Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000389.1 Hibiscus syriacus cultivar Beakdansim tig00000715_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: 2672246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 15
Found at i:1040036 original size:22 final size:22
Alignment explanation
Indices: 1040008--1040079 Score: 63
Period size: 22 Copynumber: 3.7 Consensus size: 22
1039998 ATTTTATTTT
1040008 ATTTATTTAATTTGAGATTTAA
1 ATTTATTTAATTTGAGATTTAA
*
1040030 ATTTATTTTATTT-A-ATTT--
1 ATTTATTTAATTTGAGATTTAA
1040048 A--T--TTAATTTGAGATTTAA
1 ATTTATTTAATTTGAGATTTAA
*
1040066 GTTTATTT-ATTTGA
1 ATTTATTTAATTTGA
1040080 CAATTATGCG
Statistics
Matches: 39, Mismatches: 3, Indels: 17
0.66 0.05 0.29
Matches are distributed among these distances:
14 6 0.15
15 1 0.03
16 5 0.13
18 1 0.03
20 5 0.13
21 7 0.18
22 14 0.36
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (22 bp):
ATTTATTTAATTTGAGATTTAA
Found at i:1040053 original size:9 final size:9
Alignment explanation
Indices: 1039993--1040056 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
1039983 TACACTATTC
*
1039993 TATTTATTT
1 TATTTAATT
*
1040002 TATTTTATT
1 TATTTAATT
1040011 TATTTAATT
1 TATTTAATT
1040020 TGAGATTTAA--
1 T---ATTTAATT
*
1040030 -ATTTATTT
1 TATTTAATT
1040038 TATTTAATT
1 TATTTAATT
1040047 TATTTAATT
1 TATTTAATT
1040056 T
1 T
1040057 GAGATTTAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
6 5 0.11
9 33 0.75
12 6 0.14
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (9 bp):
TATTTAATT
Found at i:1046142 original size:13 final size:13
Alignment explanation
Indices: 1046124--1046155 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1046114 TCTCATTTGG
1046124 TCTCTCTGCGCTC
1 TCTCTCTGCGCTC
1046137 TCTCTCTGCGCTC
1 TCTCTCTGCGCTC
1046150 TCTCTC
1 TCTCTC
1046156 GTCTCTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.47, G:0.12, T:0.41
Consensus pattern (13 bp):
TCTCTCTGCGCTC
Found at i:1047132 original size:15 final size:15
Alignment explanation
Indices: 1047112--1047141 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1047102 AAATGAAAAT
1047112 AATAATAATAATATA
1 AATAATAATAATATA
1047127 AATAATAATAATATA
1 AATAATAATAATATA
1047142 TATATATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAATAATAATATA
Found at i:1047171 original size:23 final size:24
Alignment explanation
Indices: 1047145--1047189 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
1047135 TAATATATAT
1047145 ATATACATAAAT-A-TTTCAAAAAC
1 ATATA-ATAAATAATTTTCAAAAAC
*
1047168 ATATAATATATAATTTTCAAAA
1 ATATAATAAATAATTTTCAAAA
1047190 TGTTTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 6 0.32
24 8 0.42
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATAATAAATAATTTTCAAAAAC
Found at i:1047300 original size:66 final size:65
Alignment explanation
Indices: 1047219--1047380 Score: 192
Period size: 66 Copynumber: 2.5 Consensus size: 65
1047209 TAATATACGA
*
1047219 ATGTTTTCAACATGTTTTCAAAATAT-TATATAAGTTTTCAAAAAAGTTTT-AAAAACTATATAA
1 ATGTTTTCAAAATGTTTTCAAAATATATATATAAGTTTTCAAAAAAGTTTTCAAAAA-T-TAT-A
1047282 TAT
63 TAT
** *
1047285 ATGTTTTCAAAATG-TTTCAAAACTATAATATATGTGTTTTCAAAAATGTTTTCAAAAATTATAT
1 ATGTTTTCAAAATGTTTTCAAAA-TAT-ATATATAAGTTTTCAAAAAAGTTTTCAAAAATTATAT
1047349 AT
64 AT
1047351 AT-TTTTCAAAATGATTTT-AAAAT-TATATAT
1 ATGTTTTCAAAATG-TTTTCAAAATATATATAT
1047381 TATATATTTT
Statistics
Matches: 86, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
63 6 0.07
64 1 0.01
65 20 0.23
66 26 0.30
67 6 0.07
68 22 0.26
69 5 0.06
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (65 bp):
ATGTTTTCAAAATGTTTTCAAAATATATATATAAGTTTTCAAAAAAGTTTTCAAAAATTATATAT
Found at i:1047323 original size:33 final size:32
Alignment explanation
Indices: 1047219--1047390 Score: 165
Period size: 33 Copynumber: 5.2 Consensus size: 32
1047209 TAATATACGA
*
1047219 ATGTTTTCAACATGTTTTCAAAATAT-TATAT
1 ATGTTTTCAAAATGTTTTCAAAATATATATAT
* * *
1047250 AAGTTTTCAAAAAAGTTTTAAAAACTATATAATAT
1 ATGTTTTC-AAAATGTTTTCAAAA-TATAT-ATAT
1047285 ATGTTTTCAAAATG-TTTCAAAACTATAATATAT
1 ATGTTTTCAAAATGTTTTCAAAA-TAT-ATATAT
*
1047318 GTGTTTTCAAAAATGTTTTCAAAA-ATTATATAT
1 ATGTTTTC-AAAATGTTTTCAAAATA-TATATAT
1047351 AT-TTTTCAAAATGATTTT-AAAATTATATATTAT
1 ATGTTTTCAAAATG-TTTTCAAAA-TATATA-TAT
*
1047384 ATATTTT
1 ATGTTTT
1047391 TTTAAAACGT
Statistics
Matches: 119, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
31 17 0.14
32 25 0.21
33 39 0.33
34 19 0.16
35 19 0.16
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (32 bp):
ATGTTTTCAAAATGTTTTCAAAATATATATAT
Found at i:1047336 original size:12 final size:12
Alignment explanation
Indices: 1047319--1047343 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1047309 ATAATATATG
1047319 TGTTTTCAAAAA
1 TGTTTTCAAAAA
1047331 TGTTTTCAAAAA
1 TGTTTTCAAAAA
1047343 T
1 T
1047344 TATATATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TGTTTTCAAAAA
Found at i:1048205 original size:82 final size:84
Alignment explanation
Indices: 1048109--1048475 Score: 401
Period size: 82 Copynumber: 4.4 Consensus size: 84
1048099 GGGAGTCTTT
* * *
1048109 GCAGATAGCCCTTCTTGACTTAAGCTATACTGCAAATGATATG-CCT-GGAGCTGAGCGTAGTCG
1 GCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCG
1048172 AACTCGAAGGTCTTGGTTG
66 AACTCGAAGGTCTTGGTTG
* * * *
1048191 GCAGATAACCCTTCTTGACTTAAG-T-TGCTGCAAATGGTGTGCCCTCGAAGCTGAGTGTAATCG
1 GCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCG
**
1048254 AACTCGGGGGTC-T--TTG
66 AACTCGAAGGTCTTGGTTG
* * * *
1048270 GCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCG
1 GCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCG
*
1048334 AACTCAAAGGTCTTGG-TG
66 AACTCGAAGGTCTTGGTTG
* * * * * * *
1048352 GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGCATAG
1 G---CAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAG
*
1048417 TCGAACTCGAAGGTCTTGGTGG
63 TCGAACTCGAAGGTCTTGGTTG
* * * * *
1048439 GCAGATAGCCCTTATGGCCTTGAGCTAAGCTGCAAAT
1 GCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAAT
1048476 AGTTTGTTTA
Statistics
Matches: 235, Mismatches: 38, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
79 25 0.11
80 40 0.17
81 20 0.09
82 50 0.21
84 30 0.13
85 35 0.15
86 33 0.14
87 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.28
Consensus pattern (84 bp):
GCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCG
AACTCGAAGGTCTTGGTTG
Found at i:1048305 original size:161 final size:164
Alignment explanation
Indices: 1048075--1048451 Score: 521
Period size: 161 Copynumber: 2.3 Consensus size: 164
1048065 TGATATGACT
* * *
1048075 TCGAAGTTGAGTGTAATCGAACTCGGGAGTCTTT-GCAGATAGCCCTTCTTGACTTAAGCTATAC
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATAC
*
1048139 TGCAAATGATATGCC-TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTTGG-CAGATAACCC
66 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGG-TGGACAGATAACCC
* *
1048202 TTCTTGACTTAAG-T-TGCTGCAAATGGTGTGCCC
130 TTCTAGACTTAAGTTATGCTGCAAATGATGTGCCC
*
1048235 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTC
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATAC
*
1048300 TGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGGTGGTCACAGATAACC
66 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGGTGG--ACAGATAACC
* * *
1048365 CTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
129 CTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCC
** * **
1048401 TCGAAGCTGAGCATAGTCGAACTCGAAGGTCTTGGTGGGCAGATAGCCCTT
1 TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT--T-GGCAGATAGCCCTT
1048452 ATGGCCTTGA
Statistics
Matches: 191, Mismatches: 16, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
160 32 0.17
161 45 0.24
162 33 0.17
164 20 0.10
165 1 0.01
166 45 0.24
168 1 0.01
169 14 0.07
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (164 bp):
TCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATAC
TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGGTGGACAGATAACCCT
TCTAGACTTAAGTTATGCTGCAAATGATGTGCCC
Found at i:1053584 original size:27 final size:26
Alignment explanation
Indices: 1053537--1053592 Score: 60
Period size: 27 Copynumber: 2.1 Consensus size: 26
1053527 AGAAAGAAAT
* *
1053537 AAAAAATAATAAAAGGTTAAATTTAAA
1 AAAAAATAATAAAAAGTTAAA-ATAAA
*
1053564 AAAAAATATTTAAAAAG-TAAAATAAA
1 AAAAAATA-ATAAAAAGTTAAAATAAA
1053590 AAA
1 AAA
1053593 TAAAGATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 7 0.28
27 12 0.48
28 6 0.24
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.23
Consensus pattern (26 bp):
AAAAAATAATAAAAAGTTAAAATAAA
Found at i:1054903 original size:3 final size:3
Alignment explanation
Indices: 1054895--1054925 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1054885 AAAAATGAAA
1054895 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1054926 TATATATACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1055067 original size:71 final size:73
Alignment explanation
Indices: 1054986--1055175 Score: 218
Period size: 71 Copynumber: 2.7 Consensus size: 73
1054976 TTTTTTTCTT
* * *
1054986 AAACTATATAATATACGAATGTTTTCAACATGTTTTCAAAA-ATATTATATAAGTTTTCAAAAAC
1 AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAACATAATATATAAGTTTTCAAAAAC
1055050 GTTTT-AA
66 GTTTTCAA
* **
1055057 AAACTATATAATATATAAATGTTTTCAAAATGTTTTCAAAACTATAATATATGTGTTTTCAAAAA
1 AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAAC-ATAATATATAAGTTTTCAAAAA
*
1055122 TGTTTTCAA
65 CGTTTTCAA
* *
1055131 AAA-T-TAT-ATATA-TAAT-TTTTCAAAATGATTTT-AAAA-ATTATATAT
1 AAACTATATAATATACAAATGTTTTCAAAATG-TTTTCAAAACATAATATAT
1055176 TATATATATT
Statistics
Matches: 106, Mismatches: 9, Indels: 12
0.83 0.07 0.09
Matches are distributed among these distances:
67 8 0.08
69 15 0.14
70 7 0.07
71 43 0.41
72 3 0.03
73 25 0.24
74 5 0.05
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (73 bp):
AAACTATATAATATACAAATGTTTTCAAAATGTTTTCAAAACATAATATATAAGTTTTCAAAAAC
GTTTTCAA
Found at i:1055089 original size:11 final size:11
Alignment explanation
Indices: 1055073--1055097 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1055063 TATAATATAT
1055073 AAATGTTTTCA
1 AAATGTTTTCA
1055084 AAATGTTTTCA
1 AAATGTTTTCA
1055095 AAA
1 AAA
1055098 CTATAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:1055127 original size:12 final size:12
Alignment explanation
Indices: 1055110--1055134 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1055100 ATAATATATG
1055110 TGTTTTCAAAAA
1 TGTTTTCAAAAA
1055122 TGTTTTCAAAAA
1 TGTTTTCAAAAA
1055134 T
1 T
1055135 TATATATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TGTTTTCAAAAA
Found at i:1055153 original size:108 final size:105
Alignment explanation
Indices: 1055005--1055200 Score: 268
Period size: 108 Copynumber: 1.8 Consensus size: 105
1054995 AATATACGAA
*
1055005 TGTTTTCAACATGTTTTCAAAAATATTATATAAGTTTTCAAAAACG-TTTTAAAAACTATATAAT
1 TGTTTTCAAAATGTTTTCAAAAATATTATATAAGTTTTC-AAAACGATTTTAAAAACTATATAAT
*
1055069 ATATAAATGTTTTCAAAATGTTTTCAAAACTATAATATATG
65 ATATAAATGTTTTCAAAACGTTTTCAAAACTATAATATATG
* * *
1055110 TGTTTTCAAAAATGTTTTCAAAAATTATATATATAATTTTTCAAAATGATTTTAAAAATTATATA
1 TGTTTTC-AAAATGTTTTCAAAAA-TAT-TATATAAGTTTTCAAAACGATTTTAAAAACTATATA
* * * *
1055175 TTATATATATTTTTTTAAAACGTTTT
63 ATATATAAATGTTTTCAAAACGTTTT
1055201 TTTTTTTAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
105 7 0.09
106 15 0.19
107 8 0.10
108 48 0.62
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.46
Consensus pattern (105 bp):
TGTTTTCAAAATGTTTTCAAAAATATTATATAAGTTTTCAAAACGATTTTAAAAACTATATAATA
TATAAATGTTTTCAAAACGTTTTCAAAACTATAATATATG
Found at i:1055173 original size:34 final size:34
Alignment explanation
Indices: 1055003--1055175 Score: 176
Period size: 34 Copynumber: 4.9 Consensus size: 34
1054993 ATAATATACG
*
1055003 AATGTTTTCAACATGTTTTCAAAAA-TAT-TATAT
1 AATGTTTTCAAAATGTTTT-AAAAATTATATATAT
*
1055036 AA-GTTTTCAAAAACGTTTTAAAAACTATATAATATAT
1 AATGTTTTC-AAAATGTTTTAAAAA-T-TAT-ATATAT
* *
1055073 AAATGTTTTCAAAATGTTTTCAAAACTATA-ATAT
1 -AATGTTTTCAAAATGTTTTAAAAATTATATATAT
*
1055107 ATGTGTTTTCAAAAATGTTTTCAAAAATTATATATAT
1 A-ATGTTTTC-AAAATGTTTT-AAAAATTATATATAT
1055144 AAT-TTTTCAAAATGATTTTAAAAATTATATAT
1 AATGTTTTCAAAATG-TTTTAAAAATTATATAT
1055176 TATATATATT
Statistics
Matches: 118, Mismatches: 9, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
32 11 0.09
33 11 0.09
34 30 0.25
35 23 0.19
36 12 0.10
37 10 0.08
38 15 0.13
39 6 0.05
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (34 bp):
AATGTTTTCAAAATGTTTTAAAAATTATATATAT
Found at i:1055278 original size:18 final size:18
Alignment explanation
Indices: 1055255--1055301 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
1055245 AAAACAATAT
*
1055255 TATGTATGTAGT-TTTAAA
1 TATGTATGTA-TATATAAA
*
1055273 TATGTATATATATATAAA
1 TATGTATGTATATATAAA
1055291 TATGTATGTAT
1 TATGTATGTAT
1055302 GTACATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (18 bp):
TATGTATGTATATATAAA
Found at i:1059805 original size:2 final size:2
Alignment explanation
Indices: 1059760--1059786 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1059750 TAATTATTGG
1059760 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1059787 AGATAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1061809 original size:30 final size:30
Alignment explanation
Indices: 1061691--1061801 Score: 98
Period size: 30 Copynumber: 3.5 Consensus size: 30
1061681 GACGAAACTT
*
1061691 TGTTTCAACAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
* ** **
1061721 TGTTTCAAGAGAATCTGTCTCAAGCGAGACAAAATT-
1 TGTTTCAAGAGAAACAATCTCAA---AG----GTTTA
1061757 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
1061787 TGTTTCAAGAGAAAC
1 TGTTTCAAGAGAAAC
1061802 TGTCTCAAGT
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
29 2 0.03
30 34 0.55
33 4 0.06
36 20 0.32
37 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTTA
Found at i:1061859 original size:133 final size:133
Alignment explanation
Indices: 1061654--1061980 Score: 521
Period size: 133 Copynumber: 2.5 Consensus size: 133
1061644 AAAATAAATT
* * *
1061654 TGTTTCAAGAGAAATTATCTCAGGTGAGACGAAACTTTGTTTC-AACAGAAACAATCTCAAAGGT
1 TGTTTCAAGAGAAACTATCTCAAGTGAGACAAAACTTTGTTTCGAA-AGAAACAATCTCAAAGGT
* *
1061718 TTATGTTTCAAGAGAATCTGTCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGG
65 TTATGTTTCAAGAGAATCGGTCTCAAGCGAGACAAAATTTGTTTAAAGAGAAACAATCTCAAAGG
1061783 TTTA
130 TTTA
*
1061787 TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAACTTTGTTTCGAAAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTATCTCAAGTGAGACAAAACTTTGTTTCGAAAGAAACAATCTCAAAGGTT
*
1061852 TATGTTTCAAGAGAATCGGTCTCAAGCGAGACAAAATTTGTTTAAAGAGAAATAATCTCAAAGGT
66 TATGTTTCAAGAGAATCGGTCTCAAGCGAGACAAAATTTGTTTAAAGAGAAACAATCTCAAAGGT
*
1061917 TTC
131 TTA
* ** * *
1061920 TGTTTCAAGAGAAACTCTCTCAACCGAGACAAAACTTTGTTTCGAGAGAAACAAACTCAAA
1 TGTTTCAAGAGAAACTATCTCAAGTGAGACAAAACTTTGTTTCGAAAGAAACAATCTCAAA
1061981 TGAGACCAAT
Statistics
Matches: 180, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
133 178 0.99
134 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (133 bp):
TGTTTCAAGAGAAACTATCTCAAGTGAGACAAAACTTTGTTTCGAAAGAAACAATCTCAAAGGTT
TATGTTTCAAGAGAATCGGTCTCAAGCGAGACAAAATTTGTTTAAAGAGAAACAATCTCAAAGGT
TTA
Found at i:1061863 original size:67 final size:67
Alignment explanation
Indices: 1061654--1061980 Score: 471
Period size: 66 Copynumber: 4.9 Consensus size: 67
1061644 AAAATAAATT
* * * * * *
1061654 TGTTTCAAGAGAAATTATCTCAGGTGAGACGAAACTTTGTTTCAACAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
1061719 TA
66 TA
*
1061721 TGTTTCAAGAGAATCTGTCTCAAGCGAGACAAAA-TTTGTTTCAAGAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
1061785 TA
66 TA
*
1061787 TGTTTCAAGAGAAACTGTCTCAAGTGAGACAAAACTTTGTTTCGAA-AGAAACAATCTCAAAGGT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTC-AAGAGAAACAATCTCAAAGGT
1061851 TTA
65 TTA
* * * *
1061854 TGTTTCAAGAGAATCGGTCTCAAGCGAGACAAAA-TTTGTTTAAAGAGAAATAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
*
1061918 TC
66 TA
* * * *
1061920 TGTTTCAAGAGAAACTCTCTCAACCGAGACAAAACTTTGTTTCGAGAGAAACAAACTCAAA
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAA
1061981 TGAGACCAAT
Statistics
Matches: 233, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
65 2 0.01
66 119 0.51
67 110 0.47
68 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
TA
Found at i:1061979 original size:37 final size:36
Alignment explanation
Indices: 1061920--1062009 Score: 99
Period size: 37 Copynumber: 2.5 Consensus size: 36
1061910 CAAAGGTTTC
*** *
1061920 TGTTTCAAGAGAAACTCTCTCAACCGAGACAAAACTT
1 TGTTTCAAGAGAAACAAACTCAAACGAGAC-AAACTT
* * * *
1061957 TGTTTCGAGAGAAACAAACTCAAATGAGACCAATTT
1 TGTTTCAAGAGAAACAAACTCAAACGAGACAAACTT
1061993 TGTTTCAAGAGAAACAA
1 TGTTTCAAGAGAAACAA
1062010 TTTCAAAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
36 20 0.45
37 24 0.55
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (36 bp):
TGTTTCAAGAGAAACAAACTCAAACGAGACAAACTT
Found at i:1061979 original size:103 final size:102
Alignment explanation
Indices: 1061879--1062185 Score: 316
Period size: 103 Copynumber: 3.0 Consensus size: 102
1061869 GGTCTCAAGC
* * * * * * *
1061879 GAGACAAAATTTGTTTAAAGAGAAATAATCTCAAAGGTTTCTGTTTCAAGAGAAACTCTCTCAAC
1 GAGACAAATTTTGTTTCAAGAGAAACAATCTCAAA-ATTTGTGTTTCAAGAGAAACTATCTCAAG
*
1061944 CGAGACAAAACTTTGTTTCGAGAGAAACAAACTCAAAT
65 CGAGACAAAACTTTGTTTTGAGAGAAACAAACTCAAAT
* * * * *
1061982 GAGACCAATTTTGTTTCAAGAGAAACAATTTCAAAATTTGTGTTTCGAGGAAAAACTGTCTCAAG
1 GAGACAAATTTTGTTTCAAGAGAAACAATCTCAAAATTTGTGTTTC-AAGAGAAACTATCTCAAG
* * *
1062047 TGAGACGAAA-TTTGTTTTTA-AGAAA-ATAATCTCAAAT
65 CGAGACAAAACTTTGTTTTGAGAGAAACA-AA-CTCAAAT
* * * * * *
1062084 GAGATCAATTTCTTGTTTCAAGTGAAACAA-CTTCAAAATTTGGGCTTCAAGGGAAACTATCTAA
1 GAGA-CAAATT-TTGTTTCAAGAGAAACAATC-TCAAAATTTGTGTTTCAAGAGAAACTATCTCA
*
1062148 AGCGAGACAAAACTTTGTTTTGAGAGAAACAATCTCAA
63 AGCGAGACAAAACTTTGTTTTGAGAGAAACAAACTCAA
1062186 GGGAGACAGA
Statistics
Matches: 165, Mismatches: 30, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
100 1 0.01
101 7 0.04
102 28 0.17
103 77 0.47
104 45 0.27
105 6 0.04
106 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (102 bp):
GAGACAAATTTTGTTTCAAGAGAAACAATCTCAAAATTTGTGTTTCAAGAGAAACTATCTCAAGC
GAGACAAAACTTTGTTTTGAGAGAAACAAACTCAAAT
Found at i:1062165 original size:104 final size:101
Alignment explanation
Indices: 1061923--1062185 Score: 287
Period size: 104 Copynumber: 2.6 Consensus size: 101
1061913 AGGTTTCTGT
* * * **
1061923 TTCAAGAGAAACTCTCTCAACCGAGACAAAACTTTGTTTCGAGAGAAACAAA-CTCAAATGAGAC
1 TTCAAGGGAAACTATCTCAAGCGAGACAAAACTTTGTTTTTA-AGAAA-AAATCTCAAATGAGAC
* * *
1061987 CAATTTTGTTTCAAGAGAAACAATTTCAAAATTTGTGT
64 CAATTTTGTTTCAAGAGAAACAACTTCAAAATTTGGGC
* * * * * *
1062025 TTCGAGGAAAAACTGTCTCAAGTGAGACGAAA-TTTGTTTTTAAGAAAATAATCTCAAATGAGAT
1 TTCAAGG-GAAACTATCTCAAGCGAGACAAAACTTTGTTTTTAAGAAAA-AATCTCAAATGAGAC
*
1062089 CAATTTCTTGTTTCAAGTGAAACAACTTCAAAATTTGGGC
64 CAA-TT-TTGTTTCAAGAGAAACAACTTCAAAATTTGGGC
* * *
1062129 TTCAAGGGAAACTATCTAAAGCGAGACAAAACTTTGTTTTGAGAGAAACAATCTCAA
1 TTCAAGGGAAACTATCTCAAGCGAGACAAAACTTTGTTTTTA-AGAAAAAATCTCAA
1062186 GGGAGACAGA
Statistics
Matches: 132, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
100 1 0.01
101 7 0.05
102 27 0.20
103 40 0.30
104 52 0.39
105 5 0.04
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (101 bp):
TTCAAGGGAAACTATCTCAAGCGAGACAAAACTTTGTTTTTAAGAAAAAATCTCAAATGAGACCA
ATTTTGTTTCAAGAGAAACAACTTCAAAATTTGGGC
Found at i:1063950 original size:18 final size:18
Alignment explanation
Indices: 1063927--1063997 Score: 124
Period size: 18 Copynumber: 3.9 Consensus size: 18
1063917 ATGTGTTCTA
1063927 AGTGGTCCGTCGGGACAT
1 AGTGGTCCGTCGGGACAT
1063945 AGTGGTCCGTCGGGACAT
1 AGTGGTCCGTCGGGACAT
*
1063963 AGTGGTCCTTCGGGACAT
1 AGTGGTCCGTCGGGACAT
*
1063981 AGTGGTCCTTCGGGACA
1 AGTGGTCCGTCGGGACA
1063998 AATTCTACGC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.17, C:0.23, G:0.37, T:0.24
Consensus pattern (18 bp):
AGTGGTCCGTCGGGACAT
Found at i:1065390 original size:21 final size:22
Alignment explanation
Indices: 1065341--1065392 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1065331 CAATCCAAGT
*
1065341 GACCCAAAACCCAACGTTACAA
1 GACCCAAAACCCAACGATACAA
1065363 GACCCAAAACCCAAC-ATAGCAA
1 GACCCAAAACCCAACGATA-CAA
1065385 -ACCCAAAA
1 GACCCAAAA
1065393 TAATAACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.50, C:0.37, G:0.08, T:0.06
Consensus pattern (22 bp):
GACCCAAAACCCAACGATACAA
Found at i:1065803 original size:21 final size:21
Alignment explanation
Indices: 1065777--1065913 Score: 174
Period size: 21 Copynumber: 6.6 Consensus size: 21
1065767 GTTTCCAGAT
1065777 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
1065798 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
1065818 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
1065839 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
1065860 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
1065881 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
1065902 TCGCAATGCGAA
1 TCGCAATGCGAA
1065914 TATGTAAATC
Statistics
Matches: 102, Mismatches: 8, Indels: 12
0.84 0.07 0.10
Matches are distributed among these distances:
20 17 0.17
21 85 0.83
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:1065952 original size:21 final size:21
Alignment explanation
Indices: 1065928--1065975 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1065918 TAAATCGCAA
1065928 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
1065949 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
1065970 TGCGAT
1 TGCGAT
1065976 TTATTCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.29
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:1066793 original size:21 final size:21
Alignment explanation
Indices: 1066769--1066988 Score: 258
Period size: 21 Copynumber: 10.6 Consensus size: 21
1066759 TTTGGAATAA
**
1066769 ATCGCAACACGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
1066790 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
*
1066810 ATCGCAATGCGATA-GTCGACT
1 ATCGCAATGCGA-ACTTCGACT
1066831 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
1066852 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
1066873 ATCGCAATGCGAA-TAT-G-CAA
1 ATCGCAATGCGAACT-TCGAC-T
*
1066893 ATCGCAATGCGATA-GTCGACT
1 ATCGCAATGCGA-ACTTCGACT
1066914 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
1066935 ATCGCAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
1066956 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
1066977 ATCGCATTGCGA
1 ATCGCAATGCGA
1066989 TTTACATATT
Statistics
Matches: 174, Mismatches: 13, Indels: 24
0.82 0.06 0.11
Matches are distributed among these distances:
19 1 0.01
20 33 0.19
21 139 0.80
22 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:1066883 original size:83 final size:83
Alignment explanation
Indices: 1066769--1066968 Score: 364
Period size: 83 Copynumber: 2.4 Consensus size: 83
1066759 TTTGGAATAA
** *
1066769 ATCGCAACACGAACTTCGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGACTATC
1 ATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGCAAATCGCAATGCGATAGTCGACTATC
1066834 GCAATGCGAACTTCGACT
66 GCAATGCGAACTTCGACT
1066852 ATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGCAAATCGCAATGCGATAGTCGACTATC
1 ATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGCAAATCGCAATGCGATAGTCGACTATC
1066917 GCAATGCGAACTTCGACT
66 GCAATGCGAACTTCGACT
*
1066935 ATCGCAATGCGAACTTCGACTATCGCAACGCGAA
1 ATCGCAATGCGAACTTCGACTATCGCAATGCGAA
1066969 CTTCGACTAT
Statistics
Matches: 113, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 113 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (83 bp):
ATCGCAATGCGAACTTCGACTATCGCAATGCGAATATGCAAATCGCAATGCGATAGTCGACTATC
GCAATGCGAACTTCGACT
Found at i:1066924 original size:104 final size:105
Alignment explanation
Indices: 1066810--1067030 Score: 340
Period size: 104 Copynumber: 2.1 Consensus size: 105
1066800 GAATATGTAA
*
1066810 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAACTTCGACTATCGCAATGCGAACTTCGACTA
1 ATCGCAATGCGATACGTCGACTATCGCAATGCGAACTTCGACTATCGCAACGCGAACTTCGACTA
*
1066874 TCGCAATGCGAATATGCA-AATCGCAATGCGATAGTCGACT
66 TCGCAATGCG-ATATACATAATCGCAATGCGATAGTCGACT
*
1066914 ATCGCAATGCGA-ACTTCGACTATCGCAATGCGAACTTCGACTATCGCAACGCGAACTTCGACTA
1 ATCGCAATGCGATACGTCGACTATCGCAATGCGAACTTCGACTATCGCAACGCGAACTTCGACTA
* * * *
1066978 TCGCATTGCGATTTACATATTCGCATTGCGATAGTCGACT
66 TCGCAATGCGATATACATAATCGCAATGCGATAGTCGACT
*
1067018 ATCGCATTGCGAT
1 ATCGCAATGCGAT
1067031 TTACATATTC
Statistics
Matches: 106, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
103 6 0.06
104 100 0.94
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (105 bp):
ATCGCAATGCGATACGTCGACTATCGCAATGCGAACTTCGACTATCGCAACGCGAACTTCGACTA
TCGCAATGCGATATACATAATCGCAATGCGATAGTCGACT
Found at i:1067003 original size:20 final size:20
Alignment explanation
Indices: 1066978--1067050 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
1066968 ACTTCGACTA
1066978 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
1066998 TCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCGAT-TTAC-A-TAT
1067019 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1067039 TCGCATTGCGAT
1 TCGCATTGCGAT
1067051 AGTCGACTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.04
20 27 0.59
21 15 0.33
22 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1067016 original size:41 final size:41
Alignment explanation
Indices: 1066971--1067098 Score: 213
Period size: 41 Copynumber: 3.1 Consensus size: 41
1066961 AACGCGAACT
1066971 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
1067012 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
* *
1067053 TCGACTATCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAG
1 TCGACTATCGCATTGCGAT-TTACATA-TTCGCATTGCGATAG
1067095 TCGA
1 TCGA
1067099 AGTTCGCGTT
Statistics
Matches: 83, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
41 61 0.73
42 22 0.27
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (41 bp):
TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAG
Found at i:1067024 original size:21 final size:21
Alignment explanation
Indices: 1066784--1067098 Score: 216
Period size: 21 Copynumber: 15.2 Consensus size: 21
1066774 AACACGAACT
1066784 TCGACTATCGCAATGCGAATA-
1 TCGACTATCGCAATGCG-ATAG
*
1066805 T-GTA-AATCGCAATGCGATAG
1 TCG-ACTATCGCAATGCGATAG
*
1066825 TCGACTATCGCAATGCGA-ACT
1 TCGACTATCGCAATGCGATA-G
*
1066846 TCGACTATCGCAATGCGA-ACT
1 TCGACTATCGCAATGCGATA-G
1066867 TCGACTATCGCAATGCGAATA-
1 TCGACTATCGCAATGCG-ATAG
*
1066888 T-G-CAAATCGCAATGCGATAG
1 TCGAC-TATCGCAATGCGATAG
*
1066908 TCGACTATCGCAATGCGA-ACT
1 TCGACTATCGCAATGCGATA-G
*
1066929 TCGACTATCGCAATGCGA-ACT
1 TCGACTATCGCAATGCGATA-G
* *
1066950 TCGACTATCGCAACGCGA-ACT
1 TCGACTATCGCAATGCGATA-G
*
1066971 TCGACTATCGCATTGCGAT--
1 TCGACTATCGCAATGCGATAG
* *
1066990 T-TACATATTCGCATTGCGATAG
1 TCGAC-TA-TCGCAATGCGATAG
*
1067012 TCGACTATCGCATTGCGAT--
1 TCGACTATCGCAATGCGATAG
* *
1067031 T-TACATATTCGCATTGCGATAG
1 TCGAC-TA-TCGCAATGCGATAG
*
1067053 TCGACTATCGCATTGCGATAG
1 TCGACTATCGCAATGCGATAG
* * *
1067074 TCCAAGT-TCGCATTGCGATAG
1 T-CGACTATCGCAATGCGATAG
1067095 TCGA
1 TCGA
1067099 AGTTCGCGTT
Statistics
Matches: 254, Mismatches: 16, Indels: 49
0.80 0.05 0.15
Matches are distributed among these distances:
18 4 0.02
19 13 0.05
20 55 0.22
21 166 0.65
22 11 0.04
23 5 0.02
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (21 bp):
TCGACTATCGCAATGCGATAG
Found at i:1067101 original size:21 final size:21
Alignment explanation
Indices: 1066997--1067112 Score: 116
Period size: 21 Copynumber: 5.6 Consensus size: 21
1066987 GATTTACATA
1066997 TTCGCATTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAC
*
1067017 TATCGCATTGCGAT-TTAC-ATA-
1 T-TCGCATTGCGATAGT-CGA-AC
1067038 TTCGCATTGCGATAGTCG-AC
1 TTCGCATTGCGATAGTCGAAC
* *
1067058 TATCGCATTGCGATAGTCCAAG
1 T-TCGCATTGCGATAGTCGAAC
*
1067080 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCGAAC
*
1067101 TTCGCGTTGCGA
1 TTCGCATTGCGA
1067113 ATCTGGAAAC
Statistics
Matches: 81, Mismatches: 6, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.01
20 16 0.20
21 61 0.75
22 3 0.04
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCGAAC
Found at i:1067804 original size:10 final size:10
Alignment explanation
Indices: 1067789--1067826 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
1067779 CTCTCTCTAA
1067789 AAAATAAAAC
1 AAAATAAAAC
1067799 AAAATAAAAC
1 AAAATAAAAC
*
1067809 AAAAATGAAA-
1 -AAAATAAAAC
1067819 AAAATAAA
1 AAAATAAA
1067827 GAATATGGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 7 0.28
10 10 0.40
11 8 0.32
ACGTcount: A:0.82, C:0.05, G:0.03, T:0.11
Consensus pattern (10 bp):
AAAATAAAAC
Found at i:1068190 original size:22 final size:22
Alignment explanation
Indices: 1068165--1068235 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
1068155 TTAATGGTAA
1068165 ATTTTTATATTATATCTCTAAT
1 ATTTTTATATTATATCTCTAAT
* **
1068187 A-TTTTATTTTCATTAAT-GGTAA-
1 ATTTTTATATT-A-T-ATCTCTAAT
1068209 ATTTTTATATTATATCTCTAAT
1 ATTTTTATATTATATCTCTAAT
1068231 ATTTT
1 ATTTT
1068236 ATTTTCATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
20 2 0.05
21 12 0.32
22 9 0.24
23 12 0.32
24 2 0.05
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.59
Consensus pattern (22 bp):
ATTTTTATATTATATCTCTAAT
Found at i:1068215 original size:44 final size:44
Alignment explanation
Indices: 1068152--1068244 Score: 186
Period size: 44 Copynumber: 2.1 Consensus size: 44
1068142 GCTGTTATGG
1068152 TCATTAATGGTAAATTTTTATATTATATCTCTAATATTTTATTT
1 TCATTAATGGTAAATTTTTATATTATATCTCTAATATTTTATTT
1068196 TCATTAATGGTAAATTTTTATATTATATCTCTAATATTTTATTT
1 TCATTAATGGTAAATTTTTATATTATATCTCTAATATTTTATTT
1068240 TCATT
1 TCATT
1068245 TCGAGTCTGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (44 bp):
TCATTAATGGTAAATTTTTATATTATATCTCTAATATTTTATTT
Found at i:1068694 original size:2 final size:2
Alignment explanation
Indices: 1068687--1068716 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1068677 ATCAAATAGC
1068687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1068717 TGACCCCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1071381 original size:24 final size:25
Alignment explanation
Indices: 1071336--1071387 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
1071326 TTCAGTATGC
*
1071336 ATTAACATCATATTTTTATTATA-A
1 ATTAAAATCATATTTTTATTATAGA
*
1071360 ATTAAAAT-ATATTTTGTGTTATAGA
1 ATTAAAATCATATTTT-TATTATAGA
1071385 ATT
1 ATT
1071388 TTTCTTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 7 0.29
24 13 0.54
25 4 0.17
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (25 bp):
ATTAAAATCATATTTTTATTATAGA
Found at i:1071485 original size:27 final size:28
Alignment explanation
Indices: 1071451--1071504 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1071441 ATAATAATAT
1071451 TTTAATAATTA-TAGTTTAATTTTATTA
1 TTTAATAATTATTAGTTTAATTTTATTA
*
1071478 TTTAATAATTATTTGTTTAATTTTATT
1 TTTAATAATTATTAGTTTAATTTTATT
1071505 TTAAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTAATAATTATTAGTTTAATTTTATTA
Found at i:1071503 original size:14 final size:14
Alignment explanation
Indices: 1071464--1071505 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1071454 AATAATTATA
1071464 GTTTAATTTTA-TT
1 GTTTAATTTTATTT
* *
1071477 ATTTAATAATTATTT
1 GTTTAAT-TTTATTT
1071492 GTTTAATTTTATTT
1 GTTTAATTTTATTT
1071506 TAAAAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
GTTTAATTTTATTT
Found at i:1071515 original size:27 final size:25
Alignment explanation
Indices: 1071448--1071508 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 25
1071438 TATATAATAA
1071448 TATTTTAATAATTATAGTTTAATTT
1 TATTTTAATAATTATAGTTTAATTT
*
1071473 TATTATTTAATAATTATTTGTTTAATTT
1 TA-T-TTTAATAATTA-TAGTTTAATTT
1071501 TATTTTAA
1 TATTTTAA
1071509 AAAATTAGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
25 2 0.06
26 6 0.19
27 12 0.38
28 12 0.38
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (25 bp):
TATTTTAATAATTATAGTTTAATTT
Found at i:1074034 original size:29 final size:29
Alignment explanation
Indices: 1073976--1074034 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1073966 TCATAATAAT
*
1073976 TTTTTAAATTTTAAAAATTAATAATCTAA
1 TTTTTAAATTTTAAAAAATAATAATCTAA
* *
1074005 TTTTTAATTTTTAAAAACATAA-AATTTAA
1 TTTTTAAATTTTAAAAA-ATAATAATCTAA
1074034 T
1 T
1074035 AATATATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (29 bp):
TTTTTAAATTTTAAAAAATAATAATCTAA
Found at i:1076237 original size:24 final size:24
Alignment explanation
Indices: 1076210--1076270 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
1076200 ATTTTACTTT
1076210 TGTATGCCCCTTCCAGACATCCAC
1 TGTATGCCCCTTCCAGACATCCAC
*
1076234 TGTATCCCCCTTCCAGACATCCAC
1 TGTATGCCCCTTCCAGACATCCAC
1076258 TGTATGCCCCTTC
1 TGTATGCCCCTTC
1076271 ATTATTCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.18, C:0.43, G:0.11, T:0.28
Consensus pattern (24 bp):
TGTATGCCCCTTCCAGACATCCAC
Found at i:1089335 original size:41 final size:41
Alignment explanation
Indices: 1089260--1089342 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
1089250 AAGTCAAAAT
* * * * *
1089260 TATCATATGAATAATGTTTATATTTGTTTCAATATATTGAG
1 TATCATATAAATAATGCTTACATTTATTTCAATATATCGAG
*
1089301 TATCATATAAATAATGCTTACATTTATTTGAATATATCGAG
1 TATCATATAAATAATGCTTACATTTATTTCAATATATCGAG
1089342 T
1 T
1089343 GGTTTCGATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (41 bp):
TATCATATAAATAATGCTTACATTTATTTCAATATATCGAG
Found at i:1099210 original size:16 final size:17
Alignment explanation
Indices: 1099185--1099225 Score: 66
Period size: 16 Copynumber: 2.5 Consensus size: 17
1099175 ACTCCCACTG
*
1099185 CTTGTACAATGTCTGGT
1 CTTGTGCAATGTCTGGT
1099202 -TTGTGCAATGTCTGGT
1 CTTGTGCAATGTCTGGT
1099218 CTTGTGCA
1 CTTGTGCA
1099226 TATCATAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.15, C:0.17, G:0.27, T:0.41
Consensus pattern (17 bp):
CTTGTGCAATGTCTGGT
Found at i:1099353 original size:25 final size:25
Alignment explanation
Indices: 1099319--1099380 Score: 106
Period size: 25 Copynumber: 2.4 Consensus size: 25
1099309 CTGTTTTGTG
1099319 TTAATGATTATAGAAAATATCATAA
1 TTAATGATTATAGAAAATATCATAA
1099344 TTAATGATTATAGAAAATATCATAA
1 TTAATGATTATAGAAAATATCATAA
*
1099369 TTACGTGATTAT
1 TTA-ATGATTAT
1099381 TTGACGATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 28 0.80
26 7 0.20
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.39
Consensus pattern (25 bp):
TTAATGATTATAGAAAATATCATAA
Found at i:1100241 original size:18 final size:19
Alignment explanation
Indices: 1100218--1100261 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1100208 CCAGTAATCC
*
1100218 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
1100236 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
1100256 TATTCC
1 TATTCC
1100262 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:1100249 original size:20 final size:20
Alignment explanation
Indices: 1100224--1100261 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1100214 ATCCTATTCC
*
1100224 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
1100244 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
1100262 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:1103080 original size:18 final size:19
Alignment explanation
Indices: 1103040--1103081 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1103030 ATATTATTTT
1103040 TATTTAAATAAAAACAGTA
1 TATTTAAATAAAAACAGTA
* *
1103059 -ATTTAATTAAAAATA-TA
1 TATTTAAATAAAAACAGTA
1103076 TATTTA
1 TATTTA
1103082 GAGGGTATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
TATTTAAATAAAAACAGTA
Found at i:1103250 original size:39 final size:41
Alignment explanation
Indices: 1103203--1103286 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 41
1103193 CATCACCTTT
* *
1103203 AAAAAATCC-ACCCCACTCAATCCGAACC-CAATTTTTTAA
1 AAAAAATCCGACCCAACTCAATCCGAACCTCAATATTTTAA
* * *
1103242 AAAAAATCCGATCTAACTCAATCCGAACCTGAATATTTTAA
1 AAAAAATCCGACCCAACTCAATCCGAACCTCAATATTTTAA
1103283 AAAA
1 AAAA
1103287 TAAAACTGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 9 0.24
40 16 0.42
41 13 0.34
ACGTcount: A:0.45, C:0.26, G:0.05, T:0.24
Consensus pattern (41 bp):
AAAAAATCCGACCCAACTCAATCCGAACCTCAATATTTTAA
Found at i:1103287 original size:39 final size:37
Alignment explanation
Indices: 1103200--1103287 Score: 95
Period size: 39 Copynumber: 2.3 Consensus size: 37
1103190 AAACATCACC
* *
1103200 TTTAAAAAATCCACCCCACTCAATCCGAACCCAATTT
1 TTTAAAAAATCCACCCAACTCAATCCGAACCCAATAT
* * *
1103237 TTTAAAAAAAATCCGATCTAACTCAATCCGAACCTGAATAT
1 TTT--AAAAAATCC-ACCCAACTCAATCCGAACC-CAATAT
1103278 TTTAAAAAAT
1 TTTAAAAAAT
1103288 AAAACTGACT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
37 3 0.07
39 16 0.38
40 16 0.38
41 7 0.17
ACGTcount: A:0.43, C:0.25, G:0.05, T:0.27
Consensus pattern (37 bp):
TTTAAAAAATCCACCCAACTCAATCCGAACCCAATAT
Found at i:1104949 original size:32 final size:31
Alignment explanation
Indices: 1104908--1104971 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 31
1104898 TTTAAATAGT
*
1104908 TATTATTTTTTATATTAAT-ATATTTATATAA
1 TATTATTTTTTAT-TAAATAATATTTATATAA
1104939 TATTATTTTTTTATTAAATAATATTTATATAA
1 TATTA-TTTTTTATTAAATAATATTTATATAA
1104971 T
1 T
1104972 TATATTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
TATTATTTTTTATTAAATAATATTTATATAA
Found at i:1104978 original size:32 final size:30
Alignment explanation
Indices: 1104908--1104971 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 30
1104898 TTTAAATAGT
1104908 TATTATTTTTTATATTAATATATTTATATAA
1 TATTATTTTTT-TATTAATATATTTATATAA
1104939 TATTATTTTTTTATTAAATAATATTTATATAA
1 TATTATTTTTTTATT-AAT-ATATTTATATAA
1104971 T
1 T
1104972 TATATTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 4 0.13
31 14 0.45
32 13 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TATTATTTTTTTATTAATATATTTATATAA
Found at i:1104981 original size:18 final size:18
Alignment explanation
Indices: 1104928--1105014 Score: 51
Period size: 18 Copynumber: 5.0 Consensus size: 18
1104918 TATATTAATA
1104928 TATTTATATAA-TATTATT
1 TATTTATATAATTA-TATT
* *
1104946 TTTTTAT-TAA--ATA-A
1 TATTTATATAATTATATT
1104960 TATTTATATAATTATATT
1 TATTTATATAATTATATT
* *
1104978 TATTTAGAATTATTA-ATT
1 TATTTA-TATAATTATATT
* *
1104996 TTTTTTTACTAATTATATT
1 TATTTATA-TAATTATATT
1105015 GTTTTGTCTA
Statistics
Matches: 52, Mismatches: 10, Indels: 13
0.69 0.13 0.17
Matches are distributed among these distances:
14 6 0.12
15 5 0.10
16 1 0.02
17 7 0.13
18 24 0.46
19 9 0.17
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (18 bp):
TATTTATATAATTATATT
Found at i:1105146 original size:17 final size:17
Alignment explanation
Indices: 1105124--1105177 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1105114 AATGTTAATA
1105124 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1105141 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1105158 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1105175 TTT
1 TTT
1105178 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:1106732 original size:21 final size:21
Alignment explanation
Indices: 1106708--1106747 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1106698 GTACATGCCC
*
1106708 AGCCCTCCACTTCATATGCTA
1 AGCCCACCACTTCATATGCTA
* *
1106729 AGCCCACCAGTTTATATGC
1 AGCCCACCACTTCATATGC
1106748 CATCTCCGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.35, G:0.12, T:0.28
Consensus pattern (21 bp):
AGCCCACCACTTCATATGCTA
Found at i:1106776 original size:42 final size:42
Alignment explanation
Indices: 1106729--1106846 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
1106719 TCATATGCTA
* * *
1106729 AGCCCACCAGTTTATATGCC-ATCTCCGCAGGGTTACATTCCG
1 AGCCCACCAGGTTACATGCCGAGC-CCGCAGGGTTACATTCCG
* *
1106771 AGCCCA-CAGGGTTACATTCCGAGCCCGCAGGGTTACATTCCT
1 AGCCCACCA-GGTTACATGCCGAGCCCGCAGGGTTACATTCCG
* *
1106813 AGCCCGCCAGGTTACATGCCTAGCCCGCAGGGTT
1 AGCCCACCAGGTTACATGCCGAGCCCGCAGGGTT
1106847 TTATACTATA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
41 2 0.03
42 59 0.91
43 4 0.06
ACGTcount: A:0.20, C:0.34, G:0.24, T:0.22
Consensus pattern (42 bp):
AGCCCACCAGGTTACATGCCGAGCCCGCAGGGTTACATTCCG
Found at i:1106782 original size:21 final size:21
Alignment explanation
Indices: 1106753--1106846 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
1106743 TATGCCATCT
1106753 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
1106774 CCACAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
1106795 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
1106816 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
1106837 CCGCAGGGTT
1 CCGCAGGGTT
1106847 TTATACTATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.19, C:0.34, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:1107413 original size:40 final size:39
Alignment explanation
Indices: 1107369--1107452 Score: 132
Period size: 39 Copynumber: 2.1 Consensus size: 39
1107359 AAATGTTTTT
* *
1107369 AAAATACAAATTATATTATTCAAAATTTAAATTTAAAATA
1 AAAATAAAAATAATATTATTC-AAATTTAAATTTAAAATA
1107409 AAAATAAAAATAATATTATTCAAATTTAAATTTAAAATA
1 AAAATAAAAATAATATTATTCAAATTTAAATTTAAAATA
*
1107448 TAAAT
1 AAAAT
1107453 TATAGTATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 22 0.54
40 19 0.46
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (39 bp):
AAAATAAAAATAATATTATTCAAATTTAAATTTAAAATA
Found at i:1107438 original size:33 final size:34
Alignment explanation
Indices: 1107397--1107471 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
1107387 TTCAAAATTT
*
1107397 AAATTTAAAATAAAAATAAAAATAATATTATTC-
1 AAATTTAAAATAAAAATAAAAATAATAGTATTCG
* * * *
1107430 AAATTTAAATTTAAAATATAAATTATAGTATTCG
1 AAATTTAAAATAAAAATAAAAATAATAGTATTCG
1107464 AAATTTAA
1 AAATTTAA
1107472 CATTAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 28 0.78
34 8 0.22
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (34 bp):
AAATTTAAAATAAAAATAAAAATAATAGTATTCG
Found at i:1107606 original size:14 final size:14
Alignment explanation
Indices: 1107587--1107616 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1107577 TTTGATCATT
*
1107587 AACATATATATTAA
1 AACATATACATTAA
1107601 AACATATACATTAA
1 AACATATACATTAA
1107615 AA
1 AA
1107617 TCAACTTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:1108283 original size:127 final size:128
Alignment explanation
Indices: 1107871--1108878 Score: 1717
Period size: 128 Copynumber: 7.9 Consensus size: 128
1107861 TTACATGATT
1107871 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** * *
1107936 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATATG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* *
1107999 TACTGATATATCTAGTGTCCACGAGGGACATGAGGGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** *
1108064 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
*
1108127 TACTGATATATCTAGTGTCCTCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1108192 TGACAAAATAATGGAAGGCGC-CCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1108254 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** *
1108319 TGACGAAATAA-GGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
1108381 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1108446 TGACGAAATAATGGAAGGCGCG-CCCTGGGAACGCGCCTTCATATGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1108508 TACTGATATATCTAGTG-CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1108572 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTTATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
1108635 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1108700 TGACGAAATAATGGAAGGCGCGCCCCCGGGAATGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1108763 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1108828 TGACG-AATAATGGAAGGCGCGCCCCTGGGAACGCGCCTTTATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
1108879 ACTCCGATTA
Statistics
Matches: 841, Mismatches: 32, Indels: 15
0.95 0.04 0.02
Matches are distributed among these distances:
126 80 0.10
127 366 0.44
128 395 0.47
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:1108408 original size:254 final size:256
Alignment explanation
Indices: 1107871--1108871 Score: 1755
Period size: 254 Copynumber: 3.9 Consensus size: 256
1107861 TTACATGATT
1107871 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** * *
1107936 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATATGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGGT
* *
1108000 ACTGATATATCTAGTGTCCACGAGGGACATGAGGGACATAATAGGGCAATGATAACATATTCTCT
130 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1108065 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
195 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
*
1108127 TACTGATATATCTAGTGTCCTCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1108192 TGACAAAATAATGGAAGGCGC-CCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
1108256 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
1108321 ACGAAATAA-GGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
1108381 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1108446 TGACGAAATAATGGAAGGCGCG-CCCTGGGAACGCGCCTTCATATGAATAGTGAAATAATAGGTA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
1108510 CTGATATATCTAGTG-CCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
* *** *
1108574 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTTATGT-GAATAGTGAAATAATAGG
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
*
1108635 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1108700 TGACGAAATAATGGAAGGCGCGCCCCCGGGAATGCGCCTTCATGTGAATAGTGAAATAATAGGTA
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
1108765 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
131 CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
* *
1108830 ACG-AATAATGGAAGGCGCGCCCCTGGGAACGCGCCTTTATGT
196 ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT
1108872 GAATAGTACT
Statistics
Matches: 716, Mismatches: 23, Indels: 13
0.95 0.03 0.02
Matches are distributed among these distances:
253 59 0.08
254 321 0.45
255 200 0.28
256 136 0.19
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.23
Consensus pattern (256 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
CTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
ACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCTGAGAAATAATAGG
Found at i:1108962 original size:8 final size:8
Alignment explanation
Indices: 1108949--1108989 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1108939 TCACAATCTT
1108949 TCAAATTC
1 TCAAATTC
1108957 TCAAATTC
1 TCAAATTC
* *
1108965 CCAAACTC
1 TCAAATTC
1108973 T-AAATTC
1 TCAAATTC
1108980 TCAAATTC
1 TCAAATTC
1108988 TC
1 TC
1108990 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:1113282 original size:16 final size:16
Alignment explanation
Indices: 1113263--1113319 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 16
1113253 TCTTTTATTA
1113263 TATTTAATATTTAATT
1 TATTTAATATTTAATT
*
1113279 TATTTAAGTATTTAAAT
1 TATTTAA-TATTTAATT
1113296 TATTTAATATTGT-ATT
1 TATTTAATATT-TAATT
*
1113312 TAATTAAT
1 TATTTAAT
1113320 TTTTTTACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (16 bp):
TATTTAATATTTAATT
Found at i:1113292 original size:17 final size:16
Alignment explanation
Indices: 1113263--1113306 Score: 70
Period size: 17 Copynumber: 2.7 Consensus size: 16
1113253 TCTTTTATTA
*
1113263 TATTTAATATTTAATT
1 TATTTAATATTTAAAT
1113279 TATTTAAGTATTTAAAT
1 TATTTAA-TATTTAAAT
1113296 TATTTAATATT
1 TATTTAATATT
1113307 GTATTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TATTTAATATTTAAAT
Found at i:1115403 original size:12 final size:12
Alignment explanation
Indices: 1115383--1115413 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1115373 GTAGCTGCTC
1115383 ACGACGACGATG
1 ACGACGACGATG
*
1115395 ACGATGACGATG
1 ACGACGACGATG
1115407 ACGACGA
1 ACGACGA
1115414 TGGTGATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.35, C:0.23, G:0.32, T:0.10
Consensus pattern (12 bp):
ACGACGACGATG
Found at i:1122609 original size:31 final size:31
Alignment explanation
Indices: 1122557--1122619 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
1122547 TATTCGGTGA
* * *
1122557 ATTCCATATGTCCTTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCCCACTAGGAACTCCC
1122588 ATTCAATATGTCATTCCCACTAGGAACTCCC
1 ATTCAATATGTCATTCCCACTAGGAACTCCC
1122619 A
1 A
1122620 AACTCTTAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.33, G:0.10, T:0.30
Consensus pattern (31 bp):
ATTCAATATGTCATTCCCACTAGGAACTCCC
Found at i:1132685 original size:7 final size:7
Alignment explanation
Indices: 1132673--1132702 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1132663 TCATGGAGGG
1132673 GGAAAGA
1 GGAAAGA
1132680 GGAAAGA
1 GGAAAGA
1132687 GGAAAGA
1 GGAAAGA
1132694 GGAAAGA
1 GGAAAGA
1132701 GG
1 GG
1132703 GAGGGGAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (7 bp):
GGAAAGA
Found at i:1138533 original size:76 final size:77
Alignment explanation
Indices: 1138385--1138539 Score: 179
Period size: 76 Copynumber: 2.0 Consensus size: 77
1138375 ACATCTTTTC
* * *
1138385 TTGCAATGCCTGTGCAAGGGCATCTGAGGCATCACCTTTAGTCTCAGCAGTATTTAAATCCAGCA
1 TTGCAATGCCTGTGCAAGGGCATCTAAGGCATAACCTTTAGTCTCAGCAGTATTTAAATACAGCA
**
1138450 TGCCCCTCT-TT
66 AACCCCTCTCTT
* * * * * *
1138461 TTGCAGTGCCTTTGCAAGGGCTTCTAAGGCACTAAGC-TTAGTCTCAGCAGTATTTGAATAGAGC
1 TTGCAATGCCTGTGCAAGGGCATCTAAGGCA-TAACCTTTAGTCTCAGCAGTATTTAAATACAGC
*
1138525 AAATCCCTCTCTT
65 AAACCCCTCTCTT
1138538 TT
1 TT
1138540 ACCTCATCTT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
76 58 0.89
77 7 0.11
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (77 bp):
TTGCAATGCCTGTGCAAGGGCATCTAAGGCATAACCTTTAGTCTCAGCAGTATTTAAATACAGCA
AACCCCTCTCTT
Found at i:1146150 original size:22 final size:22
Alignment explanation
Indices: 1146125--1146195 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 22
1146115 CCACAGTTCG
1146125 TAATTTGCACCGAAGTACCACA
1 TAATTTGCACCGAAGTACCACA
1146147 TAA-TTGTC-CCGAA-TGACCACA
1 TAATTTG-CACCGAAGT-ACCACA
** * *
1146168 TAGGTTGCATCGAAGTGCCACA
1 TAATTTGCACCGAAGTACCACA
1146190 T-ATTTG
1 TAATTTG
1146196 TCCCTTAGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
20 1 0.03
21 20 0.51
22 17 0.44
23 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (22 bp):
TAATTTGCACCGAAGTACCACA
Found at i:1146159 original size:21 final size:21
Alignment explanation
Indices: 1146134--1146233 Score: 78
Period size: 21 Copynumber: 4.7 Consensus size: 21
1146124 GTAATTTGCA
1146134 CCGAAGTACCACATAATTGTC
1 CCGAAGTACCACATAATTGTC
*
1146155 CCGAA-TGACCACATAGGTTG-C
1 CCGAAGT-ACCACATA-ATTGTC
* * *
1146176 ATCGAAGTGCCACATATTTGTC
1 -CCGAAGTACCACATAATTGTC
** * *
1146198 CCTTAGGATCACATAATTGTC
1 CCGAAGTACCACATAATTGTC
*
1146219 CCGAAGGACCACATA
1 CCGAAGTACCACATA
1146234 GACCCTCGAC
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
20 1 0.02
21 43 0.72
22 15 0.25
23 1 0.02
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (21 bp):
CCGAAGTACCACATAATTGTC
Found at i:1146211 original size:43 final size:43
Alignment explanation
Indices: 1146129--1146233 Score: 106
Period size: 43 Copynumber: 2.5 Consensus size: 43
1146119 AGTTCGTAAT
*
1146129 TTGCACCGAAGTACCACATAATTGTCCCGAATGACCACATAGG
1 TTGCACCGAAGTACCACATAATTGTCCCGAAGGACCACATAGG
* * * ** * *
1146172 TTGCATCGAAGTGCCACATATTTGTCCCTTAGGATCACATA-A
1 TTGCACCGAAGTACCACATAATTGTCCCGAAGGACCACATAGG
*
1146214 TTGTC-CCGAAGGACCACATA
1 TTG-CACCGAAGTACCACATA
1146234 GACCCTCGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
42 15 0.30
43 35 0.70
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (43 bp):
TTGCACCGAAGTACCACATAATTGTCCCGAAGGACCACATAGG
Found at i:1146359 original size:41 final size:41
Alignment explanation
Indices: 1146302--1146386 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
1146292 TTTTAATCAA
1146302 ATAATTAGGTTCAATCCTTATTCAAAGTGTTTCTTATTCAC
1 ATAATTAGGTTCAATCCTTATTCAAAGTGTTTCTTATTCAC
1146343 ATAATTAGGTTCAATCCTTATTCAAAGTGTTTCTTATTCAC
1 ATAATTAGGTTCAATCCTTATTCAAAGTGTTTCTTATTCAC
1146384 ATA
1 ATA
1146387 GCTTCTCTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (41 bp):
ATAATTAGGTTCAATCCTTATTCAAAGTGTTTCTTATTCAC
Found at i:1146872 original size:54 final size:54
Alignment explanation
Indices: 1146792--1146934 Score: 234
Period size: 54 Copynumber: 2.6 Consensus size: 54
1146782 TCATAACAAG
*
1146792 GGGTATCAATACACTCCTCAGTGTACCGATACACAAATTG-CATTCGATGTTTAA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAA-TGACATTCGATGTTTAA
* * *
1146846 GGGTATTGATACACTCCTCAGCGTACCGATACACAAATGACATTCGATGTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGACATTCGATGTTTAA
1146900 GGGTATCGATACACTCCTCAGTGTACCGATACACA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACA
1146935 CTCATACAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 2 0.02
54 80 0.98
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (54 bp):
GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGACATTCGATGTTTAA
Found at i:1151511 original size:73 final size:73
Alignment explanation
Indices: 1151417--1151554 Score: 231
Period size: 73 Copynumber: 1.9 Consensus size: 73
1151407 GAGGATGCTG
* * * *
1151417 TGGATTCTGTTCTAGTCTGAGGTTGAGAACTTGAACCTCTACTTTTATTTGATTGCGAAGAACCG
1 TGGATTCTGCTCTAGTATGAGGTTAAAAACTTGAACCTCTACTTTTATTTGATTGCGAAGAACCG
1151482 AACGATGA
66 AACGATGA
*
1151490 TGGATTCTGCTCTGGTATGAGGTTAAAAACTTGAACCTCTACTTTTATTTGATTGCGAAGAACCG
1 TGGATTCTGCTCTAGTATGAGGTTAAAAACTTGAACCTCTACTTTTATTTGATTGCGAAGAACCG
1151555 GAGGATGCAC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (73 bp):
TGGATTCTGCTCTAGTATGAGGTTAAAAACTTGAACCTCTACTTTTATTTGATTGCGAAGAACCG
AACGATGA
Found at i:1152706 original size:2 final size:2
Alignment explanation
Indices: 1152699--1152734 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1152689 ACAAAATACA
1152699 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1152735 TCAAAATCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1153163 original size:22 final size:22
Alignment explanation
Indices: 1153138--1153209 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 22
1153128 CCACAGCTCG
1153138 TAATTTGTACCGAAGTGCCACA
1 TAATTTGTACCGAAGTGCCACA
* *
1153160 TAA-TTATCCCGAA-TGACCACA
1 TAATTTGTACCGAAGTG-CCACA
** *
1153181 TAGGTTGCACCGAAGTGCCACA
1 TAATTTGTACCGAAGTGCCACA
1153203 T-ATTTGT
1 TAATTTGT
1153210 CCCATAGGAC
Statistics
Matches: 38, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
20 2 0.05
21 18 0.47
22 16 0.42
23 2 0.05
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.28
Consensus pattern (22 bp):
TAATTTGTACCGAAGTGCCACA
Found at i:1153172 original size:21 final size:22
Alignment explanation
Indices: 1153147--1153246 Score: 79
Period size: 21 Copynumber: 4.7 Consensus size: 22
1153137 GTAATTTGTA
1153147 CCGAAGTG-CCACATAATTATC
1 CCGAAGTGACCACATAATTATC
* *
1153168 CCGAA-TGACCACATAGGTT-GC
1 CCGAAGTGACCACATA-ATTATC
* *
1153189 ACCGAAGTG-CCACATATTTGTC
1 -CCGAAGTGACCACATAATTATC
1153211 CC-ATAG-GACCACATAATTATC
1 CCGA-AGTGACCACATAATTATC
*
1153232 CCGTAG-GACCACATA
1 CCGAAGTGACCACATA
1153247 GACCCTCGAC
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
20 4 0.06
21 43 0.67
22 15 0.23
23 2 0.03
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (22 bp):
CCGAAGTGACCACATAATTATC
Found at i:1153409 original size:21 final size:20
Alignment explanation
Indices: 1153380--1153426 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
1153370 ATAGAGTATA
*
1153380 TTCACATTCAATGATTCAAAG
1 TTCATATTCAATGATT-AAAG
* *
1153401 TTCATATTCACTTATTAAAG
1 TTCATATTCAATGATTAAAG
1153421 TTCATA
1 TTCATA
1153427 ACACATAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.40
Consensus pattern (20 bp):
TTCATATTCAATGATTAAAG
Found at i:1153833 original size:54 final size:54
Alignment explanation
Indices: 1153751--1153893 Score: 234
Period size: 54 Copynumber: 2.6 Consensus size: 54
1153741 TCATAACAGG
1153751 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATTG-CATTCGATGTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAA-TGACATTCGATGTTTGA
* * *
1153805 GGGTATCAATACACTCCTCAGTATACCGATACACAAATGACATTTGATGTTTGA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGACATTCGATGTTTGA
*
1153859 GGGTAACGATACACTCCTCAGTGTACCGATACACA
1 GGGTATCGATACACTCCTCAGTGTACCGATACACA
1153894 CTCATACAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
53 2 0.02
54 80 0.98
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (54 bp):
GGGTATCGATACACTCCTCAGTGTACCGATACACAAATGACATTCGATGTTTGA
Found at i:1154772 original size:17 final size:17
Alignment explanation
Indices: 1154750--1154782 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1154740 TAATCCATTT
1154750 AGACATAAATCATATCA
1 AGACATAAATCATATCA
*
1154767 AGACATATATCATATC
1 AGACATAAATCATATC
1154783 TAAGTTAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.18, G:0.06, T:0.27
Consensus pattern (17 bp):
AGACATAAATCATATCA
Found at i:1156636 original size:19 final size:19
Alignment explanation
Indices: 1156599--1156637 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1156589 CTTTGAAATC
*
1156599 TTTTATTTTCTTTCTTCTA
1 TTTTATTTTCTTTCATCTA
1156618 TTTTA-TTTCTCTTCATCTA
1 TTTTATTTTCT-TTCATCTA
1156637 T
1 T
1156638 AAATACCCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTATTTTCTTTCATCTA
Found at i:1157519 original size:21 final size:21
Alignment explanation
Indices: 1157485--1157524 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1157475 GCCACTCATA
*
1157485 TTTTAAATTAAATAAATATATT
1 TTTTAAAATAAAT-AATATATT
1157507 TTTTAAAAT-AATAATATA
1 TTTTAAAATAAATAATATA
1157525 ACAATATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 3 0.18
22 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTTTAAAATAAATAATATATT
Found at i:1158321 original size:2 final size:2
Alignment explanation
Indices: 1158314--1158340 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1158304 TCTAAAACTT
1158314 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1158341 TTTTGGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1168119 original size:83 final size:81
Alignment explanation
Indices: 1167899--1168131 Score: 236
Period size: 83 Copynumber: 2.8 Consensus size: 81
1167889 AATAATACTT
* * * * *
1167899 TAGTGGCGTTTCTT-CAACAAACGCTGCGATAGAGTTGTACTTTAGTGGCGTTTTTATACAAACG
1 TAGTGGCGTTT-TTCCAACAAACGCCGCGATAAAG-AGTACTTTAGTGG-ATTTTTATACAAATG
*
1167963 CCGTAATAAGGATCGTTTA
63 CCGTAATAAGGATAGTTTA
* * * **
1167982 TAATGGCGTTTTTCTAACAAACGCCACGATAGATTAGTA-TGTTAGTGGCATTTTTATACAAATG
1 TAGTGGCGTTTTTCCAACAAACGCCGCGATA-AAGAGTACT-TTAGTGG-ATTTTTATACAAATG
* * *
1168046 TCGTAATAGGGTTAGTTTA
63 CCGTAATAAGGATAGTTTA
* *
1168065 TAGTGGCGTTTTTCCAACAAACGCCGTGATAAAGAGTACTTTAGCGGTATTTTTTATACAAATGC
1 TAGTGGCGTTTTTCCAACAAACGCCGCGATAAAGAGTACTTTAGTGG-A-TTTTTATACAAATGC
1168130 CG
64 CG
1168132 CATAGGGTTT
Statistics
Matches: 122, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
82 15 0.12
83 107 0.88
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.35
Consensus pattern (81 bp):
TAGTGGCGTTTTTCCAACAAACGCCGCGATAAAGAGTACTTTAGTGGATTTTTATACAAATGCCG
TAATAAGGATAGTTTA
Found at i:1171439 original size:43 final size:42
Alignment explanation
Indices: 1171352--1171684 Score: 317
Period size: 43 Copynumber: 7.8 Consensus size: 42
1171342 AAGGTAATTA
* * * **
1171352 GCGGCGTTTGTATCAAAAAAATGCCGCAATAGATATGATATTTT
1 GCGGCGTTTGT-TC-CAAAAACGCCGCTATAGATATGACCTTTT
* * *
1171396 GCGGCTTTTGTATCCAAAAACGCCGCCATAGATCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATATGACCTTTT
* ** * *
1171439 GCGGTGTTTACTCC-AAAACGCCGTTATAGATATCAACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATAT-GACCTTTT
* * * * *
1171481 GCAGCGTTTGTTCAAAAAACGCAGCTATAGATTTTACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTT
* * * * *
1171523 GCGGCGTTTGTATCCTAAAATGCCGTTATATATATCAACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATAT-GACCTTTT
*
1171567 GCGGCGTTTGTTCCAAAAACGTCGCTATAGATATTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATA-TGACCTTTT
* * * *
1171610 GCAGCGTTTATTCCAAAAACACCGCTATAGATAGCGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATA-TGACCTTTT
* *
1171653 GCGGCGTTTGTTCCAAAAACACCGCGATAGAT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGAT
1171685 CTTAACCTAT
Statistics
Matches: 236, Mismatches: 48, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
41 16 0.07
42 36 0.15
43 152 0.64
44 32 0.14
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATATGACCTTTT
Found at i:1183383 original size:23 final size:22
Alignment explanation
Indices: 1183342--1183406 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
1183332 CTACATATTA
1183342 TTTTTTTGTTATTTT-TTTTAC
1 TTTTTTTGTTATTTTATTTTAC
*
1183363 TTTCTTTTGTTATTTTATTTTTC
1 TTT-TTTTGTTATTTTATTTTAC
**
1183386 TTTTTCTTGTTACATTATTTT
1 TTTTT-TTGTTATTTTATTTT
1183407 CTCTTATTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 3 0.08
22 14 0.37
23 21 0.55
ACGTcount: A:0.11, C:0.08, G:0.05, T:0.77
Consensus pattern (22 bp):
TTTTTTTGTTATTTTATTTTAC
Found at i:1183391 original size:25 final size:22
Alignment explanation
Indices: 1183345--1183397 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1183335 CATATTATTT
1183345 TTTTGTTATTTTTTTTACTTTC
1 TTTTGTTATTTTTTTTACTTTC
*
1183367 TTTTGTTATTTTATTTTTCTTT-
1 TTTTGTTATTTT-TTTTACTTTC
1183389 TTCTTGTTA
1 TT-TTGTTA
1183398 CATTATTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.09, C:0.08, G:0.06, T:0.77
Consensus pattern (22 bp):
TTTTGTTATTTTTTTTACTTTC
Found at i:1183497 original size:15 final size:17
Alignment explanation
Indices: 1183477--1183508 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1183467 CATAATATAA
1183477 TAAATT-CAAG-TAGAT
1 TAAATTACAAGATAGAT
1183492 TAAATTACAAGATAGAT
1 TAAATTACAAGATAGAT
1183509 AAAAATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (17 bp):
TAAATTACAAGATAGAT
Found at i:1186278 original size:25 final size:25
Alignment explanation
Indices: 1186224--1186278 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1186214 TAAAACGGTT
*
1186224 CGGTTCGGTTCGGTTTGGCTTTAAA
1 CGGTTCGGTTCGGTTCGGCTTTAAA
1186249 CGGTTCGGTTTTCGGTTCGG-TTTAAA
1 CGGTTCGG--TTCGGTTCGGCTTTAAA
1186275 -GGTT
1 CGGTT
1186279 TCATTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 12 0.44
26 6 0.22
27 9 0.33
ACGTcount: A:0.11, C:0.15, G:0.33, T:0.42
Consensus pattern (25 bp):
CGGTTCGGTTCGGTTCGGCTTTAAA
Found at i:1186423 original size:14 final size:14
Alignment explanation
Indices: 1186404--1186444 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 14
1186394 AAAAACCGAA
1186404 CCGAACCGAAAAAC
1 CCGAACCGAAAAAC
1186418 CCGAACCGTTAAAAAAC
1 CCGAACCG---AAAAAC
1186435 CCGAACCGAA
1 CCGAACCGAA
1186445 CAGAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 10 0.42
17 14 0.58
ACGTcount: A:0.46, C:0.34, G:0.15, T:0.05
Consensus pattern (14 bp):
CCGAACCGAAAAAC
Found at i:1196932 original size:31 final size:31
Alignment explanation
Indices: 1196897--1196975 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
1196887 TTGCTTTGTT
* *
1196897 ATGTCCCTTGACTATTATATTTTTGAAGAAA
1 ATGTCCCTCGACTATTATATATTTGAAGAAA
1196928 ATGTCCCTCGACTATTATATATTTGAAGAAA
1 ATGTCCCTCGACTATTATATATTTGAAGAAA
1196959 ATGTCCCTCGACTATTA
1 ATGTCCCTCGACTATTA
1196976 CAAGTTACAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.38
Consensus pattern (31 bp):
ATGTCCCTCGACTATTATATATTTGAAGAAA
Found at i:1197335 original size:59 final size:60
Alignment explanation
Indices: 1197211--1197344 Score: 150
Period size: 59 Copynumber: 2.2 Consensus size: 60
1197201 AATCGGGAGA
* * * *
1197211 CCATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAATCAACTCTCTATAGTCGGAGGAT
1 CCATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAACAACTCCCTATAGTC-GAGGAT
** *
1197272 -CATTTTGTAACTTTTAATAATCG-TTGACTCAACAAAACAAGTCCCTATAGTC-AGGAT
1 CCATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAACAACTCCCTATAGTCGAGGAT
1197329 GCCATTTGTGT-ACTTT
1 -CCATTT-TGTAACTTT
1197345 ACCCTAAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
57 5 0.08
59 34 0.54
60 24 0.38
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.35
Consensus pattern (60 bp):
CCATTTTGTAACTTTTAATAATCGAGGGACTCAACAAAACAACTCCCTATAGTCGAGGAT
Found at i:1197875 original size:22 final size:22
Alignment explanation
Indices: 1197823--1197877 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1197813 CTCTCTACAG
*
1197823 CGAAATCCATCCCCGTCTCCGA
1 CGAAATCCGTCCCCGTCTCCGA
1197845 CGAAATCCGTCCCCGTCTCCGA
1 CGAAATCCGTCCCCGTCTCCGA
1197867 CGAAATCCGTC
1 CGAAATCCGTC
1197878 TATCTCCATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.22, C:0.44, G:0.16, T:0.18
Consensus pattern (22 bp):
CGAAATCCGTCCCCGTCTCCGA
Found at i:1198288 original size:20 final size:20
Alignment explanation
Indices: 1198251--1198288 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1198241 CGATTTTCTC
* *
1198251 GTTGCGATTTTCATTTTCGA
1 GTTGCGATTTTAAGTTTCGA
1198271 GTTGCGATTTTAAGTTTC
1 GTTGCGATTTTAAGTTTC
1198289 AGAAATTACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.13, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATTTTAAGTTTCGA
Found at i:1199799 original size:42 final size:42
Alignment explanation
Indices: 1199709--1199807 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
1199699 CCCCCCACTT
* * *
1199709 CGAGAGCCATCACCTGATCGAGTCGATTCTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGTCGATTATACACCTCGACAA
* *
1199751 CCAGAGCCATCACCTGATCGAG-CTGATTATACACCTCTACAA
1 CGAGAGCCATCACCTGATCGAGTC-GATTATACACCTCGACAA
* *
1199793 TGAGAGCTATCACCT
1 CGAGAGCCATCACCT
1199808 ATTTCATCAC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 1 0.02
42 47 0.98
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.21
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGTCGATTATACACCTCGACAA
Found at i:1200214 original size:12 final size:12
Alignment explanation
Indices: 1200188--1200229 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1200178 TTTTCTGGCA
1200188 TTATTTATTTG-T
1 TTATTTA-TTGAT
1200200 TTATTTATTGAT
1 TTATTTATTGAT
* *
1200212 TTATGTATTAAT
1 TTATTTATTGAT
1200224 TTATTT
1 TTATTT
1200230 TTAGCGGCCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (12 bp):
TTATTTATTGAT
Found at i:1200411 original size:18 final size:19
Alignment explanation
Indices: 1200378--1200413 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1200368 CCTATCATCG
1200378 TTCAAGAGGCCCCCTATCT
1 TTCAAGAGGCCCCCTATCT
1200397 TTCAAGAGG-CCCCTATC
1 TTCAAGAGGCCCCCTATC
1200414 ACCGTTGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (19 bp):
TTCAAGAGGCCCCCTATCT
Found at i:1200426 original size:21 final size:21
Alignment explanation
Indices: 1200376--1200446 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
1200366 CACCTATCAT
* *
1200376 CGTTCAAGAGGCCCC-C-TAT
1 CGTTCAAGAGGCCCCTCACAC
*
1200395 CTTTCAAGAGGCCCCT-ATCAC
1 CGTTCAAGAGGCCCCTCA-CAC
*
1200416 CGTTGAAGAGGCCCCTCACAC
1 CGTTCAAGAGGCCCCTCACAC
1200437 CGTTCAAGAG
1 CGTTCAAGAG
1200447 ACCGATTCAC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 14 0.33
21 27 0.64
22 1 0.02
ACGTcount: A:0.24, C:0.35, G:0.21, T:0.20
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCACAC
Found at i:1201994 original size:20 final size:21
Alignment explanation
Indices: 1201948--1201994 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
1201938 CGTTGCGATG
*
1201948 GTTGCGAAAGTCAAATTCACA
1 GTTGCGAAAGTCAAATGCACA
**
1201969 -ACGCGAAAGTCAAATGCA-A
1 GTTGCGAAAGTCAAATGCACA
1201988 GTTGCGA
1 GTTGCGA
1201995 TTTTCGTGTT
Statistics
Matches: 20, Mismatches: 5, Indels: 3
0.71 0.18 0.11
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.19
Consensus pattern (21 bp):
GTTGCGAAAGTCAAATGCACA
Found at i:1203889 original size:2 final size:2
Alignment explanation
Indices: 1203882--1203931 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1203872 TGCACCTTTC
1203882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1203924 AT AC AT AT
1 AT AT AT AT
1203932 CCACGCATAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1204258 original size:30 final size:30
Alignment explanation
Indices: 1204202--1204330 Score: 224
Period size: 30 Copynumber: 4.3 Consensus size: 30
1204192 GAAGGACCTA
* *
1204202 TCCAGAGGTCACAAAGA-CCCCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1204231 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1204261 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1204291 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
1204321 TCCATAGGTC
1 TCCAGAGGTC
1204331 CCGAAGAACC
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 16 0.17
30 80 0.83
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1204347 original size:30 final size:30
Alignment explanation
Indices: 1204202--1204420 Score: 147
Period size: 30 Copynumber: 7.2 Consensus size: 30
1204192 GAAGGACCTA
* **
1204202 TCCAGAGGTCACAAAG-ACCCCGGTAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAACTG
* * * *
1204231 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAACTG
* * * *
1204261 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAACTG
* * * *
1204291 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAACTG
* *
1204321 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGT-AACTG
* ** *
1204352 TCCATATGTTC-CTTAGAACATAGGTATACTG
1 TCCATA-GGTCACAAAGAACCTAGGTA-ACTG
* * *
1204383 TCCATATGTCTCGAAAG-ACATAGGTAAAACTG
1 TCCATAGGTCAC-AAAGAACCTAGGT--AACTG
1204415 TCCATA
1 TCCATA
1204421 TGTTCCGTAG
Statistics
Matches: 165, Mismatches: 17, Indels: 13
0.85 0.09 0.07
Matches are distributed among these distances:
29 15 0.09
30 93 0.56
31 41 0.25
32 15 0.09
33 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (30 bp):
TCCATAGGTCACAAAGAACCTAGGTAACTG
Found at i:1204347 original size:60 final size:60
Alignment explanation
Indices: 1204202--1204355 Score: 220
Period size: 60 Copynumber: 2.6 Consensus size: 60
1204192 GAAGGACCTA
**
1204202 TCCAGAGGTCACAAAG-ACCCCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
* * *
1204261 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
* * *
1204321 TCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCA
1 TCCAGAGGTCACAAAGAACCTAGGT-AACTGTCCA
1204356 TATGTTCCTT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
59 15 0.18
60 60 0.71
61 9 0.11
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.21
Consensus pattern (60 bp):
TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1204426 original size:63 final size:61
Alignment explanation
Indices: 1204313--1204441 Score: 188
Period size: 63 Copynumber: 2.1 Consensus size: 61
1204303 AAAGATCCTC
* *
1204313 GGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
* *
1204374 GGTATACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGTA-ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATA
1204437 GGTAA
1 GGTAA
1204442 ACCCTCGACT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
61 5 0.08
62 25 0.41
63 31 0.51
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (61 bp):
GGTAACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATA
Found at i:1204436 original size:32 final size:31
Alignment explanation
Indices: 1204316--1204443 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
1204306 GATCCTCGGT
* * * *
1204316 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
*
1204347 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
1204378 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
1204410 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
1204441 AAC
1 AAC
1204444 CCTCGACTCT
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 4 0.05
31 51 0.62
32 23 0.28
33 4 0.05
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:1205182 original size:22 final size:22
Alignment explanation
Indices: 1205138--1205179 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1205128 TAAATCAATT
* *
1205138 TCATATAACTCTTATAATCTTC
1 TCATATAACTCTCATAACCTTC
1205160 TCATATAACT-TCATAACCTT
1 TCATATAACTCTCATAACCTT
1205180 TCTTATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (22 bp):
TCATATAACTCTCATAACCTTC
Found at i:1205653 original size:21 final size:21
Alignment explanation
Indices: 1205629--1205673 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1205619 CCATGTTCGT
* * *
1205629 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1205650 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1205671 TTG
1 TTG
1205674 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1208492 original size:2 final size:2
Alignment explanation
Indices: 1208485--1208533 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1208475 TGCACCTTTC
1208485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1208527 AT AT AT A
1 AT AT AT A
1208534 CATACATATC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1208874 original size:30 final size:30
Alignment explanation
Indices: 1208815--1208943 Score: 215
Period size: 30 Copynumber: 4.3 Consensus size: 30
1208805 GAATGACCTA
* * *
1208815 TCCAGAGGTCACAAAGA-CCCCGATAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1208844 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1208874 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1208904 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
1208934 TCCATAGGTC
1 TCCAGAGGTC
1208944 CCGAAGAACC
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
29 16 0.17
30 79 0.83
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1208960 original size:30 final size:30
Alignment explanation
Indices: 1208815--1209001 Score: 126
Period size: 30 Copynumber: 6.2 Consensus size: 30
1208805 GAATGACCTA
* ** *
1208815 TCCAGAGGTCACAAAG-ACCCCGATAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAACTG
* * * *
1208844 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAACTG
* * * *
1208874 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAACTG
* * * *
1208904 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAACTG
* *
1208934 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGT-AACTG
* * ** *
1208965 TACATATGTTC-CTTAGAACATAGGTATACTG
1 TCCATA-GGTCACAAAGAACCTAGGTA-ACTG
1208996 TCCATA
1 TCCATA
1209002 TGTCTCGAAA
Statistics
Matches: 138, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
29 15 0.11
30 90 0.65
31 30 0.22
32 3 0.02
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (30 bp):
TCCATAGGTCACAAAGAACCTAGGTAACTG
Found at i:1208960 original size:60 final size:60
Alignment explanation
Indices: 1208815--1208965 Score: 205
Period size: 60 Copynumber: 2.5 Consensus size: 60
1208805 GAATGACCTA
** *
1208815 TCCAGAGGTCACAAAG-ACCCCGATAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
* * *
1208874 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
* * *
1208934 TCCATAGGTCCCGAAGAACCTAGGTAAACTGT
1 TCCAGAGGTCACAAAGAACCTAGGT-AACTGT
1208966 ACATATGTTC
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 15 0.19
60 59 0.74
61 6 0.08
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (60 bp):
TCCAGAGGTCACAAAGAACCTAGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1208983 original size:31 final size:31
Alignment explanation
Indices: 1208929--1209056 Score: 125
Period size: 31 Copynumber: 4.1 Consensus size: 31
1208919 GATCCTCGGT
* * *
1208929 AACTGTCCATAGGTCCCGA-AGAACCTAGGTA
1 AACTGTCCATATGTTCC-ATAGAACATAGGTA
* *
1208960 AACTGTACATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
* * * *
1208991 TACTGTCCATATGTCTCGAAAG-GCATAGGTAA
1 AACTGTCCATATGT-TCCATAGAACATAGGT-A
*
1209023 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTTCCATAGAACATAGGTA
1209054 AAC
1 AAC
1209057 CCTCGACTCT
Statistics
Matches: 77, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
31 52 0.68
32 25 0.32
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCATAGAACATAGGTA
Found at i:1209794 original size:22 final size:22
Alignment explanation
Indices: 1209750--1209791 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1209740 TAAATCAATT
*
1209750 TCATATAACTCCTATAATCTTC
1 TCATATAACTCCTATAACCTTC
*
1209772 TCATATAACTTC-ATAACCTT
1 TCATATAACTCCTATAACCTT
1209792 TCTTATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.33, C:0.26, G:0.00, T:0.40
Consensus pattern (22 bp):
TCATATAACTCCTATAACCTTC
Found at i:1210265 original size:21 final size:21
Alignment explanation
Indices: 1210241--1210285 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1210231 CCATGTTCGT
* * *
1210241 TTGAGGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1210262 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1210283 TTG
1 TTG
1210286 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.13, C:0.24, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1213203 original size:20 final size:21
Alignment explanation
Indices: 1213167--1213219 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1213157 TAAAATTCGT
*
1213167 GTTGCGAATTCGAAAATCG-A
1 GTTGCGAATTTGAAAATCGCA
* *
1213187 GTTGCGAATTTGGAAATTGCA
1 GTTGCGAATTTGAAAATCGCA
1213208 -TTGCGAATTTGA
1 GTTGCGAATTTGA
1213220 CTTCCGTGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.32
Consensus pattern (21 bp):
GTTGCGAATTTGAAAATCGCA
Done.