Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008522.1 Hibiscus syriacus cultivar Beakdansim tig00111390_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: 1416293
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:155961 original size:42 final size:40
Alignment explanation
Indices: 155908--155991 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 40
155898 AATGCAAACA
*
155908 AACTTGGACTATCGCAA-CGAATTTGGAATAAATCGCAATGCG
1 AACTTGGACTATCGCAAGCGAATAT-G--TAAATCGCAATGCG
155950 AACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCG
1 AACTTGGACTATCGCAA-GCGAATATGTAAATCGCAATGCG
155991 A
1 A
155992 TAGTCGAAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
41 15 0.38
42 17 0.44
43 1 0.03
44 6 0.15
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (40 bp):
AACTTGGACTATCGCAAGCGAATATGTAAATCGCAATGCG
Found at i:155963 original size:21 final size:21
Alignment explanation
Indices: 155908--155972 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
155898 AATGCAAACA
155908 AACTTGGACTATCGCAA--CG
1 AACTTGGACTATCGCAATGCG
* *
155927 AATTTGGAATAAATCGCAATGCG
1 AACTTGGACT--ATCGCAATGCG
155950 AACTTGGACTATCGCAATGCG
1 AACTTGGACTATCGCAATGCG
155971 AA
1 AA
155973 TATGTAAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
19 8 0.21
21 20 0.53
23 10 0.26
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (21 bp):
AACTTGGACTATCGCAATGCG
Found at i:155985 original size:20 final size:20
Alignment explanation
Indices: 155936--155991 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
155926 GAATTTGGAA
155936 TAAATCGCAATGCGAACTTG
1 TAAATCGCAATGCGAACTTG
* *
155956 GACTATCGCAATGCGAA-TATG
1 TA-AATCGCAATGCGAACT-TG
155977 TAAATCGCAATGCGA
1 TAAATCGCAATGCGA
155992 TAGTCGAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (20 bp):
TAAATCGCAATGCGAACTTG
Found at i:170856 original size:11 final size:11
Alignment explanation
Indices: 170840--170865 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
170830 AATGTTTGAA
170840 ATATTTTTTTG
1 ATATTTTTTTG
170851 ATATTTTTTTG
1 ATATTTTTTTG
170862 ATAT
1 ATAT
170866 AATACTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (11 bp):
ATATTTTTTTG
Found at i:172668 original size:83 final size:83
Alignment explanation
Indices: 172573--172740 Score: 327
Period size: 83 Copynumber: 2.0 Consensus size: 83
172563 TTTTTGGTGA
172573 TTGGTGAATGATTCAAAAATTTTGAAATCTGAAGGAAATTGGTGTTGGAGATAAGGACGAGTGCA
1 TTGGTGAATGATTCAAAAATTTTGAAATCTGAAGGAAATTGGTGTTGGAGATAAGGACGAGTGCA
172638 TAATTAGGGGACAAATTT
66 TAATTAGGGGACAAATTT
*
172656 TTGGTGAATGATTCAAAAATTTTGAAATCTGAAGGAAATTGGTGTTGGAGATAGGGACGAGTGCA
1 TTGGTGAATGATTCAAAAATTTTGAAATCTGAAGGAAATTGGTGTTGGAGATAAGGACGAGTGCA
172721 TAATTAGGGGACAAATTT
66 TAATTAGGGGACAAATTT
172739 TT
1 TT
172741 AAAATTTTAA
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (83 bp):
TTGGTGAATGATTCAAAAATTTTGAAATCTGAAGGAAATTGGTGTTGGAGATAAGGACGAGTGCA
TAATTAGGGGACAAATTT
Found at i:174000 original size:20 final size:19
Alignment explanation
Indices: 173963--174023 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
173953 GTATCGATCC
*
173963 AAAACGAT-ATACCAGGTAA
1 AAAACGATAAAACC-GGTAA
* * *
173982 AAATATGATAAAATCGGTATC
1 AAA-ACGATAAAACCGGTA-A
174003 AAAACGATAAAACCGGTAA
1 AAAACGATAAAACCGGTAA
174022 AA
1 AA
174024 GGTTACCAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
19 5 0.16
20 21 0.66
21 6 0.19
ACGTcount: A:0.54, C:0.13, G:0.15, T:0.18
Consensus pattern (19 bp):
AAAACGATAAAACCGGTAA
Found at i:174111 original size:181 final size:182
Alignment explanation
Indices: 173765--174237 Score: 682
Period size: 181 Copynumber: 2.6 Consensus size: 182
173755 GATCCAAATT
* * *
173765 AAAAATGTGTCGATCCAAAACGATATAACATGTAAAACTATGACAAAACCGGTAT-AGAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACATGTAAAAATATGATAAAACCGGTATCA-AAATGAT
* * * * *
173829 AAAACCGGT-AAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACT
65 AAAACCGGTAAAAG-GATACCGGATATATTAAAAGTGTCGATACTTTAATATAAAGATCGACACT
* * *
173893 TCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
129 TCGTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* * * *
173947 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAATCGGTATCAAAACGATA
1 AAAAATGTATCGATCCAAAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
174012 AAACCGGTAAAAGGTTACCAGATATATTAAAAGTGTCGATACTTT-ATATAAAGATCGACACTTT
66 AAACCGGTAAAAGGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAAGATCGACACTTC
** *
174076 GTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* *
174128 AAAAATATATCGATCCACAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
174193 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAAGGATACCGGATATATTAAAAGTGTCGATACTTT
174238 CGTAAGTACG
Statistics
Matches: 259, Mismatches: 30, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
181 163 0.63
182 91 0.35
183 5 0.02
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACATGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAAGGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAAGATCGACACTTC
GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:174206 original size:17 final size:19
Alignment explanation
Indices: 174167--174209 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
174157 ATGTAAAAAT
174167 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
174187 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
174204 ATGATA
1 ATGATA
174210 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:176450 original size:21 final size:21
Alignment explanation
Indices: 176426--176469 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
176416 AAGACAATCA
176426 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
176447 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
176468 AG
1 AG
176470 GCATAAGGGG
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:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:178409 original size:19 final size:19
Alignment explanation
Indices: 178361--178409 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
178351 AATGTAGGGT
*
178361 TAATTTTGTAAAAGATTTA
1 TAATTTTGTATAAGATTTA
*
178380 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
*
178399 TATTTTTGTAT
1 TAATTTTGTAT
178410 GTGAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:179486 original size:199 final size:200
Alignment explanation
Indices: 178544--179680 Score: 2100
Period size: 200 Copynumber: 5.7 Consensus size: 200
178534 GTGCAACCAT
*
178544 AAAGTGTCGATCCCAAAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* *
178609 CCGGTACAAGTATATCGGTTTTATGAGAGAATATGTCTATATAATGTGTCGACACTTTTTTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
*
178674 TGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTACAACCATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATA
178739 TATAA
196 TATAA
178744 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
178809 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
178874 TGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATA
178939 TATAA
196 TATAA
178944 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* * *
179009 CCGGTACAAGTATACCAGTTTTATGATAGAATATGTCTAAATAAGGTGTCGACACTTTTTTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
179074 TGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATA
179139 TATAA
196 TATAA
179144 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
179209 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
* *
179274 TGTGTCAATATTTTTGTTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATA
179339 TATAA
196 TATAA
* *
179344 AAAGTGTCGATCCCAAAAATATCG-AACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* * *
179408 CCGGTACAAGTATACCGATTTTATGAGAAAATATGTCTAAATAATATGTCGACACTTTTTTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
*
179473 TGTGTCGATATTTTTGTTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATA
179538 TATAA
196 TATAA
* *
179543 AAAGTGTCGATCCCAAAAACATCG-AACCCAAAAGTATAATGTAATATGTAATTTTTCAATTTAA
1 AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
179607 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACAC-TTTTTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
179671 TGTGTCGATA
131 TGTGTCGATA
179681 CTAATTTAAA
Statistics
Matches: 914, Mismatches: 23, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
198 19 0.02
199 284 0.31
200 611 0.67
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (200 bp):
AAAGTGTCGATCCCAAAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
CCGGTACAAGTATACCGGTTTTATGAGAGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTT
TGTGTCGATATTTTTGGTCCAGAATGAATGGAAAACAGGGTGCAACCATAAAGTGTCGATCCATA
TATAA
Found at i:181155 original size:6 final size:6
Alignment explanation
Indices: 181144--181237 Score: 89
Period size: 6 Copynumber: 15.7 Consensus size: 6
181134 CAAGCGGTCA
* * * * *
181144 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGATG ATGACG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * * * *
181192 ATGACG ATGAAG ATGATG ACGATG ATGATG ATGATG ATGAAG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
181238 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.21
Consensus pattern (6 bp):
ATGAAG
Found at i:181241 original size:12 final size:12
Alignment explanation
Indices: 181144--181237 Score: 107
Period size: 12 Copynumber: 7.8 Consensus size: 12
181134 CAAGCGGTCA
*
181144 ATGAAGATGAAG
1 ATGACGATGAAG
*
181156 CTGACGATGAAG
1 ATGACGATGAAG
*
181168 ATGACGATGATG
1 ATGACGATGAAG
181180 ATGACGATGAAG
1 ATGACGATGAAG
181192 ATGACGATGAAG
1 ATGACGATGAAG
* * *
181204 ATGATGACGATG
1 ATGACGATGAAG
* *
181216 ATGATGATGATG
1 ATGACGATGAAG
*
181228 ATGAAGATGA
1 ATGACGATGA
181238 TGATCCAAAC
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 72 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.21
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:181241 original size:15 final size:15
Alignment explanation
Indices: 181161--181241 Score: 90
Period size: 15 Copynumber: 5.4 Consensus size: 15
181151 TGAAGCTGAC
* *
181161 GATGAAGATGACGAT
1 GATGATGATGAAGAT
* * *
181176 GATGATGACGATGAA
1 GATGATGATGAAGAT
*
181191 GATGACGATGAAGAT
1 GATGATGATGAAGAT
* *
181206 GATGACGATGATGAT
1 GATGATGATGAAGAT
181221 GATGATGATGAAGAT
1 GATGATGATGAAGAT
181236 GATGAT
1 GATGAT
181242 CCAAACAAGT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 55 1.00
ACGTcount: A:0.38, C:0.05, G:0.33, T:0.23
Consensus pattern (15 bp):
GATGATGATGAAGAT
Found at i:181241 original size:18 final size:18
Alignment explanation
Indices: 181144--181237 Score: 98
Period size: 18 Copynumber: 5.2 Consensus size: 18
181134 CAAGCGGTCA
*
181144 ATGAAGATGAAGCTGACG
1 ATGAAGATGAAGATGACG
* *
181162 ATGAAGATGACGATGATG
1 ATGAAGATGAAGATGACG
*
181180 ATGACGATGAAGATGACG
1 ATGAAGATGAAGATGACG
* * *
181198 ATGAAGATGATGACGATG
1 ATGAAGATGAAGATGACG
* * *
181216 ATGATGATGATGATGAAG
1 ATGAAGATGAAGATGACG
181234 ATGA
1 ATGA
181238 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.39, C:0.06, G:0.33, T:0.21
Consensus pattern (18 bp):
ATGAAGATGAAGATGACG
Found at i:182467 original size:16 final size:16
Alignment explanation
Indices: 182435--182468 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
182425 TATCCACAAC
* *
182435 AAAGTGTCGATTTAAA
1 AAAGTGTCGACTGAAA
182451 AAAGTGTCGACTGAAA
1 AAAGTGTCGACTGAAA
182467 AA
1 AA
182469 TGTAATAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.24
Consensus pattern (16 bp):
AAAGTGTCGACTGAAA
Found at i:182861 original size:23 final size:23
Alignment explanation
Indices: 182830--182902 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
182820 ATAGGTAAAA
*
182830 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
182853 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
182876 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
182899 ATAT
1 ATAT
182903 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:183561 original size:183 final size:183
Alignment explanation
Indices: 183281--183773 Score: 898
Period size: 183 Copynumber: 2.7 Consensus size: 183
183271 GCAATGCTAT
* *
183281 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
* *
183346 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTGTCAAAAAGTGTCGTC
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATT-TAAAAAAGTGTCGAC
*
183410 ATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
130 ATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
183464 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
*
183529 GTGTCGGTACTTTATGTCCAGATTGAAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
* *
183594 TTTACACATCGGAACTCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
131 TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
183647 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
183712 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
183774 GTAATTTTAA
Statistics
Matches: 300, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
183 296 0.99
184 4 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (183 bp):
CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
Found at i:186224 original size:25 final size:24
Alignment explanation
Indices: 186190--186301 Score: 87
Period size: 25 Copynumber: 4.8 Consensus size: 24
186180 AAATTCGCAG
186190 TACATATATAGGTATGTACAATAAC
1 TACA-ATATAGGTATGTACAATAAC
186215 TACAAGTATA--TAT-TATC-AT---
1 TACAA-TATAGGTATGTA-CAATAAC
*
186234 TA-AATTTAGGTATGTACAATAAC
1 TACAATATAGGTATGTACAATAAC
*
186257 TACATATTTAGGTATGTACAATAAC
1 TACA-ATATAGGTATGTACAATAAC
* *
186282 TACATATTTAGGTATATACA
1 TACA-ATATAGGTATGTACA
186302 TCTTTTGAGT
Statistics
Matches: 74, Mismatches: 2, Indels: 22
0.76 0.02 0.22
Matches are distributed among these distances:
17 3 0.04
18 2 0.03
19 6 0.08
20 4 0.05
22 4 0.05
23 6 0.08
24 2 0.03
25 47 0.64
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (24 bp):
TACAATATAGGTATGTACAATAAC
Found at i:186677 original size:23 final size:23
Alignment explanation
Indices: 186646--186718 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
186636 ATAGGTAAAA
*
186646 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
186669 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
186692 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
186715 ATAT
1 ATAT
186719 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:187107 original size:23 final size:23
Alignment explanation
Indices: 187076--187148 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
187066 ATAGGTAAAA
*
187076 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
187099 ATATAATGTAATAAGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
187122 ATTTAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
187145 ATAT
1 ATAT
187149 TGTAAAGTAT
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:187240 original size:430 final size:430
Alignment explanation
Indices: 186442--188170 Score: 3194
Period size: 430 Copynumber: 4.0 Consensus size: 430
186432 TTGGTTAATG
*
186442 TTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTG-
1 TTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGC
* *
186506 TAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTT--AAAAAATTGAAAC
66 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAAC
*
186569 ATAAATTACATAACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATA
131 ATAAATTACATAAC-TTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATA
*
186634 TAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAAT
195 TAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAAGTATCGTTTATATAAT
186699 GTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCA
260 GTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCA
*
186764 CCGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTAT
325 CTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTAT
186829 AGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTA
390 AGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTA
186870 TTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGC
1 TTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGC
186935 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAAC
66 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAAC
*
187000 ATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGAACACTTTCAATAT
131 ATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATAT
*
187065 AATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAAGTATCGTTTATTTAATG
196 AATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAAGTATCGTTTATATAATG
* * *
187130 TAATAGGTAGTGGTTATATTGTAAAGTATATATCTTTTTTATAAAAGTGTCTATACTTTTTTCAG
261 TAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCAC
187195 TGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATA
326 TGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATA
187260 GGCGTCTAATGATTTATTTTTTACGTTACGATATATATTA
391 GGCGTCTAATGATTTATTTTTTACGTTACGATATATATTA
187300 TTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGC
1 TTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGC
187365 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAAC
66 AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAAC
187430 ATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATAT
131 ATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATAT
187495 AATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAAGTATCGTTTATATAATG
196 AATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAAGTATCGTTTATATAATG
*
187560 TAATAGGTAGTGGTTATATTGTAGAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCAC
261 TAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCAC
187625 TGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATA
326 TGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATA
187690 GGCGTCTAATGATTTATTTTTTACGTTACGATATATATTA
391 GGCGTCTAATGATTTATTTTTTACGTTACGATATATATTA
* *
187730 TTATTAAATTAAAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTG
1 TTGTTAAATT-TAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTG
*
187795 CAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTTAAAAAAATTGAAA
65 CAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAA
*
187860 CATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACAATTTCAATA
130 CATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATA
* * *
187925 TAATATGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAACGTTTATATAAT
195 TAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAAGTATCGTTTATATAAT
* * * *
187990 GTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATATTTTTTTCA
260 GTAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCA
*
188055 CTGTGGAAAACATTAATTTAAGGTTATATTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTAT
325 CTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTAT
188120 AGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTA
390 AGGCGTCTAATGATTTATTTTTTACGTTACGATATATATTA
*
188161 TTATTAAATT
1 TTGTTAAATT
188171 AAAAACAATA
Statistics
Matches: 1267, Mismatches: 30, Indels: 5
0.97 0.02 0.00
Matches are distributed among these distances:
428 63 0.05
429 48 0.04
430 711 0.56
431 445 0.35
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (430 bp):
TTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGC
AAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAAC
ATAAATTACATAACTTTAAAAGAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATAT
AATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAAGTATCGTTTATATAATG
TAATAGGTAGTGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCAC
TGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATA
GGCGTCTAATGATTTATTTTTTACGTTACGATATATATTA
Found at i:187537 original size:23 final size:23
Alignment explanation
Indices: 187506--187578 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
187496 ATAGGTAAAA
*
187506 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* * *
187529 ATATAATGTAATAAGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
187552 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
187575 ATAT
1 ATAT
187579 TGTAGAGTAT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:187968 original size:23 final size:23
Alignment explanation
Indices: 187937--188009 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
187927 ATATGTAAAA
*
187937 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
187960 ATATAATGTAATAGGTAACGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
187983 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
188006 ATAT
1 ATAT
188010 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:189151 original size:17 final size:17
Alignment explanation
Indices: 189125--189164 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
189115 GCCCTTTCAC
*
189125 TCCCTCTCTCTTCCACT
1 TCCCTTTCTCTTCCACT
189142 TCCCTTTCTCTTCCACT
1 TCCCTTTCTCTTCCACT
189159 TCCCTT
1 TCCCTT
189165 AAAAGCTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.05, C:0.50, G:0.00, T:0.45
Consensus pattern (17 bp):
TCCCTTTCTCTTCCACT
Found at i:193558 original size:53 final size:53
Alignment explanation
Indices: 193468--193775 Score: 375
Period size: 53 Copynumber: 5.8 Consensus size: 53
193458 TGACGGGTCT
* ****
193468 GCTCCCTCTTG-TTCAGGGATTAAGGAACTCGAACAATCTTCTAAAAATGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGT-A-GAACTCGAACAATCTTCTGCCTATGGGTTC
* ** **
193522 GCTCCCTATTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGTTTACAGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTATGGGTTC
* * * * * *
193575 GTTACCTCTTGCTTCAGGGAGTAGAACTCGAAGAATCTTCTTCTTATGGGTTT
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTATGGGTTC
* *
193628 GCTCCCTTTTGCTTCAGGGAGTAAAACTCGAACAATCTTCTGCCTATGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTATGGGTTC
* *
193681 TCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTTC
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTATGGGTTC
** * *
193734 AATCCCTCTTACTTCAAGGAGTAGAACTCGAACAATCTTCTG
1 GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTG
193776 GTGTGATTCT
Statistics
Matches: 220, Mismatches: 33, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
53 200 0.91
54 11 0.05
55 9 0.04
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (53 bp):
GCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTATGGGTTC
Found at i:194216 original size:42 final size:42
Alignment explanation
Indices: 194148--194520 Score: 217
Period size: 42 Copynumber: 9.1 Consensus size: 42
194138 TCCGAGAAGG
*
194148 CTTA-AAATGACCCGGAGGACTT-ATCATC-TCGCTCGAAAGA
1 CTTACAAATGACCCGAAGGACTTCATCATCAT-GCTCGAAAGA
* *
194188 CTTACAAATTACCCGAAGGATTTCATCATCATGCTCGAAAGA
1 CTTACAAATGACCCGAAGGACTTCATCATCATGCTCGAAAGA
* * * * *
194230 CTTAC---TGA--TGAATTTG-CTTCA-CTACTCTTCGGT-G-AAGG
1 CTTACAAATGACCCGAA--GGACTTCATC-A-TCAT-GCTCGAAAGA
* * *
194268 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGA
1 CTTACAAATGACCCGAAGGACTTCATCATCATGCTCGAAAGA
** *
194310 CTTACTCATGGCCCGAAGGACTTCATCATCATGCTCGAAAGA
1 CTTACAAATGACCCGAAGGACTTCATCATCATGCTCGAAAGA
** * *
194352 CTTACTGATGGCCCGAAGGACTTCATCATCATGCTCAAAAGA
1 CTTACAAATGACCCGAAGGACTTCATCATCATGCTCGAAAGA
* * *** * * * *
194394 CTTACTAATG---GGTTTG-CTCCA-CTACTC-TTC-CGTGAAGG
1 CTTACAAATGACCCGAAGGACTTCATC-A-TCATGCTCG-AAAGA
** * * *
194432 CTTACAAATTTCTCGAAGGATTTAATCATCATGCTCGAAAGA
1 CTTACAAATGACCCGAAGGACTTCATCATCATGCTCGAAAGA
** *
194474 CTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGA
1 CTTACAAATGACCCGAAGGACTTCATCATCATGCTCGAAAGA
194516 CTTAC
1 CTTAC
194521 TGATGGCACT
Statistics
Matches: 251, Mismatches: 55, Indels: 52
0.70 0.15 0.15
Matches are distributed among these distances:
37 6 0.02
38 31 0.12
39 11 0.04
40 8 0.03
41 26 0.10
42 161 0.64
43 8 0.03
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (42 bp):
CTTACAAATGACCCGAAGGACTTCATCATCATGCTCGAAAGA
Found at i:194331 original size:20 final size:20
Alignment explanation
Indices: 194303--194374 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
194293 TCATCATGCT
194303 CGAAAGACTTACTCATGGCC
1 CGAAAGACTTACTCATGGCC
* *
194323 CGAAGGACTTCATCATCAT-GCT
1 CGAAAGACTT-A-C-TCATGGCC
*
194345 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTCATGGCC
*
194365 CGAAGGACTT
1 CGAAAGACTT
194375 CATCATCATG
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 3 0.07
20 21 0.50
21 2 0.05
22 12 0.29
23 4 0.10
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (20 bp):
CGAAAGACTTACTCATGGCC
Found at i:194337 original size:122 final size:120
Alignment explanation
Indices: 194133--194361 Score: 334
Period size: 122 Copynumber: 1.9 Consensus size: 120
194123 TTGCTCCAAC
* *
194133 ACTCTTCCGAGAAGGCTTAAAATGACCCGGAGGACTTATCATCTCGCTCGAAAGACTTACAAATT
1 ACTCTTCCGAGAAGGCTTAAAATGACCCGAAGGACTTATCATCTCGCTCGAAAGACTTACAAATG
*
194198 ACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACT
66 ACCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACT
* * * * **
194253 ACTCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCAT-GCTCGAAAGACTTACTC
1 ACTCTTCCGAGAAGGCTTA-AAATGACCCGAAGGACTT-ATCATC-TCGCTCGAAAGACTTACAA
*
194317 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATG
63 ATGACCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATG
194362 GCCCGAAGGA
Statistics
Matches: 96, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
120 17 0.18
121 15 0.16
122 63 0.66
123 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (120 bp):
ACTCTTCCGAGAAGGCTTAAAATGACCCGAAGGACTTATCATCTCGCTCGAAAGACTTACAAATG
ACCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACT
Found at i:194436 original size:122 final size:122
Alignment explanation
Indices: 194321--194654 Score: 434
Period size: 135 Copynumber: 2.6 Consensus size: 122
194311 TTACTCATGG
* *
194321 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGC
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGC
*
194386 TCAAAAGACTTACTAATGGGTTTGCTCCACTACTCTTCCGTGAAGGCTTACAAATTT
66 TCAAAAGACTTACTAATGGGTTTGCTCCACTACTCTTCCGTGAAGGCTTACAAATTA
*
194443 CTCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGC
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGC
* * *
194508 TCGAAAGACTTACTGATGGCACTTACTAATGGGTTTGCTTCACTGCTCTTCTGTGAAGGCTTACA
66 TC---A-A---A---A--G-ACTTACTAATGGGTTTGCTCCACTACTCTTCCGTGAAGGCTTACA
194573 AATTA
118 AATTA
* * * * *
194578 CCCTAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTAAGCATCATGC
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGC
*
194643 TCGAAAGACTTA
66 TCAAAAGACTTA
194655 TTGATGGCCC
Statistics
Matches: 185, Mismatches: 14, Indels: 26
0.82 0.06 0.12
Matches are distributed among these distances:
122 69 0.37
123 1 0.01
125 2 0.01
126 1 0.01
128 1 0.01
129 1 0.01
131 1 0.01
132 1 0.01
134 1 0.01
135 107 0.58
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (122 bp):
CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGC
TCAAAAGACTTACTAATGGGTTTGCTCCACTACTCTTCCGTGAAGGCTTACAAATTA
Found at i:194451 original size:164 final size:164
Alignment explanation
Indices: 194158--194527 Score: 582
Period size: 164 Copynumber: 2.3 Consensus size: 164
194148 CTTAAAATGA
* ** ** *
194158 CCCGGAGGACTT-ATCATC-TCGCTCGAAAGACTTACAAATTACCCGAAGGATTTCATCATCATG
1 CCCGAAGGACTTCATCATCAT-GCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATG
* * * *
194221 CTCGAAAGACTTACTGATGAATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCGAAG
65 CTCAAAAGACTTACTAATGAATTTGCTCCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAG
194286 GATTTAATCATCATGCTCGAAAGACTTACTCATGG
130 GATTTAATCATCATGCTCGAAAGACTTACTCATGG
194321 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGC
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGC
** * *
194386 TCAAAAGACTTACTAATGGGTTTGCTCCACTACTCTTCCGTGAAGGCTTACAAATTTCTCGAAGG
66 TCAAAAGACTTACTAATGAATTTGCTCCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAGG
*
194451 ATTTAATCATCATGCTCGAAAGACTTACTGATGG
131 ATTTAATCATCATGCTCGAAAGACTTACTCATGG
194485 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGC
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGC
194528 ACTTACTAAT
Statistics
Matches: 190, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
163 11 0.06
164 178 0.94
165 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (164 bp):
CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGC
TCAAAAGACTTACTAATGAATTTGCTCCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAGG
ATTTAATCATCATGCTCGAAAGACTTACTCATGG
Found at i:194466 original size:80 final size:80
Alignment explanation
Indices: 194188--194484 Score: 312
Period size: 80 Copynumber: 3.7 Consensus size: 80
194178 GCTCGAAAGA
* **
194188 CTTACAAATTACCCGAAGGATTTCATCATCATGCTCGAAAGACTTACTGATGAATTTGCTTCACT
1 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGGTTTGCTTCACT
*
194253 ACTCTTCGGTGAAGG
66 ACTCTTCCGTGAAGG
* ***
194268 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTCATGGCCCGAAGGACTT
1 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG---GTTTG-CTT
* * *
194333 CA-T-CATCATGCTCG-AAAGA
62 CACTAC-TC-TTC-CGTGAAGG
** ** * * * * *
194352 CTTACTGATGGCCCGAAGGACTTCATCATCATGCTCAAAAGACTTACTAATGGGTTTGCTCCACT
1 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGGTTTGCTTCACT
194417 ACTCTTCCGTGAAGG
66 ACTCTTCCGTGAAGG
* *
194432 CTTACAAATTTCTCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
194485 CCCGAAGGAC
Statistics
Matches: 172, Mismatches: 35, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
79 2 0.01
80 103 0.60
81 5 0.03
82 2 0.01
83 4 0.02
84 55 0.32
85 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (80 bp):
CTTACAAATTACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGGTTTGCTTCACT
ACTCTTCCGTGAAGG
Found at i:194469 original size:22 final size:21
Alignment explanation
Indices: 194443--194519 Score: 68
Period size: 22 Copynumber: 3.6 Consensus size: 21
194433 TTACAAATTT
*
194443 CTCGAAGGATTTAATCATCATG
1 CTCGAAGGACTT-ATCATCATG
* *
194465 CTCGAAAGACTTA-C-TGATGG
1 CTCGAAGGACTTATCATCAT-G
*
194485 CCCGAAGGACTTCATCATCATG
1 CTCGAAGGACTT-ATCATCATG
*
194507 CTCGAAAGACTTA
1 CTCGAAGGACTTA
194520 CTGATGGCAC
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
19 3 0.07
20 12 0.28
21 3 0.07
22 22 0.51
23 3 0.07
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (21 bp):
CTCGAAGGACTTATCATCATG
Found at i:194495 original size:20 final size:20
Alignment explanation
Indices: 194467--194527 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
194457 TCATCATGCT
194467 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
* * *
194487 CGAAGGACTTCATCATCAT-GCT
1 CGAAAGACTT-A-C-TGATGGCC
194509 CGAAAGACTTACTGATGGC
1 CGAAAGACTTACTGATGGC
194528 ACTTACTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
19 3 0.09
20 12 0.38
21 2 0.06
22 12 0.38
23 3 0.09
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (20 bp):
CGAAAGACTTACTGATGGCC
Found at i:194521 original size:42 final size:42
Alignment explanation
Indices: 194279--194673 Score: 268
Period size: 42 Copynumber: 9.3 Consensus size: 42
194269 TTACAAATTA
* * *
194279 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTCATGG
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
194321 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
* *
194363 CCCGAAGGACTTCATCATCATGCTCAAAAGACTTACTAATGG
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
*** * * * * ** **
194405 ---GTTTG-CTCCA-CTACTC-TTC-CGTGAAGGCTTACAAATTT
1 CCCGAAGGACTTCATC-A-TCATGCTCG-AAAGACTTACTGATGG
* * *
194443 CTCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
194485 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
* ** * * * ** **
194527 CACTTACTAATGGGTTTGCTTCA-C-TGCTCTTCTGTGAAGGCTTACAAATTA
1 C-C---CGAA-GGACTT-CATCATCATG--C-TC-G-AAAGACTTACTGATGG
* * *
194578 CCCTAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
* * * * *
194620 CCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
1 CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
194662 CCCGAAGGACTT
1 CCCGAAGGACTT
194674 ACTAAGTGCG
Statistics
Matches: 275, Mismatches: 55, Indels: 46
0.73 0.15 0.12
Matches are distributed among these distances:
37 2 0.01
38 18 0.07
39 4 0.01
41 4 0.01
42 194 0.71
43 5 0.02
44 2 0.01
45 4 0.01
46 11 0.04
47 11 0.04
48 5 0.02
49 2 0.01
50 2 0.01
51 11 0.04
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (42 bp):
CCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
Found at i:194639 original size:135 final size:135
Alignment explanation
Indices: 194393--194662 Score: 441
Period size: 135 Copynumber: 2.0 Consensus size: 135
194383 TGCTCAAAAG
* *
194393 ACTTACTAATGGGTTTGCTCCACTACTCTTCCGTGAAGGCTTACAAATTTCTCGAAGGATTTAAT
1 ACTTACTAATGGGTTTGCTCCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
* *
194458 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
66 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACTG
194523 ATGGC
131 ATGGC
* * * *
194528 ACTTACTAATGGGTTTGCTTCACTGCTCTTCTGTGAAGGCTTACAAATTACCCTAAGGATTTAAT
1 ACTTACTAATGGGTTTGCTCCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
* * *
194593 CATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTG
66 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACTG
194658 ATGGC
131 ATGGC
194663 CCGAAGGACT
Statistics
Matches: 124, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
135 124 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (135 bp):
ACTTACTAATGGGTTTGCTCCACTACTCTTCCGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAAGCATCATGCTCGAAAGACTTACTG
ATGGC
Found at i:205331 original size:12 final size:12
Alignment explanation
Indices: 205316--205357 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
205306 TTATTTAAAT
205316 GGGTATTGGGCC
1 GGGTATTGGGCC
205328 GGGTATTGGGCC
1 GGGTATTGGGCC
* *
205340 GGGAATCGGGCC
1 GGGTATTGGGCC
205352 GGGTAT
1 GGGTAT
205358 ATATATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.12, C:0.17, G:0.50, T:0.21
Consensus pattern (12 bp):
GGGTATTGGGCC
Found at i:205415 original size:24 final size:25
Alignment explanation
Indices: 205355--205467 Score: 74
Period size: 28 Copynumber: 4.5 Consensus size: 25
205345 TCGGGCCGGG
205355 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
205378 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
* * *
205402 T-T-TATTAATATTATATATATATATA
1 TATATATT-ATATTATTTAAAT-TAAA
* * *
205427 TATATATATATATATATATATATATATA
1 TATATAT-TATAT-TATTTAAAT-TAAA
205455 TATATATATATAT
1 TATATAT-TATAT
205468 ATATATATAT
Statistics
Matches: 76, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
22 4 0.05
23 8 0.11
24 24 0.32
25 4 0.05
26 1 0.01
27 7 0.09
28 28 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:205420 original size:2 final size:2
Alignment explanation
Indices: 205409--205486 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
205399 AAATTTATTA
205409 AT AT -T 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
205450 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
205487 ATTATTTTTA
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:206008 original size:20 final size:20
Alignment explanation
Indices: 205983--206021 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
205973 CTTTCTTGAA
**
205983 ATTTAAATTTTAAAAAATTT
1 ATTTAAATAATAAAAAATTT
206003 ATTTAAATAATAAAAAATT
1 ATTTAAATAATAAAAAATT
206022 AAAATATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTAAATAATAAAAAATTT
Found at i:206171 original size:8 final size:8
Alignment explanation
Indices: 206160--206185 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
206150 CCGGTGAAGG
206160 CACTGGTT
1 CACTGGTT
206168 CACTGGTT
1 CACTGGTT
206176 CACTGGTT
1 CACTGGTT
206184 CA
1 CA
206186 ACAGGATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.27, G:0.23, T:0.35
Consensus pattern (8 bp):
CACTGGTT
Found at i:207041 original size:20 final size:20
Alignment explanation
Indices: 207016--207053 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
207006 TCGATTCACC
*
207016 CCGGTTTTACCGGTTTTCAG
1 CCGGTTTTACCGATTTTCAG
207036 CCGGTTTTACCGATTTTC
1 CCGGTTTTACCGATTTTC
207054 TCATTGTCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.26, G:0.21, T:0.42
Consensus pattern (20 bp):
CCGGTTTTACCGATTTTCAG
Found at i:207386 original size:12 final size:14
Alignment explanation
Indices: 207359--207405 Score: 80
Period size: 14 Copynumber: 3.5 Consensus size: 14
207349 AATATATTAA
207359 TATATTAATAATTT
1 TATATTAATAATTT
207373 TATATT-AT-ATTT
1 TATATTAATAATTT
207385 TATATTAATAATTT
1 TATATTAATAATTT
207399 TATATTA
1 TATATTA
207406 CATTTTATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.32
13 4 0.13
14 17 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATATTAATAATTT
Found at i:207394 original size:26 final size:26
Alignment explanation
Indices: 207359--207416 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
207349 AATATATTAA
*
207359 TATATTAATAATTTTATATTATATTT
1 TATATTAATAATTTTATATTACATTT
207385 TATATTAATAATTTTATATTACATTT
1 TATATTAATAATTTTATATTACATTT
207411 TATATT
1 TATATT
207417 TTTATAATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TATATTAATAATTTTATATTACATTT
Found at i:207410 original size:12 final size:12
Alignment explanation
Indices: 207368--207416 Score: 62
Period size: 12 Copynumber: 3.9 Consensus size: 12
207358 ATATATTAAT
207368 AATTTTATATTA
1 AATTTTATATTA
*
207380 TATTTTATATTAA
1 AATTTTATATT-A
207393 TAATTTTATATTA
1 -AATTTTATATTA
*
207406 CATTTTATATT
1 AATTTTATATT
207417 TTTATAATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
12 20 0.62
13 2 0.06
14 10 0.31
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (12 bp):
AATTTTATATTA
Found at i:207555 original size:16 final size:15
Alignment explanation
Indices: 207532--207562 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
207522 TTATAAAAAA
207532 ATATTTTTAAATAAT
1 ATATTTTTAAATAAT
207547 ATATATTTTAAATAAT
1 ATAT-TTTTAAATAAT
207563 TTTAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATTTTTAAATAAT
Found at i:209047 original size:5 final size:5
Alignment explanation
Indices: 209024--209057 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
209014 TAAAAGATCT
209024 AATAA AATAA TAATGAA AATAA AATAA AATAA AA
1 AATAA AATAA -AAT-AA AATAA AATAA AATAA AA
209058 AGGAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 19 0.70
6 6 0.22
7 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:210313 original size:26 final size:25
Alignment explanation
Indices: 210263--210325 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 25
210253 GACTGAATTA
*
210263 AAATAAAATGAAATAAAACATATAAT
1 AAATAAAAT-AAATAAAAAATATAAT
210289 AAATAAAATAAA-AAAGAAATAATAAT
1 AAATAAAATAAATAAA-AAAT-ATAAT
210315 -AATAATAATAA
1 AAATAA-AATAA
210326 TATATTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 3 0.09
25 11 0.33
26 19 0.58
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (25 bp):
AAATAAAATAAATAAAAAATATAAT
Found at i:212711 original size:22 final size:22
Alignment explanation
Indices: 212659--212704 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
212649 TAGGTTCTGG
* *
212659 GGAGTAAGAAGAGATGCTAAGA
1 GGAGCAAGAAGAGATACTAAGA
212681 GGAGCAAGAAGAGATACTAAGA
1 GGAGCAAGAAGAGATACTAAGA
212703 GG
1 GG
212705 TACAAGACAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.46, C:0.07, G:0.37, T:0.11
Consensus pattern (22 bp):
GGAGCAAGAAGAGATACTAAGA
Found at i:217641 original size:2 final size:2
Alignment explanation
Indices: 217634--217778 Score: 272
Period size: 2 Copynumber: 72.5 Consensus size: 2
217624 TTTAAAACTT
217634 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
217676 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
* *
217718 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA AA 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
217760 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
217779 TTTCAAAGTG
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
2 141 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:217805 original size:36 final size:36
Alignment explanation
Indices: 217762--217934 Score: 202
Period size: 36 Copynumber: 4.7 Consensus size: 36
217752 TATATATATA
*
217762 TATATATATATATATATTTTCAAAGTGTTTTAAAAAAC
1 TATATAT-TATATATATTTTCAAAATGTTTT-AAAAAC
* * *
217800 AATATATTACATATATATTTCCAAAATGTTTTCAAAAC
1 TATATATT--ATATATATTTTCAAAATGTTTTAAAAAC
* * **
217838 TATCTAATATATATATTTTTGAAATGTTTTCAAAAAC
1 TATATATTATATATATTTTCAAAATGTTTT-AAAAAC
* *
217875 TATATATTATATATGTTTTCAAAATGTTTTCAAAAC
1 TATATATTATATATATTTTCAAAATGTTTTAAAAAC
*
217911 TATATATTATATATGTTTTCAAAA
1 TATATATTATATATATTTTCAAAA
217935 ACTATATATT
Statistics
Matches: 115, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
36 48 0.42
37 31 0.27
38 16 0.14
39 20 0.17
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (36 bp):
TATATATTATATATATTTTCAAAATGTTTTAAAAAC
Found at i:217887 original size:73 final size:69
Alignment explanation
Indices: 217766--217954 Score: 221
Period size: 75 Copynumber: 2.7 Consensus size: 69
217756 TATATATATA
* * *
217766 TATATATATATATTTTCAAAGTGTTTTAAAAAACAATATATTACATATATATTTCCAAAATGTTT
1 TATATATATATATTTTTAAA-TGTTTTCAAAAACTATATATT--ATATATATTTCCAAAATGTTT
217831 TCAAAAC
63 TCAAAAC
* *
217838 TATCTAATATATATATTTTTGAAATGTTTTCAAAAACTATATATTATATATGTTTTCAAAATGTT
1 TA--T-ATATATATATTTTT-AAATGTTTTCAAAAACTATATATTATATATATTTCCAAAATGTT
217903 TTCAAAAC
62 TTCAAAAC
217911 TATATAT-TATA----T--ATGTTTTCAAAAACTATATATTATATATATTT
1 TATATATATATATTTTTAAATGTTTTCAAAAACTATATATTATATATATTT
217955 TTGAAAACTG
Statistics
Matches: 107, Mismatches: 6, Indels: 18
0.82 0.05 0.14
Matches are distributed among these distances:
62 31 0.29
65 1 0.01
69 4 0.04
70 4 0.04
71 1 0.01
72 2 0.02
73 28 0.26
74 1 0.01
75 32 0.30
76 3 0.03
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (69 bp):
TATATATATATATTTTTAAATGTTTTCAAAAACTATATATTATATATATTTCCAAAATGTTTTCA
AAAC
Found at i:217951 original size:28 final size:26
Alignment explanation
Indices: 217898--217955 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
217888 TGTTTTCAAA
217898 ATGTTTTC-AAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATATTATAT
217923 ATGTTTTCAAAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATATTATAT
*
217949 ATATTTT
1 ATGTTTT
217956 TGAAAACTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 8 0.26
26 23 0.74
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (26 bp):
ATGTTTTCAAAAACTATATATTATAT
Found at i:217961 original size:26 final size:26
Alignment explanation
Indices: 217901--217968 Score: 91
Period size: 26 Copynumber: 2.6 Consensus size: 26
217891 TTTCAAAATG
* *
217901 TTTTCAAAACTATATATTATATATGT
1 TTTTAAAAACTATATATTATATATAT
*
217927 TTTCAAAAACTATATATTATATATAT
1 TTTTAAAAACTATATATTATATATAT
*
217953 TTTTGAAAACTGATAT
1 TTTTAAAAACT-ATAT
217969 TTAAAAAGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 32 0.89
27 4 0.11
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.47
Consensus pattern (26 bp):
TTTTAAAAACTATATATTATATATAT
Found at i:218043 original size:2 final size:2
Alignment explanation
Indices: 218038--218066 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
218028 AACTATATTA
218038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
218067 AAAAAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:218501 original size:16 final size:16
Alignment explanation
Indices: 218480--218597 Score: 164
Period size: 16 Copynumber: 7.4 Consensus size: 16
218470 GTATTACCCT
218480 ACCTGTTTTCAACCTG
1 ACCTGTTTTCAACCTG
218496 ACCTGTTTTCAACCTG
1 ACCTGTTTTCAACCTG
* * *
218512 GCTTGTTTTTAACCTG
1 ACCTGTTTTCAACCTG
218528 ACCTGTTTTCAACCTG
1 ACCTGTTTTCAACCTG
* * *
218544 GCTTGTTTTTAACCTG
1 ACCTGTTTTCAACCTG
218560 ACCTGTTTTCAACCTG
1 ACCTGTTTTCAACCTG
* *
218576 ACTTGTTTTTAACCTG
1 ACCTGTTTTCAACCTG
218592 ACCTGT
1 ACCTGT
218598 AAATGATCCA
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 87 1.00
ACGTcount: A:0.17, C:0.26, G:0.14, T:0.42
Consensus pattern (16 bp):
ACCTGTTTTCAACCTG
Found at i:218526 original size:32 final size:32
Alignment explanation
Indices: 218483--218597 Score: 212
Period size: 32 Copynumber: 3.6 Consensus size: 32
218473 TTACCCTACC
*
218483 TGTTTTCAACCTGACCTGTTTTCAACCTGGCT
1 TGTTTTTAACCTGACCTGTTTTCAACCTGGCT
218515 TGTTTTTAACCTGACCTGTTTTCAACCTGGCT
1 TGTTTTTAACCTGACCTGTTTTCAACCTGGCT
*
218547 TGTTTTTAACCTGACCTGTTTTCAACCTGACT
1 TGTTTTTAACCTGACCTGTTTTCAACCTGGCT
218579 TGTTTTTAACCTGACCTGT
1 TGTTTTTAACCTGACCTGT
218598 AAATGATCCA
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 81 1.00
ACGTcount: A:0.17, C:0.25, G:0.15, T:0.43
Consensus pattern (32 bp):
TGTTTTTAACCTGACCTGTTTTCAACCTGGCT
Found at i:218623 original size:64 final size:64
Alignment explanation
Indices: 218490--218624 Score: 164
Period size: 64 Copynumber: 2.1 Consensus size: 64
218480 ACCTGTTTTC
* ** ** **
218490 AACCTGACCTGTTTTCAACCTGGCTTGTTTTTAACCTGACCTGTTTTCAACCTGGCTTGTTTTT
1 AACCTGACCTGTTTTCAACCTGACTTGTTTTTAACCTGACCTGTAATCAACCTAACTTGTTAAT
* *
218554 AACCTGACCTGTTTTCAACCTGACTTGTTTTTAACCTGACCTGTAAATGATCC-AACTTGTTAAT
1 AACCTGACCTGTTTTCAACCTGACTTGTTTTTAACCTGACCTGT-AATCAACCTAACTTGTTAAT
*
218618 GACCTGA
1 AACCTGA
218625 TCTGATATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
64 56 0.93
65 4 0.07
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.39
Consensus pattern (64 bp):
AACCTGACCTGTTTTCAACCTGACTTGTTTTTAACCTGACCTGTAATCAACCTAACTTGTTAAT
Found at i:218888 original size:14 final size:14
Alignment explanation
Indices: 218866--218912 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
218856 TGCAAAGGAA
*
218866 AATTAATATAGTTT
1 AATTTATATAGTTT
218880 AATTTATATA----
1 AATTTATATAGTTT
218890 AA-TTATATAGTTT
1 AATTTATATAGTTT
218903 AATTTATATA
1 AATTTATATA
218913 AAGACAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:218899 original size:23 final size:24
Alignment explanation
Indices: 218865--218914 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
218855 ATGCAAAGGA
218865 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
218889 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
218912 AAA
1 AAA
218915 GACAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:219099 original size:14 final size:14
Alignment explanation
Indices: 219077--219140 Score: 76
Period size: 14 Copynumber: 4.6 Consensus size: 14
219067 TCTATTTAAA
*
219077 TTAGGGTTTATGGT
1 TTAGGGTTTATGAT
* *
219091 TTAGTGTTTATGGT
1 TTAGGGTTTATGAT
**
219105 TTAAAGTTTA-GAT
1 TTAGGGTTTATGAT
219118 TTAGGGTTTATGAT
1 TTAGGGTTTATGAT
219132 TTAGGGTTT
1 TTAGGGTTT
219141 CTATAAATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
13 10 0.23
14 33 0.77
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (14 bp):
TTAGGGTTTATGAT
Found at i:219235 original size:15 final size:15
Alignment explanation
Indices: 219215--219251 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
219205 TAATTTACTT
*
219215 TATATAGTTTTTATA
1 TATATAGTTTATATA
219230 TATATAGTTTATATA
1 TATATAGTTTATATA
219245 TAATATA
1 T-ATATA
219252 CATGGTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:219635 original size:14 final size:14
Alignment explanation
Indices: 219618--219688 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
219608 TCTATTTAAA
*
219618 TTAGGGTTTATGGT
1 TTAGGGTTTATGAT
* *
219632 TTAGTGTTTATGGT
1 TTAGGGTTTATGAT
** *
219646 TTAAAGTTTA-GAA
1 TTAGGGTTTATGAT
219659 TTAGGGTTTATGAT
1 TTAGGGTTTATGAT
* *
219673 TTAGGATTTAGGAT
1 TTAGGGTTTATGAT
219687 TT
1 TT
219689 CTATAAACTA
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
13 9 0.20
14 37 0.80
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (14 bp):
TTAGGGTTTATGAT
Found at i:219781 original size:13 final size:13
Alignment explanation
Indices: 219763--219792 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
219753 TAATTTACTT
219763 TATATAGTTTATA
1 TATATAGTTTATA
219776 TATATAGTTTATA
1 TATATAGTTTATA
219789 TATA
1 TATA
219793 CTATACATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:219797 original size:20 final size:21
Alignment explanation
Indices: 219773--219823 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
219763 TATATAGTTT
*
219773 ATATATATAGTTTATATATAC
1 ATATATATAGTTTATACATAC
* *
219794 -TATACATGGTTTATACATAC
1 ATATATATAGTTTATACATAC
219814 ATATTATATA
1 ATA-TATATA
219824 AAATTATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (21 bp):
ATATATATAGTTTATACATAC
Found at i:220057 original size:546 final size:546
Alignment explanation
Indices: 218999--220791 Score: 3262
Period size: 546 Copynumber: 3.3 Consensus size: 546
218989 TTTTAGCAAT
* * *
218999 ACATTAGTTTACAAAGG-CCAATACATAAGCCCATTCTTTTATTACAAATATATATGCATTAGTG
1 ACATTAGTTTACATAGGCCCAATGC--AAGCCCACTCTTTTATTACAAATATATATGCATTAGTG
*
219063 CTAGTCTATTTAAATTAGGGTTTATGGTTTAGTGTTTATGGTTTAAAGTTTAGATTTAGGG-TT-
64 CTAGTCTATTTAAATTAGGGTTTATGGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAGGGTTTA
*
219126 T-A--T--GATTTAGGGTTTCTATAAATTATATATTTTATTACTTTATATAGTTTATGCATAGTG
129 TGATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTG
*
219186 TTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTTTATATATATAGTTTATATATAATAT
194 TTTCTATAAACTATATAAGTAATTTACTTTATATAG--TTTATATATATAGTTTATATATACTAT
219251 ACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTA
257 ACATGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTA
219316 AATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGT
322 AATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGT
219381 TCATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAG
387 TCATAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAG
*
219446 GTTAATTCACATTAACGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAAT
452 GTTAATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAAT
219511 AAGTCCATTTGCAATAGTGCTAGTCCATTA
517 AAGTCCATTTGCAATAGTGCTAGTCCATTA
* * *
219541 ACATTAGTTTGCATAGGCCCAATGCAAGCCCACCCTTTTATTACAAATATATATGCATTAGTGTT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
219606 AGTCTATTTAAATTAGGGTTTATGGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAGGGTTTATG
66 AGTCTATTTAAATTAGGGTTTATGGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAGGGTTTATG
*
219671 ATTTAGGATTTAGGATTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
131 ATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
219736 TCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATAGTTTATATATACTATACAT
196 TCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATAGTTTATATATACTATACAT
219801 GGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATT
261 GGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATT
219866 ATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCAT
326 ATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCAT
219931 AAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTA
391 AAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTA
* *
219996 ATTCACATTAATGGCTCATTTATTTTATTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGT
456 ATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAAGT
220061 CCATTTGCAATAGTGCTAGTCCATTA
521 CCATTTGCAATAGTGCTAGTCCATTA
** *
220087 ACATTAGTTTGTATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCCTTAGTGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
* * **
220152 A-TTTCATTTAAATTAGGGTTTATGGTTTAGTGTTTATAGTTTAGTGTTTAGAATTAGGGTTTAT
66 AGTCT-ATTTAAATTAGGGTTTATGGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAGGGTTTAT
220216 GATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGT
130 GATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGT
220281 TTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATAGTTTATATATACTATACA
195 TTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATAGTTTATATATACTATACA
220346 TGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAAT
260 TGGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAAT
*
220411 TATATAAAACATGATTAATTAAGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCA
325 TATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCA
220476 TAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTT
390 TAAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTT
220541 AATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAAG
455 AATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAAG
*
220606 TCTATTTGCAATAGTGCTAGTCCATTA
520 TCCATTTGCAATAGTGCTAGTCCATTA
*
220633 ATATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
1 ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
*
220698 AGTCTATTTAAATTAGGGTTTATGGTTTAGTTTTTATGGTTTAAAGTTTAGAATTAGGGTTTATG
66 AGTCTATTTAAATTAGGGTTTATGGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAGGGTTTATG
220763 ATTTAGGATTTAGGGTTTCTATAAACTAT
131 ATTTAGGATTTAGGGTTTCTATAAACTAT
220792 GTAGACACCC
Statistics
Matches: 1206, Mismatches: 35, Indels: 16
0.96 0.03 0.01
Matches are distributed among these distances:
541 95 0.08
542 17 0.01
543 7 0.01
544 1 0.00
545 2 0.00
546 991 0.82
547 2 0.00
548 91 0.08
ACGTcount: A:0.36, C:0.09, G:0.13, T:0.43
Consensus pattern (546 bp):
ACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGCT
AGTCTATTTAAATTAGGGTTTATGGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAGGGTTTATG
ATTTAGGATTTAGGGTTTCTATAAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTT
TCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATAGTTTATATATACTATACAT
GGTTTATACATACATATTATATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATT
ATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCAT
AAATAGTAGTACATGTCATATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTA
ATTCACATTAATGGCTCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAAGT
CCATTTGCAATAGTGCTAGTCCATTA
Found at i:220186 original size:14 final size:14
Alignment explanation
Indices: 220164--220201 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
220154 TTCATTTAAA
* *
220164 TTAGGGTTTATGGT
1 TTAGTGTTTATAGT
220178 TTAGTGTTTATAGT
1 TTAGTGTTTATAGT
220192 TTAGTGTTTA
1 TTAGTGTTTA
220202 GAATTAGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.26, T:0.55
Consensus pattern (14 bp):
TTAGTGTTTATAGT
Found at i:220327 original size:13 final size:13
Alignment explanation
Indices: 220309--220338 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
220299 TAATTTACTT
220309 TATATAGTTTATA
1 TATATAGTTTATA
220322 TATATAGTTTATA
1 TATATAGTTTATA
220335 TATA
1 TATA
220339 CTATACATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:220343 original size:20 final size:21
Alignment explanation
Indices: 220319--220369 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
220309 TATATAGTTT
*
220319 ATATATATAGTTTATATATAC
1 ATATATATAGTTTATACATAC
* *
220340 -TATACATGGTTTATACATAC
1 ATATATATAGTTTATACATAC
220360 ATATTATATA
1 ATA-TATATA
220370 AAATTATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (21 bp):
ATATATATAGTTTATACATAC
Found at i:220780 original size:41 final size:40
Alignment explanation
Indices: 220704--220780 Score: 109
Period size: 41 Copynumber: 1.9 Consensus size: 40
220694 TGCTAGTCTA
* ** *
220704 TTTAAATTAGGGTTTATGGTTTAGTTTTTATGGTTTAAAG
1 TTTAAATTAGGGTTTATGATTTAGGATTTAGGGTTTAAAG
220744 TTTAGAATTAGGGTTTATGATTTAGGATTTAGGGTTT
1 TTTA-AATTAGGGTTTATGATTTAGGATTTAGGGTTT
220781 CTATAAACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 4 0.12
41 28 0.88
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.51
Consensus pattern (40 bp):
TTTAAATTAGGGTTTATGATTTAGGATTTAGGGTTTAAAG
Found at i:220837 original size:3 final size:3
Alignment explanation
Indices: 220826--220887 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
220816 TTTTTTATCG
220826 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
220871 TTA -TA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA
220888 CATTTTACAT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 4 0.07
3 47 0.87
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:228119 original size:4 final size:4
Alignment explanation
Indices: 228110--228152 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
228100 GATCGAGAAA
*
228110 ACAT ACAT ACAT ACAT ACAT ATAT AC-- ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
228153 AAATTTGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
4 33 0.94
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:228567 original size:36 final size:36
Alignment explanation
Indices: 228515--228656 Score: 141
Period size: 36 Copynumber: 4.0 Consensus size: 36
228505 TGAGAATTTT
228515 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTTC
1 AAAACAAA-TTTTGTCTCGCTTGAGACAATTTCTTTC
* * *
228552 GAAGCAAATTTTGTCTCGCTTGAGACAGCTTTC--TC
1 AAAACAAATTTTGTCTCGCTTGAGACA-ATTTCTTTC
* * * *
228587 AAAACAAATTCTGTCTCGTTTAAGACAAATTCTCTT-
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTCT-TTC
* *
228623 AAAACAAACTTCGTCTCGCTTGAGAC-ATTT-TTTC
1 AAAACAAATTTTGTCTCGCTTGAGACAATTTCTTTC
228657 CTTTGAAATA
Statistics
Matches: 84, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
33 2 0.02
34 4 0.05
35 27 0.32
36 40 0.48
37 11 0.13
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.37
Consensus pattern (36 bp):
AAAACAAATTTTGTCTCGCTTGAGACAATTTCTTTC
Found at i:228602 original size:71 final size:72
Alignment explanation
Indices: 228515--228649 Score: 175
Period size: 71 Copynumber: 1.9 Consensus size: 72
228505 TGAGAATTTT
* * * * * * *
228515 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCT-TTCGAAGCAAATTTTGTCTCGCTTGAGACA
1 AAAACAAATTTCTGTCTCGCTTAAGACAAATTCTCTT-AAAACAAACTTCGTCTCGCTTGAGACA
228579 GCTTTCTC
65 GCTTTCTC
*
228587 AAAACAAA-TTCTGTCTCGTTTAAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 AAAACAAATTTCTGTCTCGCTTAAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
228650 TTTTTTCCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
71 44 0.81
72 10 0.19
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.34
Consensus pattern (72 bp):
AAAACAAATTTCTGTCTCGCTTAAGACAAATTCTCTTAAAACAAACTTCGTCTCGCTTGAGACAG
CTTTCTC
Found at i:228801 original size:105 final size:106
Alignment explanation
Indices: 228616--228813 Score: 283
Period size: 105 Copynumber: 1.9 Consensus size: 106
228606 TTAAGACAAA
* * *
228616 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTTTCCTTTGAAATACAAATTTTGAATTT
1 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACACTTTTCCCTTTGAAATACAAATTTCGAATTT
228681 GATTCACTTAAAACAAAATTAATCTCACCTTAGATTGTTGT
66 GATTCACTTAAAACAAAATTAATCTCACCTTAGATTGTTGT
* * * *
228722 TTCTTTTAAAACAAATTTCGTCTCGCTTGAGAC-CTTTTCCCTTTGAGATCCAAATTTCGAATTT
1 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACACTTTTCCCTTTGAAATACAAATTTCGAATTT
* * *
228786 GTTTCACATT-AAACAAAGTTGATCTCAC
66 GATTCAC-TTAAAACAAAATTAATCTCAC
228814 TTGAGATCGT
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
105 48 0.59
106 33 0.41
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (106 bp):
TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACACTTTTCCCTTTGAAATACAAATTTCGAATTT
GATTCACTTAAAACAAAATTAATCTCACCTTAGATTGTTGT
Found at i:229316 original size:29 final size:29
Alignment explanation
Indices: 229144--229301 Score: 255
Period size: 29 Copynumber: 5.5 Consensus size: 29
229134 CGTTTGAGGA
*
229144 AAAAATCTTTGAGTTTGTTCCTTTCGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
229173 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
*
229202 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
*
229231 AAAAATCTTGGAGTTTGTTCCTTTTGAAT
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
** *
229260 AAAAATCTTTGAG-TTGTTTATTTTGAAA
1 AAAAATCTTTGAGTTTGTTCCTTTTGAAT
229288 AAAAATCTTTGAGT
1 AAAAATCTTTGAGT
229302 CTATTTATTT
Statistics
Matches: 122, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
28 25 0.20
29 97 0.80
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.45
Consensus pattern (29 bp):
AAAAATCTTTGAGTTTGTTCCTTTTGAAT
Found at i:229390 original size:52 final size:54
Alignment explanation
Indices: 229312--229415 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 54
229302 CTATTTATTT
**
229312 TGAAACAAAGTTTTGTCTCTCTTGAGACAA-TTT-CGTGAAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGCGAAAAAAATCTTTGAGTC
229364 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGCGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGCGAAAAAAATCTTTGAG
229416 ATTGTTTCTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 30 0.62
53 3 0.06
54 15 0.31
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (54 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGCGAAAAAAATCTTTGAGTC
Found at i:229437 original size:30 final size:30
Alignment explanation
Indices: 229403--229667 Score: 154
Period size: 30 Copynumber: 8.1 Consensus size: 30
229393 ATTTTGCGAA
*
229403 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
*
229433 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
* * ** *
229463 AAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATCT-TTGAGATTGTTTCTTTGGAAAC
*
229500 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
* * ** *
229530 AAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATCT-TTGAGATTGTTTCTTTGGAAAC
*
229567 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
* * ** *
229597 AAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAC
1 AAAA------ATCT-TTGAGATTGTTTCTTTGGAAAC
229634 AAAAATCTTTGAG-TCTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGAT-TGTTTCTTTGGAAAC
229664 AAAA
1 AAAA
229668 TTTTGTCTCT
Statistics
Matches: 176, Mismatches: 37, Indels: 44
0.68 0.14 0.17
Matches are distributed among these distances:
29 1 0.01
30 94 0.53
31 9 0.05
36 9 0.05
37 63 0.36
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTCTTTGGAAAC
Found at i:229495 original size:67 final size:67
Alignment explanation
Indices: 229420--229743 Score: 580
Period size: 67 Copynumber: 4.9 Consensus size: 67
229410 TTTGAGATTG
229420 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
229485 AA
66 AA
229487 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
229552 AA
66 AA
229554 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
229619 AA
66 AA
*
229621 TTTCTTTTGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
229686 AA
66 AA
* * * *
229688 TTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCTCTT-AAAAC-AAATGTTGTCTCT
1 TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCT-TTGGAAACAAAATTTTGTCTCT
229744 TGAGACAGTT
Statistics
Matches: 252, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
66 12 0.05
67 238 0.94
68 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (67 bp):
TTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGAT
AA
Found at i:230607 original size:31 final size:28
Alignment explanation
Indices: 230570--230665 Score: 99
Period size: 28 Copynumber: 3.3 Consensus size: 28
230560 AGACAGTTGT
230570 TTTTGAAACACATTATCTTTGAG-CTTGTTT-
1 TTTTGAAACA-A--ATCTTTGAGTC-TGTTTC
230600 TTCTTGAAACAAATCTTTGAGTCTGTTTC
1 TT-TTGAAACAAATCTTTGAGTCTGTTTC
*
230629 TTTTGAAACAAATCTTTGAAT-TGGTTTC
1 TTTTGAAACAAATCTTTGAGTCT-GTTTC
*
230657 TCTTGAAAC
1 TTTTGAAAC
230666 CATAACTCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
27 1 0.02
28 45 0.75
29 3 0.05
30 3 0.05
31 8 0.13
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (28 bp):
TTTTGAAACAAATCTTTGAGTCTGTTTC
Found at i:230615 original size:28 final size:27
Alignment explanation
Indices: 230584--230665 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 27
230574 GAAACACATT
230584 ATCTTTGAGCTTGTTTTTCTTGAAACAA
1 ATCTTTGAG-TTGTTTTTCTTGAAACAA
230612 ATCTTTGAGTCTGTTTCTT-TTGAAACAA
1 ATCTTTGAGT-TGTTT-TTCTTGAAACAA
* *
230640 ATCTTTGAATTGGTTTCTCTTGAAAC
1 ATCTTTGAGTT-GTTTTTCTTGAAAC
230666 CATAACTCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
27 3 0.06
28 43 0.90
29 2 0.04
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (27 bp):
ATCTTTGAGTTGTTTTTCTTGAAACAA
Found at i:230830 original size:46 final size:45
Alignment explanation
Indices: 230678--231041 Score: 189
Period size: 43 Copynumber: 8.5 Consensus size: 45
230668 TAACTCCTAA
* * *
230678 AGATGGCCAG-CCGTCCTCATCATGTAGGAACCGTGTCATC-CC-C
1 AGATGGCCAGAAC-TCCTCATCACGTAGGAACCGTGTCATCACCTT
* * * *
230721 AGAT---CAGAGCTCTTCATCACGTAGGAGCCGTGTCA--ACCAT
1 AGATGGCCAGAACTCCTCATCACGTAGGAACCGTGTCATCACCTT
** * *
230761 AGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATGGCCAGAAC-TCCTCATCACGTAGGAACCGTGTCATCACC-TT
* * * *
230807 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATTC-CC-C
1 AGATGGCCAGAACTCCTCATCACGTAGGAACCGTGTCA-TCACCTT
* * *
230851 AGAT---CAGATCTCCTCATCACGTAGGAGCCGTGTCA--ACCAT
1 AGATGGCCAGAACTCCTCATCACGTAGGAACCGTGTCATCACCTT
** * * *
230891 AGATAACCAGCAGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
1 AGATGGCCAGAACTCCTCATCACGTAGGAACCGTGTCATCACC-TT
* * * * * *
230937 AGATGGCTAGAACTCTTCATCACGTATGAGCAGTGTCA--ACCCT
1 AGATGGCCAGAACTCCTCATCACGTAGGAACCGTGTCATCACCTT
* ** *
230980 CGA---CCAGATTTCCTCATCACGTAGGAACCATGTCA-C-CCTT
1 AGATGGCCAGAACTCCTCATCACGTAGGAACCGTGTCATCACCTT
* * * *
231020 AGACGACCCGAACTCTTCATCA
1 AGATGGCCAGAACTCCTCATCA
231042 TGTATGAGCA
Statistics
Matches: 243, Mismatches: 54, Indels: 48
0.70 0.16 0.14
Matches are distributed among these distances:
39 4 0.02
40 62 0.26
41 29 0.12
42 1 0.00
43 70 0.29
44 7 0.03
45 6 0.02
46 61 0.25
47 3 0.01
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (45 bp):
AGATGGCCAGAACTCCTCATCACGTAGGAACCGTGTCATCACCTT
Found at i:230910 original size:130 final size:129
Alignment explanation
Indices: 230694--231014 Score: 500
Period size: 130 Copynumber: 2.5 Consensus size: 129
230684 CCAGCCGTCC
* * * * *
230694 TCATCATGTAGGAACCGTGTCATCCCCAGATCAGAGCTCTTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATCCCCAGATCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
*
230759 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCAGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
230823 TCATCACGTATGAGCCGTGTCATTCCCCAGATCAGATCTCCTCATCACGTAGGAGCCGTGTCAAC
1 TCATCACGTATGAGCCGTGTCA-TCCCCAGATCAGATCTCCTCATCACGTAGGAGCCGTGTCAAC
*
230888 CATAGATAACCAGCAGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCTAGAACTCT
65 CATAGATAACCAGCAGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
* * * * * *
230953 TCATCACGTATGAGCAGTGTCAACCCTC-GACCAGATTTCCTCATCACGTAGGAACCATGTCA
1 TCATCACGTATGAGCCGTGTCATCCC-CAGATCAGATCTCCTCATCACGTAGGAGCCGTGTCA
231015 CCCTTAGACG
Statistics
Matches: 177, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
129 52 0.29
130 125 0.71
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATCCCCAGATCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
ATAGATAACCAGCAGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:231226 original size:3 final size:3
Alignment explanation
Indices: 231213--231271 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
231203 TTTTTTATCG
231213 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
*
231258 -TA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA
231272 CATTTTACAT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 4 0.08
3 44 0.86
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:233872 original size:15 final size:15
Alignment explanation
Indices: 233852--233888 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
233842 TAATTTACTT
233852 TATATAGTTTATATA
1 TATATAGTTTATATA
233867 TATATAGTTTATATA
1 TATATAGTTTATATA
233882 TACTATA
1 TA-TATA
233889 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:234250 original size:14 final size:14
Alignment explanation
Indices: 234233--234303 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 14
234223 TCCATTTAAA
*
234233 TTAGGGTTTCTGGT
1 TTAGGGTTTATGGT
*
234247 TTAGTGTTTATGGT
1 TTAGGGTTTATGGT
** **
234261 TTAAAGTTTA-GAA
1 TTAGGGTTTATGGT
*
234274 TTAGGGTTTATGAT
1 TTAGGGTTTATGGT
* *
234288 TTAGGATTTAGGGT
1 TTAGGGTTTATGGT
234302 TT
1 TT
234304 CTATAAACTA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
13 9 0.20
14 35 0.80
ACGTcount: A:0.21, C:0.01, G:0.28, T:0.49
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:234303 original size:41 final size:40
Alignment explanation
Indices: 234227--234303 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
234217 TGTTAGTCCA
* * *
234227 TTTAAATTAGGGTTTCTGGTTTAGTGTTTATGGTTTAAAG
1 TTTAAATTAGGGTTTATGATTTAGTGTTTAGGGTTTAAAG
234267 TTTAGAATTAGGGTTTATGATTTAG-GATTTAGGGTTT
1 TTTA-AATTAGGGTTTATGATTTAGTG-TTTAGGGTTT
234304 CTATAAACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 5 0.16
41 27 0.84
ACGTcount: A:0.23, C:0.01, G:0.26, T:0.49
Consensus pattern (40 bp):
TTTAAATTAGGGTTTATGATTTAGTGTTTAGGGTTTAAAG
Found at i:234396 original size:13 final size:13
Alignment explanation
Indices: 234378--234407 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
234368 TAATTTACTT
234378 TATATAGTTTATA
1 TATATAGTTTATA
234391 TATATAGTTTATA
1 TATATAGTTTATA
234404 TATA
1 TATA
234408 CTATACATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:234412 original size:20 final size:21
Alignment explanation
Indices: 234388--234438 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
234378 TATATAGTTT
*
234388 ATATATATAGTTTATATATAC
1 ATATATATAGTTTATACATAC
* *
234409 -TATACATGGTTTATACATAC
1 ATATATATAGTTTATACATAC
234429 ATATTATATA
1 ATA-TATATA
234439 AAATTATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (21 bp):
ATATATATAGTTTATACATAC
Found at i:234446 original size:13 final size:13
Alignment explanation
Indices: 234436--234462 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
234426 TACATATTAT
234436 ATAAAATTATTTA
1 ATAAAATTATTTA
234449 ATAAAATTATTTA
1 ATAAAATTATTTA
234462 A
1 A
234463 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:234472 original size:15 final size:14
Alignment explanation
Indices: 234436--234478 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
234426 TACATATTAT
234436 ATAAAATTATTT-A
1 ATAAAATTATTTAA
234449 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
234463 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
234478 A
1 A
234479 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:234786 original size:537 final size:537
Alignment explanation
Indices: 233782--235941 Score: 3399
Period size: 521 Copynumber: 4.1 Consensus size: 537
233772 TGGTTATGAC
233782 AAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAATT
1 AAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAATT
233847 TACTTTATATAGTTTATATATATATAGTTTATATATACTATACATGGTTTATACATAC-------
66 TACTTTATATAGTTTATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTAT
233905 AT---ATTA--T-ATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAA
131 ATAAAATTATTTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAA
*
233964 TAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGCCATATTAATTTAA
196 TAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTAA
234029 ATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATGGCTCATTTATTTTGTT
261 ATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATGGCTCATTTATTTTGTT
234094 GTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTAACA
326 GTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTAACA
234159 TTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGTTAGT
391 TTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGTTAGT
* * *
234224 CCATTTAAATTAGGGTTTCTGGTTTAGTGTTTATGGTTTAAAGTTTAGAATTAGGGTTTATGATT
456 CCATTTAAATTAGGGTTTATGATTTAGTATTTA-GGTTT-AAGTTTAGAATTAGGGTTTATGATT
234289 TAGGATTTAGGGTTTCTAT
519 TAGGATTTAGGGTTTCTAT
234308 AAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAATT
1 AAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAATT
234373 TACTTTATATAG-TT-TATATATATAGTTTATATATACTATACATGGTTTATACATACATATTAT
66 TACTTTATATAGTTTATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTAT
*
234436 ATAAAATTATTTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGATGTTAAA
131 ATAAAATTATTTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAA
*
234501 TAATTAGTATGTCACATTGCATATTATATGGTTTATAAATAGTAGTACATGTCATATTAATTTAA
196 TAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTAA
234566 ATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATGGCTCATTTATTTTGTT
261 ATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATGGCTCATTTATTTTGTT
*
234631 GTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCAATAGTGCTAGTCTATTAACA
326 GTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTAACA
234696 TTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGTTAGT
391 TTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGTTAGT
* * *
234761 CCATTTAAATTAGGGTTTATGGTTTAGT-GTT-GGTTTAAAGTTTAGAATTAGGGTTTATAATTT
456 CCATTTAAATTAGGGTTTATGATTTAGTATTTAGGTTT-AAGTTTAGAATTAGGGTTTATGATTT
* *
234824 AGGGTTTAGGGTTTTTAT
520 AGGATTTAGGGTTTCTAT
234842 AAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAATT
1 AAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAATT
*
234907 TAC-------------T-T-TATATAGTTTATATATACTATACATGATTTATACATACATATTAT
66 TACTTTATATAGTTTATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTAT
*
234957 ATAAAATTATTTAATAAAATTATTTAAATATAAATTATATAAAACATGATTAATTAGGTGTTAAA
131 ATAAAATTATTTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAA
*
235022 TAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGACATATTAATTTAA
196 TAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTAA
*
235087 ATTGCATAATTTGTATTTTAGTTGCATGTTTGGTTAATTCACATTAATGGCTCATTTATTTTGTT
261 ATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATGGCTCATTTATTTTGTT
*
235152 GTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCTATTTGCAATAGTGCTAGTCCATTAACA
326 GTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTAACA
* ** * * *
235217 TTAGTTTACATAGGCCCAGTTTAAACCTACTCTTTTATTACAAATATATATGCATTAGTGCTAGT
391 TTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGTTAGT
* * ** * * *
235282 CCATTTACATTAGGGATTATGATTTAGTATTTAGTGTTTGTGATTTA-AAGTTTAGGATTTAGGG
456 CCATTTAAATTAGGGTTTATGATTTAGTATTTAG-GTTTAAG-TTTAGAA--TTAGGGTTTATGA
* *
235346 TTTATGATTTAAGGTTTCTAT
517 TTTAGGATTTAGGGTTTCTAT
* *
235367 AAACTATATATTTTACTACTTTATATAGTTTATGTATAGTGTTTCTATAAACTATATAAGTAATT
1 AAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAATT
235432 TACTTTATATAGTTTATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTAT
66 TACTTTATATAGTTTATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTAT
235497 ATAAAATTATTTAATAAAATTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTA
131 AT-AAA--A-TT-AT----TTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTA
*
235562 GGTGTTAAATAATTAATATGTCACATT-CTATATTATATGGTTCATAAATAGTAGTACATGTCAT
187 GGTGTTAAATAATTAGTATGTCACATTGC-ATATTATATGGTTCATAAATAGTAGTACATGTCAT
* * ** * *
235626 ATTAATTTCATTTGCATAATTAATATTTTAGTTGCATGTTAGGTTAATTCACATTAATAGCCCAT
251 ATTAATTTAAATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATGGCTCAT
235691 TTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCAATAGTGCTAG
316 TTATTTTGTTGTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCAATAGTGCTAG
* * *
235756 TCCATTAACATTAATTTAGATAGGCCCAATGCAAGTCCACTCTTTTATTACAAATATATATGCAT
381 TCCATTAACATTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCAT
* * * * * **
235821 TAGTGATAGTCTATTTACATTAGGGTTTATGATTTAGTATTTA-G--T-A-TTTGTGATTTAAAG
446 TAGTGTTAGTCCATTTAAATTAGGGTTTATGATTTAGTATTTAGGTTTAAGTTT-AGAATTAGGG
* * *
235881 TTTATGGTTTATGATTTAGGATTTCTAT
510 TTTATGATTTAGGATTTAGGGTTTCTAT
235909 AAACTATATATTTTATTACTTTATATAGTTTAT
1 AAACTATATATTTTATTACTTTATATAGTTTAT
235942 ATATATAGTT
Statistics
Matches: 1516, Mismatches: 72, Indels: 76
0.91 0.04 0.05
Matches are distributed among these distances:
521 381 0.25
522 3 0.00
523 5 0.00
524 50 0.03
525 94 0.06
526 77 0.05
531 2 0.00
534 119 0.08
536 3 0.00
537 335 0.22
538 1 0.00
539 1 0.00
540 46 0.03
541 3 0.00
542 63 0.04
543 1 0.00
544 3 0.00
545 3 0.00
547 1 0.00
548 1 0.00
549 324 0.21
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (537 bp):
AAACTATATATTTTATTACTTTATATAGTTTATGCATAGTGTTTCTATAAACTATATAAGTAATT
TACTTTATATAGTTTATATATATATAGTTTATATATACTATACATGGTTTATACATACATATTAT
ATAAAATTATTTAATAAAATTATTTAAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAA
TAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTACATGTCATATTAATTTAA
ATTGCATAATTTGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATGGCTCATTTATTTTGTT
GTTATGAATAAGTAATAATAAAACCCAAAAATAAGTCCATTTGCAATAGTGCTAGTCCATTAACA
TTAGTTTACATAGGCCCAATGCAAGCCCACTCTTTTATTACAAATATATATGCATTAGTGTTAGT
CCATTTAAATTAGGGTTTATGATTTAGTATTTAGGTTTAAGTTTAGAATTAGGGTTTATGATTTA
GGATTTAGGGTTTCTAT
Found at i:234822 original size:13 final size:14
Alignment explanation
Indices: 234800--234832 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
234790 TTGGTTTAAA
234800 GTTTAGAA-TTAGG
1 GTTTAGAATTTAGG
*
234813 GTTTATAATTTAGG
1 GTTTAGAATTTAGG
234827 GTTTAG
1 GTTTAG
234833 GGTTTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (14 bp):
GTTTAGAATTTAGG
Found at i:234959 original size:15 final size:17
Alignment explanation
Indices: 234923--234959 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
234913 ATATAGTTTA
234923 TATATACTATACATGAT
1 TATATACTATACATGAT
234940 T-TATAC-ATACAT-AT
1 TATATACTATACATGAT
234954 TATATA
1 TATATA
234960 AAATTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.16
15 10 0.53
16 5 0.26
17 1 0.05
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (17 bp):
TATATACTATACATGAT
Found at i:234993 original size:15 final size:15
Alignment explanation
Indices: 234955--234999 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
234945 CATACATATT
234955 ATATAAAATTATTT-A
1 ATAT-AAATTATTTAA
234970 ATA-AAATTATTTAA
1 ATATAAATTATTTAA
*
234984 ATATAAATTATATAA
1 ATATAAATTATTTAA
234999 A
1 A
235000 ACATGATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 9 0.33
14 4 0.15
15 14 0.52
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATAAATTATTTAA
Found at i:235335 original size:28 final size:28
Alignment explanation
Indices: 235304--235362 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
235294 GGGATTATGA
* * *
235304 TTTAGTATTTAGTGTTTGTGATTTAAAG
1 TTTAGGATTTAGGGTTTATGATTTAAAG
*
235332 TTTAGGATTTAGGGTTTATGATTTAAGG
1 TTTAGGATTTAGGGTTTATGATTTAAAG
235360 TTT
1 TTT
235363 CTATAAACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (28 bp):
TTTAGGATTTAGGGTTTATGATTTAAAG
Found at i:235361 original size:14 final size:14
Alignment explanation
Indices: 235317--235362 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
235307 AGTATTTAGT
* *
235317 GTTTGTGATTTAAA
1 GTTTATGATTTAAG
* *
235331 GTTTAGGATTTAGG
1 GTTTATGATTTAAG
235345 GTTTATGATTTAAG
1 GTTTATGATTTAAG
235359 GTTT
1 GTTT
235363 CTATAAACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (14 bp):
GTTTATGATTTAAG
Found at i:235417 original size:48 final size:49
Alignment explanation
Indices: 235359--235453 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 49
235349 ATGATTTAAG
** * *
235359 GTTTCTATAAACTATATATTTTA-CTACTTTATATAGTTTATGTATAGT
1 GTTTCTATAAACTATATAAGTAATCTACTTTATATAGTTTATATATAGT
*
235407 GTTTCTATAAACTATATAAGTAATTTACTTTATATAGTTTATATATA
1 GTTTCTATAAACTATATAAGTAATCTACTTTATATAGTTTATATATA
235454 TATAGTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 20 0.49
49 21 0.51
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.51
Consensus pattern (49 bp):
GTTTCTATAAACTATATAAGTAATCTACTTTATATAGTTTATATATAGT
Found at i:235457 original size:15 final size:15
Alignment explanation
Indices: 235437--235473 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
235427 TAATTTACTT
235437 TATATAGTTTATATA
1 TATATAGTTTATATA
235452 TATATAGTTTATATA
1 TATATAGTTTATATA
235467 TACTATA
1 TA-TATA
235474 CATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:235948 original size:13 final size:13
Alignment explanation
Indices: 235930--235956 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
235920 TTTATTACTT
235930 TATATAGTTTATA
1 TATATAGTTTATA
235943 TATATAGTTTATA
1 TATATAGTTTATA
235956 T
1 T
235957 GTACTATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:235998 original size:13 final size:13
Alignment explanation
Indices: 235988--236014 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
235978 TACATATTAT
235988 ATAAAATTATTTA
1 ATAAAATTATTTA
236001 ATAAAATTATTTA
1 ATAAAATTATTTA
236014 A
1 A
236015 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:236024 original size:15 final size:14
Alignment explanation
Indices: 235988--236030 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
235978 TACATATTAT
235988 ATAAAATTATTT-A
1 ATAAAATTATTTAA
236001 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
236015 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
236030 A
1 A
236031 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:236151 original size:14 final size:14
Alignment explanation
Indices: 236129--236159 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
236119 CCCATTTATA
236129 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
*
236143 TTAGTGTTTATGGT
1 TTAGGGTTTATGGT
236157 TTA
1 TTA
236160 AAGTTAGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.55
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:238699 original size:39 final size:39
Alignment explanation
Indices: 238604--238711 Score: 128
Period size: 39 Copynumber: 2.8 Consensus size: 39
238594 TTGATTCTCA
* *
238604 AAAT-ATTTCACCATAACATTATAAATTCTTAATTTCTT
1 AAATAATTTCATCATAACATTATAAATTATTAATTTCTT
*
238642 AAATAATTTCATCATAACATTTTAAATTATTAATTTCTT
1 AAATAATTTCATCATAACATTATAAATTATTAATTTCTT
** * * * *
238681 AAATTGTTTTATCCTAACAATCTAAATTATT
1 AAATAATTTCATCATAACATTATAAATTATT
238712 TCTCAAATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
38 4 0.07
39 56 0.93
ACGTcount: A:0.40, C:0.13, G:0.01, T:0.46
Consensus pattern (39 bp):
AAATAATTTCATCATAACATTATAAATTATTAATTTCTT
Found at i:238767 original size:26 final size:25
Alignment explanation
Indices: 238707--238768 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
238697 ACAATCTAAA
*
238707 TTATTTCTCAAATTATTTTTTAATTT
1 TTATTT-TTAAATTATTTTTTAATTT
**
238733 TTAAATTTAAATGTATTTCTTTAA-TT
1 TTATTTTTAAAT-TATTT-TTTAATTT
238759 TTATTTTTAA
1 TTATTTTTAA
238769 TAAATTTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 5 0.17
26 19 0.66
27 5 0.17
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (25 bp):
TTATTTTTAAATTATTTTTTAATTT
Found at i:238776 original size:16 final size:17
Alignment explanation
Indices: 238755--238786 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
238745 GTATTTCTTT
238755 AATTTTAT-TTTTAATA
1 AATTTTATCTTTTAATA
238771 AATTTTATCTTTTAAT
1 AATTTTATCTTTTAAT
238787 TATATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTTATCTTTTAATA
Found at i:241737 original size:12 final size:12
Alignment explanation
Indices: 241716--241760 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
241706 ATTATACGGT
*
241716 ATGAATAGTACC
1 ATGAACAGTACC
241728 ATGAACAGTACC
1 ATGAACAGTACC
* * *
241740 ATAAACAATGCC
1 ATGAACAGTACC
241752 ATGAACAGT
1 ATGAACAGT
241761 GCTACAGTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.44, C:0.20, G:0.16, T:0.20
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:247297 original size:20 final size:20
Alignment explanation
Indices: 247272--247310 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
247262 TTTTTATGTT
247272 AAATTATTAGGTTGTACCGC
1 AAATTATTAGGTTGTACCGC
247292 AAATTATTAGGTTGTACCG
1 AAATTATTAGGTTGTACCG
247311 AAGAATTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.36
Consensus pattern (20 bp):
AAATTATTAGGTTGTACCGC
Found at i:249501 original size:173 final size:172
Alignment explanation
Indices: 249201--249514 Score: 420
Period size: 173 Copynumber: 1.8 Consensus size: 172
249191 AAATATTTCT
* *
249201 AATAGTTCGGGGTAATTACAATGTAGTAGTGTTCATAAACTTTATTAACTATTGACAACGCATAC
1 AATAGTTCGGAGTAATTACAATGTAGTAGTGTTCATAAACTTTATTAACTATTGACAACACATAC
* *
249266 ACATCCTGCATATGTAGTTGCTCGAACCCATAATTTCAAAAGAGAACAAGACTCCCTTTAACCAC
66 ACATCCTGCAGAAGTAGTTGCTCGAACCCATAATTTCAAAAGAGAACAAGACTCCCTTTAACCAC
*
249331 TAAGACCACTCAATGGACTCATATAGAAAAGAACTTTTTGTG
131 TAAAACCACTCAATGGACTCATATAGAAAAGAACTTTTTGTG
* * * *
249373 AATAGTTTGGAGTAATTATAATGTAGTATGTGTTTC-TAAACTTTCTTAACTATTGATAACACAT
1 AATAGTTCGGAGTAATTACAATGTAGTA-GTG-TTCATAAACTTTATTAACTATTGACAACACAT
* * * * * *
249437 ACACA-CCTTGCAGAAGTAGTTGTTCGAACCTA-AGATTTCAAGAA-AGGATAAGACTTCTTTTA
64 ACACATCC-TGCAGAAGTAGTTGCTCGAACCCATA-ATTTCAA-AAGAGAACAAGACTCCCTTTA
249499 ACCACTAAAACCACTC
126 ACCACTAAAACCACTC
249515 GATAAATTCA
Statistics
Matches: 122, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
172 28 0.23
173 89 0.73
174 5 0.04
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (172 bp):
AATAGTTCGGAGTAATTACAATGTAGTAGTGTTCATAAACTTTATTAACTATTGACAACACATAC
ACATCCTGCAGAAGTAGTTGCTCGAACCCATAATTTCAAAAGAGAACAAGACTCCCTTTAACCAC
TAAAACCACTCAATGGACTCATATAGAAAAGAACTTTTTGTG
Found at i:251651 original size:17 final size:17
Alignment explanation
Indices: 251626--251668 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
251616 CCGTGTATCC
251626 ATTTTTAAAATT-TATT
1 ATTTTTAAAATTATATT
*
251642 GTTCTTT-AAATTATATT
1 ATT-TTTAAAATTATATT
251659 ATTTTTAAAA
1 ATTTTTAAAA
251669 AAATTTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
ATTTTTAAAATTATATT
Found at i:251896 original size:2 final size:2
Alignment explanation
Indices: 251889--251929 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
251879 ATATTTAATA
251889 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
251930 AGAAATCAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:252277 original size:3 final size:3
Alignment explanation
Indices: 252269--252352 Score: 80
Period size: 3 Copynumber: 27.7 Consensus size: 3
252259 TCCTTTTTAT
* * *
252269 TTA TTA TTA TTA ATA TTA TTA TTTA TTT TTA TTA TTA TTTA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA -TTA TTA TTA
* * * *
252316 TTT TTA ATA TAA TTA TTA -TA TTA ATA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
252353 TATTTTTGCA
Statistics
Matches: 64, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
2 2 0.03
3 56 0.88
4 6 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:259264 original size:11 final size:11
Alignment explanation
Indices: 259244--259401 Score: 98
Period size: 11 Copynumber: 14.3 Consensus size: 11
259234 TCACTCGAAA
259244 AAAG-AAAAAG
1 AAAGAAAAAAG
259254 AAAGAAAAAAG
1 AAAGAAAAAAG
*
259265 AAAGAAAGAA-
1 AAAGAAAAAAG
259275 AAAGAAAAAA-
1 AAAGAAAAAAG
259285 AGAAGATAAAAAG
1 A-AAGA-AAAAAG
*
259298 AGAACAAAAAAAG
1 A-AA-GAAAAAAG
* *
259311 AAAGACAAATG
1 AAAGAAAAAAG
*
259322 AAAGAAAAGA-
1 AAAGAAAAAAG
*
259332 AAAGAAAAGA-
1 AAAGAAAAAAG
*
259342 AAAGAAGAAATG
1 AAAGAA-AAAAG
259354 --AGAAAAAATG
1 AAAGAAAAAA-G
259364 AATA-AAGAAAAG
1 AA-AGAA-AAAAG
*
259376 ATAGATAAAAAG
1 AAAGA-AAAAAG
*
259388 AAAGAATAAAG
1 AAAGAAAAAAG
259399 AAA
1 AAA
259402 ATTGAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 27
0.74 0.09 0.17
Matches are distributed among these distances:
9 3 0.03
10 35 0.29
11 42 0.35
12 21 0.18
13 17 0.14
14 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.05
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:259268 original size:15 final size:15
Alignment explanation
Indices: 259240--259393 Score: 88
Period size: 15 Copynumber: 9.9 Consensus size: 15
259230 TATCTCACTC
259240 GAAAAAAGAAAAAGAAA
1 GAAAAAAG--AAAGAAA
259257 GAAAAAAGAAAGAAA
1 GAAAAAAGAAAGAAA
*
259272 G-AAAAAGAAAAAAA
1 GAAAAAAGAAAGAAA
*
259286 GAAGATAA-AAAG--A
1 GAA-AAAAGAAAGAAA
259299 GAACAAAA-AAAGAAA
1 GAA-AAAAGAAAGAAA
* *
259314 GACAAATGAAAGAAA
1 GAAAAAAGAAAGAAA
*
259329 -AGAAAAGAAAAGAAAA
1 GAAAAAAG-AAAG-AAA
259345 GAAGAAATGAGAAA-AAA
1 GAA-AAA--AGAAAGAAA
* *
259362 TGAATAAAGAAAAGATA
1 -GAAAAAAG-AAAGAAA
259379 GATAAAAAGAAAGAA
1 GA-AAAAAGAAAGAA
259394 TAAAGAAAAT
Statistics
Matches: 108, Mismatches: 14, Indels: 31
0.71 0.09 0.20
Matches are distributed among these distances:
13 11 0.10
14 21 0.19
15 28 0.26
16 16 0.15
17 21 0.19
18 6 0.06
19 3 0.03
20 2 0.02
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.05
Consensus pattern (15 bp):
GAAAAAAGAAAGAAA
Found at i:259273 original size:25 final size:25
Alignment explanation
Indices: 259240--259401 Score: 93
Period size: 25 Copynumber: 6.2 Consensus size: 25
259230 TATCTCACTC
259240 GAAA-AAAGAAAAAGAAAGAAAAAA
1 GAAAGAAAGAAAAAGAAAGAAAAAA
259264 GAAAGAAAGAAAAAGAAA-AAAAGAA
1 GAAAGAAAGAAAAAGAAAGAAAA-AA
* *
259289 GATAAAAAGAGAACAAAAAAAGAAAGACAAA
1 GA-AAGAA-AGAA-AAAGAAAG-AA-A-AAA
*
259320 TGAAAGAAA-AGAAAAGAAA-AGAAAA
1 -GAAAGAAAGA-AAAAGAAAGAAAAAA
* *
259345 G-AAGAAATGAGAAAA-AATGAATAAA
1 GAAAGAAA-GA-AAAAGAAAGAAAAAA
* *
259370 GAAAAGATAGATAAAAAGAAAGAATAAA
1 G-AAAGA-A-AGAAAAAGAAAGAAAAAA
259398 GAAA
1 GAAA
259402 ATTGAAAAGA
Statistics
Matches: 109, Mismatches: 10, Indels: 35
0.71 0.06 0.23
Matches are distributed among these distances:
23 6 0.06
24 11 0.10
25 31 0.28
26 5 0.05
27 16 0.15
28 18 0.17
29 8 0.07
30 4 0.04
31 7 0.06
32 3 0.03
ACGTcount: A:0.75, C:0.01, G:0.19, T:0.05
Consensus pattern (25 bp):
GAAAGAAAGAAAAAGAAAGAAAAAA
Found at i:261876 original size:42 final size:41
Alignment explanation
Indices: 261809--261916 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 41
261799 ACTTAGTAAG
* * * * *
261809 TCCTTCGGGCCAT-CAGTAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCAGGCCATCCA-TAAGCCTTTCAAGCAAGATG-ATAAA
* * *
261851 TCCTTCAGGTCATCTATAAGCCTTTCAAGCAAGATGATAAG
1 TCCTTCAGGCCATCCATAAGCCTTTCAAGCAAGATGATAAA
261892 TCCTTCAGGCCATCCATAAGACCTT
1 TCCTTCAGGCCATCCATAAG-CCTT
261917 CGGGCAGGAT
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 21 0.39
42 32 0.59
43 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (41 bp):
TCCTTCAGGCCATCCATAAGCCTTTCAAGCAAGATGATAAA
Found at i:262110 original size:42 final size:41
Alignment explanation
Indices: 262049--262144 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 41
262039 AAGTCCTTTT
* * **
262049 GGCCATC-AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCG
1 GGCCATCTA-TAAGCCTTTCGAACAAAATGA-TAAATCCTTCG
* *
262091 GGTCATCTATAAGCCTTTCGAACAAAATGATAAGTCCTTCG
1 GGCCATCTATAAGCCTTTCGAACAAAATGATAAATCCTTCG
*
262132 GGCCATTTATAAG
1 GGCCATCTATAAG
262145 ACATTCAGAT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
41 21 0.47
42 23 0.51
43 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (41 bp):
GGCCATCTATAAGCCTTTCGAACAAAATGATAAATCCTTCG
Found at i:262226 original size:233 final size:233
Alignment explanation
Indices: 261804--262237 Score: 647
Period size: 233 Copynumber: 1.9 Consensus size: 233
261794 TTCTTACTTA
*
261804 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTATA
* * * *
261869 AGCCTTTCAAGCAAGATGATAAGTCCTTCAGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCA
66 AGCCTTTCAAGCAAAATGATAAGTCCTTCAGGCCATCCATAAGACATTCAGACAGGATGTTTTCA
* *
261934 CATGTCTCTCGAAGAATGAGAAAAGTTTCTAATTTAAATATGAAAATTGAAACTTTTGAAAAGTA
131 CATGTCTCTCAAAAAATGAGAAAAGTTTCTAATTTAAATATGAAAATTGAAACTTTTGAAAAGTA
261999 AGAAAAGTTTCTTATCGAGTAAACAATTTCCAAAATTG
196 AGAAAAGTTTCTTATCGAGTAAACAATTTCCAAAATTG
** *
262037 GTAAGTCCTTTTGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTATA
* ** *
262102 AGCCTTTCGAA-CAAAATGATAAGTCCTTCGGGCCATTTATAAGACATTCAGATAGGATGTTTTC
66 AGCCTTTC-AAGCAAAATGATAAGTCCTTCAGGCCATCCATAAGACATTCAGACAGGATGTTTTC
* * * * * *
262166 A-AGTGTTTTTCAAAAAATGAGAAAAGTTTCTCATTTAAATATGAGAATTGAGATTTTTGAAAAG
130 ACA-TGTCTCTCAAAAAATGAGAAAAGTTTCTAATTTAAATATGAAAATTGAAACTTTTGAAAAG
*
262230 TGAGAAAA
194 TAAGAAAA
262238 CGATTTATGA
Statistics
Matches: 178, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
232 1 0.01
233 175 0.98
234 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (233 bp):
GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCAGGTCATCTATA
AGCCTTTCAAGCAAAATGATAAGTCCTTCAGGCCATCCATAAGACATTCAGACAGGATGTTTTCA
CATGTCTCTCAAAAAATGAGAAAAGTTTCTAATTTAAATATGAAAATTGAAACTTTTGAAAAGTA
AGAAAAGTTTCTTATCGAGTAAACAATTTCCAAAATTG
Found at i:262882 original size:128 final size:128
Alignment explanation
Indices: 262655--263038 Score: 405
Period size: 134 Copynumber: 2.9 Consensus size: 128
262645 GGAACATTGA
* * * * *
262655 AATGAATCAACGTCCCTAGATCTGATTTTCCCTCTAGAAGAAGCAAAATAGATCCATCTCTTTCA
1 AATGAATCAACATCCCTAGATCTGATTTTCCCTCAAGAAAAAGCAGAATAGATCC-TCTTTTTCA
* * * * * *
262720 AGATTTGATATTTCCTGAGGAAAAATGGACCAAGTTTTCCTCGATTCAATCTTCCTT-ACAATGG
65 AGATTTGATATTCCCTGAGTAACAATGGAACAAGTCTACCTC-ATTCAATCTTCCTTAACAATGG
* *
262784 AATGAATCAACATCCCTGGATCTGATTTTTCCCTCAAGAAAAAGCGGAATAGAT-CTCTTTTTCA
1 AATGAATCAACATCCCTAGATCTGA-TTTTCCCTCAAGAAAAAGCAGAATAGATCCTCTTTTTCA
* * *
262848 ATATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTGCCTCTATTCAATCTT-CTATAAAGAAC
65 AGATTTGATATTCCCTGAGTAACAATGGAACAAGTCTACCTC-ATTCAATCTTCCT-T----AAC
262912 AATGG
124 AATGG
* * * * * * *
262917 AATGAATCAACATCCCCAGATCTGATTTTCCCTTAAGTAAAAGTAGAACAAATCCCTCATTTTCA
1 AATGAATCAACATCCCTAGATCTGATTTTCCCTCAAGAAAAAGCAGAATAGAT-CCTCTTTTTCA
* * * *
262982 AGATTTGATCTTCCCTAAGTAACATTAGAACAAGTCTACCTCAGTTCAATCTTCCTT
65 AGATTTGATATTCCCTGAGTAACAATGGAACAAGTCTACCTCA-TTCAATCTTCCTT
263039 GAAGAAAAGT
Statistics
Matches: 213, Mismatches: 31, Indels: 17
0.82 0.12 0.07
Matches are distributed among these distances:
127 2 0.01
128 53 0.25
129 24 0.11
130 24 0.11
132 22 0.10
133 31 0.15
134 55 0.26
135 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (128 bp):
AATGAATCAACATCCCTAGATCTGATTTTCCCTCAAGAAAAAGCAGAATAGATCCTCTTTTTCAA
GATTTGATATTCCCTGAGTAACAATGGAACAAGTCTACCTCATTCAATCTTCCTTAACAATGG
Found at i:263256 original size:3 final size:3
Alignment explanation
Indices: 263248--263318 Score: 72
Period size: 3 Copynumber: 23.7 Consensus size: 3
263238 CTTTTATTTT
* * * *
263248 TTA TTA TTA TTA TGA TTA TTA TTA TTTA TTA ATA TTA TTA ATA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
* *
263294 TTA TTA -TA TTA ATA ATA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
263319 TATTTTAACA
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Done.