Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008495.1 Hibiscus syriacus cultivar Beakdansim tig00111338_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: 5120959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 21
Found at i:3992015 original size:61 final size:60
Alignment explanation
Indices: 3991908--3992031 Score: 149
Period size: 61 Copynumber: 2.0 Consensus size: 60
3991898 TGACACATTT
**
3991908 CTATCAAATGCACAGCTAGACCACTATTCTTTTAATCAACGATACTTAATTGTTCATCTAA
1 CTATCAAATGCACAGCTAGACCACTATTCTTTTAATCAACGATACTTAA-CCTTCATCTAA
* * * * * * * *
3991969 CTATCAAATGCATAGCTAGGCCATTATTGTTTTACTTAATGGTACTTAACCTTCATCTAA
1 CTATCAAATGCACAGCTAGACCACTATTCTTTTAATCAACGATACTTAACCTTCATCTAA
3992029 CTA
1 CTA
3992032 GCATAATTGA
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
60 12 0.23
61 41 0.77
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (60 bp):
CTATCAAATGCACAGCTAGACCACTATTCTTTTAATCAACGATACTTAACCTTCATCTAA
Found at i:3992236 original size:161 final size:161
Alignment explanation
Indices: 3991969--3992302 Score: 503
Period size: 161 Copynumber: 2.1 Consensus size: 161
3991959 GTTCATCTAA
* * *
3991969 CTATCAAATGCATAGCTAGGCCATTATTGTTTTACTTAATGGTACTTAACCTTCATCTAACTAGC
1 CTATCAAATGCATAGCTAGGCCATTATTCTTTTACTCAACGGTACTTAACCTTCATCTAACTAGC
*
3992034 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCCATTATTCTTTAACTCAACAGT-ACTTAA
66 ATAATTGACACCTTTCTGTCAAATGCACAGCTAGACCATTATTCTTTAACTCAACAGTCA-TTAA
* **
3992098 CCGTTCATCTAACTGTCATAATTGACACATTT
130 CCGTTCATATAACTAACATAATTGACACATTT
* *
3992130 CTATCAAATGTATAGCTAGGCCATTATTCTTTTACTCAACGGTACTTAACCTTTCATCTAA-TTG
1 CTATCAAATGCATAGCTAGGCCATTATTCTTTTACTCAACGGTACTTAACC-TTCATCTAACTAG
*
3992194 CCATAATTGACACCTTT-TGTCAAATGCACAGCTAGACCATTATTCTTTTACTCAACAGTCATTA
65 -CATAATTGACACCTTTCTGTCAAATGCACAGCTAGACCATTATTCTTTAACTCAACAGTCATTA
* *
3992258 ATCGTTCATATAACTAACATAATTGACACCTTT
129 ACCGTTCATATAACTAACATAATTGACACATTT
*
3992291 CTGTCAAATGCA
1 CTATCAAATGCA
3992303 CAGTTAGGGC
Statistics
Matches: 156, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
161 130 0.83
162 26 0.17
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (161 bp):
CTATCAAATGCATAGCTAGGCCATTATTCTTTTACTCAACGGTACTTAACCTTCATCTAACTAGC
ATAATTGACACCTTTCTGTCAAATGCACAGCTAGACCATTATTCTTTAACTCAACAGTCATTAAC
CGTTCATATAACTAACATAATTGACACATTT
Found at i:3992266 original size:80 final size:80
Alignment explanation
Indices: 3991972--3992310 Score: 450
Period size: 81 Copynumber: 4.2 Consensus size: 80
3991962 CATCTAACTA
* * * **
3991972 TCAAATGCATAGCTAGGCCATTATTGTTTTACTTAATGGTACTTAACC-TTCATCTAACTAGCAT
1 TCAAATGCACAGCTAGGCCATTATTCTTTTACTCAACAGTACTTAACCGTTCATCTAACT-GCAT
3992036 AATTGACACCTTTCTG
65 AATTGACACCTTTCTG
*
3992052 TCAAATGCACAGCTAGGCCATTATTCTTTAACTCAACAGTACTTAACCGTTCATCTAACTGTCAT
1 TCAAATGCACAGCTAGGCCATTATTCTTTTACTCAACAGTACTTAACCGTTCATCTAACTG-CAT
* *
3992117 AATTGACACATTTCTA
65 AATTGACACCTTTCTG
* * * * *
3992133 TCAAATGTATAGCTAGGCCATTATTCTTTTACTCAACGGTACTTAACCTTTCATCTAATTGCCAT
1 TCAAATGCACAGCTAGGCCATTATTCTTTTACTCAACAGTACTTAACCGTTCATCTAACTG-CAT
3992198 AATTGACACCTTT-TG
65 AATTGACACCTTTCTG
* * * *
3992213 TCAAATGCACAGCTAGACCATTATTCTTTTACTCAACAGT-CATTAATCGTTCATATAACTAACA
1 TCAAATGCACAGCTAGGCCATTATTCTTTTACTCAACAGTAC-TTAACCGTTCATCTAACT-GCA
3992277 TAATTGACACCTTTCTG
64 TAATTGACACCTTTCTG
*
3992294 TCAAATGCACAGTTAGG
1 TCAAATGCACAGCTAGG
3992311 GCTCAAAGGC
Statistics
Matches: 226, Mismatches: 28, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
79 1 0.00
80 110 0.49
81 115 0.51
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (80 bp):
TCAAATGCACAGCTAGGCCATTATTCTTTTACTCAACAGTACTTAACCGTTCATCTAACTGCATA
ATTGACACCTTTCTG
Found at i:3992353 original size:68 final size:68
Alignment explanation
Indices: 3992275--3992426 Score: 259
Period size: 68 Copynumber: 2.2 Consensus size: 68
3992265 ATATAACTAA
* * * *
3992275 CATAATTGACACCTTTCTGTCAAATGCACAGTTAGGGCTCAAAGGCACTTAGCCTTTCATCTAAC
1 CATAAATGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAGCCTTTCATCTAAC
3992340 TGG
66 TGG
3992343 CATAAATGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAGCCTTTCATCTAAC
1 CATAAATGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAGCCTTTCATCTAAC
3992408 TGG
66 TGG
*
3992411 CATAAATGACAACTTT
1 CATAAATGACACCTTT
3992427 TTTAAACATC
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 79 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.29
Consensus pattern (68 bp):
CATAAATGACACCTTTATGTCAAATGCACAGTTAGGCCTCAAAGGAACTTAGCCTTTCATCTAAC
TGG
Found at i:3994676 original size:42 final size:42
Alignment explanation
Indices: 3994615--3994697 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
3994605 CTGAAATCCT
* * *
3994615 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCC
1 GTGTTTGTTTCACGCAATTCGTTTTCCGAAAAATATTTTCCC
3994657 GTGTTTGTTTCACGCAATTCGTTTTCCGAAAAATATTTTCC
1 GTGTTTGTTTCACGCAATTCGTTTTCCGAAAAATATTTTCC
3994698 AGAGTTTGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (42 bp):
GTGTTTGTTTCACGCAATTCGTTTTCCGAAAAATATTTTCCC
Found at i:3994965 original size:26 final size:24
Alignment explanation
Indices: 3994903--3994965 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
3994893 ATTTTAATCA
3994903 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
3994927 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
3994950 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
3994966 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:3994967 original size:22 final size:23
Alignment explanation
Indices: 3994937--3994983 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
3994927 AAAATATATT
3994937 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
3994960 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
3994982 TA
1 TA
3994984 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:3995022 original size:23 final size:23
Alignment explanation
Indices: 3994973--3995026 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
3994963 TATATTTTTA
**
3994973 ATATTATAATAAAATAATCAATT
1 ATATTATAATAAAATAATCAAAG
*
3994996 ATATTATAATAATATAAT-ATAAG
1 ATATTATAATAAAATAATCA-AAG
3995019 ATATTATA
1 ATATTATA
3995027 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTATAATAAAATAATCAAAG
Found at i:3995129 original size:19 final size:18
Alignment explanation
Indices: 3995105--3995173 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
3995095 ATATTATTAA
3995105 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
3995124 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
3995142 ATTAGTATAATAATCTAATAAT
1 ATTA-T-TAATAA--TAATAAT
3995164 ATT-TTAATAA
1 ATTATTAATAA
3995174 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 10 0.25
19 15 0.38
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:3995188 original size:23 final size:23
Alignment explanation
Indices: 3995168--3995212 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3995158 AATAATATTT
3995168 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
3995191 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
3995213 ATATAACATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:3995604 original size:29 final size:29
Alignment explanation
Indices: 3995558--3995616 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
3995548 CTCCAGAAAT
* *
3995558 GTAATTTATTTTCTAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
*
3995587 GTAATTCATTTTCCAGAATTCAATTTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
3995616 G
1 G
3995617 AAAACCAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.17, G:0.08, T:0.42
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:3995608 original size:14 final size:14
Alignment explanation
Indices: 3995567--3995618 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
3995557 TGTAATTTAT
*
3995567 TTTCTAGAATTCAA
1 TTTCCAGAATTCAA
* *
3995581 ATTCCAGTAATTCAT
1 TTTCCAG-AATTCAA
3995596 TTTCCAGAATTCAA
1 TTTCCAGAATTCAA
3995610 TTTCCAGAA
1 TTTCCAGAA
3995619 AACCAATTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (14 bp):
TTTCCAGAATTCAA
Found at i:3997836 original size:3 final size:3
Alignment explanation
Indices: 3997823--3997861 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
3997813 AAAATACATA
3997823 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3997862 AGACCCGGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3998282 original size:137 final size:137
Alignment explanation
Indices: 3998105--3998598 Score: 546
Period size: 137 Copynumber: 3.6 Consensus size: 137
3998095 CTAATGGTAA
* * *
3998105 CTCCTACGTGATGAGGAAATCTGGTCGGTGGATGTCATGGTTCCTACATGATGAGGATGGCTAGC
1 CTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACATGGTTCCTACATGATGAGGACGGCTAGC
*
3998170 CATCTTTAGAGATAATTGAGATAACACGATTCCTACATGATGAGGAAGTCTGACTATCTAAGGGT
66 CATCTTTAGGGATAATTGAGATAACACGATTCCTACATGATGAGGAAGTCTGACTATCTAAGGGT
*
3998235 GGCGCGG
131 GACGCGG
* * * * *
3998242 CTCCTACGTGAAGAGTAGATCTGGACGGTGGATGACATGGTTTCTA-AGTGATAAGGACGGCTAG
1 CTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACATGGTTCCTACA-TGATGAGGACGGCTAG
** *
3998306 CCATCTTTAGGGATAATTGAGATAACACTTTTCCTACATGATGAGGAAGTCTGGCTATCTAAGGG
65 CCATCTTTAGGGATAATTGAGATAACACGATTCCTACATGATGAGGAAGTCTGACTATCTAAGGG
*
3998371 TGACACGG
130 TGACGCGG
* * * * * * * * *
3998379 CTCCTACGTGATGAGGATG-TATGGTCGATGTATGACACGGTTCGTACATTATGAGGACGTCCAT
1 CTCCTACGTGATGAGGA-GATCTGGTCGGTGGATGACATGGTTCCTACATGATGAGGACGGCTAG
* * * * *
3998443 CTATCTTTAGGGATAAATGGAGATAACACGGTTCCTACGTGATGAGGAAGTCT-AGTTATCTAAG
65 CCATCTTTAGGGAT-AATTGAGATAACACGATTCCTACATGATGAGGAAGTCTGA-CTATCTAAG
* * *
3998507 GTTAACGCTG
128 GGTGACGCGG
* * * ** * * *
3998517 CTCCTATGTGATGAGGAGATCTTGTCTGTGGATGACACT-GTTCCTATGTGATGAAGACGTCTGG
1 CTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACA-TGGTTCCTACATGATGAGGACGGCTAG
**
3998581 TTATCTTTAGGGATAATT
65 CCATCTTTAGGGATAATT
3998599 TGTTTCAAGG
Statistics
Matches: 294, Mismatches: 56, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
136 1 0.00
137 184 0.63
138 109 0.37
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (137 bp):
CTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACATGGTTCCTACATGATGAGGACGGCTAGC
CATCTTTAGGGATAATTGAGATAACACGATTCCTACATGATGAGGAAGTCTGACTATCTAAGGGT
GACGCGG
Found at i:3998642 original size:36 final size:35
Alignment explanation
Indices: 3998595--3998720 Score: 134
Period size: 36 Copynumber: 3.7 Consensus size: 35
3998585 CTTTAGGGAT
*
3998595 AATTTGTTTCAAGGGAAACAATCTCAAGCAAGACAA
1 AATTTGTTTCAAGAGAAACAATCTCAAG-AAGACAA
* * ***
3998631 AATTTGTTTCAAGGGAAACAATCTC-A-ATGTTTA
1 AATTTGTTTCAAGAGAAACAATCTCAAGAAGACAA
**
3998664 AA--TGTTTCAAGAGAAACTGTCTCAAGAAAGACAA
1 AATTTGTTTCAAGAGAAACAATCTCAAG-AAGACAA
3998698 AATTTGTTTCAAGAGAAACAATC
1 AATTTGTTTCAAGAGAAACAATC
3998721 CCAAAGTTTT
Statistics
Matches: 72, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
31 18 0.25
32 1 0.01
33 5 0.07
34 5 0.07
35 1 0.01
36 42 0.58
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (35 bp):
AATTTGTTTCAAGAGAAACAATCTCAAGAAGACAA
Found at i:3998771 original size:66 final size:67
Alignment explanation
Indices: 3998599--3998869 Score: 325
Period size: 66 Copynumber: 4.1 Consensus size: 67
3998589 AGGGATAATT
* ** * * *
3998599 TGTTTCAAGGGAAACAATCTCAAGCAAGACAAAATTTGTTTCAAGGGAAACAATCTC-AATGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
*
3998663 AAA
66 -TA
*
3998666 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAGAGAAACAATCCCAAA-GTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
3998730 TA
66 TA
* * * * * * **
3998732 TGTTTCAAGGGAAACTGTCTTAA-ACGAGACACAACTTGTTGCAAGAGAAATGATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGA-AAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTT
3998796 TTA
65 TTA
* * *
3998799 TGTTT-AAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAAACTCAAAGGTTT
1 TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
3998863 TA
66 TA
3998865 TGTTT
1 TGTTT
3998870 TGTTTGAAGT
Statistics
Matches: 175, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
65 1 0.01
66 105 0.60
67 67 0.38
68 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.29
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGAAAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTT
TA
Found at i:3998841 original size:21 final size:21
Alignment explanation
Indices: 3998812--3998851 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3998802 TTAAGAGAAA
*
3998812 TTGTCTCAAGAGAGACAAAAT
1 TTGTCTCAAGAGAAACAAAAT
*
3998833 TTGTTTCAAGAGAAACAAA
1 TTGTCTCAAGAGAAACAAA
3998852 CTCAAAGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.25
Consensus pattern (21 bp):
TTGTCTCAAGAGAAACAAAAT
Found at i:4006265 original size:21 final size:20
Alignment explanation
Indices: 4006233--4006271 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4006223 GTCAGTGACT
*
4006233 TTAATGCAAATTTTGAAAAC
1 TTAATGCAAATTTCGAAAAC
*
4006253 TTAATGCTCAATTTCGAAA
1 TTAATGC-AAATTTCGAAA
4006272 TAAGTTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.36
Consensus pattern (20 bp):
TTAATGCAAATTTCGAAAAC
Found at i:4007879 original size:23 final size:23
Alignment explanation
Indices: 4007819--4007903 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
4007809 CAATCTTATA
*
4007819 TGGCACTTCGATGCATTTCTACG
1 TGGCACTTCGATGCAATTCTACG
* *
4007842 CGGCACTAC-AGTGCAATTCTACG
1 TGGCACTTCGA-TGCAATTCTACG
*
4007865 TGGCAGTTCGATGCAATTCTACG
1 TGGCACTTCGATGCAATTCTACG
*
4007888 TGGGCACTTCGGTGCA
1 T-GGCACTTCGATGCA
4007904 TTTATATGAG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
22 1 0.02
23 37 0.73
24 13 0.25
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGATGCAATTCTACG
Found at i:4009059 original size:29 final size:29
Alignment explanation
Indices: 4009009--4009067 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
4008999 ATAAGCCAGC
*
4009009 CGCCACCTCCAACGCATGCTCCTATCAGT
1 CGCCACCTCCAACGCATACTCCTATCAGT
**
4009038 CGCCACCTCCAATTCATACTCCTATCAGT
1 CGCCACCTCCAACGCATACTCCTATCAGT
4009067 C
1 C
4009068 ATCATCACGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.22, C:0.44, G:0.10, T:0.24
Consensus pattern (29 bp):
CGCCACCTCCAACGCATACTCCTATCAGT
Found at i:4021696 original size:44 final size:45
Alignment explanation
Indices: 4021628--4021747 Score: 152
Period size: 49 Copynumber: 2.6 Consensus size: 45
4021618 GTAACCATGC
* *
4021628 AAATTAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGG-AA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGGAAA
* *
4021672 AAATAAGCTTATGAGCTTATGGAATTTTAAATGGTAAGTATTTTGGAAA
1 AAATAAGCTTATGAGCTTATGGAA---T-AATGGCAAGTATATTGGAAA
*
4021721 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
4021748 AAGGTAAGAA
Statistics
Matches: 66, Mismatches: 5, Indels: 9
0.82 0.06 0.11
Matches are distributed among these distances:
44 22 0.33
45 2 0.03
46 1 0.02
47 1 0.02
48 15 0.23
49 25 0.38
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGGAAA
Found at i:4024608 original size:21 final size:21
Alignment explanation
Indices: 4024584--4024637 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
4024574 ATCGAAAAAG
4024584 AAAATGAAAACGA-AGAAGAAA
1 AAAATGAAAACGAGA-AAGAAA
* *
4024605 AAAATAAAAATGAGAAAGAAA
1 AAAATGAAAACGAGAAAGAAA
4024626 AGAAATAGAAAA
1 A-AAAT-GAAAA
4024638 AAAAATGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 18 0.67
22 5 0.19
23 4 0.15
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.07
Consensus pattern (21 bp):
AAAATGAAAACGAGAAAGAAA
Found at i:4024615 original size:27 final size:28
Alignment explanation
Indices: 4024565--4024655 Score: 100
Period size: 28 Copynumber: 3.2 Consensus size: 28
4024555 TATATATTAT
*
4024565 AAGAAAA-AAATCGAAAAAGAAAATGA-A
1 AAGAAAAGAAATAGAAAAA-AAAATGAGA
*
4024592 AACGAAGAAGAAA-A-AAATAAAAATGAGA
1 AA-GAA-AAGAAATAGAAAAAAAAATGAGA
4024620 AAGAAAAGAAATAGAAAAAAAAATGAGA
1 AAGAAAAGAAATAGAAAAAAAAATGAGA
4024648 AATGAAAA
1 AA-GAAAA
4024656 AAAAATATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
26 6 0.11
27 13 0.24
28 25 0.46
29 7 0.13
30 3 0.06
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.08
Consensus pattern (28 bp):
AAGAAAAGAAATAGAAAAAAAAATGAGA
Found at i:4024626 original size:33 final size:31
Alignment explanation
Indices: 4024565--4024640 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 31
4024555 TATATATTAT
4024565 AAGAAAAAAATCGAAAAAGAAAATGAAAACGAA
1 AAGAAAAAAATC-AAAAAGAAAATGAAAA-GAA
4024598 GAAGAAAAAAAT-AAAAATGAGAAA-GAAAAGAA
1 -AAGAAAAAAATCAAAAA-GA-AAATGAAAAGAA
4024630 ATAGAAAAAAA
1 A-AGAAAAAAA
4024641 AATGAGAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
31 1 0.03
32 17 0.44
33 7 0.18
34 14 0.36
ACGTcount: A:0.75, C:0.03, G:0.16, T:0.07
Consensus pattern (31 bp):
AAGAAAAAAATCAAAAAGAAAATGAAAAGAA
Found at i:4024655 original size:15 final size:14
Alignment explanation
Indices: 4024610--4024657 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
4024600 AGAAAAAAAT
4024610 AAAAATGAGAAAGAA
1 AAAAATGAGAAAG-A
4024625 AAGAAAT-AGAAA-A
1 AA-AAATGAGAAAGA
4024638 AAAAATGAGAAATGA
1 AAAAATGAGAAA-GA
4024653 AAAAA
1 AAAAA
4024658 AAATATTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
12 4 0.14
13 8 0.28
15 13 0.45
16 4 0.14
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (14 bp):
AAAAATGAGAAAGA
Found at i:4024656 original size:18 final size:19
Alignment explanation
Indices: 4024626--4024661 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
4024616 GAGAAAGAAA
4024626 AGAAATAGAAAAAAAAATG
1 AGAAATAGAAAAAAAAATG
4024645 AGAAAT-GAAAAAAAAAT
1 AGAAATAGAAAAAAAAAT
4024662 ATTTCACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (19 bp):
AGAAATAGAAAAAAAAATG
Found at i:4031082 original size:174 final size:177
Alignment explanation
Indices: 4030733--4031082 Score: 618
Period size: 174 Copynumber: 2.0 Consensus size: 177
4030723 GTTATGAAGA
4030733 AAGCCTTTTTTGGAGGAGCTCAGGTACTCGCTAAGATAAATGGGCTAAAATTACCCTATCCAGTG
1 AAGCCTTTTTTGGAGGAGCTCAGGTACTCGCTAAGATAAATGGGCTAAAATTACCCTATCCAGTG
4030798 AACTCTGATGCGGTTAAAAGGAATTTTGCTAAAGAAAAAGAAAAAGAAAAATAATAAAATAAAAG
66 AACTCTGATGCGGTTAAAAGGAATTTTGCTAAAGAAAAAG-AAAAGAAAAATAATAAAATAAAAG
*
4030863 GAGGGTTCAAGATGAAAATCCAAAAAGGATGTCTTGAACCCAAATGGT
130 GAGGGTTCAAGATGAAAATCCAAAAAGGATGTCTTGAAACCAAATGGT
* **
4030911 AAGCCTTTTTTGGAGGAGCTCTA-GTACTCGCTGAGATGGATGGGCT-AAATTACCCTATCCAGT
1 AAGCCTTTTTTGGAGGAGCTC-AGGTACTCGCTAAGATAAATGGGCTAAAATTACCCTATCCAGT
4030974 GAACTCTGATGCGGTTAAAAGGAATTTTGCTAAAGAAAAAG-AAA-AAAAATAATAAAATAAAAG
65 GAACTCTGATGCGGTTAAAAGGAATTTTGCTAAAGAAAAAGAAAAGAAAAATAATAAAATAAAAG
4031037 GAGGGTTCAAGATGAAAATCCAAAAAGGATGTCTTGAAACCAAATG
130 GAGGGTTCAAGATGAAAATCCAAAAAGGATGTCTTGAAACCAAATG
4031083 AGGTCTCAAG
Statistics
Matches: 167, Mismatches: 4, Indels: 6
0.94 0.02 0.03
Matches are distributed among these distances:
174 64 0.38
175 3 0.02
177 58 0.35
178 41 0.25
179 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.23
Consensus pattern (177 bp):
AAGCCTTTTTTGGAGGAGCTCAGGTACTCGCTAAGATAAATGGGCTAAAATTACCCTATCCAGTG
AACTCTGATGCGGTTAAAAGGAATTTTGCTAAAGAAAAAGAAAAGAAAAATAATAAAATAAAAGG
AGGGTTCAAGATGAAAATCCAAAAAGGATGTCTTGAAACCAAATGGT
Found at i:4032471 original size:89 final size:88
Alignment explanation
Indices: 4032108--4032972 Score: 861
Period size: 89 Copynumber: 9.8 Consensus size: 88
4032098 GATGCTAAAA
* * * * ** * * *
4032108 CAAATCAATATTGAGTCTAATCTCC-CTGGAAGAGTAAAGGAGCAGATTCACCCTATTTAAGTTT
1 CAAATCAATCTCGAGTCTGATCTCCAC-GGAAGAGTAGAGGAGCAGATTCTTCTTATTTCAGATT
* *
4032172 TGGTCTTCACGAAAGAGTAGAGACG
65 TGGTCTTC-CGAAAGAGTAGCGAAG
* * * *
4032197 CAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGATGAACA-ATT-TTCTTATTTCATATTT
1 CAAATCAATCTCGAGTCTGATCTCCACGGAAGAGTAGAGGAGCAGATTCTTCTTATTTCAGATTT
*
4032260 GGTCTTCACGAAAGAGTAGCGAAA
66 GGTCTTC-CGAAAGAGTAGCGAAG
* * * * *
4032284 CAAATCAATCTCGAGTATGATATCC-CAGGAAGAGTAAAGGAG--TATTCTTTTTATTTCAGATT
1 CAAATCAATCTCGAGTCTGATCTCCAC-GGAAGAGTAGAGGAGCAGATTCTTCTTATTTCAGATT
*
4032346 TGGTATTCCGAAAGAGTAGCGAAG
65 TGGTCTTCCGAAAGAGTAGCGAAG
* * * * *
4032370 CAAATCAATCTCGAGTCTAATCACCACGGAAGAGTAGTGGAGCAGATTCTTCGTATTTTAGATTT
1 CAAATCAATCTCGAGTCTGATCTCCACGGAAGAGTAGAGGAGCAGATTCTTCTTATTTCAGATTT
* * **
4032435 TGTCTTCCTGAAATAGTATTGAAG
66 GGTCTTCC-GAAAGAGTAGCGAAG
* * * * *
4032459 CAAATCAATCTCGAGTCTAATCACCACGAAAGAGTAGTGGAGCAGATTCTTCATATTTCAGATTT
1 CAAATCAATCTCGAGTCTGATCTCCACGGAAGAGTAGAGGAGCAGATTCTTCTTATTTCAGATTT
* * * * *
4032524 TGTCTTCATGAAATAGCAGCAAAG
66 GGTCTTC-CGAAAGAGTAGCGAAG
* * * * * *
4032548 CAAATCAATCTCGTGTTTGATCTCCTCGGAAGAGTAGAGGAACA-ACT-TTCTTATTTCATATTT
1 CAAATCAATCTCGAGTCTGATCTCCACGGAAGAGTAGAGGAGCAGATTCTTCTTATTTCAGATTT
** *
4032611 TTTCTTCCTGAAATAGTAGCGAAG
66 GGTCTTCC-GAAAGAGTAGCGAAG
* * * * *
4032635 CAAATCAATCTGGAGTATGATCTCC-CTGGAATAGTAGAGGAGCAGATCCTTCTTATTTCATATT
1 CAAATCAATCTCGAGTCTGATCTCCAC-GGAAGAGTAGAGGAGCAGATTCTTCTTATTTCAGATT
*
4032699 TGGT-TTCCCGAAAGAGTAGTGAAG
65 TGGTCTT-CCGAAAGAGTAGCGAAG
* * * ** * *
4032723 CAAATCAATCTCGAGTCTGATCTCCTCGAAATAGTAGAGGAGCAGATTCACCATATTTGAGATTT
1 CAAATCAATCTCGAGTCTGATCTCCACGGAAGAGTAGAGGAGCAGATTCTTCTTATTTCAGATTT
*
4032788 GGTCTTCACGAAAGAGTAGCAAAG
66 GGTCTTC-CGAAAGAGTAGCGAAG
* * * * *
4032812 CAAATCAATCTCGAGTATGGTCAACC-CGAAAGAGTAGAGGAGCATATTCTTCTTATTTCAGATT
1 CAAATCAATCTCGAGTCTGATC-TCCACGGAAGAGTAGAGGAGCAGATTCTTCTTATTTCAGATT
* * *
4032876 TAGTCTTCACAAAAGAATAGCGAAG
65 TGGTCTTC-CGAAAGAGTAGCGAAG
* * * *
4032901 CAAATCAATCTCGAGTCTGATCACCACGGAAGAGTAGTGGAGCAGATTCTTCTAATTTTAGATTT
1 CAAATCAATCTCGAGTCTGATCTCCACGGAAGAGTAGAGGAGCAGATTCTTCTTATTTCAGATTT
4032966 GGTCTTC
66 GGTCTTC
4032973 TCAAAAGGTC
Statistics
Matches: 652, Mismatches: 105, Indels: 38
0.82 0.13 0.05
Matches are distributed among these distances:
86 54 0.08
87 157 0.24
88 105 0.16
89 333 0.51
90 3 0.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (88 bp):
CAAATCAATCTCGAGTCTGATCTCCACGGAAGAGTAGAGGAGCAGATTCTTCTTATTTCAGATTT
GGTCTTCCGAAAGAGTAGCGAAG
Found at i:4032724 original size:264 final size:264
Alignment explanation
Indices: 4032108--4032972 Score: 992
Period size: 264 Copynumber: 3.3 Consensus size: 264
4032098 GATGCTAAAA
* * * * ** * * *
4032108 CAAATCAATATTGAGTCTAATCTCC-CTGGAAGAGTAAAGGAGCAGATTCACCCTATTTAAGTTT
1 CAAATCAATCTCGAGTCTAATCACCAC-GGAAGAGTAGAGGAGCAGATTCTTCTTATTTTAGATT
* * * * *
4032172 TGGTCTTCACGAAAGAGTAGAGACGCAAATCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGAT-
65 TGGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCGAGTCTGATCTCCACGAAAGAGTAG-TG
* * *
4032236 GAACA-ATT-TTCTTATTTCATATTTGGTCTTCACGAAAGAGTAGCGAAA-CAAATCAATCTCGA
129 GAGCAGATTCTTCATATTTCAGATTTGGTCTTCACGAAAGAGTAGC-AAAGCAAATCAATCTCGA
* * * * * *
4032298 GTATGATATCCCAGGAAGAGTAAAGGAGTATTCTTT-TTATTTCAGATTTGGTATTCCGAAAGAG
193 GTATGATCTCCC-GGAAGAGTAGAGGAGCATACTTTCTTATTTCAGATTTAGTCTTCCGAAAGAG
4032362 TAGCGAAG
257 TAGCGAAG
* *
4032370 CAAATCAATCTCGAGTCTAATCACCACGGAAGAGTAGTGGAGCAGATTCTTCGTATTTTAGATTT
1 CAAATCAATCTCGAGTCTAATCACCACGGAAGAGTAGAGGAGCAGATTCTTCTTATTTTAGATTT
* * * * * *
4032435 TGTCTTCCTGAAATAGTATTGAAGCAAATCAATCTCGAGTCTAATCACCACGAAAGAGTAGTGGA
66 GGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCGAGTCTGATCTCCACGAAAGAGTAGTGGA
* * * * * *
4032500 GCAGATTCTTCATATTTCAGATTTTGTCTTCATGAAATAGCAGCAAAGCAAATCAATCTCGTGTT
131 GCAGATTCTTCATATTTCAGATTTGGTCTTCACGAAAGAGTAGCAAAGCAAATCAATCTCGAGTA
* * ** *
4032565 TGATCTCCTCGGAAGAGTAGAGGAACA-ACTTTCTTATTTCATATTTTTTCTTCCTGAAATAGTA
196 TGATCTCC-CGGAAGAGTAGAGGAGCATACTTTCTTATTTCAGATTTAGTCTTCC-GAAAGAGTA
4032629 GCGAAG
259 GCGAAG
* * * * * * * *
4032635 CAAATCAATCTGGAGTATGATCTCC-CTGGAATAGTAGAGGAGCAGATCCTTCTTATTTCATATT
1 CAAATCAATCTCGAGTCTAATCACCAC-GGAAGAGTAGAGGAGCAGATTCTTCTTATTTTAGATT
* * *
4032699 TGGT-TTCCCGAAAGAGTAGTGAAGCAAATCAATCTCGAGTCTGATCTCCTCGAAATAGTAGAGG
65 TGGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCGAGTCTGATCTCCACGAAAGAGTAGTGG
** *
4032763 AGCAGATTCACCATATTTGAGATTTGGTCTTCACGAAAGAGTAGCAAAGCAAATCAATCTCGAGT
130 AGCAGATTCTTCATATTTCAGATTTGGTCTTCACGAAAGAGTAGCAAAGCAAATCAATCTCGAGT
* * * * * *
4032828 ATGGTCAACCCGAAAGAGTAGAGGAGCATATTCTTCTTATTTCAGATTTAGTCTTCACAAAAGAA
195 ATGATC-TCCCGGAAGAGTAGAGGAGCATACT-TTCTTATTTCAGATTTAGTCTTC-CGAAAGAG
4032893 TAGCGAAG
257 TAGCGAAG
* * *
4032901 CAAATCAATCTCGAGTCTGATCACCACGGAAGAGTAGTGGAGCAGATTCTTCTAATTTTAGATTT
1 CAAATCAATCTCGAGTCTAATCACCACGGAAGAGTAGAGGAGCAGATTCTTCTTATTTTAGATTT
4032966 GGTCTTC
66 GGTCTTC
4032973 TCAAAAGGTC
Statistics
Matches: 500, Mismatches: 88, Indels: 25
0.82 0.14 0.04
Matches are distributed among these distances:
261 1 0.00
262 107 0.21
263 11 0.02
264 213 0.43
265 74 0.15
266 89 0.18
267 5 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (264 bp):
CAAATCAATCTCGAGTCTAATCACCACGGAAGAGTAGAGGAGCAGATTCTTCTTATTTTAGATTT
GGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCGAGTCTGATCTCCACGAAAGAGTAGTGGA
GCAGATTCTTCATATTTCAGATTTGGTCTTCACGAAAGAGTAGCAAAGCAAATCAATCTCGAGTA
TGATCTCCCGGAAGAGTAGAGGAGCATACTTTCTTATTTCAGATTTAGTCTTCCGAAAGAGTAGC
GAAG
Found at i:4032863 original size:353 final size:351
Alignment explanation
Indices: 4032137--4032937 Score: 964
Period size: 353 Copynumber: 2.3 Consensus size: 351
4032127 ATCTCCCTGG
* ** * * * * * ** *
4032137 AAGAGTAAAGGAGCAGATTCACCCTATTTAAGTTTTGGTCTTCACGAAAGAGTAG-AGACGCAAA
1 AAGAGTAGAGGAGCAGATTCTTCATATTTCAGATTTAGTCTTCACAAAAGAACAGCA-AAGCAAA
* * *
4032201 TCAATCTCGAGTCTGATCTCCCCGGAAGAGTAGATGAACAATTTTCTTATTTCATATTTGGTCTT
65 TCAATCTCGAGTCTGATCTCCACGGAAGAGTAGAGGAACAACTTTCTTATTTCATATTTGGTCTT
* *
4032266 CACGAAAGAGTAGCGAAACAAATCAATCTCGAGTATGATATCCCAGGAAGAGTAAAGGAGTATTC
130 CACGAAAGAGTAGCGAAACAAATCAATCTCGAGTATGATATCCCAGGAAGAGTAAAGGAGGATCC
*
4032331 TTTTTATTTCAGATTTGGTATTCCGAAAGAGTAGCGAAGCAAATCAATCTCGAGTCTAATCACCA
195 TTCTTATTTCAGATTTGGTATTCCGAAAGAGTAGCGAAGCAAATCAATCTCGAGTCTAATCACCA
* * ** * * * * ***
4032396 CGGAAGAGTAGTGGAGCAGATTCTTCGTATTTTAGATTTTGTCTTCCTGAAATAGTATTGAAGCA
260 CGAAAGAGTAGAGGAGCAGATTCACCATATTTGAGATTTGGTCTTCCTGAAAGAGTAGCAAAGCA
*
4032461 AATCAATCTCGAGTCTAATCACCACGA
325 AATCAATCTCGAGTATAATCACCACGA
* * ** * *
4032488 AAGAGTAGTGGAGCAGATTCTTCATATTTCAGATTTTGTCTTCATGAAATAGCAGCAAAGCAAAT
1 AAGAGTAGAGGAGCAGATTCTTCATATTTCAGATTTAGTCTTCACAAAAGAACAGCAAAGCAAAT
* * * **
4032553 CAATCTCGTGTTTGATCTCCTCGGAAGAGTAGAGGAACAACTTTCTTATTTCATATTTTTTCTTC
66 CAATCTCGAGTCTGATCTCCACGGAAGAGTAGAGGAACAACTTTCTTATTTCATATTTGGTCTTC
* * * * * * *
4032618 -CTGAAATAGTAGCGAAGCAAATCAATCTGGAGTATGATCTCCCTGGAATAGTAGAGGAGCAGAT
131 AC-GAAAGAGTAGCGAAACAAATCAATCTCGAGTATGATATCCCAGGAAGAGTAAAGGAG--GAT
* * * *
4032682 CCTTCTTATTTCATATTTGGT-TTCCCGAAAGAGTAGTGAAGCAAATCAATCTCGAGTCTGATCT
193 CCTTCTTATTTCAGATTTGGTATT-CCGAAAGAGTAGCGAAGCAAATCAATCTCGAGTCTAATCA
* *
4032746 CCTCGAAATAGTAGAGGAGCAGATTCACCATATTTGAGATTTGGTCTTCAC-GAAAGAGTAGCAA
257 CCACGAAAGAGTAGAGGAGCAGATTCACCATATTTGAGATTTGGTCTTC-CTGAAAGAGTAGCAA
**
4032810 AGCAAATCAATCTCGAGTATGGTCAACC-CGA
321 AGCAAATCAATCTCGAGTATAATC-ACCACGA
* * * *
4032841 AAGAGTAGAGGAGCATATTCTTCTTATTTCAGATTTAGTCTTCACAAAAGAATAGCGAAGCAAAT
1 AAGAGTAGAGGAGCAGATTCTTCATATTTCAGATTTAGTCTTCACAAAAGAACAGCAAAGCAAAT
*
4032906 CAATCTCGAGTCTGATCACCACGGAAGAGTAG
66 CAATCTCGAGTCTGATCTCCACGGAAGAGTAG
4032938 TGGAGCAGAT
Statistics
Matches: 380, Mismatches: 63, Indels: 12
0.84 0.14 0.03
Matches are distributed among these distances:
350 1 0.00
351 159 0.42
352 3 0.01
353 213 0.56
354 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (351 bp):
AAGAGTAGAGGAGCAGATTCTTCATATTTCAGATTTAGTCTTCACAAAAGAACAGCAAAGCAAAT
CAATCTCGAGTCTGATCTCCACGGAAGAGTAGAGGAACAACTTTCTTATTTCATATTTGGTCTTC
ACGAAAGAGTAGCGAAACAAATCAATCTCGAGTATGATATCCCAGGAAGAGTAAAGGAGGATCCT
TCTTATTTCAGATTTGGTATTCCGAAAGAGTAGCGAAGCAAATCAATCTCGAGTCTAATCACCAC
GAAAGAGTAGAGGAGCAGATTCACCATATTTGAGATTTGGTCTTCCTGAAAGAGTAGCAAAGCAA
ATCAATCTCGAGTATAATCACCACGA
Found at i:4036504 original size:21 final size:21
Alignment explanation
Indices: 4036478--4036520 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4036468 AACTGGTGCT
*
4036478 TGCCATACGTTAGAATGAACC
1 TGCCATACGTCAGAATGAACC
4036499 TGCCATACGTCAGAATGAACC
1 TGCCATACGTCAGAATGAACC
4036520 T
1 T
4036521 ATTCTAGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (21 bp):
TGCCATACGTCAGAATGAACC
Found at i:4039543 original size:9 final size:9
Alignment explanation
Indices: 4039525--4039554 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
4039515 CTTTGTTAAG
4039525 TTTT-TTAT
1 TTTTATTAT
4039533 TTTTATTAT
1 TTTTATTAT
4039542 TTTTATTAT
1 TTTTATTAT
4039551 TTTT
1 TTTT
4039555 TTTTTATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTATTAT
Found at i:4039564 original size:18 final size:18
Alignment explanation
Indices: 4039529--4039584 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
4039519 GTTAAGTTTT
4039529 TTATTTTTATTATT-TTTA
1 TTATTTTT-TTATTATTTA
*
4039547 TTATTTTTTTTTTATTTA
1 TTATTTTTTTATTATTTA
* *
4039565 ATATTTATTTATTATATTA
1 TTATTTTTTTATTAT-TTA
4039584 T
1 T
4039585 ATTAATATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 4 0.13
18 24 0.77
19 3 0.10
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TTATTTTTTTATTATTTA
Found at i:4041313 original size:13 final size:12
Alignment explanation
Indices: 4041292--4041361 Score: 68
Period size: 13 Copynumber: 5.2 Consensus size: 12
4041282 AACAAAAAGG
4041292 AAAAAAAAGAAA
1 AAAAAAAAGAAA
4041304 AAAAATAAAGAAA
1 AAAAA-AAAGAAA
*
4041317 AAACAAAGAGAAA
1 AAA-AAAAAGAAA
4041330 ATAAAAAAGAGAAA
1 A-AAAAAA-AGAAA
4041344 CAAAAACAAAGGAAA
1 -AAAAA-AAA-GAAA
4041359 AAA
1 AAA
4041362 GTGAAAAAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
12 5 0.10
13 20 0.41
14 17 0.35
15 7 0.14
ACGTcount: A:0.81, C:0.04, G:0.11, T:0.03
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:4041336 original size:30 final size:29
Alignment explanation
Indices: 4041296--4041359 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
4041286 AAAAGGAAAA
* * *
4041296 AAAAGAAAAAAAATAAAGAAAAAACAAAGAG
1 AAAATAAAAAAGAGAAA-AAAAAACAAAG-G
*
4041327 AAAATAAAAAAGAGAAACAAAAACAAAGG
1 AAAATAAAAAAGAGAAAAAAAAACAAAGG
4041356 AAAA
1 AAAA
4041360 AAGTGAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 5 0.17
30 10 0.34
31 14 0.48
ACGTcount: A:0.80, C:0.05, G:0.12, T:0.03
Consensus pattern (29 bp):
AAAATAAAAAAGAGAAAAAAAAACAAAGG
Found at i:4041338 original size:14 final size:13
Alignment explanation
Indices: 4041292--4041349 Score: 66
Period size: 12 Copynumber: 4.5 Consensus size: 13
4041282 AACAAAAAGG
4041292 AAAAAAAAGA-AA
1 AAAAAAAAGAGAA
*
4041304 AAAAATAA-AGAA
1 AAAAAAAAGAGAA
*
4041316 AAAACAAAGAGAA
1 AAAAAAAAGAGAA
4041329 AATAAAAAAGAGAA
1 AA-AAAAAAGAGAA
4041343 ACAAAAA
1 A-AAAAA
4041350 CAAAGGAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
11 1 0.03
12 15 0.39
13 6 0.16
14 15 0.39
15 1 0.03
ACGTcount: A:0.83, C:0.03, G:0.10, T:0.03
Consensus pattern (13 bp):
AAAAAAAAGAGAA
Found at i:4042446 original size:32 final size:32
Alignment explanation
Indices: 4042410--4042528 Score: 168
Period size: 32 Copynumber: 3.7 Consensus size: 32
4042400 AGGAACAATA
*
4042410 GGGGCACCTTTGAAGATTCAACATCAAATGTT
1 GGGGCACCTTTGGAGATTCAACATCAAATGTT
4042442 GGGGCACCTTTGGAGATTCAACATCAAATGTT
1 GGGGCACCTTTGGAGATTCAACATCAAATGTT
* * *
4042474 GGGGCATCTTTGGAGATTCAACATCGAATATT
1 GGGGCACCTTTGGAGATTCAACATCAAATGTT
**
4042506 GGGGCATATTTTGG-GATTCAACA
1 GGGGCA-CCTTTGGAGATTCAACA
4042529 CCCTGATGTG
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
32 75 0.94
33 5 0.06
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (32 bp):
GGGGCACCTTTGGAGATTCAACATCAAATGTT
Found at i:4042958 original size:110 final size:110
Alignment explanation
Indices: 4042755--4043190 Score: 626
Period size: 110 Copynumber: 4.0 Consensus size: 110
4042745 GCTCGAGTTT
* * * *
4042755 ACAGCGAA-GAGGCGACTAACTATCAACAAACAACTTTTCAGCTTCATTCAGAGCAAATTTCAAC
1 ACAGCGAATG-GGCGACTGACTATCAACAAAAAACTTTTCAGTTTCATTCAGAGCCAATTTCAAC
* *
4042819 TTCACAGCGAAGGAAATTGGACTCGAGACAACACAAGATCAACTTC
65 TTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
* *
4042865 ACAGTGAATGGGCGACTGACTATCAACAAAAAACTTTTCAGTTTCATTCAAAGCCAATTTCAACT
1 ACAGCGAATGGGCGACTGACTATCAACAAAAAACTTTTCAGTTTCATTCAGAGCCAATTTCAACT
* *
4042930 TCACAGCGAAGGATTTTGGACTCAAGACAACACAAGCTCAACTTC
66 TCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
* * * * *
4042975 ACAGCGAATGGGTGACTGACTGTCAACAAACAACCTTTCAGTTTCATTCAGAGCCAATTTTAACT
1 ACAGCGAATGGGCGACTGACTATCAACAAAAAACTTTTCAGTTTCATTCAGAGCCAATTTCAACT
* *
4043040 TCACAACGAAGGATATTGGACTCGAGACAACACATGCTCAACTTC
66 TCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
* * * *
4043085 ACAGCGAA-GAGGCGACTGAATGTCAA-AAAATAACATTTCAGTTTCATTCAGAGTCAATTTCAA
1 ACAGCGAATG-GGCGACTGACTATCAACAAAA-AACTTTTCAGTTTCATTCAGAGCCAATTTCAA
*
4043148 CTTCACAGCGAAGGATAATGGACTCGAGACAACACAAGCTCAA
64 CTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAA
4043191 TGTAGACACC
Statistics
Matches: 293, Mismatches: 30, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
109 4 0.01
110 288 0.98
111 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.22
Consensus pattern (110 bp):
ACAGCGAATGGGCGACTGACTATCAACAAAAAACTTTTCAGTTTCATTCAGAGCCAATTTCAACT
TCACAGCGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTC
Found at i:4045041 original size:2 final size:2
Alignment explanation
Indices: 4045025--4045090 Score: 116
Period size: 2 Copynumber: 33.0 Consensus size: 2
4045015 ATCTCTTGTT
4045025 TA TA TGA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4045067 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
4045091 CGGTTTTCTT
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 59 0.95
3 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:4047274 original size:21 final size:20
Alignment explanation
Indices: 4047190--4047280 Score: 101
Period size: 21 Copynumber: 4.3 Consensus size: 20
4047180 ACCAAACACG
* *
4047190 AGAAGACCGTTCATAAAGAGG
1 AGAAGACCATTCATAAAGA-C
4047211 AGAAGACCATTCATAAAGAC
1 AGAAGACCATTCATAAAGAC
* *
4047231 GAGAAGATCATTCATAAAAAC
1 -AGAAGACCATTCATAAAGAC
*
4047252 ATGAAGACCCTTCATAAAGAC
1 A-GAAGACCATTCATAAAGAC
4047273 ATGAAGAC
1 A-GAAGAC
4047281 TACTTCACAT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
20 1 0.02
21 60 0.98
ACGTcount: A:0.47, C:0.18, G:0.19, T:0.16
Consensus pattern (20 bp):
AGAAGACCATTCATAAAGAC
Found at i:4049821 original size:18 final size:20
Alignment explanation
Indices: 4049781--4049831 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
4049771 TGACATCATG
4049781 AAGAGAAAGAAGAGAAATGTAA
1 AAGAGAAA-AAGAGAAA-GTAA
4049803 AAGAGAAAAAGA-AAA-TAA
1 AAGAGAAAAAGAGAAAGTAA
4049821 AAGATGAAAAA
1 AAGA-GAAAAA
4049832 AGGAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.25
19 6 0.21
20 3 0.11
21 4 0.14
22 8 0.29
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.08
Consensus pattern (20 bp):
AAGAGAAAAAGAGAAAGTAA
Found at i:4052588 original size:37 final size:37
Alignment explanation
Indices: 4052537--4052689 Score: 186
Period size: 37 Copynumber: 4.1 Consensus size: 37
4052527 ATGAGATTGG
*
4052537 AGCAAAGTAAATCTTAAGCCTTCACCGAAAAGGAGTGA
1 AGCAAA-TCAATCTTAAGCCTTCACCGAAAAGGAGTGA
4052575 AGCAAATCAATCTTAAGCCTTCACC-AAAGAGGAGTGA
1 AGCAAATCAATCTTAAGCCTTCACCGAAA-AGGAGTGA
* *
4052612 AGCAAA-CCATCTTAAGCCTTCACCAAAAAGGAG-GAA
1 AGCAAATCAATCTTAAGCCTTCACCGAAAAGGAGTG-A
* * * *
4052648 AGCAAATCAATTTGTAAGCCTTCACTGAAGAGTAGTGA
1 AGCAAATCAATCT-TAAGCCTTCACCGAAAAGGAGTGA
4052686 AGCA
1 AGCA
4052690 CCACCTTGAG
Statistics
Matches: 101, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
35 1 0.01
36 32 0.32
37 39 0.39
38 28 0.28
39 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (37 bp):
AGCAAATCAATCTTAAGCCTTCACCGAAAAGGAGTGA
Found at i:4052631 original size:36 final size:36
Alignment explanation
Indices: 4052547--4052731 Score: 173
Period size: 36 Copynumber: 5.1 Consensus size: 36
4052537 AGCAAAGTAA
*
4052547 ATCTTAAGCCTTCACCGAAA-AGGAGTGAAGCAAATCA
1 ATCTTAAGCCTTCACC-AAAGAGGAGTGAAGCAAA-CC
4052584 ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
1 ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
* *
4052620 ATCTTAAGCCTTCACCAAAAAGGAG-GAAAGCAAATCA
1 ATCTTAAGCCTTCACCAAAGAGGAGTG-AAGCAAA-CC
* ** *
4052657 ATTTGTAAGCCTTCACTGAAGAGTAGTGAAGC--ACC
1 ATCT-TAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
* * **
4052692 ACCTTGAGCCTTCA-CAGAAGAATAGTGAAGCAAACTC
1 ATCTTAAGCCTTCACCA-AAGAGGAGTGAAGCAAAC-C
4052729 ATC
1 ATC
4052732 AGTAAGTCTT
Statistics
Matches: 123, Mismatches: 16, Indels: 18
0.78 0.10 0.11
Matches are distributed among these distances:
34 22 0.18
35 4 0.03
36 38 0.31
37 37 0.30
38 21 0.17
39 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (36 bp):
ATCTTAAGCCTTCACCAAAGAGGAGTGAAGCAAACC
Found at i:4052633 original size:73 final size:72
Alignment explanation
Indices: 4052547--4052725 Score: 220
Period size: 73 Copynumber: 2.5 Consensus size: 72
4052537 AGCAAAGTAA
4052547 ATCTTAAGCCTTCACCGAAAAGGAGTGAAGCAAATCAATCT-TAAGCCTTCACCAAAGAGGAGTG
1 ATCTTAAGCCTTCACCGAAAAGGAGTGAAGCAAATCAATCTGTAAGCCTTCACCAAAGAGGAGTG
4052611 AAGCAAACC
66 AAGC--ACC
* * ** *
4052620 ATCTTAAGCCTTCACCAAAAAGGAG-GAAAGCAAATCAATTTGTAAGCCTTCACTGAAGAGTAGT
1 ATCTTAAGCCTTCACCGAAAAGGAGTG-AAGCAAATCAATCTGTAAGCCTTCACCAAAGAGGAGT
4052684 GAAGCACC
65 GAAGCACC
* * * *
4052692 ACCTTGAGCCTTCACAGAAGAA-TAGTGAAGCAAA
1 ATCTTAAGCCTTCACCGAA-AAGGAGTGAAGCAAA
4052726 CTCATCAGTA
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
72 28 0.30
73 40 0.43
74 24 0.26
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.19
Consensus pattern (72 bp):
ATCTTAAGCCTTCACCGAAAAGGAGTGAAGCAAATCAATCTGTAAGCCTTCACCAAAGAGGAGTG
AAGCACC
Found at i:4053016 original size:40 final size:41
Alignment explanation
Indices: 4052926--4053025 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 41
4052916 TTCACAATTT
* *
4052926 ATAAGTCCTTTGGGCCATCAGTAAGTCTTTTGAGCATGATG
1 ATAAGTCCTTTGGGCCATCAGTAAGTCTTTAGAGCAAGATG
* * * * *
4052967 TTAAATCCTTCGGGTCATCTGTAAG-CTTTAGAGCAAGATG
1 ATAAGTCCTTTGGGCCATCAGTAAGTCTTTAGAGCAAGATG
4053007 ATAAGTCCTTTGGGCCATC
1 ATAAGTCCTTTGGGCCATC
4053026 CATAAAACCT
Statistics
Matches: 48, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
40 28 0.58
41 20 0.42
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (41 bp):
ATAAGTCCTTTGGGCCATCAGTAAGTCTTTAGAGCAAGATG
Found at i:4053151 original size:42 final size:42
Alignment explanation
Indices: 4053075--4053183 Score: 112
Period size: 42 Copynumber: 2.6 Consensus size: 42
4053065 AAATGAAAAA
* * * *
4053075 ATGATGTTTAAATCCTTCGGGACATCAGTAAGTCTTTCGTGC
1 ATGATGATTAAATCCTTCGGGTCATCAGTAAGTCTCTCGAGC
* ** *
4053117 ATGATGCTTAAATCCTTCGGGTCATTTGTGAGTCTCTCGAGC
1 ATGATGATTAAATCCTTCGGGTCATCAGTAAGTCTCTCGAGC
* * *
4053159 AAGA-GAGTAAATCCTTTGGGTCATC
1 ATGATGATTAAATCCTTCGGGTCATC
4053184 CATAAGACCT
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
41 17 0.31
42 38 0.69
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (42 bp):
ATGATGATTAAATCCTTCGGGTCATCAGTAAGTCTCTCGAGC
Found at i:4053373 original size:24 final size:24
Alignment explanation
Indices: 4053346--4053395 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
4053336 AGGTCCTAGG
4053346 AAGGGAGAGGTTCAAATGGCAGTC
1 AAGGGAGAGGTTCAAATGGCAGTC
4053370 AAGGGAGAGGTTCAAATGGCAGTC
1 AAGGGAGAGGTTCAAATGGCAGTC
4053394 AA
1 AA
4053396 TTCAAGGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.12, G:0.36, T:0.16
Consensus pattern (24 bp):
AAGGGAGAGGTTCAAATGGCAGTC
Found at i:4053779 original size:54 final size:54
Alignment explanation
Indices: 4053639--4053906 Score: 339
Period size: 54 Copynumber: 5.0 Consensus size: 54
4053629 TAGTGAAGCA
* * * * *
4053639 GAAGAAGATGTTCGAGTTCCATAATCCCTAGAGAAAGGGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * * *
4053693 ---GAAGATGTCTGAGTTTTATACTCCCTAGAGAAAGAGGGATCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTT
4053744 GAAGAAGATGTCCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTTCCTAG-AGAAAGAGGGAGCGAACCCGTTT
** * **
4053798 GAAGAAGATGTCTTAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCATAA
1 GAAGAAGATGTCCGAGTTCTATACTTCCTAG-AGAAAGAGGGAGCGAACCCGTTT
* *
4053852 GAAGAAGATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCTATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTT
4053906 G
1 G
4053907 TTGAAGATTT
Statistics
Matches: 186, Mismatches: 23, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
51 44 0.24
53 1 0.01
54 140 0.75
55 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (54 bp):
GAAGAAGATGTCCGAGTTCTATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTT
Found at i:4053913 original size:54 final size:54
Alignment explanation
Indices: 4053639--4053950 Score: 329
Period size: 54 Copynumber: 5.8 Consensus size: 54
4053629 TAGTGAAGCA
* * * *
4053639 GAAGAAGATGTTCGAGTTCCATAATCCCT-AGAGAAAGGGGGAGCGAACCCGTTT
1 GAAGAAGATGTTCGAGTTCTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTT
* * *
4053693 ---GAAGATG-TCTGAGTTTTATACTCCCT-AGAGAAAGAGGGATCGAACCCGTTT
1 GAAGAAGATGTTC-GAGTTCTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTT
*
4053744 GAAGAAGATGTCCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTT
* * **
4053798 GAAGAAGATG-TCTTAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCATAA
1 GAAGAAGATGTTC-GAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTT
*
4053852 GAAGAAGATGTTCGAGTTCCATACTTCCT-AGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTTCGAGTTCTATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTTT
** * *
4053906 GTTGAAGATTTTTCGAG-TCTTATAC-TCTCTGAAGAAATAGGGAGC
1 GAAGAAGA-TGTTCGAGTTC-TATACTTC-CTGAAGAAAGAGGGAGC
4053951 AGACACGATT
Statistics
Matches: 221, Mismatches: 24, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
50 2 0.01
51 43 0.19
53 2 0.01
54 144 0.65
55 29 0.13
56 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (54 bp):
GAAGAAGATGTTCGAGTTCTATACTTCCTGAAGAAAGAGGGAGCGAACCCGTTT
Found at i:4053913 original size:108 final size:108
Alignment explanation
Indices: 4053638--4053914 Score: 375
Period size: 108 Copynumber: 2.6 Consensus size: 108
4053628 GTAGTGAAGC
* * *
4053638 AGAAGAAGATGTTCGAGTTCCATAATCCCTAGAGAAAGGGGGAGCGAACCCG--T-TTGAAGATG
1 AGAAGAAGATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTTGTTGAAGATG
* * * *
4053700 TCTGAGTTTTATACTCCCTAGAGAAAGAGGGATCGAACCCGTT
66 TCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATA
* * * **
4053743 TGAAGAAGATGTCCGAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCGTTTGAAGAAGAT
1 AGAAGAAGATGTTCGAGTTCCATACTTCCTAG-AGAAAGAGGGAGCGAACCCGTTTGTTGAAGAT
* *
4053807 GTCTTAGTTCTATACTTCCT-GAAGAAAGAGGGAGCGAACCCATA
65 GTCTGAGTTCTATACTCCCTAG-AGAAAGAGGGAGCGAACCCATA
4053851 AGAAGAAGATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTTGTTGAAGAT
1 AGAAGAAGATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTTGTTGAAGAT
4053915 TTTTCGAGTC
Statistics
Matches: 147, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
104 1 0.01
105 44 0.30
107 2 0.01
108 99 0.67
109 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.23
Consensus pattern (108 bp):
AGAAGAAGATGTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCGTTTGTTGAAGATG
TCTGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCATA
Found at i:4053948 original size:55 final size:55
Alignment explanation
Indices: 4053691--4054550 Score: 597
Period size: 55 Copynumber: 15.9 Consensus size: 55
4053681 GCGAACCCGT
* * * * *
4053691 TTGAAGA-TG-TCTGAGTTTTATACTCCCT-AGAGAAAGAGGGATCGAACCCGTTTG
1 TTGAAGATTGTTC-GAGTCTTATACTCTCTGA-AGAAATAGGGAGCGAACACGTTTG
** * * *
4053745 AAGAAGA-TGTCCGAGT-TCTATACT-TCCTGAAGAAAGAGGGAGCGAACCCGTTTG
1 TTGAAGATTGTTCGAGTCT-TATACTCT-CTGAAGAAATAGGGAGCGAACACGTTTG
** * * * * **
4053799 AAGAAGA-TG-TCTTAGT-TCTATACT-TCCTGAAGAAAGAGGGAGCGAACCCATAAG
1 TTGAAGATTGTTC-GAGTCT-TATACTCT-CTGAAGAAATAGGGAGCGAACACGTTTG
** * * *
4053853 AAGAAGA-TGTTCGAGT-TCCATACT-TCCT-AGAGAAAGAGGGAGCGAACCCGTTTG
1 TTGAAGATTGTTCGAGTCT-TATACTCT-CTGA-AGAAATAGGGAGCGAACACGTTTG
* *
4053907 TTGAAGATTTTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGC-AGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-ACACGTTTG
* * * *
4053962 TTGAAGATTGTTCGAGTCTTATACTCTCTGAGGAAATAGAGAG-AAGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-ACACGTTTG
* * * ***
4054017 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAG-TAGACACAAATG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-ACACGTTTG
* * *
4054072 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAAGGAGC-AGACACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-ACACGTTTG
* *
4054127 TTGAAGATAGTTCGAGTCTTATA--CTCTGAA-AGAATAGGGAGC-AACCACGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCGAA-CACGTTTG
* *
4054180 TTGAAAATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGC-AGACACGTTTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-ACACGTTTG
** * * * * ** *
4054235 TTGAAGGCTGTTCAAGTCCTATACTCTTTGAAGGAATAGGGAGAAAACATGTTTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGAACACGTTTG
* *
4054290 TTGAAGA----TCGAGTCCTATACTCTCTGAAGGAATA-GGAGC-AGACACGTTTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGA-ACACGTTTG
* * * * * *
4054340 TTGAAGATTTTTTCAAGTCCTATACTCTCTAAAGGAATAGGGAGCGGACACGTTTG
1 TTGAAGA-TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGAACACGTTTG
* * * *
4054396 TTGAAGATTTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTG
1 TTGAAGA-TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGAACACGTTTG
* * * * *
4054452 TTGAAGA----TCTAGT-TCTATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTT-
1 TTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAGCGAACACGTTTG
** * *
4054502 TCAAAAGATT-TCTCGAGT-TCTATACTCCCTGAAGCAATAGGGAGCGAAC
1 T-TGAAGATTGT-TCGAGTCT-TATACTCTCTGAAGAAATAGGGAGCGAAC
4054551 CCGCTGGTCG
Statistics
Matches: 698, Mismatches: 73, Indels: 69
0.83 0.09 0.08
Matches are distributed among these distances:
49 1 0.00
50 20 0.03
51 63 0.09
52 2 0.00
53 49 0.07
54 139 0.20
55 344 0.49
56 80 0.11
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (55 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCGAACACGTTTG
Found at i:4054032 original size:110 final size:110
Alignment explanation
Indices: 4053901--4054459 Score: 663
Period size: 110 Copynumber: 5.1 Consensus size: 110
4053891 GGAGCGAACC
*
4053901 CGTTTGTTGAAGATTTTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGA
*
4053966 AGATTGTTCGAGTCTTATACTCTCTG-AGGAAATAGAGAGAAGACA
66 AGATTGTTCGAGTCTTATACTCTCTGAAGG-AATAGAGAGCAGACA
* * * * * *
4054011 CGATTGTTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGAGTAGACACAAATGTTGA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGA
* *
4054076 AAATTGTTCGAGTCTTATACTCTCTGAAGAAATA-AGGAGCAGACA
66 AGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGA-GAGCAGACA
* *
4054121 CGATTGTTGAAGATAGTTCGAGTCTTATA--CTCTGAA-AGAATAGGGAGCA-ACCACGATTGTT
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCAGA-CACGATTGTT
* *
4054182 GAAAATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
64 GAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACA
** * * * * * * * *
4054229 CGTTTGTTGAAGGCTGTTCAAGTCCTATACTCTTTGAAGGAATAGGGAGAAAACATGTTTGTTGA
1 CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGA
*
4054294 AGA----TCGAGTCCTATACTCTCTGAAGGAATAG-GAGCAGACA
66 AGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACA
* * * * * * *
4054334 CGTTTGTTGAAGATTTTTTCAAGTCCTATACTCTCTAAAGGAATAGGGAGCGGACACGTTTGTTG
1 CGTTTGTTGAAGA-TTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
* * * *
4054399 AAGATTTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
65 AAGA-TTGTTCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACA
4054446 CGTTTGTTGAAGAT
1 CGTTTGTTGAAGAT
4054460 CTAGTTCTAT
Statistics
Matches: 391, Mismatches: 42, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
105 21 0.05
106 74 0.19
107 2 0.01
108 91 0.23
109 1 0.00
110 150 0.38
111 31 0.08
112 21 0.05
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.30
Consensus pattern (110 bp):
CGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGA
AGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACA
Found at i:4054293 original size:163 final size:163
Alignment explanation
Indices: 4053901--4054459 Score: 673
Period size: 163 Copynumber: 3.4 Consensus size: 163
4053891 GGAGCGAACC
* * *
4053901 CGTTTGTTGAAGATTTTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGA
1 CGTTTGTTGAAGATTGTTCAAGTCCTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGA
* * *
4053966 AGATTGTTCGAGTCTTATACTCTCTG-AGGAAATAGAGAGAAGACACGATTGTTGAAAATTGTTC
66 AGATAGTTCGAGTCTTATAC-CTCTGAAGG-AATAGGGAGCA-ACACGATTGTTGAAAATTGTTC
* * *
4054030 GAGTCTTATACTCTCTGAAGAAATAGAGAGTAGACA
128 GAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
*** * * * *
4054066 CAAATGTTGAAAATTGTTCGAGTCTTATACTCTCTGAAGAAATAAGGAGCAGACACGATTGTTGA
1 CGTTTGTTGAAGATTGTTCAAGTCCTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGA
*
4054131 AGATAGTTCGAGTCTTATA-CTCTGAAAGAATAGGGAGCAACCACGATTGTTGAAAATTGTTCGA
66 AGATAGTTCGAGTCTTATACCTCTGAAGGAATAGGGAGCAA-CACGATTGTTGAAAATTGTTCGA
4054195 GTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
130 GTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
** * * * * * *
4054229 CGTTTGTTGAAGGCTGTTCAAGTCCTATACTCTTTGAAGGAATAGGGAGAAAACATGTTTGTTGA
1 CGTTTGTTGAAGATTGTTCAAGTCCTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGA
* * * *
4054294 AG--A--TCGAGTCCTATACTCTCTGAAGGAATA-GGAGCAGACACGTTTGTTGAAGATTTTTTC
66 AGATAGTTCGAGTCTTATAC-CTCTGAAGGAATAGGGAGCA-ACACGATTGTTGAA-AATTGTTC
* * * *
4054354 AAGTCCTATACTCTCTAAAGGAATAGGGAGCGGACA
128 GAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACA
* * *
4054390 CGTTTGTTGAAGATTTGTTCAAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACACGTTTGTTG
1 CGTTTGTTGAAGA-TTGTTCAAGTCCTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTG
4054455 AAGAT
65 AAGAT
4054460 CTAGTTCTAT
Statistics
Matches: 341, Mismatches: 44, Indels: 19
0.84 0.11 0.05
Matches are distributed among these distances:
159 11 0.03
160 18 0.05
161 64 0.19
162 49 0.14
163 120 0.35
164 2 0.01
165 77 0.23
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.30
Consensus pattern (163 bp):
CGTTTGTTGAAGATTGTTCAAGTCCTATACTCTCTGAAGAAATAGGGAGCAGACACGATTGTTGA
AGATAGTTCGAGTCTTATACCTCTGAAGGAATAGGGAGCAACACGATTGTTGAAAATTGTTCGAG
TCTTATACTCTCTGAAGGAATAGGGAGCAGACA
Found at i:4054740 original size:17 final size:18
Alignment explanation
Indices: 4054718--4054752 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
4054708 AAATATTAAA
4054718 ATTATTAATTATT-TATT
1 ATTATTAATTATTGTATT
4054735 ATTATTAATTATTGTATT
1 ATTATTAATTATTGTATT
4054753 GTATTTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
ATTATTAATTATTGTATT
Found at i:4054757 original size:17 final size:17
Alignment explanation
Indices: 4054720--4054757 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4054710 ATATTAAAAT
*
4054720 TATTAATTATTTATTAT
1 TATTAATTATTTATTAG
4054737 TATTAATTATTGTATT-G
1 TATTAATTATT-TATTAG
4054754 TATT
1 TATT
4054758 TTACAGGCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (17 bp):
TATTAATTATTTATTAG
Found at i:4055774 original size:14 final size:14
Alignment explanation
Indices: 4055757--4055794 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
4055747 CTCGGTTGTG
4055757 GAAAGAAGAGTAAA
1 GAAAGAAGAGTAAA
4055771 GAAAGAAGAGTAAA
1 GAAAGAAGAGTAAA
4055785 GAAAGAAGAG
1 GAAAGAAGAG
4055795 AATGGGAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.63, C:0.00, G:0.32, T:0.05
Consensus pattern (14 bp):
GAAAGAAGAGTAAA
Found at i:4062779 original size:21 final size:20
Alignment explanation
Indices: 4062733--4062783 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
4062723 GTTCAATGAG
*
4062733 TATCGATACTCAGGGTCTAG
1 TATCGATACTCAGGGTCTAA
4062753 TATCGATACTCAGGTGATC-AA
1 TATCGATACTCAGG-G-TCTAA
4062774 TATCGATACT
1 TATCGATACT
4062784 AAGGCATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 14 0.50
21 12 0.43
22 2 0.07
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (20 bp):
TATCGATACTCAGGGTCTAA
Found at i:4067115 original size:24 final size:23
Alignment explanation
Indices: 4067071--4067115 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
4067061 TTAATAACCT
*
4067071 ATTATTTTGATATTTTTTTAATC
1 ATTAGTTTGATATTTTTTTAATC
4067094 ATTAGTTT-ATATGTTTATTTAA
1 ATTAGTTTGATAT-TTT-TTTAA
4067116 GTTATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 10 0.53
24 5 0.26
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.62
Consensus pattern (23 bp):
ATTAGTTTGATATTTTTTTAATC
Found at i:4069483 original size:16 final size:16
Alignment explanation
Indices: 4069459--4069496 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
4069449 AAAGATTTTG
4069459 AAATCAGGAGTTCTGA
1 AAATCAGGAGTTCTGA
*
4069475 AAATTAGGAGTTCTGA
1 AAATCAGGAGTTCTGA
4069491 AAATCA
1 AAATCA
4069497 AGGGCATGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (16 bp):
AAATCAGGAGTTCTGA
Found at i:4079434 original size:16 final size:16
Alignment explanation
Indices: 4079413--4079443 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4079403 AACAGTAGTG
4079413 AAGCAAATCATTTGCA
1 AAGCAAATCATTTGCA
*
4079429 AAGCAAATCCTTTGC
1 AAGCAAATCATTTGC
4079444 CTTCACAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (16 bp):
AAGCAAATCATTTGCA
Found at i:4079750 original size:21 final size:22
Alignment explanation
Indices: 4079705--4079752 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
4079695 CGGTTACAAA
4079705 ACAAGGCACATAGGCCCAAGATT
1 ACAAGGCACATAGGCCC-AGATT
4079728 ACAAGGCACATAGGCCC-GATT
1 ACAAGGCACATAGGCCCAGATT
4079749 ACAA
1 ACAA
4079753 CTAAGCCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 8 0.32
23 17 0.68
ACGTcount: A:0.40, C:0.27, G:0.21, T:0.12
Consensus pattern (22 bp):
ACAAGGCACATAGGCCCAGATT
Found at i:4080436 original size:22 final size:22
Alignment explanation
Indices: 4080402--4080443 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
4080392 TAAGATACCT
*
4080402 TCAGATTTGGATTTAGGGTAAA
1 TCAGATTTGGATTGAGGGTAAA
4080424 TCAGACTTT-GATTGAGGGTA
1 TCAGA-TTTGGATTGAGGGTA
4080444 GGTTTGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (22 bp):
TCAGATTTGGATTGAGGGTAAA
Found at i:4082239 original size:133 final size:135
Alignment explanation
Indices: 4082020--4082271 Score: 386
Period size: 134 Copynumber: 1.9 Consensus size: 135
4082010 CGATGTATCA
* *
4082020 GAAAATATCCTTTGTATAGTAGCGATACGATAAACCAGGTAAAAGGGATCCAAACCATCACTTGG
1 GAAAATAGCCTTTGTATAGTAGCGATACGATAAACCAGGTAAAA-GGATCCAAACAATCACTTGG
* *
4082085 GAGGGGTGCTTTTTAGAGATGG-AAAAGGTTCTGCTCCAAGGTTGGACCGTTAACTTTCGTAAAA
65 GAGGGGTGCTTTTCAGAGATGGAAAAAGGTTCTGCTCCAAGGTTGAACCGTTAACTTTCGTAAAA
4082149 AATTTG
130 AATTTG
* *
4082155 GAAAATAGCCTTT-TGTAGTAGCGATACGGT-AACACAGGTAAACA-GATCCAAACAATCACTTG
1 GAAAATAGCCTTTGTATAGTAGCGATACGATAAAC-CAGGTAAA-AGGATCCAAACAATCACTTG
*
4082217 GGAGGGGTGCTTTTCAGTGATGGAAAAAGGTTCTGCTCCAAGGTTGAACCGTTAA
64 GGAGGGGTGCTTTTCAGAGATGGAAAAAGGTTCTGCTCCAAGGTTGAACCGTTAA
4082272 ATAACTTTCG
Statistics
Matches: 107, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
133 41 0.38
134 53 0.50
135 13 0.12
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (135 bp):
GAAAATAGCCTTTGTATAGTAGCGATACGATAAACCAGGTAAAAGGATCCAAACAATCACTTGGG
AGGGGTGCTTTTCAGAGATGGAAAAAGGTTCTGCTCCAAGGTTGAACCGTTAACTTTCGTAAAAA
ATTTG
Found at i:4085706 original size:19 final size:19
Alignment explanation
Indices: 4085682--4085731 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
4085672 CGGCCAAGAG
* **
4085682 CATGTATCTTCATTTAAAT
1 CATGTATTTTCATCAAAAT
4085701 CATGTATTTTCATCAAAAT
1 CATGTATTTTCATCAAAAT
4085720 CATGTATTTTCA
1 CATGTATTTTCA
4085732 AAGGGGATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (19 bp):
CATGTATTTTCATCAAAAT
Found at i:4101964 original size:253 final size:252
Alignment explanation
Indices: 4101516--4102021 Score: 955
Period size: 253 Copynumber: 2.0 Consensus size: 252
4101506 AGCAAGCAGA
4101516 AGGCCGCAGTGGGAAGGAATACTGTGGCATCAGATGCTGCTGAAGCAGATTGAAATGCCTTGACA
1 AGGCCGCAGTGGGAAGGAATACTGTGGCATCAGATGCTGCTGAAGCAGATTGAAATGCCTTGACA
4101581 TTTCTGGCATAGAAACAGAAAAAAATATAATTTTGTAAAAAGAACAACTAGAAAAAACGCGTGAC
66 TTTCTGGCATAGAAACAGAAAAAAATATAATTTTGTAAAAAGAACAACTAGAAAAAACGCGTGAC
4101646 TATATTTGTAACCGCCTGCTGGGGGACCATTGCCGCATAGAGGATAAGACTCACGCCGAAGGAGT
131 TATATTTGTAACCGCCTGCTGGGGGACCATTGCCGCATAGAGGATAAGACTCACGCCGAAGGAGT
4101711 GGACTCTAGGGGTATGATGGGTA-TTTGAGCACAAAAAATCTCATCATTACCGTTAGAT
196 -GACTCTAGGGGTATGATGGGTATTTTGAGCAC-AAAAATCTCATCATTACCGTTAGAT
4101769 AGGCCGCAGTGGGAAGGAATACTGTGGCATCAGATGCTGCTGAAGCAGATTGAAATGCCTTGACA
1 AGGCCGCAGTGGGAAGGAATACTGTGGCATCAGATGCTGCTGAAGCAGATTGAAATGCCTTGACA
4101834 TTTCTGGCATAGAAACAGAAAAAAATATAATTTTGTAAAAAGAACAACTAG-AAAAACGCGTGAC
66 TTTCTGGCATAGAAACAGAAAAAAATATAATTTTGTAAAAAGAACAACTAGAAAAAACGCGTGAC
4101898 TAATATTTGTAACCGCCTGCT-GGGGACCATTGCCGCATAGAAGGATAAGACTCACGCCGAAGGA
131 T-ATATTTGTAACCGCCTGCTGGGGGACCATTGCCGCATAG-AGGATAAGACTCACGCCGAAGGA
4101962 GTGACTCTAGGGGTATGATGGGTATTTTGAGCACAAAAATCTCATCATTACCGTTAGAT
194 GTGACTCTAGGGGTATGATGGGTATTTTGAGCACAAAAATCTCATCATTACCGTTAGAT
4102021 A
1 A
4102022 TTTTTATTAT
Statistics
Matches: 250, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
252 81 0.32
253 169 0.68
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (252 bp):
AGGCCGCAGTGGGAAGGAATACTGTGGCATCAGATGCTGCTGAAGCAGATTGAAATGCCTTGACA
TTTCTGGCATAGAAACAGAAAAAAATATAATTTTGTAAAAAGAACAACTAGAAAAAACGCGTGAC
TATATTTGTAACCGCCTGCTGGGGGACCATTGCCGCATAGAGGATAAGACTCACGCCGAAGGAGT
GACTCTAGGGGTATGATGGGTATTTTGAGCACAAAAATCTCATCATTACCGTTAGAT
Found at i:4109824 original size:90 final size:91
Alignment explanation
Indices: 4109637--4109864 Score: 332
Period size: 90 Copynumber: 2.5 Consensus size: 91
4109627 AAAGTTTACA
* * * * *
4109637 GATGACCCGAAGAATTTAAAAATCAAGAAACCCCTGAAGGCTTAGTTTCTTAAAATCTCATTTGA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCAGAAGGCTCAGTTTCTTAAAATCTCATTTGA
* * *
4109702 AAATATCCTGCACTGAAGGTCTTATG
66 AAACATCCTACACTGAAGGTCATATG
* * *
4109728 GATGGCCCGAAGGACTTAAAAATAAAGAAACCCCCGAAGGCTGAGTTTCTT-AAATCTCATTTGA
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCAGAAGGCTCAGTTTCTTAAAATCTCATTTGA
4109792 AAACATCCTACACTGAAGGTCATATG
66 AAACATCCTACACTGAAGGTCATATG
* *
4109818 GATGGCCCGAAGGACGTAAAAATCAAGAAACCCTAGAAGGCTCAGTT
1 GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCAGAAGGCTCAGTT
4109865 CATTAATTGT
Statistics
Matches: 123, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
90 78 0.63
91 45 0.37
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (91 bp):
GATGGCCCGAAGGACTTAAAAATCAAGAAACCCCAGAAGGCTCAGTTTCTTAAAATCTCATTTGA
AAACATCCTACACTGAAGGTCATATG
Found at i:4109987 original size:43 final size:43
Alignment explanation
Indices: 4109919--4110483 Score: 587
Period size: 43 Copynumber: 12.6 Consensus size: 43
4109909 CAAGTGTTCA
* * *
4109919 TCAAGTTTTTCATCAAGGAACCCCTACATATCACGATGGTCCC
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCC
* * **
4109962 TCAAGATTGTCATCAAGAAAACCCTACATATCACGATGGTTTC
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCC
* * *
4110005 TCATGCTTGTCATCAAGGAACCCCTACATATCATGATGGTCCC
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCC
* * **
4110048 TTAAGCTTTTCATCAAGAAACCCCTACATATCACGATGGTTTC
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCC
*
4110091 TCAAGCTTGTCATCAAATTTGTCATCAAGGAACCCCTACATATCGCGATGGTCCC
1 TCAAGCTTGTCATC-AA---G------A--AACCCCTACATATCACGATGGTCCC
* * **
4110146 TCAAGTTTTTCATCAAGAAACCCCTACATATCACGATGGTTTC
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCC
*
4110189 TCAAGCTTGTCATCAA-AGAACCCCTACATATCACGATGGTCCT
1 TCAAGCTTGTCATCAAGA-AACCCCTACATATCACGATGGTCCC
4110232 TCAAGCTTGTCATCAAATTTGTCATCAAGGAACCCCTACATATCAC-AGTGGTCCC
1 TCAAGCTTGTCATC-AA---G------A--AACCCCTACATATCACGA-TGGTCCC
* **
4110287 TCAAGCTTTTCATCAAGAAACCCCTACATATCACGATGGTTTC
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCC
* *
4110330 TCAAGCTTGTCATCAA-AGAACCCCTACATATCATGATGGTCCT
1 TCAAGCTTGTCATCAAGA-AACCCCTACATATCACGATGGTCCC
* *
4110373 TCAAGCTTGTCATCAAGGAACCCCTACATATCACGATGGTCCT
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCC
* *
4110416 TCAAGCTTGTCATCAAGAAACCCCTACATATCACAATGGTCTC
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCC
* *
4110459 TCAAGCTTTTCATCGAGAAACCCCT
1 TCAAGCTTGTCATCAAGAAACCCCT
4110484 GAAAATCAGG
Statistics
Matches: 441, Mismatches: 52, Indels: 58
0.80 0.09 0.11
Matches are distributed among these distances:
42 2 0.00
43 352 0.80
44 5 0.01
45 2 0.00
47 1 0.00
51 2 0.00
53 1 0.00
54 6 0.01
55 70 0.16
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (43 bp):
TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCC
Found at i:4110140 original size:141 final size:139
Alignment explanation
Indices: 4109968--4110472 Score: 674
Period size: 141 Copynumber: 3.7 Consensus size: 139
4109958 TCCCTCAAGA
* * ** * *
4109968 TTGTCATCAAGAAAACCCTACATATCACGATGGTTTCTCATGCTTGTCATCAAGGAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGAAACCCCTACA
* * * *
4110033 TATCATGATGGTCCCTTAAGCTTTTCATC-AAGAAACCCCTACATATCACGATGGTTTCTCAAGC
66 TATCACGATGGTCTCTCAAGCTTGTCATCAAAG-AACCCCTACATATCACGATGG--TCTCAAGC
4110097 TTGTCATCAAAT
128 TTGTCATCAAAT
* * *
4110109 TTGTCATCAAGGAACCCCTACATATCGCGATGGTCCCTCAAGTTTTTCATCAAGAAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGAAACCCCTACA
*
4110174 TATCACGATGGTTTCTCAAGCTTGTCATCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCT
66 TATCACGATGGTCTCTCAAGCTTGTCATCAAAGAACCCCTACATATCACGATGGT-C-TCAAGCT
4110239 TGTCATCAAAT
129 TGTCATCAAAT
*
4110250 TTGTCATCAAGGAACCCCTACATATCAC-AGTGGTCCCTCAAGCTTTTCATCAAGAAACCCCTAC
1 TTGTCATCAAGGAACCCCTACATATCACGA-TGGTCCCTCAAGCTTGTCATCAAGAAACCCCTAC
* *
4110314 ATATCACGATGGTTTCTCAAGCTTGTCATCAAAGAACCCCTACATATCATGATGG--TC---C--
65 ATATCACGATGGTCTCTCAAGCTTGTCATCAAAGAACCCCTACATATCACGATGGTCTCAAGCTT
**
4110372 -T--TCAAGC
130 GTCATCAAAT
*
4110379 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAGAAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGAAACCCCTACA
* *
4110444 TATCACAATGGTCTCTCAAGCTTTTCATC
66 TATCACGATGGTCTCTCAAGCTTGTCATC
4110473 GAGAAACCCC
Statistics
Matches: 335, Mismatches: 24, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
129 91 0.27
130 1 0.00
131 1 0.00
134 1 0.00
137 2 0.01
139 1 0.00
140 2 0.01
141 233 0.70
142 3 0.01
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (139 bp):
TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTGTCATCAAGAAACCCCTACA
TATCACGATGGTCTCTCAAGCTTGTCATCAAAGAACCCCTACATATCACGATGGTCTCAAGCTTG
TCATCAAAT
Found at i:4110142 original size:98 final size:98
Alignment explanation
Indices: 4110011--4110205 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
4110001 TTTCTCATGC
* *
4110011 TTGTCATCAAGGAACCCCTACATATCATGATGGTCCCTTAAGCTTTTCATCAAGAAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACA
4110076 TATCACGATGGTTTCTCAAGCTTGTCATCAAAT
66 TATCACGATGGTTTCTCAAGCTTGTCATCAAAT
* *
4110109 TTGTCATCAAGGAACCCCTACATATCGCGATGGTCCCTCAAGTTTTTCATCAAGAAACCCCTACA
1 TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACA
4110174 TATCACGATGGTTTCTCAAGCTTGTCATCAAA
66 TATCACGATGGTTTCTCAAGCTTGTCATCAAA
4110206 GAACCCCTAC
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (98 bp):
TTGTCATCAAGGAACCCCTACATATCACGATGGTCCCTCAAGCTTTTCATCAAGAAACCCCTACA
TATCACGATGGTTTCTCAAGCTTGTCATCAAAT
Found at i:4110229 original size:184 final size:182
Alignment explanation
Indices: 4109883--4110465 Score: 699
Period size: 184 Copynumber: 3.2 Consensus size: 182
4109873 GTCACGAAGG
* * *
4109883 AACCCCTACATATCACAATGATCCCTCAAG-TGTTCATCAAGTTTTTCATCAAGGAACCCCTACA
1 AACCCCTACATATCACAATGGTCTCTCAAGCTG-TCATCAA-ATTTTCATCAAGGAACCCCTACA
* *
4109947 TATCACGATGGTCCCTCAAGATTGTCATCAAGAAAACCCTACATATCACGATGGTTTCTCATGCT
64 TATCACGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCT
*
4110012 TGTCATCAAGGAACCCCTACATATCATGATGGTCCCTT-AAGCTTTTCATCAAGA
129 TGTCATCAAGGAACCCCTACATATCACGATGGT-CCTTCAAGCTTTTCATCAAGA
* *
4110066 AACCCCTACATATCACGATGGTTTCTCAAGCTTGTCATCAAATTTGTCATCAAGGAACCCCTACA
1 AACCCCTACATATCACAATGGTCTCTCAAGC-TGTCATCAAATTT-TCATCAAGGAACCCCTACA
* * *
4110131 TATCGCGATGGTCCCTCAAGTTTTTCATCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCT
64 TATCACGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCT
*
4110196 TGTCATCAAAGAACCCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAATTTGTCATCAAG
129 TGTCATCAAGGAACCCCTACATATCACGATGGTCCTTCAA----G----C---TTT-TCATCAAG
*
4110261 G
182 A
* * *
4110262 AACCCCTACATATCACAGTGGTCCCTCAA---G----C---TTTTCATCAAGAAACCCCTACATA
1 AACCCCTACATATCACAATGGTCTCTCAAGCTGTCATCAAATTTTCATCAAGGAACCCCTACATA
** * * *
4110317 TCACGATGGTTTCTCAAGCTTGTCATCAA-AGAACCCCTACATATCATGATGG-TCCTTCAAGCT
66 TCACGATGGTCCCTCAAGATTGTCATCAAGA-AACCCCTACATATCACGATGGTTTC-TCAAGCT
*
4110380 TGTCATCAAGGAACCCCTACATATCACGATGGTCCTTCAAGCTTGTCATCAAGA
129 TGTCATCAAGGAACCCCTACATATCACGATGGTCCTTCAAGCTTTTCATCAAGA
4110434 AACCCCTACATATCACAATGGTCTCTCAAGCT
1 AACCCCTACATATCACAATGGTCTCTCAAGCT
4110466 TTTCATCGAG
Statistics
Matches: 349, Mismatches: 30, Indels: 50
0.81 0.07 0.12
Matches are distributed among these distances:
172 35 0.10
173 2 0.01
176 1 0.00
180 1 0.00
183 36 0.10
184 229 0.66
185 5 0.01
188 2 0.01
192 2 0.01
195 3 0.01
196 33 0.09
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.28
Consensus pattern (182 bp):
AACCCCTACATATCACAATGGTCTCTCAAGCTGTCATCAAATTTTCATCAAGGAACCCCTACATA
TCACGATGGTCCCTCAAGATTGTCATCAAGAAACCCCTACATATCACGATGGTTTCTCAAGCTTG
TCATCAAGGAACCCCTACATATCACGATGGTCCTTCAAGCTTTTCATCAAGA
Found at i:4110584 original size:15 final size:15
Alignment explanation
Indices: 4110566--4110596 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4110556 TTCAAGTGAA
4110566 ATTGTCTCAAGGGAG
1 ATTGTCTCAAGGGAG
4110581 ATTGTCTCAAGGGAG
1 ATTGTCTCAAGGGAG
4110596 A
1 A
4110597 CAAAATTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.13, G:0.32, T:0.26
Consensus pattern (15 bp):
ATTGTCTCAAGGGAG
Found at i:4110612 original size:36 final size:36
Alignment explanation
Indices: 4110567--4110653 Score: 147
Period size: 36 Copynumber: 2.4 Consensus size: 36
4110557 TCAAGTGAAA
* *
4110567 TTGTCTCAAGGGAGATTGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAGATCGTCTCAAGGGAGACAAAAT
*
4110603 TTGTTTCAAGGGAAATCGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAGATCGTCTCAAGGGAGACAAAAT
4110639 TTGTTTCAAGGGAGA
1 TTGTTTCAAGGGAGA
4110654 CAAAATTTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 47 1.00
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (36 bp):
TTGTTTCAAGGGAGATCGTCTCAAGGGAGACAAAAT
Found at i:4110670 original size:93 final size:93
Alignment explanation
Indices: 4110567--4110822 Score: 301
Period size: 93 Copynumber: 2.8 Consensus size: 93
4110557 TCAAGTGAAA
* * *
4110567 TTGTCTCAAGGGAGATTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAA-TCGTCTCAAGGGA
1 TTGTCTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACT-GTCTCAAGGGA
4110631 GACAAAATTTGTTTCAAGGGAGACAAAAT
65 GACAAAATTTGTTTCAAGGGAGACAAAAT
*
4110660 TTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAG
1 TTGTCTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAG
*
4110725 ATAAAATTTGTTTCAA-GG-G---AAA-
66 ACAAAATTTGTTTCAAGGGAGACAAAAT
* * * * * *
4110747 CTGACTCAAGGGAGACTGTCTCAAGGGAGACAAAAAATTTCTGTTTCGAGGGAAACTATCTCAAG
1 TTGTCTCAAGGGAAACTGTCTCAAGGGAGAC--AAAA-TT-TGTTTCAAGAGAAACTGTCTCAAG
* *
4110812 TGAGATAAAAT
62 GGAGACAAAAT
4110823 CTTCTTTAAA
Statistics
Matches: 145, Mismatches: 13, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
87 27 0.19
88 3 0.02
89 4 0.03
90 2 0.01
91 32 0.22
92 2 0.01
93 74 0.51
94 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (93 bp):
TTGTCTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGGGAG
ACAAAATTTGTTTCAAGGGAGACAAAAT
Found at i:4110681 original size:57 final size:57
Alignment explanation
Indices: 4110582--4110705 Score: 223
Period size: 57 Copynumber: 2.2 Consensus size: 57
4110572 TCAAGGGAGA
*
4110582 TTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATCGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAGACAAAATTTGTTTCAAGGGAAATCGTCTCAAGGGAGACAAAAT
4110639 TTGTTTCAAGGGAGACAAAATTTGTTTCAAGGGAAA-CTGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAGGGAGACAAAATTTGTTTCAAGGGAAATC-GTCTCAAGGGAGACAAAAT
4110696 TTGTTTCAAG
1 TTGTTTCAAG
4110706 AGAAACTGTC
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
56 1 0.02
57 64 0.98
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.27
Consensus pattern (57 bp):
TTGTTTCAAGGGAGACAAAATTTGTTTCAAGGGAAATCGTCTCAAGGGAGACAAAAT
Found at i:4110684 original size:36 final size:36
Alignment explanation
Indices: 4110644--4110762 Score: 211
Period size: 36 Copynumber: 3.3 Consensus size: 36
4110634 AAAATTTGTT
4110644 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
1 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
*
4110680 TCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTC
1 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
* *
4110716 TCAAGGGAGATAAAATTTGTTTCAAGGGAAACTGAC
1 TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
4110752 TCAAGGGAGAC
1 TCAAGGGAGAC
4110763 TGTCTCAAGG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 78 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (36 bp):
TCAAGGGAGACAAAATTTGTTTCAAGGGAAACTGTC
Found at i:4110684 original size:72 final size:71
Alignment explanation
Indices: 4110608--4110781 Score: 171
Period size: 72 Copynumber: 2.4 Consensus size: 71
4110598 AAAATTTGTT
* *
4110608 TCAAGGGAAATCGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAGACAAAATTTGTTTCAAGGGA
1 TCAAGGGAAATCGTCTCAAGGGAGACAAAA-CTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGA
*
4110673 AACTGTC
65 AACTGAC
* * *
4110680 TCAAGGGAGACAAAATTTGTTTCAA--GAG---AAACTGTCTCAAGGGAGATAAAATTTGTTTCA
1 TCAA-GG-G---AAA-TCGTCTCAAGGGAGACAAAACTGTCTCAAGGGAGACAAAATTTGTTTCA
4110740 AGGGAAACTGAC
60 AGGGAAACTGAC
*
4110752 TCAAGGGAGA-CTGTCTCAAGGGAGACAAAA
1 TCAAGGGAAATC-GTCTCAAGGGAGACAAAA
4110782 AATTTCTGTT
Statistics
Matches: 81, Mismatches: 9, Indels: 25
0.70 0.08 0.22
Matches are distributed among these distances:
66 6 0.07
67 2 0.02
68 3 0.04
70 1 0.01
71 5 0.06
72 45 0.56
73 5 0.06
74 1 0.01
76 3 0.04
77 3 0.04
78 7 0.09
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (71 bp):
TCAAGGGAAATCGTCTCAAGGGAGACAAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAA
ACTGAC
Found at i:4110765 original size:51 final size:54
Alignment explanation
Indices: 4110701--4110816 Score: 141
Period size: 55 Copynumber: 2.2 Consensus size: 54
4110691 AAAATTTGTT
* *
4110701 TCAAGAGAAACTGTCTCAAGGGAG-ATAAAA-TT-TGTTTCAAGGGAAACTGA-C
1 TCAAGAGAGACTGTCTCAAGGGAGAAAAAAATTTCTGTTTCAAGGGAAACT-ATC
* *
4110752 TCAAGGGAGACTGTCTCAAGGGAGACAAAAAATTTCTGTTTCGAGGGAAACTATC
1 TCAAGAGAGACTGTCTCAAGGGAGA-AAAAAATTTCTGTTTCAAGGGAAACTATC
*
4110807 TCAAGTGAGA
1 TCAAGAGAGA
4110817 TAAAATCTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
51 22 0.40
53 5 0.09
54 3 0.05
55 25 0.45
ACGTcount: A:0.37, C:0.15, G:0.25, T:0.23
Consensus pattern (54 bp):
TCAAGAGAGACTGTCTCAAGGGAGAAAAAAATTTCTGTTTCAAGGGAAACTATC
Found at i:4110775 original size:15 final size:15
Alignment explanation
Indices: 4110737--4110777 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
4110727 AAAATTTGTT
*
4110737 TCAAGGGAAACTGAC
1 TCAAGGGAGACTGAC
*
4110752 TCAAGGGAGACTGTC
1 TCAAGGGAGACTGAC
4110767 TCAAGGGAGAC
1 TCAAGGGAGAC
4110778 AAAAAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.34, C:0.20, G:0.32, T:0.15
Consensus pattern (15 bp):
TCAAGGGAGACTGAC
Found at i:4110908 original size:36 final size:35
Alignment explanation
Indices: 4110868--4111059 Score: 132
Period size: 36 Copynumber: 5.1 Consensus size: 35
4110858 TCTTTCAAGT
*
4110868 AAAATAGTCTCAAGTGAGATAAATCTTTTTTTAAG
1 AAAAAAGTCTCAAGTGAGATAAATCTTTTTTTAAG
* * * * *
4110903 AAAAATAATCTTAAGTTAAATAAATCTTCTTTTTTCGAG
1 AAAAA-AGTCTCAAGTGAGATAAATC-T-TTTTTT-AAG
* * *
4110942 TAAAAAATGTCTCAAGCGAGACAAATCTTGTTTTAAG
1 -AAAAAA-GTCTCAAGTGAGATAAATCTTTTTTTAAG
* ** * *
4110979 AAAAACAATCTTGAGTGAAATAAATCTTCTTATTTCGAG
1 AAAAA-AGTCTCAAGTGAGATAAATCTT-TT-TTT-AAG
* *
4111018 TAAAAAATGTCTCAAGTGAGACAAATCTTATTTTAAG
1 -AAAAAA-GTCTCAAGTGAGATAAATCTTTTTTTAAG
4111055 AAAAA
1 AAAAA
4111060 CAATCTGTAG
Statistics
Matches: 116, Mismatches: 29, Indels: 23
0.69 0.17 0.14
Matches are distributed among these distances:
35 4 0.03
36 41 0.35
37 7 0.06
38 17 0.15
39 8 0.07
40 39 0.34
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (35 bp):
AAAAAAGTCTCAAGTGAGATAAATCTTTTTTTAAG
Found at i:4110947 original size:40 final size:39
Alignment explanation
Indices: 4110830--4111051 Score: 113
Period size: 40 Copynumber: 5.8 Consensus size: 39
4110820 AATCTTCTTT
* * *
4110830 AAAAAATCTTGAGTGAAATGAAATGC--CTTCTTTCAAGTA
1 AAAAAATCTTAAGTGAAAT-AAAT-CTTCTTTTTTCGAGTA
* * * * *
4110869 AAATAGTCTCAAGTGAGATAAATC-T-TTTTTT-AAG-A
1 AAAAAATCTTAAGTGAAATAAATCTTCTTTTTTCGAGTA
*
4110904 AAAATAATCTTAAGTTAAATAAATCTTCTTTTTTCGAGTA
1 AAAA-AATCTTAAGTGAAATAAATCTTCTTTTTTCGAGTA
* * * * * * *
4110944 AAAAATGTCTCAAGCGAGACAAATC-T-TGTTTT-AAG-A
1 AAAAA-ATCTTAAGTGAAATAAATCTTCTTTTTTCGAGTA
* *
4110980 AAAACAATCTTGAGTGAAATAAATCTTCTTATTTCGAGTA
1 AAAA-AATCTTAAGTGAAATAAATCTTCTTTTTTCGAGTA
* * * * *
4111020 AAAAATGTCTCAAGTGAGACAAATCTTATTTT
1 AAAAA-ATCTTAAGTGAAATAAATCTTCTTTT
4111052 AAGAAAAACA
Statistics
Matches: 134, Mismatches: 36, Indels: 25
0.69 0.18 0.13
Matches are distributed among these distances:
35 4 0.03
36 37 0.28
37 11 0.08
38 19 0.14
39 21 0.16
40 42 0.31
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (39 bp):
AAAAAATCTTAAGTGAAATAAATCTTCTTTTTTCGAGTA
Found at i:4110968 original size:76 final size:76
Alignment explanation
Indices: 4110830--4111190 Score: 403
Period size: 76 Copynumber: 4.8 Consensus size: 76
4110820 AATCTTCTTT
* * * * * *
4110830 AAAA-AATCTTGAGTGAAATGAAATGCCTTCTTTCAAGTAAAATA-GTCTCAAGTGAGATAAATC
1 AAAACAATCTTGAGTAAAATGAAATGTCTTTTTTCGAGTAAAAAATGTCTCAAGTGAGACAAATC
*
4110893 TTTTTTTAAGA
66 TTGTTTTAAGA
* * * * *
4110904 AAAATAATCTTAAGTTAAAT-AAATCTTCTTTTTTCGAGTAAAAAATGTCTCAAGCGAGACAAAT
1 AAAACAATCTTGAGTAAAATGAAAT-GTCTTTTTTCGAGTAAAAAATGTCTCAAGTGAGACAAAT
4110968 CTTGTTTTAAGA
65 CTTGTTTTAAGA
* * *
4110980 AAAACAATCTTGAGTGAAAT-AAATCTTCTTATTTCGAGTAAAAAATGTCTCAAGTGAGACAAAT
1 AAAACAATCTTGAGTAAAATGAAAT-GTCTTTTTTCGAGTAAAAAATGTCTCAAGTGAGACAAAT
*
4111044 CTTATTTTAAGA
65 CTTGTTTTAAGA
* ** * *
4111056 AAAACAATC-TGTAGTAAAATGAAATGTCTTGTTTT-GAATAAAACCTGTTTCAAGCGAGACAAA
1 AAAACAATCTTG-AGTAAAATGAAATGTCTT-TTTTCGAGTAAAAAATGTCTCAAGTGAGACAAA
*
4111119 TATTGTTTTAAGA
64 TCTTGTTTTAAGA
* * * *
4111132 AAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCAAGTAAAACA-GTCTCAAGTGAGAC
1 AAAACAATCTTGAGTAAAATGAAATGTCTTTTTTCGAGTAAAAAATGTCTCAAGTGAGAC
4111191 GACTTTGTTT
Statistics
Matches: 246, Mismatches: 33, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
74 8 0.03
75 45 0.18
76 184 0.75
77 9 0.04
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (76 bp):
AAAACAATCTTGAGTAAAATGAAATGTCTTTTTTCGAGTAAAAAATGTCTCAAGTGAGACAAATC
TTGTTTTAAGA
Found at i:4111059 original size:152 final size:151
Alignment explanation
Indices: 4110830--4111190 Score: 482
Period size: 152 Copynumber: 2.4 Consensus size: 151
4110820 AATCTTCTTT
* *
4110830 AAAA-AATCTTGAGTGAAATGAAATGC-CTTCTTTCAAGTAAAATAGTCTCAAGTGAGATAAATC
1 AAAACAATCTTGAGTGAAATGAAAT-CTCTTCTTTCAAGTAAAAAAGTCTCAAGTGAGACAAATC
* * * * *
4110893 TTTTTTTAAGAAAAATAATCT-TAAGTTAAAT-AAATCTTCTT-TTTTCGAGTAAAAAATGTCTC
65 TTATTTTAAGAAAAACAATCTGT-AGTAAAATGAAAT-GTCTTGTTTT-GAATAAAAAATGTCTC
*
4110955 AAGCGAGACAAATCTTGTTTTAAGA
127 AAGCGAGACAAATATTGTTTTAAGA
* *
4110980 AAAACAATCTTGAGTGAAAT-AAATCTTCTTATTTCGAGTAAAAAATGTCTCAAGTGAGACAAAT
1 AAAACAATCTTGAGTGAAATGAAATC-TCTTCTTTCAAGTAAAAAA-GTCTCAAGTGAGACAAAT
** *
4111044 CTTATTTTAAGAAAAACAATCTGTAGTAAAATGAAATGTCTTGTTTTGAATAAAACCTGTTTCAA
64 CTTATTTTAAGAAAAACAATCTGTAGTAAAATGAAATGTCTTGTTTTGAATAAAAAATGTCTCAA
4111109 GCGAGACAAATATTGTTTTAAGA
129 GCGAGACAAATATTGTTTTAAGA
* * *
4111132 AAAACAATCTTGAGTCAAATGAAATGTCTTCTTTCAAGTAAAACAGTCTCAAGTGAGAC
1 AAAACAATCTTGAGTGAAATGAAATCTCTTCTTTCAAGTAAAAAAGTCTCAAGTGAGAC
4111191 GACTTTGTTT
Statistics
Matches: 185, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
149 1 0.01
150 8 0.04
151 44 0.24
152 119 0.64
153 13 0.07
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (151 bp):
AAAACAATCTTGAGTGAAATGAAATCTCTTCTTTCAAGTAAAAAAGTCTCAAGTGAGACAAATCT
TATTTTAAGAAAAACAATCTGTAGTAAAATGAAATGTCTTGTTTTGAATAAAAAATGTCTCAAGC
GAGACAAATATTGTTTTAAGA
Found at i:4111566 original size:32 final size:32
Alignment explanation
Indices: 4111530--4111592 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
4111520 ATATTAAATG
*
4111530 CCCCAATATTCGATATTGAATCTCCAAAGATA
1 CCCCAACATTCGATATTGAATCTCCAAAGATA
* * *
4111562 CCCCAACATTTGATGTTGAATCTTCAAAGAT
1 CCCCAACATTCGATATTGAATCTCCAAAGAT
4111593 GTCCTCTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.30
Consensus pattern (32 bp):
CCCCAACATTCGATATTGAATCTCCAAAGATA
Found at i:4111771 original size:24 final size:23
Alignment explanation
Indices: 4111718--4111771 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
4111708 TCTTTTATTT
4111718 TCAAA-AGTTTTGAAAATATCAA
1 TCAAAGAGTTTTGAAAATATCAA
* * *
4111740 TTAGAAGAGTTTTGAAAAATGTTAA
1 TCA-AAGAGTTTTG-AAAATATCAA
4111765 TCAAAGA
1 TCAAAGA
4111772 ATTAATTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 2 0.08
23 2 0.08
24 11 0.44
25 10 0.40
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (23 bp):
TCAAAGAGTTTTGAAAATATCAA
Found at i:4112618 original size:37 final size:34
Alignment explanation
Indices: 4112538--4112676 Score: 74
Period size: 36 Copynumber: 4.1 Consensus size: 34
4112528 TCATCCCTTT
* * *
4112538 TTCTTTTCTTTTTTCTTTTTTTATTTGTTTTTATGT
1 TTCTTTTC-TTTTTCTTTTTCTATTTCTTTTT-TTT
* **
4112574 TTCTTTT-TTTTTC-TTTTCTTTTTCTTTTTCCT
1 TTCTTTTCTTTTTCTTTTTCTATTTCTTTTTTTT
** * * *
4112606 TT-TGCTCTTTTT-TTTCTCT-TTTATTTTTTTG
1 TTCTTTTCTTTTTCTTTTTCTATTTCTTTTTTTT
* *
4112637 TTCTATTTCTTTTTTTCTTTTT-TCTTTCTCTTTTTT
1 TTCT-TTTC--TTTTTCTTTTTCTATTTCTTTTTTTT
4112673 TTCT
1 TTCT
4112677 AATTGGATCT
Statistics
Matches: 77, Mismatches: 18, Indels: 16
0.69 0.16 0.14
Matches are distributed among these distances:
31 12 0.16
32 14 0.18
33 15 0.19
34 6 0.08
35 6 0.08
36 24 0.31
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (34 bp):
TTCTTTTCTTTTTCTTTTTCTATTTCTTTTTTTT
Found at i:4112650 original size:32 final size:30
Alignment explanation
Indices: 4112535--4112676 Score: 90
Period size: 32 Copynumber: 4.4 Consensus size: 30
4112525 TTCTCATCCC
* *
4112535 TTTTTCTTTTC-TTTTTTCTTTTTTTATTTG
1 TTTTTCTTTTCTTTTTTTC-TCTTTTATTTT
* * *
4112565 TTTTTATGTTTCTTTTTTTTTCTTTTCTTTTT
1 TTTTTCT-TTTCTTTTTTTCTCTTTT-ATTTT
4112597 CTTTTTCCTTTTGCTCTTTTTTTTCTCTTTTATTTT
1 -TTTTT-C-TTT--TC-TTTTTTTCTCTTTTATTTT
* *
4112633 TTTGTTCTATTTCTTTTTTTCTTTTTTCTTTCT
1 TTT-TTCT-TTTCTTTTTTTCTCTTTTATTT-T
*
4112666 CTTTT-TTTTCT
1 TTTTTCTTTTCT
4112677 AATTGGATCT
Statistics
Matches: 89, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
30 11 0.12
31 10 0.11
32 27 0.30
33 10 0.11
34 3 0.03
35 7 0.08
36 8 0.09
37 13 0.15
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (30 bp):
TTTTTCTTTTCTTTTTTTCTCTTTTATTTT
Found at i:4113708 original size:6 final size:6
Alignment explanation
Indices: 4113692--4113765 Score: 51
Period size: 6 Copynumber: 11.5 Consensus size: 6
4113682 AAATGTTTAA
* **
4113692 AAATG- AAATGC AAATGC AAAATGC AAAGATGT AAATGC GGATGC AAAATGC
1 AAATGC AAATGC AAATGC -AAATGC -AA-ATGC AAATGC AAATGC -AAATGC
*
4113743 AAAGATGC AAATGC AGATGC AAA
1 -AA-ATGC AAATGC AAATGC AAA
4113766 AATGTTGATC
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
5 5 0.09
6 24 0.43
7 20 0.36
8 7 0.12
ACGTcount: A:0.50, C:0.12, G:0.22, T:0.16
Consensus pattern (6 bp):
AAATGC
Found at i:4113729 original size:27 final size:27
Alignment explanation
Indices: 4113697--4113766 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
4113687 TTTAAAAATG
* *
4113697 AAATGCAAATGCAAAATGCAAAGATGT
1 AAATGCAGATGCAAAATGCAAAGATGC
*
4113724 AAATGCGGATGCAAAATGCAAAGATGC
1 AAATGCAGATGCAAAATGCAAAGATGC
4113751 AAATGCAGATGCAAAA
1 AAATGCAGATGCAAAA
4113767 ATGTTGATCC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.50, C:0.13, G:0.21, T:0.16
Consensus pattern (27 bp):
AAATGCAGATGCAAAATGCAAAGATGC
Found at i:4113769 original size:14 final size:13
Alignment explanation
Indices: 4113697--4113766 Score: 63
Period size: 13 Copynumber: 5.2 Consensus size: 13
4113687 TTTAAAAATG
*
4113697 AAATGCAAATGCA
1 AAATGCAGATGCA
*
4113710 AAATGCAAAGATG-T
1 AAATGC--AGATGCA
*
4113724 AAATGCGGATGCA
1 AAATGCAGATGCA
4113737 AAATGCAAAGATGC-
1 AAATGC--AGATGCA
4113751 AAATGCAGATGCA
1 AAATGCAGATGCA
4113764 AAA
1 AAA
4113767 ATGTTGATCC
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
12 10 0.22
13 15 0.33
14 12 0.26
15 9 0.20
ACGTcount: A:0.50, C:0.13, G:0.21, T:0.16
Consensus pattern (13 bp):
AAATGCAGATGCA
Found at i:4115758 original size:2 final size:2
Alignment explanation
Indices: 4115751--4115816 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
4115741 GTACAATGTA
4115751 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
4115793 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
4115817 TAATATGTAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4132280 original size:24 final size:25
Alignment explanation
Indices: 4132252--4132299 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
4132242 ATCCAGGCAG
4132252 ATTTCT-GTCATGATCAGAGATCGA
1 ATTTCTAGTCATGATCAGAGATCGA
4132276 ATTTCTAGGTCATGATCAGAGATC
1 ATTTCTA-GTCATGATCAGAGATC
4132300 CAGTGAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 6 0.27
26 16 0.73
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (25 bp):
ATTTCTAGTCATGATCAGAGATCGA
Found at i:4132567 original size:20 final size:20
Alignment explanation
Indices: 4132530--4132572 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4132520 ATTCCACCTC
* *
4132530 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGATCCTAA
*
4132550 ATGCATCTAAATGATCCTAA
1 ATGCAACTAAATGATCCTAA
4132570 ATG
1 ATG
4132573 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGATCCTAA
Found at i:4142563 original size:27 final size:27
Alignment explanation
Indices: 4142532--4142583 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
4142522 ATCCAGGCAG
4142532 ATTTCTCGGTCATGATCAGAGATCCGA
1 ATTTCTCGGTCATGATCAGAGATCCGA
*
4142559 ATTTCTCGGTCATGATTAGAGATCC
1 ATTTCTCGGTCATGATCAGAGATCC
4142584 TGTGAAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (27 bp):
ATTTCTCGGTCATGATCAGAGATCCGA
Found at i:4142852 original size:20 final size:20
Alignment explanation
Indices: 4142815--4142857 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4142805 ATTCCACCTC
* *
4142815 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGATCCTAA
*
4142835 ATGCATCTAAATGATCCTAA
1 ATGCAACTAAATGATCCTAA
4142855 ATG
1 ATG
4142858 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGATCCTAA
Found at i:4150895 original size:31 final size:31
Alignment explanation
Indices: 4150857--4150917 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
4150847 TAGTTGTATG
* *
4150857 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGCAAAACTAA
4150888 AATTATTTAAATCTCAGTATTGCAAAACTA
1 AATTATTTAAATCTCAGTATTGCAAAACTA
4150918 TTTTAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:4151598 original size:21 final size:21
Alignment explanation
Indices: 4151574--4151644 Score: 124
Period size: 21 Copynumber: 3.4 Consensus size: 21
4151564 GAAATTGTGA
*
4151574 TCGGGTAGGAACAAAAGCATG
1 TCGGGTAGGAACAAAAACATG
4151595 TCGGGTAGGAACAAAAACATG
1 TCGGGTAGGAACAAAAACATG
*
4151616 TCGAGTAGGAACAAAAACATG
1 TCGGGTAGGAACAAAAACATG
4151637 TCGGGTAG
1 TCGGGTAG
4151645 ATATCTTGCG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.39, C:0.14, G:0.31, T:0.15
Consensus pattern (21 bp):
TCGGGTAGGAACAAAAACATG
Found at i:4152260 original size:46 final size:46
Alignment explanation
Indices: 4152188--4152279 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
4152178 CAGATAATCC
4152188 TTACGATAGAGGACCTCAGTACGGAGCAGACCCAACAAAAGTGAAG
1 TTACGATAGAGGACCTCAGTACGGAGCAGACCCAACAAAAGTGAAG
* *
4152234 TTACGATAGAGGACCTCAGTAGGGAGCAGACCCAACGAAAGTGAAG
1 TTACGATAGAGGACCTCAGTACGGAGCAGACCCAACAAAAGTGAAG
4152280 CGGTCATCCG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.28, T:0.13
Consensus pattern (46 bp):
TTACGATAGAGGACCTCAGTACGGAGCAGACCCAACAAAAGTGAAG
Found at i:4158633 original size:16 final size:16
Alignment explanation
Indices: 4158612--4158644 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4158602 TGCTGTCCAT
4158612 TGAAGACCATGACACC
1 TGAAGACCATGACACC
4158628 TGAAGACCATGACACC
1 TGAAGACCATGACACC
4158644 T
1 T
4158645 AAATGCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.30, G:0.18, T:0.15
Consensus pattern (16 bp):
TGAAGACCATGACACC
Found at i:4158980 original size:19 final size:20
Alignment explanation
Indices: 4158956--4159006 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
4158946 TGGCCAAGAA
*
4158956 CATGTATCTTCATT-AAAAT
1 CATGTATTTTCATTAAAAAT
*
4158975 CATGTATTTTTATTAAAAAT
1 CATGTATTTTCATTAAAAAT
4158995 CATGTATTTTCA
1 CATGTATTTTCA
4159007 AAGAGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:4159559 original size:16 final size:14
Alignment explanation
Indices: 4159527--4159585 Score: 70
Period size: 15 Copynumber: 4.3 Consensus size: 14
4159517 CCTTTGATAA
*
4159527 CATTTCTTTCCTTT
1 CATTTCTTTCATTT
4159541 CATTTTCTTATCATTT
1 CA-TTTCTT-TCATTT
4159557 CATTTCTTT-ATTT
1 CATTTCTTTCATTT
4159570 CATTTC-TT-ATTT
1 CATTTCTTTCATTT
4159582 CATT
1 CATT
4159586 AATCATTTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
12 10 0.24
13 10 0.24
14 3 0.07
15 12 0.29
16 7 0.17
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.64
Consensus pattern (14 bp):
CATTTCTTTCATTT
Found at i:4163116 original size:19 final size:20
Alignment explanation
Indices: 4163092--4163142 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
4163082 TGTCCAAGGG
*
4163092 CATGTATCTTCATT-AAAAT
1 CATGTATTTTCATTAAAAAT
4163111 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
4163131 CATGTATTTTCA
1 CATGTATTTTCA
4163143 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:4163692 original size:15 final size:14
Alignment explanation
Indices: 4163670--4163728 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 14
4163660 CCTTTGATAA
*
4163670 CATTTCTTTCCTTT
1 CATTTCTTTCATTT
4163684 CATTTTCTTATCATTT
1 CA-TTTCTT-TCATTT
4163700 CATTTCTTT-ATTT
1 CATTTCTTTCATTT
*
4163713 CGTTTC-TT-ATTT
1 CATTTCTTTCATTT
4163725 CATT
1 CATT
4163729 AATCATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
12 9 0.22
13 9 0.22
14 3 0.08
15 12 0.30
16 7 0.17
ACGTcount: A:0.14, C:0.20, G:0.02, T:0.64
Consensus pattern (14 bp):
CATTTCTTTCATTT
Found at i:4166166 original size:43 final size:42
Alignment explanation
Indices: 4166089--4166299 Score: 251
Period size: 43 Copynumber: 5.0 Consensus size: 42
4166079 TAATTAGCGA
**
4166089 CGTTTGCATCCAAAAATACCGCTATAGATCTGACCTTTTGCGG
1 CGTTTGC-TCCAAAAACGCCGCTATAGATCTGACCTTTTGCGG
* * *
4166132 TGTTTGCTCCAAAAACGCCGCTAAAGATCTTGACCTTTTGCAG
1 CGTTTGCTCCAAAAACGCCGCTATAGATC-TGACCTTTTGCGG
* *
4166175 CGTTTGTTCCAAAAACGCCGCTATAGATCCGACCTTTTGCGG
1 CGTTTGCTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGG
* ** * *
4166217 CGTTTTCTCCAAAAACGTTGTTATAGATCTAGACCTATTGCGG
1 CGTTTGCTCCAAAAACGCCGCTATAGATCT-GACCTTTTGCGG
* ** *
4166260 CGTTTGTTTAAAAAATGCCGCTATAGATCTGACCTTTTGC
1 CGTTTGCTCCAAAAACGCCGCTATAGATCTGACCTTTTGC
4166300 CGCCAAAAAT
Statistics
Matches: 140, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
42 63 0.45
43 77 0.55
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (42 bp):
CGTTTGCTCCAAAAACGCCGCTATAGATCTGACCTTTTGCGG
Found at i:4166245 original size:85 final size:85
Alignment explanation
Indices: 4166097--4166299 Score: 280
Period size: 85 Copynumber: 2.4 Consensus size: 85
4166087 GACGTTTGCA
* *
4166097 TCCAAAAATACCGCTATAGATCTGACCTTTTGCGGTGTTTGCTCCAAAAACGCCGCTAAAGATCT
1 TCCAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGCTCCAAAAACGCCGCTAAAGATCT
* *
4166162 TGACCTTTTGCAGCGTTTGT
66 AGACCTATTGCAGCGTTTGT
* * * ** * *
4166182 TCCAAAAACGCCGCTATAGATCCGACCTTTTGCGGCGTTTTCTCCAAAAACGTTGTTATAGATCT
1 TCCAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGCTCCAAAAACGCCGCTAAAGATCT
*
4166247 AGACCTATTGCGGCGTTTGT
66 AGACCTATTGCAGCGTTTGT
**
4166267 TTAAAAAATGCCGCTATAGATCTGACCTTTTGC
1 TCCAAAAATGCCGCTATAGATCTGACCTTTTGC
4166300 CGCCAAAAAT
Statistics
Matches: 102, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 102 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (85 bp):
TCCAAAAATGCCGCTATAGATCTGACCTTTTGCGGCGTTTGCTCCAAAAACGCCGCTAAAGATCT
AGACCTATTGCAGCGTTTGT
Found at i:4166400 original size:42 final size:42
Alignment explanation
Indices: 4166314--4166400 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
4166304 AAAAATGCCA
* * * *
4166314 CTATAGATCTCGACATATTGCGGCGTTTTTGGACAAATGTCG
1 CTATAGATCTAGACATATTGCGGCGTTTTTGCACAAACGCCG
* *
4166356 CTATAGATCTAGACATATTGCGGCTTTTTTTCACAAACGCCG
1 CTATAGATCTAGACATATTGCGGCGTTTTTGCACAAACGCCG
4166398 CTA
1 CTA
4166401 ACTTTAGTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (42 bp):
CTATAGATCTAGACATATTGCGGCGTTTTTGCACAAACGCCG
Found at i:4171246 original size:10 final size:10
Alignment explanation
Indices: 4171231--4171304 Score: 55
Period size: 10 Copynumber: 7.3 Consensus size: 10
4171221 AAATAATTAT
4171231 TATTTTAGTA
1 TATTTTAGTA
4171241 TATTTTAGTA
1 TATTTTAGTA
**
4171251 TATTATTAAGGG
1 TATT-TT-AGTA
* *
4171263 CAGTTTT-GGA
1 TA-TTTTAGTA
4171273 TA-TTTA-TA
1 TATTTTAGTA
4171281 TTATTTTAGTA
1 -TATTTTAGTA
4171292 TATTTTAGTA
1 TATTTTAGTA
4171302 TAT
1 TAT
4171305 CTAGCATTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
8 4 0.08
9 2 0.04
10 34 0.67
11 4 0.08
12 5 0.10
13 2 0.04
ACGTcount: A:0.30, C:0.01, G:0.14, T:0.55
Consensus pattern (10 bp):
TATTTTAGTA
Found at i:4175513 original size:3 final size:3
Alignment explanation
Indices: 4175507--4175558 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
4175497 AAAAAAAATA
*
4175507 AAT AAT AAT AAT AAT AAT AAAT ACT AAT AAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
4175552 AAT AAT A
1 AAT AAT A
4175559 TTTTTTTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4175527 original size:19 final size:19
Alignment explanation
Indices: 4175503--4175558 Score: 89
Period size: 19 Copynumber: 3.1 Consensus size: 19
4175493 CTGCAAAAAA
4175503 AATAAATAATAATAATAAT
1 AATAAATAATAATAATAAT
*
4175522 AATAAATACTAATAATAAT
1 AATAAATAATAATAATAAT
4175541 AAT-AATAATAA-AATAAT
1 AATAAATAATAATAATAAT
4175558 A
1 A
4175559 TTTTTTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.20
18 7 0.20
19 21 0.60
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (19 bp):
AATAAATAATAATAATAAT
Found at i:4175922 original size:84 final size:83
Alignment explanation
Indices: 4175804--4175969 Score: 224
Period size: 84 Copynumber: 2.0 Consensus size: 83
4175794 TGTCAGATCT
* *
4175804 TTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGTAGCTGAGC
1 TTTGGTTGGAAAATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTG-AGCTGAGC
**
4175869 GTAGTCGAACTCGAAGGTC
65 GTAACCGAACTCGAAGGTC
* * * * * *
4175888 TTTGGTTGGAAAATAACCTTTCTTGCCTTGAGCTATGTTGCAAATGATGTGCCTTGAGCTGAGTG
1 TTTGGTTGGAAAATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGCG
*
4175953 TAACCGAGCTCGAAGGT
66 TAACCGAACTCGAAGGT
4175970 TTGGTGTTTC
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
83 22 0.31
84 49 0.69
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (83 bp):
TTTGGTTGGAAAATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGAGCTGAGCG
TAACCGAACTCGAAGGTC
Found at i:4176049 original size:36 final size:36
Alignment explanation
Indices: 4176006--4176576 Score: 491
Period size: 36 Copynumber: 16.2 Consensus size: 36
4175996 AATGTTTTTT
* *
4176006 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
4176042 TTTCAAGAGAAACATAT-T-AA-A-AG-----ATTGGTG
1 TTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT--TG
* * *
4176072 TTTCAATAGAAACTGTCTCAACAAAGACAAAACTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTG
* *
4176109 TTTCAAGGGAAA-TTTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* *
4176144 TTTCAAGAGAAACTGTCTCAAGAGTGACAAAACTTAG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTG
* * * *
4176181 TTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* *
4176217 TTTCAAG-GAGAACATAT-TC-A-A-AG----ATTTTG
1 TTTCAAGAGA-AAC-TGTCTCAAGAGAGACAAAATTTG
*
4176246 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
4176282 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* *
4176318 TTTCAAGGGTAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
4176354 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTC-A-AGAG----AGACAAAATTTG
*
4176396 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTG
* * * **
4176433 TTCCAAAAGAAACTGTCTCAAGGGAGATGAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* *
4176469 TTT-AATGTA-AAACATAT-TC-A-A-AG----ATTTTG
1 TTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAATTTG
* *
4176498 TTTCAAGGGGAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
4176534 TTTCAAGGGAAACTGTC-CTAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTC-AAGAGAGACAAAATTTG
4176570 TTTCAAG
1 TTTCAAG
4176577 TAAATTAGTC
Statistics
Matches: 441, Mismatches: 47, Indels: 94
0.76 0.08 0.16
Matches are distributed among these distances:
28 7 0.02
29 33 0.07
30 20 0.05
31 4 0.01
32 5 0.01
33 8 0.02
35 24 0.05
36 217 0.49
37 80 0.18
38 5 0.01
39 2 0.00
40 4 0.01
41 1 0.00
42 31 0.07
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:4176265 original size:138 final size:135
Alignment explanation
Indices: 4176105--4176364 Score: 403
Period size: 137 Copynumber: 1.9 Consensus size: 135
4176095 AAGACAAAAC
* *
4176105 TTTGTTTCAAGGGAAATTTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGTG
1 TTTGTTTCAAGGGAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAG
* *
4176170 ACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGAGAACATATT
66 ACAAAA-TTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA-GAGAACATATT
4176235 CAAAGAT
129 CAAAGAT
*
4176242 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAA-TGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* * ** *
4176307 GACAAAATTTGTTTCAAGGGTAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAA
65 GACAAAATTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAA
4176365 ACTGTCTCAA
Statistics
Matches: 112, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
136 5 0.04
137 55 0.49
138 52 0.46
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.27
Consensus pattern (135 bp):
TTTGTTTCAAGGGAAATGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAG
ACAAAATTAGTTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAACATATTCA
AAGAT
Found at i:4176310 original size:174 final size:174
Alignment explanation
Indices: 4176013--4176408 Score: 555
Period size: 174 Copynumber: 2.2 Consensus size: 174
4176003 TTTTTTCAAG
*
4176013 AGAAACTGTCTCAAGGGAGACAAAATTTTTTTCAAGAGAAACATATTAAAAGATTGGTGTTTCAA
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACATATTAAAAGATTGGTGTTTCAA
* *
4176078 TAGAAACTGTCTCAACAAAGACAAAACTTTGTTTCAAGGGAAATTTCTCAAGAGAGACAAAATTT
66 GAGAAACTGTCTCAACAAAGACAAAACTTTGTTTCAAGGGAAATGTCTCAAGAGAGACAAAATTT
*
4176143 GTTTCAAGAGAAACTGTCTCAAGAGTGACAAAACTTAGTTCCAAA
131 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAA
* * *
4176188 AGAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAG-GAGAACATATTCAAAGATT-TTGTTTCA
1 AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGA-AACATATTAAAAGATTGGTGTTTCA
* * *
4176251 AGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
65 AGAGAAACTGTCTCAACAAAGACAAAACTTTGTTTCAAGGGAAA-TGTCTCAAGAGAGACAAAAT
* * * * *
4176315 TTGTTTCAAGGGTAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG
129 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAA
4176361 AGAAACTGTCTCAAGAGAGACAAAGACAAAATTTGTTTCAAGAGAAAC
1 AGAAACTGTCTCAAG-G-G----AGACAAAATTTGTTTCAAGAGAAAC
4176409 TGTCTCAAGA
Statistics
Matches: 196, Mismatches: 16, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
173 39 0.20
174 84 0.43
175 50 0.26
179 21 0.11
180 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (174 bp):
AGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACATATTAAAAGATTGGTGTTTCAA
GAGAAACTGTCTCAACAAAGACAAAACTTTGTTTCAAGGGAAATGTCTCAAGAGAGACAAAATTT
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAA
Found at i:4176361 original size:21 final size:21
Alignment explanation
Indices: 4176263--4176363 Score: 73
Period size: 21 Copynumber: 5.4 Consensus size: 21
4176253 GGAAACTGTC
4176263 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* *
4176284 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
4176299 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
* * *
4176320 TCAAG-G-G---TAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
4176335 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
4176356 TCAAGAGA
1 TCAAGAGA
4176364 AACTGTCTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 24
0.63 0.11 0.26
Matches are distributed among these distances:
15 16 0.28
16 7 0.12
17 2 0.03
19 2 0.03
20 7 0.12
21 24 0.41
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:4176514 original size:252 final size:246
Alignment explanation
Indices: 4176082--4176576 Score: 807
Period size: 252 Copynumber: 2.0 Consensus size: 246
4176072 TTTCAATAGA
* *
4176082 AACTGTCTCAACAAAGACAAAACTTTGTTTCAAGGGAAATTTCTCAAGAGAGACAAAATTTGTTT
1 AACTGTCTCAACAAAGACAAAACTTTGTTTCAAGAGAAATGTCTCAAGAGAGACAAAATTTGTTT
*
4176147 CAAGAGAAACTGTCTCAAGAGTGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAA
66 CAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAA
*
4176212 ATTTGTTTCAAGGAGAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
131 ATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
4176277 ATTTGTTTCAAGGGAAACTGT-CTCAAGAGAGACAAAATTTGTTTCAAGGGT
196 ATTTGTTTCAAGGGAAACTGTCCT-AAGAGAGACAAAATTTGTTTCAAGGGT
* *
4176328 AACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAGACAAAA
1 AACTGTCTCAACAAAGACAAAACTTTGTTTCAAGAGAAA-TGTCTC-A-AGAG----AGACAAAA
4176392 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
59 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
* * *
4176457 AGATGAAATTTGTTT-AATGTAAAACATATTCAAAGATTTTGTTTCAAGGGGAACTGTCTCAAGA
124 AGACGAAATTTGTTTCAA-GGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGA
4176521 GAGACAAAATTTGTTTCAAGGGAAACTGTCCTAAGAGAGACAAAATTTGTTTCAAG
188 GAGACAAAATTTGTTTCAAGGGAAACTGTCCTAAGAGAGACAAAATTTGTTTCAAG
4176577 TAAATTAGTC
Statistics
Matches: 231, Mismatches: 9, Indels: 12
0.92 0.04 0.05
Matches are distributed among these distances:
245 15 0.06
246 25 0.11
247 1 0.00
248 4 0.02
251 2 0.01
252 182 0.79
253 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (246 bp):
AACTGTCTCAACAAAGACAAAACTTTGTTTCAAGAGAAATGTCTCAAGAGAGACAAAATTTGTTT
CAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGAA
ATTTGTTTCAAGGAAAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
ATTTGTTTCAAGGGAAACTGTCCTAAGAGAGACAAAATTTGTTTCAAGGGT
Found at i:4176817 original size:116 final size:116
Alignment explanation
Indices: 4176662--4176891 Score: 365
Period size: 116 Copynumber: 2.0 Consensus size: 116
4176652 CCTGAAGATG
* * *
4176662 AATGTTGCTGGTGGGTACGATTCCCTTCATCGTGAAGTTGAAACCGTGGATGGACCC-TTCATTG
1 AATGTTGCTGGTGAGCACGATTCCCTTCATCATGAAGTTGAAACCGTGGATGG-CCCTTTCATTG
*
4176726 TGAAGTTGAGCTTTGAA-TTGAATATCCTTCATCGTGAAGTTGAAATCCAATA
65 TGAAGTTGAGCCTT-AACTTGAATATCCTTCATCGTGAAGTTGAAATCCAATA
* * *
4176778 AATGTTGTTGGTGAGCACGATTCCCTTCGTCATGAAGTTGAAACCGTGGATGGCCCTTTCGTTGT
1 AATGTTGCTGGTGAGCACGATTCCCTTCATCATGAAGTTGAAACCGTGGATGGCCCTTTCATTGT
4176843 GAAGTTGAGCCTTAACTTGAATATCCTTCATCGTGAAGTTGAAATCCAA
66 GAAGTTGAGCCTTAACTTGAATATCCTTCATCGTGAAGTTGAAATCCAA
4176892 GCTTGTATTG
Statistics
Matches: 105, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
115 5 0.05
116 100 0.95
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (116 bp):
AATGTTGCTGGTGAGCACGATTCCCTTCATCATGAAGTTGAAACCGTGGATGGCCCTTTCATTGT
GAAGTTGAGCCTTAACTTGAATATCCTTCATCGTGAAGTTGAAATCCAATA
Found at i:4177492 original size:31 final size:33
Alignment explanation
Indices: 4177425--4177512 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 33
4177415 TTCACATCTG
*
4177425 GATGTTGAATC-CACAAATATGCCCCAATATTC
1 GATGTTGAATCTCACAAATATGCCCCAACATTC
*
4177457 GATGTTGAATCTC-CGAAA-ATG-CCCAACATTT
1 GATGTTGAATCTCAC-AAATATGCCCCAACATTC
* *
4177488 GATGTTGAATCT-TCAAAGATGCCCC
1 GATGTTGAATCTCACAAATATGCCCC
4177513 CATTGTTCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
30 3 0.06
31 24 0.49
32 18 0.37
33 4 0.08
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (33 bp):
GATGTTGAATCTCACAAATATGCCCCAACATTC
Found at i:4178595 original size:25 final size:26
Alignment explanation
Indices: 4178538--4178599 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
4178528 TGTTTTTGTC
*
4178538 TCTCTTTT-TTATTTTCTCTTTGCTTT
1 TCTCTTTTGTTTTTTTCTCTTT-CTTT
4178564 T-TC-TTTGTTTTTTTCTCTTT-TTT
1 TCTCTTTTGTTTTTTTCTCTTTCTTT
4178587 TCTCTTTTGTTTT
1 TCTCTTTTGTTTT
4178600 GATTTGATCT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
23 4 0.12
24 5 0.16
25 22 0.69
26 1 0.03
ACGTcount: A:0.02, C:0.16, G:0.05, T:0.77
Consensus pattern (26 bp):
TCTCTTTTGTTTTTTTCTCTTTCTTT
Found at i:4179392 original size:16 final size:18
Alignment explanation
Indices: 4179361--4179394 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
4179351 CAGTCGTTTA
4179361 AAAGATTGAGAAAACATG
1 AAAGATTGAGAAAACATG
4179379 AAAGATT-A-AAAACATG
1 AAAGATTGAGAAAACATG
4179395 TTCAAACAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 1 0.06
18 7 0.44
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18
Consensus pattern (18 bp):
AAAGATTGAGAAAACATG
Found at i:4187045 original size:3 final size:3
Alignment explanation
Indices: 4187039--4187085 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
4187029 AAAATATTAT
* *
4187039 TAA TAA TAA TAA TAAA TAC TAA TAC TAA TAA TAA TAA -AA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4187084 TA
1 TA
4187086 TTTTTTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:4187067 original size:22 final size:23
Alignment explanation
Indices: 4187042--4187085 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
4187032 ATATTATTAA
*
4187042 TAATAATAAT-AAATACTAATAC
1 TAATAATAATAAAATAATAATAC
4187064 TAATAATAATAAAATAATAATA
1 TAATAATAATAAAATAATAATA
4187086 TTTTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (23 bp):
TAATAATAATAAAATAATAATAC
Done.