Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1929
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: 264168
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:214785 original size:52 final size:52
Alignment explanation
Indices: 214729--214853 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
214719 CACTGATCTT
* *
214729 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGAAACACTATAAAA
*
214781 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGAAACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGAAACACTATAAAA
*
214833 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
214854 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGAAACACTATAAAA
Found at i:222185 original size:21 final size:21
Alignment explanation
Indices: 222159--222199 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
222149 TAATCTTCAC
222159 AAAAAAAAAAACAAAAAAACA
1 AAAAAAAAAAACAAAAAAACA
* *
222180 AAAAAAAAAAAGAGAAAAAC
1 AAAAAAAAAAACAAAAAAAC
222200 CCCTTTTCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAACAAAAAAACA
Found at i:223176 original size:30 final size:31
Alignment explanation
Indices: 223140--223221 Score: 121
Period size: 30 Copynumber: 2.7 Consensus size: 31
223130 ATACCTTTTT
223140 AAAGTCCACGACTCAGTGGCATTTTGTC-TC
1 AAAGTCCACGACTCAGTGGCATTTTGTCTTC
* *
223170 AAAGTCCACGACTCAGTGGCATTTTTTCTTT
1 AAAGTCCACGACTCAGTGGCATTTTGTCTTC
* *
223201 AAAGTCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCA
223222 CCTTGTTCCT
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 27 0.57
31 20 0.43
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCATTTTGTCTTC
Found at i:223263 original size:61 final size:62
Alignment explanation
Indices: 223198--223780 Score: 495
Period size: 61 Copynumber: 8.9 Consensus size: 62
223188 GCATTTTTTC
* * * *
223198 TTTAAAGTCCACAACTCCGTGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACC-CG
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACCTCT
* *
223259 TTT-AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCATGGCACCTTTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTT-AAGCCCACAACTCCGTGGCACC----T
223323 CT
61 CT
* *
223325 TTTAAAGCCCACAACTCTGTAGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTT
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTT--AAGCCCACAACTCCGTGGCACC--
223390 TTTCT
60 --TCT
**
223395 GTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGCCTCCGTGGCA-CT
1 -TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTC-CTTTT--AAGCCCACAACTCCGTGGCACCT
223459 C-
61 CT
* *
223460 TTTAAAGCCCACAACTCCGTGGCACCTTCTT-CTTTTCAAAGCCCACAACTCTGTGGCACCTTCT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTT--AAGCCCACAACTCCGTGGCA-C--C-
223524 TCT
60 TCT
* * * *
223527 TTTCAAAGCCCACGACTCCGTGGCA-C-TCTT--TTTAAAGCCCACAACTCCGTGGCACTCTTT
1 TTT-AAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGCCCACAACTCCGTGGCAC-CTCT
* * *
223587 TTCCTCCTAAGCCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCACAACTCCGTGGCACC-
1 TT--T--AAAGCCCACAACTCCGTGGCAC-CTTTTTCCTTTTAAGCCCACAACTCCGTGGCACCT
223651 CT
61 CT
* * * * *
223653 TTT-AAGCCCATAACTCCGTGGCACTTTTTTCATCTTTAAGTCCATAACTCCGTGGCACCTTTTT
1 TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT-TTTAAGCCCACAACTCCGTGGCACC-----
223717 TTTCT
60 --TCT
*
223722 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCA
1 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CCTTTTAAGCCCACAACTCCGTGGCA
223781 TCTTTCTCCC
Statistics
Matches: 443, Mismatches: 40, Indels: 68
0.80 0.07 0.12
Matches are distributed among these distances:
60 41 0.09
61 90 0.20
62 2 0.00
63 43 0.10
64 26 0.06
65 5 0.01
66 18 0.04
67 24 0.05
68 49 0.11
69 10 0.02
70 51 0.12
71 82 0.19
72 2 0.00
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.32
Consensus pattern (62 bp):
TTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTTTTAAGCCCACAACTCCGTGGCACCTCT
Found at i:223270 original size:27 final size:27
Alignment explanation
Indices: 223232--223283 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
223222 CCTTGTTCCT
*
223232 TTTAAGTCCACAACTCCGTGGCACCCG
1 TTTAAGCCCACAACTCCGTGGCACCCG
223259 TTTAAGCCCACAACTCCGTGGCACC
1 TTTAAGCCCACAACTCCGTGGCACC
223284 TTTTTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (27 bp):
TTTAAGCCCACAACTCCGTGGCACCCG
Found at i:223301 original size:34 final size:34
Alignment explanation
Indices: 223262--223785 Score: 511
Period size: 34 Copynumber: 15.7 Consensus size: 34
223252 GCACCCGTTT
223262 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTA
*
223296 AAGCCCACAACTCCATGGCACCTTTTTC-TTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTA
* * *
223329 AAGCCCACAACTCTGTAGCACTCTTTTTCCCTTTTCA
1 AAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTTTA
*
223366 AAGCCCACAACTCCGTGGCACCTTTTTCTGTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTA
223400 AAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCA
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCT-TTTT-A
**
223437 AAGCCCACGCCTCCGTGGCA-C----TC--TTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTA
* *
223464 AAGCCCACAACTCCGTGGCACCTTCTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTA
* * *
223498 AAGCCCACAACTCTGTGGCACCTTCTTCTTTTCA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTA
*
223532 AAGCCCACGACTCCGTGGCA-C----TCTTTTTA
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTA
* **
223561 AAGCCCACAACTCCGTGGCACTCTTTTTCCTCCT-
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTTA
* * *
223595 AAGCCCACAACTCTGTGGCACTCTTTTTCCTTCT-
1 AAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTTA
223629 AAGCCCACAACTCCGTGGCACC-----C-TTTT-
1 AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTA
* * *
223656 AAGCCCATAACTCCGTGGCACTTTTTTCATCTTT-
1 AAGCCCACAACTCCGTGGCACCTTTTTC-TTTTTA
* * *
223690 AAGTCCATAACTCCGTGGCACCTTTTTTTTCTTTTA
1 AAGCCCACAACTCCGTGGCACC-TTTTTCT-TTTTA
*
223726 AAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT-
1 AAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTTA
* *
223761 AAGTCCACAACTCCGTGGCATCTTT
1 AAGCCCACAACTCCGTGGCACCTTT
223786 CTCCCTTCCT
Statistics
Matches: 418, Mismatches: 40, Indels: 64
0.80 0.08 0.12
Matches are distributed among these distances:
27 42 0.10
28 5 0.01
29 26 0.06
31 3 0.01
32 3 0.01
33 25 0.06
34 193 0.46
35 40 0.10
36 38 0.09
37 43 0.10
ACGTcount: A:0.20, C:0.35, G:0.12, T:0.33
Consensus pattern (34 bp):
AAGCCCACAACTCCGTGGCACCTTTTTCTTTTTA
Found at i:223516 original size:132 final size:132
Alignment explanation
Indices: 223195--223785 Score: 497
Period size: 131 Copynumber: 4.5 Consensus size: 132
223185 GTGGCATTTT
* * *
223195 TTCTTTAAAGTCCACAACTCCGTGGCACCTTGTTCCTTTT--AAGTCCACAACTCCGTGGCACC-
1 TTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCCTTTTCAAAGCCCACAACTCCGTGGCACCT
223257 ---C-GTTT-AAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAACTCCATGGCA
66 TTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTTAAAGCCCACAACTCCATGGCA
223316 CC
131 CC
* * *
223318 TTTTTCTTTTAAAGCCCACAACTCTGTAGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTG
1 ---TTC-TTTAAAGCCCACAACTCCGTGGCAC-CTTCTT-CCTTTTCAAAGCCCACAACTCCGTG
**
223383 GCACCTTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTCTTTTCAAAGCCCACGCC
60 GCACC-TTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCT-TTTT-AAAGCCCACAAC
*
223448 TCCGTGGCA-C
122 TCCATGGCACC
*
223458 -TCTTTAAAGCCCACAACTCCGTGGCACCTTCTT-CTTTTCAAAGCCCACAACTCTGTGGCACCT
1 TTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCCTTTTCAAAGCCCACAACTCCGTGGCACCT
* *
223521 TCTTCT-TTTCAAAGCCCACGACTCCGTGGCA--C----TCTTTTTAAAGCCCACAACTCCGTGG
66 T-TTCTGTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTTAAAGCCCACAACTCCATGG
223579 CACTC
129 CAC-C
* * * * *
223584 TTTTTCCTCCTAAGCCCACAACTCTGTGGCACTCTTTTTCC--TTCTAAGCCCACAACTCCGTGG
1 TTCTT--T--AAAGCCCACAACTCCGTGGCAC-CTTCTTCCTTTTCAAAGCCCACAACTCCGTGG
* * * *
223647 CACC----CT-TTT-AAGCCCATAACTCCGTGGCACT-TTTTTCATCTTT-AAGTCCATAACTCC
61 CACCTTTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC-TTTTTAAAGCCCACAACTCC
*
223704 GTGGCACC
125 ATGGCACC
* *
223712 TTTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT--AAGTCCACAACTCC
1 ------TTC-TTTAAAGCCCACAACTCCGTGGCAC-CTTCTT-CCTTTTCAAAGCCCACAACTCC
*
223775 GTGGCATCTTT
57 GTGGCACCTTT
223786 CTCCCTTCCT
Statistics
Matches: 388, Mismatches: 31, Indels: 83
0.77 0.06 0.17
Matches are distributed among these distances:
124 37 0.10
125 4 0.01
126 12 0.03
127 25 0.06
128 6 0.02
129 28 0.07
130 5 0.01
131 97 0.25
132 79 0.20
133 2 0.01
134 9 0.02
135 25 0.06
136 3 0.01
137 4 0.01
138 21 0.05
139 8 0.02
140 5 0.01
141 18 0.05
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.33
Consensus pattern (132 bp):
TTCTTTAAAGCCCACAACTCCGTGGCACCTTCTTCCTTTTCAAAGCCCACAACTCCGTGGCACCT
TTTCTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTTAAAGCCCACAACTCCATGGCA
CC
Found at i:223602 original size:97 final size:95
Alignment explanation
Indices: 223136--223753 Score: 580
Period size: 97 Copynumber: 6.3 Consensus size: 95
223126 TCAAATACCT
* * * * * * *
223136 TTTTAAAGTCCACGACTCAGTGGCA-T-TTTGTCTCAAAGTCCACGACTCAGTGGCA--TTTTTT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTT-T-T-AAAGCCCACAACTCCGTGGCACCTTTTTC
* * *
223197 CTTTAAAGTCCACAACTCCGTGGCACCTTGTTCC
63 CTTTTAAGCCCACAACTCCGTGGCACCTT-TTTC
* ** *
223231 TTTT-AAGTCCACAACTCCGTGGCAC-CCGTTT-AAGCCCACAACTCCGTGGCACCTTTTTCTTT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTT
*
223293 TTAAAGCCCACAACTCCATGGCACCTTTTTC
66 TT-AAGCCCACAACTCCGTGGCACCTTTTTC
* *
223324 TTTTAAAGCCCACAACTCTGTAGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCT
1 TTTTAAAGCCCACAACTCCGTGGCACTC----T---TTTT-AAAGCCCACAACTCCGTGGCACCT
223389 TTTT-CTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCTC
58 TTTTCCT-TTT-AAGCCCACAACTCCGTGGCAC-C-TTTT-TC
** *
223431 TTTTCAAAGCCCACGCCTCCGTGGCACTC--TTTAAAGCCCACAACTCCGTGGCACCTTCTT-CT
1 TTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT
* *
223493 TTTCAAAGCCCACAACTCTGTGGCACCTTCTTC
65 TTT--AAGCCCACAACTCCGTGGCACCTTTTTC
*
223526 TTTTCAAAGCCCACGACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 TTTT-AAAGCCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCAC-CTTTTTCC
** *
223591 TCCTAAGCCCACAACTCTGTGGCACTCTTTTTCC
64 TTTTAAGCCCACAACTCCGTGGCAC-CTTTTT-C
* * * * *
223625 TTCT-AAGCCCACAACTCCGTGGCAC-CCTTTT-AAGCCCATAACTCCGTGGCACTTTTTTCATC
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCT-
* *
223687 TTTAAGTCCATAACTCCGTGGCACCTTTTTTTTC
65 TTTAAGCCCACAACTCCGTGGCACC---TTTTTC
223721 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
223754 CCCTTTTAAG
Statistics
Matches: 444, Mismatches: 45, Indels: 65
0.80 0.08 0.12
Matches are distributed among these distances:
91 17 0.04
93 16 0.04
94 67 0.15
95 75 0.17
96 12 0.03
97 96 0.22
98 65 0.15
99 10 0.02
102 3 0.01
103 1 0.00
104 51 0.11
105 1 0.00
106 4 0.01
107 6 0.01
108 20 0.05
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (95 bp):
TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCTT
TTAAGCCCACAACTCCGTGGCACCTTTTTC
Found at i:223682 original size:27 final size:27
Alignment explanation
Indices: 223623--223676 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
223613 CACTCTTTTT
*
223623 CCTTCTAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
*
223650 CCTTTTAAGCCCATAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
223677 TTTTTTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.41, G:0.15, T:0.22
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCGTGGCAC
Found at i:223726 original size:35 final size:34
Alignment explanation
Indices: 223651--223785 Score: 155
Period size: 35 Copynumber: 3.9 Consensus size: 34
223641 CCGTGGCACC
*
223651 CTTTTAAGCCCATAACTCCGTGGCACTTTTTTCAT
1 CTTTTAAGCCCACAACTCCGTGGCACTTTTTT-AT
* * *
223686 C-TTTAAGTCCATAACTCCGTGGCACCTTTTTTTT
1 CTTTTAAGCCCACAACTCCGTGGCA-CTTTTTTAT
**
223720 CTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 CTTTT-AAGCCCACAACTCCGTGGCACT-TTTTTAT
*
223756 CTTTTAAGTCCACAACTCCGTGGCATCTTT
1 CTTTTAAGCCCACAACTCCGTGGCA-CTTT
223786 CTCCCTTCCT
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
34 24 0.27
35 34 0.39
36 30 0.34
ACGTcount: A:0.19, C:0.30, G:0.12, T:0.39
Consensus pattern (34 bp):
CTTTTAAGCCCACAACTCCGTGGCACTTTTTTAT
Found at i:223791 original size:34 final size:34
Alignment explanation
Indices: 223649--223792 Score: 155
Period size: 36 Copynumber: 4.1 Consensus size: 34
223639 CTCCGTGGCA
*
223649 CCCTTTTAAGCCCATAACTCCGTGGCA-CTTTTT
1 CCCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
* * * * *
223682 TCATCTTTAAGTCCATAACTCCGTGGCACCTTTTTT
1 CCCT-TTTAAGCCCACAACTCCGTGGCATC-TTTTT
**
223718 TTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCCTTTT-AAGCCCACAACTCCGTGGCA-TCTTTTT
* *
223754 CCCTTTTAAGTCCACAACTCCGTGGCATCTTTCT
1 CCCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
223788 CCCTT
1 CCCTT
223793 CCTAAAGCCC
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
33 2 0.02
34 33 0.35
35 23 0.24
36 35 0.37
37 1 0.01
ACGTcount: A:0.18, C:0.33, G:0.11, T:0.38
Consensus pattern (34 bp):
CCCTTTTAAGCCCACAACTCCGTGGCATCTTTTT
Found at i:223799 original size:71 final size:70
Alignment explanation
Indices: 223656--223805 Score: 187
Period size: 71 Copynumber: 2.1 Consensus size: 70
223646 GCACCCTTTT
* * * **
223656 AAGCCCATAACTCCGTGGCACTTTTTTCATCTTTAAGTCCATAACTCCGTGGCACCTTTTTTTTC
1 AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTCTCCC
*
223721 TTTTA
66 TTCTA
* *
223726 AAGCCCACAACTCCGTGGCACTCTTTTTC-CCTTTTAAGTCCACAACTCCGTGGCATC-TTTCTC
1 AAGCCCACAACTCCGTGGCACT-TTTTTCATC-TTTAAGTCCACAACTCCGTGGCACCTTTTCTC
223789 CCTTCCTA
64 CCTT-CTA
223797 AAGCCCACA
1 AAGCCCACA
223806 CAAGTTGGTG
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
70 29 0.42
71 40 0.58
ACGTcount: A:0.21, C:0.33, G:0.11, T:0.35
Consensus pattern (70 bp):
AAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACCTTTTCTCCC
TTCTA
Found at i:223833 original size:33 final size:35
Alignment explanation
Indices: 223790--223859 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 35
223780 ATCTTTCTCC
*
223790 CTTCCTAAAGCCCACACAAGTTGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
223824 CTTCC-AAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
223858 CT
1 CT
223860 AAGCCCAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 23 0.68
34 11 0.32
ACGTcount: A:0.26, C:0.36, G:0.17, T:0.21
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:223936 original size:49 final size:49
Alignment explanation
Indices: 223859--224476 Score: 600
Period size: 49 Copynumber: 12.9 Consensus size: 49
223849 GCAACCCTTC
* *
223859 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGTATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* *
223908 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* *
223951 TAAGTCCAATATCGCTGGCCTTCAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* * * * *
224000 TAAGTCCAATGTAGCTAGCCTTGACTCAACACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
*
224043 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* *
224092 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* * *
224135 TAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* * * ** * *
224184 TAAGTTCAATGTAGCTGGCCTTGAATCAACACGTTGACATCTTTTTGGCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATC---TT--CATCTT
* *
224238 TAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* *
224287 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* * *
224330 TAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* * * * *
224379 TAAGTTCAATGTAGCTGGCCTTGAATCAACACATTGACATCTTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATC-----T-TCATCTT
* * * * *
224434 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTT
224477 TATCACTTTT
Statistics
Matches: 461, Mismatches: 73, Indels: 70
0.76 0.12 0.12
Matches are distributed among these distances:
43 148 0.32
45 4 0.01
47 4 0.01
49 221 0.48
50 1 0.00
51 2 0.00
52 2 0.00
54 39 0.08
55 40 0.09
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
Found at i:224021 original size:92 final size:92
Alignment explanation
Indices: 223854--224414 Score: 870
Period size: 92 Copynumber: 6.0 Consensus size: 92
223844 CGGTGGCAAC
* *
223854 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGTATCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
223919 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* *
223947 CCTTTAAGTCCAATATCGCTGGCCTTCAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
* * *
224012 AGCTAGCCTTGACTCAACACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
224039 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
224104 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
224131 CCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGT
1 CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
*
224196 AGCTGGCCTTGAATCAACACGTTGACATCTTTTTGGCA
66 AGCTGGCCTTGAAT---CA----G-CA-C--ATTGGCA
* *
224234 CCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
224299 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
224326 CCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGT
1 CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
*
224391 AGCTGGCCTTGAATCAACACATTG
66 AGCTGGCCTTGAATCAGCACATTG
224415 ACATCTTTTT
Statistics
Matches: 432, Mismatches: 25, Indels: 23
0.90 0.05 0.05
Matches are distributed among these distances:
92 335 0.78
93 4 0.01
94 1 0.00
95 4 0.01
96 1 0.00
99 1 0.00
100 4 0.01
101 1 0.00
103 81 0.19
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:224365 original size:195 final size:194
Alignment explanation
Indices: 223854--224476 Score: 987
Period size: 195 Copynumber: 3.2 Consensus size: 194
223844 CGGTGGCAAC
* *
223854 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGTATCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
* * *
223919 TAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTCAATCAGCATA
65 TAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATA
* * *
223984 TTGGCATCTTCATCTTTAAGTCCAATGTAGCTAGCCTTGACTC-A-AC---ACA-----TTGGCA
130 TTGGCATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAACACTTGACATCTTTTTGGCA
*
224039 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
224104 AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATAT
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATAT
224169 TGGCATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAACACGTTGACATCTTTTTGGCA
131 TGGCATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAACAC-TTGACATCTTTTTGGCA
* *
224234 CCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
224299 AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATAT
66 AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATAT
**
224364 TGGCATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAACACATTGACATCTTTTTTCTC
131 TGGCATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAACAC-TTGACATC-TTTTTGGC
224429 A
194 A
* * * *
224430 TCTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTT
1 CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTT
224477 TATCACTTTT
Statistics
Matches: 409, Mismatches: 17, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
184 159 0.39
185 5 0.01
186 2 0.00
190 3 0.01
195 190 0.46
196 50 0.12
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (194 bp):
CCTTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATAT
TGGCATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAACACTTGACATCTTTTTGGCA
Found at i:225284 original size:13 final size:13
Alignment explanation
Indices: 225266--225290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
225256 CATAAAATGT
225266 TGTATCGATACAA
1 TGTATCGATACAA
225279 TGTATCGATACA
1 TGTATCGATACA
225291 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:225290 original size:33 final size:33
Alignment explanation
Indices: 225247--225315 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
225237 TCAACGATTG
225247 GTATCAATACATAAAATGTTGTATCGATACAAT
1 GTATCAATACATAAAATGTTGTATCGATACAAT
* *** *
225280 GTATCGATACATATTTTTTTGTATCGATACAAT
1 GTATCAATACATAAAATGTTGTATCGATACAAT
225313 GTA
1 GTA
225316 AGCTACTGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (33 bp):
GTATCAATACATAAAATGTTGTATCGATACAAT
Found at i:225374 original size:13 final size:13
Alignment explanation
Indices: 225356--225380 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
225346 ATTACTCACA
225356 TGTATCGATACAT
1 TGTATCGATACAT
225369 TGTATCGATACA
1 TGTATCGATACA
225381 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:225445 original size:52 final size:52
Alignment explanation
Indices: 225389--225513 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
225379 CACTGATCTT
*
225389 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
225441 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
225493 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
225514 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:228664 original size:27 final size:28
Alignment explanation
Indices: 228625--228797 Score: 107
Period size: 33 Copynumber: 5.8 Consensus size: 28
228615 TTTTTTTTTC
* * *
228625 TAAGTCAATAACTCTGTGGCA-CCCTTT
1 TAAGTCCACAACTCCGTGGCATCCCTTT
* **
228652 TAAGTTCACAACTCTATGGCATCTTTTTCCTTT
1 TAAGTCCACAACTCCGTGGCATC-----CCTTT
*
228685 TAAGTCCACAACTCCGTGGCATATTTTTCCTTT
1 TAAGTCCACAACTCCGTGGC--A---TCCCTTT
*
228718 TAAGTCCACAACTCCATGGCA-CCCTTT
1 TAAGTCCACAACTCCGTGGCATCCCTTT
* *
228745 TAAGTCCACAACTCCGTGGAACATTTTCTTTT
1 TAAGTCCACAACTCCGTGG--CA--TCCCTTT
*
228777 TAAGTCCATAACTCCGTGGCA
1 TAAGTCCACAACTCCGTGGCA
228798 CCTTGTTCCT
Statistics
Matches: 116, Mismatches: 14, Indels: 29
0.73 0.09 0.18
Matches are distributed among these distances:
27 40 0.34
28 1 0.01
29 2 0.02
30 2 0.02
31 1 0.01
32 22 0.19
33 46 0.40
35 1 0.01
38 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.35
Consensus pattern (28 bp):
TAAGTCCACAACTCCGTGGCATCCCTTT
Found at i:228684 original size:33 final size:33
Alignment explanation
Indices: 228647--229423 Score: 739
Period size: 33 Copynumber: 23.9 Consensus size: 33
228637 TCTGTGGCAC
* **
228647 CCTTTTAAGTTCACAACTCTATGGCATCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
*
228680 CCTTTTAAGTCCACAACTCCGTGGCATATTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
*
228713 CCTTTTAAGTCCACAACTCCATGGCA-C-----
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* *
228740 CCTTTTAAGTCCACAACTCCGTGG-AACATTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* * * *
228772 CTTTTTAAGTCCATAACTCCGTGGCACCTTGTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* * *
228805 CCTTTTACGTCCATAACTCCGTGGCA-CATTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* * * * * * *
228837 CTTTTTAAATCTACGACTTCGTGGTACTCTTTTC
1 CCTTTTAAGTCCACAACTCCGTGGCA-TCTTTTT
* * *
228871 CCTTTTAAGTCCACAACTCTC-TGGTACCTTGTT
1 CCTTTTAAGTCCACAACTC-CGTGGCATCTTTTT
* * * *
228904 CCTTTTAAGTCCATAAATCCGTGGCACCTTGTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* *
228937 CCTTTTAAGTCCACAACTCCATGGTA-C-----
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
228964 CCTTTTAAGTCCACAACTCCGTGGCA-CTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* ** * ** *
228996 CTTTTTAAGTCCATGACTTCGTGGTGTTCTTTTC
1 CCTTTTAAGTCCACAACTCCGTGG-CATCTTTTT
*
229030 CCTTTTAAGTCCACAACTCCATGGCATCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
*
229063 CCTTTTAAGTCCACAACTCCATGGCATCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* *
229096 CCTTTTAAGTCCATAACTCCGTGGCA-CCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* * * * *
229128 CTTTTTAAGTCAACAACTCCATGGCACCTTGTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* * * *
229161 CCTTTTACGTCCATAACTCCATGGCA-CCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* ** **
229193 CTTTTTAAGTCCATGACTCTATGGCATTCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCA-TCTTTTT
* *
229227 CCTTTTAAGTCCACAACTCCGTGGCACCTTATT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
*
229260 CCTTTTAAGTCCACAACTCCGTGGCA-CCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* * *
229292 CTTTTTAAGTCCACGACTCTGTGGCATTCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCA-TCTTTTT
229326 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
* * *
229359 CCTTTTAAGCCCACAACTTCGTGGCATCCCTCTTT
1 CCTTTTAAGTCCACAACTCCGTGGCAT--CTTTTT
* * * *
229394 CC-TGTAAGTCCATAACTCCTTGGCACCTTT
1 CCTTTTAAGTCCACAACTCCGTGGCATCTTT
229424 AAGTCCAATA
Statistics
Matches: 615, Mismatches: 104, Indels: 51
0.80 0.14 0.07
Matches are distributed among these distances:
26 1 0.00
27 49 0.08
32 149 0.24
33 289 0.47
34 119 0.19
35 8 0.01
ACGTcount: A:0.20, C:0.29, G:0.12, T:0.39
Consensus pattern (33 bp):
CCTTTTAAGTCCACAACTCCGTGGCATCTTTTT
Found at i:229557 original size:48 final size:48
Alignment explanation
Indices: 229420--229928 Score: 369
Period size: 48 Copynumber: 10.8 Consensus size: 48
229410 TCCTTGGCAC
* * *
229420 CTTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTAGCACCTTTAC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTAT
* * * * *
229469 CATCTTGAGTCCAATATTGCTGGCCTTGAACCAGCGTATTGGCACCTTGT
1 C-T-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTAT
* * *
229519 CTCTAAGACCAATGTCGCTGGCCTTGAATCAGCATATTGG---C--A-
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTAT
* *
229561 ---TAAG-CCTAATATCGTTGGCCTTGAATCAGCATATTAGCACCTTAT
1 CTTTAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTAT
* * * *
229606 CTTTAAGACCAATGTCTCTGGCCTTGAATCAGCACATTGG---C--A-
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTAT
* * *
229648 C---AAGCCCAATATCGCTAGACTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-AT
*
229694 CTTTAAGTCC-ATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTAT
* * * *
229742 CTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-AT
** * * * *
229791 CTTTAAGTCTGATATCGTTGGCTTTGAATCAGCATATTGGCATCTTTAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTTAT
* * * ** * *
229840 CATTCCTTAGCCCAATGTCGCTGGCCTTGTCTCAGCACATTGGCA--TTCTT
1 C-TT--TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-AT
* * ** *
229890 CTTCAATTTTAATATCGCTGGCCTTGAATCAGCACATTG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTG
229929 TCATTCTTCG
Statistics
Matches: 359, Mismatches: 70, Indels: 64
0.73 0.14 0.13
Matches are distributed among these distances:
38 2 0.01
39 61 0.17
42 3 0.01
43 1 0.00
44 1 0.00
45 3 0.01
46 1 0.00
47 27 0.08
48 103 0.29
49 83 0.23
50 9 0.03
51 36 0.10
52 29 0.08
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (48 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTAT
Found at i:229627 original size:87 final size:87
Alignment explanation
Indices: 229479--229832 Score: 368
Period size: 87 Copynumber: 3.9 Consensus size: 87
229469 CATCTTGAGT
* * * * *
229479 CCAATATTGCTGGCCTTGAACCAGCGTATTGGCACCTTGTCTCTAAGACCAATGTCGCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTGGCCTT
*
229544 GAATCAGCATATTGGCATAAGC
66 GAATCAGCATATTGGCACAAGC
* * * *
229566 CTAATATCGTTGGCCTTGAATCAGCATATTAGCACCTTATCTTTAAGACCAATGTCTCTGGCCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTGGCCTT
*
229631 GAATCAGCACATTGGCACAAGC
66 GAATCAGCATATTGGCACAAGC
* * * *
229653 CCAATATCGCTAGACTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCC-ATATCGCTGGCCT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGACCAATGTCGCTGGCCT
*
229717 TGAATCAGCATATTGGCACCGTCATCTTTAAGA
65 TGAATCAGCATATT-G----G-CA-C---AAGC
* * * * ** * * *
229750 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCTGATATCGTTGGCTT
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGACCAATGTCGCTGGCCT
229815 TGAATCAGCATATTGGCA
65 TGAATCAGCATATTGGCA
229833 TCTTTAACAT
Statistics
Matches: 226, Mismatches: 29, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
87 133 0.59
88 12 0.05
92 3 0.01
93 3 0.01
94 1 0.00
97 49 0.22
98 25 0.11
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (87 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAATGTCGCTGGCCTT
GAATCAGCATATTGGCACAAGC
Found at i:229781 original size:49 final size:49
Alignment explanation
Indices: 229653--229928 Score: 272
Period size: 49 Copynumber: 5.6 Consensus size: 49
229643 TGGCACAAGC
* * *
229653 CCAATATCGCTAGACTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
229702 CC-ATATCGCTGGCCTTGAATCAGCATATTGGCACCGTCATCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
229750 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
** * * * * * *
229799 CTGATATCGTTGGCTTTGAATCAGCATATTGGCATCTTTAACATTCCTT-AGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CCTT--CA-TCTTTAAGT
* ** * * *
229851 CCAATGTCGCTGGCCTTGTCTCAGCACATTGGCA--TTCTTCTTCAATT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
**
229898 TTAATATCGCTGGCCTTGAATCAGCACATTG
1 CCAATATCGCTGGCCTTGAATCAGCACATTG
229929 TCATTCTTCG
Statistics
Matches: 184, Mismatches: 37, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
46 3 0.02
47 28 0.15
48 44 0.24
49 73 0.40
50 2 0.01
52 30 0.16
53 4 0.02
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (49 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
Found at i:231172 original size:13 final size:13
Alignment explanation
Indices: 231154--231178 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
231144 ACATAAGTGT
231154 TGTATCGATACAA
1 TGTATCGATACAA
231167 TGTATCGATACA
1 TGTATCGATACA
231179 TAAGCTACTC
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:231245 original size:13 final size:13
Alignment explanation
Indices: 231227--231254 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
231217 CATTATTCAA
231227 TGTATCGATACAT
1 TGTATCGATACAT
231240 TGTATCGATACAT
1 TGTATCGATACAT
231253 TG
1 TG
231255 ATTTTTGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:231267 original size:33 final size:33
Alignment explanation
Indices: 231207--231272 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
231197 GCCAAGGAAA
*
231207 TGTATCGATACATTATTCAATGTATCGATACAT
1 TGTATCGATACATTATTCAATGCATCGATACAT
**
231240 TGTATCGATACATTGATT-TTTGCATCGATACAT
1 TGTATCGATACATT-ATTCAATGCATCGATACAT
231273 CTGGGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTATTCAATGCATCGATACAT
Found at i:237609 original size:13 final size:13
Alignment explanation
Indices: 237591--237615 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
237581 AATAAAATGT
237591 TGTATCGATACAA
1 TGTATCGATACAA
237604 TGTATCGATACA
1 TGTATCGATACA
237616 TTTTTTTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:237767 original size:52 final size:52
Alignment explanation
Indices: 237711--237835 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
237701 CACTGATCTT
*
237711 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTA-TAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
237762 GTGTATCGATACATGCAGGAAAATTTGCCCAGATGTATCGATACACTATTAAA
1 -TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
237815 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
237836 CTTTTCATAT
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
52 64 0.94
53 4 0.06
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:245477 original size:31 final size:31
Alignment explanation
Indices: 245436--245938 Score: 232
Period size: 31 Copynumber: 15.9 Consensus size: 31
245426 CTTCAAATAC
* *
245436 CTTCTTAAAGTCCATGACTCCGTGGCACCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
*
245467 CTTCTCAAAGTCCACGACTCAGTGGCATCCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCA-CCTT
* *
245499 -TTCTTCAAAGTCCACGACTCAGTGGCAATCTT
1 CTTC-TCAAAGTCCACGACTCCGTGGC-ACCTT
*
245531 -TGCTCAAAGTCCACGACTCCGTGGCACCTTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACC-TT
* *
245562 CTT-TCAAAGCCCACAACTCCGTGGCACTCTTTTT
1 CTTCTCAAAGTCCACGACTCCGTGGCAC-C---TT
* *
245596 CCTTTTTAAAGTCCACGACTCCGTGGCACCTT
1 -CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* * *
245628 CTTTTCAAAGCCCACAACTCCGTGGCACC--
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* * * *
245657 CTT-T-TAAGCCCACAACTCCGTGGCACTTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* * * *
245686 TTTCATCTTTAAGTCCACAACTCCGTGCCACC--
1 CTTC-TC--AAAGTCCACGACTCCGTGGCACCTT
* * * *
245718 CTTCT--AAGCCCACAACTCCATGGCACTTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* * * *
245747 TTTCATCTTTAAGTCCACAACTCTGTGGCACCTTTTT
1 CTTC-TC--AAAGTCCACGACTCCGTGGCACC---TT
* * * *
245784 CTTTTTAAAGCCCACAACTCCGTGGCACCTTTTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACC---TT
* * *
245818 CTTTTTAAAGCCCAC-AGCTCCGTGGCACTCTT
1 CTTCTCAAAGTCCACGA-CTCCGTGGCAC-CTT
** * *
245850 -TTCCCGTTTAAGCCCACAACTCCGTGGCACC--
1 CTT--C-TCAAAGTCCACGACTCCGTGGCACCTT
* * *
245881 CTT-T-TAAGTCCACAACTCAGTGGCACCTT
1 CTTCTCAAAGTCCACGACTCCGTGGCACCTT
* *
245910 C-TCATCAAAGTCCACAACTTCGTGGCACC
1 CTTC-TCAAAGTCCACGACTCCGTGGCACC
245939 CTTTTAAAGC
Statistics
Matches: 388, Mismatches: 45, Indels: 78
0.76 0.09 0.15
Matches are distributed among these distances:
27 60 0.15
28 3 0.01
29 9 0.02
30 4 0.01
31 122 0.31
32 42 0.11
33 3 0.01
34 113 0.29
35 6 0.02
36 22 0.06
37 4 0.01
ACGTcount: A:0.21, C:0.35, G:0.14, T:0.30
Consensus pattern (31 bp):
CTTCTCAAAGTCCACGACTCCGTGGCACCTT
Found at i:245704 original size:34 final size:33
Alignment explanation
Indices: 245568--246066 Score: 265
Period size: 34 Copynumber: 15.6 Consensus size: 33
245558 CTTTCTTTCA
*
245568 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTT
1 AAGCCCACAACTCCGTGGCACT-TTTTT-CTCTTT
* * * *
245603 AAAGTCCACGACTCCGTGGCACCTTCTTT-TC--A
1 -AAGCCCACAACTCCGTGGCA-CTTTTTTCTCTTT
*
245635 AAGCCCACAACTCCGTGGCAC-----CCT-TTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCTCTTT
245662 AAGCCCACAACTCCGTGGCACTTTTTTCATCTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTC-TCTTT
* *
245696 AAGTCCACAACTCCGTGCCAC------C-CTTCT
1 AAGCCCACAACTCCGTGGCACTTTTTTCTCTT-T
*
245723 AAGCCCACAACTCCATGGCACTTTTTTCATCTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTC-TCTTT
* * * *
245757 AAGTCCACAACTCTGTGGCACCTTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCTCTTT
* *
245790 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1 -AAGCCCACAACTCCGTGGCACTTTTTTCTCTTT
* * *
245824 AAAGCCCACAGCTCCGTGGCACTCTTTTCCCGTTT
1 -AAGCCCACAACTCCGTGGCACTTTTTTCTC-TTT
*
245859 AAGCCCACAACTCCGTGGCAC-----CCT-TTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCTCTTT
* * * **
245886 AAGTCCACAACTCAGTGGCAC---CTTCTCATCA
1 AAGCCCACAACTCCGTGGCACTTTTTTCTC-TTT
* * *
245917 AAGTCCACAACTTCGTGGCAC-----CCT-TTT
1 AAGCCCACAACTCCGTGGCACTTTTTTCTCTTT
** *
245944 AAAGCCCACAACTTTGTGGCACTCGTTTTC-CTTTT
1 -AAGCCCACAACTCCGTGGCACT-TTTTTCTC-TTT
* *
245979 AAGTCCACGACTCCGTGGCACCCTTTTTTC-CTTT
1 AAGCCCACAACTCCGTGGCA--CTTTTTTCTCTTT
* *
246013 AAAGCCCACAACTACGTGGCACTCTTTTC-CTTTT
1 -AAGCCCACAACTCCGTGGCACTTTTTTCTC-TTT
* * *
246047 AAGTCCACAAGTCGGTGGCA
1 AAGCCCACAACTCCGTGGCA
246067 ACCATTCTCT
Statistics
Matches: 368, Mismatches: 56, Indels: 81
0.73 0.11 0.16
Matches are distributed among these distances:
26 4 0.01
27 63 0.17
28 20 0.05
29 5 0.01
30 1 0.00
31 38 0.10
32 1 0.00
33 30 0.08
34 148 0.40
35 32 0.09
36 24 0.07
37 2 0.01
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.31
Consensus pattern (33 bp):
AAGCCCACAACTCCGTGGCACTTTTTTCTCTTT
Found at i:245711 original size:61 final size:61
Alignment explanation
Indices: 245639--245851 Score: 266
Period size: 61 Copynumber: 3.4 Consensus size: 61
245629 TTTTCAAAGC
245639 CCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGT
* * *
245700 CCACAACTCCGTGCCACCCTTCTAAGCCCACAACTCCATGGCACTTTTTTCATCTTTAAGT
1 CCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGT
* * *
245761 CCACAACTCTGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTC-TTTTTA
1 CCACAACTCCGTGGCACC-----C-TTTT-AAGCCCACAACTCCGTGGCACTTTTTTCATCTTT-
*
245825 AAGC
58 AAGT
* *
245829 CCACAGCTCCGTGGCACTCTTTT
1 CCACAACTCCGTGGCACCCTTTT
245852 CCCGTTTAAG
Statistics
Matches: 131, Mismatches: 13, Indels: 15
0.82 0.08 0.09
Matches are distributed among these distances:
61 74 0.56
62 4 0.03
63 1 0.01
66 1 0.01
67 7 0.05
68 44 0.34
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.32
Consensus pattern (61 bp):
CCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGT
Found at i:245873 original size:163 final size:156
Alignment explanation
Indices: 245568--246030 Score: 475
Period size: 163 Copynumber: 2.9 Consensus size: 156
245558 CTTTCTTTCA
* * * * *
245568 AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTTAAAGTCCACGACTCCGTGGCACCTTCTTTT
1 AAGCCCACAACTCCATGGCACT-TTTTTCATCTTT-AAGTCCACAACTCTGTGGCACCTTCTTTT
* * * *
245633 CAAAGCCCACAACTCCGTGGCACC----CTTTTAAGCCCACAACTCCGTGGCACTTTTTTCATCT
64 TAAAGCCCACAACTCCGTGGCACCTTTTCTTTTAAGCCCACAGCTCCGTGGCACTCTTTTC-CCT
*
245694 TTAAGTCCACAACTCCGTGCCACCCTTCT
128 TTAAGCCCACAACTCCGTGCCACCCTTCT
245723 AAGCCCACAACTCCATGGCACTTTTTTCATCTTTAAGTCCACAACTCTGTGGCACCTTTTTCTTT
1 AAGCCCACAACTCCATGGCACTTTTTTCATCTTTAAGTCCACAACTCTGTGGCACC---TTCTTT
245788 TTAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAGCTCCGTGGCACTCTTTTC
63 TTAAAGCCCACAACTCCGTGGCACC-TTTTC-TTTT-AAGCCCACAGCTCCGTGGCACTCTTTTC
* *
245853 CCGTTTAAGCCCACAACTCCGTGGCACCCTTTT
125 CC-TTTAAGCCCACAACTCCGTGCCACCCTTCT
* * * *
245886 AAGTCCACAACT-CAGTGGCAC-CTTCTCATC--AAAGTCCACAACT-TCGTGGCACC--C-TTT
1 AAGCCCACAACTCCA-TGGCACTTTTTTCATCTTTAAGTCCACAACTCT-GTGGCACCTTCTTTT
** * *
245943 TAAAGCCCACAACTTTGTGGCACTCGTTTTCCTTTTAAGTCCAC-GACTCCGTGGCACCCTTTTT
64 TAAAGCCCACAACTCCGTGGCAC-C-TTTT-CTTTTAAGCCCACAG-CTCCGTGGCACTC-TTTT
* *
246007 TCCTTTAAAGCCCACAACTACGTG
124 CCCTTT-AAGCCCACAACTCCGTG
246031 GCACTCTTTT
Statistics
Matches: 267, Mismatches: 23, Indels: 36
0.82 0.07 0.11
Matches are distributed among these distances:
153 21 0.08
154 56 0.21
155 53 0.20
156 31 0.12
159 1 0.00
160 20 0.07
161 1 0.00
162 14 0.05
163 70 0.26
ACGTcount: A:0.21, C:0.35, G:0.13, T:0.31
Consensus pattern (156 bp):
AAGCCCACAACTCCATGGCACTTTTTTCATCTTTAAGTCCACAACTCTGTGGCACCTTCTTTTTA
AAGCCCACAACTCCGTGGCACCTTTTCTTTTAAGCCCACAGCTCCGTGGCACTCTTTTCCCTTTA
AGCCCACAACTCCGTGCCACCCTTCT
Found at i:246165 original size:49 final size:49
Alignment explanation
Indices: 246112--246763 Score: 919
Period size: 49 Copynumber: 13.6 Consensus size: 49
246102 CCTTCTAACC
* *
246112 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
*
246161 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGC
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
246204 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
246253 CCAATGTAGCTGGCCTTCAATCAGCATATTGGCACCTTCATCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
246302 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
246345 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
246394 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
246443 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* * *
246492 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
*
246541 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
246590 CCAATGTAGCTAGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
246638 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
* *
246681 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGT
1 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CATCTTTAAGT
*
246733 TCAATGTAGCTGGCCTTGAATCAGCACATTG
1 CCAATGTAGCTGGCCTTGAATCAGCACATTG
246764 ACATCCTTTT
Statistics
Matches: 542, Mismatches: 40, Indels: 39
0.87 0.06 0.06
Matches are distributed among these distances:
43 118 0.22
45 3 0.01
47 2 0.00
48 44 0.08
49 338 0.62
50 1 0.00
52 36 0.07
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGT
Found at i:246366 original size:141 final size:141
Alignment explanation
Indices: 246112--246772 Score: 1010
Period size: 141 Copynumber: 4.6 Consensus size: 141
246102 CCTTCTAACC
246112 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
*
246177 TGAATCAGCACATTGGCACCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
66 TGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
246242 CATCTTTAAGT
131 CATCTTTAAGT
* *
246253 CCAATGTAGCTGGCCTTCAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
*
246318 TGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT
66 TGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
246383 CATCTTTAAGT
131 CATCTTTAAGT
*
246394 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
*
246459 TGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
66 TGAATCAGCACATTGGCACC-T-----TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
*
246524 CACCTTTATCTTTAAGT
125 CACCTTCATCTTTAAGT
* * * *
246541 CCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTAGCCT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
* *
246606 TGAATCAGCACATTGGCACCTCACCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGC
66 TGAATCAGCACATTGG-----CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGC
246671 A----C--CTTTAAGT
126 ACCTTCATCTTTAAGT
*
246681 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGG
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCAATGTAGCTGG
*
246746 CCTTGAATCAGCACATTGACATCCTTT
63 CCTTGAATCAGCACATTGGCA-CCTTT
246773 TTCTCATTTT
Statistics
Matches: 480, Mismatches: 25, Indels: 32
0.89 0.05 0.06
Matches are distributed among these distances:
138 2 0.00
139 5 0.01
140 41 0.09
141 218 0.45
142 3 0.01
143 40 0.08
146 38 0.08
147 128 0.27
151 1 0.00
152 4 0.01
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (141 bp):
CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCT
TGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT
CATCTTTAAGT
Found at i:246751 original size:52 final size:53
Alignment explanation
Indices: 246673--246794 Score: 165
Period size: 52 Copynumber: 2.3 Consensus size: 53
246663 ACATTGGCAC
* *
246673 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCCAT
* *
246725 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCC-TTTTC-CAT
* *
246780 TTTTAAGCCCAATAT
1 CTTTAAGTCCAATAT
246795 CGTTGGTCGT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
52 38 0.64
53 2 0.03
54 5 0.08
55 14 0.24
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCCAT
Found at i:247891 original size:52 final size:52
Alignment explanation
Indices: 247835--247959 Score: 216
Period size: 52 Copynumber: 2.4 Consensus size: 52
247825 CACTGATCTT
*
247835 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTA-TAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
247886 GTGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 -TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
247939 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
247960 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
52 66 0.94
53 4 0.06
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:254580 original size:51 final size:51
Alignment explanation
Indices: 254525--254671 Score: 172
Period size: 50 Copynumber: 2.9 Consensus size: 51
254515 TATCCCCTGA
* * *
254525 TGAAAAATTAATATTTTGGAGATAAAAATGGGGTTTGAGTATCCCCAATGG
1 TGAAAAATTGATATTTTGGAAATAAAAATGGGGTTAGAGTATCCCCAATGG
* * *
254576 TGAAAGATCGATATTTTGAAAATAAAACA--GGGTTAGAGTATCCCCAATGG
1 TGAAAAATTGATATTTTGGAAATAAAA-ATGGGGTTAGAGTATCCCCAATGG
* * * * *
254626 TGAAAAGTTGATATTTTGGAAACAAAATTGGGGTTGGAATATCCCC
1 TGAAAAATTGATATTTTGGAAATAAAAATGGGGTTAGAGTATCCCC
254672 TCAAAAATAA
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
50 42 0.53
51 36 0.46
52 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.29
Consensus pattern (51 bp):
TGAAAAATTGATATTTTGGAAATAAAAATGGGGTTAGAGTATCCCCAATGG
Found at i:254839 original size:128 final size:131
Alignment explanation
Indices: 254686--254956 Score: 309
Period size: 128 Copynumber: 2.1 Consensus size: 131
254676 AAATAACAGT
* * *
254686 GTTGGAGTAT-CCTCGATGGTGGAAAATCGGTGTTTTAGAAACAAAACCAAGGTTAGAGTATCCC
1 GTTGGAGTATCCCTCGATAGTAGAAAATCGATGTTTTAGAAACAAAACCAAGGTTAGAGTATCCC
* * * * *
254750 TTAAAAAATAACAGGGTTTGAGTATCTCTGCT-GAT-AAAAAATGATGTTTTAAAAATAAAATGA
66 TTAAAAAATAACAGGGTTAGAGTATCCCCGATAG-TGAAAAAATGATGTTTTAAAAATAAAATCA
254813 G-
130 GA
* * * ** *
254814 GTTGGAGTATCCCT-GATAGTAGAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCCTCGATAGTAGAAAATCGATGTTTTAGAAACAAAACCAAGGTTAGAGTATCCC
*** * * * *
254878 TTTGGAAATAATAGGGTTAGAGTATCCCCGATAGTGAAAAATTGGTGTTTTAGAAATAAAATCAG
66 TTAAAAAATAACAGGGTTAGAGTATCCCCGATAGTGAAAAAATGATGTTTTAAAAATAAAATCAG
254943 A
131 A
254944 GTTGGAGTATCCC
1 GTTGGAGTATCCC
254957 CTCAGAAATA
Statistics
Matches: 118, Mismatches: 21, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
128 76 0.64
129 29 0.25
130 13 0.11
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.30
Consensus pattern (131 bp):
GTTGGAGTATCCCTCGATAGTAGAAAATCGATGTTTTAGAAACAAAACCAAGGTTAGAGTATCCC
TTAAAAAATAACAGGGTTAGAGTATCCCCGATAGTGAAAAAATGATGTTTTAAAAATAAAATCAG
A
Found at i:254949 original size:79 final size:78
Alignment explanation
Indices: 254813--255092 Score: 314
Period size: 79 Copynumber: 3.6 Consensus size: 78
254803 AATAAAATGA
*
254813 GGTTGGAGTATCCCTGATAGT-AGAAAATTGATGTTTTAGAAATAAAATCGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCGATAGTGA-AAAATTGATGTTTTAGAAATAAAATC-GGGTTGGAGTATCC
* **
254877 CTTTGGAAATAATAG
64 CTTCGGAAATAACGG
* * *
254892 GGTTAGAGTATCCCCGATAGTGAAAAATTGGTGTTTTAGAAATAAAATCAGAGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATAGTGAAAAATTGATGTTTTAGAAATAAAATC-GGGTTGGAGTATCCC
* *
254957 CTCAGAAATAACGG
65 TTCGGAAATAACGG
** * * *
254971 GGTTGGAGTATCCCTAATGGTCAAAAATTGATGTTTTAAAAATAAAACTCGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCGATAGTGAAAAATTGATGTTTTAGAAATAAAA-TCGGGTTGGAGTATCCC
*
255036 TTCGAAAATAACGG
65 TTCGGAAATAACGG
* * * * *
255050 GGTTTGAGTATCCTCGAT-GATG-GAAATCGGTGTTTTAGAAATA
1 GGTTGGAGTATCCCCGATAG-TGAAAAATTGATGTTTTAGAAATA
255093 GAAACATCAA
Statistics
Matches: 168, Mismatches: 30, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
78 18 0.11
79 147 0.88
80 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (78 bp):
GGTTGGAGTATCCCCGATAGTGAAAAATTGATGTTTTAGAAATAAAATCGGGTTGGAGTATCCCT
TCGGAAATAACGG
Found at i:254954 original size:207 final size:210
Alignment explanation
Indices: 254589--255036 Score: 514
Period size: 207 Copynumber: 2.2 Consensus size: 210
254579 AAGATCGATA
* * * ** * *
254589 TTTTGAAAATAAAAC-AGGGTTAGAGTATCCCCAATGGT-GAAAAGTTGATATTTTGGAAACAAA
1 TTTTAAAAATAAAACTCGGGTTGGAGTATCCCTGATAGTAGAAAAGTTGATATTTTAGAAACAAA
* * * * * *
254652 ATTGGGGTTGGAATATCCCCTCAAAAATAACAGTGTTGGAGTATCCTCGATGGTGGAAAATCGGT
66 ATCGGGGTTGGAATATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATAGTGAAAAATCGGT
* * * **
254717 GTTTTAGAAACAAAACCAAGGTTAGAGTATCCCTTAAAAAATAACAGGGTTTGAGTATCTCTGCT
131 GTTTTAGAAACAAAACCAAGGTTAGAGTATCCCCTAAAAAATAACAGGGTTGGAGTATCCCTAAT
254782 GAT-AAAAAATGATG
196 GATCAAAAAATGATG
* *
254796 TTTTAAAAATAAAA-T-GAGGTTGGAGTATCCCTGATAGTAGAAAA-TTGATGTTTTAGAAATAA
1 TTTTAAAAATAAAACTCG-GGTTGGAGTATCCCTGATAGTAGAAAAGTTGATATTTTAGAAACAA
* * *** * *
254858 AATCGGGGTTGGAGTATCCCTTTGGAAATAATAGGGTTAGAGTATCCCCGATAGTGAAAAATTGG
65 AATCGGGGTTGGAATATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATAGTGAAAAATCGG
* * * * * *
254923 TGTTTTAGAAATAAAATC-AGAGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCTA
130 TGTTTTAGAAACAAAACCAAG-GTTAGAGTATCCCCTAAAAAATAACAGGGTTGGAGTATCCCTA
* *
254987 ATGGTCAAAAATTGATG
194 ATGATCAAAAAATGATG
255004 TTTTAAAAATAAAACTCGGGTTGGAGTATCCCT
1 TTTTAAAAATAAAACTCGGGTTGGAGTATCCCT
255037 TCGAAAATAA
Statistics
Matches: 200, Mismatches: 34, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
206 3 0.01
207 151 0.75
208 29 0.14
209 16 0.08
210 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (210 bp):
TTTTAAAAATAAAACTCGGGTTGGAGTATCCCTGATAGTAGAAAAGTTGATATTTTAGAAACAAA
ATCGGGGTTGGAATATCCCCTCAAAAATAACAGGGTTAGAGTATCCCCGATAGTGAAAAATCGGT
GTTTTAGAAACAAAACCAAGGTTAGAGTATCCCCTAAAAAATAACAGGGTTGGAGTATCCCTAAT
GATCAAAAAATGATG
Found at i:259949 original size:17 final size:18
Alignment explanation
Indices: 259927--259974 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
259917 TTTCTTTGTG
259927 AAAGAAAAAAAGAAAA-A
1 AAAGAAAAAAAGAAAAGA
*
259944 AAAGAACAAAAGAAAAGA
1 AAAGAAAAAAAGAAAAGA
*
259962 AAA-AAGAAAAGAA
1 AAAGAAAAAAAGAA
259975 TGAAAGGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 24 0.86
18 4 0.14
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAAGAAAAGA
Found at i:259955 original size:25 final size:25
Alignment explanation
Indices: 259927--259974 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
259917 TTTCTTTGTG
259927 AAAGAAAA-AAAGAAAAAAAAGAACA
1 AAAGAAAAGAAA-AAAAAAAAGAACA
*
259952 AAAGAAAAGAAAAAAGAAAAGAA
1 AAAGAAAAGAAAAAAAAAAAGAA
259975 TGAAAGGGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (25 bp):
AAAGAAAAGAAAAAAAAAAAGAACA
Found at i:259972 original size:12 final size:12
Alignment explanation
Indices: 259927--259974 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
259917 TTTCTTTGTG
259927 AAAGAAAA-AAA
1 AAAGAAAAGAAA
*
259938 GAAAAAAAAGAACA
1 -AAAGAAAAGAA-A
259952 AAAGAAAAGAAA
1 AAAGAAAAGAAA
259964 AAAGAAAAGAA
1 AAAGAAAAGAA
259975 TGAAAGGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 19 0.59
13 12 0.38
14 1 0.03
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:259980 original size:25 final size:25
Alignment explanation
Indices: 259925--259980 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
259915 ATTTTCTTTG
259925 TGAAAGAAAAAAAGAAAAAAAAGAA
1 TGAAAGAAAAAAAGAAAAAAAAGAA
** *
259950 CAAAAGAAAAGAAA-AAAGAAAAGAA
1 TGAAAGAAAA-AAAGAAAAAAAAGAA
259975 TGAAAG
1 TGAAAG
259981 GGATGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 22 0.88
26 3 0.12
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (25 bp):
TGAAAGAAAAAAAGAAAAAAAAGAA
Found at i:262290 original size:13 final size:13
Alignment explanation
Indices: 262272--262297 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
262262 CATTTTTTGG
262272 TGTATCGATACAT
1 TGTATCGATACAT
262285 TGTATCGATACAT
1 TGTATCGATACAT
262298 ACTTTGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:262312 original size:32 final size:33
Alignment explanation
Indices: 262252--262315 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
262242 TACAAGCTAA
**
262252 TGTATCGATACATTTTTTGGTGTATCGATACAT
1 TGTATCGATACATACTTTGGTGTATCGATACAT
262285 TGTATCGATACATACTTT-GTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
262316 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.27, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Done.