Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008082.1 Hibiscus syriacus cultivar Beakdansim tig00110584_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: 6025995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 28
Found at i:2733249 original size:7 final size:7
Alignment explanation
Indices: 2733236--2733268 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2733226 GTCAAAGGAA
2733236 GTCAACG
1 GTCAACG
*
2733243 ATCAACG
1 GTCAACG
2733250 GTC-ACG
1 GTCAACG
2733256 GTCAACG
1 GTCAACG
2733263 GTCAAC
1 GTCAAC
2733269 AGTCGGGTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.30, C:0.30, G:0.24, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:2733332 original size:19 final size:18
Alignment explanation
Indices: 2733293--2733361 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 18
2733283 AGTAGGGTCG
* *
2733293 GGTCAGACCGGTTAAATC
1 GGTCAGACCGGTCAAACC
*
2733311 GGTTCAGACCGATCAAACC
1 GG-TCAGACCGGTCAAACC
*
2733330 GGTCGAAACCGGTCAAACC
1 GGTC-AGACCGGTCAAACC
2733349 GGTCAGAACCGGT
1 GGTCAG-ACCGGT
2733362 TGAAAACTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
18 5 0.12
19 37 0.88
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:2733340 original size:10 final size:9
Alignment explanation
Indices: 2733293--2733381 Score: 70
Period size: 9 Copynumber: 9.3 Consensus size: 9
2733283 AGTAGGGTCG
*
2733293 GGTCAGACC
1 GGTCAAACC
* *
2733302 GGTTAAATC
1 GGTCAAACC
*
2733311 GGTTCAGACC
1 GG-TCAAACC
*
2733321 GATCAAACC
1 GGTCAAACC
2733330 GGTCGAAACC
1 GGTC-AAACC
2733340 GGTCAAACC
1 GGTCAAACC
2733349 GGTCAGAACC
1 GGTCA-AACC
* *
2733359 GGTTGAAAACT
1 GG-T-CAAACC
2733370 GGTCAAACC
1 GGTCAAACC
2733379 GGT
1 GGT
2733382 TTCCAACCCT
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
9 34 0.55
10 21 0.34
11 6 0.10
12 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.27, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2733380 original size:20 final size:21
Alignment explanation
Indices: 2733344--2733382 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2733334 GAAACCGGTC
2733344 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
2733365 AAACTGGTCA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
2733383 TCCAACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:2734279 original size:22 final size:21
Alignment explanation
Indices: 2734251--2734295 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
2734241 TTGGTGCTGG
2734251 AAACAAGAT-AAGAAATAAGATA
1 AAACAAGATAAAG-AA-AAGATA
2734273 AAACAAGATAAAGAAAAGATA
1 AAACAAGATAAAGAAAAGATA
2734294 AA
1 AA
2734296 GGAATTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 8 0.36
22 11 0.50
23 3 0.14
ACGTcount: A:0.71, C:0.04, G:0.13, T:0.11
Consensus pattern (21 bp):
AAACAAGATAAAGAAAAGATA
Found at i:2735295 original size:163 final size:162
Alignment explanation
Indices: 2735006--2735331 Score: 593
Period size: 163 Copynumber: 2.0 Consensus size: 162
2734996 ATGTGATGGT
2735006 CTTTATGTGTTTAGTAGAGGTTTCTTCTTTTAGGAACTGATTTCTTGTAGTCTTGAAATCTTCTT
1 CTTTATGTGTTTAGTAGAGGTTTCTTCTTTTAGGAACTGATTTCTTGTAGTCTTGAAATCTTCTT
2735071 TTGCATACAAGTCTGTAATATGATGTTTAGGTTGAAATTCAACGTGGTGTCGACCACTGTTTGCT
66 TTGCATACAAGTCTGTAATATGATGTTTAGGTTGAAATTCAACGTGGTGTCGACCACTGTTTGCT
*
2735136 TTCTC-TGA-TTCTCCAGATATTTTCTCCATG
131 TTCTCATGATTTCTCCAGATAATTTCTCCATG
2735166 CTTTATGTGTTTTAGTAGAGGTTTCTTCTTTGTAGGAACTGATTTCTTGTAGTCTTGAAATCTTC
1 CTTTATGTG-TTTAGTAGAGGTTTCTTCTTT-TAGGAACTGATTTCTTGTAGTCTTGAAATCTTC
2735231 TTTTGCATACAAGTCTTGTAATATGATGTTTAGGTTGAAATTCAACGTGGTGTCGACCACTGTTT
64 TTTTGCATACAAGTC-TGTAATATGATGTTTAGGTTGAAATTCAACGTGGTGTCGACCACTGTTT
2735296 GCTTTCTCTATGATTTCTCCAGATAATTTCTCCATG
128 GCTTTCTC-ATGATTTCTCCAGATAATTTCTCCATG
2735332 GTTTTATTCG
Statistics
Matches: 159, Mismatches: 1, Indels: 6
0.96 0.01 0.04
Matches are distributed among these distances:
160 9 0.06
161 21 0.13
162 48 0.30
163 57 0.36
165 3 0.02
166 21 0.13
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (162 bp):
CTTTATGTGTTTAGTAGAGGTTTCTTCTTTTAGGAACTGATTTCTTGTAGTCTTGAAATCTTCTT
TTGCATACAAGTCTGTAATATGATGTTTAGGTTGAAATTCAACGTGGTGTCGACCACTGTTTGCT
TTCTCATGATTTCTCCAGATAATTTCTCCATG
Found at i:2738166 original size:19 final size:19
Alignment explanation
Indices: 2738144--2738185 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2738134 TTTTTTGAAA
2738144 TTTTGACTTTTTTAT-TTTT
1 TTTTGACTTTTTT-TGTTTT
*
2738163 TTTTGCCTTTTTTTGTTTT
1 TTTTGACTTTTTTTGTTTT
2738182 TTTT
1 TTTT
2738186 TTGAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.05, C:0.07, G:0.07, T:0.81
Consensus pattern (19 bp):
TTTTGACTTTTTTTGTTTT
Found at i:2739565 original size:26 final size:26
Alignment explanation
Indices: 2739531--2739582 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2739521 AATGACGTTC
2739531 AATGCGTGTCATAAATGA-GCGTCATA
1 AATGCGTGTCATAAAT-ACGCGTCATA
* *
2739557 AATGTGTGTCATAGATACGCGTCATA
1 AATGCGTGTCATAAATACGCGTCATA
2739583 TATTCATGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (26 bp):
AATGCGTGTCATAAATACGCGTCATA
Found at i:2742011 original size:4 final size:4
Alignment explanation
Indices: 2742004--2742054 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
2741994 TGAAAAAAAG
* *
2742004 AAAT AAAT --AT AAAA AAAT AAGT AAAT AAAAT AAAT AAAT AAAT AAAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT -AAAT
2742052 AAA
1 AAA
2742055 CAAAACGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 2 0.05
4 29 0.74
5 8 0.21
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2742011 original size:17 final size:16
Alignment explanation
Indices: 2741991--2742117 Score: 67
Period size: 17 Copynumber: 7.2 Consensus size: 16
2741981 AAAACAAACA
*
2741991 AAATGAAAAAAAGAAAT
1 AAAT-AAAAAAATAAAT
*
2742008 AAATATAAAAAAATAAGT
1 -AA-ATAAAAAAATAAAT
2742026 AAATAAAATAAATAAAT
1 AAATAAAA-AAATAAAT
* *
2742043 AAATAAAATAAACAAAACG
1 AAATAAAA-AAA-TAAA-T
*
2742062 AAACGAAACGAAAATAAA-
1 AAA-TAAA--AAAATAAAT
* *
2742080 AGAATAAAAAAATGAAG
1 A-AATAAAAAAATAAAT
2742097 ACAATAAAAAAATGAAAT
1 A-AATAAAAAAAT-AAAT
2742115 AAA
1 AAA
2742118 ACATAGGAAA
Statistics
Matches: 87, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
16 13 0.15
17 35 0.40
18 22 0.25
19 7 0.08
20 6 0.07
21 3 0.03
22 1 0.01
ACGTcount: A:0.74, C:0.04, G:0.08, T:0.14
Consensus pattern (16 bp):
AAATAAAAAAATAAAT
Found at i:2742035 original size:13 final size:13
Alignment explanation
Indices: 2742004--2742059 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
2741994 TGAAAAAAAG
*
2742004 AAATAAATATAAAA
1 AAATAAATA-AATA
*
2742018 AAATAAGTAAATA
1 AAATAAATAAATA
2742031 AAATAAATAAAT-
1 AAATAAATAAATA
*
2742043 AAATAAAATAAACA
1 AAAT-AAATAAATA
2742057 AAA
1 AAA
2742060 CGAAACGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
12 4 0.11
13 21 0.58
14 11 0.31
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (13 bp):
AAATAAATAAATA
Found at i:2743499 original size:18 final size:20
Alignment explanation
Indices: 2743447--2743520 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 20
2743437 ATGTAAATAA
*
2743447 ATAATAATAAATATAGATGAAT
1 ATAAT-ATAAATATAGAT-TAT
* *
2743469 ATATTATGTAATAT-GATT-T
1 ATAATAT-AAATATAGATTAT
*
2743488 ATAATATAAATATATATTAT
1 ATAATATAAATATAGATTAT
2743508 ATAATAT-AATATA
1 ATAATATAAATATA
2743521 ATAACATTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
18 5 0.12
19 16 0.37
20 8 0.19
21 5 0.12
22 9 0.21
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
ATAATATAAATATAGATTAT
Found at i:2748899 original size:22 final size:23
Alignment explanation
Indices: 2748867--2748921 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
2748857 GTAAAGGGCA
* *
2748867 TGGACGTGGTGGAAGTCGTGGT-
1 TGGACGAGGTGGAAGTCGCGGTC
2748889 TGGACGAGGTGGAAGTCGCGGTC
1 TGGACGAGGTGGAAGTCGCGGTC
2748912 GTGGACGAGG
1 -TGGACGAGG
2748922 CAGGAATTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.69
24 9 0.31
ACGTcount: A:0.16, C:0.13, G:0.51, T:0.20
Consensus pattern (23 bp):
TGGACGAGGTGGAAGTCGCGGTC
Found at i:2755595 original size:14 final size:13
Alignment explanation
Indices: 2755558--2755591 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2755548 TCATCTCCAC
* *
2755558 TTTTATTTCTTTA
1 TTTTCTTTCATTA
2755571 TTTTCTTTCATTA
1 TTTTCTTTCATTA
2755584 TTTTCTTT
1 TTTTCTTT
2755592 TCATAATGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTTCATTA
Found at i:2756165 original size:9 final size:9
Alignment explanation
Indices: 2756151--2756211 Score: 56
Period size: 9 Copynumber: 6.7 Consensus size: 9
2756141 ATTCTTCTAC
2756151 TTTATTTAT
1 TTTATTTAT
2756160 TTTATTTAT
1 TTTATTTAT
*
2756169 TTTTTCATTAT
1 TTTAT--TTAT
2756180 TTTCATTTA-
1 TTT-ATTTAT
2756189 -TTATTTAGT
1 TTTATTTA-T
2756198 TTTA-TTAT
1 TTTATTTAT
2756206 TTTATT
1 TTTATT
2756212 ACCTTCATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
7 5 0.12
8 7 0.16
9 17 0.40
10 6 0.14
11 7 0.16
12 1 0.02
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTATTTAT
Found at i:2756169 original size:13 final size:11
Alignment explanation
Indices: 2756152--2756208 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 11
2756142 TTCTTCTACT
2756152 TTATTTATTTTA
1 TTATTT-TTTTA
*
2756164 TTTATTTTTTCA
1 -TTATTTTTTTA
2756176 TTATTTTCATTTA
1 TTATTTT--TTTA
2756189 TTATTTAGTTTTA
1 TTATTT--TTTTA
2756202 TTATTTT
1 TTATTTT
2756209 ATTACCTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 8 0.21
12 4 0.11
13 25 0.66
15 1 0.03
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (11 bp):
TTATTTTTTTA
Found at i:2758023 original size:29 final size:28
Alignment explanation
Indices: 2757970--2758026 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
2757960 CTAGCAACTC
*
2757970 AAAAAATAATATATTAATATTATATTTT
1 AAAAAATAATATATTAATATAATATTTT
*
2757998 AAAAAATAA-ATTATTAGTAATAATATTTT
1 AAAAAATAATA-TATTAAT-ATAATATTTT
2758027 TGTGTTGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 1 0.04
28 15 0.60
29 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
AAAAAATAATATATTAATATAATATTTT
Found at i:2758676 original size:15 final size:15
Alignment explanation
Indices: 2758658--2758687 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2758648 TTTTAAGATA
*
2758658 TATTTTTATTTTATT
1 TATTTTTATTCTATT
2758673 TATTTTTATTCTATT
1 TATTTTTATTCTATT
2758688 GAATAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTTTATTCTATT
Found at i:2759269 original size:28 final size:28
Alignment explanation
Indices: 2759228--2759300 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
2759218 AACTAAAAAT
* *
2759228 TTATGAAATTATAAAAATTATGGGTCCT-AA
1 TTAT-AAA-TATAAAAATTAGGGGT-ATGAA
*
2759258 TTATAAATATAAAAAATAGGGGTATGAA
1 TTATAAATATAAAAATTAGGGGTATGAA
2759286 TTATAAATA-AAAAAT
1 TTATAAATATAAAAAT
2759301 GGGGGGGGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
27 6 0.16
28 25 0.66
29 3 0.08
30 4 0.11
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (28 bp):
TTATAAATATAAAAATTAGGGGTATGAA
Found at i:2762084 original size:30 final size:29
Alignment explanation
Indices: 2762040--2762097 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
2762030 ATTTTCAAAT
* *
2762040 TATTATATATTTTATATATTTTTTATTTTTG
1 TATTATATAATTTATA-ATTTATT-TTTTTG
2762071 TATT-TATAATTTATAATTTATTTTTTT
1 TATTATATAATTTATAATTTATTTTTTT
2762098 CTTCCTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.20
29 6 0.24
30 10 0.40
31 4 0.16
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.71
Consensus pattern (29 bp):
TATTATATAATTTATAATTTATTTTTTTG
Found at i:2762136 original size:26 final size:27
Alignment explanation
Indices: 2762094--2762155 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
2762084 TAATTTATTT
*
2762094 TTTTCTTCCTTAAAATTGTATAAATTCA
1 TTTTCTT-CTTAAAATTGTAGAAATTCA
* *
2762122 TTTTCTT-TTAAAATTTTAGAAATTCG
1 TTTTCTTCTTAAAATTGTAGAAATTCA
2762148 TTTGTCTT
1 TTT-TCTT
2762156 AATATGATCC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 19 0.63
27 4 0.13
28 7 0.23
ACGTcount: A:0.27, C:0.11, G:0.06, T:0.55
Consensus pattern (27 bp):
TTTTCTTCTTAAAATTGTAGAAATTCA
Found at i:2762388 original size:32 final size:32
Alignment explanation
Indices: 2762347--2762418 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
2762337 AGAGTGAATA
2762347 CAAATTTATACCCACAGCAGCTGAAATTTATT
1 CAAATTTATACCCACAGCAGCTGAAATTTATT
*
2762379 CAAATTTATACCCACTGCAGCTGAAATTTATT
1 CAAATTTATACCCACAGCAGCTGAAATTTATT
2762411 CAAATTTA
1 CAAATTTA
2762419 CACCTTAATC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (32 bp):
CAAATTTATACCCACAGCAGCTGAAATTTATT
Found at i:2763150 original size:31 final size:31
Alignment explanation
Indices: 2763082--2763169 Score: 124
Period size: 31 Copynumber: 2.9 Consensus size: 31
2763072 CTTCCTGGAT
* *
2763082 TTTAGATAAAATATTAATTTAA-CCATAAAA
1 TTTAAATAAAATATTAATTTAACCCTTAAAA
* *
2763112 TTTAAATAAAATAATAATTTAACCCTTAAAC
1 TTTAAATAAAATATTAATTTAACCCTTAAAA
*
2763143 TTTAAATAAAATATTAATTTGACCCTT
1 TTTAAATAAAATATTAATTTAACCCTT
2763170 GAATATGTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 20 0.39
31 31 0.61
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (31 bp):
TTTAAATAAAATATTAATTTAACCCTTAAAA
Found at i:2764017 original size:14 final size:13
Alignment explanation
Indices: 2763998--2764056 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 13
2763988 TTCTTCGATA
2763998 TTAAAAATAAATAT
1 TTAAAAAT-AATAT
2764012 TTAAAAATAATAT
1 TTAAAAATAATAT
**
2764025 TT-ATTAT-ATAT
1 TTAAAAATAATAT
2764036 TT-AAAA-AATAT
1 TTAAAAATAATAT
*
2764047 TTAACAATAA
1 TTAAAAATAA
2764057 AAATACAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 14 0.38
12 6 0.16
13 9 0.24
14 8 0.22
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAAAATAATAT
Found at i:2764029 original size:17 final size:14
Alignment explanation
Indices: 2763998--2764027 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2763988 TTCTTCGATA
2763998 TTAAAAATAAATAT
1 TTAAAAATAAATAT
2764012 TTAAAAAT-AATAT
1 TTAAAAATAAATAT
2764025 TTA
1 TTA
2764028 TTATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TTAAAAATAAATAT
Found at i:2765482 original size:3 final size:3
Alignment explanation
Indices: 2765474--2765553 Score: 142
Period size: 3 Copynumber: 26.7 Consensus size: 3
2765464 TATTATAAAT
*
2765474 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2765522 TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2765554 TGGATAAAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2766021 original size:114 final size:114
Alignment explanation
Indices: 2765800--2766320 Score: 961
Period size: 114 Copynumber: 4.5 Consensus size: 114
2765790 GCTCTTGATG
2765800 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-T
2765865 TCCTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
62 T-CTCTGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
2765919 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
2765984 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
2766033 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* *
2766098 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAACATGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
2766147 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
*
2766212 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAACAGGTTGAACA
66 TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
*
2766261 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
2766321 CTACCTTGCA
Statistics
Matches: 398, Mismatches: 4, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
114 336 0.84
115 2 0.01
116 21 0.05
119 39 0.10
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (114 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGAATGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACA
Found at i:2767079 original size:50 final size:50
Alignment explanation
Indices: 2767006--2767146 Score: 273
Period size: 50 Copynumber: 2.8 Consensus size: 50
2766996 CTTACCAAAA
*
2767006 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
2767056 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
2767106 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
2767147 GGCAAATTCA
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 90 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (50 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
Found at i:2767253 original size:50 final size:50
Alignment explanation
Indices: 2767189--2767329 Score: 273
Period size: 50 Copynumber: 2.8 Consensus size: 50
2767179 TCTGTTAAAC
2767189 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
*
2767239 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
2767289 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
2767330 GGCAAATTCA
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 90 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (50 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
Found at i:2767278 original size:183 final size:183
Alignment explanation
Indices: 2767006--2767462 Score: 887
Period size: 183 Copynumber: 2.5 Consensus size: 183
2766996 CTTACCAAAA
*
2767006 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
2767071 AAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAG
66 AAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAG
2767136 AAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTAAAC
131 AAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTAAAC
2767189 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
*
2767254 AAAGAACACTTCCAGAAGATGCTATTTTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAG
66 AAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAG
*
2767319 AAGATGCTATTGGCAAATTCATCTTCTAAATTCATTGATTGGTTCTGTTAAAC
131 AAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTAAAC
2767372 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
2767437 AAAGAACACTTCCAGAAGATGCTATT
66 AAAGAACACTTCCAGAAGATGCTATT
2767463 GGCAAATTCA
Statistics
Matches: 271, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
183 271 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (183 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAG
AAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTAAAC
Found at i:2768599 original size:1 final size:1
Alignment explanation
Indices: 2768588--2768659 Score: 90
Period size: 1 Copynumber: 72.0 Consensus size: 1
2768578 TTGACCCCTC
* * * * * *
2768588 TTTTTTCTTTTTTTTTTTTTTTTTTTTCTTTTCTTTTTTTTTTTCTTTTTCTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2768653 TTTTTTT
1 TTTTTTT
2768660 CTTCAAGCAT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (1 bp):
T
Found at i:2768617 original size:28 final size:30
Alignment explanation
Indices: 2768586--2768659 Score: 113
Period size: 26 Copynumber: 2.6 Consensus size: 30
2768576 CCTTGACCCC
2768586 TCTTTTTTCTTTTTTTTTTT-TTTTT-TTT
1 TCTTTTTTCTTTTTTTTTTTCTTTTTCTTT
2768614 TC--TTTTCTTTTTTTTTTTCTTTTTCTTT
1 TCTTTTTTCTTTTTTTTTTTCTTTTTCTTT
2768642 TCTTTTTT-TTTTTTTTTT
1 TCTTTTTTCTTTTTTTTTT
2768660 CTTCAAGCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
26 16 0.38
27 5 0.12
28 7 0.17
29 10 0.24
30 4 0.10
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (30 bp):
TCTTTTTTCTTTTTTTTTTTCTTTTTCTTT
Found at i:2768624 original size:23 final size:23
Alignment explanation
Indices: 2768588--2768659 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
2768578 TTGACCCCTC
2768588 TTTTTTC-TTT-TTTTTTTTTTT
1 TTTTTTCTTTTCTTTTTTTTTTT
2768609 TTTTTTCTTTTCTTTTTTTTTTT
1 TTTTTTCTTTTCTTTTTTTTTTT
*
2768632 CTTTTTCTTTTCTTTTTTTTTTT
1 TTTTTTCTTTTCTTTTTTTTTTT
2768655 TTTTT
1 TTTTT
2768660 CTTCAAGCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.15
22 3 0.06
23 37 0.79
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (23 bp):
TTTTTTCTTTTCTTTTTTTTTTT
Found at i:2768660 original size:28 final size:28
Alignment explanation
Indices: 2768586--2768662 Score: 120
Period size: 28 Copynumber: 2.8 Consensus size: 28
2768576 CCTTGACCCC
*
2768586 TCTTTTTTCTTTTTTTTTT-TTTTTTTTT
1 TCTTTTTT-TTTTTTTTTTCTTTTTCTTT
*
2768614 TCTTTTCTTTTTTTTTTTCTTTTTCTTT
1 TCTTTTTTTTTTTTTTTTCTTTTTCTTT
2768642 TCTTTTTTTTTTTTTTTTCTT
1 TCTTTTTTTTTTTTTTTTCTT
2768663 CAAGCATAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 10 0.22
28 35 0.78
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (28 bp):
TCTTTTTTTTTTTTTTTTCTTTTTCTTT
Found at i:2779948 original size:14 final size:13
Alignment explanation
Indices: 2779929--2780027 Score: 57
Period size: 13 Copynumber: 7.9 Consensus size: 13
2779919 TTCTTCGATA
2779929 TTAAAAATAAATAT
1 TTAAAAAT-AATAT
2779943 TTAAAAATAATAT
1 TTAAAAATAATAT
**
2779956 TT-ATTAT-ATAT
1 TTAAAAATAATAT
2779967 TT-AAAA-AATAT
1 TTAAAAATAATAT
* *
2779978 TTAACAATAA-AA
1 TTAAAAATAATAT
* * * *
2779990 ATACAAATACTAC
1 TTAAAAATAATAT
*
2780003 TAAAATAAT-ATAT
1 TTAAA-AATAATAT
2780016 TTAAAAATAATA
1 TTAAAAATAATA
2780028 AGATAAATGA
Statistics
Matches: 62, Mismatches: 17, Indels: 13
0.67 0.18 0.14
Matches are distributed among these distances:
11 14 0.23
12 16 0.26
13 21 0.34
14 11 0.18
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAAATAATAT
Found at i:2781421 original size:3 final size:3
Alignment explanation
Indices: 2781413--2781498 Score: 154
Period size: 3 Copynumber: 28.7 Consensus size: 3
2781403 TAATATAAAT
*
2781413 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2781461 TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2781499 TGGATAAAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2795812 original size:17 final size:17
Alignment explanation
Indices: 2795792--2795827 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2795782 CAATCAACAG
*
2795792 GTCGGTTCAGTCAACGA
1 GTCGGGTCAGTCAACGA
*
2795809 GTCGGGTCAGTCAATGA
1 GTCGGGTCAGTCAACGA
2795826 GT
1 GT
2795828 TAGGTCAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.25
Consensus pattern (17 bp):
GTCGGGTCAGTCAACGA
Found at i:2795833 original size:17 final size:17
Alignment explanation
Indices: 2795798--2795841 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2795788 ACAGGTCGGT
* *
2795798 TCAGTCAACGAGTCGGG
1 TCAGTCAATGAGTCAGG
*
2795815 TCAGTCAATGAGTTAGG
1 TCAGTCAATGAGTCAGG
*
2795832 TCAATCAATG
1 TCAGTCAATG
2795842 GGTCTAGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (17 bp):
TCAGTCAATGAGTCAGG
Found at i:2800804 original size:9 final size:9
Alignment explanation
Indices: 2800790--2800819 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
2800780 GAATTTATTA
2800790 AAAGTTTTC
1 AAAGTTTTC
2800799 AAAGTTTTC
1 AAAGTTTTC
*
2800808 AAAATTTTC
1 AAAGTTTTC
2800817 AAA
1 AAA
2800820 AATAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (9 bp):
AAAGTTTTC
Found at i:2805705 original size:3 final size:3
Alignment explanation
Indices: 2805697--2805745 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
2805687 ATGCACAAAT
**
2805697 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2805745 T
1 T
2805746 GGTGTCGGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2814207 original size:3 final size:3
Alignment explanation
Indices: 2814199--2814223 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2814189 AAACAAAATT
2814199 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
2814224 GGGACAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2814592 original size:133 final size:134
Alignment explanation
Indices: 2814345--2815232 Score: 916
Period size: 134 Copynumber: 6.7 Consensus size: 134
2814335 GGAATATGAT
* * * * * * *
2814345 GAGGGATTTATTCCGCTTCTTCTTGGGGGAAAATCATATCTGGGGGCGTTGATTCATTCCACTAT
1 GAGGGATCTGTTCCACTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTGT
** * ** ** *
2814410 TGCTCAGGGAAGATTGAATCGAGCCAGACTTGTTCCTTTGTTACTCAGGGAATGTCAAATCTTGA
66 CACTCAAGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
2814475 GAA-A
131 -AAGA
* * * *
2814479 GAGGGATCTGTTCCGCTTCTTCTTGAGGGAAAATCAGATCT-GGGACGTTAATTCATTTCATTGT
1 GAGGGATCTGTTCCACTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTGT
*** ** * *
2814543 TGTTCTGGGAAGATTGAATTGAGGAAGACTTGTTCCACTGTTACACAGGGAATATCAAATCTTGA
66 CACTCAAGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
2814608 AAGA
131 AAGA
* * * *
2814612 GAGGGA-CATGTTCCACTTCTTCTTGAGGGAAAATCAGATATGGGGATGTTAATTCATTTCACTG
1 GAGGGATC-TGTTCCACTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTG
* * * * *
2814676 TCACTGATGAAAGATTGAATCGAGGAAGACTTGTTCCACTATTACTTAGGGAATATCAAATCTTG
65 TCACTCAAGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTG
*
2814741 AAAAA
130 AAAGA
* * * * ** * * *
2814746 GAGGGTTATGTTCCACTTATTCTTGAGGGAAAATCAAATCTCAGGACATTGATTCATTCCATTAT
1 GAGGGATCTGTTCCACTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTGT
* ** * *
2814811 CACTCAATGAAGATTGAATTAAGGCAGACTTGTTCCACTTTTACTCAGGGAATATCAAATCTTGA
66 CACTCAAGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
*
2814876 AAAA
131 AAGA
* * * *
2814880 GAGGGATATGTTCTC-CTTCTTCTTGAGGGAAAATCAAATATGGGGGATGTTGATTCATTCCACT
1 GAGGGATCTGTTC-CACTTCTTCTTGAGGGAAAATCAGATCT-GGGGACGTTGATTCATTCCACT
** * *
2814944 GTCACTCAAGGAAGATTGAATCG-GGTTCGACTTGTTTCACTATTACTCAGGGAATATCAAATCT
64 GTCACTCAAGGAAGATTGAATCGAGG-AAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCT
2815008 TGAAAGA
128 TGAAAGA
* * * ** * *
2815015 GATGGATTTGTT-C-C-GCTTCTTGAGGGAAAATCAGATCTGGGGATATTGATTCATT-TATTGT
1 GAGGGATCTGTTCCACTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTGT
* **** * * ** *
2815076 CACTCAAAGAAGATTGAATCGAATTCGACTTGTTCCATTGTTACTTAAAGAATATCAAATCTTGG
66 CACTCAAGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
*
2815141 AATA
131 AAGA
* * *
2815145 -AGTGGATCTGTTCCATTTTTTCTTGAGGGAAAATCAGATATGGGGACGTTGATTCATTCCACTG
1 GAG-GGATCTGTTCCACTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTG
2815209 TCACTC-AGGAAAGATTGAATCGAG
65 TCACTCAAGG-AAGATTGAATCGAG
2815233 TTCATTCGCT
Statistics
Matches: 636, Mismatches: 104, Indels: 28
0.83 0.14 0.04
Matches are distributed among these distances:
129 1 0.00
130 69 0.11
131 17 0.03
132 24 0.04
133 152 0.24
134 286 0.45
135 87 0.14
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (134 bp):
GAGGGATCTGTTCCACTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTGT
CACTCAAGGAAGATTGAATCGAGGAAGACTTGTTCCACTGTTACTCAGGGAATATCAAATCTTGA
AAGA
Found at i:2824246 original size:28 final size:28
Alignment explanation
Indices: 2824179--2824247 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
2824169 ACAAATAATA
**
2824179 AAAATAAATAAAACATGGGGACTAAATT
1 AAAATAAATAAAACACAGGGACTAAATT
* *
2824207 -AAGTAAATTAAAACTACATGGAC-AAATT
1 AAAATAAA-TAAAAC-ACAGGGACTAAATT
2824235 AAAATAAATAAAA
1 AAAATAAATAAAA
2824248 ATTTGAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
27 6 0.18
28 16 0.48
29 11 0.33
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.22
Consensus pattern (28 bp):
AAAATAAATAAAACACAGGGACTAAATT
Found at i:2826743 original size:2 final size:2
Alignment explanation
Indices: 2826738--2826777 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2826728 ATAATGTTAA
2826738 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
2826778 TCGTAAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2829712 original size:40 final size:40
Alignment explanation
Indices: 2829660--2829741 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
2829650 ATATTTTATA
* *
2829660 AAATATTGATAAAATAAGTTAGAGTGATTAAAATATAAAT
1 AAATATTAATAAAATAAATTAGAGTGATTAAAATATAAAT
2829700 AAATATTAATAAAATAAATTAGAGTGATTAAAATATAAAT
1 AAATATTAATAAAATAAATTAGAGTGATTAAAATATAAAT
2829740 AA
1 AA
2829742 TTTAAAAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.32
Consensus pattern (40 bp):
AAATATTAATAAAATAAATTAGAGTGATTAAAATATAAAT
Found at i:2829731 original size:19 final size:19
Alignment explanation
Indices: 2829669--2829734 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
2829659 AAAATATTGA
*
2829669 TAAAATAAGTTAGAGTGAT
1 TAAAATAAATTAGAGTGAT
* * * * *
2829688 TAAAATATAAATAAATATTAA
1 TAAAATA-AATTAGA-GTGAT
2829709 TAAAATAAATTAGAGTGAT
1 TAAAATAAATTAGAGTGAT
2829728 TAAAATA
1 TAAAATA
2829735 TAAATAATTT
Statistics
Matches: 34, Mismatches: 11, Indels: 4
0.69 0.22 0.08
Matches are distributed among these distances:
19 16 0.47
20 9 0.26
21 9 0.26
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.32
Consensus pattern (19 bp):
TAAAATAAATTAGAGTGAT
Found at i:2829739 original size:21 final size:21
Alignment explanation
Indices: 2829673--2829739 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
2829663 TATTGATAAA
*
2829673 ATAAGTTAGAGTGATTAAAAT
1 ATAAATTAGAGTGATTAAAAT
* *
2829694 ATAAA-TA-AAT-ATTAATAAA
1 ATAAATTAGAGTGATTAA-AAT
2829713 ATAAATTAGAGTGATTAAAAT
1 ATAAATTAGAGTGATTAAAAT
2829734 ATAAAT
1 ATAAAT
2829740 AATTTAAAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
18 5 0.14
19 9 0.24
20 4 0.11
21 14 0.38
22 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (21 bp):
ATAAATTAGAGTGATTAAAAT
Found at i:2835720 original size:20 final size:20
Alignment explanation
Indices: 2835695--2835733 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2835685 TTAAAATCAC
2835695 GATGTTACACATCGTTTCAT
1 GATGTTACACATCGTTTCAT
2835715 GATGTTACACATCGTTTCA
1 GATGTTACACATCGTTTCA
2835734 CGACGGGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (20 bp):
GATGTTACACATCGTTTCAT
Found at i:2837634 original size:60 final size:61
Alignment explanation
Indices: 2837560--2837688 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 61
2837550 ATAGTTTGGT
* * *
2837560 GACCATATTGTAACTTTTAATGGTCAAGGGACTCAACAAAATAATACCCTA-TAGTCAAGG
1 GACCATTTTATAACTTTTAATAGTCAAGGGACTCAACAAAATAATACCCTATTAGTCAAGG
* ** * * * * *
2837620 GAGCATTTTATAACTTTTGGTAGTCGATGGATTCAACAAAGTAATACCCTATTAGTCGAGG
1 GACCATTTTATAACTTTTAATAGTCAAGGGACTCAACAAAATAATACCCTATTAGTCAAGG
2837681 GACCATTT
1 GACCATTT
2837689 GTGTATTTCA
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
60 41 0.73
61 15 0.27
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (61 bp):
GACCATTTTATAACTTTTAATAGTCAAGGGACTCAACAAAATAATACCCTATTAGTCAAGG
Found at i:2838596 original size:24 final size:23
Alignment explanation
Indices: 2838565--2838626 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
2838555 ATATACAATA
* *
2838565 AATAATATTATTTATTAACAAAAT
1 AATAATATTATTTA-AAACAAAAG
*
2838589 AATAATATTACTTTAAAACAATAG
1 AATAATATTA-TTTAAAACAAAAG
2838613 AATAAT-TTATTTAA
1 AATAATATTATTTAA
2838627 TATTATTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.15
23 3 0.09
24 22 0.65
25 4 0.12
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (23 bp):
AATAATATTATTTAAAACAAAAG
Found at i:2840852 original size:16 final size:17
Alignment explanation
Indices: 2840833--2840886 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
2840823 ATTTTTTTTA
*
2840833 GTTTTTATTCTA-TATT
1 GTTTTTATACTATTATT
*
2840849 GTTTTT-TACTATTTTT
1 GTTTTTATACTATTATT
2840865 GTTTTTAT-C-ATTATTT
1 GTTTTTATACTATTA-TT
2840881 GTTTTT
1 GTTTTT
2840887 TCATTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 7 0.22
16 24 0.75
17 1 0.03
ACGTcount: A:0.15, C:0.06, G:0.07, T:0.72
Consensus pattern (17 bp):
GTTTTTATACTATTATT
Found at i:2840871 original size:15 final size:16
Alignment explanation
Indices: 2840862--2840895 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
2840852 TTTTACTATT
2840862 TTTGTTTTTATCATTA
1 TTTGTTTTTATCATTA
2840878 TTTGTTTTT-TCATTA
1 TTTGTTTTTATCATTA
2840893 TTT
1 TTT
2840896 TATTTAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.15, C:0.06, G:0.06, T:0.74
Consensus pattern (16 bp):
TTTGTTTTTATCATTA
Found at i:2843464 original size:20 final size:20
Alignment explanation
Indices: 2843441--2843482 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2843431 CATTTCACAT
* * *
2843441 TTTGCATTCTCATTTTTGCA
1 TTTGCATGCGCATCTTTGCA
2843461 TTTGCATGCGCATCTTTGCA
1 TTTGCATGCGCATCTTTGCA
2843481 TT
1 TT
2843483 AACACATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (20 bp):
TTTGCATGCGCATCTTTGCA
Found at i:2845707 original size:36 final size:36
Alignment explanation
Indices: 2845612--2845735 Score: 117
Period size: 36 Copynumber: 3.3 Consensus size: 36
2845602 CAACATTTCC
* *
2845612 AAACAAATTTTGTCTCGATTGAGACAG--TCCCATCG
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCCC-TTG
* *
2845647 AAACAAAAGATTTTATCTCGCTTGAGATAGTTTCCCTTG
1 AAAC--AA-ATTTTGTCTCGCTTGAGACAGTTTCCCTTG
* * *
2845686 AAACAAATTTTGTCTCCCTTGAGGCAGTTTCTCTTG
1 AAACAAATTTTGTCTCGCTTGAGACAGTTTCCCTTG
2845722 AAACATAATCTTTG
1 AAACA-AAT-TTTG
2845736 AAAACGTTTC
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
35 4 0.05
36 30 0.41
37 7 0.10
38 22 0.30
39 6 0.08
40 4 0.05
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (36 bp):
AAACAAATTTTGTCTCGCTTGAGACAGTTTCCCTTG
Found at i:2845788 original size:36 final size:36
Alignment explanation
Indices: 2845741--2846219 Score: 393
Period size: 37 Copynumber: 13.6 Consensus size: 36
2845731 CTTTGAAAAC
2845741 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * * *
2845777 GTTTCCCTTGAAA-AAA-GTTGTCTCCCATGAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
2845811 GTTTCACTTGAAACAAATTTAGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
2845847 ATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGATA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* * *
2845884 GTTTCCCTTGAAACAAAGTTTTATCTCCCTTGAAACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
*
2845921 GTTTCCCTTGAAACAAAGTTTTGTCTCCCTTGAG-CTA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGAC-A
* * *
2845958 GTTTCCCTTGAAATAAATTTCGTCTCTTTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* ** * *
2845994 G-TTCTCTTGAAACATAA-----AATAT-TTGA-ATA
1 GTTTCCCTTGAAACA-AATTTTGTCTCTCTTGAGACA
*
2846023 TGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA
1 -GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* ** **
2846060 GTTTCTCTTGAAACACAA-----AATCT-TTGA-ATTT
1 GTTTCCCTTGAAACA-AATTTTGTCTCTCTTGAGA-CA
*
2846091 GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
2846127 ATTTCTCTTGAAACAAAGTTTTGTCTCTCTAGAGACA
1 GTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
* ** * * *
2846164 GTTTCTCTCAAAACAAATTTTATCTCACTTGAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
2846200 GTCTT-TCTTTAAACAAATTT
1 GT-TTCCCTTGAAACAAATTT
2846220 CTTTTTATTC
Statistics
Matches: 358, Mismatches: 59, Indels: 52
0.76 0.13 0.11
Matches are distributed among these distances:
29 2 0.01
30 10 0.03
31 32 0.09
32 3 0.01
34 26 0.07
35 22 0.06
36 126 0.35
37 137 0.38
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:2845841 original size:21 final size:20
Alignment explanation
Indices: 2845817--2845879 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 20
2845807 GATAGTTTCA
2845817 CTTGAAACAAATTTAGTCTCT
1 CTTGAAACAAATTT-GTCTCT
*
2845838 CTTGAGAC-AA-TT-TC-C-
1 CTTGAAACAAATTTGTCTCT
2845853 CTTGAAACAAAGTTTTGTCTCT
1 CTTGAAACAAA--TTTGTCTCT
2845875 CTTGA
1 CTTGA
2845880 GATAGTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
15 7 0.21
16 3 0.09
17 2 0.06
19 4 0.12
20 4 0.12
21 8 0.24
22 5 0.15
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (20 bp):
CTTGAAACAAATTTGTCTCT
Found at i:2845915 original size:22 final size:21
Alignment explanation
Indices: 2845887--2845953 Score: 74
Period size: 22 Copynumber: 3.4 Consensus size: 21
2845877 TGAGATAGTT
2845887 TCCCTTGAAACAAAGTTTTATC
1 TCCCTTGAAACAAAGTTTT-TC
2845909 TCCCTTGAAAC--AG---TT-
1 TCCCTTGAAACAAAGTTTTTC
2845924 TCCCTTGAAACAAAGTTTTGTC
1 TCCCTTGAAACAAAGTTTT-TC
2845946 TCCCTTGA
1 TCCCTTGA
2845954 GCTAGTTTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
15 11 0.29
16 1 0.03
17 3 0.08
20 3 0.08
21 1 0.03
22 19 0.50
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (21 bp):
TCCCTTGAAACAAAGTTTTTC
Found at i:2846618 original size:91 final size:91
Alignment explanation
Indices: 2846429--2846738 Score: 491
Period size: 91 Copynumber: 3.4 Consensus size: 91
2846419 AAGATAAACC
*
2846429 GATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGA--GAG-AGAAGTTCA
1 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
2846491 TAATGAGAAGAACTTGTTCAACCTTG
66 TAATGAGAAGAACTTGTTCAACCTTG
* *
2846517 GATCAACATTTCCAGTGGAGAGATCATAATGAGAAGAACTTATCCAACGAGGGAGAAGAAGTTCA
1 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
*
2846582 TAATGAGAAGAACTTGTTCAACGTTG
66 TAATGAGAAGAACTTGTTCAACCTTG
* * * * *
2846608 GTTCAACATTTCCATTGGAGAGTTCATAATGAGAATAACTCATCTAATGAGGGAGAAGAAGTTCA
1 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
*
2846673 TAATGAGAAGAACTTGCTCAACCTTG
66 TAATGAGAAGAACTTGTTCAACCTTG
* *
2846699 GATCAACATTTCGAGTGGAGAGTTCATAATGAGCAGAACT
1 GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACT
2846739 TGTTCGACCT
Statistics
Matches: 201, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
88 47 0.23
90 3 0.01
91 151 0.75
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.25
Consensus pattern (91 bp):
GATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTG
Found at i:2846749 original size:52 final size:52
Alignment explanation
Indices: 2846667--2846790 Score: 194
Period size: 52 Copynumber: 2.4 Consensus size: 52
2846657 AGGGAGAAGA
* *
2846667 AGTTCATAATGAGAAGAACTTGCTCAACCTTGGATCAACATTTCGAGTGGAG
1 AGTTCATAATGAGAAGAACTTGCTCAACCTTGGATCAACATTTCCAGTAGAG
* * * *
2846719 AGTTCATAATGAGCAGAACTTGTTCGACCTTGGCTCAACATTTCCAGTAGAG
1 AGTTCATAATGAGAAGAACTTGCTCAACCTTGGATCAACATTTCCAGTAGAG
2846771 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
2846791 CATCCAACAA
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (52 bp):
AGTTCATAATGAGAAGAACTTGCTCAACCTTGGATCAACATTTCCAGTAGAG
Found at i:2846758 original size:143 final size:143
Alignment explanation
Indices: 2846571--2846881 Score: 460
Period size: 143 Copynumber: 2.2 Consensus size: 143
2846561 CAACGAGGGA
* * * *
2846571 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACGTTGGTTCAACATTTCCATTGGAGAGTTCATA
1 GAAG-AGTTCATAATGAGAAGAACTTGTTCAACCTTGGCTCAACATTTCCAGTAGAGAGTTCATA
* * **
2846636 ATGAGAATAACTCATCTAATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGCTCAACCTTGGA
65 ATGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGCTCAACCTTGGA
*
2846701 TCAACATTTCGAGT
130 TCAACATTTCCAGT
* * *
2846715 GGAGAGTTCATAATGAGCAGAACTTGTTCGACCTTGGCTCAACATTTCCAGTAGAGAGTTCATAA
1 GAAGAGTTCATAATGAGAAGAACTTGTTCAACCTTGGCTCAACATTTCCAGTAGAGAGTTCATAA
* * *
2846780 TGAGAAGAACTCATCCAACAAGGGATAAGAAGTTTATAATGAGAAGAACTTGTTCAACCTTGGAT
66 TGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGCTCAACCTTGGAT
*
2846845 CTACATTTCCAGT
131 CAACATTTCCAGT
*
2846858 GAAGAGTCCATAATGAGAAGAACT
1 GAAGAGTTCATAATGAGAAGAACT
2846882 AGTCTAACGA
Statistics
Matches: 148, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
143 145 0.98
144 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (143 bp):
GAAGAGTTCATAATGAGAAGAACTTGTTCAACCTTGGCTCAACATTTCCAGTAGAGAGTTCATAA
TGAGAAGAACTCATCCAACAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGCTCAACCTTGGAT
CAACATTTCCAGT
Found at i:2846879 original size:91 final size:91
Alignment explanation
Indices: 2846719--2846932 Score: 279
Period size: 91 Copynumber: 2.4 Consensus size: 91
2846709 TCGAGTGGAG
* * *
2846719 AGTTCATAATGAGCAGAACTTGTTCGACCTTGGCTCAACATTTCCAGTAGAGAGTTCATAATGAG
1 AGTTCATAATGAGAAGAACTTGTTCGACCTTGGATCAACATTTCCAGTAGAGAGTCCATAATGAG
*
2846784 AAGAACTCA-TCCAACAAGGGATAAGA
66 AAGAACT-AGTCCAACAAGGGAGAAGA
* * *
2846810 AGTTTATAATGAGAAGAACTTGTTCAACCTTGGATCTACATTTCCAGT-GAAGAGTCCATAATGA
1 AGTTCATAATGAGAAGAACTTGTTCGACCTTGGATCAACATTTCCAGTAG-AGAGTCCATAATGA
* * **
2846874 GAAGAACTAGTCTAACGAGGGAGGGGA
65 GAAGAACTAGTCCAACAAGGGAGAAGA
* *
2846901 AGTTCATGATGAGAATAACTTGTTCGACCTTG
1 AGTTCATAATGAGAAGAACTTGTTCGACCTTG
2846933 CACCGACATC
Statistics
Matches: 106, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
90 2 0.02
91 104 0.98
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (91 bp):
AGTTCATAATGAGAAGAACTTGTTCGACCTTGGATCAACATTTCCAGTAGAGAGTCCATAATGAG
AAGAACTAGTCCAACAAGGGAGAAGA
Found at i:2846896 original size:234 final size:234
Alignment explanation
Indices: 2846485--2846932 Score: 673
Period size: 234 Copynumber: 1.9 Consensus size: 234
2846475 ACGAGAGAGA
*
2846485 AGTTCATAATGAGAAGAACTTGTTCAACCTTGGATCAACATTTCCAGTGGAGAGATCATAATGAG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTGGATCAACATTTCCAGTAGAGAGATCATAATGAG
* * * *
2846550 AAGAACTTATCCAACGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACGTTGGTTCAAC
66 AAGAACTCATCCAACAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGATCAAC
* * * * *
2846615 ATTTCCATTGGAGAGTTCATAATGAGAATAACTCATCTAATGAGGGAGAAGAAGTTCATAATGAG
131 ATTTCCAGTGAAGAGTCCATAATGAGAAGAACTCATCTAACGAGGGAGAAGAAGTTCATAATGAG
2846680 AAGAACTTGCTCAACCTTGGATCAACATTTCGAGTGGAG
196 AAGAACTTGCTCAACCTTGGATCAACATTTCGAGTGGAG
* * * *
2846719 AGTTCATAATGAGCAGAACTTGTTCGACCTTGGCTCAACATTTCCAGTAGAGAGTTCATAATGAG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTGGATCAACATTTCCAGTAGAGAGATCATAATGAG
* * *
2846784 AAGAACTCATCCAACAAGGGATAAGAAGTTTATAATGAGAAGAACTTGTTCAACCTTGGATCTAC
66 AAGAACTCATCCAACAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGATCAAC
** *
2846849 ATTTCCAGTGAAGAGTCCATAATGAGAAGAACT-AGTCTAACGAGGGAGGGGAAGTTCATGATGA
131 ATTTCCAGTGAAGAGTCCATAATGAGAAGAACTCA-TCTAACGAGGGAGAAGAAGTTCATAATGA
* * *
2846913 GAATAACTTGTTCGACCTTG
195 GAAGAACTTGCTCAACCTTG
2846933 CACCGACATC
Statistics
Matches: 190, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
233 1 0.01
234 189 0.99
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (234 bp):
AGTTCATAATGAGAAGAACTTGTTCAACCTTGGATCAACATTTCCAGTAGAGAGATCATAATGAG
AAGAACTCATCCAACAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTGGATCAAC
ATTTCCAGTGAAGAGTCCATAATGAGAAGAACTCATCTAACGAGGGAGAAGAAGTTCATAATGAG
AAGAACTTGCTCAACCTTGGATCAACATTTCGAGTGGAG
Found at i:2847271 original size:88 final size:89
Alignment explanation
Indices: 2847170--2847374 Score: 297
Period size: 88 Copynumber: 2.3 Consensus size: 89
2847160 TGACTTCTCG
* * *
2847170 TTCGATTCAATCGCAGAAGGAGGTGGATCGACATTTTTATTTTGCTCAAATCCATTGTAGAAGTA
1 TTCGATTCAATCGCAGAAGGAGGTGGATCGACATTTTTATTTTACTCAAATCCATTGCAGAAGGA
*
2847235 GTTGGATCAACATCAA-ATTTTTT
66 GTTGGATCAACATCAATATTTTTC
* * *
2847258 TTCGACTCCATCGCAGAAAGAGGTGGATCGACATTTTTATTTTACTCAAATCCATTGCAGAAGGA
1 TTCGATTCAATCGCAGAAGGAGGTGGATCGACATTTTTATTTTACTCAAATCCATTGCAGAAGGA
*
2847323 GTTGGATCAGCATCAATATTTTTC
66 GTTGGATCAACATCAATATTTTTC
* * *
2847347 TT-GATTCTATCACAGAAGGAGGTCGATC
1 TTCGATTCAATCGCAGAAGGAGGTGGATC
2847375 AGCATCAACA
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
88 95 0.92
89 8 0.08
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (89 bp):
TTCGATTCAATCGCAGAAGGAGGTGGATCGACATTTTTATTTTACTCAAATCCATTGCAGAAGGA
GTTGGATCAACATCAATATTTTTC
Found at i:2847285 original size:44 final size:45
Alignment explanation
Indices: 2847170--2847423 Score: 149
Period size: 44 Copynumber: 5.8 Consensus size: 45
2847160 TGACTTCTCG
* * **** *
2847170 TTCGATTCAATCGCAGAAGGAGGTGGATCGACATTTTTATTTTGC
1 TTCGATTCCATCGCAGAAGGAGGTGGATCAACATCAACATTTTTC
* * * * * * *
2847215 -TCAAATCCATTGTAGAAGTAGTTGGATCAACATCAA-ATTTTTT
1 TTCGATTCCATCGCAGAAGGAGGTGGATCAACATCAACATTTTTC
* * * **** *
2847258 TTCGACTCCATCGCAGAAAGAGGTGGATCGACATTTTTATTTTAC
1 TTCGATTCCATCGCAGAAGGAGGTGGATCAACATCAACATTTTTC
* * * * * *
2847303 -TCAAATCCATTGCAGAAGGAGTTGGATCAGCATCAATATTTTTC
1 TTCGATTCCATCGCAGAAGGAGGTGGATCAACATCAACATTTTTC
* * * * * *
2847347 TT-GATTCTATCACAGAAGGAGGTCGATCAGCATCAACA-TCTCC
1 TTCGATTCCATCGCAGAAGGAGGTGGATCAACATCAACATTTTTC
* *
2847390 TTCGATTCCATCGCAGAATGAGGTGAATCAACAT
1 TTCGATTCCATCGCAGAAGGAGGTGGATCAACAT
2847424 TTTTATTTTG
Statistics
Matches: 152, Mismatches: 53, Indels: 9
0.71 0.25 0.04
Matches are distributed among these distances:
43 10 0.07
44 136 0.89
45 6 0.04
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (45 bp):
TTCGATTCCATCGCAGAAGGAGGTGGATCAACATCAACATTTTTC
Found at i:2848258 original size:19 final size:19
Alignment explanation
Indices: 2848174--2848246 Score: 110
Period size: 19 Copynumber: 3.8 Consensus size: 19
2848164 AAGAACCAAG
*
2848174 AGTGCATCGATGCATGGTC
1 AGTGCATCGATGCATGATC
*
2848193 AGTGCATTGATGCATGATC
1 AGTGCATCGATGCATGATC
*
2848212 AGTGCATCGATGCATGATT
1 AGTGCATCGATGCATGATC
*
2848231 AGTGCATCAATGCATG
1 AGTGCATCGATGCATG
2848247 GTTTGTGCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (19 bp):
AGTGCATCGATGCATGATC
Found at i:2848755 original size:13 final size:13
Alignment explanation
Indices: 2848739--2848772 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
2848729 TTGAAAATTA
2848739 CTCCCCCTATATT
1 CTCCCCCTATATT
2848752 CTCCCCCTATATT
1 CTCCCCCTATATT
2848765 CTCCCCCT
1 CTCCCCCT
2848773 TTTTGTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.12, C:0.53, G:0.00, T:0.35
Consensus pattern (13 bp):
CTCCCCCTATATT
Found at i:2851053 original size:23 final size:22
Alignment explanation
Indices: 2851021--2851087 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
2851011 ATAGTGTATT
2851021 GATGCACATTCAAGGAATGCATC
1 GATGCACATTCAAGG-ATGCATC
* *
2851044 GGTGCACATTCATA-G-TGTATC
1 GATGCACATTCA-AGGATGCATC
2851065 GATGCACATTCAAGGGATGCATC
1 GATGCACATTCAA-GGATGCATC
2851088 AGTACACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
20 1 0.03
21 16 0.44
22 1 0.03
23 17 0.47
24 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (22 bp):
GATGCACATTCAAGGATGCATC
Found at i:2851070 original size:21 final size:21
Alignment explanation
Indices: 2850993--2851076 Score: 82
Period size: 21 Copynumber: 4.0 Consensus size: 21
2850983 AAACCTGACG
* *
2850993 AGTGTATCGATGTAC-TGCAT
1 AGTGTATCGATGCACATTCAT
*
2851013 AGTGTATTGATGCACATTCA-
1 AGTGTATCGATGCACATTCAT
* *
2851033 AGGAATGCATCGGTGCACATTCAT
1 A-G--TGTATCGATGCACATTCAT
2851057 AGTGTATCGATGCACATTCA
1 AGTGTATCGATGCACATTCA
2851077 AGGGATGCAT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
20 14 0.27
21 20 0.39
23 16 0.31
24 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.31
Consensus pattern (21 bp):
AGTGTATCGATGCACATTCAT
Found at i:2851073 original size:44 final size:44
Alignment explanation
Indices: 2851010--2851113 Score: 156
Period size: 44 Copynumber: 2.4 Consensus size: 44
2851000 CGATGTACTG
* * *
2851010 CATAGTGTATTGATGCACATTCAAGGAATGCATCGGTGCACATT
1 CATAGTGTATCGATGCACATTCAAGGAATGCATCAGTACACATT
* *
2851054 CATAGTGTATCGATGCACATTCAAGGGATGCATCAGTACACTTT
1 CATAGTGTATCGATGCACATTCAAGGAATGCATCAGTACACATT
2851098 C-TAGTGTATCGATGCA
1 CATAGTGTATCGATGCA
2851114 TTTTGCACAA
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
43 15 0.27
44 40 0.73
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (44 bp):
CATAGTGTATCGATGCACATTCAAGGAATGCATCAGTACACATT
Found at i:2852655 original size:23 final size:23
Alignment explanation
Indices: 2852628--2852676 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2852618 TGGTGGTTGG
2852628 TTTAATGGATAT-TTAAACTTTAT
1 TTTAATGG-TATGTTAAACTTTAT
* *
2852651 TTTAATGGTATGTTTAAGTTTAT
1 TTTAATGGTATGTTAAACTTTAT
2852674 TTT
1 TTT
2852677 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATGTTAAACTTTAT
Found at i:2862855 original size:23 final size:23
Alignment explanation
Indices: 2862828--2862876 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2862818 TGGTGGTTGG
2862828 TTTAATGG-ATATTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
* *
2862851 TTTAATGGTATGTTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
2862874 TTT
1 TTT
2862877 GATTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:2867946 original size:131 final size:130
Alignment explanation
Indices: 2867712--2868081 Score: 483
Period size: 131 Copynumber: 2.8 Consensus size: 130
2867702 ATTAATATTG
* * *
2867712 AAAATAATGACATCTCTTCATTTCAATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAAGTCA
1 AAAATAGTGA-ATCTCTTCATTTAAATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
* * * * * *
2867777 TTTATTCTCGATT-AGAGATAATTAGATATCATCATTTTCTCTCGAATCAATATTTATTTTTAAG
65 TTTATTCTCAATTGA-AAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAG
2867841 AC
129 AC
* *
2867843 AAAATGGTGATATCTCTTCATTTGAATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
1 AAAATAGTGA-ATCTCTTCATTTAAATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
* * **
2867908 GTTATTCTCTATTGAAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAATT
65 TTTATTCTCAATTGAAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAGA
2867973 C
130 C
* * *
2867974 GAAATAGTGAATTCTCTTCATTTAAATCGGAGTAATAAATGACTAG-TTTAAGGCGTGAGAGGTC
1 AAAATAGTGAA-TCTCTTCATTTAAATTGGAGTAATAAATGACT-GCTTTAAGGCATGAGAGGTC
* * * *
2868038 ATTTATTATCAATTGGAAATAATTAGATCTTATTGTTTTCTCTC
64 ATTTATTCTCAATTGAAAATAATTAGATATTATCGTTTTCTCTC
2868082 TTGGAATTAT
Statistics
Matches: 211, Mismatches: 25, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
130 1 0.00
131 208 0.99
132 2 0.01
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (130 bp):
AAAATAGTGAATCTCTTCATTTAAATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
TTATTCTCAATTGAAAATAATTAGATATTATCGTTTTCTCTCGAATCAATATTGAATTTTAAGAC
Found at i:2873772 original size:29 final size:29
Alignment explanation
Indices: 2873737--2873818 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
2873727 AAACTAAATT
* *
2873737 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
2873766 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
2873795 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
2873819 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:2878540 original size:29 final size:29
Alignment explanation
Indices: 2878505--2878586 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
2878495 AAACTAAATT
* *
2878505 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
2878534 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
2878563 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
2878587 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:2881258 original size:40 final size:39
Alignment explanation
Indices: 2881156--2881410 Score: 163
Period size: 40 Copynumber: 6.3 Consensus size: 39
2881146 TTTTTTGAAT
* * * *
2881156 AAACGCCGGTAAATACTCATACTTTAGTGGTGTTTTTATAT
1 AAACGCCGCTAAAGAC-CATACTTTAGT-GCGTTTTTATAC
** ** * * *
2881197 AATTGTTGCTAAATACTATACTTTAGTGTCGTTTGTATAC
1 AAACGCCGCTAAAGACCATACTTTAGTG-CGTTTTTATAC
* * *
2881237 AAACGCCGCCAAAGACCATACTTTAGTGGCATTTTTGTAC
1 AAACGCCGCTAAAGACCATACTTTAGT-GCGTTTTTATAC
* * * * *
2881277 GAACCCCGCTAAAGACTCGTACTTTAGCGCGTTTTTATCC
1 AAACGCCGCTAAAGAC-CATACTTTAGTGCGTTTTTATAC
* ** * *
2881317 AAATGCCGCTAAAGGTTCATACTTTAGTG-GTTTTTAGCAT
1 AAACGCCGCTAAA-GACCATACTTTAGTGCGTTTTTA-TAC
* *
2881357 AAACGCCGCTAAATACTCATATTTTAGTG-GTATTTTTATAC
1 AAACGCCGCTAAAGAC-CATACTTTAGTGCG--TTTTTATAC
*
2881398 AAACACCGCTAAA
1 AAACGCCGCTAAA
2881411 AGCTTGTACT
Statistics
Matches: 161, Mismatches: 45, Indels: 16
0.73 0.20 0.07
Matches are distributed among these distances:
39 8 0.05
40 112 0.70
41 35 0.22
42 6 0.04
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (39 bp):
AAACGCCGCTAAAGACCATACTTTAGTGCGTTTTTATAC
Found at i:2885499 original size:26 final size:24
Alignment explanation
Indices: 2885444--2885500 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
2885434 CATTTTATGA
*
2885444 TATTTT-TAAATAAATAAATATTT
1 TATTTTATAAATAAATAAATAATT
*
2885467 TATTTTTATAAATTATATAAATTAATT
1 TA-TTTTATAAA-TAAATAAA-TAATT
2885494 TATTTTA
1 TATTTTA
2885501 ATTATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 2 0.07
24 4 0.14
25 4 0.14
26 12 0.43
27 6 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTTTATAAATAAATAAATAATT
Found at i:2886741 original size:46 final size:49
Alignment explanation
Indices: 2886667--2886757 Score: 127
Period size: 46 Copynumber: 1.9 Consensus size: 49
2886657 TTTTATTTTC
* *
2886667 TTTTTCCTAAATAAATGCATGCGAACTAGAAATCATGCA-GTTAGGTTAA
1 TTTTTCCTAAACAAATGCATGCGAACTAGAAAGCATG-AGGTTAGGTTAA
2886716 TTTTTCC-AAACAAA-GCATG-GAACTAGAAAGCATGAGGTTAGG
1 TTTTTCCTAAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
2886758 ATTTATACCT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 1 0.03
46 20 0.51
47 5 0.13
48 6 0.15
49 7 0.18
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (49 bp):
TTTTTCCTAAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGGTTAA
Found at i:2894564 original size:74 final size:75
Alignment explanation
Indices: 2894407--2894578 Score: 213
Period size: 74 Copynumber: 2.3 Consensus size: 75
2894397 ATCAACAAGA
* * *
2894407 AGCAAATGTTGGGGTATGCTAAAAGCCCATTTCAATCAGACTCAAGAATATTGACTCATTTTGAA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACTCATTTTGAA
*
2894472 CATTTGTATC
66 CATCTGTATC
* * * * *
2894482 AGCAAATGTTGGGACATGCTGAAAGCCC-TTTTAATCAGAATCAGGAATGTTG-GTACATTTTGA
1 AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACT-CATTTTGA
* *
2894545 ACGTCTGTATT
65 ACATCTGTATC
*
2894556 AGCCAATGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
2894579 GACCCATAAC
Statistics
Matches: 83, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
73 1 0.01
74 57 0.69
75 25 0.30
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (75 bp):
AGCAAATGTTGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACTCATTTTGAA
CATCTGTATC
Found at i:2895952 original size:22 final size:22
Alignment explanation
Indices: 2895926--2895983 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
2895916 TACATCTACA
*
2895926 CTCTTCAAAGATGATAGATTCT
1 CTCTTCAAAGATGATAAATTCT
2895948 CTCTTCAAAGATGATAAATTCT
1 CTCTTCAAAGATGATAAATTCT
* *
2895970 CTTTTCAAATATGA
1 CTCTTCAAAGATGA
2895984 AAGCTTCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
CTCTTCAAAGATGATAAATTCT
Found at i:2896898 original size:73 final size:73
Alignment explanation
Indices: 2896811--2896976 Score: 269
Period size: 73 Copynumber: 2.3 Consensus size: 73
2896801 AGGAATAAGA
* ** *
2896811 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTTAATTCATCACTCGATGGATTAACATTG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACATTG
2896876 CCAGGTAG
66 CCAGGTAG
* * *
2896884 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTTCTCGAATTCATCACTTGATGGATCAGCATTG
1 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACATTG
2896949 CCAGGTAG
66 CCAGGTAG
2896957 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
2896977 CATCTGAATA
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 86 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (73 bp):
AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGGATCAACATTG
CCAGGTAG
Found at i:2897017 original size:40 final size:39
Alignment explanation
Indices: 2896959--2897055 Score: 149
Period size: 39 Copynumber: 2.5 Consensus size: 39
2896949 CCAGGTAGAG
* *
2896959 TTCATAATGAGAAGAACTCATCTGAATAAGGAAGAAGAAA
1 TTCATAATGAGAAGAACTCATCTAAAGAA-GAAGAAGAAA
* *
2896999 TTCATAATGAGAATAACTCATCTAAAGAAGAAGAAGAAG
1 TTCATAATGAGAAGAACTCATCTAAAGAAGAAGAAGAAA
2897038 TTCATAATGAGAAGAACT
1 TTCATAATGAGAAGAACT
2897056 TGTTCAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
39 26 0.50
40 26 0.50
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.22
Consensus pattern (39 bp):
TTCATAATGAGAAGAACTCATCTAAAGAAGAAGAAGAAA
Found at i:2897043 original size:39 final size:40
Alignment explanation
Indices: 2896957--2897055 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
2896947 TGCCAGGTAG
* *
2896957 AGTTCATAATGAGAAGAACTCATCTGAATAAGGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGA
* *
2896997 AATTCATAATGAGAATAACTCATCTAAAGAA-GAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGA
2897036 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
2897056 TGTTCAATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 26 0.49
40 27 0.51
ACGTcount: A:0.49, C:0.10, G:0.19, T:0.21
Consensus pattern (40 bp):
AGTTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGA
Found at i:2897176 original size:17 final size:17
Alignment explanation
Indices: 2897154--2897195 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
2897144 TCTGAAGAGG
2897154 AAGAAGAAATTCATAAT
1 AAGAAGAAATTCATAAT
2897171 AAGAAGAAATTCATAAT
1 AAGAAGAAATTCATAAT
*
2897188 GAGAAGAA
1 AAGAAGAA
2897196 TTTGTTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.60, C:0.05, G:0.17, T:0.19
Consensus pattern (17 bp):
AAGAAGAAATTCATAAT
Found at i:2897290 original size:146 final size:141
Alignment explanation
Indices: 2897029--2897324 Score: 382
Period size: 146 Copynumber: 2.1 Consensus size: 141
2897019 TCTAAAGAAG
* ** * *
2897029 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATTTTTTTTGCATGACTCTATCACAGAAGGAG
1 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAA-TCCTTTTGCATGACGCTATCACAGAAAGAG
* *
2897094 ATAGATCAGCACCAACATTTCCAGATGAAGTTCATAATGAGAAGAGCTCATCTGAAGAGGAAGAA
65 ATAGATCAGCACCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAA
2897159 GAAATTCATAAT
130 GAAATTCATAAT
*
2897171 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAA-CCTTTTGC-TCGACGCTATCACAGAAAGAG
1 AAGAAGAAATTCATAATGAGAAGAACTTGTTCAATCCTTTTGCAT-GACGCTATCACAGAAAGAG
*
2897234 ATAGATCAACATCAACATCAACATTTCCAGAA-AGAGTTCATAATGAGAAGAACTCATCTGAAGA
65 ATAGAT---CAGC-AC--CAACATTTCCAGAAGA-AGTTCATAATGAGAAGAACTCATCTGAAGA
* *
2897298 GGAAGAGGAAGTTCATAAT
123 GGAAGAAGAAATTCATAAT
*
2897317 GAGAAGAA
1 AAGAAGAA
2897325 TTTGTTCAAC
Statistics
Matches: 134, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
139 1 0.01
140 29 0.22
142 32 0.24
143 3 0.02
144 2 0.01
145 1 0.01
146 66 0.49
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.24
Consensus pattern (141 bp):
AAGAAGAAATTCATAATGAGAAGAACTTGTTCAATCCTTTTGCATGACGCTATCACAGAAAGAGA
TAGATCAGCACCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAG
AAATTCATAAT
Found at i:2899412 original size:23 final size:23
Alignment explanation
Indices: 2899373--2899416 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2899363 CATTTTCTGA
*
2899373 TATTTATAAGTAAATAAATATCT
1 TATTTATAAGAAAATAAATATCT
2899396 TATTTATAA-AAATATAAATAT
1 TATTTATAAGAAA-ATAAATAT
2899417 TTTCTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
TATTTATAAGAAAATAAATATCT
Found at i:2917834 original size:57 final size:57
Alignment explanation
Indices: 2917743--2917864 Score: 208
Period size: 57 Copynumber: 2.1 Consensus size: 57
2917733 AATCACGATA
* *
2917743 CATAAATGTGTGTCATTTTCATTTATGACAGGGGCTTCAATGACACGCAATGTAAGT
1 CATAAATGTGTGTCATCTTCATTTATGACAGGGGCTTCAATGACACACAATGTAAGT
* *
2917800 CATAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACGCACAATGTAAGT
1 CATAAATGTGTGTCATCTTCATTTATGACAGGGGCTTCAATGACACACAATGTAAGT
2917857 CATAAATG
1 CATAAATG
2917865 CACGTCATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (57 bp):
CATAAATGTGTGTCATCTTCATTTATGACAGGGGCTTCAATGACACACAATGTAAGT
Found at i:2917871 original size:13 final size:13
Alignment explanation
Indices: 2917855--2917902 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
2917845 CACAATGTAA
*
2917855 GTCATAAATGCAC
1 GTCATAAATGCGC
2917868 GTCATAAATGCGC
1 GTCATAAATGCGC
2917881 GTCATAAATGCGC
1 GTCATAAATGCGC
*
2917894 TTCATAAAT
1 GTCATAAAT
2917903 TTATAACGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:2917877 original size:26 final size:26
Alignment explanation
Indices: 2917848--2917902 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2917838 AATGACGCAC
*
2917848 AATGTAAGTCATAAATGCACGTCATA
1 AATGCAAGTCATAAATGCACGTCATA
** * *
2917874 AATGCGCGTCATAAATGCGCTTCATA
1 AATGCAAGTCATAAATGCACGTCATA
2917900 AAT
1 AAT
2917903 TTATAACGCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (26 bp):
AATGCAAGTCATAAATGCACGTCATA
Found at i:2920805 original size:35 final size:35
Alignment explanation
Indices: 2920751--2920825 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
2920741 TTCATATTCA
**
2920751 AAATTCCAAAAAACATCAATTACATTCTAAACCCC
1 AAATTCCAAAAAACATCAATTACATTAAAAACCCC
* * *
2920786 AAATTCCAAAATAA-TTCAATTATATTAAAAACCCT
1 AAATTCCAAAA-AACATCAATTACATTAAAAACCCC
2920821 AAATT
1 AAATT
2920826 AAAGTATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 32 0.94
36 2 0.06
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (35 bp):
AAATTCCAAAAAACATCAATTACATTAAAAACCCC
Found at i:2923954 original size:43 final size:43
Alignment explanation
Indices: 2923889--2923977 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
2923879 ATGAAAAATT
2923889 CCATTGCTTGTAGGAGAAGTGGTAGCTCATTATATGACTGATC
1 CCATTGCTTGTAGGAGAAGTGGTAGCTCATTATATGACTGATC
*
2923932 CCATTGCTTGTAGGAGAGGTGGTAGCTCATTATATGACTGATC
1 CCATTGCTTGTAGGAGAAGTGGTAGCTCATTATATGACTGATC
2923975 CCA
1 CCA
2923978 ATCACCATAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (43 bp):
CCATTGCTTGTAGGAGAAGTGGTAGCTCATTATATGACTGATC
Found at i:2925272 original size:25 final size:25
Alignment explanation
Indices: 2925244--2925293 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
2925234 GATTGAAGAA
*
2925244 GAAAGGAGTGTTTTATGTAAGAGAT
1 GAAAGGAGTGTGTTATGTAAGAGAT
2925269 GAAAGGAGTGTGTTATGTAAGAGAT
1 GAAAGGAGTGTGTTATGTAAGAGAT
2925294 TGAAGATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.30
Consensus pattern (25 bp):
GAAAGGAGTGTGTTATGTAAGAGAT
Found at i:2926693 original size:2 final size:2
Alignment explanation
Indices: 2926686--2926710 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2926676 GCTATTAAGC
2926686 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 A
2926711 AATAATGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2927929 original size:3 final size:3
Alignment explanation
Indices: 2927921--2928031 Score: 163
Period size: 3 Copynumber: 37.0 Consensus size: 3
2927911 TGGGCTGCAA
* * *
2927921 AAT AAT AAT AA- ACACT AAT ATT AAC ATT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2927966 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2928014 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
2928032 TGTGTGAAGT
Statistics
Matches: 98, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
2 3 0.03
3 93 0.95
4 1 0.01
5 1 0.01
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2934316 original size:3 final size:3
Alignment explanation
Indices: 2934308--2934355 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
2934298 TGGCCTGCAA
* *
2934308 AAT AAT AAT AAT AACT AAT ATTT AAT ATT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AA-T AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
2934354 AA
1 AA
2934356 AGTTAAACGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.82
4 5 0.13
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:2934444 original size:3 final size:3
Alignment explanation
Indices: 2934436--2934492 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
2934426 TTTTTACATT
* * * *
2934436 TTA TTA TTA TTA TTA TTA TTA TTA -TA TAA ATA TTAA ATA TTA GTTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA -TTA
2934482 TTA TTA TTA TT
1 TTA TTA TTA TT
2934493 TTGCAGGCCA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.05
3 37 0.86
4 4 0.09
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:2935132 original size:3 final size:3
Alignment explanation
Indices: 2935124--2935153 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2935114 ACATACATTT
2935124 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2935154 AAATGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2935497 original size:177 final size:178
Alignment explanation
Indices: 2935195--2935543 Score: 398
Period size: 177 Copynumber: 2.0 Consensus size: 178
2935185 GGGTGTCTAT
* * ** * *
2935195 AAACACGAACGAGGAAATGTTCGTGTTCGCTCGTTTAACTTTAATCGAACTTACGAATGAACGTA
1 AAACACGAACGAGGAAATGTTCATGTTCACTCGTTTAACTTTAATCGAACAAACGAACGAACATA
* ** *
2935260 AACAACTAAACGAACATAATTTCTTGTTTGTGTTTGTTCATTAAGAAAGGCAGTTTGTTTGTGGT
66 AACAACTAAACGAACATAATTTCTTGTTTGTGTTTATTCATTAAGAAAGGCAACTTGTTTGTAGT
* *
2935325 CGTTTATG-TTGTTGGCTAAAGTGATAAACT-AACACAAGCGAACAAAC
131 CGTTCATGTTTGTTCGCTAAAGTGATAAA-TGAACACAAGCGAACAAAC
* * * *
2935372 AAACACGAACGA-GAGTATGTTCATGTTCATTCGTTTAACTTTAATCGAACAAATGAACGAATAT
1 AAACACGAACGAGGA-AATGTTCATGTTCACTCGTTTAACTTTAATCGAACAAACGAACGAACAT
** * * * * * * * *
2935436 GTATAACTAAACGAACTTAATTTTTTGTTTGTGTTTATTCGTTAAGGAATGTAACTTGTTTGTAT
65 AAACAACTAAACGAACATAATTTCTTGTTTGTGTTTATTCATTAAGAAAGGCAACTTGTTTGTAG
* * *
2935501 TCGTTCATGTTTGTTCGTTAAATTGGTAAATGAACACAAGCGA
130 TCGTTCATGTTTGTTCGCTAAAGTGATAAATGAACACAAGCGA
2935544 TGTAAAAAGC
Statistics
Matches: 140, Mismatches: 29, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
176 2 0.01
177 111 0.79
178 27 0.19
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35
Consensus pattern (178 bp):
AAACACGAACGAGGAAATGTTCATGTTCACTCGTTTAACTTTAATCGAACAAACGAACGAACATA
AACAACTAAACGAACATAATTTCTTGTTTGTGTTTATTCATTAAGAAAGGCAACTTGTTTGTAGT
CGTTCATGTTTGTTCGCTAAAGTGATAAATGAACACAAGCGAACAAAC
Found at i:2939742 original size:16 final size:16
Alignment explanation
Indices: 2939721--2939754 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2939711 GTTTGCTTCA
2939721 ATGTACATAATCAATT
1 ATGTACATAATCAATT
2939737 ATGTACATAATCAATT
1 ATGTACATAATCAATT
2939753 AT
1 AT
2939755 AAGGGAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
ATGTACATAATCAATT
Found at i:2942535 original size:21 final size:21
Alignment explanation
Indices: 2942510--2942558 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
2942500 TTCTAAGGGT
2942510 ATCGATATATTTTTATAAGGC
1 ATCGATATATTTTTATAAGGC
2942531 ATCGATATATTTTTATAAGGC
1 ATCGATATATTTTTATAAGGC
2942552 ATCGATA
1 ATCGATA
2942559 CTCAAAGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (21 bp):
ATCGATATATTTTTATAAGGC
Found at i:2944716 original size:83 final size:81
Alignment explanation
Indices: 2944539--2944828 Score: 361
Period size: 83 Copynumber: 3.5 Consensus size: 81
2944529 TATTGTTATA
* * ** * *
2944539 AAGTATCAATATTTTATATTTTGAATTGATTTCTTAATTATTTTAACTTTTTAATGTTAGAAAGT
1 AAGTATAAATATTTTATATTTCGAA-CCATTTCTTAATTATTTTAACTTTTTATTGTTACAAAGT
*
2944604 ATCAATCATCATAGATT
65 ATCGATCATCATAGATT
* *
2944621 AAGTATAAATATTTTATATTTCGAACCATTTTCTTAATTATTTAAACTTTTTTATTGTTTCAAAG
1 AAGTATAAATATTTTATATTTCGAACCA-TTTCTTAATTATTTTAAC-TTTTTATTGTTACAAAG
2944686 TATCGATCATCATAGATT
64 TATCGATCATCATAGATT
** * * *
2944704 AAGTATTGATATTTTTTATTTCAAACTGATTTCTTAATTATTTTAAC-TTTTATTGTTACAAAGT
1 AAGTATAAATATTTTATATTTCGAAC-CATTTCTTAATTATTTTAACTTTTTATTGTTACAAAGT
2944768 ATCGATCATCATAGATT
65 ATCGATCATCATAGATT
*
2944785 AAGTATCAAA-ATTTTATATTTTGAACTGC-TTTCTTAATTATTTT
1 AAGTAT-AAATATTTTATATTTCGAAC--CATTTCTTAATTATTTT
2944829 TTTCTTGATT
Statistics
Matches: 180, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
81 68 0.38
82 41 0.23
83 70 0.39
84 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.49
Consensus pattern (81 bp):
AAGTATAAATATTTTATATTTCGAACCATTTCTTAATTATTTTAACTTTTTATTGTTACAAAGTA
TCGATCATCATAGATT
Found at i:2944799 original size:81 final size:82
Alignment explanation
Indices: 2944539--2944828 Score: 388
Period size: 81 Copynumber: 3.5 Consensus size: 82
2944529 TATTGTTATA
* * * * *
2944539 AAGTATCAATATTTTATATTTTGAATTGATTTCTTAATTATTTTAACTTTTTAATGTTAGAAAGT
1 AAGTATCAAAATTTTATATTTCGAACTGATTTCTTAATTATTTTAACTTTTTATTGTTACAAAGT
*
2944604 ATCAATCATCATAGATT
66 ATCGATCATCATAGATT
* * *
2944621 AAGTAT-AAATATTTTATATTTCGAAC-CATTTTCTTAATTATTTAAACTTTTTTATTGTTTCAA
1 AAGTATCAAA-ATTTTATATTTCGAACTGA-TTTCTTAATTATTTTAAC-TTTTTATTGTTACAA
2944684 AGTATCGATCATCATAGATT
63 AGTATCGATCATCATAGATT
** * * *
2944704 AAGTATTGATATTTTTTATTTCAAACTGATTTCTTAATTATTTTAAC-TTTTATTGTTACAAAGT
1 AAGTATCAAAATTTTATATTTCGAACTGATTTCTTAATTATTTTAACTTTTTATTGTTACAAAGT
2944768 ATCGATCATCATAGATT
66 ATCGATCATCATAGATT
* *
2944785 AAGTATCAAAATTTTATATTTTGAACTGCTTTCTTAATTATTTT
1 AAGTATCAAAATTTTATATTTCGAACTGATTTCTTAATTATTTT
2944829 TTTCTTGATT
Statistics
Matches: 180, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
81 73 0.41
82 37 0.21
83 68 0.38
84 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.08, T:0.49
Consensus pattern (82 bp):
AAGTATCAAAATTTTATATTTCGAACTGATTTCTTAATTATTTTAACTTTTTATTGTTACAAAGT
ATCGATCATCATAGATT
Found at i:2945355 original size:187 final size:186
Alignment explanation
Indices: 2945017--2945865 Score: 829
Period size: 187 Copynumber: 4.6 Consensus size: 186
2945007 CAATTGTATA
* * *
2945017 TATTATAAATATTCATAACATTTTAAACTTTTAACTTATTTTCTTTTCGCT-TGAATGTCCAAGG
1 TATTATAGATATTCATAACATTTTAGA-TTTTAACTTATTTTCTTATCG-TGTGAATGTCCAAGG
*** * * *
2945081 CCCCATTTTCTTAAATTCTTG-TAATATTTTAGGCACAACCCATTTTACTAATAAAAATATTAAT
64 CCCCATCAGCTTAAATTC-TGATAACATTTTAGGCACAACCCATTTTATTAATAAAAATATTAAC
* * * * * *
2945145 GTTCTAGATCACAACCTACTTTCTTAGTAAACCATGTCATTATTGGACACAACCATATT
128 ATTCCAGATCACAACCTACTTTCTTAGTGAACCATGACATTCTTGGACACAACCTTATT
* * * * *
2945204 TATTATAGATATTCATAACATTTTCAGCTTTTAACTTATTTTCTTATAGTGTTAATGTCAAAGTC
1 TATTATAGATATTCATAACATTTT-AGATTTTAACTTATTTTCTTATCGTGTGAATGTCCAAGGC
* * * * * *
2945269 TCCATTAGCTTAAATTCTGTTAACATTTTAGACACAACCTATTTTATTAATAAAAAAATTAACAT
65 CCCATCAGCTTAAATTCTGATAACATTTTAGGCACAACCCATTTTATTAATAAAAATATTAACAT
* * **
2945334 TCCAGATCGCAA-CTGACTTTCTTAGTGAACCATGACATTGTTTGG-CACAATTTTATT
130 TCCAGATCACAACCT-ACTTTCTTAGTGAACCATGACATT-CTTGGACACAACCTTATT
* *
2945391 TATTATATATATTCATAACATTTTAGTTTTTAACTTATTTTCTTATCGTGTGAACT-TCCAAGGC
1 TATTATAGATATTCATAACATTTTAGATTTTAACTTATTTTCTTATCGTGTGAA-TGTCCAAGGC
* * * *** * *
2945455 CCCGTCAACTTAAATTTTGATAACATTTTAGGTGTAACCCATTTTGTTAATAAAAATATTAGCAT
65 CCCATCAGCTTAAATTCTGATAACATTTTAGGCACAACCCATTTTATTAATAAAAATATTAACAT
* * * * *
2945520 TCCATATCACAACATACTTTCTTTGTGAACCATGAAATTCTTGGGAGCA-AGCC-TATT
130 TCCAGATCACAACCTACTTTCTTAGTGAACCATGACATTCTT-GGA-CACAACCTTATT
* * * * * * *
2945577 TATTATAGATATAT-ACAACATTTTCATATATTAGCTTATTTTGTTATCGTGAGAATGTCTAAGG
1 TATTATAGATAT-TCATAACATTTT-AGATTTTAACTTATTTTCTTATCGTGTGAATGTCCAAGG
* * * *
2945641 CCCCATCAGCTTAAACTCTAATAACATTTTAGGCGCAACCTATTTTATTAATAAAAATATTAACA
64 CCCCATCAGCTTAAATTCTGATAACATTTTAGGCACAACCCATTTTATTAATAAAAATATTAACA
* ** * * *
2945706 TTACAGATTGCAACCTACTTTCTTAGTGAA-CATTACATTCTTGGGCACAAACTTATT
129 TTCCAGATCACAACCTACTTTCTTAGTGAACCATGACATTCTTGGACACAACCTTATT
* * * * ** * * * *
2945763 TCTTATATATATTCATAACGTTTTAGATTTTAACTTAATTGGTTATCATGGGAAT-TACTAAGGT
1 TATTATAGATATTCATAACATTTTAGATTTTAACTTATTTTCTTATCGTGTGAATGT-CCAAGGC
* * *
2945827 CCCATCAGCTTAAACTCT-AGTAACATTTAAGACACAACC
65 CCCATCAGCTTAAATTCTGA-TAACATTTTAGGCACAACC
2945866 TAAAATATTA
Statistics
Matches: 544, Mismatches: 100, Indels: 38
0.80 0.15 0.06
Matches are distributed among these distances:
184 4 0.01
185 71 0.13
186 180 0.33
187 282 0.52
188 7 0.01
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (186 bp):
TATTATAGATATTCATAACATTTTAGATTTTAACTTATTTTCTTATCGTGTGAATGTCCAAGGCC
CCATCAGCTTAAATTCTGATAACATTTTAGGCACAACCCATTTTATTAATAAAAATATTAACATT
CCAGATCACAACCTACTTTCTTAGTGAACCATGACATTCTTGGACACAACCTTATT
Found at i:2945730 original size:373 final size:372
Alignment explanation
Indices: 2945006--2945799 Score: 954
Period size: 373 Copynumber: 2.1 Consensus size: 372
2944996 TACAGAGCGT
* * * * *
2945006 ACAATTGTATATATTATAAATATTCATAACATTTTAAACTTTTAACTTATTTTCTTTTCGCTTGA
1 ACAATTTTATTTATTATATATATTCATAACATTTTAGA-TTTTAACTTATTTTCTTATCGCTTGA
*** *
2945071 ATGTCCAAGGCCCCATTTTCTTAAATTCTTGTAATATTTTAGGCACAACCCATTTTACTAATAAA
65 ATGTCCAAGGCCCCATCAACTTAAATTCTTGTAACATTTTAGGCACAACCCATTTTACTAATAAA
** * * **
2945136 AATATTAATGTTCTAGATCACAACCTACTTTCTTAGTAAACCATGTCATTATTGGACACAACCAT
130 AATATTAACATTCCAGATCACAACATACTTTCTTAGTAAACCATGAAATTATTGGACACAACCAT
* * * **
2945201 ATTTATTATAGATATTCATAACATTTTCAGCTTTTAACTTATTTTCTTATAGTGTTAATGTCAAA
195 ATTTATTATAGATATTCACAACATTTTCAGATATTAACTTATTTTCTTATAGTGAGAATGTCAAA
* * * * **
2945266 GTCTCCATTAGCTTAAATTCTGTTAACATTTTAGACACAACCTATTTTATTAATAAAAAAATTAA
260 GGCCCCATCAGCTTAAACTCTAATAACATTTTAGACACAACCTATTTTATTAATAAAAAAATTAA
* * *
2945331 CATTCCAGATCGCAACTGACTTTCTTAGTGAACCATGACATTGTTTGGC
325 CATTACAGATCGCAACTGACTTTCTTAGTGAA-CATGACATTCTTGGGC
*
2945380 ACAATTTTATTTATTATATATATTCATAACATTTTAGTTTTTAACTTATTTTCTTATCG-TGTGA
1 ACAATTTTATTTATTATATATATTCATAACATTTTAGATTTTAACTTATTTTCTTATCGCT-TGA
* *** **
2945444 ACT-TCCAAGGCCCCGTCAACTTAAATT-TTGATAACATTTTAGGTGTAACCCATTTTGTTAATA
65 A-TGTCCAAGGCCCCATCAACTTAAATTCTTG-TAACATTTTAGGCACAACCCATTTTACTAATA
* * * * * *
2945507 AAAATATTAGCATTCCATATCACAACATACTTTCTTTGTGAACCATGAAATTCTTGGGAGCA-AG
128 AAAATATTAACATTCCAGATCACAACATACTTTCTTAGTAAACCATGAAATTATT-GGA-CACAA
* * * *
2945571 CC-TATTTATTATAGATATAT-ACAACATTTTCATATATTAGCTTATTTTGTTATCGTGAGAATG
191 CCATATTTATTATAGATAT-TCACAACATTTTCAGATATTAACTTATTTTCTTATAGTGAGAATG
* * * *
2945634 TCTAAGGCCCCATCAGCTTAAACTCTAATAACATTTTAGGCGCAACCTATTTTATTAATAAAAAT
255 TCAAAGGCCCCATCAGCTTAAACTCTAATAACATTTTAGACACAACCTATTTTATTAATAAAAAA
* *
2945699 ATTAACATTACAGATTGCAACCT-ACTTTCTTAGTGAACATTACATTCTTGGGC
320 ATTAACATTACAGATCGCAA-CTGACTTTCTTAGTGAACATGACATTCTTGGGC
** * *
2945752 ACAAACTTATTTCTTATATATATTCATAACGTTTTAGATTTTAACTTA
1 ACAATTTTATTTATTATATATATTCATAACATTTTAGATTTTAACTTA
2945800 ATTGGTTATC
Statistics
Matches: 356, Mismatches: 57, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
372 60 0.17
373 251 0.71
374 43 0.12
375 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (372 bp):
ACAATTTTATTTATTATATATATTCATAACATTTTAGATTTTAACTTATTTTCTTATCGCTTGAA
TGTCCAAGGCCCCATCAACTTAAATTCTTGTAACATTTTAGGCACAACCCATTTTACTAATAAAA
ATATTAACATTCCAGATCACAACATACTTTCTTAGTAAACCATGAAATTATTGGACACAACCATA
TTTATTATAGATATTCACAACATTTTCAGATATTAACTTATTTTCTTATAGTGAGAATGTCAAAG
GCCCCATCAGCTTAAACTCTAATAACATTTTAGACACAACCTATTTTATTAATAAAAAAATTAAC
ATTACAGATCGCAACTGACTTTCTTAGTGAACATGACATTCTTGGGC
Found at i:2945955 original size:77 final size:77
Alignment explanation
Indices: 2945861--2946018 Score: 235
Period size: 77 Copynumber: 2.1 Consensus size: 77
2945851 ATTTAAGACA
*
2945861 CAACCTAAAATATTAATAATATTAATGACATTTACTATATATAACTAATTTTCTTACCCTTCATA
1 CAACCTAAAATATTAATAATATTAATGACATTTACTATATATAACTAATTTTATTACCCTTCATA
*
2945926 ATATTTTACGTG
66 AAATTTTACGTG
* * * * * *
2945938 CAACCTAAAATCTTAATAATATTCATGACATTTACTGTTTATAACTTATTTTATTACGCTTCATA
1 CAACCTAAAATATTAATAATATTAATGACATTTACTATATATAACTAATTTTATTACCCTTCATA
*
2946003 AAATTTTAGGTG
66 AAATTTTACGTG
2946015 CAAC
1 CAAC
2946019 TTGTCATATT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (77 bp):
CAACCTAAAATATTAATAATATTAATGACATTTACTATATATAACTAATTTTATTACCCTTCATA
AAATTTTACGTG
Found at i:2948449 original size:24 final size:24
Alignment explanation
Indices: 2948392--2948449 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
2948382 AAACTATTGT
*
2948392 TATAATTAATTTTAATTATTTTCA
1 TATAATTAATATTAATTATTTTCA
2948416 TAT-ATATAATATTAATTATTATT-A
1 TATAAT-TAATATTAATTATT-TTCA
*
2948440 TTTAATTAAT
1 TATAATTAAT
2948450 TTTTTATGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 2 0.07
24 23 0.79
25 4 0.14
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TATAATTAATATTAATTATTTTCA
Found at i:2949961 original size:28 final size:29
Alignment explanation
Indices: 2949929--2949985 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
2949919 ATTTTGACTC
*
2949929 CCCCAA-TTTCTATTGTTAATTATACTTT
1 CCCCAATTTTCTATTGGTAATTATACTTT
*
2949957 CCCCAATTTTCTATTGGTATTTATACTTT
1 CCCCAATTTTCTATTGGTAATTATACTTT
2949986 GTCCCTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (29 bp):
CCCCAATTTTCTATTGGTAATTATACTTT
Found at i:2950159 original size:28 final size:29
Alignment explanation
Indices: 2950127--2950182 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2950117 TTTTGCCTCG
*
2950127 CCCAA-TTCCTATTGTTAATTATACTTTC
1 CCCAATTTCCTATTGGTAATTATACTTTC
* *
2950155 CCCAATTTTCTATTGGTATTTATACTTT
1 CCCAATTTCCTATTGGTAATTATACTTT
2950183 GTCCCTTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.50
Consensus pattern (29 bp):
CCCAATTTCCTATTGGTAATTATACTTTC
Found at i:2950173 original size:197 final size:196
Alignment explanation
Indices: 2949820--2950215 Score: 704
Period size: 197 Copynumber: 2.0 Consensus size: 196
2949810 AGGGATAGAG
2949820 CTATCTAGTGGCTCAGTGGCCACTGCCCCCTTAATTTTTTATCATTAAAAAACATAAGGAAAAAT
1 CTATCTAGTGGCTCAGTGGCCACTGCCCCCTTAATTTTTTATCATTAAAAAACATAAGGAAAAAT
*
2949885 ACCTATTTAGAATTTTAAAGTTTGATTTATCTTGATTTTGACTCCCCCAATTTCTATTGTTAATT
66 ACCTATTTAGAATTTTAAAGTTTGATTTATCTTGATTTTGACTCCCCCAATTCCTATTGTTAATT
2949950 ATACTTTCCCCAATTTTCTATTGGTATTTATACTTTGTCCCTTTGAACTAGATCCTAACTCTGTC
131 ATACTTTCCCCAATTTTCTATTGGTATTTATACTTTGTCCCTTTGAACTAGATCCTAACTCTGTC
2950015 C
196 C
*
2950016 CTATCTAGTGGCTCAG-GATGCCACTGCCCCCTTAATTTTTTATCATTAAGAAACATAAGGAAAA
1 CTATCTAGTGGCTCAGTG--GCCACTGCCCCCTTAATTTTTTATCATTAAAAAACATAAGGAAAA
* * * *
2950080 ATACCTATTTAGAATTTTAATGTTTGATTTATTTTGATTTTGCCTCGCCCAATTCCTATTGTTAA
64 ATACCTATTTAGAATTTTAAAGTTTGATTTATCTTGATTTTGACTCCCCCAATTCCTATTGTTAA
*
2950145 TTATACTTTCCCCAATTTTCTATTGGTATTTATACTTTGTCCCTTTGAACTAGATCCTAGCTCTG
129 TTATACTTTCCCCAATTTTCTATTGGTATTTATACTTTGTCCCTTTGAACTAGATCCTAACTCTG
2950210 TCC
194 TCC
2950213 CTA
1 CTA
2950216 CGTGTTCGGT
Statistics
Matches: 191, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
195 1 0.01
196 16 0.08
197 174 0.91
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.41
Consensus pattern (196 bp):
CTATCTAGTGGCTCAGTGGCCACTGCCCCCTTAATTTTTTATCATTAAAAAACATAAGGAAAAAT
ACCTATTTAGAATTTTAAAGTTTGATTTATCTTGATTTTGACTCCCCCAATTCCTATTGTTAATT
ATACTTTCCCCAATTTTCTATTGGTATTTATACTTTGTCCCTTTGAACTAGATCCTAACTCTGTC
C
Found at i:2950266 original size:12 final size:12
Alignment explanation
Indices: 2950242--2950282 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2950232 ATGTTCACGA
*
2950242 ATAAGCTCGTTT
1 ATAAGCTCATTT
*
2950254 ATGAGCTCATTT
1 ATAAGCTCATTT
*
2950266 ATAAGCTTATTT
1 ATAAGCTCATTT
2950278 ATAAG
1 ATAAG
2950283 TATGCTTATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (12 bp):
ATAAGCTCATTT
Found at i:2952638 original size:22 final size:21
Alignment explanation
Indices: 2952612--2952660 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2952602 GTTAAAAAGT
2952612 GTTTTGATGAATATTTTC-TAAA
1 GTTTTGATG-AT-TTTTCATAAA
*
2952634 GTTTTAATGATTTTTCATAAA
1 GTTTTGATGATTTTTCATAAA
*
2952655 TTTTTG
1 GTTTTG
2952661 TTCATCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.29, C:0.04, G:0.12, T:0.55
Consensus pattern (21 bp):
GTTTTGATGATTTTTCATAAA
Found at i:2953074 original size:14 final size:14
Alignment explanation
Indices: 2953055--2953082 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2953045 TACTTATTCT
2953055 CCATTGTTGAATTA
1 CCATTGTTGAATTA
2953069 CCATTGTTGAATTA
1 CCATTGTTGAATTA
2953083 TTTTTGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (14 bp):
CCATTGTTGAATTA
Found at i:2953733 original size:20 final size:19
Alignment explanation
Indices: 2953685--2953757 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
2953675 AATGTGTTTA
* * *
2953685 AAAGTTTCGATACTTTCAC
1 AAAGTTTCGAAACTTCCTC
2953704 AAAGTTTCGAAACTTCCTC
1 AAAGTTTCGAAACTTCCTC
* * *
2953723 ACAATTTTCGAAATTTTCTTC
1 A-AAGTTTCGAAA-CTTCCTC
2953744 AAAGTTTCGAAACT
1 AAAGTTTCGAAACT
2953758 GTATGTGCAG
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 18 0.41
20 20 0.45
21 6 0.14
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.37
Consensus pattern (19 bp):
AAAGTTTCGAAACTTCCTC
Found at i:2954207 original size:19 final size:19
Alignment explanation
Indices: 2954179--2954233 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
2954169 TACTGTTCAT
* * *
2954179 AGTTTGGAAACTTTGTAAG
1 AGTTTCGAAACTTTGCAAA
* *
2954198 AGTTTTGAAACTTTACAAA
1 AGTTTCGAAACTTTGCAAA
2954217 AGTTTCGAAACTTTGCA
1 AGTTTCGAAACTTTGCA
2954234 CCCATAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (19 bp):
AGTTTCGAAACTTTGCAAA
Found at i:2955086 original size:2 final size:2
Alignment explanation
Indices: 2955079--2955125 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2955069 GGCTTTACAC
2955079 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
2955121 AT AT A
1 AT AT A
2955126 AGCTTAATGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2955329 original size:13 final size:13
Alignment explanation
Indices: 2955300--2955328 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2955290 TTTTTTAAAT
2955300 AAAATATTATTTA
1 AAAATATTATTTA
2955313 AAAATATT-TTTA
1 AAAATATTATTTA
2955325 AAAA
1 AAAA
2955329 AAATATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAAATATTATTTA
Found at i:2958770 original size:26 final size:26
Alignment explanation
Indices: 2958730--2958786 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
2958720 ACTTTACAAT
2958730 TGTTGAAATTCACTCATCATATAGAG
1 TGTTGAAATTCACTCATCATATAGAG
* *
2958756 TGTTGAAATTTACTCGTCATATAGAG
1 TGTTGAAATTCACTCATCATATAGAG
2958782 TGTTG
1 TGTTG
2958787 CAATAGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (26 bp):
TGTTGAAATTCACTCATCATATAGAG
Found at i:2959247 original size:22 final size:22
Alignment explanation
Indices: 2959195--2959248 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 22
2959185 TTCTGGGCTC
* *
2959195 GAGTATCGATACTGGAAGAACA
1 GAGTATCGATACCGAAAGAACA
* *
2959217 -A-TAGCGATACCGAAAGAATA
1 GAGTATCGATACCGAAAGAACA
2959237 GAGTATCGATAC
1 GAGTATCGATAC
2959249 TATAATACCA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 15 0.60
21 2 0.08
22 8 0.32
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.19
Consensus pattern (22 bp):
GAGTATCGATACCGAAAGAACA
Found at i:2959271 original size:34 final size:34
Alignment explanation
Indices: 2959233--2959318 Score: 154
Period size: 34 Copynumber: 2.5 Consensus size: 34
2959223 ATACCGAAAG
2959233 AATAGAGTATCGATACTATAATACCAGCGGTGGA
1 AATAGAGTATCGATACTATAATACCAGCGGTGGA
* *
2959267 AATAGAGTATCGATACTGTAATACCATCGGTGGA
1 AATAGAGTATCGATACTATAATACCAGCGGTGGA
2959301 AATAGAGTATCGATACTA
1 AATAGAGTATCGATACTA
2959319 CCCCTACAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.26
Consensus pattern (34 bp):
AATAGAGTATCGATACTATAATACCAGCGGTGGA
Found at i:2962108 original size:54 final size:54
Alignment explanation
Indices: 2962047--2962547 Score: 679
Period size: 54 Copynumber: 9.3 Consensus size: 54
2962037 TGTGTACTAT
* * ** *
2962047 AGGCACTATGTGTGCAACTCACGGAATTCTTCATAAGTTGATGAACAATTGTAT
1 AGGCACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTAC
**
2962101 AGGCACTATGTGTGCAACCCACATAATTCATCATAAGTTGATGAACAACCGTAC
1 AGGCACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTAC
*
2962155 AGG-AGCTATGTGTGCAACCCACAGAATTCATCATAAGTTGATGAACAACCGTAC
1 AGGCA-CTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTAC
* * ** *
2962209 AAGCACTATGTGTGCAGCCCACAAAATTCATCATATA-TTGATGAATAACCGTAC
1 AGGCACTATGTGTGCAACCCACGGAATTCATCATA-AGTTGATGAACAACCGTAC
* * *
2962263 ATGCACTATGTGTGCAACCCATGGAATTCATCATATGTTGATGAACAACCGTAC
1 AGGCACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTAC
* * * *
2962317 AGGCACTATGTGTGCAACCCATGAAATTCATCATATGTTGATGAACTACCGTAC
1 AGGCACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTAC
* *
2962371 AGGCACTATGTGTACAACCCACGGAATTCATTATAAGTTGATGAACAACCGTAC
1 AGGCACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTAC
*
2962425 AGGCACTATGTGTGCAACTCACGGAATTCATCATATA-TTGATGAACAA-CGTAC
1 AGGCACTATGTGTGCAACCCACGGAATTCATCATA-AGTTGATGAACAACCGTAC
* * * *
2962478 AGGCACTATGTGTGCAACTCACGGAATTCATCTTGTA-TTGATGAACAACCGTAT
1 AGGCACTATGTGTGCAACCCACGGAATTCATCAT-AAGTTGATGAACAACCGTAC
*
2962532 AGGCACTACGTGTGCA
1 AGGCACTATGTGTGCA
2962548 TCTTAATAAA
Statistics
Matches: 405, Mismatches: 35, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
53 51 0.13
54 351 0.87
55 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (54 bp):
AGGCACTATGTGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCGTAC
Found at i:2973363 original size:32 final size:32
Alignment explanation
Indices: 2973285--2973371 Score: 88
Period size: 32 Copynumber: 2.7 Consensus size: 32
2973275 TTAGTATTTT
* * *
2973285 TTTAAATAGTTATTATTTTTTATATTAATATA
1 TTTATATAATTATTATTTTTTATATAAATATA
* *
2973317 TTTATGTAAATATTATTTTTTAT-TAAAATAATA
1 TTTATATAATTATTATTTTTTATAT-AAAT-ATA
2973350 TTT-TATAATTATTATTTATTTA
1 TTTATATAATTATTATTT-TTTA
2973372 GAATTATTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
31 1 0.02
32 34 0.76
33 10 0.22
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (32 bp):
TTTATATAATTATTATTTTTTATATAAATATA
Done.