Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007815.1 Hibiscus syriacus cultivar Beakdansim tig00110147_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 279268
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:4034 original size:11 final size:11
Alignment explanation
Indices: 4020--4076 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
4010 AGGATGATTT
4020 AATGGTGATGA
1 AATGGTGATGA
4031 AATGGTGATGGA
1 AATGGTGAT-GA
4043 ATATGGTGATGA
1 A-ATGGTGATGA
* *
4055 TATAGGCG-TGA
1 AAT-GGTGATGA
4066 TAATGGTGATG
1 -AATGGTGATG
4077 GACAGATTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
11 17 0.46
12 12 0.32
13 8 0.22
ACGTcount: A:0.32, C:0.02, G:0.37, T:0.30
Consensus pattern (11 bp):
AATGGTGATGA
Found at i:16724 original size:13 final size:13
Alignment explanation
Indices: 16706--16730 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16696 AAGAAAATCT
16706 AAAGAAAGCAAAC
1 AAAGAAAGCAAAC
16719 AAAGAAAGCAAA
1 AAAGAAAGCAAA
16731 ATGCAAAGAA
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:0.72, C:0.12, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAGAAAGCAAAC
Found at i:22658 original size:19 final size:19
Alignment explanation
Indices: 22626--22673 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
22616 AAATACCTTT
22626 CCATTTCA-TTTGTAAGAA
1 CCATTTCACTTTGTAAGAA
22644 CCATTTCACTTTGTAAGAA
1 CCATTTCACTTTGTAAGAA
*
22663 CCAATTCACTT
1 CCATTTCACTT
22674 ATGAAGCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (19 bp):
CCATTTCACTTTGTAAGAA
Found at i:23149 original size:24 final size:22
Alignment explanation
Indices: 23115--23159 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
23105 TCCACAAGAC
* *
23115 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGAAATTTAAAAGG
23137 ATGTACCTCTTGAAATTTAAAAG
1 ATGT-CCT-TTGAAATTTAAAAG
23160 AATGAGCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 3 0.16
24 12 0.63
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (22 bp):
ATGTCCTTTGAAATTTAAAAGG
Found at i:25381 original size:24 final size:21
Alignment explanation
Indices: 25347--25389 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
25337 TCCACAAGAC
*
25347 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
25369 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
25390 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:30261 original size:17 final size:18
Alignment explanation
Indices: 30229--30263 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
30219 AATTTTGATG
*
30229 AATGGATATTCATCTTTT
1 AATGGATATACATCTTTT
30247 AATGGA-ATACATCTTTT
1 AATGGATATACATCTTTT
30264 GGCCGAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
AATGGATATACATCTTTT
Found at i:63514 original size:13 final size:13
Alignment explanation
Indices: 63496--63520 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63486 AAGAAAATAT
63496 AAAGAAAGAAAAC
1 AAAGAAAGAAAAC
63509 AAAGAAAGAAAA
1 AAAGAAAGAAAA
63521 ATGCAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAAC
Found at i:65388 original size:16 final size:16
Alignment explanation
Indices: 65364--65395 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
65354 TAGTTAGCTC
65364 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
*
65380 ATTTTCATTCTAACAT
1 ATTTGCATTCTAACAT
65396 TGGTGGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:69766 original size:35 final size:35
Alignment explanation
Indices: 69727--69816 Score: 117
Period size: 35 Copynumber: 2.5 Consensus size: 35
69717 GGTGGTTATA
69727 ATAGGCGTGAAATGGTGATCGAAGATGGTAATGAT
1 ATAGGCGTGAAATGGTGATCGAAGATGGTAATGAT
* * * * *
69762 ATAGGCGTGCAATGGTAATGGAAGATGGTGATGTT
1 ATAGGCGTGAAATGGTGATCGAAGATGGTAATGAT
*
69797 GTAGGCGTGAAAATGGTGAT
1 ATAGGCGTG-AAATGGTGAT
69817 ATTTAGGTAG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
35 38 0.83
36 8 0.17
ACGTcount: A:0.31, C:0.06, G:0.37, T:0.27
Consensus pattern (35 bp):
ATAGGCGTGAAATGGTGATCGAAGATGGTAATGAT
Found at i:71277 original size:13 final size:14
Alignment explanation
Indices: 71254--71282 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
71244 ATAAGATACT
71254 ATCTGTTCATCACC
1 ATCTGTTCATCACC
71268 ATCT-TTCATCACC
1 ATCTGTTCATCACC
71281 AT
1 AT
71283 TTTTTCACGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.24, C:0.34, G:0.03, T:0.38
Consensus pattern (14 bp):
ATCTGTTCATCACC
Found at i:75538 original size:165 final size:165
Alignment explanation
Indices: 75249--75580 Score: 515
Period size: 165 Copynumber: 2.0 Consensus size: 165
75239 CAGTCTTCCC
* *
75249 TTGAAATTGAGGAATTTTGATTTTGATGTTGCTCATATTATCATCAACATTGGCACGCCTAGGTC
1 TTGAAATTGAAGAATCTTGATTTTGATGTTGCTCATATTATCATCAACATTGGCACGCCTAGGTC
*
75314 TTTGTATCAATTCTGGTTCTTCATCATCATAAGGATTTGGAACATCATCTTCGGGAAGAGGTTGT
66 TTTGTATCAATGCTGGTTCTTCATCATCATAAGGATTTGGAACATCATCTTCGGGAAGAGGTTGT
*
75379 TGCCTCCAAGGAGTATCATTGTTTCT-GGTTTATGG
131 TACCTCCAAGGAGTATCATTGTTT-TGGGTTTATGG
* * *
75414 TTGAAATTGAAGAATCTTGATTTTTATGTTGCTCATGTTATCATCAACATTGGCACGCCTGGGT-
1 TTGAAATTGAAGAATCTTGATTTTGATGTTGCTCATATTATCATCAACATTGGCACGCCTAGGTC
* * ** *
75478 TATTGTATCAATGCTGGTTCTTCTTCATCATAAGGATTTGGGACATTTTCTTCTGGAAGAGGTTG
66 T-TTGTATCAATGCTGGTTCTTCATCATCATAAGGATTTGGAACATCATCTTCGGGAAGAGGTTG
*
75543 TTACCTCCGAGGAGTATCATTGTTTTGGGTTTATGG
130 TTACCTCCAAGGAGTATCATTGTTTTGGGTTTATGG
75579 TT
1 TT
75581 TATCTTGTAT
Statistics
Matches: 152, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
164 2 0.01
165 150 0.99
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.40
Consensus pattern (165 bp):
TTGAAATTGAAGAATCTTGATTTTGATGTTGCTCATATTATCATCAACATTGGCACGCCTAGGTC
TTTGTATCAATGCTGGTTCTTCATCATCATAAGGATTTGGAACATCATCTTCGGGAAGAGGTTGT
TACCTCCAAGGAGTATCATTGTTTTGGGTTTATGG
Found at i:76262 original size:26 final size:26
Alignment explanation
Indices: 76212--76275 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
76202 CTTGGCTTGC
76212 TTTTCTCTTTT-TGAAATCTTTTTCT
1 TTTTCTCTTTTCTGAAATCTTTTTCT
76237 TTTTCTTCTTTTCTG-AAT-TTTCTTCT
1 TTTTC-TCTTTTCTGAAATCTTT-TTCT
*
76263 TTTTGTCTTTTCT
1 TTTTCTCTTTTCT
76276 TTCTTTTTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 16 0.46
26 17 0.49
27 2 0.06
ACGTcount: A:0.08, C:0.17, G:0.05, T:0.70
Consensus pattern (26 bp):
TTTTCTCTTTTCTGAAATCTTTTTCT
Found at i:76279 original size:17 final size:15
Alignment explanation
Indices: 76228--76284 Score: 60
Period size: 17 Copynumber: 3.5 Consensus size: 15
76218 CTTTTTGAAA
*
76228 TCTTTTTCTTTTTCT
1 TCTTTTTGTTTTTCT
*
76243 TCTTTTCTGAATTTTCT
1 TCTTTT-TG-TTTTTCT
76260 TCTTTTTGTCTTTTCTT
1 TCTTTTTGT-TTTTC-T
76277 TCTTTTTG
1 TCTTTTTG
76285 CACTCCAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 6 0.17
16 8 0.23
17 21 0.60
ACGTcount: A:0.04, C:0.18, G:0.05, T:0.74
Consensus pattern (15 bp):
TCTTTTTGTTTTTCT
Found at i:83126 original size:58 final size:58
Alignment explanation
Indices: 83061--83186 Score: 207
Period size: 58 Copynumber: 2.2 Consensus size: 58
83051 TTCAAATTGA
*
83061 CGCCAAATGGGATAGGAGATGATGCTTAGCCGAATAGTTAAATGGCTCTTCATCTTGG
1 CGCCAAATGGGAGAGGAGATGATGCTTAGCCGAATAGTTAAATGGCTCTTCATCTTGG
* * *
83119 CGCCAAATGGGAGAGGAGATGATGCTTGGCCGAATGGTTAAATGGCTCTTTATCTTGG
1 CGCCAAATGGGAGAGGAGATGATGCTTAGCCGAATAGTTAAATGGCTCTTCATCTTGG
83177 CGCCTAAATG
1 CGCC-AAATG
83187 AACCCACATG
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 58 0.92
59 5 0.08
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.27
Consensus pattern (58 bp):
CGCCAAATGGGAGAGGAGATGATGCTTAGCCGAATAGTTAAATGGCTCTTCATCTTGG
Found at i:86972 original size:25 final size:26
Alignment explanation
Indices: 86934--87000 Score: 109
Period size: 25 Copynumber: 2.6 Consensus size: 26
86924 CCCTAGAACA
* *
86934 CCCATGTGCTTTGCATATGATCAG-C
1 CCCATGTGCCTTGCATATGACCAGAC
86959 CCCATGTGCCTTGCATATGACCAGAC
1 CCCATGTGCCTTGCATATGACCAGAC
86985 CCCATGTGCCTTGCAT
1 CCCATGTGCCTTGCAT
87001 GTGGGTTCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
25 22 0.56
26 17 0.44
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.28
Consensus pattern (26 bp):
CCCATGTGCCTTGCATATGACCAGAC
Found at i:87883 original size:23 final size:23
Alignment explanation
Indices: 87855--87908 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
87845 AAAAATCAAC
* *
87855 AAAGAAAGTGAAGCACTCAAAAG
1 AAAGAAAATCAAGCACTCAAAAG
*
87878 AAAGAAAAATCCAGCACTCAAAAG
1 AAAG-AAAATCAAGCACTCAAAAG
87902 -AAGAAAA
1 AAAGAAAA
87909 AGCAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 16 0.59
ACGTcount: A:0.61, C:0.15, G:0.17, T:0.07
Consensus pattern (23 bp):
AAAGAAAATCAAGCACTCAAAAG
Found at i:90930 original size:25 final size:26
Alignment explanation
Indices: 90892--90955 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
90882 CCCTATAACA
* * *
90892 CCCATGTGCTTTGCATATGATCAG-C
1 CCCATGTGCCTTGCAAATGACCAGCC
90917 CCCATGTGCCTTGCAAATGACCAGCC
1 CCCATGTGCCTTGCAAATGACCAGCC
90943 CCCATGTGCCTTG
1 CCCATGTGCCTTG
90956 TATGTGGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
25 21 0.60
26 14 0.40
ACGTcount: A:0.19, C:0.34, G:0.20, T:0.27
Consensus pattern (26 bp):
CCCATGTGCCTTGCAAATGACCAGCC
Found at i:92432 original size:19 final size:21
Alignment explanation
Indices: 92389--92440 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
92379 GAAACCCCTT
92389 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
92410 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
92429 TGAAGATACATG
1 TGAAAATACATG
92441 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:96559 original size:19 final size:21
Alignment explanation
Indices: 96516--96567 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
96506 GAAACCCCTT
96516 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
96537 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
96556 TGAAGATACATG
1 TGAAAATACATG
96568 CTCTTGGTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:97906 original size:33 final size:33
Alignment explanation
Indices: 97864--97932 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
97854 GTTGATAAAT
*
97864 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
97897 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
97930 GAA
1 GAA
97933 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:102369 original size:33 final size:33
Alignment explanation
Indices: 102327--102395 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
102317 GTTGATAAAT
*
102327 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
102360 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
102393 GAA
1 GAA
102396 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:104966 original size:91 final size:90
Alignment explanation
Indices: 104786--104966 Score: 206
Period size: 91 Copynumber: 2.0 Consensus size: 90
104776 CCTAGAACAC
104786 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATAGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATAGATCATTTAGGCGCCAAGATG
** * *
104851 AAGAGTTCTCTCCTTATTCGGCCAAG
66 AAGACATCTATCC-TATTCAGCCAAG
** * * * *
104877 CCATGTGTTTTGCATGTGATCAG-CCCCATGTGCCTTGTATAT-GACTCCATTTAGGTGCCAAGA
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATAGA-T-CATTTAGGCGCCAAGA
104940 TGAATGACCATCTATCC-ATTCAGCCAA
64 TGAA-GA-CATCTATCCTATTCAGCCAA
104967 ACACCATTAC
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
89 2 0.03
90 19 0.25
91 47 0.62
92 2 0.03
93 6 0.08
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (90 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATAGATCATTTAGGCGCCAAGATG
AAGACATCTATCCTATTCAGCCAAG
Found at i:111979 original size:15 final size:15
Alignment explanation
Indices: 111944--111972 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
111934 GTGCTTCAAC
111944 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
111958 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
111973 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:115169 original size:36 final size:36
Alignment explanation
Indices: 115121--115225 Score: 151
Period size: 35 Copynumber: 2.9 Consensus size: 36
115111 ACTACCTAAA
115121 CATCACCATCTTCCATCACCATTTTCACGCCTATAAT
1 CATCACCATCTTCCATCACCA-TTTCACGCCTATAAT
* *
115158 -ATCACCATCTTCCATTACCATTGCACGCCTAT-AT
1 CATCACCATCTTCCATCACCATTTCACGCCTATAAT
* *
115192 CATTACCATCTTCTATCACCATTTCACGCCTATA
1 CATCACCATCTTCCATCACCATTTCACGCCTATA
115226 TAACCACCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
34 2 0.03
35 39 0.65
36 19 0.32
ACGTcount: A:0.27, C:0.36, G:0.04, T:0.33
Consensus pattern (36 bp):
CATCACCATCTTCCATCACCATTTCACGCCTATAAT
Found at i:116826 original size:13 final size:13
Alignment explanation
Indices: 116808--116865 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 13
116798 ACTATCTGTT
116808 CATCACCATCTTC
1 CATCACCATCTTC
*
116821 CATCACCAT-TTT
1 CATCACCATCTTC
* **
116833 CA-CACC-TATAA
1 CATCACCATCTTC
116844 CATCACCATCTTC
1 CATCACCATCTTC
116857 CATCACCAT
1 CATCACCAT
116866 TGCACGCCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
10 1 0.03
11 7 0.19
12 8 0.22
13 20 0.56
ACGTcount: A:0.29, C:0.41, G:0.00, T:0.29
Consensus pattern (13 bp):
CATCACCATCTTC
Found at i:116925 original size:35 final size:35
Alignment explanation
Indices: 116807--116960 Score: 182
Period size: 35 Copynumber: 4.3 Consensus size: 35
116797 TACTATCTGT
*
116807 TCATCACCATCTTCCATCACCATTTTCACACCTATA
1 TCATCACCATCTTCCATCACCA-TTGCACACCTATA
* *
116843 ACATCACCATCTTCCATCACCATTGCACGCCTATATTA
1 TCATCACCATCTTCCATCACCATTGCACACC--TA-TA
* **
116881 TCATCACCATCTTCTATCACCATTGCACGTCTATA
1 TCATCACCATCTTCCATCACCATTGCACACCTATA
* * * *
116916 TCATCACCATCTTCTATCAGCATTTCATACCTATA
1 TCATCACCATCTTCCATCACCATTGCACACCTATA
116951 TCATCACCAT
1 TCATCACCAT
116961 TCCCTTATCA
Statistics
Matches: 104, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
35 49 0.47
36 23 0.22
37 2 0.02
38 30 0.29
ACGTcount: A:0.28, C:0.36, G:0.03, T:0.33
Consensus pattern (35 bp):
TCATCACCATCTTCCATCACCATTGCACACCTATA
Found at i:116949 original size:73 final size:74
Alignment explanation
Indices: 116807--116956 Score: 194
Period size: 73 Copynumber: 2.0 Consensus size: 74
116797 TACTATCTGT
* *
116807 TCATCACCATCTTCCATCACCATTTTCACACCTATAACATCACCATCTTCCATCACCATTGCACG
1 TCATCACCATCTTCCATCACCATTTGCACACCTATAACATCACCATCTTCCATCACCATTGCACA
*
116872 CCTATATTA
66 CCTATATCA
* ** * * * * *
116881 TCATCACCATCTTCTATCACCA-TTGCACGTCTATATCATCACCATCTTCTATCAGCATTTCATA
1 TCATCACCATCTTCCATCACCATTTGCACACCTATAACATCACCATCTTCCATCACCATTGCACA
116945 CCTATATCA
66 CCTATATCA
116954 TCA
1 TCA
116957 CCATTCCCTT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
73 44 0.68
74 21 0.32
ACGTcount: A:0.28, C:0.35, G:0.03, T:0.33
Consensus pattern (74 bp):
TCATCACCATCTTCCATCACCATTTGCACACCTATAACATCACCATCTTCCATCACCATTGCACA
CCTATATCA
Found at i:117307 original size:52 final size:52
Alignment explanation
Indices: 117229--117333 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 52
117219 ATCGGGAAAT
*
117229 AACAAGGTTGCCAACTTCTCCATTATTGAAGAAGCCTGATCAGCCCTACATC
1 AACAAGGTTACCAACTTCTCCATTATTGAAGAAGCCTGATCAGCCCTACATC
* * *
117281 AACAAGGTTACCAACTTCTCCATTATTGAAGAAGCCTGGTTAGCCTTACATC
1 AACAAGGTTACCAACTTCTCCATTATTGAAGAAGCCTGATCAGCCCTACATC
117333 A
1 A
117334 TATTGTGTCC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (52 bp):
AACAAGGTTACCAACTTCTCCATTATTGAAGAAGCCTGATCAGCCCTACATC
Found at i:117481 original size:14 final size:13
Alignment explanation
Indices: 117461--117520 Score: 63
Period size: 14 Copynumber: 4.6 Consensus size: 13
117451 ATAAGTAATG
117461 AAATGAAAGAATA
1 AAATGAAAGAATA
117474 AGAATGAAATGAA-A
1 A-AATGAAA-GAATA
*
117488 AAAT--AAGAATG
1 AAATGAAAGAATA
117499 AAATGAAAGAATA
1 AAATGAAAGAATA
117512 AGAATGAAA
1 A-AATGAAA
117521 TGAAATAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
10 3 0.08
11 6 0.15
13 11 0.28
14 16 0.41
15 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (13 bp):
AAATGAAAGAATA
Found at i:117481 original size:19 final size:19
Alignment explanation
Indices: 117451--117525 Score: 132
Period size: 19 Copynumber: 3.9 Consensus size: 19
117441 GAATAATAAT
117451 ATAAGTAATGAAATGAAAGA
1 ATAAG-AATGAAATGAAAGA
*
117471 ATAAGAATGAAATGAAAAA
1 ATAAGAATGAAATGAAAGA
117490 ATAAGAATGAAATGAAAGA
1 ATAAGAATGAAATGAAAGA
117509 ATAAGAATGAAATGAAA
1 ATAAGAATGAAATGAAA
117526 TAAAGAAAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
19 48 0.91
20 5 0.09
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (19 bp):
ATAAGAATGAAATGAAAGA
Found at i:119436 original size:69 final size:69
Alignment explanation
Indices: 119325--119480 Score: 276
Period size: 69 Copynumber: 2.3 Consensus size: 69
119315 TCCTTATAAG
*
119325 TCACGCCCTTTGGATGAAAAATCATTTCCCTTTGGTTTTCAATAGGCACGACTCTTGATTCTTGA
1 TCACGTCCTTTGGATGAAAAATCATTTCCCTTTGGTTTTCAATAGGCACGACTCTTGATTCTTGA
*
119390 TGGA
66 TAGA
* *
119394 TCACGTCCTTTGGATGAAAAATCATTTCCCTTTGGTTTTCAATAGGCATGACTCTTTATTCTTGA
1 TCACGTCCTTTGGATGAAAAATCATTTCCCTTTGGTTTTCAATAGGCACGACTCTTGATTCTTGA
119459 TAGA
66 TAGA
119463 TCACGTCCTTTGGATGAA
1 TCACGTCCTTTGGATGAA
119481 GAGTTACCAT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
69 83 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.38
Consensus pattern (69 bp):
TCACGTCCTTTGGATGAAAAATCATTTCCCTTTGGTTTTCAATAGGCACGACTCTTGATTCTTGA
TAGA
Found at i:126540 original size:12 final size:12
Alignment explanation
Indices: 126525--126572 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
126515 CAAAAAAAAC
126525 AAAAAAAGGC--
1 AAAAAAAGGCAA
*
126535 AAAAAAAGGTAAA
1 AAAAAAAGG-CAA
126548 AAAAAAAGGCAA
1 AAAAAAAGGCAA
*
126560 AAAAAAAGCCAA
1 AAAAAAAGGCAA
126572 A
1 A
126573 TTTCAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
10 9 0.28
12 14 0.44
13 9 0.28
ACGTcount: A:0.75, C:0.08, G:0.15, T:0.02
Consensus pattern (12 bp):
AAAAAAAGGCAA
Found at i:126551 original size:13 final size:13
Alignment explanation
Indices: 126535--126566 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
126525 AAAAAAAGGC
*
126535 AAAAAAAGGTAAA
1 AAAAAAAGGCAAA
126548 AAAAAAAGGCAAA
1 AAAAAAAGGCAAA
126561 AAAAAA
1 AAAAAA
126567 GCCAAATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.03
Consensus pattern (13 bp):
AAAAAAAGGCAAA
Found at i:133059 original size:13 final size:13
Alignment explanation
Indices: 133037--133066 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
133027 ACTAAACACC
133037 TTTC-ACATACCT
1 TTTCAACATACCT
133049 TTTCAACATACCT
1 TTTCAACATACCT
133062 TTTCA
1 TTTCA
133067 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:139334 original size:22 final size:22
Alignment explanation
Indices: 139309--139362 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
139299 ATTGGAGTGC
139309 AAAAAGAAAAGAT-AAAAAGAAG
1 AAAAAGAAAA-ATAAAAAAGAAG
*
139331 AAAAA-AAAATTCAAAAAAGAAG
1 AAAAAGAAAAAT-AAAAAAGAAG
139353 -AAAAGAAAAA
1 AAAAAGAAAAA
139363 GAAGTTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
20 1 0.04
21 8 0.30
22 18 0.67
ACGTcount: A:0.80, C:0.02, G:0.13, T:0.06
Consensus pattern (22 bp):
AAAAAGAAAAATAAAAAAGAAG
Found at i:143982 original size:19 final size:20
Alignment explanation
Indices: 143958--144008 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
143948 CGGCCAAGAG
* *
143958 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
143977 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
143997 CATGTATTTTCA
1 CATGTATTTTCA
144009 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:145401 original size:21 final size:21
Alignment explanation
Indices: 145374--145426 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
145364 TCATCTTGAA
145374 AAAAAAAAGAATTCCGAAAATT
1 AAAAAAAA-AATTCCGAAAATT
*
145396 AAAAAAAAAATTCTGAAAATT
1 AAAAAAAAAATTCCGAAAATT
*
145417 AAAAAGAAAA
1 AAAAAAAAAA
145427 GAAAAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 21 0.72
22 8 0.28
ACGTcount: A:0.70, C:0.06, G:0.08, T:0.17
Consensus pattern (21 bp):
AAAAAAAAAATTCCGAAAATT
Found at i:149364 original size:11 final size:13
Alignment explanation
Indices: 149332--149361 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
149322 TGGCCAAAGA
149332 TGAAAAGGTATGT
1 TGAAAAGGTATGT
149345 TGAAAAGGTATG-
1 TGAAAAGGTATGT
149357 TGAAA
1 TGAAA
149362 GGTGTCTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:151392 original size:13 final size:13
Alignment explanation
Indices: 151374--151400 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
151364 TCTTAGATTA
151374 CTATCTAAAGGGT
1 CTATCTAAAGGGT
151387 CTATCTAAAGGGT
1 CTATCTAAAGGGT
151400 C
1 C
151401 CAAGTCCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (13 bp):
CTATCTAAAGGGT
Found at i:151741 original size:16 final size:16
Alignment explanation
Indices: 151709--151746 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
151699 AACAAAAAGC
*
151709 AACAAGAAAGAAGAAA
1 AACAAGAAAAAAGAAA
151725 AACAA-AAAAAAGAAA
1 AACAAGAAAAAAGAAA
*
151740 AAAAAGA
1 AACAAGA
151747 CTCCTACAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (16 bp):
AACAAGAAAAAAGAAA
Found at i:158239 original size:10 final size:10
Alignment explanation
Indices: 158226--158294 Score: 66
Period size: 10 Copynumber: 6.5 Consensus size: 10
158216 TTTTTTAAAA
*
158226 TTTTGGTTTT
1 TTTTGTTTTT
158236 TTTTGTTTTT
1 TTTTGTTTTT
*
158246 TTGCCTTTTTTTT
1 TT---TTGTTTTT
**
158259 TTTTGCCTTT
1 TTTTGTTTTT
158269 TTTTGTTTTTT
1 TTTTG-TTTTT
158280 TTTTGTTTTT
1 TTTTGTTTTT
158290 TTTTG
1 TTTTG
158295 AAAAAAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
10 31 0.65
11 8 0.17
13 9 0.19
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.83
Consensus pattern (10 bp):
TTTTGTTTTT
Found at i:158254 original size:15 final size:15
Alignment explanation
Indices: 158236--158291 Score: 62
Period size: 15 Copynumber: 3.8 Consensus size: 15
158226 TTTTGGTTTT
158236 TTTTGTTTTTTTGCC
1 TTTTGTTTTTTTGCC
*
158251 TTTTTTTTTTTTGCC
1 TTTTGTTTTTTTGCC
**
158266 TTTT-TTTGTTTT-TT
1 TTTTGTTT-TTTTGCC
158280 TTTTGTTTTTTT
1 TTTTGTTTTTTT
158292 TTGAAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
14 11 0.31
15 25 0.69
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (15 bp):
TTTTGTTTTTTTGCC
Found at i:161377 original size:33 final size:33
Alignment explanation
Indices: 161335--161403 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
161325 GTTGATGAAT
*
161335 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
161368 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
161401 GAA
1 GAA
161404 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:161444 original size:36 final size:36
Alignment explanation
Indices: 161374--161486 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
161364 AATGGAAGGA
* * *
161374 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGAGATGGAATATGG
* *
161409 TGATGATATAGGCGTGATAATGGCGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGAGATGGAATATGG
* *
161445 TGATTATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGAGATGGAATATGG
161481 TGATGA
1 TGATGA
161487 AAATAGTATC
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
35 16 0.23
36 53 0.77
ACGTcount: A:0.27, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGAGATGGAATATGG
Found at i:165796 original size:33 final size:33
Alignment explanation
Indices: 165754--165822 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
165744 GTTGATGAAT
*
165754 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
165787 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
165820 GAA
1 GAA
165823 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:165863 original size:36 final size:36
Alignment explanation
Indices: 165793--165905 Score: 156
Period size: 36 Copynumber: 3.2 Consensus size: 36
165783 AATGGAAGGA
* *
165793 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
165828 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
** * *
165864 TTTTGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
165900 TGATGA
1 TGATGA
165906 AAATAGTATC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 16 0.24
36 52 0.76
ACGTcount: A:0.27, C:0.04, G:0.35, T:0.35
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:169489 original size:13 final size:13
Alignment explanation
Indices: 169467--169496 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
169457 ACTAAACACC
169467 TTTC-ACATACCT
1 TTTCAACATACCT
169479 TTTCAACATACCT
1 TTTCAACATACCT
169492 TTTCA
1 TTTCA
169497 TATTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:171849 original size:11 final size:11
Alignment explanation
Indices: 171833--171890 Score: 73
Period size: 11 Copynumber: 5.1 Consensus size: 11
171823 ATTGGAGTGC
171833 AAAAAAAAG-A
1 AAAAAAAAGAA
171843 AAAAAAAAGAA
1 AAAAAAAAGAA
171854 AAAAAAAAGAA
1 AAAAAAAAGAA
171865 TCAGAAAAAAAGAA
1 --A-AAAAAAAGAA
*
171879 AAGAAAAAGAA
1 AAAAAAAAGAA
171890 A
1 A
171891 TTCAAAAGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
10 9 0.21
11 22 0.51
12 1 0.02
13 1 0.02
14 10 0.23
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:171861 original size:25 final size:25
Alignment explanation
Indices: 171833--171886 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
171823 ATTGGAGTGC
*
171833 AAAAAAAAGAAAAAAAAAGAAAAAA
1 AAAAAAAACAAAAAAAAAGAAAAAA
* * * *
171858 AAAAGAATCAGAAAAAAAGAAAAGA
1 AAAAAAAACAAAAAAAAAGAAAAAA
171883 AAAA
1 AAAA
171887 GAAATTCAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (25 bp):
AAAAAAAACAAAAAAAAAGAAAAAA
Found at i:171897 original size:25 final size:24
Alignment explanation
Indices: 171843--171889 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
171833 AAAAAAAAGA
171843 AAAAAAAAGAAAAAAAAAAGAATC
1 AAAAAAAAGAAAAAAAAAAGAATC
*
171867 AGAAAAAAAGAAAAGAAAAAGAA
1 A-AAAAAAAGAAAAAAAAAAGAA
171890 ATTCAAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAAAAAGAATC
Found at i:175306 original size:13 final size:13
Alignment explanation
Indices: 175284--175313 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
175274 ACTAAACACC
175284 TTTC-ACATACCT
1 TTTCAACATACCT
175296 TTTCAACATACCT
1 TTTCAACATACCT
175309 TTTCA
1 TTTCA
175314 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:180728 original size:15 final size:15
Alignment explanation
Indices: 180692--180721 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
180682 GTGCTTCAAC
180692 TTTCTTT-CTTTTCT
1 TTTCTTTGCTTTTCT
180706 TTTCTTTGCTTTTCT
1 TTTCTTTGCTTTTCT
180721 T
1 T
180722 CTTTTTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTCTTTGCTTTTCT
Found at i:181714 original size:23 final size:23
Alignment explanation
Indices: 181684--181727 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
181674 CTAAATGATC
181684 CATATGCAAGGCACATGGGTGGT
1 CATATGCAAGGCACATGGGTGGT
181707 CATATGCAAGGCACATGGGTG
1 CATATGCAAGGCACATGGGTG
181728 TTCTAGGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.20
Consensus pattern (23 bp):
CATATGCAAGGCACATGGGTGGT
Found at i:181861 original size:22 final size:18
Alignment explanation
Indices: 181815--181858 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
181805 GTCTCCTTCA
181815 AGCTAGCTTGAGTTGTGG
1 AGCTAGCTTGAGTTGTGG
181833 AGCTAGCTTGAGTTGTGG
1 AGCTAGCTTGAGTTGTGG
181851 AGCTAGCT
1 AGCTAGCT
181859 AGCAAACATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.18, C:0.14, G:0.36, T:0.32
Consensus pattern (18 bp):
AGCTAGCTTGAGTTGTGG
Found at i:188101 original size:36 final size:36
Alignment explanation
Indices: 188054--188138 Score: 161
Period size: 36 Copynumber: 2.4 Consensus size: 36
188044 GATACAATCT
188054 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
188090 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
188126 TTCCATCACCATT
1 GTCCATCACCATT
188139 TCATCACCAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.29, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:188126 original size:11 final size:11
Alignment explanation
Indices: 188057--188148 Score: 71
Period size: 11 Copynumber: 7.8 Consensus size: 11
188047 ACAATCTGTC
188057 CATCACCATTAT
1 CATCACCA-TAT
*
188069 CA-CGCCTATAT
1 CATCACC-ATAT
188080 CATCACCATAGT
1 CATCACCATA-T
188092 CCATCACCATTAT
1 -CATCACCA-TAT
*
188105 CA-CGCCTATAT
1 CATCACC-ATAT
188116 CATCACCATATT
1 CATCACCATA-T
*
188128 CCATCACCATTT
1 -CATCACCATAT
188140 CATCACCAT
1 CATCACCAT
188149 TAAATCATCC
Statistics
Matches: 66, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
11 31 0.47
12 15 0.23
13 18 0.27
14 2 0.03
ACGTcount: A:0.30, C:0.37, G:0.03, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:188689 original size:11 final size:11
Alignment explanation
Indices: 188675--188767 Score: 55
Period size: 11 Copynumber: 7.9 Consensus size: 11
188665 AGGATGATTT
188675 AATGGTGATGA
1 AATGGTGATGA
188686 AATGGTGATGGA
1 AATGGTGAT-GA
188698 ATATGGTGATGA
1 A-ATGGTGATGA
* *
188710 TATAGGCG-TGA
1 AAT-GGTGATGA
188721 TAATGGTGATGGA
1 -AATGGTGAT-GA
*
188734 CTATGGTGATGA
1 -AATGGTGATGA
* *
188746 TATAGGCG-TGA
1 AAT-GGTGATGA
188757 TAATGGTGATG
1 -AATGGTGATG
188768 GACAGATTGT
Statistics
Matches: 64, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
11 26 0.41
12 20 0.31
13 18 0.28
ACGTcount: A:0.30, C:0.03, G:0.37, T:0.30
Consensus pattern (11 bp):
AATGGTGATGA
Found at i:188705 original size:13 final size:12
Alignment explanation
Indices: 188676--188745 Score: 58
Period size: 11 Copynumber: 5.8 Consensus size: 12
188666 GGATGATTTA
188676 ATGGTGATGAA-
1 ATGGTGATGAAT
188687 ATGGTGATGGAAT
1 ATGGTGAT-GAAT
188700 ATGGTGATG-AT
1 ATGGTGATGAAT
*
188711 ATAGGCG-TG-AT
1 AT-GGTGATGAAT
*
188722 AATGGTGATGGACT
1 -ATGGTGAT-GAAT
188736 ATGGTGATGA
1 ATGGTGATGA
188746 TATAGGCGTG
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
11 19 0.39
12 12 0.24
13 17 0.35
14 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
ATGGTGATGAAT
Found at i:188770 original size:36 final size:36
Alignment explanation
Indices: 188686--188770 Score: 161
Period size: 36 Copynumber: 2.4 Consensus size: 36
188676 ATGGTGATGA
*
188686 AATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGGACTATGGTGATGATATAGGCGTGAT
188722 AATGGTGATGGACTATGGTGATGATATAGGCGTGAT
1 AATGGTGATGGACTATGGTGATGATATAGGCGTGAT
188758 AATGGTGATGGAC
1 AATGGTGATGGAC
188771 AGATTGTATC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.29
Consensus pattern (36 bp):
AATGGTGATGGACTATGGTGATGATATAGGCGTGAT
Found at i:190778 original size:13 final size:12
Alignment explanation
Indices: 190759--190844 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
190749 ATATGGGCGT
190759 GATATGGTGATG
1 GATATGGTGATG
190771 GAATATGGTGAT-
1 G-ATATGGTGATG
*
190783 GATATAGGCG-T-
1 GATAT-GGTGATG
190794 GATAATGGTGATG
1 GAT-ATGGTGATG
190807 GACTATGGTGAT-
1 GA-TATGGTGATG
*
190819 GATATAGGCG-T-
1 GATAT-GGTGATG
190830 GATAATGGTGATG
1 GAT-ATGGTGATG
190843 GA
1 GA
190845 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:190814 original size:36 final size:36
Alignment explanation
Indices: 190741--190845 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
190731 AATTATAAGT
* * *
190741 TGGTGATAATATGGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
190776 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
190812 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
190846 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:195782 original size:24 final size:24
Alignment explanation
Indices: 195728--195784 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
195718 AGGATAGGCT
*
195728 AGAAAAGG-TTAAGAAAGATGATA
1 AGAAAAGGAATAAGAAAGATGATA
**
195751 AGGTAAGGAATAAGAAAAGATGA-A
1 AGAAAAGGAATAAG-AAAGATGATA
195775 AGAAAAGGAA
1 AGAAAAGGAA
195785 ATGAAATAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 6 0.22
24 13 0.48
25 8 0.30
ACGTcount: A:0.60, C:0.00, G:0.28, T:0.12
Consensus pattern (24 bp):
AGAAAAGGAATAAGAAAGATGATA
Found at i:196259 original size:15 final size:16
Alignment explanation
Indices: 196223--196260 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
196213 TGATAATTAA
196223 GAAATGAAAAGTAATG
1 GAAATGAAAAGTAATG
* *
196239 GAAATGGAAAG-AATT
1 GAAATGAAAAGTAATG
196254 GAAATGA
1 GAAATGA
196261 TAGAATAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.18
Consensus pattern (16 bp):
GAAATGAAAAGTAATG
Found at i:196435 original size:22 final size:23
Alignment explanation
Indices: 196407--196458 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
196397 ATTTATAAGT
*
196407 TGGTGATAATATGGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
196429 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
196452 TGGTGAT
1 TGGTGAT
196459 GGACTATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 19 0.70
23 8 0.30
ACGTcount: A:0.27, C:0.04, G:0.37, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:198077 original size:9 final size:9
Alignment explanation
Indices: 198063--198095 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
198053 GTGCTTCAAC
198063 TTTCTTTCT
1 TTTCTTTCT
198072 TTTCTTTCT
1 TTTCTTTCT
*
198081 TTGCTTT-T
1 TTTCTTTCT
198089 TTTCTTT
1 TTTCTTT
198096 TGAATGCTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:198097 original size:14 final size:14
Alignment explanation
Indices: 198062--198095 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
198052 AGTGCTTCAA
198062 CTTTCTTT-CTTTT
1 CTTTCTTTGCTTTT
198075 CTTTCTTTGCTTTT
1 CTTTCTTTGCTTTT
198089 -TTTCTTT
1 CTTTCTTT
198096 TGAATGCTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (14 bp):
CTTTCTTTGCTTTT
Found at i:211560 original size:24 final size:21
Alignment explanation
Indices: 211526--211568 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
211516 TCCACAAGAC
*
211526 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
211548 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
211569 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:214365 original size:30 final size:31
Alignment explanation
Indices: 214312--214371 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
214302 CTTAGCTTTA
***
214312 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCACTTAGATATCATT
*
214342 TATTATGTTTTCATATCACTTAGATATCAT
1 TATTATGTTTACATATCACTTAGATATCAT
214372 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCACTTAGATATCATT
Found at i:216377 original size:24 final size:21
Alignment explanation
Indices: 216342--216384 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
216332 GGCTCATTCT
*
216342 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
216365 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
216385 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:222273 original size:16 final size:16
Alignment explanation
Indices: 222252--222298 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
222242 TCTTCCACCT
222252 ATGTTAGAATGCAAAA
1 ATGTTAGAATGCAAAA
222268 ATGTTAGAATGCAAAA
1 ATGTTAGAATGCAAAA
222284 ATGTTAGAATGCAAA
1 ATGTTAGAATGCAAA
222299 TGAGCTAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (16 bp):
ATGTTAGAATGCAAAA
Found at i:224390 original size:14 final size:14
Alignment explanation
Indices: 224367--224402 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
224357 TTATAAGTTG
224367 GTGATAATATAGGC
1 GTGATAATATAGGC
* *
224381 GTGATGATATAGGT
1 GTGATAATATAGGC
224395 GTGATAAT
1 GTGATAAT
224403 GTTGATGGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.31, T:0.33
Consensus pattern (14 bp):
GTGATAATATAGGC
Found at i:233324 original size:13 final size:12
Alignment explanation
Indices: 233305--233390 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
233295 ATATAGACGT
233305 GATATGGTGATG
1 GATATGGTGATG
233317 GAATATGGTGAT-
1 G-ATATGGTGATG
*
233329 GATATAGGCG-T-
1 GATAT-GGTGATG
233340 GATAATGGTGATG
1 GAT-ATGGTGATG
233353 GACTATGGTGAT-
1 GA-TATGGTGATG
*
233365 GATATAGGCG-T-
1 GATAT-GGTGATG
233376 GATAATGGTGATG
1 GAT-ATGGTGATG
233389 GA
1 GA
233391 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:233360 original size:36 final size:36
Alignment explanation
Indices: 233287--233391 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
233277 ATTTATAAGT
* * *
233287 TGGTGATAATATAGACGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
233322 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
233358 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
233392 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.30, C:0.05, G:0.35, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:236539 original size:16 final size:16
Alignment explanation
Indices: 236518--236550 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
236508 TTCTTCCACC
236518 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
236534 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
236550 T
1 T
236551 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:244162 original size:19 final size:19
Alignment explanation
Indices: 244138--244181 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
244128 TAATGAATAT
244138 AAATGATGAAAGAAAAAAG
1 AAATGATGAAAGAAAAAAG
*
244157 AAATGATGAAAGAAAAAGG
1 AAATGATGAAAGAAAAAAG
244176 AAATGA
1 AAATGA
244182 AGATAACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (19 bp):
AAATGATGAAAGAAAAAAG
Found at i:245112 original size:17 final size:17
Alignment explanation
Indices: 245078--245118 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
245068 TGTTTCCATT
245078 TATCAT-TTATTATGAA
1 TATCATGTTATTATGAA
245094 TATCATGTTATATAT-AA
1 TATCATGTTAT-TATGAA
245111 TATTCATG
1 TA-TCATG
245119 CAAATAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 6 0.27
17 8 0.36
18 8 0.36
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (17 bp):
TATCATGTTATTATGAA
Found at i:247385 original size:16 final size:16
Alignment explanation
Indices: 247364--247396 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
247354 TTCTTCCACC
247364 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
247380 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
247396 T
1 T
247397 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:250491 original size:215 final size:211
Alignment explanation
Indices: 250101--250529 Score: 822
Period size: 215 Copynumber: 2.0 Consensus size: 211
250091 TTCTTCTACA
250101 AATGAAATGGAAAGCTATTTAGGCCTAAGAGATGTCTAGGATGCACATACAAGATTTAATGATTG
1 AATGAAATGGAAAGCTATTTAGGCCTAAGAGATGTCTAGGATGCACATACAAGATTTAATGATTG
250166 ATCATCCTTAAGTAGATACAATGTACGTCCCCTGCAAGTTCATGGACTAATAAAATAAATGAATG
66 ATCATCCTTAAGTAGATACAATGTACGTCCCCTGCAAGTTCATGGACTAATAAAATAAATGAATG
250231 TTCATCCATTTAAGTGAATACATCTTCATAGCCGAATTCATCCTCTCTTGATGTGAACATGTTGG
131 TTCATCCATTTAAGTGAATACATCTTCATAGCCGAATTCATCCTCTCTTGATGTGAACATGTTGG
250296 TTCATTTCCTTGCATG
196 TTCATTTCCTTGCATG
250312 AATGAAATGGAAAGCTATTTATAGGCCTAAGAGATGTCTAGGATGCACATACAAGATTTAATGAT
1 AATGAAATGGAAAGCTA-TT-TAGGCCTAAGAGATGTCTAGGATGCACATACAAGATTTAATGAT
250377 TGATCATCCTTAAGTAGATACAATGTACGTCCCCTATGCAAGTTCATGGACTAATAAAATAAATG
64 TGATCATCCTTAAGTAGATACAATGTACGTCCCC--TGCAAGTTCATGGACTAATAAAATAAATG
250442 AATGTTCATCCATTTAAGTGAATACATCTTCATAGCCGAATTCATCCTCTCTTGATGTGAACATG
127 AATGTTCATCCATTTAAGTGAATACATCTTCATAGCCGAATTCATCCTCTCTTGATGTGAACATG
250507 TTGGTTCATTTCCTTGCATG
192 TTGGTTCATTTCCTTGCATG
250527 AAT
1 AAT
250530 TTGGAGGAAT
Statistics
Matches: 214, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
211 17 0.08
212 2 0.01
213 78 0.36
215 117 0.55
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (211 bp):
AATGAAATGGAAAGCTATTTAGGCCTAAGAGATGTCTAGGATGCACATACAAGATTTAATGATTG
ATCATCCTTAAGTAGATACAATGTACGTCCCCTGCAAGTTCATGGACTAATAAAATAAATGAATG
TTCATCCATTTAAGTGAATACATCTTCATAGCCGAATTCATCCTCTCTTGATGTGAACATGTTGG
TTCATTTCCTTGCATG
Found at i:250977 original size:16 final size:16
Alignment explanation
Indices: 250956--250988 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
250946 TTCTTCCACC
250956 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
250972 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
250988 T
1 T
250989 GAGCTAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:254484 original size:16 final size:16
Alignment explanation
Indices: 254463--254495 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
254453 TTCTTCCACC
254463 TATGTTAGAATGCAAA
1 TATGTTAGAATGCAAA
*
254479 TATGTTAGAATGTAAA
1 TATGTTAGAATGCAAA
254495 T
1 T
254496 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.36
Consensus pattern (16 bp):
TATGTTAGAATGCAAA
Found at i:255609 original size:33 final size:33
Alignment explanation
Indices: 255567--255635 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
255557 GTTGATGAAT
*
255567 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
255600 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
255633 GAA
1 GAA
255636 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:255640 original size:13 final size:12
Alignment explanation
Indices: 255621--255717 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
255611 TTATTGGCGT
255621 GATATGGTGATG
1 GATATGGTGATG
255633 GAATATGGTGAT-
1 G-ATATGGTGATG
*
255645 GATATAGG-CAT-
1 GATAT-GGTGATG
255656 GATAATGGTGATG
1 GAT-ATGGTGATG
255669 GACTATGGTGAT-
1 GA-TATGGTGATG
*
255681 GATATAGGCG-T-
1 GATAT-GGTGATG
*
255692 GATAATGGAGATG
1 GAT-ATGGTGATG
255705 GATTATGGTGATG
1 GA-TATGGTGATG
255718 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:255669 original size:36 final size:36
Alignment explanation
Indices: 255606--255718 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
255596 AATGGAAGGA
* *
255606 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
255641 TGATGATATAGGCATGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
255677 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
255713 TGATGA
1 TGATGA
255719 AAATAGTATC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 15 0.21
36 55 0.79
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:257056 original size:23 final size:22
Alignment explanation
Indices: 257013--257062 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
257003 AATAAAGGGT
*
257013 AATAATATAAGTAATGAAAATA
1 AATAATATAAGAAATGAAAATA
257035 AATAATAATAATGAAATG-AAATA
1 AATAAT-ATAA-GAAATGAAAATA
257058 AATAA
1 AATAA
257063 AAAGATAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 6 0.24
23 14 0.56
24 5 0.20
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (22 bp):
AATAATATAAGAAATGAAAATA
Found at i:263009 original size:13 final size:12
Alignment explanation
Indices: 262990--263075 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
262980 AAATAGGCGT
262990 GATATGGTGATG
1 GATATGGTGATG
263002 GAATATGGTGAT-
1 G-ATATGGTGATG
*
263014 GATATAGGCG-T-
1 GATAT-GGTGATG
263025 GATAATGGTGATG
1 GAT-ATGGTGATG
263038 GACTATGGTGAT-
1 GA-TATGGTGATG
*
263050 GATATAGGCG-T-
1 GATAT-GGTGATG
263061 GATAATGGTGATG
1 GAT-ATGGTGATG
263074 GA
1 GA
263076 CATATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:263045 original size:36 final size:36
Alignment explanation
Indices: 262972--263076 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
262962 ATTTATAAGT
* * *
262972 TGGTGATAAAATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
263007 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
263043 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
263077 ATATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.29
36 47 0.71
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:272191 original size:24 final size:24
Alignment explanation
Indices: 272156--272206 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
272146 TCACTTCAAG
* *
272156 TTGAAGATTCAAGAAACATGTCTT
1 TTGAAGAATCAAGAAACATGACTT
* *
272180 TTGAAGAATCAATAAACGTGACTT
1 TTGAAGAATCAAGAAACATGACTT
272204 TTG
1 TTG
272207 GTGATCCACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (24 bp):
TTGAAGAATCAAGAAACATGACTT
Found at i:278724 original size:11 final size:11
Alignment explanation
Indices: 278691--278778 Score: 58
Period size: 11 Copynumber: 7.8 Consensus size: 11
278681 ACAATCTGTC
278691 CATCACCATTAT
1 CATCACCA-TAT
*
278703 CA-CGCCTATAT
1 CATCACC-ATAT
278714 CATCACCATAT
1 CATCACCATAT
278725 CCATCACCATAT
1 -CATCACCATAT
*
278737 CA-CACCAATAA
1 CATCACC-ATAT
278748 CATCATCC-T-T
1 CATCA-CCATAT
* *
278758 CCATTACCATTT
1 -CATCACCATAT
278770 CATCACCAT
1 CATCACCAT
278779 TAAATCATCC
Statistics
Matches: 61, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
10 6 0.10
11 33 0.54
12 20 0.33
13 2 0.03
ACGTcount: A:0.33, C:0.38, G:0.01, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:278731 original size:12 final size:12
Alignment explanation
Indices: 278689--278737 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
278679 ATACAATCTG
278689 TCCATCACCATTA
1 TCCATCACCA-TA
*
278702 T-CA-CGCCTATA
1 TCCATCACC-ATA
278713 T-CATCACCATA
1 TCCATCACCATA
278724 TCCATCACCATA
1 TCCATCACCATA
278736 TC
1 TC
278738 ACACCAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 12 0.39
12 18 0.58
13 1 0.03
ACGTcount: A:0.31, C:0.39, G:0.02, T:0.29
Consensus pattern (12 bp):
TCCATCACCATA
Done.