Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold175
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: 1254584
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 2 of 8
Found at i:178952 original size:11 final size:11
Alignment explanation
Indices: 178911--178952 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
178901 GAACAGTGAG
178911 AAGAAAAAGAGA
1 AAGAAAAA-AGA
* *
178923 AATAAAAGAGA
1 AAGAAAAAAGA
178934 AAGAAAAAAGA
1 AAGAAAAAAGA
178945 AAGAAAAA
1 AAGAAAAA
178953 TAGTGAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 20 0.77
12 6 0.23
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:181858 original size:33 final size:32
Alignment explanation
Indices: 181816--182058 Score: 249
Period size: 33 Copynumber: 7.6 Consensus size: 32
181806 CGTTATGACA
* *
181816 CCACACAAGTCGGTGGCAACCTTTTTTTAAAGC
1 CCACACAAGTCGGTGGCAACC-TTCTCTAAAGC
* * **
181849 CCACACAAGTCGATGGTAACCCCCTTCTAAAGC
1 CCACACAAGTCGGTGGCAACCTTC-TCTAAAGC
* * *
181882 CCACACAAGTCGGTGGCCACCCT-TCAAAAGC
1 CCACACAAGTCGGTGGCAACCTTCTCTAAAGC
* * *
181913 TCACACGAGTCGATGGCAACCTTTCTCTAAAGC
1 CCACACAAGTCGGTGGCAACC-TTCTCTAAAGC
*
181946 CCACACAAGTCAGTGGCAACCTTTCTCTAAAGC
1 CCACACAAGTCGGTGGCAACC-TTCTCTAAAGC
* * *
181979 CCACACAAGTCAGTGGCAACCCT-TC-AAAGT
1 CCACACAAGTCGGTGGCAACCTTCTCTAAAGC
* * * *
182009 CCACACAAGTTGTTGGCAACCCTCTCAAAAGC
1 CCACACAAGTCGGTGGCAACCTTCTCTAAAGC
182041 CCACACAAGTCGGTGGCA
1 CCACACAAGTCGGTGGCA
182059 TCTCCTTCTA
Statistics
Matches: 176, Mismatches: 29, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
30 24 0.14
31 28 0.16
32 22 0.12
33 102 0.58
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.19
Consensus pattern (32 bp):
CCACACAAGTCGGTGGCAACCTTCTCTAAAGC
Found at i:181926 original size:64 final size:65
Alignment explanation
Indices: 181816--182074 Score: 271
Period size: 64 Copynumber: 4.0 Consensus size: 65
181806 CGTTATGACA
* * ** *
181816 CCACACAAGTCGGTGGCAACCTTTTTTTAAAGCCCACACAAGTCGATGGTAACCCCCTTCTAAAG
1 CCACACAAGTCGGTGGCAACCTCTCTCAAAAGCCCACACAAGTCGATGGCAA-CCCCTTCTAAAG
181881 C
65 C
* * * **
181882 CCACACAAGTCGGTGGCCACC-CT-TCAAAAGCTCACACGAGTCGATGGCAACCTTTCTCTAAAG
1 CCACACAAGTCGGTGGCAACCTCTCTCAAAAGCCCACACAAGTCGATGGCAACCCCT-TCTAAAG
181945 C
65 C
* * *
181946 CCACACAAGTCAGTGGCAACCTTTCTCTAAAGCCCACACAAGTC-AGTGGCAA-CCCTTC-AAAG
1 CCACACAAGTCGGTGGCAACCTCTCTCAAAAGCCCACACAAGTCGA-TGGCAACCCCTTCTAAAG
*
182008 T
65 C
* * * * *
182009 CCACACAAGTTGTTGGCAACC-CTCTCAAAAGCCCACACAAGTCGGTGGCATCTCCTTCT-AAGC
1 CCACACAAGTCGGTGGCAACCTCTCTCAAAAGCCCACACAAGTCGATGGCAACCCCTTCTAAAGC
182072 CCA
1 CCA
182075 ATGTTGTTGG
Statistics
Matches: 159, Mismatches: 27, Indels: 17
0.78 0.13 0.08
Matches are distributed among these distances:
62 25 0.16
63 36 0.23
64 51 0.32
65 5 0.03
66 42 0.26
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (65 bp):
CCACACAAGTCGGTGGCAACCTCTCTCAAAAGCCCACACAAGTCGATGGCAACCCCTTCTAAAGC
Found at i:181983 original size:97 final size:95
Alignment explanation
Indices: 181816--182074 Score: 294
Period size: 97 Copynumber: 2.7 Consensus size: 95
181806 CGTTATGACA
* * * *
181816 CCACACAAGTCGGTGGCAACCTTTTTTTAAAGCCCACACAAGTCGATGGTAACCCCCTTCTAAAG
1 CCACACAAGTCGATGGCAACCTTTCTCTAAAGCCCACACAAGTCG-TGGCAACCCCCTTCTAAAG
* *
181881 CCCACACAAGTCGGTGGCCACCCTTCAAAAG-
65 CCCACACAAGTCAGTGGCAACCCTTC-AAAGT
* **
181912 CTCACACGAGTCGATGGCAACCTTTCTCTAAAGCCCACACAAGTCAGTGGCAA-CCTTTCTCTAA
1 C-CACACAAGTCGATGGCAACCTTTCTCTAAAGCCCACACAAGTC-GTGGCAACCCCCT-TCTAA
181976 AGCCCACACAAGTCAGTGGCAACCCTTCAAAGT
63 AGCCCACACAAGTCAGTGGCAACCCTTCAAAGT
* * * * * *
182009 CCACACAAGTTGTTGGCAACC-CTCTCAAAAGCCCACACAAGTCGGTGGC-ATCTCCTTCT-AAG
1 CCACACAAGTCGATGGCAACCTTTCTCTAAAGCCCACACAAGTC-GTGGCAACCCCCTTCTAAAG
182071 CCCA
65 CCCA
182075 ATGTTGTTGG
Statistics
Matches: 140, Mismatches: 18, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
93 7 0.05
94 4 0.03
95 27 0.19
96 25 0.18
97 76 0.54
98 1 0.01
ACGTcount: A:0.29, C:0.34, G:0.17, T:0.20
Consensus pattern (95 bp):
CCACACAAGTCGATGGCAACCTTTCTCTAAAGCCCACACAAGTCGTGGCAACCCCCTTCTAAAGC
CCACACAAGTCAGTGGCAACCCTTCAAAGT
Found at i:182149 original size:59 final size:54
Alignment explanation
Indices: 182057--182220 Score: 154
Period size: 59 Copynumber: 3.0 Consensus size: 54
182047 AAGTCGGTGG
*** * * *
182057 CATCTCCTTCTAAGCCCAATGTTGTTGGCCTTGAATCAACACATAGGCACTTGTCAAAC
1 CATCT-CTTCTAAGCCCAATGTCACTAGCCTTGAATCAACACATTGGCACCT-T---AC
** *
182116 CATCTCTTTCTAAGCCCAATGTCACTAGCCTTGAATCAGTACATTGGCACCCTTAT
1 CATCTC-TTCTAAGCCCAATGTCACTAGCCTTGAATCAACACATTGGCA-CCTTAC
*
182172 CA--TCTT-TAAGTCCAATGTCACTAGCCTTGAATCAACACATTGGCACCTT
1 CATCTCTTCTAAGCCCAATGTCACTAGCCTTGAATCAACACATTGGCACCTT
182221 TGTCATCTTT
Statistics
Matches: 91, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
51 4 0.04
52 36 0.40
53 2 0.02
54 2 0.02
56 3 0.03
58 1 0.01
59 41 0.45
60 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.30
Consensus pattern (54 bp):
CATCTCTTCTAAGCCCAATGTCACTAGCCTTGAATCAACACATTGGCACCTTAC
Found at i:182198 original size:52 final size:52
Alignment explanation
Indices: 182126--182322 Score: 188
Period size: 52 Copynumber: 3.8 Consensus size: 52
182116 CATCTCTTTC
*
182126 TAAGCCCAATGTCACTAGCCTTGAATCAGTACATTGGCACCCTTATCATCTT
1 TAAGCCCAATGTCACTAGCCTTGAATCAGCACATTGGCACCCTTATCATCTT
* * * *
182178 TAAGTCCAATGTCACTAGCCTTGAATCAACACATTGGCACCTTTGTCATCTT
1 TAAGCCCAATGTCACTAGCCTTGAATCAGCACATTGGCACCCTTATCATCTT
**** * * * * * * *
182230 TAAGTTTGATATCACTGGCCTTAAATTAGTATATTGGCA--CTTCT-AT-TAT
1 TAAGCCCAATGTCACTAGCCTTGAATCAGCACATTGGCACCCTTATCATCT-T
*
182279 TAAGCCCAATGTCACT-GACCTTGAATCAGCACATTGGTACCCTT
1 TAAGCCCAATGTCACTAG-CCTTGAATCAGCACATTGGCACCCTT
182323 GTATCAATAC
Statistics
Matches: 114, Mismatches: 27, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
48 2 0.02
49 30 0.26
50 3 0.03
51 3 0.03
52 76 0.67
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (52 bp):
TAAGCCCAATGTCACTAGCCTTGAATCAGCACATTGGCACCCTTATCATCTT
Found at i:183411 original size:33 final size:33
Alignment explanation
Indices: 183374--183440 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
183364 TTCAACGATT
183374 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
183407 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
183440 T
1 T
183441 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:183412 original size:13 final size:13
Alignment explanation
Indices: 183394--183418 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
183384 CATAAAATGT
183394 TGTATCGATACAA
1 TGTATCGATACAA
183407 TGTATCGATACA
1 TGTATCGATACA
183419 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:190815 original size:27 final size:27
Alignment explanation
Indices: 190780--190850 Score: 119
Period size: 27 Copynumber: 2.7 Consensus size: 27
190770 GTTCTTTTCC
190780 AAAAAAAGAAACAAAACAAAAAAGA-AA
1 AAAAAAAGAAACAAAA-AAAAAAGACAA
190807 AAAAAAAGAAACAAAAAAAAAAGACAA
1 AAAAAAAGAAACAAAAAAAAAAGACAA
190834 AAAAAAAGAAA-AAAAAA
1 AAAAAAAGAAACAAAAAA
190851 TGAAAAACCC
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
26 14 0.33
27 29 0.67
ACGTcount: A:0.87, C:0.06, G:0.07, T:0.00
Consensus pattern (27 bp):
AAAAAAAGAAACAAAAAAAAAAGACAA
Found at i:190839 original size:38 final size:39
Alignment explanation
Indices: 190779--190855 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 39
190769 TGTTCTTTTC
*
190779 CAAAAAAAGAAACAAAACAAAAAAGAAAAAAAAAAGAAA
1 CAAAAAAAAAAACAAAACAAAAAAGAAAAAAAAAAGAAA
*
190818 CAAAAAAAAAAGAC-AAA-AAAAAAGAAAAAAAAATGAAA
1 CAAAAAAAAAA-ACAAAACAAAAAAGAAAAAAAAAAGAAA
190856 AACCCCTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 20 0.57
39 13 0.37
40 2 0.06
ACGTcount: A:0.84, C:0.06, G:0.08, T:0.01
Consensus pattern (39 bp):
CAAAAAAAAAAACAAAACAAAAAAGAAAAAAAAAAGAAA
Found at i:190857 original size:1 final size:1
Alignment explanation
Indices: 190780--190850 Score: 61
Period size: 1 Copynumber: 71.0 Consensus size: 1
190770 GTTCTTTTCC
* * * * * * * * *
190780 AAAAAAAGAAACAAAACAAAAAAGAAAAAAAAAAGAAACAAAAAAAAAAGACAAAAAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
190845 AAAAAA
1 AAAAAA
190851 TGAAAAACCC
Statistics
Matches: 52, Mismatches: 18, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.87, C:0.06, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:190857 original size:12 final size:11
Alignment explanation
Indices: 190780--190857 Score: 79
Period size: 11 Copynumber: 7.2 Consensus size: 11
190770 GTTCTTTTCC
190780 AAAAAAAGAAA
1 AAAAAAAGAAA
* *
190791 CAAAACA-AAA
1 AAAAAAAGAAA
*
190801 AAGAAAA-AAA
1 AAAAAAAGAAA
* *
190811 AAAGAAACAAA
1 AAAAAAAGAAA
190822 AAAAAAAGACAA
1 AAAAAAAGA-AA
190834 AAAAAAAGAAA
1 AAAAAAAGAAA
*
190845 AAAAAATGAAA
1 AAAAAAAGAAA
190856 AA
1 AA
190858 CCCCTTTTCA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
10 15 0.27
11 29 0.53
12 11 0.20
ACGTcount: A:0.86, C:0.05, G:0.08, T:0.01
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:191820 original size:31 final size:31
Alignment explanation
Indices: 191782--191906 Score: 128
Period size: 32 Copynumber: 4.0 Consensus size: 31
191772 CAATTCTTCA
*
191782 AATCTCTTC-TCAAAGCCCATGACTCAGTGG
1 AATCTCTTCTTCAAAGCCCACGACTCAGTGG
*
191812 TAATCTCTTC-TCAAAGTCCACGACTCAGTGG
1 -AATCTCTTCTTCAAAGCCCACGACTCAGTGG
* * *
191843 CATCTTTTTCTTCAAAGTCCACGACTCAGTGG
1 AATC-TCTTCTTCAAAGCCCACGACTCAGTGG
* * * *
191875 CAACCTTTTCTTCAAAGCCCACAACTCCGTGG
1 -AATCTCTTCTTCAAAGCCCACGACTCAGTGG
191907 CACCTTTTTA
Statistics
Matches: 82, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
30 3 0.04
31 32 0.39
32 45 0.55
33 2 0.02
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (31 bp):
AATCTCTTCTTCAAAGCCCACGACTCAGTGG
Found at i:191972 original size:69 final size:67
Alignment explanation
Indices: 191824--192264 Score: 373
Period size: 69 Copynumber: 6.7 Consensus size: 67
191814 ATCTCTTCTC
* * * * * * *
191824 AAAGTCCACGACTCAGTGGCATCTTTTTC--TTCAAAGTCCACGACTCAGTGGCAACC-TTTTC-
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGC-ACCTTTTTCT
*
191885 TTC
65 TTT
* * *
191888 AAAGCCCACAACTCCGTGGCACCTTTTTATTTTTAAAGCCCACAACTTCGTGGCACTCTTTTTCC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTTTT--
191953 CTTTT
63 CTTTT
* * * * *
191958 -AAGTCCACAACTCCGTGGCACCTTGTTCCTTTC-AAGTCCACGACTCCGTGGCACC---TTCTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTT
192018 TT
66 TT
* * * *
192020 CAAAGCCCACAATTTCGTGGCAACCTTATTTCTTCTCAAAGCCCACCACTCCGTGGCA-CTTTTT
1 -AAAGCCCACAACTCCGTGGC-ACCTT-TTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
192084 CTTTT
63 CTTTT
*
192089 CAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTCTTT
1 -AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTTCAAAGCCCACAACTCCGTGGCAC-CTTT
192154 TTCCCTTTT
61 TT--CTTTT
* *
192163 AAAGTCCACGACTCCGTGGCACC---TTCTTTTCAAAGCCCACAACTCCGTGGCACC-----CTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTT
192220 TT
66 TT
* * *
192222 -AAGCCCACAACTCTGTGGCACCTTTCTC-CTTCTAAAGCCCACA
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTC-AAAGCCCACA
192265 TAAGTCGGTG
Statistics
Matches: 311, Mismatches: 40, Indels: 55
0.77 0.10 0.14
Matches are distributed among these distances:
58 19 0.06
59 5 0.02
60 3 0.01
61 12 0.04
62 5 0.02
64 42 0.14
65 7 0.02
66 27 0.09
67 51 0.16
68 23 0.07
69 59 0.19
70 27 0.09
72 7 0.02
73 19 0.06
74 5 0.02
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.31
Consensus pattern (67 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTT
TT
Found at i:192060 original size:36 final size:34
Alignment explanation
Indices: 191817--192264 Score: 377
Period size: 32 Copynumber: 13.5 Consensus size: 34
191807 AGTGGTAATC
* * * * *
191817 TCTTCTCAAAGTCCACGACTCAGTGGCATCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
* * *
191851 TC--TTCAAAGTCCACGACTCAGTGGCAACC-TTT
1 TCTTTTCAAAGCCCACAACTCCGTGGC-ACCTTTT
191883 TC--TTCAAAGCCCACAACTCCGTGGCACCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
* * *
191915 TATTTTTAAAGCCCACAACTTCGTGGCACTCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTTT
* *
191950 TCCCTTTT--AAGTCCACAACTCCGTGGCACCTTGT
1 T--CTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
* * *
191984 TCCTTTC-AAGTCCACGACTCCGTGGCACC---T
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
* *
192014 TCTTTTCAAAGCCCACAATTTCGTGGCAACCTTATT
1 TCTTTTCAAAGCCCACAACTCCGTGGC-ACCTT-TT
* *
192050 TCTTCTCAAAGCCCACCACTCCGTGGCA-CTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
*
192083 TCTTTTCAAAGCCCACAACTCTGTGGCACTCTTTT
1 TCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTTT
192118 TCCCTTTTCAAAGCCCACAACTCCGTGGCACTCTTTT
1 T--CTTTTCAAAGCCCACAACTCCGTGGCAC-CTTTT
* *
192155 TCCCTTTT-AAAGTCCACGACTCCGTGGCACC---T
1 T--CTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
192187 TCTTTTCAAAGCCCACAACTCCGTGGCACC----
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
* *
192217 -CTTTT--AAGCCCACAACTCTGTGGCACCTTTC
1 TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
*
192248 TC-CTTCTAAAGCCCACA
1 TCTTTTC-AAAGCCCACA
192265 TAAGTCGGTG
Statistics
Matches: 354, Mismatches: 33, Indels: 54
0.80 0.07 0.12
Matches are distributed among these distances:
27 21 0.06
29 5 0.01
30 12 0.03
31 41 0.12
32 61 0.17
33 50 0.14
34 42 0.12
35 33 0.09
36 44 0.12
37 45 0.13
ACGTcount: A:0.21, C:0.35, G:0.13, T:0.31
Consensus pattern (34 bp):
TCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
Found at i:192082 original size:133 final size:131
Alignment explanation
Indices: 191824--192252 Score: 391
Period size: 133 Copynumber: 3.2 Consensus size: 131
191814 ATCTCTTCTC
* * * *
191824 AAAGTCCACGACTCAGTGGCATCTTTTTC-TTCAAAGTCCACGACTCAGTGGCAACCTTTTCTTC
1 AAAGTCCACAACTCAGTGGCACCTTTTCCTTTCAAAGTCCACGACTCCGTGGC-ACCTTTTCTTC
* * *
191888 AAAGCCCACAACTCCGTGGCACCTTTTTATTTTTAAAGCCCACAACTTCGTGGCACTCTTTTTCC
65 AAAGCCCACAACTCCGTGGCACCTTTTTATTCTCAAAGCCCACAACTCCGTGGCAC-CTTTTT--
191953 CTTTT
127 CTTTT
*
191958 -AAGTCCACAACTCCGTGGCACCTTGTTCCTTTC-AAGTCCACGACTCCGTGGCACCTTCTT-TT
1 AAAGTCCACAACTCAGTGGCACCTT-TTCCTTTCAAAGTCCACGACTCCGTGGCACCTT-TTCTT
* * * *
192020 CAAAGCCCACAATTTCGTGGCAACCTTATTTCTTCTCAAAGCCCACCACTCCGTGGCA-CTTTTT
64 CAAAGCCCACAACTCCGTGGC-ACCTT-TTTATTCTCAAAGCCCACAACTCCGTGGCACCTTTTT
192084 CTTTT
127 CTTTT
* * * *
192089 CAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTCTTT
1 -AAAGTCCACAACTCAGTGGCAC-C-TTTT-CC-TTTCAAAGTCCACGACTCCGTGGCAC-C-TT
* * * *
192154 TTCCCTTTTAAAGTCCACGACTCCGTGGCACC-TTCT-TT-TCAAAGCCCACAACTCCGTGGCAC
59 TT--C-TTCAAAGCCCACAACTCCGTGGCACCTTTTTATTCTCAAAGCCCACAACTCCGTGGCAC
192216 C-----CTTTT
121 CTTTTTCTTTT
* *
192222 -AAGCCCACAACTCTGTGGCACCTTTCTCCTT
1 AAAGTCCACAACTCAGTGGCACCTTT-TCCTT
192253 CTAAAGCCCA
Statistics
Matches: 252, Mismatches: 23, Indels: 46
0.79 0.07 0.14
Matches are distributed among these distances:
128 2 0.01
129 5 0.02
130 2 0.01
131 26 0.10
133 77 0.31
134 31 0.12
135 32 0.13
136 4 0.02
137 41 0.16
138 6 0.02
139 4 0.02
140 1 0.00
141 3 0.01
142 18 0.07
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.32
Consensus pattern (131 bp):
AAAGTCCACAACTCAGTGGCACCTTTTCCTTTCAAAGTCCACGACTCCGTGGCACCTTTTCTTCA
AAGCCCACAACTCCGTGGCACCTTTTTATTCTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
T
Found at i:192187 original size:27 final size:28
Alignment explanation
Indices: 192156--192243 Score: 115
Period size: 27 Copynumber: 3.1 Consensus size: 28
192146 CACTCTTTTT
* *
192156 CCCTTTTAAAGTCCACGACTCCGTGGCA
1 CCCTTTTAAAGCCCACAACTCCGTGGCA
192184 CCTTCTTTTCAAAGCCCACAACTCCGTGGCA
1 CC--CTTTT-AAAGCCCACAACTCCGTGGCA
*
192215 CCCTTTT-AAGCCCACAACTCTGTGGCA
1 CCCTTTTAAAGCCCACAACTCCGTGGCA
192242 CC
1 CC
192244 TTTCTCCTTC
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
27 21 0.39
28 2 0.04
29 5 0.09
30 5 0.09
31 21 0.39
ACGTcount: A:0.22, C:0.39, G:0.15, T:0.25
Consensus pattern (28 bp):
CCCTTTTAAAGCCCACAACTCCGTGGCA
Found at i:192394 original size:43 final size:43
Alignment explanation
Indices: 192331--192512 Score: 247
Period size: 43 Copynumber: 4.1 Consensus size: 43
192321 GCACCTTCTT
*
192331 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
192374 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA-C
* * *
192418 TTTTTCTTTAAATCCAATGTAGCTGGCCTTGAATCAGCACATTGACAC
1 -----CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
192466 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
192509 CTTT
1 CTTT
192513 TCCATCTTTA
Statistics
Matches: 121, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
43 82 0.68
44 1 0.01
48 1 0.01
49 37 0.31
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:192449 original size:92 final size:92
Alignment explanation
Indices: 192292--192565 Score: 467
Period size: 92 Copynumber: 2.9 Consensus size: 92
192282 TTCTAAGCCT
*
192292 AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATGTAGCTGGCCTTG
1 AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAGTCCAATGTAGCTGGCCTTG
*
192357 AATCAGCACATTGGCACCTTTAAGTCC
66 AATCAGCACATTGACACCTTTAAGTCC
* *
192384 AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAATCCAATGTAGCTGGCCTTG
1 AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAGTCCAATGTAGCTGGCCTTG
192449 AATCAGCACATTGACACCTTTAAGTCC
66 AATCAGCACATTGACACCTTTAAGTCC
*
192476 AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGTAGCTGGCC
1 AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTT---TCTTTAAGTCCAATGTAGCTGGCC
192541 TTGAATCAGCACATTGACATCCTTT
63 TTGAATCAGCACATTGACA-CCTTT
192566 TTCTCATCTT
Statistics
Matches: 171, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
92 125 0.73
95 41 0.24
96 5 0.03
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (92 bp):
AATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAGTCCAATGTAGCTGGCCTTG
AATCAGCACATTGACACCTTTAAGTCC
Found at i:192703 original size:43 final size:43
Alignment explanation
Indices: 192640--192821 Score: 256
Period size: 43 Copynumber: 4.1 Consensus size: 43
192630 TCACCTTCAT
*
192640 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
192683 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
192726 CTTTTTCTTGAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACAC
1 C----T-TT-AAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
*
192775 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
192818 CTTT
1 CTTT
192822 TCCATCTTTA
Statistics
Matches: 123, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
43 81 0.66
44 2 0.02
45 1 0.01
47 1 0.01
48 2 0.02
49 36 0.29
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:192788 original size:92 final size:93
Alignment explanation
Indices: 192639--192874 Score: 402
Period size: 92 Copynumber: 2.5 Consensus size: 93
192629 CTCACCTTCA
* *
192639 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGG
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACACCTTTAAGTCCAATATAGCTGG
192704 CCTTGAATCAGCATATTGGCACCTTTT-
66 CCTTGAATCAGCATATTGGCACCTTTTC
*
192731 TCTTGAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACACCTTTAAGTCCAATATAGCTGG
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACACCTTTAAGTCCAATATAGCTGG
192796 CCTTGAATCAGCATATTGGCACCTTTTCC
66 CCTTGAATCAGCATATTGGCACCTTTT-C
*
192825 ATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 -TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACA-CCTTT
192875 TTCTCATCTT
Statistics
Matches: 135, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
92 89 0.66
95 41 0.30
96 5 0.04
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (93 bp):
TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGACACCTTTAAGTCCAATATAGCTGG
CCTTGAATCAGCATATTGGCACCTTTTC
Found at i:192881 original size:309 final size:309
Alignment explanation
Indices: 192322--192994 Score: 1283
Period size: 309 Copynumber: 2.2 Consensus size: 309
192312 AGCATATTGG
*
192322 CACCTTCTTCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAAT
1 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAAT
*
192387 ATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTTAAATCCAATGTAGCTGGCCTTGAAT
66 ATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTGAAATCCAATGTAGCTGGCCTTGAAT
192452 CAGCACATTGACACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCA
131 CAGCACATTGACACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCA
192517 TCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCC
196 TCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCC
192582 CAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCT
261 CAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCT
192631 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAAT
1 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAAT
*
192696 ATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTGAAGTCCAATGTAGCTGGCCTTGAAT
66 ATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTGAAATCCAATGTAGCTGGCCTTGAAT
192761 CAGCACATTGACACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCA
131 CAGCACATTGACACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCA
192826 TCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCC
196 TCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCC
192891 CAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCT
261 CAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCT
* * * *
192940 CATCTTCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTT
1 CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
192995 CATCATCTTT
Statistics
Matches: 357, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
309 357 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (309 bp):
CACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAAT
ATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTTCTTGAAATCCAATGTAGCTGGCCTTGAAT
CAGCACATTGACACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCA
TCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAGCC
CAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCT
Found at i:192986 original size:67 final size:68
Alignment explanation
Indices: 192878--193004 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
192868 ATCCTTTTTC
* * *
192878 TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
192942 TCT
66 TCT
* * * *
192945 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTT
193005 AAAACCCAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.39
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:193802 original size:33 final size:33
Alignment explanation
Indices: 193765--193831 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
193755 TTCAACGATT
193765 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
193798 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
193831 T
1 T
193832 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:193803 original size:13 final size:13
Alignment explanation
Indices: 193785--193809 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
193775 CATAAAATGT
193785 TGTATCGATACAA
1 TGTATCGATACAA
193798 TGTATCGATACA
1 TGTATCGATACA
193810 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:197578 original size:26 final size:26
Alignment explanation
Indices: 197542--197593 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
197532 AATGATAGTT
197542 CTCCCATCATGCTCATCTCGAATTCA
1 CTCCCATCATGCTCATCTCGAATTCA
197568 CTCCCATCATGCTCATCTCGAATTCA
1 CTCCCATCATGCTCATCTCGAATTCA
197594 TCTTGCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.38, G:0.08, T:0.31
Consensus pattern (26 bp):
CTCCCATCATGCTCATCTCGAATTCA
Found at i:200412 original size:26 final size:26
Alignment explanation
Indices: 200383--200434 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
200373 ATTTAGAGAT
200383 AGTTTTCTTGTGTTTAGAATTCATTG
1 AGTTTTCTTGTGTTTAGAATTCATTG
200409 AGTTTTCTTGTGTTTAGAATTCATTG
1 AGTTTTCTTGTGTTTAGAATTCATTG
200435 CCTTAAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.54
Consensus pattern (26 bp):
AGTTTTCTTGTGTTTAGAATTCATTG
Found at i:200814 original size:3 final size:3
Alignment explanation
Indices: 200806--200839 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
200796 CGAGTCAACT
* *
200806 TCA TCA TCA TCA TTA TCA TCA TCA TCT TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
200840 TGTTGATGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (3 bp):
TCA
Found at i:202554 original size:20 final size:21
Alignment explanation
Indices: 202527--202600 Score: 84
Period size: 20 Copynumber: 3.7 Consensus size: 21
202517 TTCTACCCAG
202527 ATGTATCGATACATTTTTCGA
1 ATGTATCGATACATTTTTCGA
*
202548 A-GTATCGATACA-TGTT-GA
1 ATGTATCGATACATTTTTCGA
* *
202566 ATATATTGATACATTTTTC-A
1 ATGTATCGATACATTTTTCGA
*
202586 ATGTATCGATGCATT
1 ATGTATCGATACATT
202601 CTATTTTCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
18 3 0.07
19 12 0.28
20 27 0.63
21 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (21 bp):
ATGTATCGATACATTTTTCGA
Found at i:203955 original size:18 final size:20
Alignment explanation
Indices: 203897--203948 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
203887 ATCGATACAA
**
203897 TGTATCGATACATG-TTCAT
1 TGTATCGATACATGATAAAT
*
203916 TATATCGATACATGATAAAT
1 TGTATCGATACATGATAAAT
203936 TGTATCGATACAT
1 TGTATCGATACAT
203949 AAAATTGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATGATAAAT
Found at i:204024 original size:24 final size:24
Alignment explanation
Indices: 203992--204061 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
203982 AATACATTAC
203992 TGTTCATCACTATTCATGTATCAT
1 TGTTCATCACTATTCATGTATCAT
* * *
204016 TGTTTATCACTGTTCATGTATCAC
1 TGTTCATCACTATTCATGTATCAT
* *
204040 TATTCATTAC-AGTTCATGTATC
1 TGTTCATCACTA-TTCATGTATC
204062 GATACAGTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (24 bp):
TGTTCATCACTATTCATGTATCAT
Found at i:204595 original size:35 final size:36
Alignment explanation
Indices: 204528--204596 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
204518 AGTGATTGTG
**
204528 AGGTTCTATCTTAGCCTTTGAAAAAGATAGGGAGAA
1 AGGTTCTATCTTAGCCCATGAAAAAGATAGGGAGAA
204564 AGGTTCTATCTTAGCCCATG-AAAAGATAGGGAG
1 AGGTTCTATCTTAGCCCATGAAAAAGATAGGGAG
204597 GTTTTTATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 13 0.42
36 18 0.58
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (36 bp):
AGGTTCTATCTTAGCCCATGAAAAAGATAGGGAGAA
Found at i:204611 original size:32 final size:34
Alignment explanation
Indices: 204527--204611 Score: 102
Period size: 36 Copynumber: 2.5 Consensus size: 34
204517 AAGTGATTGT
**
204527 GAGGTTCTATCTTAGCCTTTGAAAAAGATAGGGA
1 GAGGTTCTATCTTAGCCCATGAAAAAGATAGGGA
204561 GAAAGGTTCTATCTTAGCCCATG-AAAAGATAGGGA
1 G--AGGTTCTATCTTAGCCCATGAAAAAGATAGGGA
* *
204596 G-GTTTTTATCTTAGCC
1 GAGGTTCTATCTTAGCC
204612 TTAAAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
32 13 0.29
34 1 0.02
35 13 0.29
36 18 0.40
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.31
Consensus pattern (34 bp):
GAGGTTCTATCTTAGCCCATGAAAAAGATAGGGA
Found at i:206235 original size:21 final size:21
Alignment explanation
Indices: 206193--206251 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
206183 GAACTAGAGG
206193 AGAAAATGAATGAGTTAGAAA
1 AGAAAATGAATGAGTTAGAAA
206214 AGAAAA-GAAATGAGTT-GCAAA
1 AGAAAATG-AATGAGTTAG-AAA
206235 ATGAAAATG-ATGAGTTA
1 A-GAAAATGAATGAGTTA
206252 ACTAATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
20 2 0.06
21 25 0.76
22 5 0.15
23 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.24, T:0.20
Consensus pattern (21 bp):
AGAAAATGAATGAGTTAGAAA
Found at i:207202 original size:13 final size:13
Alignment explanation
Indices: 207184--207208 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
207174 CAAAGAAAAT
207184 TATATCGATACAC
1 TATATCGATACAC
207197 TATATCGATACA
1 TATATCGATACA
207209 ATTTTGATAT
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:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
TATATCGATACAC
Found at i:207616 original size:29 final size:30
Alignment explanation
Indices: 207564--207623 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
207554 CTAGGTTTTG
*
207564 TGTGTTGGTTTCATTCAGAAATATTTGTAT
1 TGTGTTGGTTTCATTCAAAAATATTTGTAT
207594 TGTGTTGGTTT-ATTCAAAAATATTTGTAT
1 TGTGTTGGTTTCATTCAAAAATATTTGTAT
207623 T
1 T
207624 CAAAATTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.52
Consensus pattern (30 bp):
TGTGTTGGTTTCATTCAAAAATATTTGTAT
Found at i:209178 original size:24 final size:24
Alignment explanation
Indices: 209144--209194 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
209134 TAATTGATAC
*
209144 ATCACTGTTCATCACTATTCATGT
1 ATCACTATTCATCACTATTCATGT
* *
209168 ATCACTATTCATCACTGTTTATGT
1 ATCACTATTCATCACTATTCATGT
209192 ATC
1 ATC
209195 GATATAGTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.24, G:0.08, T:0.43
Consensus pattern (24 bp):
ATCACTATTCATCACTATTCATGT
Found at i:209304 original size:20 final size:19
Alignment explanation
Indices: 209258--209304 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
209248 AATTTTAAGT
*
209258 GCATGTATCGATACATTAT
1 GCATGTATCGATACATTAA
*
209277 GAATTGTATCGATACATTGAA
1 GCA-TGTATCGATACATT-AA
209298 GCATGTA
1 GCATGTA
209305 AGTACGGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (19 bp):
GCATGTATCGATACATTAA
Found at i:209708 original size:36 final size:33
Alignment explanation
Indices: 209660--209752 Score: 100
Period size: 36 Copynumber: 2.8 Consensus size: 33
209650 AAGTGATTGT
209660 GAGGTTCTATCTTAGCCTTTGAAAAAGATAGGGA
1 GAGGTTCTATCTTAGCC-TTGAAAAAGATAGGGA
* *
209694 GAAAGGTTCTATCTTAGCCCGTG-AAAATATAGGGA
1 G--AGGTTCTATCTTAG-CCTTGAAAAAGATAGGGA
**
209729 G-CTTTCTATCTTAGCCTTGAAAAA
1 GAGGTTCTATCTTAGCCTTGAAAAA
209753 TAGTGTTGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
31 4 0.08
32 15 0.30
34 1 0.02
35 12 0.24
36 16 0.32
37 2 0.04
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (33 bp):
GAGGTTCTATCTTAGCCTTGAAAAAGATAGGGA
Found at i:209753 original size:32 final size:33
Alignment explanation
Indices: 209663--209754 Score: 98
Period size: 32 Copynumber: 2.7 Consensus size: 33
209653 TGATTGTGAG
* *
209663 GTTCTATCTTAGCCTTTGAAAAAGATAGGGAGAAAG
1 GTTCTATCTTAGCC-TTGAAAAATATAGGGAG--AC
*
209699 GTTCTATCTTAGCCCGTG-AAAATATAGGGAG-C
1 GTTCTATCTTAG-CCTTGAAAAATATAGGGAGAC
*
209731 TTTCTATCTTAGCCTTGAAAAATA
1 GTTCTATCTTAGCCTTGAAAAATA
209755 GTGTTGTAAG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
31 4 0.08
32 17 0.35
35 12 0.24
36 14 0.29
37 2 0.04
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.32
Consensus pattern (33 bp):
GTTCTATCTTAGCCTTGAAAAATATAGGGAGAC
Found at i:213320 original size:7 final size:7
Alignment explanation
Indices: 213308--213374 Score: 50
Period size: 7 Copynumber: 9.3 Consensus size: 7
213298 ATAGGAAGGG
213308 AGAAAAA
1 AGAAAAA
213315 AGAAAAA
1 AGAAAAA
213322 A-AAGAGGAA
1 AGAA-A--AA
213331 AG-AAAA
1 AGAAAAA
213337 AG-AAAA
1 AGAAAAA
213343 AGAAAAA
1 AGAAAAA
*
213350 AGGAAATA
1 A-GAAAAA
*
213358 AGAAGAA
1 AGAAAAA
213365 AGAGAAAA
1 AGA-AAAA
213373 AG
1 AG
213375 GGAAATGAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
6 12 0.24
7 21 0.43
8 12 0.24
9 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.01
Consensus pattern (7 bp):
AGAAAAA
Found at i:213378 original size:24 final size:24
Alignment explanation
Indices: 213303--213380 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 24
213293 AAGAGATAGG
*
213303 AAGGGAGA-AAAAAGAAAAA-AAA
1 AAGGGAAATAAAAAGAAAAAGAAA
* *
213325 GA-GGAAAGAAAAAGAAAAAGAAA
1 AAGGGAAATAAAAAGAAAAAGAAA
* * *
213348 AAAGGAAATAAGAAGAAAGAGAAA
1 AAGGGAAATAAAAAGAAAAAGAAA
213372 AAGGGAAAT
1 AAGGGAAAT
213381 GAGGTAGCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
21 4 0.09
22 12 0.26
23 4 0.09
24 26 0.57
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03
Consensus pattern (24 bp):
AAGGGAAATAAAAAGAAAAAGAAA
Found at i:218257 original size:164 final size:160
Alignment explanation
Indices: 217933--218444 Score: 473
Period size: 164 Copynumber: 3.1 Consensus size: 160
217923 AGTTTTTAAC
* *
217933 TTTAAAATTCTTTAAATATTATCATTTAATTACCAT-TAAATCAGTTTTGAAACA-TTCATTTAT
1 TTTAAAATTCATTAAATATCATCATTTAATTA--ATGTAAATCAGTTTTGAAA-ATTTCATTTAT
** * *
217996 TTTCTCAAGTTTTTTTATTTTTCCTTAAAATCCCTTTATTTTTAAAAAATGAAAATTTCTATCCA
63 TTTCTTGAGTTTTTTTATTTTTTCTTAAAAT---TTTATTTTTAAAAAACGAAAATTTCTATCCA
*
218061 GAAATGTTTTCGGGAGATTTTTCTCAGTTTAAAATTT
125 GAAATGTTTTAGGGAGATTTTTCTCAGTTT-AAATTT
* * *
218098 TTT-TAATTCATTAAATATCATCATTTAATTTAATGTAAATCAGTTTTGAAATTTTCATTTACTT
1 TTTAAAATTCATTAAATATCATCATTTAA-TTAATGTAAATCAGTTTTGAAAATTTCATTTATTT
* ** *
218162 TCTTGAGTTTTTTTATTTTTTCTTGAAATTTTATTTTTCCAAAAAACGAAGTTTTCTACTCCATA
65 TCTTGAGTTTTTTTATTTTTTCTTAAAATTTTATTTTT--AAAAAACGAAAATTTCTA-TCCAGA
* * *
218227 AATTTTTTGAGGGGGATCTTTT-T-GGTTTAAATTT
127 AATGTTTT-AGGGAGAT-TTTTCTCAGTTTAAATTT
* * *
218261 TTTAAAATTCATCAAATATCATCATTTAATTCATAGTAAATCATTTTTGAAAAATTT-ATTTATT
1 TTTAAAATTCATTAAATATCATCATTTAATTAAT-GTAAATCAGTTTTG-AAAATTTCATTTATT
* ** * ** * *
218325 TTCATGAG-TTTTCCATTTTTTCTTAAAATTTTTCTATTCTTAAAAAATCG-AGTTTTCTGTTTC
64 TTCTTGAGTTTTTTTATTTTTTCTTAAAA--TTT-TATTTTTAAAAAA-CGAAAATTTCT-ATCC
* * * * *
218388 ATAAATGTTTTAGGACAAATTTTTCTCAGTCTAAAATT
124 AGAAATGTTTTAGG-GAGATTTTTCTCAGTTTAAATTT
*
218426 TTTAAAATTCATTTAATAT
1 TTTAAAATTCATTAAATAT
218445 TGTCATTAAA
Statistics
Matches: 289, Mismatches: 39, Indels: 38
0.79 0.11 0.10
Matches are distributed among these distances:
161 9 0.03
163 54 0.19
164 167 0.58
165 49 0.17
166 10 0.03
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (160 bp):
TTTAAAATTCATTAAATATCATCATTTAATTAATGTAAATCAGTTTTGAAAATTTCATTTATTTT
CTTGAGTTTTTTTATTTTTTCTTAAAATTTTATTTTTAAAAAACGAAAATTTCTATCCAGAAATG
TTTTAGGGAGATTTTTCTCAGTTTAAATTT
Found at i:221042 original size:164 final size:163
Alignment explanation
Indices: 220798--221376 Score: 480
Period size: 165 Copynumber: 3.5 Consensus size: 163
220788 TCTTATGAAA
* * * * *
220798 AAAAATGCAAAACTCAT-AAAATAAATTGAATTTTGTAAAACTAATTTAATGTGAATTTAATG-T
1 AAAAATG-AAAACTCATGAAAATAAA-TGAATTTT-TAAAAATGATTTACTATGAATTAAATGAT
* * * * ** * * *
220861 CATTATTAGATGAATTTTAAAAATTTTAAATCGAGACAAATTTCT-CCGAAAACATTTACG-GGA
63 GA-TATTTGATGAATTTTAAAAATTTTAAATCGAAAAAAATCCCTCCCAAAAAAATTTACGAGCA
* * *
220924 TAGAAAACTCAACTTTTT-GGGAATAGGG-GAATTTTAA-G
127 -A-AAAACTCAA-TTTTTCGGAAACAGGGAG-ATTTCAAGG
* * *
220962 AGAAAATGAAAACTCATGAAAATAAATGAATTTTTCAAAATTGACTCACTATGAATTAAATGATG
1 A-AAAATGAAAACTCATGAAAATAAATGAATTTTT-AAAAATGATTTACTATGAATTAAATGATG
*
221027 ATATTTGATGAATTTTAAAAATTTTAAATCGAAAAAAATCCCTCCCAAAAAAATTTATGAAGCAA
64 ATATTTGATGAATTTTAAAAATTTTAAATCGAAAAAAATCCCTCCCAAAAAAATTTACG-AGCAA
* *
221092 AAAACTCTATTTTTCGGAAACATGGAGATTTCAAGG
128 AAAACTCAATTTTTCGGAAACAGGGAGATTTCAAGG
* *
221128 AAAAATAAAAAATTCA-GAAAAATAAATGAATTTTTTAAAAATGATTTACTATGAATTAAATGAT
1 AAAAAT-GAAAACTCATG-AAAATAAATGAA-TTTTTAAAAATGATTTACTATGAATTAAATGAT
* * * * * * *
221192 GATATTTGATGAATTTTTAAAATTTTAAA-CTTAGAAAAATCCCT-TCAAAAACATTTATGGAGT
63 GATATTTGATGAATTTTAAAAATTTTAAATC-GAAAAAAATCCCTCCCAAAAAAATTTA-CGAGC
* ** * * *
221255 AAAAAACTCGATTTTTCAAAAATAGAGAGATTTCAAAG
126 AAAAAACTCAATTTTTCGGAAACAGGGAGATTTCAAGG
* * * * *
221293 AAAAATGAGAAACTTAAGAAAATAAATAAATTTTTTAAAACTGATTTA--ATGGTAATTACATGA
1 AAAAATGA-AAACTCATGAAAATAAATGAA-TTTTTAAAAATGATTTACTAT-G-AATTAAATGA
* * *
221356 TAATATTTAAAGAATTTTAAA
62 TGATATTTGATGAATTTTAAA
221377 GTTAAAAACT
Statistics
Matches: 345, Mismatches: 51, Indels: 37
0.80 0.12 0.09
Matches are distributed among these distances:
163 3 0.01
164 81 0.23
165 165 0.48
166 89 0.26
167 7 0.02
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (163 bp):
AAAAATGAAAACTCATGAAAATAAATGAATTTTTAAAAATGATTTACTATGAATTAAATGATGAT
ATTTGATGAATTTTAAAAATTTTAAATCGAAAAAAATCCCTCCCAAAAAAATTTACGAGCAAAAA
ACTCAATTTTTCGGAAACAGGGAGATTTCAAGG
Found at i:221328 original size:165 final size:164
Alignment explanation
Indices: 220959--221376 Score: 495
Period size: 165 Copynumber: 2.5 Consensus size: 164
220949 GGGGAATTTT
* * * * * *
220959 AAGAGAAAATGAAAACTCATGAAAATAAATGAATTTTTCAAAATTGACTCACTATGAATTAAATG
1 AAGA-AAAATGAAAACTTAAGAAAATAAATGAATTTTTTAAAAATGATTTACTATGAATTAAATG
221024 ATGATATTTGATGAATTTTAAAAATTTTAAATCGAAAAAAATCCCTCCCAAAAAAATTTATGAAG
65 ATGATATTTGATGAATTTTAAAAATTTTAAATCGAAAAAAATCCCTCCCAAAAAAATTTATGAAG
* *
221089 CAAAAAACTCTATTTTTCGGAAACATGGAGATTTCA
130 CAAAAAACTCGATTTTTC-GAAAAATGGAGATTTCA
* * * *
221125 AGGAAAAATAAAAAATTCAGAAAAATAAATGAATTTTTTAAAAATGATTTACTATGAATTAAATG
1 AAGAAAAATGAAAACTTAAG-AAAATAAATGAATTTTTTAAAAATGATTTACTATGAATTAAATG
* * * * * *
221190 ATGATATTTGATGAATTTTTAAAATTTTAAA-CTTAGAAAAATCCCT-TCAAAAACATTTATGGA
65 ATGATATTTGATGAATTTTAAAAATTTTAAATC-GAAAAAAATCCCTCCCAAAAAAATTTATGAA
*
221253 GTAAAAAACTCGATTTTTC-AAAAATAGAGAGATTTCA
129 GCAAAAAACTCGATTTTTCGAAAAAT-G-GAGATTTCA
* * *
221290 AAGAAAAATGAGAAACTTAAGAAAATAAATAAATTTTTTAAAACTGATTTA--ATGGTAATTACA
1 AAGAAAAATGA-AAACTTAAGAAAATAAATGAATTTTTTAAAAATGATTTACTAT-G-AATTAAA
* * *
221353 TGATAATATTTAAAGAATTTTAAA
63 TGATGATATTTGATGAATTTTAAA
221377 GTTAAAAACT
Statistics
Matches: 215, Mismatches: 30, Indels: 15
0.83 0.12 0.06
Matches are distributed among these distances:
163 7 0.03
164 2 0.01
165 115 0.53
166 91 0.42
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (164 bp):
AAGAAAAATGAAAACTTAAGAAAATAAATGAATTTTTTAAAAATGATTTACTATGAATTAAATGA
TGATATTTGATGAATTTTAAAAATTTTAAATCGAAAAAAATCCCTCCCAAAAAAATTTATGAAGC
AAAAAACTCGATTTTTCGAAAAATGGAGATTTCA
Found at i:224733 original size:93 final size:93
Alignment explanation
Indices: 224590--224774 Score: 370
Period size: 93 Copynumber: 2.0 Consensus size: 93
224580 GAAAGGAAGA
224590 TATTGTCACTGCAACATCAATAGATGCCCTTTATATTGAGCCACATGAAGATATTCCTGAATCTT
1 TATTGTCACTGCAACATCAATAGATGCCCTTTATATTGAGCCACATGAAGATATTCCTGAATCTT
224655 TATTTCAATTATTTGAATTTGTGAATGT
66 TATTTCAATTATTTGAATTTGTGAATGT
224683 TATTGTCACTGCAACATCAATAGATGCCCTTTATATTGAGCCACATGAAGATATTCCTGAATCTT
1 TATTGTCACTGCAACATCAATAGATGCCCTTTATATTGAGCCACATGAAGATATTCCTGAATCTT
224748 TATTTCAATTATTTGAATTTGTGAATG
66 TATTTCAATTATTTGAATTTGTGAATG
224775 CTACTTACAT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (93 bp):
TATTGTCACTGCAACATCAATAGATGCCCTTTATATTGAGCCACATGAAGATATTCCTGAATCTT
TATTTCAATTATTTGAATTTGTGAATGT
Found at i:229019 original size:22 final size:23
Alignment explanation
Indices: 228980--229030 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
228970 GTCCTAAGAT
*
228980 AAAAAAAAAGTAAGAAAA-AAAC
1 AAAAAAAAAGTAAAAAAAGAAAC
*
229002 AAAAAAAAAG-ACAAAAAAGAAAG
1 AAAAAAAAAGTA-AAAAAAGAAAC
229025 AAAAAA
1 AAAAAA
229031 CTCAGATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.60
23 9 0.36
ACGTcount: A:0.84, C:0.04, G:0.10, T:0.02
Consensus pattern (23 bp):
AAAAAAAAAGTAAAAAAAGAAAC
Found at i:229029 original size:12 final size:12
Alignment explanation
Indices: 228975--229030 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 12
228965 AGGGTGTCCT
*
228975 AAGATAAAAAAA
1 AAGACAAAAAAA
* *
228987 AAG-TAAGAAAA
1 AAGACAAAAAAA
228998 AA-ACAAAAAAA
1 AAGACAAAAAAA
229009 AAGACAAAAAAGA
1 AAGACAAAAAA-A
229022 AAGA-AAAAA
1 AAGACAAAAA
229031 CTCAGATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
11 17 0.45
12 16 0.42
13 5 0.13
ACGTcount: A:0.82, C:0.04, G:0.11, T:0.04
Consensus pattern (12 bp):
AAGACAAAAAAA
Found at i:230921 original size:13 final size:13
Alignment explanation
Indices: 230903--230927 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
230893 ACCAAGAACA
230903 TGTATCGATACAT
1 TGTATCGATACAT
230916 TGTATCGATACA
1 TGTATCGATACA
230928 AAGCAATATA
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:230925 original size:32 final size:33
Alignment explanation
Indices: 230884--230948 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
230874 CAATTCAGTG
* *
230884 TGTATCGATACCAAG-AACATGTATCGATACAT
1 TGTATCGATACAAAGCAACATATATCGATACAT
*
230916 TGTATCGATACAAAGCAATATATATCGATACAT
1 TGTATCGATACAAAGCAACATATATCGATACAT
230949 CTGGGTGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (33 bp):
TGTATCGATACAAAGCAACATATATCGATACAT
Found at i:231627 original size:25 final size:25
Alignment explanation
Indices: 231593--231649 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
231583 TAAAACTCTT
231593 CCTTAATAAGATTTTTCTTTCTCCC
1 CCTTAATAAGATTTTTCTTTCTCCC
231618 CCTTAATAAGATTTTTCTTTCTCCC
1 CCTTAATAAGATTTTTCTTTCTCCC
231643 CCTTAAT
1 CCTTAAT
231650 CAGAAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.21, C:0.28, G:0.04, T:0.47
Consensus pattern (25 bp):
CCTTAATAAGATTTTTCTTTCTCCC
Found at i:233672 original size:13 final size:13
Alignment explanation
Indices: 233654--233688 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
233644 AGTGCCCTTG
233654 TATCAATACAATA
1 TATCAATACAATA
*
233667 TATCAATACAATG
1 TATCAATACAATA
*
233680 TATCGATAC
1 TATCAATAC
233689 TAAGATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (13 bp):
TATCAATACAATA
Found at i:239821 original size:13 final size:13
Alignment explanation
Indices: 239803--239827 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
239793 ACCAAGAACA
239803 TGTATCAATACAT
1 TGTATCAATACAT
239816 TGTATCAATACA
1 TGTATCAATACA
239828 AAGCAATATG
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:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (13 bp):
TGTATCAATACAT
Found at i:240427 original size:28 final size:28
Alignment explanation
Indices: 240395--240483 Score: 106
Period size: 28 Copynumber: 3.2 Consensus size: 28
240385 CAAAAGAAAG
** ** *
240395 CCACATTAGTTGGCATTTATGTTAAAAC
1 CCACATTAGTTGGCACATAAATCAAAAC
*
240423 CCACATTAGTTGGCACATAAATCAAAGC
1 CCACATTAGTTGGCACATAAATCAAAAC
* *
240451 CCACATTAGTTGGCACATGAATCAAAGC
1 CCACATTAGTTGGCACATAAATCAAAAC
240479 CCACA
1 CCACA
240484 CCATAAATCA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.25
Consensus pattern (28 bp):
CCACATTAGTTGGCACATAAATCAAAAC
Found at i:240623 original size:28 final size:28
Alignment explanation
Indices: 240583--240658 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
240573 ATTTACCTTA
*
240583 AAGCCCATATTAGTTGGCACATGAATCG
1 AAGCCCATATTAGTTGGCACATGAATCC
* * * *
240611 AAGCCCATATTAGCTGGCACCTTATTCC
1 AAGCCCATATTAGTTGGCACATGAATCC
* *
240639 AAGCCCATACTAGTTAGCAC
1 AAGCCCATATTAGTTGGCAC
240659 TTAAGTTAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (28 bp):
AAGCCCATATTAGTTGGCACATGAATCC
Found at i:240726 original size:39 final size:39
Alignment explanation
Indices: 240682--240756 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
240672 CACACTAGCT
240682 GGCAACTTATTAGGAGGTTAAACCTTACAAAAAAATGTG
1 GGCAACTTATTAGGAGGTTAAACCTTACAAAAAAATGTG
240721 GGCAACTTATTAGGAGGTTAAACCTTACAAAAAAAT
1 GGCAACTTATTAGGAGGTTAAACCTTACAAAAAAAT
240757 CATCTATTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (39 bp):
GGCAACTTATTAGGAGGTTAAACCTTACAAAAAAATGTG
Found at i:241339 original size:13 final size:14
Alignment explanation
Indices: 241303--241341 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
241293 AGATTAGAGT
241303 TGAAAAAAAAAAGA
1 TGAAAAAAAAAAGA
**
241317 TGAACTAAAAAA-A
1 TGAAAAAAAAAAGA
241330 TGAAAAAAAAAA
1 TGAAAAAAAAAA
241342 CAAGCTTTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (14 bp):
TGAAAAAAAAAAGA
Found at i:241751 original size:51 final size:50
Alignment explanation
Indices: 241687--241791 Score: 140
Period size: 51 Copynumber: 2.1 Consensus size: 50
241677 ATCTTGAACC
* * * *
241687 AAAAAAGAAAAAAAAAAGAAGGAGAGAGGAAAAGAGAAGAAAGAAAAA-AG
1 AAAAAAAAAAAAAAAAAGAAGAAGAAAGAAAAAGAGAAGAAA-AAAAAGAG
*
241737 AAAAAAAAAGAAAAAAATGAAGAAGAAAGAAAAAGAGAAGAAAAAAAAGAG
1 AAAAAAAAA-AAAAAAAAGAAGAAGAAAGAAAAAGAGAAGAAAAAAAAGAG
241788 AAAA
1 AAAA
241792 GAGATGGCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
50 13 0.27
51 35 0.73
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (50 bp):
AAAAAAAAAAAAAAAAAGAAGAAGAAAGAAAAAGAGAAGAAAAAAAAGAG
Found at i:241769 original size:29 final size:30
Alignment explanation
Indices: 241727--241791 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
241717 AAAGAGAAGA
241727 AAGAAAAAAGAAAAA-AAAAGAAAAAAATG
1 AAGAAAAAAGAAAAAGAAAAGAAAAAAATG
* * *
241756 AAGAAGAAAGAAAAAGAGAAGAAAAAAAAG
1 AAGAAAAAAGAAAAAGAAAAGAAAAAAATG
241786 -AGAAAA
1 AAGAAAA
241792 GAGATGGCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (30 bp):
AAGAAAAAAGAAAAAGAAAAGAAAAAAATG
Found at i:242127 original size:15 final size:16
Alignment explanation
Indices: 242096--242133 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
242086 ATATTTGAGA
242096 TTTTTTATATTATTAC
1 TTTTTTATATTATTAC
*
242112 TTTTTTATGTTA-TAC
1 TTTTTTATATTATTAC
*
242127 TTGTTTA
1 TTTTTTA
242134 ATGTGTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (16 bp):
TTTTTTATATTATTAC
Found at i:245101 original size:21 final size:23
Alignment explanation
Indices: 245077--245120 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
245067 TAATAAATGT
245077 TTTTAAGA-T-AAAATATTAATA
1 TTTTAAGAGTAAAAATATTAATA
*
245098 TTTTAATAGTAAAAATATTAATA
1 TTTTAAGAGTAAAAATATTAATA
245121 GAAATAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 1 0.05
23 12 0.60
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (23 bp):
TTTTAAGAGTAAAAATATTAATA
Found at i:245116 original size:17 final size:17
Alignment explanation
Indices: 245093--245135 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
245083 GATAAAATAT
245093 TAATATTTTAATAGTAAA
1 TAATATTTTAATAG-AAA
245111 -AATA--TTAATAGAAA
1 TAATATTTTAATAGAAA
245125 TAATATTTTAA
1 TAATATTTTAA
245136 ATATTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.14
15 11 0.50
17 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
TAATATTTTAATAGAAA
Found at i:245348 original size:26 final size:27
Alignment explanation
Indices: 245312--245368 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
245302 TTAAATGTTA
* * *
245312 AGTATTTAATATTAATA-TAATATTTT
1 AGTATTAAATACTAATATTAAAATTTT
*
245338 AGTATTAAATACTATTATTAAAATTTT
1 AGTATTAAATACTAATATTAAAATTTT
245365 AGTA
1 AGTA
245369 CTTTAATAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (27 bp):
AGTATTAAATACTAATATTAAAATTTT
Found at i:245353 original size:18 final size:19
Alignment explanation
Indices: 245316--245358 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
245306 ATGTTAAGTA
245316 TTTAATATTAATATAATAT
1 TTTAATATTAATATAATAT
* *
245335 TTTAGTATTAA-ATACTAT
1 TTTAATATTAATATAATAT
245353 TATTAA
1 T-TTAA
245359 AATTTTAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TTTAATATTAATATAATAT
Found at i:260804 original size:3 final size:3
Alignment explanation
Indices: 260796--260821 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
260786 ATAGTGGATT
260796 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
260822 GATAACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:261507 original size:84 final size:84
Alignment explanation
Indices: 261348--261507 Score: 205
Period size: 84 Copynumber: 1.9 Consensus size: 84
261338 TTAATCTCAT
* ** * *
261348 TTTTTAGGGATTATTTAATAATTTAATTATCCTTCTATTTTCATTTTTATGTCTCAGATTTGGGA
1 TTTTTAAGGATTATTTAATAATTTAACAATCCTTCTATTTTCATATTTATATCTCAGATTTGGGA
*
261413 GATCATGAGAAGATGAAAA
66 GATCACGAGAAGATGAAAA
* * **
261432 TTTTTAAGGATTATTTGATAATTTAACAATCTCTT-TATTTTCATATTTATATTTTGGATTTGGG
1 TTTTTAAGGATTATTTAATAATTTAACAATC-CTTCTATTTTCATATTTATATCTCAGATTTGGG
*
261496 AGATTACGAGAA
65 AGATCACGAGAA
261508 CATCCCAAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
84 61 0.95
85 3 0.05
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (84 bp):
TTTTTAAGGATTATTTAATAATTTAACAATCCTTCTATTTTCATATTTATATCTCAGATTTGGGA
GATCACGAGAAGATGAAAA
Found at i:262863 original size:3 final size:3
Alignment explanation
Indices: 262855--262895 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
262845 CTTCAATTTA
262855 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
262896 AGATTTTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:266843 original size:2 final size:2
Alignment explanation
Indices: 266836--266860 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
266826 CCACAGATTC
266836 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
266861 TGCAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:267624 original size:19 final size:19
Alignment explanation
Indices: 267602--267694 Score: 50
Period size: 20 Copynumber: 4.8 Consensus size: 19
267592 AAAAATTATG
267602 AATTTATTTAAAATTTAAA
1 AATTTATTTAAAATTTAAA
* * * *
267621 AATTTTATTATACAGTTGAGA
1 AA-TTTATT-TAAAATTTAAA
*
267642 AA-TTATTAAGAAAATTTAAA
1 AATTTATT--TAAAATTTAAA
*
267662 AATTTTAATT-AAA-TT-AA
1 AA-TTTATTTAAAATTTAAA
267679 AATTTATGTTAAAATT
1 AATTTAT-TTAAAATT
267695 AATATGTTAA
Statistics
Matches: 54, Mismatches: 12, Indels: 16
0.66 0.15 0.20
Matches are distributed among these distances:
16 4 0.07
17 6 0.11
18 5 0.09
19 11 0.20
20 15 0.28
21 9 0.17
22 4 0.07
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.44
Consensus pattern (19 bp):
AATTTATTTAAAATTTAAA
Found at i:267772 original size:15 final size:15
Alignment explanation
Indices: 267732--267776 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
267722 AATAAAAAAT
267732 TAAATTAA-ATTTAAA
1 TAAATTAATA-TTAAA
267747 TAAATT-ATATTAAA
1 TAAATTAATATTAAA
267761 -AAATTAATTATTAAA
1 TAAATTAA-TATTAAA
267776 T
1 T
267777 TTTAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.19
14 7 0.27
15 14 0.54
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAATTAATATTAAA
Found at i:268071 original size:23 final size:22
Alignment explanation
Indices: 268022--268072 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
268012 AAATAGTTTA
268022 AATTTATTTTATTTTAAGATGT
1 AATTTATTTTATTTTAAGATGT
*
268044 GATTTATTTTTATTTATAAGAT-T
1 AATTTA-TTTTATTT-TAAGATGT
268067 AATTTA
1 AATTTA
268073 ATTAAAGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.20
23 14 0.56
24 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (22 bp):
AATTTATTTTATTTTAAGATGT
Found at i:268391 original size:23 final size:22
Alignment explanation
Indices: 268337--268380 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
268327 AATTTTAGAA
* *
268337 AAGAAAGGAGGAAAAAAGAAAG
1 AAGAAAGAAGAAAAAAAGAAAG
268359 AAGCAAAGAAGAAAAAAAGAAA
1 AAG-AAAGAAGAAAAAAAGAAA
268381 TGAGAGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (22 bp):
AAGAAAGAAGAAAAAAAGAAAG
Found at i:269081 original size:158 final size:157
Alignment explanation
Indices: 268550--269457 Score: 847
Period size: 158 Copynumber: 5.9 Consensus size: 157
268540 ATTAAATCAA
* * * * * * *
268550 AAAAATAAAAAGACTTAGTTTGATGTGGTTTTGGGTTATA-TATTTGTTCAATATGAAATACTCA
1 AAAAATAAAAAAACTTAGTTTAACGTGGTTTTGGATTATATTTTTTGTTTAATATGAAATACTCG
* * * *
268614 TTTAAATATCTTTTGATATTGTTTGAG-TTTTCTAATATTATTAATTTTTTAT-ACAT-CTTGC-
66 TTTAAATACCTCTTGATATTGTTTAAGATTTT-TAATATTATTAATTTTTTATGGCATGCTT-CT
* *
268675 TTAATATGTCAAAATATGTTTAACATGTC
129 TTAATATATCAAAATATGTTTAATATGTC
* * * *
268704 AAAAATAAAAAAAACTTAGTTTAACATAGTTTTGAATTATATTTTTTGTTTAACATGAAATACTC
1 AAAAAT-AAAAAAACTTAGTTTAACGTGGTTTTGGATTATATTTTTTGTTTAATATGAAATACTC
* ** **
268769 GTTTAAATACCT-TTAGATGTTGTTTAAGATTTTTAATATTATTAATTTTTTATGGCACACTTGG
65 GTTTAAATACCTCTT-GATATTGTTTAAGATTTTTAATATTATTAATTTTTTATGGCATGCTTCT
* * *
268833 TTGATTTGTCAAAATATGTTTAATATGTC
129 TTAATATATCAAAATATGTTTAATATGTC
* * * * *
268862 AAAAACAAAAAAAAAACTTGGTTTAACATGATTTTAGG-TTATATTTTTTGTTTAATATGAAATG
1 --AAA-AATAAAAAAACTTAGTTTAACGTGGTTTT-GGATTATATTTTTTGTTTAATATGAAATA
* * * * *
268926 CTCGTTTAGATGCCTCTTGATATTGTTTGAGATTTATAATATTATTAAATTTTGTATGGCATGCT
62 CTCGTTTAAATACCTCTTGATATTGTTTAAGATTTTTAATATTATT-AATTTTTTATGGCATGCT
*
268991 TCTTTAATATATCAAAATATGTTTAATATATC
126 TCTTTAATATATCAAAATATGTTTAATATGTC
* * * *
269023 AAAAATAAAAAGACTTAGTTTAACGTGGTTTTGGATTGTATTTTTTATTTAATATGAAATGCTCG
1 AAAAATAAAAAAACTTAGTTTAACGTGGTTTTGGATTATATTTTTTGTTTAATATGAAATACTCG
* ** * * * * * * *
269088 TTTAGATGGCTCTTAATGTTGTTTGAGATTTTTGATATTATTCATTTTTTATAGCATGCTTATTT
66 TTTAAATACCTCTTGATATTGTTTAAGATTTTTAATATTATTAATTTTTTATGGCATGCTTCTTT
*
269153 AATATGTCAAAA-A----T-A-A-G--
131 AATATATCAAAATATGTTTAATATGTC
* * * * *
269170 ------AAAAAACCTTAGTTTAACGTGGTTTTAGATTATATTTTTTGTTTAATATAAAATATTTG
1 AAAAATAAAAAAACTTAGTTTAACGTGGTTTTGGATTATATTTTTTGTTTAATATGAAATACTCG
* ** * * * * * *
269229 TTTAGATGTCTCTTGATATTGTTAAAAATTTCTGATATTATTAGTTTTTTTATGGCATGCTTGTT
66 TTTAAATACCTCTTGATATTGTTTAAGATTTTTAATATTATTA-ATTTTTTATGGCATGCTTCTT
269294 TAATATATCAAAATATGTTTAATATGTC
130 TAATATATCAAAATATGTTTAATATGTC
* *** * * * *
269322 AAACATAAAAAAACTTAGTTTGGTGTGATTTTGGATTATATTTTTTATTTAGTATGAAATGCGT-
1 AAAAATAAAAAAACTTAGTTTAACGTGGTTTTGGATTATATTTTTTGTTTAATATGAAATAC-TC
* * * *
269386 GTTTAAATACCTATTGATGTTGTTTAAGATTTTTGATATTATTAATTTTTTTATGGCATGCTTGT
65 GTTTAAATACCTCTTGATATTGTTTAAGATTTTTAATATTATTAA-TTTTTTATGGCATGCTTCT
269451 TTAATAT
129 TTAATAT
269458 TATTAATTTT
Statistics
Matches: 621, Mismatches: 100, Indels: 62
0.79 0.13 0.08
Matches are distributed among these distances:
141 85 0.14
142 30 0.05
143 1 0.00
147 1 0.00
148 1 0.00
149 1 0.00
150 2 0.00
151 1 0.00
152 1 0.00
154 6 0.01
155 29 0.05
156 62 0.10
157 38 0.06
158 225 0.36
159 4 0.01
160 88 0.14
161 46 0.07
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (157 bp):
AAAAATAAAAAAACTTAGTTTAACGTGGTTTTGGATTATATTTTTTGTTTAATATGAAATACTCG
TTTAAATACCTCTTGATATTGTTTAAGATTTTTAATATTATTAATTTTTTATGGCATGCTTCTTT
AATATATCAAAATATGTTTAATATGTC
Found at i:269232 original size:141 final size:138
Alignment explanation
Indices: 269012--269306 Score: 376
Period size: 141 Copynumber: 2.1 Consensus size: 138
269002 TCAAAATATG
* * *
269012 TTTAATATATCAAAAATAAAAAGACTTAGTTTAACGTGGTTTTGGATTGTATTTTTTATTTAATA
1 TTTAATATATCAAAAATAAAAAAACTTAGTTTAACGTGGTTTTAGATTATATTTTTTATTTAATA
* * * ** * *
269077 TGAAATGCTCGTTTAGATGGCTCTTAATGTTGTTTGAGATTTTTGATATTATTCA-TTTTTTATA
66 TAAAATACTCGTTTAGATGGCTCTTAATATTGTTAAAAATTTCTGATATTATT-AGTTTTTTATA
269141 GCATGCTTA
130 GCATGCTTA
* *
269150 TTTAATATGTCAAAAATAAGAAAAAACCTTAGTTTAACGTGGTTTTAGATTATATTTTTTGTTTA
1 TTTAATATATCAAAAAT-A-AAAAAA-CTTAGTTTAACGTGGTTTTAGATTATATTTTTTATTTA
* * * *
269215 ATATAAAATATTTGTTTAGATGTCTCTTGATATTGTTAAAAATTTCTGATATTATTAGTTTTTTT
63 ATATAAAATACTCGTTTAGATGGCTCTTAATATTGTTAAAAATTTCTGATATTATTAG-TTTTTT
* *
269280 ATGGCATGCTTG
127 ATAGCATGCTTA
269292 TTTAATATATCAAAA
1 TTTAATATATCAAAA
269307 TATGTTTAAT
Statistics
Matches: 133, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
138 16 0.12
139 1 0.01
140 6 0.05
141 80 0.60
142 30 0.23
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (138 bp):
TTTAATATATCAAAAATAAAAAAACTTAGTTTAACGTGGTTTTAGATTATATTTTTTATTTAATA
TAAAATACTCGTTTAGATGGCTCTTAATATTGTTAAAAATTTCTGATATTATTAGTTTTTTATAG
CATGCTTA
Found at i:269408 original size:299 final size:300
Alignment explanation
Indices: 268851--269457 Score: 840
Period size: 299 Copynumber: 2.0 Consensus size: 300
268841 TCAAAATATG
* *
268851 TTTAATATGTCAAAAACAAAAAAAAAACTTGGTTTAACATGATTTTAGGTTATATTTTTTGTTTA
1 TTTAATATGTCAAAAACAAAAAAAAAACTTAGTTTAACATGATTTTAGATTATATTTTTTGTTTA
* * ** *
268916 ATATGAAATGCTCGTTTAGATGCCTCTTGATATTGTTTGAGATTTATAATATTATTAAATTTTGT
66 ATATAAAATACTCGTTTAGATGCCTCTTGATATTGTTAAAAATTTATAATATTATTAAATTTTGT
*
268981 ATGGCATGCTTCTTTAATATATCAAAATATGTTTAATATATCAAAAATAAAAAGACTTAGTTTAA
131 ATGGCATGCTTCTTTAATATATCAAAATATGTTTAATATATCAAAAATAAAAAAACTTAGTTTAA
* * * ** *
269046 CGTGGTTTTGGATTGTATTTTTTATTTAATATGAAATGCTCGTTTAGATGGCTCTTAATGTTGTT
196 CGTGATTTTGGATTATATTTTTTATTTAATATGAAATGCTCGTTTAAATACCTATTAATGTTGTT
* *
269111 TGAGATTTTTGATATTATTCA-TTTTTTATAGCATGCTTA
261 TAAGATTTTTGATATTATTAATTTTTTTATAGCATGCTTA
* * * * *
269150 TTTAATATGTCAAAAATAAGAAAAAACCTTAGTTTAACGTGGTTTTAGATTATATTTTTTGTTTA
1 TTTAATATGTCAAAAACAAAAAAAAAACTTAGTTTAACATGATTTTAGATTATATTTTTTGTTTA
* * * * * ** *
269215 ATATAAAATATTTGTTTAGATGTCTCTTGATATTGTTAAAAATTTCTGATATTATTAGTTTTTTT
66 ATATAAAATACTCGTTTAGATGCCTCTTGATATTGTTAAAAATTTATAATATTATTAAATTTTGT
* * * **
269280 ATGGCATGCTTGTTTAATATATCAAAATATGTTTAATATGTCAAACATAAAAAAACTTAGTTTGG
131 ATGGCATGCTTCTTTAATATATCAAAATATGTTTAATATATCAAAAATAAAAAAACTTAGTTTAA
* * *
269345 TGTGATTTTGGATTATATTTTTTATTTAGTATGAAATGCGT-GTTTAAATACCTATTGATGTTGT
196 CGTGATTTTGGATTATATTTTTTATTTAATATGAAATGC-TCGTTTAAATACCTATTAATGTTGT
* *
269409 TTAAGATTTTTGATATTATTAATTTTTTTATGGCATGCTTG
260 TTAAGATTTTTGATATTATTAATTTTTTTATAGCATGCTTA
269450 TTTAATAT
1 TTTAATAT
269458 TATTAATTTT
Statistics
Matches: 267, Mismatches: 39, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
299 242 0.91
300 25 0.09
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (300 bp):
TTTAATATGTCAAAAACAAAAAAAAAACTTAGTTTAACATGATTTTAGATTATATTTTTTGTTTA
ATATAAAATACTCGTTTAGATGCCTCTTGATATTGTTAAAAATTTATAATATTATTAAATTTTGT
ATGGCATGCTTCTTTAATATATCAAAATATGTTTAATATATCAAAAATAAAAAAACTTAGTTTAA
CGTGATTTTGGATTATATTTTTTATTTAATATGAAATGCTCGTTTAAATACCTATTAATGTTGTT
TAAGATTTTTGATATTATTAATTTTTTTATAGCATGCTTA
Found at i:272128 original size:96 final size:96
Alignment explanation
Indices: 271975--272244 Score: 296
Period size: 96 Copynumber: 2.8 Consensus size: 96
271965 AAAAAAACAG
* * * * *
271975 GGTTGGAGTATCCCTTTGGAGGAATAGGGTT-GAAGTGTCCTCGATAATTG-CAATTTAAGCAAA
1 GGTTGGAGTATCCC-CTAGAGGAATAGGGTTGGAA-TGTCCCCGATGA-TGACAGTTTAAGCAAA
*
272038 AATAAAATTTAAATCTTAACGAGTTTAAAAATGA
63 AATAAAATTTAAATCTTAACGAGTTTAAAAAGGA
* * *
272072 GGTTGGAGTATCCCCTAGAGGAATAAGGTTGGAATGCCCCCGATGATGACAGTTTAAGTAAAAAT
1 GGTTGGAGTATCCCCTAGAGGAATAGGGTTGGAATGTCCCCGATGATGACAGTTTAAGCAAAAAT
*
272137 AAAATTTAAATCTTGACGAGTTTAAAAAGGA
66 AAAATTTAAATCTTAACGAGTTTAAAAAGGA
* * * * * *
272168 GGTTAGAGTATCCCCTCGAATGAAT-GGGTTTGGAGTGTCCCTGATGATGA-TGATTTAAGCAAA
1 GGTTGGAGTATCCCCTAG-AGGAATAGGG-TTGGAATGTCCCCGATGATGACAG-TTTAAGCAAA
**
272231 AATATGATTTAAAT
63 AATAAAATTTAAAT
272245 ATTGAAAATG
Statistics
Matches: 147, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
95 2 0.01
96 84 0.57
97 61 0.41
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (96 bp):
GGTTGGAGTATCCCCTAGAGGAATAGGGTTGGAATGTCCCCGATGATGACAGTTTAAGCAAAAAT
AAAATTTAAATCTTAACGAGTTTAAAAAGGA
Found at i:276470 original size:87 final size:86
Alignment explanation
Indices: 276129--276516 Score: 348
Period size: 88 Copynumber: 4.4 Consensus size: 86
276119 TTTTTTATGA
* * *** * *
276129 AGAATGAGGTTGGAGTATCCTCTCGGAATAGTGGGGATGGAATTACTTTAAAGATAAAACTATAT
1 AGAATGGGGTTGGAGTATCC-CTCGGAATAGTGGGGATGGAATTTC-CCCAAGATAAAATTATAC
* **
276194 GAAGGGTAAATTTGAAATTTTTGGG
64 GAA-GGAAAATTTG-AATTTTTGTT
* * * * * * *
276219 AGAACGGAGTTAGAGTATTCCTTTGGAGTAGTGGGGATGGAATTTCCCTAAGGATAAAATTATAC
1 AGAATGGGGTTGGAGTA-TCCCTCGGAATAGTGGGGATGGAATTTCCCCAA-GATAAAATTATAC
* *
276284 AAAGGAAAATTTGAAATTTTGTT
64 GAAGGAAAATTTGAATTTTTGTT
* * * ** *
276307 AGAATAGGGTTGAAGTATCCCTTTGGAAT-GCTGAAGATGGAGTTTCCCCAAAGATAAAATTATA
1 AGAATGGGGTTGGAGTATCCC-TCGGAATAG-TGGGGATGGAATTTCCCC-AAGATAAAATTATA
* *
276371 TGAAGGAAAATTTGAATTTTTGCT
63 CGAAGGAAAATTTGAATTTTTGTT
* *
276395 AGAATGGGGTTGGAGTATCACCTCGAAATAGTGGGGATGGAGTTTCCCCAAGATAAAATTATACG
1 AGAATGGGGTTGGAGTATC-CCTCGGAATAGTGGGGATGGAATTTCCCCAAGATAAAATTATACG
* *
276460 AAGGAAAATTTAAATTTTTATT
65 AAGGAAAATTTGAATTTTTGTT
** *
276482 AGAATAAGGTTGGAGTGTCCTCTTC-GAATAGTGGG
1 AGAATGGGGTTGGAGTATCC-C-TCGGAATAGTGGG
276517 AATAGAGTTT
Statistics
Matches: 242, Mismatches: 47, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
86 1 0.00
87 64 0.26
88 111 0.46
89 16 0.07
90 47 0.19
91 3 0.01
ACGTcount: A:0.34, C:0.09, G:0.26, T:0.31
Consensus pattern (86 bp):
AGAATGGGGTTGGAGTATCCCTCGGAATAGTGGGGATGGAATTTCCCCAAGATAAAATTATACGA
AGGAAAATTTGAATTTTTGTT
Found at i:280034 original size:21 final size:22
Alignment explanation
Indices: 280008--280050 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
279998 TAATCAACAC
280008 TCAATA-AATAATTAAA-TAAAT
1 TCAATATAA-AATTAAATTAAAT
280029 TCAATATAAAATTAAATTAAAT
1 TCAATATAAAATTAAATTAAAT
280051 GAATAATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (22 bp):
TCAATATAAAATTAAATTAAAT
Found at i:281827 original size:10 final size:10
Alignment explanation
Indices: 281812--281853 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
281802 AGTATCGATA
*
281812 CATCACAGTT
1 CATCACTGTT
281822 CATCACTGTT
1 CATCACTGTT
*
281832 CATAACTGTT
1 CATCACTGTT
*
281842 CATAACTGTT
1 CATCACTGTT
281852 CA
1 CA
281854 GGTATCACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.36
Consensus pattern (10 bp):
CATCACTGTT
Found at i:281897 original size:13 final size:13
Alignment explanation
Indices: 281879--281917 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
281869 CACTATTCAG
*
281879 GTATCGATGCATT
1 GTATCGATACATT
*
281892 GTATCGATACACT
1 GTATCGATACATT
281905 GTATCGATACATT
1 GTATCGATACATT
281918 ATGAATAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:284031 original size:21 final size:21
Alignment explanation
Indices: 284007--284068 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
283997 TAATATTCTT
* *
284007 GAAAAGAAATTAAGTGAATTA
1 GAAAAGAAAATAAATGAATTA
284028 GAAAAGAAAATAAATGAATTA
1 GAAAAGAAAATAAATGAATTA
** **
284049 GAGGAGAAAAGGAATGAATT
1 GAAAAGAAAATAAATGAATT
284069 GCAAATGGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (21 bp):
GAAAAGAAAATAAATGAATTA
Found at i:287653 original size:17 final size:17
Alignment explanation
Indices: 287628--287665 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
287618 TATCGATACA
*
287628 TCACAGTTCATCACTGT
1 TCACAGTTCATAACTGT
*
287645 TCACTGTTCATAACTGT
1 TCACAGTTCATAACTGT
287662 TCAC
1 TCAC
287666 GTATCACTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (17 bp):
TCACAGTTCATAACTGT
Found at i:287709 original size:13 final size:13
Alignment explanation
Indices: 287691--287715 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
287681 ATTGTTCAGA
287691 TATCGATACATTG
1 TATCGATACATTG
287704 TATCGATACATT
1 TATCGATACATT
287716 ATGAATAGTA
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:0.12, T:0.40
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:288224 original size:32 final size:32
Alignment explanation
Indices: 288183--288274 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 32
288173 CAAGTGATTA
*
288183 AGAGGTTCTATCTTAGCCTTGAAAGATAGTGT
1 AGAGGTTCTATCTTAGCCTTGAAAGATAGGGT
*
288215 AGAGGTTCTATCTTCGCCTTTGTAAAAGATAGGGT
1 AGAGGTTCTATCTTAGCC-TTG--AAAGATAGGGT
* * *
288250 ATAAGGTTATACCTTAGCCTT-AAAG
1 A-GAGGTTCTATCTTAGCCTTGAAAG
288275 GTAAACAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
32 21 0.42
33 3 0.06
35 13 0.26
36 13 0.26
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (32 bp):
AGAGGTTCTATCTTAGCCTTGAAAGATAGGGT
Found at i:288341 original size:18 final size:18
Alignment explanation
Indices: 288315--288357 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
288305 CCACTTGGCA
*
288315 AGGAAGTGCCAAGGAGAG
1 AGGACGTGCCAAGGAGAG
*
288333 AGGACGTGCCTAGGAGAG
1 AGGACGTGCCAAGGAGAG
288351 AGGACGT
1 AGGACGT
288358 AAGTGCCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.14, G:0.44, T:0.09
Consensus pattern (18 bp):
AGGACGTGCCAAGGAGAG
Found at i:290174 original size:15 final size:17
Alignment explanation
Indices: 290146--290178 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
290136 GTAACACTTC
290146 TTTTTTCACTATTAAAA
1 TTTTTTCACTATTAAAA
290163 TTTTTTC-C-ATTAAAA
1 TTTTTTCACTATTAAAA
290178 T
1 T
290179 AGACAAATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTTTCACTATTAAAA
Found at i:291074 original size:166 final size:166
Alignment explanation
Indices: 290775--291226 Score: 511
Period size: 166 Copynumber: 2.7 Consensus size: 166
290765 ATCTATGCAT
* * *
290775 CATATATTAGCCTTATCAACTTCTTTCATATCAGAAAAAATCTAATTCCCATT-AGTAATGTATG
1 CATATATTAGTCTTATCAACTTCTTTCATATAAGAAAAAATCTAATTCCCATTAAG-AATCTATG
* * * * * * * * *
290839 TAATAATCACATTTATTTC-AAAATAGAATCCATGTATTAGTCTCATTTTTTAGATTCCAATATA
65 CATTTATCATATTTA-TTCAAAAATAGAATCCATGCATTAGTCTCATCTTTCAAATTCCAATACA
* * * *
290903 TACATTAGTTTATTCCTTGCAGTCTGACTTTTATAATC
129 TACATTAGTTTATTCCTTGCAGTATAACATTTACAATC
*
290941 CATATATTAGTCTTATCAACTT-TTTACATATAAGAAAAAATCTGATTCCCATTAAGAATCTATG
1 CATATATTAGTCTTATCAACTTCTTT-CATATAAGAAAAAATCTAATTCCCATTAAGAATCTATG
* * *
291005 CATTTATCATATTCATTCAAAAATAGAATCTATGCATTAGTC-CTATCTTTCAAACTT-CAATCC
65 CATTTATCATATTTATTCAAAAATAGAATCCATGCATTAGTCTC-ATCTTTCAAA-TTCCAATAC
*
291068 ATACATTAGTTTATTCCTTGCAGTATAACATTTGCAATC
128 ATACATTAGTTTATTCCTTGCAGTATAACATTTACAATC
** * * * * * * *
291107 CATGCATTACTCTTATCAACTTCTTTCAAATCAA-AAAAAATTTTATTCTCATTAAGAATTTATA
1 CATATATTAGTCTTATCAACTTCTTTCATAT-AAGAAAAAATCTAATTCCCATTAAGAATCTATG
* * *
291171 CATGTATCATATTTATTTAAAAATAGAATCCATGCATTAGTCTCATCTTTGAAATT
65 CATTTATCATATTTATTCAAAAATAGAATCCATGCATTAGTCTCATCTTTCAAATT
291227 TTAATAAAAA
Statistics
Matches: 243, Mismatches: 35, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
165 9 0.04
166 224 0.92
167 10 0.04
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.40
Consensus pattern (166 bp):
CATATATTAGTCTTATCAACTTCTTTCATATAAGAAAAAATCTAATTCCCATTAAGAATCTATGC
ATTTATCATATTTATTCAAAAATAGAATCCATGCATTAGTCTCATCTTTCAAATTCCAATACATA
CATTAGTTTATTCCTTGCAGTATAACATTTACAATC
Found at i:291259 original size:39 final size:39
Alignment explanation
Indices: 291215--291298 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 39
291205 CATTAGTCTC
* * * *
291215 ATCTTTGAAATTTTAATAAAAAATTTATATATTACTCAT
1 ATCTTTGAAATTCTAATAAAAAATCTATATAATACTAAT
* * *
291254 ATCTTTTAGATTCTAATAAATAATCTATATAATACTAAT
1 ATCTTTGAAATTCTAATAAAAAATCTATATAATACTAAT
291293 ATCTTT
1 ATCTTT
291299 CAAAATCCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (39 bp):
ATCTTTGAAATTCTAATAAAAAATCTATATAATACTAAT
Found at i:291644 original size:14 final size:14
Alignment explanation
Indices: 291625--291669 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
291615 TAATTTGTAA
291625 AAAAAACATATTTT
1 AAAAAACATATTTT
*
291639 AAAAAATAT-TTTCT
1 AAAAAACATATTT-T
291653 AAAAAAACATATTTT
1 -AAAAAACATATTTT
291668 AA
1 AA
291670 GAGTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.12
14 11 0.42
15 9 0.35
16 3 0.12
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAAAACATATTTT
Found at i:291900 original size:6 final size:6
Alignment explanation
Indices: 291859--291899 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
291849 CACTTTACTA
* *
291859 TAAAAC TAAAAC TAAAAC TCAAAC TAAAAC TAAAAT TAAAA
1 TAAAAC TAAAAC TAAAAC TAAAAC TAAAAC TAAAAC TAAAA
291900 TGCAGTTCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.66, C:0.15, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAC
Found at i:293494 original size:20 final size:20
Alignment explanation
Indices: 293465--293507 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
293455 TGCAATCTTA
293465 AAAAATTATAATAAATAGAAT
1 AAAAATTATAATAAATA-AAT
293486 AAAAA-TATAATAAATAAAT
1 AAAAATTATAATAAATAAAT
293505 AAA
1 AAA
293508 TAAACAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 11 0.50
21 5 0.23
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAATTATAATAAATAAAT
Found at i:293498 original size:23 final size:22
Alignment explanation
Indices: 293463--293517 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
293453 ATTGCAATCT
*
293463 TAAAAAATTAT-AATAAATAGAA
1 TAAAAAATAATAAATAAATA-AA
293485 TAAAAATATAATAAATAAATAAA
1 TAAAAA-ATAATAAATAAATAAA
293508 TAAACAAATA
1 TAAA-AAATA
293518 TTGTTTGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 6 0.21
23 13 0.45
24 10 0.34
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
TAAAAAATAATAAATAAATAAA
Found at i:294062 original size:19 final size:19
Alignment explanation
Indices: 294025--294063 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
294015 TAATTTTATC
*
294025 ATTATGTAAAATAAGATTA
1 ATTATGTAAAATAAAATTA
294044 ATTAT-TAAAATCAAAATTA
1 ATTATGTAAAAT-AAAATTA
294063 A
1 A
294064 AAAAAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (19 bp):
ATTATGTAAAATAAAATTA
Found at i:294500 original size:2 final size:2
Alignment explanation
Indices: 294493--294520 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
294483 ATTTAATTAG
294493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
294521 CATAAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:294680 original size:22 final size:23
Alignment explanation
Indices: 294655--294702 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
294645 AACTCAACTT
294655 AATAATTAAACAAATT-AATTCA
1 AATAATTAAACAAATTAAATTCA
* *
294677 AAT-ATTTATCAAATTAAATTCA
1 AATAATTAAACAAATTAAATTCA
294699 AATA
1 AATA
294703 GCTAAGGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.35
Consensus pattern (23 bp):
AATAATTAAACAAATTAAATTCA
Found at i:295082 original size:14 final size:16
Alignment explanation
Indices: 295051--295088 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
295041 TTAGTGATCC
*
295051 AAATAAAATCATTCAA
1 AAATTAAATCATTCAA
295067 AAATTAAAT-ATT-AA
1 AAATTAAATCATTCAA
295081 AAATTAAA
1 AAATTAAA
295089 GATAATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.48
15 3 0.14
16 8 0.38
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATTAAATCATTCAA
Found at i:295777 original size:25 final size:25
Alignment explanation
Indices: 295749--295797 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
295739 GAAACTAACT
295749 TAAC-TCTCAAATAATAACTTATTTA
1 TAACTTCTC-AATAATAACTTATTTA
* *
295774 TAACTTTTCAATAGTAACTTATTT
1 TAACTTCTCAATAATAACTTATTT
295798 CTATTTCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (25 bp):
TAACTTCTCAATAATAACTTATTTA
Found at i:299815 original size:21 final size:21
Alignment explanation
Indices: 299791--299838 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
299781 GAAAGAAAAC
*
299791 GTAATAGTCA-TAATATATCTT
1 GTAATAGTCACCAAT-TATCTT
*
299812 GTAATTGTCACCAATTATCTT
1 GTAATAGTCACCAATTATCTT
*
299833 GAAATA
1 GTAATA
299839 ATCGAATTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (21 bp):
GTAATAGTCACCAATTATCTT
Found at i:302238 original size:33 final size:33
Alignment explanation
Indices: 302173--302238 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
302163 AAATTCCCAG
**
302173 ATGTATCGATACAAAGATCAATGTATTGATACA
1 ATGTATCGATACAAAGATCAATGTATCAATACA
**
302206 ATGTATCGATACATTGAAT-AATGTATCAATACA
1 ATGTATCGATACAAAG-ATCAATGTATCAATACA
302239 TTTCCTTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (33 bp):
ATGTATCGATACAAAGATCAATGTATCAATACA
Found at i:302275 original size:43 final size:43
Alignment explanation
Indices: 302227--302324 Score: 178
Period size: 43 Copynumber: 2.3 Consensus size: 43
302217 CATTGAATAA
*
302227 TGTATCAATACATTTCCTTGGCAGAAGCTTTGTAGCGATACAT
1 TGTATCGATACATTTCCTTGGCAGAAGCTTTGTAGCGATACAT
*
302270 TGTATCGATACATTTCCTTGGCAGCAGCTTTGTAGCGATACAT
1 TGTATCGATACATTTCCTTGGCAGAAGCTTTGTAGCGATACAT
302313 TGTATCGATACA
1 TGTATCGATACA
302325 ACACTTATGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 53 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (43 bp):
TGTATCGATACATTTCCTTGGCAGAAGCTTTGTAGCGATACAT
Found at i:316968 original size:8 final size:8
Alignment explanation
Indices: 316951--317044 Score: 70
Period size: 8 Copynumber: 11.5 Consensus size: 8
316941 ATCATTCGCC
316951 AAAA-AAA
1 AAAACAAA
316958 AAAACAAA
1 AAAACAAA
*
316966 AAAAGAAGAA
1 AAAA-CA-AA
316976 AAAACAAA
1 AAAACAAA
316984 AAAACAACA
1 AAAACAA-A
316993 AAAA-AACA
1 AAAACAA-A
317001 AAAACACAA
1 AAAACA-AA
*
317010 AAAA-ACA
1 AAAACAAA
*
317017 AAGA-AAA
1 AAAACAAA
*
317024 ACAACAAA
1 AAAACAAA
317032 AAAACAACA
1 AAAACAA-A
317041 AAAA
1 AAAA
317045 GGGTCCAGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
7 12 0.17
8 34 0.48
9 18 0.25
10 7 0.10
ACGTcount: A:0.84, C:0.13, G:0.03, T:0.00
Consensus pattern (8 bp):
AAAACAAA
Found at i:316968 original size:11 final size:11
Alignment explanation
Indices: 316951--317044 Score: 77
Period size: 11 Copynumber: 8.4 Consensus size: 11
316941 ATCATTCGCC
316951 AAAAAAAAA-A
1 AAAAAAAAACA
* *
316961 ACAAAAAAA-G
1 AAAAAAAAACA
*
316971 AAGAAAAAACA
1 AAAAAAAAACA
*
316982 AAAAAACAACA
1 AAAAAAAAACA
316993 AAAAAACAAA-A
1 AAAAAA-AAACA
317004 ACACAAAAAAACA
1 A-A-AAAAAAACA
317017 AAGAAAAACAACA
1 AA-AAAAA-AACA
*
317030 AAAAAACAACA
1 AAAAAAAAACA
317041 AAAA
1 AAAA
317045 GGGTCCAGAT
Statistics
Matches: 68, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
10 15 0.22
11 25 0.37
12 16 0.24
13 12 0.18
ACGTcount: A:0.84, C:0.13, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:316979 original size:18 final size:19
Alignment explanation
Indices: 316955--317044 Score: 107
Period size: 18 Copynumber: 4.8 Consensus size: 19
316945 TTCGCCAAAA
*
316955 AAAAAAACAAAAAAAGAA-
1 AAAAAAACAAAAAAACAAC
*
316973 GAAAAAACAAAAAAACAAC
1 AAAAAAACAAAAAAACAAC
316992 AAAAAAAC--AAAAAC-AC
1 AAAAAAACAAAAAAACAAC
317008 AAAAAAACAAAGAAAAACAAC
1 AAAAAAAC-AA-AAAAACAAC
317029 AAAAAAACAACAAAAA
1 AAAAAAACAA-AAAAA
317045 GGGTCCAGAT
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
16 10 0.16
17 6 0.10
18 16 0.26
19 7 0.11
20 13 0.21
21 10 0.16
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAAACAAC
Found at i:317024 original size:37 final size:37
Alignment explanation
Indices: 316955--317044 Score: 121
Period size: 37 Copynumber: 2.4 Consensus size: 37
316945 TTCGCCAAAA
*
316955 AAAAAAACAAAAAAAGAAGAAAAAACAAAAAAACAAC
1 AAAAAAACAAAAAAACAAGAAAAAACAAAAAAACAAC
*
316992 AAAAAAACAAAAACAC-A-AAAAAACAAAGAAAAACAAC
1 AAAAAAACAAAAAAACAAGAAAAAAC-AA-AAAAACAAC
317029 AAAAAAACAACAAAAA
1 AAAAAAACAA-AAAAA
317045 GGGTCCAGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
35 7 0.15
36 3 0.06
37 33 0.70
38 4 0.09
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.00
Consensus pattern (37 bp):
AAAAAAACAAAAAAACAAGAAAAAACAAAAAAACAAC
Found at i:317044 original size:1 final size:1
Alignment explanation
Indices: 316951--317035 Score: 53
Period size: 1 Copynumber: 85.0 Consensus size: 1
316941 ATCATTCGCC
* * * * * * * * * *
316951 AAAAAAAAAAACAAAAAAAGAAGAAAAAACAAAAAAACAACAAAAAAACAAAAACACAAAAAAAC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
317016 AAAGAAAAACAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAA
317036 CAACAAAAAG
Statistics
Matches: 58, Mismatches: 26, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.85, C:0.12, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:318000 original size:28 final size:27
Alignment explanation
Indices: 317948--318022 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
317938 ATCTTCAATG
* * *
317948 GAATCAAGAAAAGTGCTGATCCCCAAG-A
1 GAATCAAGAAAATTGC-AATTCCC-AGTA
*
317976 GAATCATGACAAATTGCAATTCCCAGTA
1 GAATCAAGA-AAATTGCAATTCCCAGTA
*
318004 GAATCAAGAAACTTGCAAT
1 GAATCAAGAAAATTGCAAT
318023 GGCTTTGTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 11 0.28
28 22 0.56
29 6 0.15
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (27 bp):
GAATCAAGAAAATTGCAATTCCCAGTA
Found at i:318551 original size:27 final size:27
Alignment explanation
Indices: 318506--318635 Score: 145
Period size: 27 Copynumber: 4.9 Consensus size: 27
318496 AATCTATGGC
* * * *
318506 CCACAACTCCATGGTACCCTTTTAAAT
1 CCACGACTCCGTGGCACCCTTTTAAGT
* *
318533 CCATGACTCCGTGGCACCCTTTTAAGC
1 CCACGACTCCGTGGCACCCTTTTAAGT
*
318560 CCACGACTCCGTGGTACCCTTTTAAGT
1 CCACGACTCCGTGGCACCCTTTTAAGT
* * *
318587 CCATGACTCTGTGGCACCCTTGTAAGT
1 CCACGACTCCGTGGCACCCTTTTAAGT
* *
318614 CCACAACT-CGTGGCACCTTTTT
1 CCACGACTCCGTGGCACCCTTTT
318636 CTTCTCAAAA
Statistics
Matches: 85, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
26 11 0.13
27 74 0.87
ACGTcount: A:0.21, C:0.34, G:0.16, T:0.29
Consensus pattern (27 bp):
CCACGACTCCGTGGCACCCTTTTAAGT
Found at i:318590 original size:54 final size:54
Alignment explanation
Indices: 318504--318635 Score: 185
Period size: 54 Copynumber: 2.5 Consensus size: 54
318494 CAAATCTATG
* *
318504 GCCCACAACTCCATGGTACCCTTTTAAATCCATGACTCCGTGGCACCCTTTTAA
1 GCCCACAACTCCGTGGTACCCTTTTAAATCCATGACTCCGTGGCACCCTTGTAA
* * *
318558 GCCCACGACTCCGTGGTACCCTTTTAAGTCCATGACTCTGTGGCACCCTTGTAA
1 GCCCACAACTCCGTGGTACCCTTTTAAATCCATGACTCCGTGGCACCCTTGTAA
* * *
318612 GTCCACAACT-CGTGGCACCTTTTT
1 GCCCACAACTCCGTGGTACCCTTTT
318636 CTTCTCAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
53 12 0.17
54 57 0.83
ACGTcount: A:0.20, C:0.34, G:0.17, T:0.29
Consensus pattern (54 bp):
GCCCACAACTCCGTGGTACCCTTTTAAATCCATGACTCCGTGGCACCCTTGTAA
Found at i:318726 original size:32 final size:30
Alignment explanation
Indices: 318637--318728 Score: 78
Period size: 32 Copynumber: 2.9 Consensus size: 30
318627 CACCTTTTTC
* * *
318637 TTCTCAAAAGCCCATACAAGTTAGTGGCAAT
1 TTCTCAAAAACCCACACAAG-TGGTGGCAAT
* * *
318668 TGTCT-TAAAACTCACATAAGTCGGTGGCAACT
1 T-TCTCAAAAACCCACACAAGT-GGTGGCAA-T
318700 TTCTCAAAAACCCACACAAGCTGGTGGCA
1 TTCTCAAAAACCCACACAAG-TGGTGGCA
318729 TCTCCTTGTA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
30 1 0.02
31 21 0.45
32 24 0.51
33 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (30 bp):
TTCTCAAAAACCCACACAAGTGGTGGCAAT
Found at i:318795 original size:49 final size:50
Alignment explanation
Indices: 318737--319043 Score: 210
Period size: 49 Copynumber: 6.1 Consensus size: 50
318727 CATCTCCTTG
* *
318737 TAAGTCCAATGTCGTTGGCCTTGAATCAGCATATTGGCA-CTTTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTCATCTT
* * * * *
318786 TAAGTCCAATGTTGCTGGCATTGAATCAGCACATTAGCACCTTTGTCATTTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATC-TT-TCATCTT
* * * * * * *
318838 TAAG-CCTAATATCGCTGACCTTGAATCAGTATATTGGCATTTTTAATATT
1 TAAGTCC-AATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTCATCTT
* * * * * * *
318888 CCT-AGCCCAAAGTCACTAG-CTTGAATCAGCACATTGGTATTTTTTTGATCTT
1 --TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA--TCTTTCATCTT
* * * * * *
318940 CAAGTCTAATGTTGCTGGCCTTTATTCAGCACATTAGCA-CTTTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTCATCTT
* ** * *
318989 TAAGTCCAATGTTGCTGGCCTTGAATCAATACATTTGCACCTTTGTCATCTT
1 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATC-TT-TCATCTT
319041 TAA
1 TAA
319044 ACCTAATACC
Statistics
Matches: 197, Mismatches: 47, Indels: 25
0.73 0.17 0.09
Matches are distributed among these distances:
49 74 0.38
50 24 0.12
51 26 0.13
52 73 0.37
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (50 bp):
TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTTCATCTT
Found at i:319833 original size:13 final size:13
Alignment explanation
Indices: 319815--319840 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
319805 CATTAATAAA
319815 TGTATCGATACAT
1 TGTATCGATACAT
319828 TGTATCGATACAT
1 TGTATCGATACAT
319841 GCAGGCAAAT
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:324226 original size:20 final size:21
Alignment explanation
Indices: 324187--324235 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
324177 TAATTTATAT
*
324187 CGATACAAACAGTAAATGTAC
1 CGATACATACAGTAAATGTAC
* *
324208 CGATACATA-AGTGAATGTAT
1 CGATACATACAGTAAATGTAC
324228 CGATACAT
1 CGATACAT
324236 GCCTAAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (21 bp):
CGATACATACAGTAAATGTAC
Found at i:326581 original size:33 final size:33
Alignment explanation
Indices: 326544--326610 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
326534 TTCAACGATT
326544 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
***
326577 TGTATCGATACATATTTTGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
326610 T
1 T
326611 TTAAGCTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:326582 original size:13 final size:13
Alignment explanation
Indices: 326564--326588 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
326554 CATAAAATGT
326564 TGTATCGATACAA
1 TGTATCGATACAA
326577 TGTATCGATACA
1 TGTATCGATACA
326589 TATTTTGTTG
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:326669 original size:13 final size:13
Alignment explanation
Indices: 326651--326675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
326641 ATTACTCAAA
326651 TGTATCGATACAT
1 TGTATCGATACAT
326664 TGTATCGATACA
1 TGTATCGATACA
326676 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:334786 original size:76 final size:78
Alignment explanation
Indices: 334652--334812 Score: 229
Period size: 76 Copynumber: 2.1 Consensus size: 78
334642 TCGGGGATAT
* *
334652 TCCAACTCCGATTTTATTTCAAAACACCAACTTTTCACAATCGGGGATACTCCAACCCCGTTATT
1 TCCAACCCCGATTTTATTTCAAAACACCAACTTTTCACAATCGGGGATACTCCAACCCCATTATT
334717 TCCGAGGGGACAC
66 TCCGAGGGGACAC
* * *
334730 TCCAACCCCGGTTTTATTTCTAAAACATCAA-TTTT-TC-ATCGGGGATACTCCAACCCCATTAT
1 TCCAACCCCGATTTTATTTC-AAAACACCAACTTTTCACAATCGGGGATACTCCAACCCCATTAT
* *
334792 TTTCGAGGGGATAC
65 TTCCGAGGGGACAC
334806 TCCAACC
1 TCCAACC
334813 TCGTTATTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
76 43 0.57
77 1 0.01
78 22 0.29
79 9 0.12
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (78 bp):
TCCAACCCCGATTTTATTTCAAAACACCAACTTTTCACAATCGGGGATACTCCAACCCCATTATT
TCCGAGGGGACAC
Found at i:334802 original size:28 final size:28
Alignment explanation
Indices: 334770--334842 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
334760 ATTTTTCATC
334770 GGGGATACTCCAACCCCATTATTTTCGA
1 GGGGATACTCCAACCCCATTATTTTCGA
* *
334798 GGGGATACTCCAACCTCGTTATTTTCGA
1 GGGGATACTCCAACCCCATTATTTTCGA
*
334826 GGGGATACCCCAACCCC
1 GGGGATACTCCAACCCC
334843 GGTTTTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.25
Consensus pattern (28 bp):
GGGGATACTCCAACCCCATTATTTTCGA
Found at i:334811 original size:129 final size:129
Alignment explanation
Indices: 334543--334795 Score: 318
Period size: 129 Copynumber: 2.0 Consensus size: 129
334533 GTTTCATTCT
* * * * *
334543 AAAACATCAATTTTTCATAATCCGGGATACTCCAACCCCGTTATTTCCGAGGAGATACTTCAACC
1 AAAACACCAACTTTTCACAATCCGGGATACTCCAACCCCGTTATTTCCGAGGAGACACTCCAACC
* * * * * *
334608 CTGATTTTATTTTTGAAACACCAATTCTCCGCAATCGGGGATATTCCAACTCCGATTTTATTTC
66 CCGATTTTATTTCTAAAACACCAATTCTCCGCAATCGGGGATACTCCAACTCCCATTATATTTC
* *
334672 AAAACACCAACTTTTCACAATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACC
1 AAAACACCAACTTTTCACAATCCGGGATACTCCAACCCCGTTATTTCCGAGGAGACACTCCAACC
* * **
334737 CCGGTTTTATTTCTAAAACATCAATT-T-TTC-ATCGGGGATACTCCAAC-CCCATTAT-TTTC
66 CCGATTTTATTTCTAAAACACCAATTCTCCGCAATCGGGGATACTCCAACTCCCATTATATTTC
334796 GAGGGGATAC
Statistics
Matches: 107, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
124 4 0.04
125 6 0.06
126 16 0.15
127 1 0.01
128 1 0.01
129 79 0.74
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (129 bp):
AAAACACCAACTTTTCACAATCCGGGATACTCCAACCCCGTTATTTCCGAGGAGACACTCCAACC
CCGATTTTATTTCTAAAACACCAATTCTCCGCAATCGGGGATACTCCAACTCCCATTATATTTC
Found at i:334919 original size:107 final size:104
Alignment explanation
Indices: 334694--334922 Score: 325
Period size: 104 Copynumber: 2.2 Consensus size: 104
334684 TTTCACAATC
*
334694 GGGGATACTCCAACCCCGTTATTTCCGAGGGGACACTCCAACCCCGGTTTTATTTCTAAAACATC
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGACACCCCAACCCCGGTTTTATTTCTAAAACATC
* *
334759 AATTTTTCATCGGGGATACTCCAACCCCATTATTTTCGA
66 AATTTTTAATCGGGGATACTCCAACCCCATTATTTCCGA
* * * *
334798 GGGGATACTCCAACCTCGTTATTTTCGAGGGGATACCCCAACCCCGGTTTTAATTT-TAAAATAT
1 GGGGATACTCCAACCCCGTTATTTCCGAGGGGACACCCCAACCCCGGTTTT-ATTTCTAAAACAT
* * *
334862 TAATTTCTCATAATCGGGGATACTCTAATCCCATTATTTCCGA
65 CAATTT-T--TAATCGGGGATACTCCAACCCCATTATTTCCGA
334905 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
334923 GTTTTATTTC
Statistics
Matches: 110, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
104 59 0.54
105 5 0.05
107 46 0.42
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.30
Consensus pattern (104 bp):
GGGGATACTCCAACCCCGTTATTTCCGAGGGGACACCCCAACCCCGGTTTTATTTCTAAAACATC
AATTTTTAATCGGGGATACTCCAACCCCATTATTTCCGA
Found at i:334937 original size:79 final size:79
Alignment explanation
Indices: 334798--334969 Score: 213
Period size: 79 Copynumber: 2.2 Consensus size: 79
334788 TTATTTTCGA
* * * *
334798 GGGGATACTCCAACCTCGTTATTTTCGAGGGGATACCCCAACCCCGGTTTTAATTTTAAAATATT
1 GGGGATACTCCAACCTCATTATTTCCGAGGGGATACCCCAACCCCGGTTTTAATTTTAAAACATC
334863 AATTTCTCATAATC
66 AATTTCTCATAATC
* *
334877 GGGGATACTCTAATCC-CATTATTTCCGAGGGGATACTCCAACCCCGGTTTT-ATTTCTAAAACA
1 GGGGATACTCCAA-CCTCATTATTTCCGAGGGGATACCCCAACCCCGGTTTTAATTT-TAAAACA
* * *
334940 TCAATTTTTTATAGTC
64 TCAATTTCTCATAATC
* *
334956 GAGGATACTTCAAC
1 GGGGATACTCCAAC
334970 ATTGTTATCG
Statistics
Matches: 79, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
78 5 0.06
79 72 0.91
80 2 0.03
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (79 bp):
GGGGATACTCCAACCTCATTATTTCCGAGGGGATACCCCAACCCCGGTTTTAATTTTAAAACATC
AATTTCTCATAATC
Done.