Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005294.1 Hibiscus syriacus cultivar Beakdansim tig00011985_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: 212260
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 2
Found at i:2885 original size:2 final size:2
Alignment explanation
Indices: 2878--2920 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2868 TAAAAGCGCT
2878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2920 T
1 T
2921 TATCCCAATT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5128 original size:30 final size:30
Alignment explanation
Indices: 5073--5157 Score: 118
Period size: 30 Copynumber: 2.9 Consensus size: 30
5063 ATGTTGATCT
* * *
5073 GAATGAAGGT-TTGCTGGGGATTTGAAGGA
1 GAATGAGGGTATTGATGGGAATTTGAAGGA
* *
5102 GGATGAGGTTATTGATGGGAATTTGAAGGA
1 GAATGAGGGTATTGATGGGAATTTGAAGGA
5132 GAATGAGGGTATTGATGGGAATTTGA
1 GAATGAGGGTATTGATGGGAATTTGA
5158 GTGAAACTCT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
29 7 0.15
30 41 0.85
ACGTcount: A:0.29, C:0.01, G:0.40, T:0.29
Consensus pattern (30 bp):
GAATGAGGGTATTGATGGGAATTTGAAGGA
Found at i:22129 original size:30 final size:30
Alignment explanation
Indices: 22093--22165 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
22083 CCCGAAGGAC
22093 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
22123 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
22153 CTGTCCATAGGTC
1 CTATCCAGAGGTC
22166 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:22189 original size:31 final size:31
Alignment explanation
Indices: 22151--22276 Score: 137
Period size: 31 Copynumber: 4.1 Consensus size: 31
22141 GATCCTCGGT
* *
22151 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
22182 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * **
22213 TACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* *
22244 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
22275 AA
1 AA
22277 ACCCTCGACT
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
30 1 0.01
31 82 0.99
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:23578 original size:64 final size:62
Alignment explanation
Indices: 23445--23605 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 62
23435 TAATGAAGGT
* * *
23445 ATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* *
23510 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
23574 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
23606 CCTTAAACAA
Statistics
Matches: 85, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
63 1 0.01
64 58 0.68
65 23 0.27
66 3 0.04
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:26859 original size:30 final size:30
Alignment explanation
Indices: 26823--26895 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
26813 CCCGAAGGAC
26823 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
26853 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
26883 CTGTCCATAGGTC
1 CTATCCAGAGGTC
26896 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:26935 original size:31 final size:31
Alignment explanation
Indices: 26878--26987 Score: 141
Period size: 31 Copynumber: 3.6 Consensus size: 31
26868 AAAGATCCTC
* * ** *
26878 GGTA-ACTGTCCATAGGTCCCGAAGAACCTA
1 GGTATACTGTCCATATGTTCCTTAGAACATA
* *
26908 GGTAAACTGTTCATATGTTCCTTAGAACATA
1 GGTATACTGTCCATATGTTCCTTAGAACATA
*
26939 GGTATATTGTCCATATGTTCCTTAGAACATA
1 GGTATACTGTCCATATGTTCCTTAGAACATA
26970 GGTATACTGTCCATATGT
1 GGTATACTGTCCATATGT
26988 CTCGAAAGAC
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
30 4 0.06
31 65 0.94
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (31 bp):
GGTATACTGTCCATATGTTCCTTAGAACATA
Found at i:27000 original size:31 final size:31
Alignment explanation
Indices: 26878--27004 Score: 132
Period size: 31 Copynumber: 4.1 Consensus size: 31
26868 AAAGATCCTC
* * * *
26878 GGTA-ACTGTCCATAGGTCCCGAAGAACCTA
1 GGTATACTGTCCATATGTTCCTAAGAACATA
* * *
26908 GGTAAACTGTTCATATGTTCCTTAGAACATA
1 GGTATACTGTCCATATGTTCCTAAGAACATA
* *
26939 GGTATATTGTCCATATGTTCCTTAGAACATA
1 GGTATACTGTCCATATGTTCCTAAGAACATA
**
26970 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTATACTGTCCATATGT-TCCTAAGAACATA
27001 GGTA
1 GGTA
27005 AAACCCTCGA
Statistics
Matches: 82, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
30 4 0.05
31 74 0.90
32 4 0.05
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Consensus pattern (31 bp):
GGTATACTGTCCATATGTTCCTAAGAACATA
Found at i:28286 original size:64 final size:63
Alignment explanation
Indices: 28172--28295 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 63
28162 TTAATGAAGG
* * *
28172 TATGCATCGATGCATAAATTCTATTCGATGTTTGTATTTAATGGGGATGCATCGATGCACTCCT
1 TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGAATGCATCGATGCACTCCT
* *
28236 TATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TAATGCATCGATGCAC
1 TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGAATGCATCGATGCAC
28296 ATGTAGTGCA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
64 43 0.81
65 7 0.13
66 3 0.06
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (63 bp):
TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGAATGCATCGATGCACTCCT
Found at i:28306 original size:64 final size:62
Alignment explanation
Indices: 28171--28313 Score: 164
Period size: 64 Copynumber: 2.2 Consensus size: 62
28161 TTTAATGAAG
* * *
28171 GTATGCATCGATGCATAAATTCTATTCGATGTTTGTATTTAATGGGGATGCATCGATGCACTCC
1 GTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGAATGCATCGATGCACT-C
* * *
28235 TTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TAATGCATCGATGCACAT-
1 GTATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGAATGCATCGATGCAC-TC
28298 GTAGTGCATCGATGCA
1 GTA-TGCATCGATGCA
28314 CCTTAAACAA
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
63 2 0.03
64 55 0.81
65 8 0.12
66 3 0.04
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (62 bp):
GTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGAATGCATCGATGCACTC
Found at i:31561 original size:30 final size:30
Alignment explanation
Indices: 31525--31621 Score: 185
Period size: 30 Copynumber: 3.2 Consensus size: 30
31515 CCCGAAGGAC
31525 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
31555 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
31585 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
31615 CTGTCCA
1 CTATCCA
31622 TAAGTCCCGA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:31644 original size:60 final size:60
Alignment explanation
Indices: 31525--31644 Score: 168
Period size: 60 Copynumber: 2.0 Consensus size: 60
31515 CCCGAAGGAC
* * * *
31525 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAAGTCACAAAGAACCTAGGTAA
* * * *
31585 CTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAAGTCCCGAAGAACCTAGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAAGTCACAAAGAACCTAGGTAA
31645 ACTGTCCATA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (60 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAAGTCACAAAGAACCTAGGTAA
Found at i:31648 original size:31 final size:31
Alignment explanation
Indices: 31613--31738 Score: 137
Period size: 31 Copynumber: 4.1 Consensus size: 31
31603 GATCCTCGGT
* *
31613 AACTGTCCATAAGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
31644 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * **
31675 TACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* *
31706 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGTA
31737 AA
1 AA
31739 ACCCTCGACT
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
30 1 0.01
31 82 0.99
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:32401 original size:2 final size:2
Alignment explanation
Indices: 32394--32430 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
32384 ATACAATTCC
*
32394 TA TA TA TA TG 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 TA TA T
32431 CTAACTCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33051 original size:64 final size:63
Alignment explanation
Indices: 32938--33078 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 63
32928 GCACTACACC
* *
32938 ATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGGATGCATCGATGTACTCCTT
1 ATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGAATGCATCGATGTACTCCTT
* * * * * *
33002 ATGCATTGATGCATAAATCCTATTCGATGTTTACTTTTTAAAT-TAATGCATCGATGCACTGCAT
1 ATGCATCGATGCATAAATCCTATTCGATGTTT-CTATTT-AATGGAATGCATCGATGTACTCCTT
*
33066 GTGCATCGATGCA
1 ATGCATCGATGCA
33079 CTTTAAACAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
64 58 0.89
65 4 0.06
66 3 0.05
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (63 bp):
ATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGAATGCATCGATGTACTCCTT
Found at i:43198 original size:15 final size:15
Alignment explanation
Indices: 43178--43206 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43168 TGGCCGACCG
43178 AACCGAATTAACCAT
1 AACCGAATTAACCAT
43193 AACCGAATTAACCA
1 AACCGAATTAACCA
43207 AACTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (15 bp):
AACCGAATTAACCAT
Found at i:43655 original size:182 final size:183
Alignment explanation
Indices: 43333--43718 Score: 627
Period size: 182 Copynumber: 2.1 Consensus size: 183
43323 TTTTCTAATT
* * * *
43333 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAATAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTCAAAAAAAATTTACAATTAATTTAAATAATATATAAT
*
43397 TATAAAATAAAAATTTTAGATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTA-ATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* *
43462 GGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AGCCCATATTTTA
130 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGG-TTGAGCCCATATGTTA
43516 TATATAATATATTTAATATTTTTTAATT-AAAAAACAATTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTCAAAAAA-AATTTACAATTAATTTAAATAATATATAA
*
43580 TTATAAAATAAAAAATTT-ATATAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
65 TTATAAAATAAAAAATTTAATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
* *
43644 GGATCTTAAATTATTAATTGGGTTTTAAATTATTTGGGTTGAGCTCATATGTTA
130 GGATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
43698 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
43719 AAAATTTAAT
Statistics
Matches: 190, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
181 2 0.01
182 113 0.59
183 13 0.07
184 62 0.33
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (183 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAATTTACAATTAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAATAAAATTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATTG
GATCTTAAATTATTAATTGGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
Found at i:59091 original size:19 final size:19
Alignment explanation
Indices: 59053--59091 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
59043 ATCAAAACCT
*
59053 ATTTCATGTAAAACAGACA
1 ATTTCATGTAAAACAAACA
* *
59072 ATTTCATGTGAAATAAACA
1 ATTTCATGTAAAACAAACA
59091 A
1 A
59092 GCATTTAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (19 bp):
ATTTCATGTAAAACAAACA
Found at i:61001 original size:32 final size:32
Alignment explanation
Indices: 60951--61022 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
60941 AATGGTGGTT
* * *
60951 GATGTGAGTTAATTTCAGTA-CTTGTCGGCTCA
1 GATGTGGGATAATTTCAGTAGCTT-TCGGATCA
*
60983 GCTGTGGGATAATTTCAGTAGCTTTCGGATCA
1 GATGTGGGATAATTTCAGTAGCTTTCGGATCA
61015 GATGTGGG
1 GATGTGGG
61023 TGGAGCAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 31 0.91
33 3 0.09
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.35
Consensus pattern (32 bp):
GATGTGGGATAATTTCAGTAGCTTTCGGATCA
Found at i:62520 original size:11 final size:11
Alignment explanation
Indices: 62504--62528 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
62494 ACTATTCATA
62504 TGTTCCAAAAT
1 TGTTCCAAAAT
62515 TGTTCCAAAAT
1 TGTTCCAAAAT
62526 TGT
1 TGT
62529 CAAGAGACCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (11 bp):
TGTTCCAAAAT
Found at i:65677 original size:3 final size:3
Alignment explanation
Indices: 65671--65734 Score: 62
Period size: 3 Copynumber: 22.0 Consensus size: 3
65661 AAAAAATTTG
* * **
65671 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TGA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
65715 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
65735 CGAAAAAAAC
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.09
3 45 0.85
4 3 0.06
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:65954 original size:43 final size:43
Alignment explanation
Indices: 65890--66222 Score: 195
Period size: 46 Copynumber: 7.8 Consensus size: 43
65880 TGGTGGGGAC
* **
65890 GACACTGCTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGT
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTCATCTAAGGGT
* ****
65933 GACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA---T
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTCATCTAAGGGT
* *
65973 GACACGACTCATACGTGATGAAGAGTTCTGG-CTATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTC-ATCT-AAGG-G-T
* * * * *
66019 AACACGGTTCCTACGTGATGAGGACGG-CTGGTTATCT-AGGGT
1 GACACGGCTCATACGTGATGAAGA-GGTCTGGTCATCTAAGGGT
* *
66061 GACACGGCTCATACGTGATGAAGAGATCTGG---TCT-GGGGAT
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTCATCTAAGGG-T
* * * * *
66101 GACACGGTTCCTACATGATGAGGACGG-CTGGCCATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGA-GGTCTGGTCATCT-AAGG-G-T
* * * * * * *
66147 AACACGGTTCCTACGTGATGAGGACGG-CTGGTTATCTATGGTT
1 GACACGGCTCATACGTGATGAAGA-GGTCTGGTCATCTAAGGGT
* * *
66190 GACACGGCTCCTACGTGATGAGGAGATCTGGTC
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTC
66223 TGGGGATGAC
Statistics
Matches: 228, Mismatches: 43, Indels: 38
0.74 0.14 0.12
Matches are distributed among these distances:
39 7 0.03
40 55 0.24
41 4 0.02
42 26 0.11
43 63 0.28
44 3 0.01
45 5 0.02
46 64 0.28
47 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (43 bp):
GACACGGCTCATACGTGATGAAGAGGTCTGGTCATCTAAGGGT
Found at i:66055 original size:46 final size:45
Alignment explanation
Indices: 66000--66266 Score: 208
Period size: 40 Copynumber: 6.2 Consensus size: 45
65990 ATGAAGAGTT
*
66000 CTGGCTATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
1 CTGGCTATCT-AAGGTGATGACACGGTTCCTACGTGATGAGGACGG
* * * * *
66046 CTGGTTATCT-AGG-G-TGACACGGCTCATACGTGATGAAGA-GAT
1 CTGGCTATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACG-G
* *
66088 CTGG---TCT--GGGGATGACACGGTTCCTACATGATGAGGACGG
1 CTGGCTATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACGG
* *
66128 CTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
1 CTGGCTATCT-AAGGTGATGACACGGTTCCTACGTGATGAGGACGG
* * * *
66174 CTGGTTATCTATGGT--TGACACGGCTCCTACGTGATGAGGA-GAT
1 CTGGCTATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACG-G
* * *
66217 CTGG---TCT--GGGGATGACGCGGTTCCTACATGATGAGGACGG
1 CTGGCTATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACGG
* *
66257 TTGGCCATCT
1 CTGGCTATCT
66267 TTAGGAGTTA
Statistics
Matches: 178, Mismatches: 26, Indels: 37
0.74 0.11 0.15
Matches are distributed among these distances:
38 4 0.02
39 4 0.02
40 53 0.30
41 3 0.02
42 26 0.15
43 34 0.19
44 3 0.02
45 4 0.02
46 47 0.26
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.25
Consensus pattern (45 bp):
CTGGCTATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACGG
Found at i:66120 original size:40 final size:40
Alignment explanation
Indices: 65932--66253 Score: 177
Period size: 40 Copynumber: 7.6 Consensus size: 40
65922 CATCTAAGGG
* *
65932 TGACACGGCTCATACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCCTACGTGATGAGGAG-TCTGGTTCTGGGG-A
* * * *
65972 TGACACGACTCATACGTGATGAAGAGTTCTGGCTATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAGGAG-TCTGG-T-TCT---GGGGA
* * * *
66018 TAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGG-
1 TGACACGGCTCCTACGTGATGAGGA-GTCTGG-T-TCTGGGGA
* *
66060 TGACACGGCTCATACGTGATGAAGAGATCTGG-TCTGGGGA
1 TGACACGGCTCCTACGTGATGAGGAG-TCTGGTTCTGGGGA
* * * * *
66100 TGACACGGTTCCTACATGATGAGGACGGCTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAGGA-GTCTGG--TTCT---GGGGA
* * * ** *
66146 TAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
1 TGACACGGCTCCTACGTGATGAGGA-GTCTGG-T-TCTGGGGA
66189 TGACACGGCTCCTACGTGATGAGGAGATCTGG-TCTGGGGA
1 TGACACGGCTCCTACGTGATGAGGAG-TCTGGTTCTGGGGA
* * *
66229 TGACGCGGTTCCTACATGATGAGGA
1 TGACACGGCTCCTACGTGATGAGGA
66254 CGGTTGGCCA
Statistics
Matches: 222, Mismatches: 41, Indels: 38
0.74 0.14 0.13
Matches are distributed among these distances:
39 6 0.03
40 82 0.37
41 2 0.01
42 26 0.12
43 35 0.16
46 67 0.30
47 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (40 bp):
TGACACGGCTCCTACGTGATGAGGAGTCTGGTTCTGGGGA
Found at i:66138 original size:82 final size:84
Alignment explanation
Indices: 65972--66138 Score: 221
Period size: 82 Copynumber: 2.0 Consensus size: 84
65962 GGTCGGGGAA
* * *
65972 TGACACGACTCATACGTGATGAAGAGTTCTGGCTATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGACTCATACGTGATGAAGAGATCTGG--ATCT--AGGGGATAACACGGTTCCTACATGA
**
66037 TGAGGACGGCTGGTTATCTAGGG
62 TGAGGACGGCTGGCCATCTAGGG
* *
66060 TGACACGGCTCATACGTGATGAAGAGATCTGG-TCT-GGGGATGACACGGTTCCTACATGATGAG
1 TGACACGACTCATACGTGATGAAGAGATCTGGATCTAGGGGATAACACGGTTCCTACATGATGAG
66123 GACGGCTGGCCATCTA
66 GACGGCTGGCCATCTA
66139 AAGGTGATAA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
82 39 0.54
85 3 0.04
88 30 0.42
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.25
Consensus pattern (84 bp):
TGACACGACTCATACGTGATGAAGAGATCTGGATCTAGGGGATAACACGGTTCCTACATGATGAG
GACGGCTGGCCATCTAGGG
Found at i:66249 original size:129 final size:128
Alignment explanation
Indices: 65917--66266 Score: 533
Period size: 128 Copynumber: 2.7 Consensus size: 128
65907 ATGAAGAGGT
* **
65917 CTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGGAATGACACGAC
1 CTGGTTATCT-AGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGG-ATGACACGGT
* * * * *
65981 TCATACGTGATGAAGA-GTTCTGGCTATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG
64 TCCTACATGATGAGGACG-GCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG
66045 G
128 G
66046 CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTC
1 CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTC
66111 CTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
66 CTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
* * * *
66174 CTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACGCGGTT
1 CTGGTTATCTA-GGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTT
*
66239 CCTACATGATGAGGACGGTTGGCCATCT
65 CCTACATGATGAGGACGGCTGGCCATCT
66267 TTAGGAGTTA
Statistics
Matches: 205, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
128 115 0.56
129 90 0.44
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (128 bp):
CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTC
CTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
Found at i:66329 original size:28 final size:28
Alignment explanation
Indices: 66279--66332 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
66269 AGGAGTTATG
* *
66279 GTTTCAAGAGAAACCAAATCAAAGATTT
1 GTTTCAAAAGAAACCAAACCAAAGATTT
66307 GTTTCAAAAGAAA-CAAACCCAAAGAT
1 GTTTCAAAAGAAACCAAA-CCAAAGAT
66333 GATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (28 bp):
GTTTCAAAAGAAACCAAACCAAAGATTT
Found at i:66688 original size:15 final size:15
Alignment explanation
Indices: 66664--66707 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
66654 AAGATGATCT
*
66664 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
66679 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
66694 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
66708 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:67054 original size:28 final size:28
Alignment explanation
Indices: 67013--67081 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
67003 TTAAGAGAGA
*
67013 CAAAG-TTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
*
67041 CAAAGATTTTTTTCAAAAGAAACAATCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
67069 CAAAGATTTTTTT
1 CAAAGATTTTTTT
67082 TTTTTCTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 34 0.89
29 4 0.11
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:67255 original size:29 final size:29
Alignment explanation
Indices: 67193--67347 Score: 219
Period size: 29 Copynumber: 5.5 Consensus size: 29
67183 AAATAAATAG
* *
67193 ACTCAAAGA--TTT-TTCAAAA-GAAACA
1 ACTCAAAGATTTTTATTTAAAAGGAACCA
* *
67218 ACTCAAAGATATTTATTCAAAAGGAACCA
1 ACTCAAAGATTTTTATTTAAAAGGAACCA
* *
67247 ACTCCAAGATTTTTATTTAAAAGGAACAA
1 ACTCAAAGATTTTTATTTAAAAGGAACCA
*
67276 ACTCAAAGATTTTTATTTAAAAGGAACAA
1 ACTCAAAGATTTTTATTTAAAAGGAACCA
67305 ACTCAAAGATTTTTATTTAAAAGGAACCA
1 ACTCAAAGATTTTTATTTAAAAGGAACCA
67334 ACTCAAAGATTTTT
1 ACTCAAAGATTTTT
67348 TTAAGAGAAA
Statistics
Matches: 119, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
25 9 0.08
27 3 0.03
28 7 0.06
29 100 0.84
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTTAAAAGGAACCA
Found at i:68053 original size:28 final size:28
Alignment explanation
Indices: 68021--68096 Score: 134
Period size: 28 Copynumber: 2.7 Consensus size: 28
68011 TGTAACATGC
*
68021 ATGTATGTGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
*
68049 ATGTATGAATTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
68077 ATGTATGAGTTGATGTATGT
1 ATGTATGAGTTGATGTATGT
68097 TTCTCAATCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (28 bp):
ATGTATGAGTTGATGTATGTATATATGT
Found at i:68092 original size:12 final size:12
Alignment explanation
Indices: 68030--68095 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
68020 CATGTATGTG
68030 TTGATGTATGTATA
1 TTGATGTATG-A-A
68044 TATGTATGTATGAA
1 T-TG-ATGTATGAA
68058 TTGATGTATGTATA
1 TTGATGTATG-A-A
*
68072 TATGTATGTATGAG
1 T-TG-ATGTATGAA
68086 TTGATGTATG
1 TTGATGTATG
68096 TTTCTCAATC
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
12 14 0.31
13 5 0.11
14 6 0.13
15 6 0.13
16 14 0.31
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (12 bp):
TTGATGTATGAA
Found at i:68096 original size:4 final size:4
Alignment explanation
Indices: 68033--68083 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
68023 GTATGTGTTG
* * *
68033 ATGT ATGT ATAT ATGT ATGT ATGA AT-T GATGT ATGT ATAT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT -ATGT ATGT ATGT ATGT ATGT
68081 ATG
1 ATG
68084 AGTTGATGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 38 0.97
5 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:69275 original size:12 final size:11
Alignment explanation
Indices: 69247--69284 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
69237 TCTTCTTTTG
*
69247 TTCTTTGCTTT
1 TTCTTTGATTT
69258 TTCTTTGATTT
1 TTCTTTGATTT
69269 TTGCTTTGATTT
1 TT-CTTTGATTT
69281 TTCT
1 TTCT
69285 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:69980 original size:26 final size:26
Alignment explanation
Indices: 69902--69983 Score: 86
Period size: 26 Copynumber: 3.4 Consensus size: 26
69892 TTTCAAGGTG
69902 GAAAGAATGTTTCAAGGTCTCAAAGA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
**
69928 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
*
69949 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
*
69974 GATAGAATGT
1 GAAAGAATGT
69984 CAAAAATTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
20 13 0.30
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 22 0.51
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (26 bp):
GAAAGAATGTTTCAAGGTCTCAAAGA
Found at i:69982 original size:46 final size:45
Alignment explanation
Indices: 69890--69983 Score: 143
Period size: 46 Copynumber: 2.1 Consensus size: 45
69880 ATAAATACAG
* * *
69890 TGTTTCAAGGTGGAAAGAATGTTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
*
69935 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
69981 TGT
1 TGT
69984 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 11 0.25
46 33 0.75
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:72264 original size:31 final size:32
Alignment explanation
Indices: 72208--72269 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
72198 TGACAAAATG
72208 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
72240 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
72270 CATGCAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:76055 original size:3 final size:3
Alignment explanation
Indices: 76049--76115 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
76039 AAAAAATTTG
* * **
76049 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TGA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
76093 TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
76116 CGAAAAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.09
3 48 0.86
4 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:76336 original size:43 final size:43
Alignment explanation
Indices: 76272--76604 Score: 195
Period size: 46 Copynumber: 7.8 Consensus size: 43
76262 TGGTGGGGAC
* **
76272 GACACTGCTCATACGCAATGAAGAGGTCTGGTCATCTAAGGGT
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTCATCTAAGGGT
* ****
76315 GACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAA---T
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTCATCTAAGGGT
* *
76355 GACACGACTCATACGTGATGAAGAGTTCTGG-CTATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTC-ATCT-AAGG-G-T
* * * * *
76401 AACACGGTTCCTACGTGATGAGGACGG-CTGGTTATCT-AGGGT
1 GACACGGCTCATACGTGATGAAGA-GGTCTGGTCATCTAAGGGT
* *
76443 GACACGGCTCATACGTGATGAAGAGATCTGG---TCT-GGGGAT
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTCATCTAAGGG-T
* * * * *
76483 GACACGGTTCCTACATGATGAGGACGG-CTGGCCATCTAAAGGTGAT
1 GACACGGCTCATACGTGATGAAGA-GGTCTGGTCATCT-AAGG-G-T
* * * * * * *
76529 AACACGGTTCCTACGTGATGAGGACGG-CTGGTTATCTATGGTT
1 GACACGGCTCATACGTGATGAAGA-GGTCTGGTCATCTAAGGGT
* * *
76572 GACACGGCTCCTACGTGATGAGGAGATCTGGTC
1 GACACGGCTCATACGTGATGAAGAGGTCTGGTC
76605 TGGGGATGAC
Statistics
Matches: 228, Mismatches: 43, Indels: 38
0.74 0.14 0.12
Matches are distributed among these distances:
39 7 0.03
40 55 0.24
41 4 0.02
42 26 0.11
43 63 0.28
44 3 0.01
45 5 0.02
46 64 0.28
47 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (43 bp):
GACACGGCTCATACGTGATGAAGAGGTCTGGTCATCTAAGGGT
Found at i:76437 original size:46 final size:45
Alignment explanation
Indices: 76382--76648 Score: 217
Period size: 40 Copynumber: 6.2 Consensus size: 45
76372 ATGAAGAGTT
*
76382 CTGGCTATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
1 CTGGCTATCT-AAGGTGATGACACGGTTCCTACGTGATGAGGACGG
* * * * *
76428 CTGGTTATCT-AGG-G-TGACACGGCTCATACGTGATGAAGA-GAT
1 CTGGCTATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACG-G
* *
76470 CTGG---TCT--GGGGATGACACGGTTCCTACATGATGAGGACGG
1 CTGGCTATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACGG
* *
76510 CTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
1 CTGGCTATCT-AAGGTGATGACACGGTTCCTACGTGATGAGGACGG
* * * *
76556 CTGGTTATCTATGGT--TGACACGGCTCCTACGTGATGAGGA-GAT
1 CTGGCTATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACG-G
* * *
76599 CTGG---TCT--GGGGATGACGCGGTTCCTACATGATGAGGACGG
1 CTGGCTATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACGG
*
76639 CTGGCCATCT
1 CTGGCTATCT
76649 TTAGGAGTTA
Statistics
Matches: 179, Mismatches: 25, Indels: 37
0.74 0.10 0.15
Matches are distributed among these distances:
38 4 0.02
39 4 0.02
40 54 0.30
41 3 0.02
42 26 0.15
43 34 0.19
44 3 0.02
45 4 0.02
46 47 0.26
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.25
Consensus pattern (45 bp):
CTGGCTATCTAAGGTGATGACACGGTTCCTACGTGATGAGGACGG
Found at i:76502 original size:40 final size:40
Alignment explanation
Indices: 76314--76635 Score: 177
Period size: 40 Copynumber: 7.6 Consensus size: 40
76304 CATCTAAGGG
* *
76314 TGACACGGCTCATACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCCTACGTGATGAGGAG-TCTGGTTCTGGGG-A
* * * *
76354 TGACACGACTCATACGTGATGAAGAGTTCTGGCTATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAGGAG-TCTGG-T-TCT---GGGGA
* * * *
76400 TAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGG-
1 TGACACGGCTCCTACGTGATGAGGA-GTCTGG-T-TCTGGGGA
* *
76442 TGACACGGCTCATACGTGATGAAGAGATCTGG-TCTGGGGA
1 TGACACGGCTCCTACGTGATGAGGAG-TCTGGTTCTGGGGA
* * * * *
76482 TGACACGGTTCCTACATGATGAGGACGGCTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAGGA-GTCTGG--TTCT---GGGGA
* * * ** *
76528 TAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
1 TGACACGGCTCCTACGTGATGAGGA-GTCTGG-T-TCTGGGGA
76571 TGACACGGCTCCTACGTGATGAGGAGATCTGG-TCTGGGGA
1 TGACACGGCTCCTACGTGATGAGGAG-TCTGGTTCTGGGGA
* * *
76611 TGACGCGGTTCCTACATGATGAGGA
1 TGACACGGCTCCTACGTGATGAGGA
76636 CGGCTGGCCA
Statistics
Matches: 222, Mismatches: 41, Indels: 38
0.74 0.14 0.13
Matches are distributed among these distances:
39 6 0.03
40 82 0.37
41 2 0.01
42 26 0.12
43 35 0.16
46 67 0.30
47 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (40 bp):
TGACACGGCTCCTACGTGATGAGGAGTCTGGTTCTGGGGA
Found at i:76520 original size:82 final size:84
Alignment explanation
Indices: 76354--76520 Score: 221
Period size: 82 Copynumber: 2.0 Consensus size: 84
76344 GGTCGGGGAA
* * *
76354 TGACACGACTCATACGTGATGAAGAGTTCTGGCTATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGACTCATACGTGATGAAGAGATCTGG--ATCT--AGGGGATAACACGGTTCCTACATGA
**
76419 TGAGGACGGCTGGTTATCTAGGG
62 TGAGGACGGCTGGCCATCTAGGG
* *
76442 TGACACGGCTCATACGTGATGAAGAGATCTGG-TCT-GGGGATGACACGGTTCCTACATGATGAG
1 TGACACGACTCATACGTGATGAAGAGATCTGGATCTAGGGGATAACACGGTTCCTACATGATGAG
76505 GACGGCTGGCCATCTA
66 GACGGCTGGCCATCTA
76521 AAGGTGATAA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
82 39 0.54
85 3 0.04
88 30 0.42
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.25
Consensus pattern (84 bp):
TGACACGACTCATACGTGATGAAGAGATCTGGATCTAGGGGATAACACGGTTCCTACATGATGAG
GACGGCTGGCCATCTAGGG
Found at i:76631 original size:129 final size:128
Alignment explanation
Indices: 76299--76648 Score: 542
Period size: 128 Copynumber: 2.7 Consensus size: 128
76289 ATGAAGAGGT
* **
76299 CTGGTCATCTAAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGGAATGACACGAC
1 CTGGTTATCT-AGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGG-ATGACACGGT
* * * * *
76363 TCATACGTGATGAAGA-GTTCTGGCTATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG
64 TCCTACATGATGAGGACG-GCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACG
76427 G
128 G
76428 CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTC
1 CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTC
76493 CTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
66 CTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
* * * *
76556 CTGGTTATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACGCGGTT
1 CTGGTTATCTA-GGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTT
76621 CCTACATGATGAGGACGGCTGGCCATCT
65 CCTACATGATGAGGACGGCTGGCCATCT
76649 TTAGGAGTTA
Statistics
Matches: 206, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
128 115 0.56
129 91 0.44
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (128 bp):
CTGGTTATCTAGGGTGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTC
CTACATGATGAGGACGGCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGG
Found at i:76711 original size:28 final size:28
Alignment explanation
Indices: 76661--76714 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
76651 AGGAGTTATG
* *
76661 GTTTCAAGAGAAACCAAATCAAAGATTT
1 GTTTCAAAAGAAACCAAACCAAAGATTT
76689 GTTTCAAAAGAAA-CAAACCCAAAGAT
1 GTTTCAAAAGAAACCAAA-CCAAAGAT
76715 GATATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (28 bp):
GTTTCAAAAGAAACCAAACCAAAGATTT
Found at i:77070 original size:15 final size:15
Alignment explanation
Indices: 77046--77088 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
77036 AAGATGATCT
*
77046 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
77061 TGTTTCAAGAG-AAA
1 TGTTTCAAGAGAAAA
*
77075 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
77089 CGACTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.33
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:77434 original size:28 final size:28
Alignment explanation
Indices: 77393--77461 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
77383 TTAAGAGAGA
*
77393 CAAAG-TTTTGTTTCCAAAGAAACAAACT
1 CAAAGATTTT-TTTCAAAAGAAACAAACT
*
77421 CAAAGATTTTTTTCAAAAGAAACAATCT
1 CAAAGATTTTTTTCAAAAGAAACAAACT
77449 CAAAGATTTTTTT
1 CAAAGATTTTTTT
77462 TTTTTTCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 34 0.89
29 4 0.11
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (28 bp):
CAAAGATTTTTTTCAAAAGAAACAAACT
Found at i:77636 original size:29 final size:29
Alignment explanation
Indices: 77574--77728 Score: 219
Period size: 29 Copynumber: 5.5 Consensus size: 29
77564 AAATGAATAG
* *
77574 ACTCAAAGA--TTT-TTCAAAA-GAAACA
1 ACTCAAAGATTTTTATTTAAAAGGAACCA
* *
77599 ACTCAAAGATATTTATTCAAAAGGAACCA
1 ACTCAAAGATTTTTATTTAAAAGGAACCA
* *
77628 ACTCCAAGATTTTTATTTAAAAGGAACAA
1 ACTCAAAGATTTTTATTTAAAAGGAACCA
*
77657 ACTCAAAGATTTTTATTTAAAAGGAACAA
1 ACTCAAAGATTTTTATTTAAAAGGAACCA
77686 ACTCAAAGATTTTTATTTAAAAGGAACCA
1 ACTCAAAGATTTTTATTTAAAAGGAACCA
77715 ACTCAAAGATTTTT
1 ACTCAAAGATTTTT
77729 TTAAGAGAAA
Statistics
Matches: 119, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
25 9 0.08
27 3 0.03
28 7 0.06
29 100 0.84
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTTAAAAGGAACCA
Found at i:78436 original size:28 final size:28
Alignment explanation
Indices: 78404--78479 Score: 134
Period size: 28 Copynumber: 2.7 Consensus size: 28
78394 TGTAACATGC
*
78404 ATGTATGTGTTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
*
78432 ATGTATGAATTGATGTATGTATATATGT
1 ATGTATGAGTTGATGTATGTATATATGT
78460 ATGTATGAGTTGATGTATGT
1 ATGTATGAGTTGATGTATGT
78480 TTCTCAATCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (28 bp):
ATGTATGAGTTGATGTATGTATATATGT
Found at i:78475 original size:12 final size:12
Alignment explanation
Indices: 78413--78478 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
78403 CATGTATGTG
78413 TTGATGTATGTATA
1 TTGATGTATG-A-A
78427 TATGTATGTATGAA
1 T-TG-ATGTATGAA
78441 TTGATGTATGTATA
1 TTGATGTATG-A-A
*
78455 TATGTATGTATGAG
1 T-TG-ATGTATGAA
78469 TTGATGTATG
1 TTGATGTATG
78479 TTTCTCAATC
Statistics
Matches: 45, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
12 14 0.31
13 5 0.11
14 6 0.13
15 6 0.13
16 14 0.31
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (12 bp):
TTGATGTATGAA
Found at i:78479 original size:4 final size:4
Alignment explanation
Indices: 78416--78466 Score: 59
Period size: 4 Copynumber: 12.8 Consensus size: 4
78406 GTATGTGTTG
* * *
78416 ATGT ATGT ATAT ATGT ATGT ATGA AT-T GATGT ATGT ATAT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT -ATGT ATGT ATGT ATGT ATGT
78464 ATG
1 ATG
78467 AGTTGATGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
4 38 0.97
5 1 0.03
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (4 bp):
ATGT
Found at i:79658 original size:12 final size:11
Alignment explanation
Indices: 79630--79667 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
79620 TCTTCTTTTG
*
79630 TTCTTTGCTTT
1 TTCTTTGATTT
79641 TTCTTTGATTT
1 TTCTTTGATTT
79652 TTGCTTTGATTT
1 TT-CTTTGATTT
79664 TTCT
1 TTCT
79668 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:80363 original size:26 final size:26
Alignment explanation
Indices: 80285--80366 Score: 86
Period size: 26 Copynumber: 3.4 Consensus size: 26
80275 TTTCAAGGTG
80285 GAAAGAATGTTTCAAGGTCTCAAAGA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
**
80311 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
*
80332 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATGTTTCAAGGTCTCAAAGA
*
80357 GATAGAATGT
1 GAAAGAATGT
80367 CAAAAATTGG
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
20 13 0.30
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 22 0.51
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (26 bp):
GAAAGAATGTTTCAAGGTCTCAAAGA
Found at i:80365 original size:46 final size:45
Alignment explanation
Indices: 80273--80366 Score: 143
Period size: 46 Copynumber: 2.1 Consensus size: 45
80263 ATAAATACAG
* * *
80273 TGTTTCAAGGTGGAAAGAATGTTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
*
80318 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
80364 TGT
1 TGT
80367 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 11 0.25
46 33 0.75
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:82641 original size:30 final size:31
Alignment explanation
Indices: 82588--82647 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
82578 TGACAAAATG
82588 ACACAAACAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAGAGAAGAAATAAGTTAGTAT
82619 ACACAAACAAA-AG-AGAAAATAAGTTAGTA
1 ACACAAACAAAGAGAAG-AAATAAGTTAGTA
82648 CATGCAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 2 0.07
30 15 0.54
31 11 0.39
ACGTcount: A:0.60, C:0.10, G:0.15, T:0.15
Consensus pattern (31 bp):
ACACAAACAAAGAGAAGAAATAAGTTAGTAT
Found at i:86441 original size:3 final size:3
Alignment explanation
Indices: 86433--86499 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
86423 AAAAAATTTG
* * **
86433 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TGA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
86477 TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
86500 CGAAAAAAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 5 0.09
3 48 0.86
4 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:88009 original size:5 final size:5
Alignment explanation
Indices: 87999--88025 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
87989 GTACTCTTTC
87999 TTCTT TTCTT TTCTT TTCTT TTCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TT
88026 TTTCATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:93324 original size:2 final size:2
Alignment explanation
Indices: 93317--93351 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
93307 ATAATTTGTT
93317 TA 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 TA T
93352 CAATTTCGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:96507 original size:3 final size:3
Alignment explanation
Indices: 96499--96576 Score: 106
Period size: 3 Copynumber: 26.0 Consensus size: 3
96489 CCATTTGTTT
*
96499 TTA TTA TTA TTA TTA TTA TTA TT- TATA CTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
*
96543 GTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
96577 CAGGCCCAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
2 3 0.04
3 62 0.93
4 2 0.03
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:97736 original size:14 final size:13
Alignment explanation
Indices: 97696--97770 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 13
97686 CTATTTATTT
*
97696 ATATTTTAATTTA
1 ATATTTTAATTCA
*
97709 ATATTTAAATTTCA
1 ATATTTTAA-TTCA
97723 ATATGTTTAATTCA
1 ATAT-TTTAATTCA
* *
97737 ATGTTCTAATT-A
1 ATATTTTAATTCA
*
97749 TTATTTT-ATT-A
1 ATATTTTAATTCA
*
97760 TTATTTTAATT
1 ATATTTTAATT
97771 TAGTCATATA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
11 11 0.22
12 8 0.16
13 14 0.27
14 14 0.27
15 4 0.08
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.59
Consensus pattern (13 bp):
ATATTTTAATTCA
Found at i:98153 original size:23 final size:22
Alignment explanation
Indices: 98127--98180 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
98117 TTCTAAGTAA
*
98127 ATAAATATCTTATTTATAAAAAT
1 ATAAATAT-ATATTTATAAAAAT
*
98150 ATAAAAAATATATTTATAAAAAT
1 AT-AAATATATATTTATAAAAAT
98173 -T-AATATAT
1 ATAAATATAT
98181 TTTCTTGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 6 0.22
22 1 0.04
23 15 0.56
24 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATAAATATATATTTATAAAAAT
Found at i:103983 original size:19 final size:19
Alignment explanation
Indices: 103959--104007 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
103949 TTTTAAAGGG
103959 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
103978 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
*
103997 ATGCATTGATG
1 ATGCATCGATG
104008 TTTCTTCTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:112373 original size:18 final size:20
Alignment explanation
Indices: 112341--112381 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
112331 AGATTCCAAG
112341 TTTATCTTTTCGAAATTCAA
1 TTTATCTTTTCGAAATTCAA
112361 TTTAT-TTTT-GAAATTCAA
1 TTTATCTTTTCGAAATTCAA
112379 TTT
1 TTT
112382 GTTCTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.57
19 4 0.19
20 5 0.24
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTATCTTTTCGAAATTCAA
Found at i:113894 original size:20 final size:20
Alignment explanation
Indices: 113832--113894 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
113822 TCCAGATAAA
113832 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
113852 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
113871 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
113891 GTTC
1 GTTC
113895 GACCTTAGCT
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
18 3 0.10
19 10 0.33
20 14 0.47
21 3 0.10
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:114224 original size:3 final size:3
Alignment explanation
Indices: 114216--114302 Score: 92
Period size: 3 Copynumber: 30.0 Consensus size: 3
114206 CCATTTGTTT
* * *
114216 TTA TTA TTA TTA TTA ATA ATA ATA TT- TTA TTA TT- TTA TT- TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
114259 CTA TTA TTA TTA TT- TTA TTA TTA TTA ATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
114303 CAGGCCTAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
2 7 0.10
3 66 0.90
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:114249 original size:23 final size:24
Alignment explanation
Indices: 114216--114302 Score: 106
Period size: 26 Copynumber: 3.6 Consensus size: 24
114206 CCATTTGTTT
*
114216 TTATTATTATTATTAATAATAATA
1 TTATTATTATTATTATTAATAATA
* *
114240 TT-TTATTATT-TTATTTATACTA
1 TTATTATTATTATTATTAATAATA
*
114262 TTATTATTATTTTATTATTATTAATA
1 TTATTATTA--TTATTATTAATAATA
114288 TTATTATTATTATTA
1 TTATTATTATTATTA
114303 CAGGCCTAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
22 11 0.21
23 14 0.26
24 8 0.15
25 2 0.04
26 18 0.34
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATTATTATTATTATTAATAATA
Found at i:114263 original size:17 final size:17
Alignment explanation
Indices: 114243--114302 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
114233 AATAATATTT
114243 TATTATT-TTATTTATAC
1 TATTATTATTATTT-TAC
*
114260 TATTATTATTATTTTAT
1 TATTATTATTATTTTAC
* *
114277 TATTATTAATATTATTAT
1 TATTATTATTATT-TTAC
114295 TATTATTA
1 TATTATTA
114303 CAGGCCTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
17 21 0.54
18 18 0.46
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTATTATTTTAC
Found at i:115661 original size:14 final size:13
Alignment explanation
Indices: 115621--115695 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 13
115611 CTATTTATTT
*
115621 ATATTTTAATTTA
1 ATATTTTAATTCA
*
115634 ATATTTAAATTTCA
1 ATATTTTAA-TTCA
115648 ATATGTTTAATTCA
1 ATAT-TTTAATTCA
* *
115662 ATGTTCTAATT-A
1 ATATTTTAATTCA
*
115674 TTATTTT-ATT-A
1 ATATTTTAATTCA
*
115685 TTATTTTAATT
1 ATATTTTAATT
115696 TAGTCATATA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
11 11 0.22
12 8 0.16
13 14 0.27
14 14 0.27
15 4 0.08
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.59
Consensus pattern (13 bp):
ATATTTTAATTCA
Found at i:116078 original size:23 final size:22
Alignment explanation
Indices: 116038--116105 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 22
116028 TATTTTTCTG
*
116038 ATATTTATAAGTAA-ATAAATAT
1 ATATTTATAA-AAATATAAATAT
* *
116060 CTTATTTATAAAAATATAAAAAAT
1 -ATATTTATAAAAATAT-AAATAT
116084 ATATTTATAAAAAT-T-AATAT
1 ATATTTATAAAAATATAAATAT
116104 AT
1 AT
116106 TTTCTTGGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 6 0.16
22 3 0.08
23 24 0.63
24 5 0.13
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (22 bp):
ATATTTATAAAAATATAAATAT
Found at i:127111 original size:3 final size:3
Alignment explanation
Indices: 127103--127212 Score: 195
Period size: 3 Copynumber: 36.7 Consensus size: 3
127093 TTTTTATCCA
127103 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
127151 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
127198 TAT TAA TAT ATAT TA
1 TAT TAT TAT -TAT TA
127213 AATATACATA
Statistics
Matches: 103, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.02
3 98 0.95
4 3 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:127719 original size:16 final size:16
Alignment explanation
Indices: 127660--127729 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
127650 CCATCCTGAA
* * *
127660 AAAAAAACACACACAG
1 AAAAAAACAGAGAAAG
*
127676 AAAAAAA-AGAGAGAG
1 AAAAAAACAGAGAAAG
* * * *
127691 ACAGAACCGGAGAAAG
1 AAAAAAACAGAGAAAG
*
127707 AAAAAAACAGAGAAAC
1 AAAAAAACAGAGAAAG
127723 AAAAAAA
1 AAAAAAA
127730 AACTACTAAC
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
15 9 0.22
16 31 0.77
ACGTcount: A:0.70, C:0.13, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAACAGAGAAAG
Found at i:127847 original size:28 final size:27
Alignment explanation
Indices: 127803--127864 Score: 106
Period size: 28 Copynumber: 2.3 Consensus size: 27
127793 AGAAGAGAAA
127803 CTTACCGAGAAGCCCCGACCACCGGAT
1 CTTACCGAGAAGCCCCGACCACCGGAT
127830 CTTACCGAGGAAGCCCCGACCACCGGAT
1 CTTACCGA-GAAGCCCCGACCACCGGAT
*
127858 CTCACCG
1 CTTACCG
127865 GAACCTTCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 8 0.24
28 25 0.76
ACGTcount: A:0.24, C:0.42, G:0.23, T:0.11
Consensus pattern (27 bp):
CTTACCGAGAAGCCCCGACCACCGGAT
Found at i:128694 original size:13 final size:13
Alignment explanation
Indices: 128678--128723 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
128668 TTTAAATAAA
128678 TAAATATTTATTT
1 TAAATATTTATTT
*
128691 TAAATAAATTATTT
1 TAAAT-ATTTATTT
128705 T-AATATTTATTT
1 TAAATATTTATTT
*
128717 TCAATAT
1 TAAATAT
128724 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 8 0.28
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:128713 original size:21 final size:23
Alignment explanation
Indices: 128663--128713 Score: 56
Period size: 21 Copynumber: 2.3 Consensus size: 23
128653 TGTTGTTAAA
128663 AATATTTTAAATAAATAAATATTT
1 AATA-TTTAAATAAATAAATATTT
*
128687 -AT-TTTAAATAAAT-TAT-TTT
1 AATATTTAAATAAATAAATATTT
128706 AATATTTA
1 AATATTTA
128714 TTTTCAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
19 3 0.12
20 4 0.17
21 15 0.62
23 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATATTTAAATAAATAAATATTT
Found at i:128856 original size:90 final size:92
Alignment explanation
Indices: 128690--128877 Score: 231
Period size: 90 Copynumber: 2.1 Consensus size: 92
128680 AATATTTATT
* * * *
128690 TTAAATAAATTATTTTAATATTTATTTTCAATATCAAAGAAAAGGACAGTCTTAATACAACTGGA
1 TTAAATAAATTATTTTAATATTAATTATCAATATCAAAGAAAAGGACAGTCTTAAGACAACTAGA
*
128755 TGTCCTATTCTGATA-TTTTAAAAAAA
66 AGTCCTATTCTGATATTTTTAAAAAAA
* * * *
128781 TTAAATAATTTATTTTAA-ATTAATTATCAATATCAAAGAAAA-GAGCTGTCTTAAGGCACCTAG
1 TTAAATAAATTATTTTAATATTAATTATCAATATCAAAGAAAAGGA-CAGTCTTAAGACAACTAG
* * *
128844 AAGTTCTTTTCTGATATTTTTAAATAAA
65 AAGTCCTATTCTGATATTTTTAAAAAAA
128872 -TAAATA
1 TTAAATA
128878 TTTTTTATAT
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
89 2 0.02
90 54 0.65
91 27 0.33
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.39
Consensus pattern (92 bp):
TTAAATAAATTATTTTAATATTAATTATCAATATCAAAGAAAAGGACAGTCTTAAGACAACTAGA
AGTCCTATTCTGATATTTTTAAAAAAA
Found at i:129386 original size:21 final size:23
Alignment explanation
Indices: 129362--129403 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
129352 TTTCAATTAT
129362 TATTTAT-T-TATTATTTTATAA
1 TATTTATATGTATTATTTTATAA
*
129383 TATTTATATGTTTTATTTTAT
1 TATTTATATGTATTATTTTAT
129404 TTGCAAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 1 0.06
23 10 0.56
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TATTTATATGTATTATTTTATAA
Found at i:140032 original size:10 final size:9
Alignment explanation
Indices: 140015--140077 Score: 76
Period size: 9 Copynumber: 7.0 Consensus size: 9
140005 ATTATGCTTG
140015 AAGAAAAAA
1 AAGAAAAAA
140024 AATGAAAAAA
1 AA-GAAAAAA
* *
140034 AAG-AGAAG
1 AAGAAAAAA
140042 AA-AAAAAA
1 AAGAAAAAA
140050 AAGAAAAAA
1 AAGAAAAAA
140059 AAGAAAAAAA
1 AAG-AAAAAA
140069 AAGAAAAAA
1 AAGAAAAAA
140078 GGGGGGTCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
8 10 0.22
9 18 0.39
10 18 0.39
ACGTcount: A:0.86, C:0.00, G:0.13, T:0.02
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:140034 original size:11 final size:10
Alignment explanation
Indices: 140015--140077 Score: 72
Period size: 10 Copynumber: 5.9 Consensus size: 10
140005 ATTATGCTTG
140015 AAGAAAAAAA
1 AAGAAAAAAA
*
140025 ATGAAAAAAA
1 AAGAAAAAAA
140035 AGAGAAGAAAAAA
1 A-AG-A-AAAAAA
*
140048 AAAAGAAAAAA
1 AAGA-AAAAAA
140059 AAGAAAAAAA
1 AAGAAAAAAA
140069 AAGAAAAAA
1 AAGAAAAAA
140078 GGGGGGTCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
10 25 0.54
11 12 0.26
12 2 0.04
13 7 0.15
ACGTcount: A:0.86, C:0.00, G:0.13, T:0.02
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:140044 original size:14 final size:13
Alignment explanation
Indices: 140018--140070 Score: 60
Period size: 12 Copynumber: 4.3 Consensus size: 13
140008 ATGCTTGAAG
*
140018 AAAAAA-AATGAA
1 AAAAAAGAAAGAA
140030 AAAAAAGAGAAG-A
1 AAAAAAGA-AAGAA
140043 AAAAAA-AAAGAA
1 AAAAAAGAAAGAA
140055 AAAAAAGAAA-AA
1 AAAAAAGAAAGAA
140067 AAAA
1 AAAA
140071 GAAAAAAGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
11 3 0.08
12 20 0.56
13 11 0.31
14 2 0.06
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (13 bp):
AAAAAAGAAAGAA
Found at i:140417 original size:16 final size:16
Alignment explanation
Indices: 140398--140434 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
140388 CAATTATATC
140398 TATTTCAAATTCAATT
1 TATTTCAAATTCAATT
* *
140414 TATTTGAGATTCAATT
1 TATTTCAAATTCAATT
140430 TATTT
1 TATTT
140435 TTGGAAATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54
Consensus pattern (16 bp):
TATTTCAAATTCAATT
Found at i:140446 original size:19 final size:18
Alignment explanation
Indices: 140404--140452 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
140394 TATCTATTTC
140404 AAATTCAATTTA--TTTG
1 AAATTCAATTTATTTTTG
*
140420 AGATTCAATTTATTTTTGG
1 AAATTCAATTTATTTTT-G
140439 AAATTCAATTTATT
1 AAATTCAATTTATT
140453 CTTTTCTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
18 3 0.11
19 14 0.50
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (18 bp):
AAATTCAATTTATTTTTG
Found at i:141361 original size:83 final size:83
Alignment explanation
Indices: 141222--141515 Score: 518
Period size: 83 Copynumber: 3.5 Consensus size: 83
141212 CAATATACTC
* *
141222 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAATCAATCATTGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-TAGAACCAATCATTGAAT
141286 TTGAAAGATGAATTTGCCA
65 TTGAAAGATGAATTTGCCA
141305 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCATTGAATT
141370 TGAAAGATGAATTTGCCA
66 TGAAAGATGAATTTGCCA
*
141388 ATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCATTGAATT
*
141453 TGGAAGATGAATTTGCCA
66 TGAAAGATGAATTTGCCA
* *
141471 ATAACATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
141516 ATAGGAACTA
Statistics
Matches: 203, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
83 199 0.98
84 4 0.02
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.38
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGAACCAATCATTGAATT
TGAAAGATGAATTTGCCA
Found at i:142443 original size:113 final size:113
Alignment explanation
Indices: 142243--142796 Score: 959
Period size: 113 Copynumber: 4.9 Consensus size: 113
142233 ATTCAAATCT
142243 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
* **
142308 GAAGAAGTTCATAATGATAAGAATTTGTTCAACCTTTTGTCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
142356 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
142421 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* *
142469 ATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
142534 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* * *
142582 ATCATTTGATGGATCATCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
142647 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
* *
142695 ATCAATTGATGGATTATCTTTT-CAG-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAA
1 ATCACTTGATGGATTATCTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * *
142758 AGAAGAAGTTCATAATAAGAAGAACTTGTTCAACTTTTT
65 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
142797 GCATAATTCT
Statistics
Matches: 425, Mismatches: 15, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
111 2 0.00
112 72 0.17
113 351 0.83
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (113 bp):
ATCACTTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTC
Found at i:143123 original size:3 final size:3
Alignment explanation
Indices: 143115--143167 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
143105 TTTTTATCCA
*
143115 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
143163 TAT TA
1 TAT TA
143168 AATATATATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:144664 original size:13 final size:13
Alignment explanation
Indices: 144648--144686 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
144638 ATACAATAAA
144648 TAAATATTTATTT
1 TAAATATTTATTT
*
144661 TAAATAAATTATTT
1 TAAAT-ATTTATTT
144675 T-AATATTTATTT
1 TAAATATTTATTT
144687 ATCAATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.30
13 8 0.35
14 8 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:144839 original size:98 final size:96
Alignment explanation
Indices: 144660--144847 Score: 227
Period size: 98 Copynumber: 1.9 Consensus size: 96
144650 AATATTTATT
* *
144660 TTAAATAAATTATTTTAATATTTATTTATCAATATCAAAGAAAAGGACAGTCTTAATACAACTGG
1 TTAAATAAATTATTTTAATATTTATTTATCAATATCAAAGAAAAGGACAGTCTTAAGACAACTAG
* *
144725 ATGTCCTATTCTGATATTTTGAAATTAAAAA
66 AAGTCCTATTCCGATATTTTGAAATTAAAAA
* * * *
144756 TTAAATAATTTATTTTTAA-ATTAGTATTTATCAATATCAAAGAAAA-GAGCTGTCTTAAGGCAC
1 TTAAATAAATTA-TTTTAATATT--TATTTATCAATATCAAAGAAAAGGA-CAGTCTTAAGACAA
* * *
144819 CTAGAAGTTCTTTTCCGATATTTTTAAAT
62 CTAGAAGTCCTATTCCGATATTTTGAAAT
144848 AAATAAATAT
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
96 14 0.18
97 8 0.10
98 55 0.71
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (96 bp):
TTAAATAAATTATTTTAATATTTATTTATCAATATCAAAGAAAAGGACAGTCTTAAGACAACTAG
AAGTCCTATTCCGATATTTTGAAATTAAAAA
Found at i:149257 original size:21 final size:21
Alignment explanation
Indices: 149231--149387 Score: 194
Period size: 21 Copynumber: 7.5 Consensus size: 21
149221 GTTTCCAGAT
**
149231 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGAACTTGGACTA
149252 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
149273 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
149293 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
149314 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
149335 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
149356 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
* *
149377 TTGCATTGCGA
1 TCGCAATGCGA
149388 TTTACATATT
Statistics
Matches: 119, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
20 16 0.13
21 103 0.87
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:149345 original size:104 final size:104
Alignment explanation
Indices: 149231--149428 Score: 285
Period size: 104 Copynumber: 1.9 Consensus size: 104
149221 GTTTCCAGAT
** *
149231 TCGCAATGCGATTTTGGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-A-A-
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCAATGCG-AT-T-TACATAT
149293 TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTA
63 TCGCAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTA
* *
149335 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATTGCATTGCGATTTACATATTCG
1 TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCAATGCGATTTACATATTCG
* *
149400 CATTGCGATAGTCGACTATCGCATTGCGA
66 CAATGCGATAGTCGACTATCGCAATGCGA
149429 TAGTCCAAAA
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
101 2 0.02
102 2 0.02
103 3 0.04
104 77 0.92
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (104 bp):
TCGCAATGCGAACTTGGACTATCGCAATGCGAACTTCGACTATCGCAATGCGATTTACATATTCG
CAATGCGATAGTCGACTATCGCAATGCGAACTTGGACTA
Found at i:149423 original size:21 final size:21
Alignment explanation
Indices: 149231--149433 Score: 120
Period size: 21 Copynumber: 9.8 Consensus size: 21
149221 GTTTCCAGAT
** *
149231 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGATAGTCGACTA
* *
149252 TCGCAATGCGA-ACTTGGACTA
1 TCGCAATGCGATA-GTCGACTA
*
149273 TCGCAATGCGAATA-T-GTA-AA
1 TCGCAATGCG-ATAGTCG-ACTA
149293 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGATAGTCGACTA
* *
149314 TCGCAATGCGA-ACTTGGACTA
1 TCGCAATGCGATA-GTCGACTA
* *
149335 TCGCAATGCGA-ACTTGGACTA
1 TCGCAATGCGATA-GTCGACTA
*
149356 TCGCAATGCGA-ACTTCGACTA
1 TCGCAATGCGATA-GTCGACTA
* * *
149377 TTGCATTGCGAT--T-TACATA
1 TCGCAATGCGATAGTCGAC-TA
*
149396 TTCGCATTGCGATAGTCGACTA
1 -TCGCAATGCGATAGTCGACTA
*
149418 TCGCATTGCGATAGTC
1 TCGCAATGCGATAGTC
149434 CAAAATCGCA
Statistics
Matches: 157, Mismatches: 11, Indels: 28
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.01
19 6 0.04
20 26 0.17
21 116 0.74
22 4 0.03
23 3 0.02
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (21 bp):
TCGCAATGCGATAGTCGACTA
Found at i:149441 original size:21 final size:21
Alignment explanation
Indices: 149397--149443 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
149387 ATTTACATAT
* **
149397 TCGCATTGCGATAGTCGACTA
1 TCGCATTGCGATAGTCCAAAA
149418 TCGCATTGCGATAGTCCAAAA
1 TCGCATTGCGATAGTCCAAAA
149439 TCGCA
1 TCGCA
149444 ACGACTGGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAAA
Found at i:150201 original size:21 final size:21
Alignment explanation
Indices: 150169--150224 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
150159 GCGAATATGT
*
150169 AAATCGCATTGCGATAGTCCA
1 AAATCGTATTGCGATAGTCCA
**
150190 AGTTCGTATTGCGATAGTCCA
1 AAATCGTATTGCGATAGTCCA
150211 AAATCGTATTGCGA
1 AAATCGTATTGCGA
150225 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (21 bp):
AAATCGTATTGCGATAGTCCA
Found at i:157599 original size:36 final size:35
Alignment explanation
Indices: 157558--157662 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 35
157548 AAAGGTCTTC
157558 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTTTT
1 GTGTTTCAAGAGAAACA-TTTCAAAGGTTTTTTTTT
*
157594 GTGTTTCAAGAGAAAAAATTTCAAAGGTTTTTTTTT
1 GTGTTTCAAGAG-AAACATTTCAAAGGTTTTTTTTT
157630 GTGTTTCAAGAGAAACGATTTCAAAGGTTTTTT
1 GTGTTTCAAGAGAAAC-ATTTCAAAGGTTTTTT
157663 AAGAGAAACT
Statistics
Matches: 65, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
35 3 0.05
36 58 0.89
37 4 0.06
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (35 bp):
GTGTTTCAAGAGAAACATTTCAAAGGTTTTTTTTT
Found at i:157757 original size:67 final size:63
Alignment explanation
Indices: 157631--157775 Score: 159
Period size: 67 Copynumber: 2.2 Consensus size: 63
157621 TTTTTTTTTG
* * * *
157631 TGTTTCAAGAGAAACGATTTCAAAGGTTTTTTAAGAGAAACTGTCTCAAAGGAGGCAAAATTT
1 TGTTTCAAGAGAAACGATTTCAAAGATTTTTTAAGAGAAACTGTCTCAAAGGAGACAAAACTA
*
157694 TGTTTCAAGAGAAAC-ATATTTAAAGATTGGTGTTTCAAGAGAAACTGTCTC-AAGAGAGACAAA
1 TGTTTCAAGAGAAACGAT-TTCAAAGATT--T-TTT-AAGAGAAACTGTCTCAAAG-GAGACAAA
157757 ACTA
60 ACTA
* *
157761 TGTTGCAAGGGAAAC
1 TGTTTCAAGAGAAAC
157776 TGTCTCAAGA
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
62 2 0.03
63 23 0.33
65 1 0.01
66 6 0.09
67 37 0.54
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (63 bp):
TGTTTCAAGAGAAACGATTTCAAAGATTTTTTAAGAGAAACTGTCTCAAAGGAGACAAAACTA
Found at i:157784 original size:37 final size:36
Alignment explanation
Indices: 157724--157916 Score: 172
Period size: 37 Copynumber: 5.1 Consensus size: 36
157714 TAAAGATTGG
157724 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TA
* * *
157761 TGTTGCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATA
* *
157797 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAACACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAG------ACAAAATA
* * *
157839 TGTTTAAAGAGGAACTATCTCAAGAGAGACAAAACT-
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TA
* * * * * *
157875 TAGTTCCAAAAAAAACTGTCTCAAGGGAGACGAAATT
1 T-GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATA
157912 TGTTT
1 TGTTT
157917 AATGTAAAAC
Statistics
Matches: 130, Mismatches: 17, Indels: 19
0.78 0.10 0.11
Matches are distributed among these distances:
36 37 0.28
37 59 0.45
42 34 0.26
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATA
Found at i:157838 original size:42 final size:41
Alignment explanation
Indices: 157724--157873 Score: 165
Period size: 42 Copynumber: 3.9 Consensus size: 41
157714 TAAAGATTGG
* *
157724 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC----TA
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACAAAATT
* * *
157761 TGTTGCAAGGGAAACTGTCTCAAGAGAG-----ACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACAAAATT
157797 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAACACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAA-ACAAAATT
* *
157839 TGTTTAAAGAGGAACTATCTCAAGAGAGACAAAAC
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAC
157874 TTAGTTCCAA
Statistics
Matches: 95, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
32 2 0.02
36 26 0.27
37 26 0.27
41 2 0.02
42 39 0.41
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.21
Consensus pattern (41 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACAAAATT
Found at i:158247 original size:60 final size:60
Alignment explanation
Indices: 158179--158314 Score: 209
Period size: 60 Copynumber: 2.3 Consensus size: 60
158169 ATACTTCTTC
* *
158179 GTGAAGTTGAAATCCAAGTGTTGTTTCAACAAATCGACTTTGAGTTGGATATCATTCGTT
1 GTGAAGTTGAAATCCAAGTATTGCTTCAACAAATCGACTTTGAGTTGGATATCATTCGTT
* * * * *
158239 GTGAAGTTGAAATCCAAGTATTGCTTCACCAAATTGGCTTTGAGTTGGATATCCTTTGTT
1 GTGAAGTTGAAATCCAAGTATTGCTTCAACAAATCGACTTTGAGTTGGATATCATTCGTT
158299 GTGAAGTTGAAATCCA
1 GTGAAGTTGAAATCCA
158315 TTCTCGAGTA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (60 bp):
GTGAAGTTGAAATCCAAGTATTGCTTCAACAAATCGACTTTGAGTTGGATATCATTCGTT
Found at i:159039 original size:23 final size:23
Alignment explanation
Indices: 159013--159057 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
159003 CACCACAGCT
*
159013 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
159036 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
159058 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:160734 original size:21 final size:21
Alignment explanation
Indices: 160704--160748 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
160694 ATTCTGTCGT
* *
160704 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
160725 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
160746 TTG
1 TTG
160749 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:164006 original size:23 final size:23
Alignment explanation
Indices: 163980--164024 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
163970 CACCACAGCT
*
163980 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
164003 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
164025 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:165689 original size:21 final size:21
Alignment explanation
Indices: 165659--165703 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
165649 ATTCTGTCGT
* *
165659 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
165680 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
165701 TTG
1 TTG
165704 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:167055 original size:31 final size:32
Alignment explanation
Indices: 167007--167089 Score: 96
Period size: 31 Copynumber: 2.6 Consensus size: 32
166997 ATCAGGGTGC
* * * *
167007 TGAATCCCCGAAGATGCCCTAATATTCGATGT
1 TGAATCTCCAAAGATGCCCCAACATTCGATGT
*
167039 T-AATCTCCAAAGATGCCCCAACATTTGATGT
1 TGAATCTCCAAAGATGCCCCAACATTCGATGT
* *
167070 TGAATCTTCAAAGGTGCCCC
1 TGAATCTCCAAAGATGCCCC
167090 CATTGTTCCT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 26 0.60
32 17 0.40
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (32 bp):
TGAATCTCCAAAGATGCCCCAACATTCGATGT
Found at i:168151 original size:20 final size:20
Alignment explanation
Indices: 168128--168195 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 20
168118 TTTTTCTATA
168128 TTTTTCCTTTATTTTTGC-T
1 TTTTTCCTTTATTTTTGCTT
* *
168147 TTTTTCTTTTCTTTTTGCTT
1 TTTTTCCTTTATTTTTGCTT
* *
168167 TTTTT-CTTTGTTTTTCTCTT
1 TTTTTCCTTTATTTTT-GCTT
168187 TTTTTCCTT
1 TTTTTCCTT
168196 CTCTTTTTGT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 24 0.59
20 14 0.34
21 3 0.07
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.78
Consensus pattern (20 bp):
TTTTTCCTTTATTTTTGCTT
Found at i:171216 original size:21 final size:20
Alignment explanation
Indices: 171183--171237 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
171173 GGCTAAAAGG
* *
171183 AAAAAGTTG-AAAAGTTGAA
1 AAAAAATTGAAAAAGCTGAA
171202 ATAAAAATTGAAAAAGCTGAA
1 A-AAAAATTGAAAAAGCTGAA
*
171223 AAGAAGATTGAAAAA
1 AA-AAAATTGAAAAA
171238 AATGTGTAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 8 0.27
21 21 0.70
ACGTcount: A:0.62, C:0.02, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAAAATTGAAAAAGCTGAA
Found at i:171261 original size:2 final size:2
Alignment explanation
Indices: 171254--171298 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
171244 TAGAAAACAA
171254 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
171296 AT A
1 AT A
171299 AATGATAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:171388 original size:16 final size:15
Alignment explanation
Indices: 171367--171458 Score: 53
Period size: 16 Copynumber: 5.9 Consensus size: 15
171357 TATAGTAAAA
*
171367 AAATAAAAATAGTAT
1 AAATAAAAATAATAT
*
171382 AATATAATAATAATAT
1 AA-ATAAAAATAATAT
* * *
171398 AAATAAATAACAAAAA
1 AAATAAA-AATAATAT
171414 AATATAGAAAATAA-AT
1 AA-ATA-AAAATAATAT
*
171430 AAA-AAATAATTATAT
1 AAATAAA-AATAATAT
* *
171445 ATATAATAATAATA
1 AAATAAAAATAATA
171459 ATAAGGGTTA
Statistics
Matches: 58, Mismatches: 12, Indels: 14
0.69 0.14 0.17
Matches are distributed among these distances:
13 2 0.03
14 5 0.09
15 17 0.29
16 25 0.43
17 7 0.12
18 2 0.03
ACGTcount: A:0.68, C:0.01, G:0.02, T:0.28
Consensus pattern (15 bp):
AAATAAAAATAATAT
Found at i:171417 original size:24 final size:22
Alignment explanation
Indices: 171394--171450 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
171384 TATAATAATA
171394 ATATAAATAAATAACAAAAAAAT
1 ATATAAATAAATAA-AAAAAAAT
* *
171417 ATAGAAAATAAATAAAAAATAATT
1 ATA-TAAATAAATAAAAAA-AAAT
*
171441 ATATATATAA
1 ATATAAATAA
171451 TAATAATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
ATATAAATAAATAAAAAAAAAT
Found at i:180414 original size:105 final size:105
Alignment explanation
Indices: 180232--180435 Score: 399
Period size: 105 Copynumber: 1.9 Consensus size: 105
180222 ACTTTCTAAA
*
180232 GTGGAGCAATTGAACAAATTTTAATCTTTAGTTCTTCGAATATTAAATGAATTAAGGATTCTTTT
1 GTGGAGAAATTGAACAAATTTTAATCTTTAGTTCTTCGAATATTAAATGAATTAAGGATTCTTTT
180297 AACTCTTCAAGAATTATAGATTTTTGACATATGAAAAAAG
66 AACTCTTCAAGAATTATAGATTTTTGACATATGAAAAAAG
180337 GTGGAGAAATTGAACAAATTTTAATCTTTAGTTCTTCGAATATTAAATGAATTAAGGATTCTTTT
1 GTGGAGAAATTGAACAAATTTTAATCTTTAGTTCTTCGAATATTAAATGAATTAAGGATTCTTTT
180402 AACTCTTCAAGAATTATAGATTTTTGACATATGA
66 AACTCTTCAAGAATTATAGATTTTTGACATATGA
180436 CAAGATTAGA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.39
Consensus pattern (105 bp):
GTGGAGAAATTGAACAAATTTTAATCTTTAGTTCTTCGAATATTAAATGAATTAAGGATTCTTTT
AACTCTTCAAGAATTATAGATTTTTGACATATGAAAAAAG
Found at i:181119 original size:8 final size:7
Alignment explanation
Indices: 181094--181182 Score: 56
Period size: 8 Copynumber: 11.7 Consensus size: 7
181084 AATCAAGAAC
181094 AAAAAAG
1 AAAAAAG
181101 AAAAGAAG
1 AAAA-AAG
181109 CAAAAAAG
1 -AAAAAAG
181117 CAAAAAA-
1 -AAAAAAG
*
181124 AACAAAG
1 AAAAAAG
181131 -AAAAAG
1 AAAAAAG
181137 AAAAACAAG
1 -AAAA-AAG
181146 AAAAAAAGG
1 -AAAAAA-G
181155 AAAAAAG
1 AAAAAAG
*
181162 AGCAAAAAT
1 A--AAAAAG
*
181171 CAAAAAG
1 AAAAAAG
181178 AAAAA
1 AAAAA
181183 GGGACAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
6 10 0.15
7 15 0.22
8 24 0.36
9 18 0.27
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:181122 original size:9 final size:9
Alignment explanation
Indices: 181094--181169 Score: 61
Period size: 9 Copynumber: 8.4 Consensus size: 9
181084 AATCAAGAAC
181094 AAAAAAG-A
1 AAAAAAGCA
*
181102 AAAGAAGC-
1 AAAAAAGCA
181110 AAAAAAGCA
1 AAAAAAGCA
*
181119 AAAAAAACAA
1 AAAAAAGC-A
181129 AGAAAAAG-A
1 A-AAAAAGCA
181138 AAAACAAG-A
1 AAAA-AAGCA
*
181147 AAAAAAGGA
1 AAAAAAGCA
181156 AAAAAGAGCA
1 AAAAA-AGCA
181166 AAAA
1 AAAA
181170 TCAAAAAGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
8 19 0.34
9 23 0.41
10 9 0.16
11 5 0.09
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAGCA
Found at i:181146 original size:15 final size:16
Alignment explanation
Indices: 181121--181150 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
181111 AAAAAGCAAA
181121 AAAAACAAAGAAAAAG
1 AAAAACAAAGAAAAAG
181137 AAAAAC-AAGAAAAA
1 AAAAACAAAGAAAAA
181151 AAGGAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAACAAAGAAAAAG
Found at i:181861 original size:23 final size:22
Alignment explanation
Indices: 181819--181861 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
181809 CCATCAATCT
* *
181819 TTTGAGCATCCAATGCCAAACC
1 TTTGAGCATCAAATGACAAACC
181841 TTTGAGCATCAAATGAACAAA
1 TTTGAGCATCAAATG-ACAAA
181862 AATGCCAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (22 bp):
TTTGAGCATCAAATGACAAACC
Found at i:182760 original size:37 final size:38
Alignment explanation
Indices: 182701--182825 Score: 145
Period size: 37 Copynumber: 3.4 Consensus size: 38
182691 ACTCAAGATT
* *
182701 GTTT-TTCTTAAAAC-ATATTTTGTCTTCCTTGAGACA
1 GTTTCTTCTTGAAACAAAATTTTGTCTTCCTTGAGACA
* * *
182737 GTTTCTT-TTGGAACTAAGTTTTGTC-TCTCTTGAGACA
1 GTTTCTTCTTGAAACAAAATTTTGTCTTC-CTTGAGACA
*
182774 G-TTCTTCTTGAAACAAAATTTTGTCTCCCTTGAGACA
1 GTTTCTTCTTGAAACAAAATTTTGTCTTCCTTGAGACA
182811 GTTTC-TCTTGAAACA
1 GTTTCTTCTTGAAACA
182826 TAAACATCGA
Statistics
Matches: 75, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
36 16 0.21
37 55 0.73
38 4 0.05
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.43
Consensus pattern (38 bp):
GTTTCTTCTTGAAACAAAATTTTGTCTTCCTTGAGACA
Found at i:182902 original size:37 final size:37
Alignment explanation
Indices: 182855--182927 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
182845 CCTTGAAATG
* *
182855 AATTTTGTCTCTCTTGAGATAGTTTC-CTTTGAAACAA
1 AATTTTGTCTCCCTTGAGACAGTTTCTC-TTGAAACAA
182892 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
182928 TAAACATTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 32 0.97
38 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
Found at i:182990 original size:36 final size:35
Alignment explanation
Indices: 182943--183063 Score: 116
Period size: 36 Copynumber: 3.3 Consensus size: 35
182933 ATTGAAAACA
* *
182943 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAAT-AATTTTGTCTCCCTTGAGACAG
* * *
182979 TTTCCCTTGAAACAAAGTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAA-TAATTTTGTCTCCCTTGAGACAG
** * *
183015 TTTCTTTTTGAACTAAGTTTTATCTCCCTTGAGACAG
1 TTTC-CCTTGAAATAA-TTTTGTCTCCCTTGAGACAG
*
183052 TTTCTCTTGAAA
1 TTTCCCTTGAAA
183064 CAACACAATT
Statistics
Matches: 68, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
36 42 0.62
37 26 0.38
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (35 bp):
TTTCCCTTGAAATAATTTTGTCTCCCTTGAGACAG
Found at i:183026 original size:102 final size:102
Alignment explanation
Indices: 182755--183019 Score: 453
Period size: 102 Copynumber: 2.6 Consensus size: 102
182745 TGGAACTAAG
* *
182755 TTTTGTCTCTCTTGAGACAG-TTCTTCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 TTTTGTCTCTCTTGAGATAGTTTC-CCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCT
182819 TGAAACATAAACATCGAAAACATTTCCCTTGAAATGAA
65 TGAAACATAAACATCGAAAACATTTCCCTTGAAATGAA
*
182857 TTTTGTCTCTCTTGAGATAGTTTCCTTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
1 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
*
182922 GAAACATAAACATTGAAAACATTTCCCTTGAAATGAA
66 GAAACATAAACATCGAAAACATTTCCCTTGAAATGAA
* *
182959 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAAC-AAAGTTCGTCTCCCTTGAGACAGTTTCT
1 TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
183020 TTTTGAACTA
Statistics
Matches: 155, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
101 26 0.17
102 126 0.81
103 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (102 bp):
TTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTT
GAAACATAAACATCGAAAACATTTCCCTTGAAATGAA
Found at i:183431 original size:106 final size:106
Alignment explanation
Indices: 183303--183946 Score: 915
Period size: 106 Copynumber: 6.1 Consensus size: 106
183293 ATATCGTGCC
* *
183303 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
183368 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
183409 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
183474 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
183515 ACTCCAGACAACGCAAGTTCAACTGCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * **
183580 AATTTCGGATCCAATTTCAACTTCACGGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
183621 ACTCGAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCACTGGCTG-------ACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
183679 AATTTCAGATCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
183720 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
183785 AATTTCGGATCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * * * *
183826 ACTCGAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGTTGGCTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
183891 AATTTCAGAGCCAATTTCAACTTCACAGCGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
183932 CCTCAAAACAACGCA
1 ACTCCAGACAACGCA
183947 GCTTGCATTT
Statistics
Matches: 482, Mismatches: 49, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
99 88 0.18
106 394 0.82
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:183761 original size:205 final size:206
Alignment explanation
Indices: 183303--183946 Score: 957
Period size: 205 Copynumber: 3.1 Consensus size: 206
183293 ATATCGTGCC
* *
183303 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * * * * *
183368 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCGGATCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAGCACAAGTTCAACT
* * *
183433 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
131 TCACAACGAAGGGGCCGCTGGCTG------AACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
183498 ACAACGAAGGATATTGG
190 ACAACGAAGGATATTGG
* * *
183515 ACTCCAGACAACGCAAGTTCAACTGCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
183580 AATTTCGGATCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAGACAGCACAAGTTCAACT
66 AATTTCGGATCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAGCACAAGTTCAACT
* * *
183645 TCACAACGAAGGGGCCACTGGCTG-ACAACTTCCCAATTTCAGATCCAATTTCAACTTCACAACG
131 TCACAACGAAGGGGCCGCTGGCTGAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
183709 AAGGATATTGG
196 AAGGATATTGG
*
183720 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
183785 AATTTCGGATCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAGCACAAGTTCAACT
66 AATTTCGGATCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAGCACAAGTTCAACT
*
183850 TCACAACGAAGGGGCCGTTGGCTGTCAACAAATAACTTCTCAATTTCAGAGCCAATTTCAACTTC
131 TCACAACGAAGGGGCCGCTGGCTG--AAC----AACTTCTCAATTTCAGAGCCAATTTCAACTTC
* *
183915 ACAGCGGAGGATATTGG
190 ACAACGAAGGATATTGG
* *
183932 CCTCAAAACAACGCA
1 ACTCAAGACAACGCA
183947 GCTTGCATTT
Statistics
Matches: 395, Mismatches: 30, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
205 198 0.50
208 2 0.01
212 195 0.49
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (206 bp):
ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCGGATCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAGCACAAGTTCAACT
TCACAACGAAGGGGCCGCTGGCTGAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGG
Found at i:183928 original size:311 final size:311
Alignment explanation
Indices: 183358--183931 Score: 941
Period size: 311 Copynumber: 1.8 Consensus size: 311
183348 TTGTCAACAA
*
183358 ACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
1 ACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
*
183423 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAA
* *
183488 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTGCACGACGAAGGGA
131 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTGCACAACGAAGGGA
* * * * * *
183553 CCGCTGGTTGTCAATAAACAATTTCCCAATTTCGGATCCAATTTCAACTTCACGGCGAAGGATAT
196 CCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
183618 TGGACTCGAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCACTGGCTG
261 TGGACTCGAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCACTGGCTG
*
183669 ACAACTTCCCAATTTCAGATCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
1 ACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
* * *
183734 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGATCCAA
66 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAA
* * * * *
183799 TTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAGCACAAGTTCAACTTCACAACGAAGGGG
131 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTGCACAACGAAGGGA
* * * *
183864 CCGTTGGCTGTCAACAAATAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCGGAGGATAT
196 CCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
183929 TGG
261 TGG
183932 CCTCAAAACA
Statistics
Matches: 240, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
311 240 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.23
Consensus pattern (311 bp):
ACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAA
TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTGCACAACGAAGGGA
CCGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATAT
TGGACTCGAGACAGCACAAGTTCAACTTCACAACGAAGGGGCCACTGGCTG
Found at i:188462 original size:32 final size:32
Alignment explanation
Indices: 188425--188493 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
188415 ATTTAATTAT
*
188425 TGATGTGACATAA-ATCATGTTATCATCTTAGG
1 TGATGTGACA-AATATCACGTTATCATCTTAGG
* *
188457 TGATGTGACAAATATCACGTTATCATTTTGGG
1 TGATGTGACAAATATCACGTTATCATCTTAGG
188489 TGATG
1 TGATG
188494 CGTTAACCGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 2 0.06
32 31 0.94
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.38
Consensus pattern (32 bp):
TGATGTGACAAATATCACGTTATCATCTTAGG
Found at i:190373 original size:23 final size:23
Alignment explanation
Indices: 190347--190415 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
190337 CACCACAGCT
* *
190347 CGTATAATTGCACCGAAGTGTCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
190370 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
190393 TGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
190416 TATAATAATG
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:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:191087 original size:21 final size:21
Alignment explanation
Indices: 191063--191105 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
191053 TCATATTCGT
* *
191063 TTGAGGGGGAATCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
* *
191084 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
191105 T
1 T
191106 AGCCCATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGAACCGATTCCCC
Done.