Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007800.1 Hibiscus syriacus cultivar Beakdansim tig00110114_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: 4652821
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 23
Found at i:966150 original size:19 final size:19
Alignment explanation
Indices: 966128--966183 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
966118 GGAAATGGCT
966128 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
966147 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
966161 ATCGCAGTGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
966180 ATCG
1 ATCG
966184 TAACGAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
14 9 0.31
15 1 0.03
16 2 0.07
17 2 0.07
18 1 0.03
19 14 0.48
ACGTcount: A:0.45, C:0.20, G:0.21, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:966216 original size:33 final size:33
Alignment explanation
Indices: 966128--966207 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
966118 GGAAATGGCT
*
966128 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
* *
966161 ATCGCAGTGCGAAATGAAAATCGTAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
966194 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
966208 CACAAATCGC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
Found at i:966264 original size:33 final size:33
Alignment explanation
Indices: 966222--966311 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
966212 AATCGCATTG
* * * *
966222 CGATTTTCATTTCACTTTGCGATTTTTTCGTTA
1 CGATTTTCATTTCGCATTGCGATATTGTCGTTA
* *
966255 CGATTTTCATTTCGCACTGCGATATTGTCGTTG
1 CGATTTTCATTTCGCATTGCGATATTGTCGTTA
966288 CGATTTTCATTTCGCATTGCGATA
1 CGATTTTCATTTCGCATTGCGATA
966312 GCCATTTCCG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.47
Consensus pattern (33 bp):
CGATTTTCATTTCGCATTGCGATATTGTCGTTA
Found at i:966309 original size:19 final size:19
Alignment explanation
Indices: 966214--966310 Score: 72
Period size: 19 Copynumber: 5.6 Consensus size: 19
966204 GAAACACAAA
966214 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
966233 TCACTTTGCGA-TTT--TT
1 TCGCATTGCGATTTTCATT
*
966249 TCG--TTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
966266 TCGCACTGCGA---T-ATT
1 TCGCATTGCGATTTTCATT
966281 GTCG--TTGCGATTTTCATT
1 -TCGCATTGCGATTTTCATT
966299 TCGCATTGCGAT
1 TCGCATTGCGAT
966311 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 7, Indels: 24
0.66 0.08 0.27
Matches are distributed among these distances:
14 10 0.17
15 6 0.10
16 8 0.14
17 9 0.15
18 6 0.10
19 20 0.34
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:966350 original size:21 final size:20
Alignment explanation
Indices: 966295--966338 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
966285 TTGCGATTTT
*
966295 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
966314 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
966334 CATTT
1 CATTT
966339 TTCGTGTTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:966886 original size:18 final size:18
Alignment explanation
Indices: 966863--966911 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
966853 TGTCGTTGTG
966863 GAGGTGTATAG-TCTGGGT
1 GAGGTG-ATAGCTCTGGGT
*
966881 GAGGTGATAGCTTTGGGT
1 GAGGTGATAGCTCTGGGT
*
966899 GAGGTGATGGCTC
1 GAGGTGATAGCTC
966912 CCGAAGTGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.16, C:0.08, G:0.45, T:0.31
Consensus pattern (18 bp):
GAGGTGATAGCTCTGGGT
Found at i:968284 original size:20 final size:20
Alignment explanation
Indices: 968232--968273 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
968222 ATAGTTTCTT
* *
968232 AAAATGAAAATCGCAACACG
1 AAAATGACAATCGCAACGCG
968252 AAAATGACAATCGCAACGCG
1 AAAATGACAATCGCAACGCG
968272 AA
1 AA
968274 TTTGACTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.21, G:0.17, T:0.10
Consensus pattern (20 bp):
AAAATGACAATCGCAACGCG
Found at i:968582 original size:22 final size:22
Alignment explanation
Indices: 968552--968595 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
968542 GATGGAGATA
*
968552 GACGGATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
*
968574 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
968596 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:968881 original size:41 final size:41
Alignment explanation
Indices: 968762--968893 Score: 162
Period size: 41 Copynumber: 3.2 Consensus size: 41
968752 CGCTTTGAAA
*
968762 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * *
968803 ATC-TAGTTGCGA--AAGTAAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCA-TTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * *
968843 ATCGTATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
968884 ATCGCATTGC
1 ATCGCATTGC
968894 AATTTTCCAA
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
39 3 0.04
40 31 0.40
41 41 0.53
42 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:968888 original size:20 final size:20
Alignment explanation
Indices: 968782--968893 Score: 100
Period size: 20 Copynumber: 5.5 Consensus size: 20
968772 GATTATGTAT
*
968782 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
968802 TATCTAGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
968822 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** ** *
968842 TATCGTATTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
968863 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
968883 TATCGCATTGC
1 TATCGCGTTGC
968894 AATTTTCCAA
Statistics
Matches: 74, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
19 3 0.04
20 57 0.77
21 12 0.16
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:968915 original size:41 final size:41
Alignment explanation
Indices: 968822--968917 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
968812 CGAAAGTAAG
* * * ** *
968822 TATCGCGTTGCGAAAGTCAGTATCGTATTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCAAA
968863 TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTT-CAAA
*
968905 T-TCGCATTGCGAT
1 TATCGCGTTGCGAT
968918 TTACTTATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCAAA
Found at i:968933 original size:20 final size:20
Alignment explanation
Indices: 968904--968956 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
968894 AATTTTCCAA
968904 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
*
968924 ATTTGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACTT
968944 ATTCGCATTGCGA
1 ATTCGCATTGCGA
968957 ATTGGGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.43
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACTT
Found at i:968998 original size:21 final size:22
Alignment explanation
Indices: 968946--968998 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
968936 ATTTACTTAT
968946 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
968967 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
968988 TCGCATTGCGA
1 TCGCATTGCGA
968999 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:970101 original size:32 final size:32
Alignment explanation
Indices: 970031--970101 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
970021 TGGCCTTGGG
* * * * * *
970031 TAGGCTCTAAGGCTCCAAGGCATTTCCTTGGG
1 TAGGCTCTAAGGCCCCAAGACACTCCCTTAGA
970063 TAGGCTCTAAGGCCCCAAGACACTCCCTTAGA
1 TAGGCTCTAAGGCCCCAAGACACTCCCTTAGA
*
970095 TTGGCTC
1 TAGGCTC
970102 CTACGACTAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.25
Consensus pattern (32 bp):
TAGGCTCTAAGGCCCCAAGACACTCCCTTAGA
Found at i:970842 original size:130 final size:130
Alignment explanation
Indices: 970609--970869 Score: 504
Period size: 130 Copynumber: 2.0 Consensus size: 130
970599 ATGGAATGGC
*
970609 CGGTTTGAGTATTTAATGAATACTATTAGAATTGGGCTAGGGTACTTGCCCCCAAAATAAAGGTG
1 CGGTTTGAGTATTTAATGAATACTAGTAGAATTGGGCTAGGGTACTTGCCCCCAAAATAAAGGTG
970674 CCACCAATTGGATTTGGAGCCTACATAATTCATTTTTAAATAAATTTTGTTATTATAATATTTTA
66 CCACCAATTGGATTTGGAGCCTACATAATTCATTTTTAAATAAATTTTGTTATTATAATATTTTA
970739 CGGTTTGAGTATTTAATGAATACTAGTAGAATTGGGCTAGGGTACTTGCCCCCAAAATAAAGGTG
1 CGGTTTGAGTATTTAATGAATACTAGTAGAATTGGGCTAGGGTACTTGCCCCCAAAATAAAGGTG
*
970804 CCACCAATTGGATTTGGAGCCTACATAATTTATTTTTAAATAAATTTTGTTATTATAATATTTTA
66 CCACCAATTGGATTTGGAGCCTACATAATTCATTTTTAAATAAATTTTGTTATTATAATATTTTA
970869 C
1 C
970870 TATATTTAAA
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 129 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (130 bp):
CGGTTTGAGTATTTAATGAATACTAGTAGAATTGGGCTAGGGTACTTGCCCCCAAAATAAAGGTG
CCACCAATTGGATTTGGAGCCTACATAATTCATTTTTAAATAAATTTTGTTATTATAATATTTTA
Found at i:970919 original size:23 final size:24
Alignment explanation
Indices: 970876--970920 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
970866 TTACTATATT
970876 TAAATTTATAAAAAAAACTAAATA
1 TAAATTTATAAAAAAAACTAAATA
* *
970900 TAAATTT-TAAAACAATCTAAA
1 TAAATTTATAAAAAAAACTAAA
970921 GTATTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (24 bp):
TAAATTTATAAAAAAAACTAAATA
Found at i:977822 original size:22 final size:22
Alignment explanation
Indices: 977783--977825 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
977773 TTTGGATTTG
*
977783 CAAAACGTGATCATATTTGTAA
1 CAAAACGTGATCAGATTTGTAA
**
977805 CAAAACGTGATTGGATTTGTA
1 CAAAACGTGATCAGATTTGTA
977826 TGCTAACATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (22 bp):
CAAAACGTGATCAGATTTGTAA
Found at i:979054 original size:24 final size:26
Alignment explanation
Indices: 979003--979059 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
978993 TAGTCGAGTA
* *
979003 ATATATCAGATACCATTGATTAATAT
1 ATATAACAGATACCAGTGATTAATAT
*
979029 ATATAACAGATACCAGTGGTTAATAT
1 ATATAACAGATACCAGTGATTAATAT
979055 ATATA
1 ATATA
979060 TATATGTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (26 bp):
ATATAACAGATACCAGTGATTAATAT
Found at i:993397 original size:30 final size:31
Alignment explanation
Indices: 993323--993389 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
993313 TTATTGAGGC
* * * *
993323 CAAACTAATAATTTATCTAAAATTTAGAGGT
1 CAAATTAATATTTTATCTAAAACTTAGAGAT
*
993354 TAAATTAATATTTTATCTAAAACTTA-AGAT
1 CAAATTAATATTTTATCTAAAACTTAGAGAT
993384 CAAATT
1 CAAATT
993390 GGTATTTTGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (31 bp):
CAAATTAATATTTTATCTAAAACTTAGAGAT
Found at i:998448 original size:3 final size:3
Alignment explanation
Indices: 998440--998504 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
998430 ATAAATAAGC
998440 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
998488 ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA AT
998505 TACAATTAGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:998976 original size:134 final size:134
Alignment explanation
Indices: 998794--999058 Score: 440
Period size: 134 Copynumber: 2.0 Consensus size: 134
998784 GCCATCTAAA
*
998794 GGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAGGGTGACACGGCTCCTACGT
1 GGTGATAACACGGTTCCTACGTGATGAGGACGACTGGCTATCTAAGGGTGACACGGCTCCTACGT
* * * * *
998859 GATGAGGAGGTCTGGTCGAGGGATGGCACAGTTCCTACGTGATGAAGACGGCTGGCCATCTTTAG
66 GATGAAGAGATCTGGTCGAGGGATGACACAGTTCCTACGTAATGAAGACGACTGGCCATCTTTAG
998924 GAGT
131 GAGT
* *
998928 GGTGATAACTCGGTTCCTACGTGATGAGGACGGCTGGCTATCTAAGGGTGACACGGCTCCTACGT
1 GGTGATAACACGGTTCCTACGTGATGAGGACGACTGGCTATCTAAGGGTGACACGGCTCCTACGT
* *
998993 GATGAAGAGATCTGGTCGAGGGATGACACGGTTCCTACGTAATGAGGACGACTGGCCATCTTTAG
66 GATGAAGAGATCTGGTCGAGGGATGACACAGTTCCTACGTAATGAAGACGACTGGCCATCTTTAG
999058 G
131 G
999059 GATCATGGTT
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
134 121 1.00
ACGTcount: A:0.23, C:0.20, G:0.34, T:0.24
Consensus pattern (134 bp):
GGTGATAACACGGTTCCTACGTGATGAGGACGACTGGCTATCTAAGGGTGACACGGCTCCTACGT
GATGAAGAGATCTGGTCGAGGGATGACACAGTTCCTACGTAATGAAGACGACTGGCCATCTTTAG
GAGT
Found at i:999159 original size:31 final size:28
Alignment explanation
Indices: 999066--999162 Score: 101
Period size: 28 Copynumber: 3.4 Consensus size: 28
999056 AGGGATCATG
* *
999066 GTTTCAAGAGAAATC-GATTCAAAGATTT
1 GTTTCAAAAGAAA-CAGACTCAAAGATTT
999094 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
999122 GTTTCAAGAA-AAACA-AGCTCAAAGATAATGT
1 GTTTCAA-AAGAAACAGA-CTCAAAGAT--T-T
999153 GTTTCAAAAG
1 GTTTCAAAAG
999163 CAACTGTCTC
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
27 2 0.03
28 45 0.75
29 2 0.03
30 3 0.05
31 8 0.13
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.27
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATTT
Found at i:999751 original size:31 final size:31
Alignment explanation
Indices: 999701--999761 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 31
999691 AAGGGAAACG
999701 ACTCAAAGATGGTTTTATTT-TAAGAGAAACAA
1 ACTCAAAGAT-GTTTTATTTCT-AGAGAAACAA
999733 ACTCAAAGAT-TTTGTATTTCTAGAGAAAC
1 ACTCAAAGATGTTT-TATTTCTAGAGAAAC
999762 TGCCTCAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 3 0.11
31 13 0.48
32 11 0.41
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (31 bp):
ACTCAAAGATGTTTTATTTCTAGAGAAACAA
Found at i:1000136 original size:120 final size:121
Alignment explanation
Indices: 999996--1000281 Score: 337
Period size: 120 Copynumber: 2.4 Consensus size: 121
999986 CAAAGGTTGG
** * *
999996 TTTTTCATTAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTTAA-AGAAATAAACTAAAAGATG
1 TTTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATATG-TTTTAAGAGAAACAAACTAAAAGATG
* * ** * * *
1000060 ATTTTGTTAGTAGAAACAAACTCAAAGA-TTTT-TTCAAAAGGAATAGACTCCAAGAT
65 ATTTTCTCAAAAGAAA-AAACTCAAAGATTTTTATTCAAAAGGAACAAACTCAAAGAT
* * * * **
1000116 TTTTTCAAGAGAAACTGTCTCAAGAGAAACAAAATATGTTTTAAGAGAAACATACTCAAAGATTT
1 TTTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATATGTTTTAAGAGAAACAAACTAAAAGATGA
* *
1000181 TTTTCTCAAAAGAAATAACTCAAAGATTTTTATTCAAAATGAACAAACTCAAAGAT
66 TTTTCTCAAAAGAAAAAACTCAAAGATTTTTATTCAAAAGGAACAAACTCAAAGAT
1000237 TTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-ATCGTTTTAA
1 TT-TTTCAAAAGAAACTGTCTCAAGAGAGACAAAATAT-GTTTTAA
1000282 AATATTCAAA
Statistics
Matches: 141, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
119 16 0.11
120 64 0.45
121 24 0.17
122 37 0.26
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.30
Consensus pattern (121 bp):
TTTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATATGTTTTAAGAGAAACAAACTAAAAGATGA
TTTTCTCAAAAGAAAAAACTCAAAGATTTTTATTCAAAAGGAACAAACTCAAAGAT
Found at i:1000202 original size:29 final size:27
Alignment explanation
Indices: 1000169--1000251 Score: 105
Period size: 29 Copynumber: 3.0 Consensus size: 27
1000159 AGAGAAACAT
1000169 ACTCAAAGATTTTTTTCTCAAAAGAAATA
1 ACTCAAAGATTTTTTT-TCAAAAGAAA-A
*
1000198 ACTCAAAGATTTTTATTCAAAATGAACAA
1 ACTCAAAGATTTTTTTTCAAAA-GAA-AA
*
1000227 ACTCAAAGA-TTTGTTTCAAAAGAAA
1 ACTCAAAGATTTTTTTTCAAAAGAAA
1000252 CTGTCTCAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
26 1 0.02
27 3 0.06
28 16 0.33
29 28 0.57
30 1 0.02
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.31
Consensus pattern (27 bp):
ACTCAAAGATTTTTTTTCAAAAGAAAA
Found at i:1000260 original size:28 final size:28
Alignment explanation
Indices: 1000161--1000253 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 28
1000151 ATGTTTTAAG
1000161 AGAAAC-ATACTCAAAGATTTTTTTCTCAAA
1 AGAAACTA-ACTCAAAGA-TTTTTT-TCAAA
1000191 AGAAA-TAACTCAAAGATTTTTATTCAAA
1 AGAAACTAACTCAAAGATTTTT-TTCAAA
* *
1000219 ATG-AACAAACTCAAAGATTTGTTTCAAA
1 A-GAAACTAACTCAAAGATTTTTTTCAAA
1000247 AGAAACT
1 AGAAACT
1000254 GTCTCAAGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
27 1 0.02
28 23 0.42
29 25 0.45
30 6 0.11
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (28 bp):
AGAAACTAACTCAAAGATTTTTTTCAAA
Found at i:1000270 original size:122 final size:119
Alignment explanation
Indices: 999965--1000282 Score: 336
Period size: 120 Copynumber: 2.6 Consensus size: 119
999955 TGAGACGAAT
* * **
999965 TTTTTTC-AAAGGAAACAATCTCAAAGGTTGGTTTTTCATTAGAAACTGTCTCAAGAGAGACAAA
1 TTTTTTCAAAAGG-AACAAACTCAAA-GAT--TTTTTCAAAAGAAACTGTCTCAAGAGAGACAAA
* * * * **
1000029 ATTTGTTTTTAAAGAAATAAACTAAAAGATGATTTTGTTAGTAGAAACAAACTCAAAGA
62 ATATG-TTTTAAAGAAACAAACTAAAAGATGATTTTCTCAAAAGAAACAAACTCAAAGA
* * * * *
1000088 TTTTTTCAAAAGGAATAGACTCCAAGATTTTTTCAAGAGAAACTGTCTCAAGAGAAACAAAATAT
1 TTTTTTCAAAAGGAACAAACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATAT
* * ** *
1000153 GTTTTAAGAGAAACATACTCAAAGATTTTTTTCTCAAAAGAAA-TAACTCAAAGA
66 GTTTTAA-AGAAACAAACTAAAAGATGATTTTCTCAAAAGAAACAAACTCAAAGA
*
1000207 TTTTTATTCAAAATGAACAAACTCAAAGATTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA
1 -TTTT-TTCAAAAGGAACAAACTCAAAGATTT-TTTCAAAAGAAACTGTCTCAAGAGAGACAAAA
1000272 -ATCGTTTTAAA
63 TAT-GTTTTAAA
1000283 ATATTCAAAG
Statistics
Matches: 164, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
119 16 0.10
120 64 0.39
121 25 0.15
122 39 0.24
123 15 0.09
124 5 0.03
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.31
Consensus pattern (119 bp):
TTTTTTCAAAAGGAACAAACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATAT
GTTTTAAAGAAACAAACTAAAAGATGATTTTCTCAAAAGAAACAAACTCAAAGA
Found at i:1000519 original size:36 final size:36
Alignment explanation
Indices: 1000479--1000560 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
1000469 AAAGGAAAAA
* * *
1000479 TGTCTCAAGCGAGACGAAGTTTG-TTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAA-AGAAAT
* * *
1000515 TGTCTTAAGTGATACAAACTTTGTTTTTAAAGAAAT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
1000551 TGTCTCAAGC
1 TGTCTCAAGC
1000561 AAAACAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 31 0.84
37 6 0.16
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
Found at i:1000568 original size:36 final size:36
Alignment explanation
Indices: 1000479--1000573 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 36
1000469 AAAGGAAAAA
* * * *
1000479 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
* * * *
1000515 TGTCTTAAGTGATACAAACTTTGTTTTTAA-AGAAAT
1 TGTCTCAAGCGAAACAAAATTTG-TTTTAAGAGAAAT
*
1000551 TGTCTCAAGCAAAACAAAATTTG
1 TGTCTCAAGCGAAACAAAATTTG
1000574 AGAAAACGAT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
36 41 0.87
37 6 0.13
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.35
Consensus pattern (36 bp):
TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
Found at i:1000696 original size:36 final size:35
Alignment explanation
Indices: 1000663--1000780 Score: 139
Period size: 36 Copynumber: 3.3 Consensus size: 35
1000653 AGTGAGACGG
1000663 AATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAA
1 AATTTGTTTTT-AAGAAATTGTCTCAAACGAGACAA
* *
1000699 AATTTGTTTTT-AGAAAGCTGTCTCAAGCGAGACAA
1 AATTTGTTTTTAAGAAA-TTGTCTCAAACGAGACAA
** * *
1000734 AATTTGCTTTGAAAGAAATTGTCTCAAGCGATACAAA
1 AATTTG-TTTTTAAGAAATTGTCTCAAACGAGAC-AA
1000771 AATTTGTTTT
1 AATTTGTTTT
1000781 AAAATTCTCA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
34 5 0.07
35 22 0.31
36 31 0.44
37 13 0.18
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (35 bp):
AATTTGTTTTTAAGAAATTGTCTCAAACGAGACAA
Found at i:1001142 original size:4 final size:4
Alignment explanation
Indices: 1001126--1001179 Score: 69
Period size: 4 Copynumber: 14.2 Consensus size: 4
1001116 ATGCAAATTT
* *
1001126 TATG TAT- TATG TATG TATG --TG TATA TATG TATG TATG TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1001171 TATG TATG T
1 TATG TATG T
1001180 TTTCTCGATC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 2 0.05
3 3 0.07
4 38 0.88
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:1001166 original size:16 final size:16
Alignment explanation
Indices: 1001126--1001179 Score: 83
Period size: 16 Copynumber: 3.3 Consensus size: 16
1001116 ATGCAAATTT
1001126 TATGTAT-TATGTATG
1 TATGTATATATGTATG
1001141 TATGTGTATATATGTATG
1 TA--TGTATATATGTATG
1001159 TATGTATATATGTATG
1 TATGTATATATGTATG
1001175 TATGT
1 TATGT
1001180 TTTCTCGATC
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.06
16 19 0.53
17 5 0.14
18 10 0.28
ACGTcount: A:0.28, C:0.00, G:0.20, T:0.52
Consensus pattern (16 bp):
TATGTATATATGTATG
Found at i:1008440 original size:3 final size:3
Alignment explanation
Indices: 1008432--1008508 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
1008422 ATAAATAAGC
1008432 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1008480 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1008509 TACAATTAGA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1011648 original size:15 final size:14
Alignment explanation
Indices: 1011628--1011663 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
1011618 ATATGGATTG
1011628 ATTTATTTTAAAATA
1 ATTTATTTT-AAATA
1011643 ATTTATTTTAAATA
1 ATTTATTTTAAATA
1011657 ATTTATT
1 ATTTATT
1011664 AGTATGGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1011657 original size:14 final size:15
Alignment explanation
Indices: 1011566--1011663 Score: 101
Period size: 15 Copynumber: 6.2 Consensus size: 15
1011556 TATTAAAATA
1011566 ATTTT-AAATAATTT
1 ATTTTAAAATAATTT
*
1011580 ATTATAAAATAATTT
1 ATTTTAAAATAATTT
1011595 ATTTTAAAATAATTT
1 ATTTTAAAATAATTT
*
1011610 ATTATAAAATATGGATTGATTT
1 ATT-TTAAA-AT--A---ATTT
1011632 ATTTTAAAATAATTT
1 ATTTTAAAATAATTT
1011647 ATTTT-AAATAATTT
1 ATTTTAAAATAATTT
1011661 ATT
1 ATT
1011664 AGTATGGATT
Statistics
Matches: 72, Mismatches: 4, Indels: 16
0.78 0.04 0.17
Matches are distributed among these distances:
14 16 0.22
15 35 0.49
16 4 0.06
17 2 0.03
18 1 0.01
19 1 0.01
20 2 0.03
21 4 0.06
22 7 0.10
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATTTTAAAATAATTT
Found at i:1011681 original size:32 final size:32
Alignment explanation
Indices: 1011643--1011794 Score: 146
Period size: 32 Copynumber: 5.4 Consensus size: 32
1011633 TTTTAAAATA
1011643 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1011675 ATTTATTTT--A-AA---A-TA-TA--GATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1011697 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1011729 ATTTATTTT-AA-AA--TA-T-G-A---ATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
1011751 ATTTATTTTAAATAATTTATTAGTATGTATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
1011783 ATTTATTTTAAA
1 ATTTATTTTAAA
1011795 ATATAGATTG
Statistics
Matches: 99, Mismatches: 1, Indels: 40
0.71 0.01 0.29
Matches are distributed among these distances:
22 27 0.27
23 2 0.02
24 5 0.05
25 5 0.05
26 4 0.04
27 2 0.02
28 4 0.04
29 5 0.05
30 5 0.05
31 2 0.02
32 38 0.38
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:1011709 original size:54 final size:54
Alignment explanation
Indices: 1011643--1011811 Score: 304
Period size: 54 Copynumber: 3.1 Consensus size: 54
1011633 TTTTAAAATA
1011643 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1011697 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT-GAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAG-ATTG
* *
1011751 ATTTATTTTAAATAATTTATTAGTATGTATTAATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
1011805 ATTTATT
1 ATTTATT
1011812 ATTGTAGTTG
Statistics
Matches: 111, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
53 1 0.01
54 109 0.98
55 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
Found at i:1011745 original size:22 final size:22
Alignment explanation
Indices: 1011720--1011762 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1011710 AATTTATTAG
*
1011720 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
1011742 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
1011763 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:1011769 original size:108 final size:105
Alignment explanation
Indices: 1011591--1011811 Score: 315
Period size: 108 Copynumber: 2.1 Consensus size: 105
1011581 TTATAAAATA
1011591 ATTTATTTTAAAATAATTTATTATAAAATATGGATTGATTTATTTTAAAATAATTTATTTTAAAT
1 ATTTATTTTAAAATAATTTATTAT-AAATATGGATTGATTTATTTTAAAATAATTTATTTTAAAT
*
1011656 AATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTG
65 AATTTATTAGTATGGATTAATTTATTTTAAAATATAGATTG
*
1011697 ATTTATTTT-AAATAATTTA-T-T-AGTATGGATTGATTTATTTTAAAATATGAATTGATTTATT
1 ATTTATTTTAAAATAATTTATTATAAATATGGATTGATTTATTTT-AAA-AT--A---ATTTATT
*
1011758 TTAAATAATTTATTAGTATGTATTAATTTATTTTAAAATATAGATTG
59 TTAAATAATTTATTAGTATGGATTAATTTATTTTAAAATATAGATTG
1011805 ATTTATT
1 ATTTATT
1011812 ATTGTAGTTG
Statistics
Matches: 105, Mismatches: 3, Indels: 12
0.88 0.03 0.10
Matches are distributed among these distances:
101 19 0.18
102 3 0.03
103 3 0.03
104 1 0.01
105 11 0.10
106 9 0.09
108 59 0.56
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (105 bp):
ATTTATTTTAAAATAATTTATTATAAATATGGATTGATTTATTTTAAAATAATTTATTTTAAATA
ATTTATTAGTATGGATTAATTTATTTTAAAATATAGATTG
Found at i:1011844 original size:134 final size:135
Alignment explanation
Indices: 1011688--1012433 Score: 829
Period size: 134 Copynumber: 5.5 Consensus size: 135
1011678 TATTTTAAAA
1011688 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
1 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
* *
1011753 TTATTTTAAATAATTTATTAGTATGTATTAATTTATTTTAAAATATAGATTGATTTA-TTATTGT
66 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTTATTGT
1011817 AGTT-G
131 A-TTAG
* * * * *
1011822 TATGGATTGGTTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
1011887 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTA-TTATTGT
66 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTTATTGT
1011951 AGTT-G
131 A-TTAG
** *
1011956 TATAGATTGATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTTAAATAT-AGATTGA
1 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGA-ATTGA
* * *
1012020 TTTA--TT--AT--TGTAGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
65 TTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT-AA-AA--TA-TAG-ATTGATTTA
*
1012078 TTTATT-T-TTAAA
123 TTTATTGTATT-AG
* *
1012090 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
*
1012155 TTATTTTAAATAATTTATTAGTAT-AATTTGATTTATTTTAAAATATAGATTGATTTATTTTAAA
66 TTATTTTAAATAATTTATTAGTATGGA-TTGATTTATTTTAAAATATAGATTGATTTA-TTT--A
*
1012219 TAATTTATTAG
127 T--TGTATTAG
1012230 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT-AGATTGA
1 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGA-ATTGA
* * * * *
1012294 TTTA--TT--AT--TGTAGTT-GTACGGATTGATTTATTTTAAATAATTTATTGGTATGAATTGA
65 TTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT-AA-AA--TATAGAT-TG-ATTTA
* * *
1012352 TTTATTTTA-AAA
123 TTTATTGTATTAG
* * * *
1012364 TATAGATTAATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATGTGAATTAAT
1 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
1012429 TTATT
66 TTATT
1012434 ATTGTAGTTG
Statistics
Matches: 531, Mismatches: 42, Indels: 76
0.82 0.06 0.12
Matches are distributed among these distances:
128 22 0.04
129 4 0.01
130 4 0.01
132 6 0.01
133 3 0.01
134 345 0.65
135 21 0.04
136 8 0.02
137 4 0.01
138 11 0.02
139 11 0.02
140 90 0.17
141 2 0.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (135 bp):
TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGAT
TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTTATTGT
ATTAG
Found at i:1011848 original size:80 final size:79
Alignment explanation
Indices: 1011742--1012416 Score: 429
Period size: 80 Copynumber: 8.3 Consensus size: 79
1011732 TATTTTAAAA
* *
1011742 TATGAATTGATTTATTTTAAATAATTTATTAGTATGTATTAATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATAGATTGAT
1011807 TTATTATTGTAGTT-G
66 TTATTATT-TA-TTAG
* * * *
1011822 TATGGATTGGTTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATAGATTGAT
1011887 TTATTTTAAATAATTTATTAG
66 TTA---T---T-ATTTATTAG
** * * *
1011908 TATGGATTGATTTATTTTAAA-ATATAGATT-G-ATTTATT-ATTGTAGTTGTATAGAT-T-GAT
1 TATGGATTGATTTATTTTAAATA-ATTTATTAGTATGTATTGATT-TA-TTTTA-AAATATAGAT
* *
1011967 TTATTTTAAATAATTTATTAG
62 TGA-TTT--ATTATTTATTAG
** ** * * **
1011988 TATATATTGATTTATTTTTAAAT-ATAGATT-G-ATTTATT-ATTGTAGTTGTATGGAT-T-GAT
1 TATGGATTGATTTA-TTTTAAATAATTTATTAGTATGTATTGATT-TA-TTTTA-AAATATAGAT
* *
1012047 TTATTTTAAATAATTTATTAG
62 TGA-TTT--ATTATTTATTAG
** * * ** * * * *
1012068 TATGGATTGATTTATTTTTAAAT-ATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATT
1 TATGGATTGATTTA-TTTTAAATAATTTATTAGTATGTA-TTGATTTATTTTA-AAATATAGATT
* *
1012130 GATTTA-T-TTTA-AAA
63 GATTTATTATTTATTAG
*
1012144 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-AATTTGATTTATTTTAAAATATAGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTA-TTGATTTATTTTAAAATATAGATTGA
1012208 TTTATTTTAAATAATTTATTAG
65 TTTA---T---T-ATTTATTAG
* *
1012230 TATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATAGATTGAT
1012295 TTATTATTGTAGTT-G
66 TTATTATT-TA-TTAG
* * * *
1012310 TACGGATTGATTTATTTTAAATAATTTATTGGTATGAATTGATTTATTTTAAAATATAGATTAAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATAGATTGAT
1012375 TTATTTTAAATAATTTATTAG
66 TTA---T---T-ATTTATTAG
*
1012396 TATAGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1012417 ATGTGAATTA
Statistics
Matches: 496, Mismatches: 54, Indels: 84
0.78 0.09 0.13
Matches are distributed among these distances:
75 8 0.02
76 34 0.07
77 16 0.03
78 2 0.00
79 4 0.01
80 244 0.49
81 17 0.03
82 6 0.01
83 7 0.01
84 13 0.03
85 17 0.03
86 120 0.24
87 8 0.02
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (79 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATAGATTGAT
TTATTATTTATTAG
Found at i:1011872 original size:32 final size:32
Alignment explanation
Indices: 1011822--1011928 Score: 117
Period size: 32 Copynumber: 3.7 Consensus size: 32
1011812 ATTGTAGTTG
*
1011822 TATGGATTGGTTTATTTTAAATAATTTATTAA
1 TATGGATTGATTTATTTTAAATAATTTATTAA
*
1011854 TATGAATTGATTTA-TTT---T-A---A--AA
1 TATGGATTGATTTATTTTAAATAATTTATTAA
*
1011876 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAA
1011908 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1011929 ATATAGATTG
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
22 15 0.25
23 3 0.05
24 1 0.02
26 1 0.02
27 2 0.03
28 1 0.02
30 1 0.02
31 3 0.05
32 34 0.56
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAA
Found at i:1011877 original size:22 final size:22
Alignment explanation
Indices: 1011852--1011896 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1011842 ATAATTTATT
1011852 AATATGAATTGATTTATTTTAA
1 AATATGAATTGATTTATTTTAA
*
1011874 AATATGGATTGATTTATTTTAA
1 AATATGAATTGATTTATTTTAA
1011896 A
1 A
1011897 TAATTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
AATATGAATTGATTTATTTTAA
Found at i:1011892 original size:54 final size:54
Alignment explanation
Indices: 1011822--1012433 Score: 550
Period size: 54 Copynumber: 11.3 Consensus size: 54
1011812 ATTGTAGTTG
* *
1011822 TATGGATTGGTTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
*
1011876 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
* *
1011930 TATAGATTGATTTA--TT--AT--TGTAGTT-GTAT-AGATTGATTTATTTT-AAA
1 TATGGATTGATTTATTTTAAATAATTTA-TTAGTATGA-ATTGATTTATTTTAAAA
** * * * * * * ***
1011977 TAATTTATT-AGTATATATTGATTTATTT-TTAAATAT-AGATTGATTTATTATTGTAGTTG
1 T-ATGGATTGA-TTTATTTTAAATAATTTATT-AGTATGA-ATTGATTTA-T-TT-TA-AAA
* *
1012036 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
*
1012090 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
1012144 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-AATTTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAA-TTGATTTATTTTAAAA
*
1012198 TATAGATTGATTTATTTTAAATAATTTATTAGTAT-AGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTA-TTT---TAA---A--A
* * ***
1012261 GTATGGATTGATTTATTTT-AA-AA--TA-TAG-ATTG-ATTTA-TTATTGTAGTTG
1 -TATGGATTGATTTATTTTAAATAATTTATTAGTA-TGAATTGATTTATTTTA-AAA
* *
1012310 TACGGATTGATTTATTTTAAATAATTTATTGGTATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
* *
1012364 TATAGATTAATTTATTTTAAATAATTTATTAGTAT-AGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTTAAAA
* * *
1012418 TGTGAATTAATTTATT
1 TATGGATTGATTTATT
1012434 ATTGTAGTTG
Statistics
Matches: 463, Mismatches: 51, Indels: 88
0.77 0.08 0.15
Matches are distributed among these distances:
47 5 0.01
48 45 0.10
49 4 0.01
50 6 0.01
52 7 0.02
53 8 0.02
54 293 0.63
55 13 0.03
56 6 0.01
57 5 0.01
58 38 0.08
59 8 0.02
60 2 0.00
61 1 0.00
62 2 0.00
63 3 0.01
64 17 0.04
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAA
Found at i:1011986 original size:214 final size:214
Alignment explanation
Indices: 1011747--1012159 Score: 754
Period size: 214 Copynumber: 1.9 Consensus size: 214
1011737 TAAAATATGA
*
1011747 ATTGATTTATTTTAAATAATTTATTAGTATGTATTAATTTATTTTAAAATATAGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATTAGTATATATTAATTTATTTTAAAATATAGATTGATTTATT
*
1011812 ATTGTAGTTGTATGGATTGGTTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAAT
66 ATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAAT
1011877 ATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATT
131 ATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATT
1011942 TATTATTGTAGTTGTATAG
196 TATTATTGTAGTTGTATAG
* *
1011961 ATTGATTTATTTTAAATAATTTATTAGTATATATTGATTTATTTTTAAATATAGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATTAGTATATATTAATTTATTTTAAAATATAGATTGATTTATT
* * *
1012026 ATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAT
66 ATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAAT
*
1012091 ATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATT
131 ATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATT
1012156 TATT
196 TATT
1012160 TTAAATAATT
Statistics
Matches: 191, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
214 191 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.54
Consensus pattern (214 bp):
ATTGATTTATTTTAAATAATTTATTAGTATATATTAATTTATTTTAAAATATAGATTGATTTATT
ATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAATATGAATTGATTTATTTTAAAAT
ATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATT
TATTATTGTAGTTGTATAG
Found at i:1012012 original size:18 final size:18
Alignment explanation
Indices: 1011961--1012022 Score: 51
Period size: 18 Copynumber: 3.7 Consensus size: 18
1011951 AGTTGTATAG
1011961 ATTGATTTA-TTTTAAAT
1 ATTGATTTATTTTTAAAT
** *
1011978 A---ATTTATTAGTATAT
1 ATTGATTTATTTTTAAAT
1011993 ATTGATTTATTTTTAAAT
1 ATTGATTTATTTTTAAAT
* *
1012011 ATAGATTGATTT
1 ATTGATTTATTT
1012023 ATTATTGTAG
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
14 5 0.15
15 6 0.18
17 1 0.03
18 21 0.64
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.56
Consensus pattern (18 bp):
ATTGATTTATTTTTAAAT
Found at i:1012076 original size:32 final size:32
Alignment explanation
Indices: 1012035--1012282 Score: 178
Period size: 32 Copynumber: 7.7 Consensus size: 32
1012025 TATTGTAGTT
1012035 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1012067 GTATGGATTGATTTATTTTTAAATATGGATTGATTTA
1 GTATGGATTGATTTA-TTTTAAATA---ATTTA-TTA
* ** * * * * *
1012104 -TTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATT--T-T-AAATAATTTA--TT--A
*
1012143 ATATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1012175 GTAT-AATTTGATTTATTTT--A-AA---A-TA
1 GTATGGA-TTGATTTATTTTAAATAATTTATTA
1012200 -TA--GATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1012229 GTATAGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1012261 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
1012283 ATATAGATTG
Statistics
Matches: 170, Mismatches: 22, Indels: 48
0.71 0.09 0.20
Matches are distributed among these distances:
22 12 0.07
23 1 0.01
24 3 0.02
25 4 0.02
26 1 0.01
28 1 0.01
29 4 0.02
30 3 0.02
31 1 0.01
32 79 0.46
33 9 0.05
34 2 0.01
35 2 0.01
36 24 0.14
37 8 0.05
38 2 0.01
39 3 0.02
40 11 0.06
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:1012109 original size:21 final size:22
Alignment explanation
Indices: 1012068--1012112 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1012058 AATTTATTAG
1012068 TATGGATTGATTTATTTTTAAA
1 TATGGATTGATTTATTTTTAAA
1012090 TATGGATTGATTTA-TTTTAAA
1 TATGGATTGATTTATTTTTAAA
1012111 TA
1 TA
1012113 ATTTATTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTTAAA
Found at i:1012147 original size:22 final size:22
Alignment explanation
Indices: 1012122--1012164 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1012112 AATTTATTAG
1012122 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1012144 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1012165 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1012186 original size:86 final size:81
Alignment explanation
Indices: 1012090--1012416 Score: 345
Period size: 86 Copynumber: 3.9 Consensus size: 81
1012080 TATTTTTAAA
* * * * *
1012090 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAATATGGATTGA
1 TATGAATTGATTTATTTT-AA-AA--TA-TAG-ATTGATTTATTTATTTTAGTAGTATGGATTGA
1012154 TTTATTTTAAATAATTTATTAG
60 TTTATTTTAAATAATTTATTAG
* *
1012176 TAT-AATTTGATTTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTAGTATAGATTGA
1 TATGAA-TTGATTTATTTTAAAATATAGATTGATTTA-TTT--AT--TTTAGTAGTATGGATTGA
1012240 TTTATTTTAAATAATTTATTAG
60 TTTATTTTAAATAATTTATTAG
* * * *
1012262 TATGGATTGATTTATTTTAAAATATAGATTGATTTA-TTATTGTAGTTGTACGGATTGATTTATT
1 TATGAATTGATTTATTTTAAAATATAGATTGATTTATTTATTTTAGTAGTATGGATTGATTTATT
*
1012326 TTAAATAATTTATTGG
66 TTAAATAATTTATTAG
* * *
1012342 TATGAATTGATTTATTTTAAAATATAGATTAATTTATTTTAAATAATTTATTAGTATAGATTGAT
1 TATGAATTGATTTATTTTAAAATATAGATTGATTTA-TTT--AT--TTTAGTAGTATGGATTGAT
1012407 TTATTTTAAA
61 TTATTTTAAA
1012417 ATGTGAATTA
Statistics
Matches: 207, Mismatches: 20, Indels: 28
0.81 0.08 0.11
Matches are distributed among these distances:
80 75 0.36
81 6 0.03
82 6 0.03
83 2 0.01
84 6 0.03
85 7 0.03
86 104 0.50
87 1 0.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (81 bp):
TATGAATTGATTTATTTTAAAATATAGATTGATTTATTTATTTTAGTAGTATGGATTGATTTATT
TTAAATAATTTATTAG
Found at i:1012226 original size:14 final size:14
Alignment explanation
Indices: 1012207--1012259 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
1012197 ATATAGATTG
1012207 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
1012221 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
1012239 ATTTATTTTAAATA
1 ATTTATTTTAAATA
1012253 ATTTATT
1 ATTTATT
1012260 AGTATGGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
14 16 0.52
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.29
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:1012356 original size:32 final size:31
Alignment explanation
Indices: 1012315--1012416 Score: 98
Period size: 32 Copynumber: 3.5 Consensus size: 31
1012305 AGTTGTACGG
1012315 ATTGATTTATTTTAAATAATTTATTGGTATGA
1 ATTGATTTATTTTAAATAATTTATT-GTATGA
1012347 ATTGATTTATTTT-AA-AA--TA---TA-G-
1 ATTGATTTATTTTAAATAATTTATTGTATGA
*
1012369 ATTAATTTATTTTAAATAATTTATTAGTAT-A
1 ATTGATTTATTTTAAATAATTTATT-GTATGA
1012400 GATTGATTTATTTTAAA
1 -ATTGATTTATTTTAAA
1012417 ATGTGAATTA
Statistics
Matches: 57, Mismatches: 2, Indels: 22
0.70 0.02 0.27
Matches are distributed among these distances:
22 12 0.21
23 3 0.05
24 4 0.07
26 2 0.04
28 2 0.04
30 4 0.07
31 2 0.04
32 28 0.49
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (31 bp):
ATTGATTTATTTTAAATAATTTATTGTATGA
Found at i:1012471 original size:166 final size:165
Alignment explanation
Indices: 1011747--1012416 Score: 544
Period size: 166 Copynumber: 4.1 Consensus size: 165
1011737 TAAAATATGA
* * * * * *
1011747 ATTGATTTATTTTAAATAATTTATTAGTATGTATTAATTTATTTTAAAATATAGATTGATTTATT
1 ATTGATTTATTTTAAATAATTAATTAG-ATGGATTGATTTATTGTAAAATATAGATTAATTTAGT
* * *
1011812 ATTGTAGTTGTATGGATTGGTTTATTTTAAATAATTTATTAATATGAA-TTGATTTATTTTAAAA
65 ATTGTAGTTGTACGGATTGATTTATTTTAAATAATTTATTAGTAT-AATTTGATTTATTTTAAAA
* * *
1011876 TATGGATTGATTTATTTTAAATAATTTATTAGTATGG
129 TATAGATTAATTTATTTTAAATAATTTATTAGTATAG
** * *
1011913 ATTGATTTATTTT-AA-AATATAGATT-GATTTATT-ATTGTAGTTGTATAGAT-T-GATTTATT
1 ATTGATTTATTTTAAATAAT-TA-ATTAGATGGATTGATT-TA-TTGTA-AAATATAGA-TTAAT
* *** * *
1011972 TTAAATAATT-TA-TTAGTATATATTGATTTATTTT---TAA-ATA-TAG-ATTGATTT-A-TTA
60 TT-AGT-ATTGTAGTT-GTACGGATTGATTTATTTTAAATAATTTATTAGTA-TAATTTGATTTA
* *** * * *
1012027 TTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGG
121 TTTTA-AAATATAGATTAATTTATTTTAAATAATTTATTAGTATAG
** ** * * * * * * *
1012073 ATTGATTTATTTTTAAAT-ATGGATT-GATTTATTTTAAATAATT-TATTAGTATGGATTGATTT
1 ATTGATTTA-TTTTAAATAATTAATTAGATGGA--TTGATTTATTGTA-AAATATAGATTAATTT
*** *
1012135 A-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATAATTTGATTTATTTTAA
62 AGTATTGTAGTTGTACGGATTGATTTATTTTAAATAATTTATTAGTATAATTTGATTTATTTTAA
*
1012196 AATATAGATTGATTTATTTTAAATAATTTATTAGTATAG
127 AATATAGATTAATTTATTTTAAATAATTTATTAGTATAG
* * * *
1012235 ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATT
1 ATTGATTTATTTTAAATAATTAATTAG-ATGGATTGATTTATTGTAAAATATAGATTAATTTAGT
*
1012300 ATTGTAGTTGTACGGATTGATTTATTTTAAATAATTTATTGGTATGAA-TTGATTTATTTTAAAA
65 ATTGTAGTTGTACGGATTGATTTATTTTAAATAATTTATTAGTAT-AATTTGATTTATTTTAAAA
1012364 TATAGATTAATTTATTTTAAATAATTTATTAGTATAG
129 TATAGATTAATTTATTTTAAATAATTTATTAGTATAG
1012401 ATTGATTTATTTTAAA
1 ATTGATTTATTTTAAA
1012417 ATGTGAATTA
Statistics
Matches: 412, Mismatches: 55, Indels: 74
0.76 0.10 0.14
Matches are distributed among these distances:
156 16 0.04
157 4 0.01
159 11 0.03
160 65 0.16
161 33 0.08
162 83 0.20
163 19 0.05
164 18 0.04
165 18 0.04
166 140 0.34
167 5 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (165 bp):
ATTGATTTATTTTAAATAATTAATTAGATGGATTGATTTATTGTAAAATATAGATTAATTTAGTA
TTGTAGTTGTACGGATTGATTTATTTTAAATAATTTATTAGTATAATTTGATTTATTTTAAAATA
TAGATTAATTTATTTTAAATAATTTATTAGTATAG
Found at i:1012483 original size:31 final size:31
Alignment explanation
Indices: 1012448--1012507 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1012438 TAGTTGTAAT
* * *
1012448 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAATATTGCAAAACTAA
1012479 AATTATTTAAATCTCAATATTGCAAAACT
1 AATTATTTAAATCTCAATATTGCAAAACT
1012508 CTTTTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATCTCAATATTGCAAAACTAA
Found at i:1017490 original size:35 final size:34
Alignment explanation
Indices: 1017405--1017491 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
1017395 AAAATAATTT
*
1017405 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
1017439 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
1017477 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1017492 ATTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:1019790 original size:16 final size:16
Alignment explanation
Indices: 1019769--1019818 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
1019759 TTTATATTTG
*
1019769 TAAAATATTAATTAAA
1 TAAAATATTAAATAAA
* *
1019785 TAAAATATTAAACAAT
1 TAAAATATTAAATAAA
1019801 TAAAATAATTAAATAAA
1 TAAAAT-ATTAAATAAA
1019818 T
1 T
1019819 TACTAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAATATTAAATAAA
Found at i:1019842 original size:33 final size:30
Alignment explanation
Indices: 1019771--1019848 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 30
1019761 TATATTTGTA
* *
1019771 AAATATTAATTAAATAAAATATTAAACAATT
1 AAATA-TAATTAAATAAAATATAAAAAAATT
*
1019802 AAA-ATAATTAAATAAATTACTAAAAAAATACT
1 AAATATAATTAAATAAAATA-TAAAAAAAT--T
*
1019834 AAATATAATAAAATA
1 AAATATAATTAAATA
1019849 TACCTTAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 14 0.36
30 8 0.21
31 3 0.08
32 4 0.10
33 10 0.26
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (30 bp):
AAATATAATTAAATAAAATATAAAAAAATT
Found at i:1020762 original size:145 final size:143
Alignment explanation
Indices: 1020517--1020853 Score: 414
Period size: 145 Copynumber: 2.3 Consensus size: 143
1020507 TAGTTTTGTG
* * *
1020517 ATTTAGTCCCTAATTTCCTTATT-CTTCAATT-TCACATTCATTTTAAGTCCATTTTTACCAAAT
1 ATTTAGTCTCTAATTTTCTTATTCCTTCAATTCT-AC-TTCATTTTAAGTCTATTTTTACCAAAT
* * *
1020580 TTGAACCACATGCTCCTAAACCATCGCAGAATACATATGTGCTTTCAATTAATCTTTTT-AATAA
64 TTCAACCACATGCTCCAAAACCATCGCAGAATACATATGTGCTTTCAATT--CCTTTTTGAATAA
* *
1020644 TATTTTTAAATTTTTTA
127 CATTTTTAAATTTTTCA
* * * **
1020661 GTTTAGTCTCTAATTTTCTTATTCCTTCAATTGCTTCTCCATTTTAAGTCTATTTTTATTAAATT
1 ATTTAGTCTCTAATTTTCTTATTCCTTCAATT-CTACTTCATTTTAAGTCTATTTTTACCAAATT
** *
1020726 TCAACCACATGCTCCAAAACCATCTTAGAATACATATGTGCTTTCAATTCCTTTTTGTATAACAT
65 TCAACCACATGCTCCAAAACCATCGCAGAATACATATGTGCTTTCAATTCCTTTTTGAATAACAT
*
1020791 TTTTTAATTTTTCA
130 TTTTAAATTTTTCA
* *
1020805 ATTTAGTCT-TGATTTTCTTATTCCTT-AATTCATCCTTCATTTTAAGTCT
1 ATTTAGTCTCTAATTTTCTTATTCCTTCAATTC-TACTTCATTTTAAGTCT
1020854 TGTCGTAACC
Statistics
Matches: 167, Mismatches: 21, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
141 1 0.01
142 19 0.11
143 22 0.13
144 46 0.28
145 77 0.46
146 1 0.01
147 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.47
Consensus pattern (143 bp):
ATTTAGTCTCTAATTTTCTTATTCCTTCAATTCTACTTCATTTTAAGTCTATTTTTACCAAATTT
CAACCACATGCTCCAAAACCATCGCAGAATACATATGTGCTTTCAATTCCTTTTTGAATAACATT
TTTAAATTTTTCA
Found at i:1021602 original size:2 final size:2
Alignment explanation
Indices: 1021595--1021637 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1021585 AAAAATAAAC
1021595 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
1021637 A
1 A
1021638 AAATTTAGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1021765 original size:27 final size:27
Alignment explanation
Indices: 1021694--1021755 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 27
1021684 ATATATAAAG
*
1021694 AAAATAATAATA-AGTAGAAAAAGAAATA
1 AAAATAAAAATATA-TA-AAAAAGAAATA
*
1021722 AAAATAAAAATATATAAAAAATAAAT-
1 AAAATAAAAATATATAAAAAAGAAATA
1021748 AAAATAAA
1 AAAATAAA
1021756 GAGAATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 8 0.26
27 9 0.29
28 13 0.42
29 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (27 bp):
AAAATAAAAATATATAAAAAAGAAATA
Found at i:1023820 original size:84 final size:84
Alignment explanation
Indices: 1023637--1024441 Score: 921
Period size: 84 Copynumber: 9.6 Consensus size: 84
1023627 AACTTGACAA
* * * * * * *
1023637 TTTTGTTGTCAGATAGCCCTTCTTGCCTTGAGATATGCTGTAAATTTGATTTACCTAT-GAGCTG
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAA--TGATGTGCCT-TGGAGCTG
* * * *
1023701 AGTGTAATCAAACTTGAAGGTC
63 AGCGTAGTCGAACTCGAAGGTC
* * * * * * * *
1023723 TTTGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCATTTGAACTGAAC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
1023788 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * *
1023807 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACAAATGATGTGCCTTGTAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
1023872 GTAGTCAAACTCGAAGGTT
66 GTAGTCGAACTCGAAGGTC
* * * *
1023891 TTTTGTTGGCAGATAACCCTTCCT-GCCTTGAGCTATGTTGCAAATTATATACCTTGGAGCTGAG
1 TTTTGTTGGCAGATAACCCTT-CTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAG
*
1023955 CGTAGTCGAACTCGAAGGGC
65 CGTAGTCGAACTCGAAGGTC
* * *
1023975 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
1024040 GTAGTCGAACTTGATGGTC
66 GTAGTCGAACTCGAAGGTC
* *
1024059 TTTTGTTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
1024124 GTAGTCGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * *
1024143 TTTGGTTGGCAGATAACCCTTTTAGCCTTGAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* * *
1024208 ATAATCGAACTCGAAAGTC
66 GTAGTCGAACTCGAAGGTC
* * ** * ** ** * * * * * *
1024227 TTTTGTTGCCAAATAGTCATTCTTTCCTTGATATATGTTGTAAATAATGTGTCTTAGAGTTGAGC
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
1024292 GTAGTTGAACTCGAAGGTC
66 GTAGTCGAACTCGAAGGTC
* * * * *
1024311 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGTCTTAGAGCTGAGT
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
* *
1024376 GTAGTCGAACTCAAAGGCC
66 GTAGTCGAACTCGAAGGTC
* * * * *
1024395 TTTTGTTGGAAAATAATCATTCTTGCCTTGAGCTATGCTGCAAATGA
1 TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGA
1024442 ACACGATATC
Statistics
Matches: 609, Mismatches: 107, Indels: 8
0.84 0.15 0.01
Matches are distributed among these distances:
83 3 0.00
84 568 0.93
85 2 0.00
86 36 0.06
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (84 bp):
TTTTGTTGGCAGATAACCCTTCTAGCCTTGAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCGAAGGTC
Found at i:1024663 original size:124 final size:124
Alignment explanation
Indices: 1024500--1024735 Score: 357
Period size: 124 Copynumber: 1.9 Consensus size: 124
1024490 TGGTGGGTAG
*** *
1024500 GATTCCCTTTATCGTGAAGTTGAAACCGTAGAGGGCCCCTTCATTGTGAAGTTGAACCTCGAATT
1 GATTCCCTTTATCGTGAAGTTGAAACCGTAGACAACCCCTTCATTGTAAAGTTGAACCTCGAATT
* * * *
1024565 GGATATCTTTTGTCGTGAAGTTGAAATCTAATTTAAAGATGAATGTTACTGGTGAGAAT
66 GGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAGAAT
* * *
1024624 GATTCCCTTCT-TCGTGAAGTTGAAACCGTAGACAACCCCTTCGTTGTAAAGTTGAGCCTTGAAT
1 GATTCCCTT-TATCGTGAAGTTGAAACCGTAGACAACCCCTTCATTGTAAAGTTGAACCTCGAAT
1024688 TGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTT
65 TGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTT
1024736 GCTTCGAGTC
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
124 99 0.99
125 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (124 bp):
GATTCCCTTTATCGTGAAGTTGAAACCGTAGACAACCCCTTCATTGTAAAGTTGAACCTCGAATT
GGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTACTGGTGAGAAT
Found at i:1025065 original size:240 final size:242
Alignment explanation
Indices: 1024635--1025099 Score: 639
Period size: 240 Copynumber: 1.9 Consensus size: 242
1024625 ATTCCCTTCT
*
1024635 TCGTGAAGTTGAAACCGTAGACAACCCCTTCGTTGTAAAGTTGAGCCTTGAATTGGATATCCTTC
1 TCGTGAAGTTGAAACCGTAGACAACCCCTTCGTTGTAAAGTTGAGCCTTGAATTGAATATCCTTC
* * *
1024700 GTCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGCTTCGAGTCCAATATTCTTCACCGTGAA
66 GTCGTGAAGTTAAAATCCAAGCT----ATG-ATATTGCTTCGAGTCCAATATTCTTCACCGTGAA
* * *
1024765 GTTGAAATTAGCTTTGAATGAAACTGGGAAGCCCCTTCCCCGTGAAGTTGAGCTTTGAATTAGAC
126 GTTGAAATTAGCTCTGAATGAAACTGGGAAGCCCCTTCACCGTGAAGTTGAACTTTGAATTAGAC
* * *
1024830 ATCTTTCATTGTGAAGTTGAAATCCAATCTAGAATTGGCATAATATCTTTCG
191 ATCATTCATCGTGAAGTTAAAATCCAATCTAGAATTGGCATAATATCTTTCG
* * ** * *
1024882 TCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGACTTGAATATCCTTC
1 TCGTGAAGTTGAAACCGTAGACAACCCCTTCGTTGTAAAGTTGAGCCTTGAATTGAATATCCTTC
* * *
1024947 GTTGTGAAGTTAAAATCCAAGCT-TG-TATTGTTTCGAGTCCAATA-TCATTCGCCGTGAAGTTG
66 GTCGTGAAGTTAAAATCCAAGCTATGATATTGCTTCGAGTCCAATATTC-TTCACCGTGAAGTTG
* * * *
1025009 AAATTGGCTCTGAATGAAACTTGGAAGCCCCTTCACCGTGAAGTTGAACTTTGAATTGGATATCA
130 AAATTAGCTCTGAATGAAACTGGGAAGCCCCTTCACCGTGAAGTTGAACTTTGAATTAGACATCA
*
1025074 TTCGTCGTGAAGTTAAAATCCAATCT
195 TTCATCGTGAAGTTAAAATCCAATCT
1025100 TGTGTAGATG
Statistics
Matches: 193, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
239 2 0.01
240 111 0.58
242 2 0.01
247 78 0.40
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (242 bp):
TCGTGAAGTTGAAACCGTAGACAACCCCTTCGTTGTAAAGTTGAGCCTTGAATTGAATATCCTTC
GTCGTGAAGTTAAAATCCAAGCTATGATATTGCTTCGAGTCCAATATTCTTCACCGTGAAGTTGA
AATTAGCTCTGAATGAAACTGGGAAGCCCCTTCACCGTGAAGTTGAACTTTGAATTAGACATCAT
TCATCGTGAAGTTAAAATCCAATCTAGAATTGGCATAATATCTTTCG
Found at i:1025201 original size:287 final size:287
Alignment explanation
Indices: 1024880--1025545 Score: 1026
Period size: 287 Copynumber: 2.3 Consensus size: 287
1024870 TAATATCTTT
* *
1024880 CGTCGTGAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGACTTGAATATCCT
1 CGTCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGACTTGAATATCCT
* * *
1024945 TCGTTGTGAAGTTAAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCATTCGCCGTGAAGTTGA
66 TCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCATTCGCCATGAAGTTGA
* * *
1025010 AATTGGCTCTGAATGAAACTTGGAAGCCCCTTCACCGTGAAGTTGAACTTTGAATTGGATATCAT
131 AATTAGCTCTGAATGAAACTAGGAAGCCCCTTCACCGTGAAGTTGAACTTCGAATTGGATATCAT
* * * *
1025075 TCGTCGTGAAGTTAAAATCCAATCTTGTGTAGATGGGCACGATATTCTTCGCCGTGAAGTTGAAA
196 TCGTCGTGAAGTTAAAATCCAATCTTATATAGATGGGCACGATATCCTTCGCCGTGAAGTTAAAA
1025140 TCGTAGATTTGTGGGCACGATATCCTC
261 TCGTAGATTTGTGGGCACGATATCCTC
* *
1025167 CGTCGTGGACTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTAACTTGAATATCCT
1 CGTCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGACTTGAATATCCT
* *
1025232 TCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCCTTCGTCATGAAGTTGA
66 TCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCATTCGCCATGAAGTTGA
* * * *
1025297 AATTAGCTCTGAATGAAACTAGGAAGCCCCTTCTCTGTGAAGTTGAGCTTCGAATTGGATATCCT
131 AATTAGCTCTGAATGAAACTAGGAAGCCCCTTCACCGTGAAGTTGAACTTCGAATTGGATATCAT
* *
1025362 TCGTCGTGAAGTTGAAATCCAATCTTATATAGATGGGCACGATATCCTTCGTCGTGAAGTTAAAA
196 TCGTCGTGAAGTTAAAATCCAATCTTATATAGATGGGCACGATATCCTTCGCCGTGAAGTTAAAA
* * *
1025427 TTGTGGATTTGTGGGCATGATATCCTC
261 TCGTAGATTTGTGGGCACGATATCCTC
* * * * * * *
1025454 CGTCATGGAGTTGAAACCGCGGATGGCCCTTTCGTCGTGAAGTTGAGCCTTGAATTGGATATCCT
1 CGTCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGACTTGAATATCCT
* *
1025519 CCGTCGTGAAGTTGAAATCCAATCTTG
66 TCGTCGTGAAGTTGAAATCCAAGCTTG
1025546 AGAAAGTTGG
Statistics
Matches: 343, Mismatches: 36, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
287 343 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (287 bp):
CGTCGTGGAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAGTTGAGCCTTGACTTGAATATCCT
TCGTCGTGAAGTTGAAATCCAAGCTTGTATTGTTTCGAGTCCAATATCATTCGCCATGAAGTTGA
AATTAGCTCTGAATGAAACTAGGAAGCCCCTTCACCGTGAAGTTGAACTTCGAATTGGATATCAT
TCGTCGTGAAGTTAAAATCCAATCTTATATAGATGGGCACGATATCCTTCGCCGTGAAGTTAAAA
TCGTAGATTTGTGGGCACGATATCCTC
Found at i:1030959 original size:12 final size:12
Alignment explanation
Indices: 1030938--1030968 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
1030928 ACGTATATAC
1030938 AATAATATAAAAA
1 AATAA-ATAAAAA
1030951 AATAAATAAAAA
1 AATAAATAAAAA
1030963 AATAAA
1 AATAAA
1030969 CATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (12 bp):
AATAAATAAAAA
Found at i:1034204 original size:15 final size:15
Alignment explanation
Indices: 1034184--1034255 Score: 72
Period size: 16 Copynumber: 4.7 Consensus size: 15
1034174 ATTTTACATT
* *
1034184 TTAATCATTCAGCGC
1 TTAATCATTCAACAC
*
1034199 TTAATCATTCAACAT
1 TTAATCATTCAACAC
* *
1034214 TTGAATCATTCAATAT
1 TT-AATCATTCAACAC
*
1034230 TTGAATCATTCAACGC
1 TT-AATCATTCAACAC
1034246 TTAATCATTC
1 TTAATCATTC
1034256 TGAAGTAAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
15 22 0.45
16 27 0.55
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (15 bp):
TTAATCATTCAACAC
Found at i:1034222 original size:16 final size:16
Alignment explanation
Indices: 1034168--1034243 Score: 82
Period size: 16 Copynumber: 4.8 Consensus size: 16
1034158 ACAGAGCATC
**
1034168 TGAATCATTTTACATT
1 TGAATCATTCAACATT
* * **
1034184 TTAATCATTCAGCGCT
1 TGAATCATTCAACATT
1034200 T-AATCATTCAACATT
1 TGAATCATTCAACATT
*
1034215 TGAATCATTCAATATT
1 TGAATCATTCAACATT
1034231 TGAATCATTCAAC
1 TGAATCATTCAAC
1034244 GCTTAATCAT
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
15 12 0.25
16 36 0.75
ACGTcount: A:0.34, C:0.18, G:0.07, T:0.41
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:1034782 original size:60 final size:60
Alignment explanation
Indices: 1034651--1034830 Score: 177
Period size: 60 Copynumber: 3.0 Consensus size: 60
1034641 CATGTAGTTT
* * * ** *
1034651 GGGATGAAATTGGAATGTTCAAAAAGTTTGGGGACTAATTTAGAATGAAAGTTGTAGTTTA
1 GGGATGAAATTGGAATATTC-AAAAGTTTGAGGACTAATTTAGAATAAAAGTCATAATTTA
* *
1034712 TGGATGAAATTGAAATATTCAAAAGTTTGAGGACTAATTTAGAATAATAAG-CATAATTTA
1 GGGATGAAATTGGAATATTCAAAAGTTTGAGGACTAATTTAGAATAA-AAGTCATAATTTA
* * * * * * *
1034772 GGGATAAAATTGGAATA-TCTAAAGTTTAGAGG-CCAATTTAAAATGAATGTCATACTTTA
1 GGGATGAAATTGGAATATTCAAAAGTTT-GAGGACTAATTTAGAATAAAAGTCATAATTTA
1034831 AGAACATATG
Statistics
Matches: 99, Mismatches: 17, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
58 2 0.02
59 28 0.28
60 49 0.49
61 20 0.20
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.33
Consensus pattern (60 bp):
GGGATGAAATTGGAATATTCAAAAGTTTGAGGACTAATTTAGAATAAAAGTCATAATTTA
Found at i:1039915 original size:18 final size:19
Alignment explanation
Indices: 1039880--1039916 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1039870 CACGGAATGT
1039880 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1039900 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1039917 GGATTACTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:1040141 original size:37 final size:37
Alignment explanation
Indices: 1040068--1040142 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
1040058 GTCCGAAAAT
* *
1040068 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
*
1040105 ATTTATATAATGTTT-TTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-AT-TTTCTTTAAAAAATTAAAAATCATAAA
1040142 A
1 A
1040143 AATGTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 16 0.48
39 3 0.09
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:1041766 original size:15 final size:15
Alignment explanation
Indices: 1041742--1041773 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1041732 TGGCAGATCT
*
1041742 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
1041757 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
1041772 AA
1 AA
1041774 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:1046153 original size:60 final size:60
Alignment explanation
Indices: 1046009--1046154 Score: 143
Period size: 60 Copynumber: 2.4 Consensus size: 60
1045999 AAGTTTGAGT
* * * *
1046009 ATCAATTTAGAATGAGAGTCATAGTTTAGAAATAAAATTGAAAGTTTCAAAAGTACAATG
1 ATCAATTTAAAATGAAAGTCATAATTTAGAAATAAAATTGAAAATTTCAAAAGTACAATG
* * * * * * **
1046069 ATTAATATAAAATGAAGGTTATAATTTAGGAATAAAATT-AAAATATTCAATAATTTGAA-G
1 ATCAATTTAAAATGAAAGTCATAATTTAGAAATAAAATTGAAAAT-TTCAA-AAGTACAATG
*
1046129 ATCAATTTAAAATTAAAGTCATAATT
1 ATCAATTTAAAATGAAAGTCATAATT
1046155 CAAGGACATA
Statistics
Matches: 67, Mismatches: 17, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
59 4 0.06
60 58 0.87
61 5 0.07
ACGTcount: A:0.49, C:0.05, G:0.12, T:0.34
Consensus pattern (60 bp):
ATCAATTTAAAATGAAAGTCATAATTTAGAAATAAAATTGAAAATTTCAAAAGTACAATG
Found at i:1052168 original size:19 final size:20
Alignment explanation
Indices: 1052141--1052214 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
1052131 ATGTATTTTA
*
1052141 TGCACCGATGCAC-ATGTAG
1 TGCATCGATGCACGATGTAG
* *
1052160 TGCATCGATGCACCGATAGGGAA
1 TGCATCGATGCA-CGAT--GTAG
*
1052183 TGCATCGATACACTG-TGTAG
1 TGCATCGATGCAC-GATGTAG
1052203 TGCATCGATGCA
1 TGCATCGATGCA
1052215 TACCTTCATT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 11 0.26
20 14 0.33
21 2 0.05
22 2 0.05
23 14 0.33
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (20 bp):
TGCATCGATGCACGATGTAG
Found at i:1053183 original size:103 final size:103
Alignment explanation
Indices: 1052959--1053176 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
1052949 GTCGAGGGTC
1052959 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
1053024 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1053062 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
1053127 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1053165 TATGTGGTCCTT
1 TATGTGGTCCTT
1053177 ATGGACAGTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1053226 original size:23 final size:23
Alignment explanation
Indices: 1053193--1053258 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
1053183 AGTATTATAT
*
1053193 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* * *
1053216 GGCACTCCGGTGCAATTATATGT
1 GGCACTACGGTGCAATTATACGC
* *
1053239 GGCACTTCGGTGCAAGTATA
1 GGCACTACGGTGCAATTATA
1053259 TGAGCTGTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.23, C:0.24, G:0.27, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1053259 original size:23 final size:23
Alignment explanation
Indices: 1053183--1053260 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
1053173 CCTTATGGAC
*
1053183 AGTATTATATGGCACTACGGTGCA
1 AGTA-TATGTGGCACTACGGTGCA
* * * * *
1053207 ATTCTACGCGGCACTCCGGTGCA
1 AGTATATGTGGCACTACGGTGCA
* *
1053230 ATTATATGTGGCACTTCGGTGCA
1 AGTATATGTGGCACTACGGTGCA
1053253 AGTATATG
1 AGTATATG
1053261 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 41 0.95
24 2 0.05
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (23 bp):
AGTATATGTGGCACTACGGTGCA
Found at i:1059101 original size:103 final size:103
Alignment explanation
Indices: 1058917--1059131 Score: 376
Period size: 103 Copynumber: 2.1 Consensus size: 103
1058907 GTCGAGGGTC
1058917 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCCGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCCGGTGAGACACATAC
* * *
1058982 TTGGTCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
1059020 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCCGGTGAGACACATAC
*
1059085 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
1059123 TATGTGGTC
1 TATGTGGTC
1059132 ATTATGGATA
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCCGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:1059217 original size:23 final size:23
Alignment explanation
Indices: 1059150--1059218 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1059140 TAATATTATA
* * *
1059150 TGGCACTACGGTACAATTCTACG
1 TGGCACTACGGTGCAATTATATG
* *
1059173 CGGCACTCCGGTGCAATTATATG
1 TGGCACTACGGTGCAATTATATG
*
1059196 TGGCACTTCGGTGCAATTATATG
1 TGGCACTACGGTGCAATTATATG
1059219 AGTTGTGGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATATG
Found at i:1061551 original size:30 final size:30
Alignment explanation
Indices: 1061510--1061570 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1061500 TATCAATGAA
*
1061510 GAAGGTGGTGAAGCTGGTACAGCTGAAGAT
1 GAAGATGGTGAAGCTGGTACAGCTGAAGAT
*
1061540 GAAGATGGTGAAGTTGGTACAGCTGAAGAT
1 GAAGATGGTGAAGCTGGTACAGCTGAAGAT
1061570 G
1 G
1061571 TTGAGTCGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.08, G:0.39, T:0.21
Consensus pattern (30 bp):
GAAGATGGTGAAGCTGGTACAGCTGAAGAT
Found at i:1069995 original size:7 final size:7
Alignment explanation
Indices: 1069983--1070012 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
1069973 AAGTAAATCT
1069983 AGGCTTA
1 AGGCTTA
1069990 AGGCTTA
1 AGGCTTA
1069997 AGGCTTA
1 AGGCTTA
1070004 AGGCTTA
1 AGGCTTA
1070011 AG
1 AG
1070013 AGGTACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (7 bp):
AGGCTTA
Found at i:1073874 original size:15 final size:17
Alignment explanation
Indices: 1073825--1073874 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 17
1073815 CATGCATATA
*
1073825 ATTATCTTATTTCCTATC
1 ATTATCATATTT-CTATC
1073843 ATTATCATATTAT-TATC
1 ATTATCATATT-TCTATC
1073860 A-T-TCATATTTCTATC
1 ATTATCATATTTCTATC
1073875 TCTTGTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 1 0.03
15 11 0.38
16 1 0.03
17 5 0.17
18 10 0.34
19 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTATCATATTTCTATC
Found at i:1074297 original size:32 final size:32
Alignment explanation
Indices: 1074181--1074302 Score: 117
Period size: 32 Copynumber: 3.8 Consensus size: 32
1074171 ATGTAAACTA
* *
1074181 TCCATATGTTCC-ATAGAACATAGGT-ATATTG
1 TCCATATGTTCCGAAAG-ACATAGGTAATTTTG
* * * *
1074212 TCTATATGTCCCGAAAGACATAGGTAAATCTG
1 TCCATATGTTCCGAAAGACATAGGTAATTTTG
*
1074244 TCCATAT-ATCTCGAAAGACATAGGTAATTTTG
1 TCCATATGTTC-CGAAAGACATAGGTAATTTTG
*
1074276 TCCATATGTTCCG-TAGAACATAGGTAA
1 TCCATATGTTCCGAAAG-ACATAGGTAA
1074303 ACCCTCGAAT
Statistics
Matches: 73, Mismatches: 13, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
31 21 0.29
32 50 0.68
33 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (32 bp):
TCCATATGTTCCGAAAGACATAGGTAATTTTG
Found at i:1076482 original size:21 final size:21
Alignment explanation
Indices: 1076458--1076500 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1076448 ACCTTAAATC
1076458 TTCTTTAAATATGATTAAACA
1 TTCTTTAAATATGATTAAACA
1076479 TTCTTTAAATATGATTAAACA
1 TTCTTTAAATATGATTAAACA
1076500 T
1 T
1076501 ACACTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (21 bp):
TTCTTTAAATATGATTAAACA
Found at i:1078437 original size:32 final size:32
Alignment explanation
Indices: 1078386--1078472 Score: 122
Period size: 32 Copynumber: 2.8 Consensus size: 32
1078376 ATTCCTTATA
*
1078386 ACATAGGTATA-CTGTCCATATGTCCCGAAAG
1 ACATAGGTAAATCTGTCCATATGTCCCGAAAG
1078417 ACATAGGTAAATCTGTCCATATGTCCCGAAAG
1 ACATAGGTAAATCTGTCCATATGTCCCGAAAG
* * * *
1078449 ACATAGCTAATTCTATTCATATGT
1 ACATAGGTAAATCTGTCCATATGT
1078473 TTCATAGAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 10 0.20
32 40 0.80
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (32 bp):
ACATAGGTAAATCTGTCCATATGTCCCGAAAG
Found at i:1087274 original size:23 final size:23
Alignment explanation
Indices: 1087248--1087295 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1087238 ATAAAGTACA
*
1087248 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
1087271 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
1087294 AT
1 AT
1087296 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:1087807 original size:23 final size:23
Alignment explanation
Indices: 1087781--1087843 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1087771 ATATAACCAC
1087781 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1087804 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1087827 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1087844 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1088238 original size:23 final size:23
Alignment explanation
Indices: 1088212--1088274 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1088202 ATATAACTAC
1088212 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1088235 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
1088258 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1088275 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1088448 original size:431 final size:431
Alignment explanation
Indices: 1087606--1088700 Score: 2077
Period size: 431 Copynumber: 2.5 Consensus size: 431
1087596 ATGTTTATTG
*
1087606 TTTTTAATTTAATAATAATATATATCGTAACGT-AAAAATAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
*
1087670 AAATTAATATCTTAAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
*
1087735 TATAGACACTTTTATAAAAAAGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
1087800 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
1087865 TGTCCATACTTTTTATAAAAATGATCGATACTTTGTTTAAAGTTATGTAATTTATGTTTCAATTT
261 TGTCCATACTTTTTATAAAAATGATCGATACTTTGTTTAAAGTTATGTAATTTATGTTTCAATTT
*
1087930 TTTTTAATAGTTTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
326 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
1087995 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
391 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
1088036 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
* *
1088101 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATATTTTCCACATTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
* *
1088166 TATAGACACTTTTATAAAAAGGATAAATACTTTACAATATAACTACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
1088231 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
1088296 TGTCCATACTTTTTATAAAAATGATCGATACTTCT-TTTAAAGTTATGTAATTTATGTTTCAATT
261 TGTCCATACTTTTTATAAAAATGATCGATACTT-TGTTTAAAGTTATGTAATTTATGTTTCAATT
*
1088360 TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAA
325 TTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAA
1088425 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
390 ATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
1088467 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
*
1088532 AAATTAATATCTTAAAACTCACTCAAAAGGTAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
66 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
1088597 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
131 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
1088662 ACGATACCTATTACATTATATAAGCGCTACCTATTACAT
196 ACGATACCTATTACATTATATAAGCGCTACCTATTACAT
1088701 AATGTTTTCC
Statistics
Matches: 649, Mismatches: 14, Indels: 3
0.97 0.02 0.00
Matches are distributed among these distances:
430 33 0.05
431 615 0.95
432 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (431 bp):
TTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAGAAATCATTAGACGCCTATAATTACT
AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAA
ACGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
TGTCCATACTTTTTATAAAAATGATCGATACTTTGTTTAAAGTTATGTAATTTATGTTTCAATTT
TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAAAA
TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
Found at i:1088669 original size:23 final size:23
Alignment explanation
Indices: 1088643--1088700 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1088633 ATATAACCAC
1088643 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
1088666 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
1088689 TACCTATTACAT
1 TACCTATTACAT
1088701 AATGTTTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1088967 original size:325 final size:325
Alignment explanation
Indices: 1088377--1088999 Score: 1237
Period size: 325 Copynumber: 1.9 Consensus size: 325
1088367 ATAGTGTTTC
1088377 ATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTG
1 ATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTG
1088442 ATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAG
66 ATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAG
*
1088507 AAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGGTAACCTTAAA
131 AAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAA
1088572 TTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATAT
196 TTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATAT
1088637 AACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATA
261 AACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATA
1088702 ATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTG
1 ATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTG
1088767 ATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAG
66 ATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAG
1088832 AAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAA
131 AAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAA
1088897 TTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATAT
196 TTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATAT
1088962 AACCACTACCTATTACATTATATAAACGATACCTATTA
261 AACCACTACCTATTACATTATATAAACGATACCTATTA
1089000 TAAGCGCTAC
Statistics
Matches: 297, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
325 297 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (325 bp):
ATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTG
ATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATAATATATATCGTAACGTAAAAAAG
AAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAA
TTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAAAGGATAGATACTTTACAATAT
AACCACTACCTATTACATTATATAAACGATACCTATTACATTATATAAGCGCTACCTATTACATA
Found at i:1089409 original size:16 final size:16
Alignment explanation
Indices: 1089384--1089417 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1089374 ATCTATTACA
*
1089384 TTTTTCAATCGACACT
1 TTTTTAAATCGACACT
1089400 TTTTTAAATCGACACT
1 TTTTTAAATCGACACT
1089416 TT
1 TT
1089418 GTTGTGGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.06, T:0.47
Consensus pattern (16 bp):
TTTTTAAATCGACACT
Found at i:1090619 original size:3 final size:3
Alignment explanation
Indices: 1090611--1090685 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
1090601 ACTTGTTTGG
* * * * *
1090611 ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC GTC AGC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* * *
1090659 ATC GTC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1090686 GTCAACTTCA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.24, C:0.33, G:0.07, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:1090686 original size:12 final size:12
Alignment explanation
Indices: 1090615--1090702 Score: 95
Period size: 12 Copynumber: 7.3 Consensus size: 12
1090605 GTTTGGATCA
* *
1090615 TCATCATCATCA
1 TCATCTTCATCG
* * *
1090627 TCATCATCGTCA
1 TCATCTTCATCG
1090639 TCATCTTCATCG
1 TCATCTTCATCG
*
1090651 TCAGCTTCATCG
1 TCATCTTCATCG
*
1090663 TCATCATCATCG
1 TCATCTTCATCG
1090675 TCATCTTCATCG
1 TCATCTTCATCG
* *
1090687 TCAACTTCATCT
1 TCATCTTCATCG
1090699 TCAT
1 TCAT
1090703 TGACCGCTTG
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 65 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.38
Consensus pattern (12 bp):
TCATCTTCATCG
Found at i:1092527 original size:199 final size:199
Alignment explanation
Indices: 1092178--1092937 Score: 1342
Period size: 199 Copynumber: 3.8 Consensus size: 199
1092168 CGACACAAAC
*
1092178 TAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAG
1 TAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAG
1092243 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATA
66 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATA
* *
1092308 TATGGATCGACACCTTATGGTTGCACACTGTTTTCCATTCATTCTGGACCAAAAATATCGACACT
131 TATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACT
*
1092373 GTTT
196 ATTT
* *
1092377 TAAATGGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCAGTATACTTGTACCGGTTAG
1 TAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAG
*
1092442 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTAGGATCGACACTTTTTATA
66 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATA
*
1092507 TATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAATTATCGACACT
131 TATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACT
*
1092572 TTTT
196 ATTT
*
1092576 TAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATCGGTATACTTGTACCGGTTAG
1 TAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAG
*
1092641 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTACA
66 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATA
1092706 TATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACAC-
131 TATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACT
***
1092770 AAAC
196 ATTT
* *
1092774 TAAACAAGTGTCGACGCATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
1 TAAA-TAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTA
1092839 GATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGATCGACACTTTTTA
65 GATTGAAAAATTACATATTACATTATACTTTTGGG-TTCGATGTTTTTGGGATCGACACTTTTTA
*
1092904 TATATGGTTCGACACTTTATGGTTGCACCCTGTT
129 TATATGGATCGACACTTTATGGTTGCACCCTGTT
1092938 GGCCATATTG
Statistics
Matches: 536, Mismatches: 23, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
198 4 0.01
199 471 0.88
200 61 0.11
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (199 bp):
TAAATAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATACTTGTACCGGTTAG
ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGTTTTTGGGATCGACACTTTTTATA
TATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAAATATCGACACT
ATTT
Found at i:1093102 original size:19 final size:19
Alignment explanation
Indices: 1093056--1093104 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1093046 TTATATTCAC
*
1093056 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
1093075 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
1093094 ATACAAAATTA
1 ATACAAAATTA
1093105 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:1094700 original size:21 final size:21
Alignment explanation
Indices: 1094675--1094715 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1094665 CCTCCTCATT
1094675 TCTTCCATCTCTTCTTCTTCC
1 TCTTCCATCTCTTCTTCTTCC
* *
1094696 TCTTCCCTCTTTTCTTCTTC
1 TCTTCCATCTCTTCTTCTTC
1094716 ATATTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.02, C:0.41, G:0.00, T:0.56
Consensus pattern (21 bp):
TCTTCCATCTCTTCTTCTTCC
Found at i:1094938 original size:33 final size:33
Alignment explanation
Indices: 1094901--1094964 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
1094891 TCTTAATATC
*
1094901 ACCCCTTAACACCCCAACTTCTTTCACCACTTT
1 ACCCCTCAACACCCCAACTTCTTTCACCACTTT
* *
1094934 ACCCCTCAACACCTCTACTTCTTTCACCACT
1 ACCCCTCAACACCCCAACTTCTTTCACCACT
1094965 CCATCTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
ACCCCTCAACACCCCAACTTCTTTCACCACTTT
Found at i:1095023 original size:21 final size:21
Alignment explanation
Indices: 1094998--1095041 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1094988 CCCCTTATGC
1094998 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
* *
1095019 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTGTATCTTCGACT
1095040 CT
1 CT
1095042 TGATTGTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.32, G:0.11, T:0.41
Consensus pattern (21 bp):
CTCTCAAGTGTATCTTCGACT
Found at i:1097102 original size:24 final size:24
Alignment explanation
Indices: 1097065--1097117 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1097055 CCGTTCTATC
1097065 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
1097089 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
1097113 TATTT
1 TATTT
1097118 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:1097278 original size:17 final size:18
Alignment explanation
Indices: 1097256--1097298 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1097246 ATATATCCGG
1097256 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
1097273 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
1097293 TATCAT
1 TATCAT
1097299 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:1097316 original size:20 final size:19
Alignment explanation
Indices: 1097261--1097307 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1097251 TCCGGTATCA
1097261 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
1097280 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
1097301 TTTTACC
1 TTTTACC
1097308 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:1097532 original size:181 final size:182
Alignment explanation
Indices: 1097228--1097700 Score: 666
Period size: 181 Copynumber: 2.6 Consensus size: 182
1097218 CGTACTTACG
* * *
1097228 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACCTTTTACCGGTTTTATCATTTTGATACCGGTTT
** *
1097293 TATCATATTTTTACCTGTTATATCGTTGTT-GATCGATATTTTTTTTTAAAGTATCGACACATTA
66 TATCATATTTTTACCTGTTATATCGTT-TTGGATCGATACATTTTTTAAAAGTATCGACACATTA
* *
1097357 TAGGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAATGTCGATCCTTATA-T
130 TAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATATT
* * *
1097409 AAAGTATCGACACTTTTAATATATCCGGTAACCTTTTACCGGTTTTATCGTTTTGATACCGATTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACCTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
1097474 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * * * *
1097539 AGGATTTAAAATTGCTTCTCTTTTAAATTCACGAAGTGTCGATTCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATATT
* * *
1097591 AAAGTACCGACACTTTAAATGTATCCGGTAGCGC-TTTACCGGTTTTATCATTTCT-ATACCGGT
1 AAAGTATCGACACTTTAAATATATCCGGTAAC-CTTTTACCGGTTTTATCATTT-TGATACCGGT
* * *
1097654 TTTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
64 TTTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
1097701 AATTTGGATC
Statistics
Matches: 260, Mismatches: 28, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
180 2 0.01
181 159 0.61
182 97 0.37
183 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACCTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAATGTCGATCCTTATATT
Found at i:1099648 original size:16 final size:18
Alignment explanation
Indices: 1099612--1099648 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1099602 AAAGCTTAAA
1099612 AGTGTGCTTACATGATAT
1 AGTGTGCTTACATGATAT
*
1099630 AGTGT-CTTA-ATGCTAT
1 AGTGTGCTTACATGATAT
1099646 AGT
1 AGT
1099649 ATTATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 4 0.22
18 5 0.28
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.41
Consensus pattern (18 bp):
AGTGTGCTTACATGATAT
Found at i:1103372 original size:2 final size:2
Alignment explanation
Indices: 1103365--1103397 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1103355 TAACCGCCGG
1103365 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1103398 TGACCAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1115530 original size:15 final size:15
Alignment explanation
Indices: 1115507--1115536 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1115497 CAAACTTATC
1115507 TTTGATTTTGGTTTT
1 TTTGATTTTGGTTTT
*
1115522 TTTGTTTTTGGTTTT
1 TTTGATTTTGGTTTT
1115537 GTGAATACGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.00, G:0.20, T:0.77
Consensus pattern (15 bp):
TTTGATTTTGGTTTT
Found at i:1122860 original size:33 final size:32
Alignment explanation
Indices: 1122818--1122921 Score: 118
Period size: 33 Copynumber: 3.0 Consensus size: 32
1122808 AAAAATGGTT
1122818 TTCAAAGTTTGGTAAATGTTTATTTGAAAATTG
1 TTCAAAGTTTGGTAAATGTTT-TTTGAAAATTG
*
1122851 TTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGGTTT
1 TTCAAAGTTTGGTAAATGTTT-TTTG-AAAA---TTG
* *
1122888 TTCAAAGTTTGGTAGATGTTTGTTGAAATATTG
1 TTCAAAGTTTGGTAAATGTTTTTTGAAA-ATTG
1122921 T
1 T
1122922 AATGGGATAA
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
33 28 0.46
34 4 0.07
35 3 0.05
36 4 0.07
37 22 0.36
ACGTcount: A:0.30, C:0.04, G:0.20, T:0.46
Consensus pattern (32 bp):
TTCAAAGTTTGGTAAATGTTTTTTGAAAATTG
Found at i:1122901 original size:37 final size:37
Alignment explanation
Indices: 1122802--1122908 Score: 143
Period size: 33 Copynumber: 3.0 Consensus size: 37
1122792 TGACAACCAA
1122802 CTTTGAAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
* *
1122839 ATTTG-AAAA---TTGTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
*
1122872 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
1122909 GTTGAAATAT
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
33 26 0.43
34 4 0.07
35 4 0.07
37 26 0.43
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.45
Consensus pattern (37 bp):
CTTTGAAAAATGGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:1124040 original size:27 final size:27
Alignment explanation
Indices: 1124002--1124061 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
1123992 CTGGTATTGA
1124002 GTGAAGAAATTCGACGAAGAGAATCGG
1 GTGAAGAAATTCGACGAAGAGAATCGG
1124029 GTGAAGAAATTCGACGAAGAGAATCGG
1 GTGAAGAAATTCGACGAAGAGAATCGG
1124056 GTGAAG
1 GTGAAG
1124062 CATCAACCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.40, C:0.10, G:0.35, T:0.15
Consensus pattern (27 bp):
GTGAAGAAATTCGACGAAGAGAATCGG
Found at i:1124160 original size:15 final size:15
Alignment explanation
Indices: 1124136--1124167 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1124126 AGGCAGATCG
*
1124136 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
1124151 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
1124166 AA
1 AA
1124168 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:1127489 original size:35 final size:37
Alignment explanation
Indices: 1127443--1127535 Score: 127
Period size: 35 Copynumber: 2.6 Consensus size: 37
1127433 AAATTAAAAG
1127443 TTCAAAGTTTGGTAAATGTTTATTTG-AAAA-TGGTT
1 TTCAAAGTTTGGTAAATGTTTATTTGAAAAATTGGTT
* * *
1127478 TTCAAAGTTTGGTAAATGATTCTTTGAAAAATTGTTT
1 TTCAAAGTTTGGTAAATGTTTATTTGAAAAATTGGTT
* *
1127515 TTCAGAGTTTGGTAGATGTTT
1 TTCAAAGTTTGGTAAATGTTT
1127536 GTTGAAATAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
35 24 0.48
36 4 0.08
37 22 0.44
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.46
Consensus pattern (37 bp):
TTCAAAGTTTGGTAAATGTTTATTTGAAAAATTGGTT
Found at i:1127541 original size:36 final size:35
Alignment explanation
Indices: 1127443--1127548 Score: 117
Period size: 35 Copynumber: 2.9 Consensus size: 35
1127433 AAATTAAAAG
*
1127443 TTCAAAGTTTGGTAAATGTTTATTTG-AAAA-TGGTT
1 TTCAAAGTTTGGTAAATG-TT-TTTGAAAAATTGTTT
1127478 TTCAAAGTTTGGTAAATGATTCTTTGAAAAATTGTTT
1 TTCAAAGTTTGGTAAATG-TT-TTTGAAAAATTGTTT
* * *
1127515 TTCAGAGTTTGGTAGATGTTTGTTGAAATATTGT
1 TTCAAAGTTTGGTAAATGTTT-TTGAAAAATTGT
1127549 AATGGGATAA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
35 25 0.40
36 17 0.27
37 20 0.32
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (35 bp):
TTCAAAGTTTGGTAAATGTTTTTGAAAAATTGTTT
Found at i:1131787 original size:14 final size:15
Alignment explanation
Indices: 1131766--1131803 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
1131756 CTTTTGGGCT
1131766 CTTTCCTTTAT-TTTC
1 CTTTCCTTT-TCTTTC
1131781 C-TTCCTTTTCTTTC
1 CTTTCCTTTTCTTTC
1131795 CTTTCCTTT
1 CTTTCCTTT
1131804 CATCAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 1 0.05
14 12 0.57
15 8 0.38
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.66
Consensus pattern (15 bp):
CTTTCCTTTTCTTTC
Found at i:1141392 original size:22 final size:22
Alignment explanation
Indices: 1141367--1141421 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1141357 CTGTTAATAT
* *
1141367 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1141389 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1141411 CGGGAGTTATA
1 CAGGAGTTATA
1141422 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1144809 original size:29 final size:29
Alignment explanation
Indices: 1144776--1144864 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 29
1144766 AAAATTTATT
1144776 TATTAATTTATTCCCATCAACCATATATA
1 TATTAATTTATTCCCATCAACCATATATA
* **
1144805 TATT-ATGTTA---CCTTCAATAATATATA
1 TATTAAT-TTATTCCCATCAACCATATATA
* *
1144831 AAATAATTTATTCCCATCAACCATATATA
1 TATTAATTTATTCCCATCAACCATATATA
1144860 TATTA
1 TATTA
1144865 TGTTACCTTG
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
26 18 0.40
27 2 0.04
28 2 0.04
29 23 0.51
ACGTcount: A:0.40, C:0.17, G:0.01, T:0.42
Consensus pattern (29 bp):
TATTAATTTATTCCCATCAACCATATATA
Found at i:1148201 original size:14 final size:14
Alignment explanation
Indices: 1148179--1148231 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
1148169 TTACAATACC
*
1148179 TAAATCTTAAATCT
1 TAAACCTTAAATCT
1148193 TAAACCTTAAAT-T
1 TAAACCTTAAATCT
* *
1148206 ATAAACCATAAATCA
1 -TAAACCTTAAATCT
1148221 TAAA-CTTAAAT
1 TAAACCTTAAAT
1148232 TGTACTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
13 7 0.21
14 26 0.79
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAACCTTAAATCT
Found at i:1149972 original size:10 final size:11
Alignment explanation
Indices: 1149935--1149972 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
1149925 GCACTTGAGA
1149935 TTGAATCGAGT
1 TTGAATCGAGT
*
1149946 TTGAATCAAGT
1 TTGAATCGAGT
1149957 TTGAATCGAG-
1 TTGAATCGAGT
1149967 TTGAAT
1 TTGAAT
1149973 TGGGCTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.37
Consensus pattern (11 bp):
TTGAATCGAGT
Found at i:1153898 original size:15 final size:15
Alignment explanation
Indices: 1153878--1153907 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1153868 TTCTGCTTCA
1153878 GAAGAATCTCCTTGT
1 GAAGAATCTCCTTGT
1153893 GAAGAATCTCCTTGT
1 GAAGAATCTCCTTGT
1153908 TCAACCTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (15 bp):
GAAGAATCTCCTTGT
Found at i:1159744 original size:20 final size:20
Alignment explanation
Indices: 1159719--1159853 Score: 112
Period size: 20 Copynumber: 6.7 Consensus size: 20
1159709 AATTGGGAAA
1159719 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1159739 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1159759 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* * *
1159780 ATCGCAACGAGATATTGACT
1 ATCGCAATGCGATACTGACT
* * *
1159800 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
1159820 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
1159840 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1159854 TTTCAAAGCG
Statistics
Matches: 95, Mismatches: 15, Indels: 9
0.80 0.13 0.08
Matches are distributed among these distances:
19 4 0.04
20 65 0.68
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1159781 original size:61 final size:61
Alignment explanation
Indices: 1159716--1159853 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
1159706 ACGAATTGGG
* * *
1159716 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * * * *
1159777 AAAATCGCAACGAGATATTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
1159838 ATAATCGCAATGCGAT
1 AAAATCGCAATGCGAT
1159854 TTTCAAAGCG
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 65 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (61 bp):
AAAATCGCAATGCGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1160049 original size:22 final size:22
Alignment explanation
Indices: 1160021--1160064 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1160011 CACTCTCTCA
1160021 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
1160043 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
1160065 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.45, G:0.18, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGGCGAAATCCGTC
Done.