCATCTGAATCA
382 ATTCATCTAACCAAATCTCAGCCACATTGGATTTAAG-GATTTGTTTTTACGAGCATCTGAATCA
* * * * * * * *
173039 TTTTTCGATTTAATCATG-AATAAATGCAGATAAAACTCGAAAATCGATATTACAAGTGTGAAAA
446 TGTTTCGATTTAATCA-GAAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTG-AAA
* * *
173103 AG-TCTTCATTCTTTTTAGCGA-TGAATTATATATTTTTATTAGTATTGTGGCAAAAAATTTAGG
509 AGCTCTTCATTC-TTTT-GC-ATTGAATTATATATTTTTATAAGTATTATGGCTAAAAATTTAGG
* * * * * **
173166 AAAAATATTACGGGTCAA-CTTTTCGAAAAATTTTAGCCGAAAT-ATGTA-T-ATTATCATAGTT
571 AAAAATCTTTCGGGTCAATTTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCATAGTT
* * *
173227 TTTGGTTAAAAAACGCGTTCTGAGATCCC
636 TTTGGCTAAAAAACGCGTTCCGAGACCCC
* * * ** *** *
173256 GGCCCAATTTTATATGATTTTTTTTGACAAGACTCCTTGAAATATC-----T-A--T-A-C---T
1 AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
* * * * * * *
173308 -T-AGCTACATTGGATTTAATGTTTTGTTTTCACGAGCATCTGAATCATGTTTCAATTTAGTCAT
66 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAG
** * * *
173371 AAATTAATTTTGATAAAATTGGAAAAACGATATTAGAGGCGTGAAAAGCTTTTCATTCTTTTTGG
131 AAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAACTCTTCATT-TTTTTGG
* * * * *
173436 CGTTGAATTATACA-TTTTTAAGAGTATTATGGCTAAAAATTTAAGAAAAATCTTTCGGGTCAAA
195 CGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTTAGGAAAAATCTTTCGGGTCAAT
* * *
173500 TTTTTGCAAAATTTTAACCGAAATCCTGTACT-A-CATCACACTTTTTGGCTAAAAAACGCGTTC
260 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAACGCGTTC
*
173563 CGGGACCCCGACACAGTTTTGCATGATTTTTGGCGCCAAGACTCC-TGAAATATCTATATTCATC
325 CGGG-CCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATC
* *
173627 TAACCAAATCTCAGTCACATTGGATTTAAGGATTGGTTTTTACGAGCATCTGAATCATGTTTCGA
389 TAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGA
* * *
173692 TTTAATCAGAAAATAATTCAGATAAAATTGGAAAAACGATATTAGAAGCATGAAAAGCTCTTAAT
454 TTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCTCTTCAT
*** * *
173757 TCTTTTTTTGTTGAATTATATAATTTTTATGAGTATTGTGGCTAAAAATTTAGGAAAAATCTTTC
519 TC-TTTTGCATTGAATTATAT-ATTTTTATAAGTATTATGGCTAAAAATTTAGGAAAAATCTTTC
* * *
173822 GGGTCAATTTTTTTGCAAAATTATAGCCAAAATCGTGTACTAACCATCATAGTTTTTGGCTAAAA
582 GGGTCAATTTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCATAGTTTTTGGCTAAAA
*
173887 AACGCGTT-CTAGACCCC
647 AACGCGTTCCGAGACCCC
** * *
173904 AGCTCAGTTTTGCATGATTTTTATCGCCAAGACTCCTTCAAATATCTACATTCATCTAACCAAAT
1 AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
* * *
173969 CTCAGCCACATTGGATTTAAGGATTCGTTTTTACAAGCATGTGAATCATGTTTCGATTTAATCAG
66 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAG
* * * * * *
174034 ACATTAATTCAGATTAAATTAGAAAAACGATATTAAAAGCGTGAAAAGCTCTTCATTATTTCTGG
131 AAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAACTCTTCATT-TTTTTGG
* * * *
174099 CGTTGAATTATATA-TTTTTATGAGTATTGTTGCTAAAAGTTTAGGAGAAATCTTCCGGGTCAAT
195 CGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTTAGGAAAAATCTTTCGGGTCAAT
* *
174163 TTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATCACAGTTTTTGGCTAAAAAACGCGTTT
260 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAACGCGTTC
* ** * *
174228 CGGGACCACGGCGACTTAGTTTTGCATGATTTTTGGCGTGAAGACTCCTTAAAATATATATATTC
325 CGGG-CC-C--CGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTC
174293 ATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTT
386 ATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTT
* *
174358 CGATTGAA-CATGAAATTAATTCAGATAAAATTGGAAAAACGATAATAGAAGCGTGAAAAGCTCT
451 CGATTTAATCA-GAAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCTCT
* * * *
174422 TCATTCTATATGTCATTTAATTATATATGTTTTATAAGTTTTATGGCTAAGAATTTAGGAAAAAT
515 TCATTCT-TTTG-CATTGAATTATATAT-TTTTATAAGTATTATGGCTAAAAATTTAGGAAAAAT
* *
174487 CTTTCGGGTCAATTTTTTTGCAAAATTTGAGCCGAAATCGTGTACTAACCATCATAGTTTTTGGC
577 CTTTCGGGTCAATTTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCATAGTTTTTGGC
* *
174552 TAAAAAACGCGTTCCGGGGCCCC
642 TAAAAAACGCGTTCCGAGACCCC
* * * * * *
174575 AGCTTAGTTTTGCATGATTTTTGGCGTCAAGACTTCTTGAAATATATTTATTCTTCTAACCAAAT
1 AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
* * * *
174640 CTCAGCCACATTAGATTTAAGGATTTGTTTTTACAAGCATTTGAATCATGTTTCGATTTAATCAT
66 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAG
* * * * * *
174705 AAATTACTTCAGAGATAATTGGAAAATCAATATTAGAAGCGTGAAAAACTCTTCATTCTTTTTGC
131 AAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAACTCTTCATT-TTTTTGG
* * * ** *
174770 CGTTGAATTATATATTTTTTATCATTATTTTTTTCTAAAAATTTAGGAAAAATCTTTCGGATCAA
195 CGTTGAATTATATATTTTTTATGAGTA-TTGTGGCTAAAAATTTAGGAAAAATCTTTCGGGTCAA
174835 TTTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAACGCGT
259 -TTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAACGCGT
* * * * *
174900 TCCCGGGCCCC-AGCTCAGCTTTGCATGATTTTTGGTGCCAAGACTTCTTGAAATATATTTATTC
323 T-CCGGGCCCCGA-CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTC
* * * *
174964 TTCTAACCAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTCACGAGCTTCTGAATCATGTTT
386 ATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTT
* ** *
175029 GGATTTAATCAGAAATTAGCTCAGATAAAATTGGAAAAAC-AGTATTAGAAGCGTGAAAATCTCT
451 CGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACGA-TATTAGAAGCGTGAAAAGCTCT
* * * *
175093 TCAATCTTTTTGGAGTTTAATTATATATTTTTATGAGTA-TATTGGCTAAAAATTTAGGAAAAAT
515 TCATTC-TTTTGCA-TTGAATTATATATTTTTATAAGTATTA-TGGCTAAAAATTTAGGAAAAAT
* *
175157 CTTTCGGGTCAATTTTTTTTGCAAAATTTTAGCCGAAATCAAGTATTAACCATCATAGTTTTTGG
577 CTTTCGGGTCAA-TTTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCATAGTTTTTGG
175222 CTAAAAAACGCGTTCCG-GAGCCCC
641 CTAAAAAACGCGTTCCGAGA-CCCC
* * *
175246 AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTTCTTGAAATATCTTTATTCTTCTAACCAAAA
1 AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACC-AAA
* *
175311 TCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGGGCATCTGAATCATGTTTCGATTTAATCA
65 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCA
* * *
175376 GAAATTAAATCAGATAAAATTGGAAAAAC-AGTATTAGAAGCATGAAAATCTCTTCAATTTTTTT
130 GAAATTAATTCAGATAAAATTGGAAAAACGA-TATTAGAAGCGTGAAAAACTCTTC-ATTTTTTT
175440 GGCGTTGAATTATATATTTTTTATGAGTATAT-TGGCTAAAAATTTAGGAAAAAAT-TTTCGGGT
193 GGCGTTGAATTATATATTTTTTATGAGTAT-TGTGGCTAAAAATTTAGG-AAAAATCTTTCGGGT
* * * *
175503 CAATTTTTTGC-AAATTTTAGCCGAAATCGTGTACTAACCATAATAGTTTTTTGCTAAAAATCGC
256 CAATTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAACGC
* * * * * *
175567 GCTCCGGGGCTCC-AGCTCAATTTTGCATGATTTTTGGCGCCAAAACTTCTTGAAATATCTTTAT
321 GTTCC-GGGCCCCGA-CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATAT
* * * * *
175631 TCTTCTAACAAAATCTCAGTCACATTAGATTTAAGGATTTGTTTTTATGAGCATCTGAATCATGT
384 TCATCTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGT
* * * * *
175696 ATAGATTTAATCAGAAATTAAATCAGATAAAATTGGAAAAA-AAGTATTAGAAGCGTGAAAATCT
449 TTCGATTTAATCAGAAATTAATTCAGATAAAATTGGAAAAACGA-TATTAGAAGCGTGAAAAGCT
* *
175760 CTTCAATCTTCTTGGCGTTGAATTATATATTTTTATAAGTAT
513 CTTCATTCTT-TT-GCATTGAATTATATATTTTTATAAGTAT
175802 ATT
Statistics
Matches: 2207, Mismatches: 273, Indels: 125
0.85 0.10 0.05
Matches are distributed among these distances:
644 20 0.01
645 195 0.09
646 52 0.02
647 5 0.00
648 51 0.02
649 180 0.08
650 16 0.01
651 4 0.00
652 17 0.01
653 1 0.00
654 1 0.00
655 1 0.00
656 2 0.00
657 1 0.00
658 2 0.00
659 1 0.00
661 1 0.00
662 5 0.00
663 208 0.09
664 11 0.00
665 35 0.02
666 1 0.00
668 40 0.02
669 399 0.18
670 172 0.08
671 520 0.24
672 161 0.07
673 35 0.02
674 66 0.03
675 4 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (664 bp):
AGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAAT
CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATCAG
AAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAACTCTTCATTTTTTTGGC
GTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTTAGGAAAAATCTTTCGGGTCAATT
TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAAACGCGTTCC
GGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTA
ACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATT
TAATCAGAAATTAATTCAGATAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCTCTTCATTC
TTTTGCATTGAATTATATATTTTTATAAGTATTATGGCTAAAAATTTAGGAAAAATCTTTCGGGT
CAATTTTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCATAGTTTTTGGCTAAAAAACG
CGTTCCGAGACCCC
Done.