Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008292.1 Hibiscus syriacus cultivar Beakdansim tig00110956_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: 1591938
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 6 of 8
Found at i:1053514 original size:18 final size:18
Alignment explanation
Indices: 1053491--1053525 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1053481 GCAGCCACTG
1053491 CAGCCATATATAATGCCA
1 CAGCCATATATAATGCCA
*
1053509 CAGCCATATATGATGCC
1 CAGCCATATATAATGCC
1053526 GTCATCGCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (18 bp):
CAGCCATATATAATGCCA
Found at i:1055640 original size:102 final size:104
Alignment explanation
Indices: 1055452--1055664 Score: 295
Period size: 110 Copynumber: 2.0 Consensus size: 104
1055442 ATTAACAAAA
* * *
1055452 TTAATTTTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
1055517 AATTAAAACGTTAAAATGTTACCGTATCAGCATAGTGTCGAGATAT
66 AATTAAAAC------A-GTTACCGTATCAGCAAAGTGTAGAGATAT
*
1055563 TTAATTCTTAATCTAATAATCATGCTTTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1055627 AATTAAAAC-GTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACAGTTACCGTATCAGCAAAGTGTAGAGATAT
1055665 ATGATTTCCA
Statistics
Matches: 96, Mismatches: 6, Indels: 9
0.86 0.05 0.08
Matches are distributed among these distances:
102 27 0.28
110 36 0.38
111 33 0.34
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (104 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACAGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:1055996 original size:50 final size:51
Alignment explanation
Indices: 1055953--1056068 Score: 171
Period size: 51 Copynumber: 2.3 Consensus size: 51
1055943 TATAGCGTAA
* ** *
1055953 TGCAGGGGCCGCGCTATACCC-ACATGGCGCCAGCTCACCGTATAGCACGG
1 TGCAGGGGGCGCGCTATACCCTACATGGCGCCAAATCACCGTATAGCGCGG
* *
1056003 TGCAGGGGGCGCGCTATACCCTACGTGGCGCCAAATCATCGTATAGCGCGG
1 TGCAGGGGGCGCGCTATACCCTACATGGCGCCAAATCACCGTATAGCGCGG
1056054 TGCAGGGGGCGCGCT
1 TGCAGGGGGCGCGCT
1056069 TTACTGCTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 20 0.34
51 39 0.66
ACGTcount: A:0.18, C:0.32, G:0.34, T:0.16
Consensus pattern (51 bp):
TGCAGGGGGCGCGCTATACCCTACATGGCGCCAAATCACCGTATAGCGCGG
Found at i:1059146 original size:14 final size:14
Alignment explanation
Indices: 1059127--1059157 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1059117 TGTTCAATGT
1059127 TTTTGCATTATTTC
1 TTTTGCATTATTTC
1059141 TTTTGCATTATTTC
1 TTTTGCATTATTTC
1059155 TTT
1 TTT
1059158 GGCAAGAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTTGCATTATTTC
Found at i:1060337 original size:15 final size:15
Alignment explanation
Indices: 1060317--1060398 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
1060307 TTTCAGAAAA
1060317 TGAATTACTGGAATT
1 TGAATTACTGGAATT
1060332 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
1060347 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
1060362 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
1060377 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
1060391 TGAATTAC
1 TGAATTAC
1060399 ATTTCTGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:1060351 original size:30 final size:30
Alignment explanation
Indices: 1060317--1060398 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
1060307 TTTCAGAAAA
**
1060317 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
1060347 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
1060377 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
1060399 ATTTCTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:1060376 original size:45 final size:44
Alignment explanation
Indices: 1060312--1060398 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
1060302 TGGTTTTTCA
**
1060312 GAAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTG
1060357 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1060399 ATTTCTGGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (44 bp):
GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTG
Found at i:1060404 original size:20 final size:20
Alignment explanation
Indices: 1060381--1060450 Score: 140
Period size: 20 Copynumber: 3.5 Consensus size: 20
1060371 GGAATTTGAA
1060381 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1060401 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1060421 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1060441 TTCTGGAAAA
1 TTCTGGAAAA
1060451 CATCTGGAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:1060732 original size:22 final size:23
Alignment explanation
Indices: 1060707--1060750 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1060697 GATTATTTTA
1060707 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
1060729 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
1060751 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:1060755 original size:22 final size:22
Alignment explanation
Indices: 1060711--1060767 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
1060701 ATTTTATATA
* *
1060711 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
1060732 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
1060754 ATATTTTAAATATT
1 ATATTATAAATATT
1060768 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:1060766 original size:52 final size:51
Alignment explanation
Indices: 1060647--1060767 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 51
1060637 TAAAAAAATT
**
1060647 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
1060698 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
1060752 ATATATTTTAAATATT
1 ATATATTTTAAATATT
1060768 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.33
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:1061015 original size:42 final size:42
Alignment explanation
Indices: 1060956--1061071 Score: 205
Period size: 42 Copynumber: 2.8 Consensus size: 42
1060946 ATGAATTACA
* *
1060956 TTCCGGAAAACGAATTACGTGAAATAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
1060998 TTCCGGAAAACAAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1061040 TTCCGGAAAACGAATTACGTGAAACAAACACG
1 TTCCGGAAAACGAATTACGTGAAACAAACACG
1061072 AAAATTCAGA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:1066422 original size:30 final size:30
Alignment explanation
Indices: 1066388--1066477 Score: 144
Period size: 30 Copynumber: 3.0 Consensus size: 30
1066378 CCCGAAGGAC
1066388 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1066418 CTATCCAGAGGTCATAAAGTTCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* * *
1066448 CTGTCCATAGGTCATAAAGATCATCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1066478 ACTGTCCATA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1069068 original size:22 final size:22
Alignment explanation
Indices: 1069042--1069089 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1069032 TTCAGTATTC
1069042 GTCCCGAAAGACTACTATATAT
1 GTCCCGAAAGACTACTATATAT
* *
1069064 GTCCCGAATGACTGCTATATAT
1 GTCCCGAAAGACTACTATATAT
1069086 GTCC
1 GTCC
1069090 TGTAGGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (22 bp):
GTCCCGAAAGACTACTATATAT
Found at i:1069121 original size:15 final size:15
Alignment explanation
Indices: 1069101--1069133 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1069091 GTAGGACCAT
1069101 TACGTCCCGAAGGAC
1 TACGTCCCGAAGGAC
1069116 TACGTCCCGAAGGAC
1 TACGTCCCGAAGGAC
1069131 TAC
1 TAC
1069134 AATACCCTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.15
Consensus pattern (15 bp):
TACGTCCCGAAGGAC
Found at i:1069788 original size:35 final size:35
Alignment explanation
Indices: 1069741--1069810 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
1069731 TTCATTTAGG
*
1069741 GGGGAATTGATACCCCCCA-AGGGGAATCTGTTCCC
1 GGGGAATCGATA-CCCCCAGAGGGGAATCTGTTCCC
*
1069776 GGGGAATCGATACCCCCAGGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCAGAGGGGAATCTGTTCCC
1069811 CCTGCACATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 6 0.19
35 26 0.81
ACGTcount: A:0.21, C:0.29, G:0.31, T:0.19
Consensus pattern (35 bp):
GGGGAATCGATACCCCCAGAGGGGAATCTGTTCCC
Found at i:1071321 original size:21 final size:21
Alignment explanation
Indices: 1071273--1071321 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1071263 TAAATCCAAA
1071273 TCTTAAACTCTAAACAATAAC
1 TCTTAAACTCTAAACAATAAC
* * *
1071294 TCCTAAACTCTAAACATTATC
1 TCTTAAACTCTAAACAATAAC
1071315 TCTTAAA
1 TCTTAAA
1071322 TTATACATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (21 bp):
TCTTAAACTCTAAACAATAAC
Found at i:1071352 original size:14 final size:14
Alignment explanation
Indices: 1071329--1071373 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
1071319 AAATTATACA
*
1071329 TAAACTTTAAATCT
1 TAAACCTTAAATCT
1071343 TAAACCTTAAAT-T
1 TAAACCTTAAATCT
*
1071356 TAAACCCTAAATCT
1 TAAACCTTAAATCT
1071370 TAAA
1 TAAA
1071374 AAAAAAACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.43
14 16 0.57
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAACCTTAAATCT
Found at i:1080850 original size:2 final size:2
Alignment explanation
Indices: 1080843--1080869 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1080833 CTCTTTATTT
1080843 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1080870 TTTTATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1081799 original size:23 final size:24
Alignment explanation
Indices: 1081768--1081814 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1081758 GTCGAAGATG
*
1081768 TTAAATATTTTTTTCAA-TATTTT
1 TTAAATATTATTTTCAATTATTTT
*
1081791 TTAATTATTATTTTCAATTATTTT
1 TTAAATATTATTTTCAATTATTTT
1081815 CATATATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (24 bp):
TTAAATATTATTTTCAATTATTTT
Found at i:1081804 original size:13 final size:13
Alignment explanation
Indices: 1081773--1081812 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
1081763 AGATGTTAAA
*
1081773 TATTTTTTTCAA-
1 TATTATTTTCAAT
1081785 TATT-TTTT-AAT
1 TATTATTTTCAAT
1081796 TATTATTTTCAAT
1 TATTATTTTCAAT
1081809 TATT
1 TATT
1081813 TTCATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 8 0.32
12 8 0.32
13 7 0.28
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTTTCAAT
Found at i:1081822 original size:23 final size:24
Alignment explanation
Indices: 1081768--1081823 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 24
1081758 GTCGAAGATG
* *
1081768 TTAA-ATATTTTTTTCAATATTTT
1 TTAATATATTATTTTCAATATATT
1081791 TTAAT-TATTATTTTCAAT-TATT
1 TTAATATATTATTTTCAATATATT
*
1081813 TTCATATATTA
1 TTAATATATTA
1081824 CGAATTGAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (24 bp):
TTAATATATTATTTTCAATATATT
Found at i:1081823 original size:13 final size:12
Alignment explanation
Indices: 1081771--1081823 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
1081761 GAAGATGTTA
*
1081771 AATATTTTTTTC
1 AATATTATTTTC
1081783 AATATT-TTTT-
1 AATATTATTTTC
1081793 AATTATTATTTTC
1 AA-TATTATTTTC
1081806 -A-ATTATTTTC
1 AATATTATTTTC
1081816 ATATATTA
1 A-ATATTA
1081824 CGAATTGAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
10 11 0.31
11 8 0.23
12 12 0.34
13 4 0.11
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (12 bp):
AATATTATTTTC
Found at i:1083480 original size:17 final size:18
Alignment explanation
Indices: 1083460--1083493 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1083450 AAATTTTAAG
*
1083460 TATAATTTTAAA-AAAAT
1 TATAAATTTAAATAAAAT
1083477 TATAAATTTAAATAAAA
1 TATAAATTTAAATAAAA
1083494 ATTGATAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TATAAATTTAAATAAAAT
Found at i:1090199 original size:27 final size:28
Alignment explanation
Indices: 1090134--1090377 Score: 120
Period size: 27 Copynumber: 8.8 Consensus size: 28
1090124 CCAGAATTTA
* *
1090134 GATTGAAGCACAGAGGTGCTCAGTCATA
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
**
1090162 G-TTGGCTGCACAGAGGTG-TCAGTCCTC
1 GATT-GAAGCACAGAGGTGCTCAGTCCTC
* * *
1090189 GATTGAAGCACAGAAGTGCTCAATCATC
1 GATTGAAGCACAGAGGTGCTCAGTCCTC
*
1090217 --TTAGCTA-CACAGAGGTG-TCAGCTCC-C
1 GATT-G-AAGCACAGAGGTGCTCAG-TCCTC
* * *
1090243 -AGCTGAAGCACAGAGGTGCTCAGTCATTT
1 GA-TTGAAGCACAGAGGTGCTCAGTC-CTC
** * *
1090272 TTTTTAACTGCACAGAGGTG-TCAGTTCTC
1 GATTGAA--GCACAGAGGTGCTCAGTCCTC
*
1090301 GATTGAAGCACAGAGGTGCTCAATCACT-
1 GATTGAAGCACAGAGGTGCTCAGTC-CTC
* *
1090329 -TTTGGCTA-CACAGAGGTG-TCAG-CTCTC
1 GATT-G-AAGCACAGAGGTGCTCAGTC-CTC
1090356 GATTGAAGCACAGAGGTGCTCA
1 GATTGAAGCACAGAGGTGCTCA
1090378 ATCGTTAATT
Statistics
Matches: 159, Mismatches: 34, Indels: 46
0.67 0.14 0.19
Matches are distributed among these distances:
26 11 0.07
27 73 0.46
28 48 0.30
29 11 0.07
30 5 0.03
31 11 0.07
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (28 bp):
GATTGAAGCACAGAGGTGCTCAGTCCTC
Found at i:1090208 original size:55 final size:55
Alignment explanation
Indices: 1090134--1090380 Score: 286
Period size: 55 Copynumber: 4.5 Consensus size: 55
1090124 CCAGAATTTA
* ** * *
1090134 GATTGAAGCACAGAGGTGCTCAGTCATAGTTGGCTGCACAGAGGTGTCAGTCCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTC
* *
1090189 GATTGAAGCACAGAAGTGCTCAATCA-TCTTAGCTACACAGAGGTGTCAGCTCC-C
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAG-TCCTC
* * * * *
1090243 -AGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 GA-TTGAAGCACAGAGGTGCTCAATCA---TTTTTAGCTACACAGAGGTGTCAGTCCTC
* *
1090301 GATTGAAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAG-CTCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTC-CTC
1090356 GATTGAAGCACAGAGGTGCTCAATC
1 GATTGAAGCACAGAGGTGCTCAATC
1090381 GTTAATTCTA
Statistics
Matches: 163, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
53 1 0.01
54 41 0.25
55 75 0.46
57 2 0.01
58 43 0.26
59 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTC
Found at i:1090396 original size:55 final size:55
Alignment explanation
Indices: 1090080--1090401 Score: 265
Period size: 55 Copynumber: 5.8 Consensus size: 55
1090070 CTTGATTTTA
* * * * *
1090080 GATTGTAGCACAGAGGTGCTCAATCATTCCAA---T-GCACAGAGGTGCCAGAATTTA
1 GATTGAAGCACAGAGGTGCTCAATCATT--AATTCTAGCACAGAGGTGTCAG-CTCTC
* *
1090134 GATTGAAGCACAGAGGTGCTCAGTCA-TAGTTGGCT-GCACAGAGGTGTCAG-TCCTC
1 GATTGAAGCACAGAGGTGCTCAATCATTAATT--CTAGCACAGAGGTGTCAGCT-CTC
* * *
1090189 GATTGAAGCACAGAAGTGCTCAATCATCTTA-GCTA-CACAGAGGTGTCAGCTC-C
1 GATTGAAGCACAGAGGTGCTCAATCAT-TAATTCTAGCACAGAGGTGTCAGCTCTC
* * * ** * *
1090242 CAGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 GA-TTGAAGCACAGAGGTGCTCAATCATTAATTCT-A--GCACAGAGGTGTCAGCTCTC
1090301 GATTGAAGCACAGAGGTGCTCAATCACTT--TTGGCTA-CACAGAGGTGTCAGCTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA-TTAATT--CTAGCACAGAGGTGTCAGCTCTC
*
1090356 GATTGAAGCACAGAGGTGCTCAATCGTTAATTCTAGCACAGAGGTG
1 GATTGAAGCACAGAGGTGCTCAATCATTAATTCTAGCACAGAGGTG
1090402 CTATGGATTC
Statistics
Matches: 220, Mismatches: 25, Indels: 45
0.76 0.09 0.16
Matches are distributed among these distances:
51 1 0.00
53 5 0.02
54 70 0.32
55 80 0.36
56 17 0.08
57 3 0.01
58 39 0.18
59 5 0.02
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCATTAATTCTAGCACAGAGGTGTCAGCTCTC
Found at i:1090632 original size:81 final size:81
Alignment explanation
Indices: 1090497--1090653 Score: 260
Period size: 81 Copynumber: 1.9 Consensus size: 81
1090487 CGAGTTACAA
*
1090497 AGAATGGTTCACACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGTTAC
1 AGAATGGTTCACACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTAC
* *
1090562 TGAGCCGGTTGCACCG
66 CGAGCCAGTTGCACCG
* * *
1090578 AGAATGGTTCGCACACGAAATGGCGGATCGACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTAC
1 AGAATGGTTCACACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTAC
1090643 CGAGCCAGTTG
66 CGAGCCAGTTG
1090654 TGCAAGAGAC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 70 1.00
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (81 bp):
AGAATGGTTCACACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTAC
CGAGCCAGTTGCACCG
Found at i:1098733 original size:21 final size:20
Alignment explanation
Indices: 1098700--1098741 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1098690 TTAATTATTT
*
1098700 AAAAAATTAAATAAAATATA
1 AAAAAATTAAATAAAAAATA
*
1098720 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
1098741 A
1 A
1098742 TTTTTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAATTAAATAAAAAATA
Found at i:1103438 original size:18 final size:17
Alignment explanation
Indices: 1103395--1103456 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
1103385 TAGCGTTTAT
* *
1103395 TTAGAATTTGTGAAGGA
1 TTAGAATCTGTGAAGAA
*
1103412 TTAAAAATCTGTGAAAGAA
1 TT-AGAATCTGTG-AAGAA
* *
1103431 TTAGAATCTGTCAGGAA
1 TTAGAATCTGTGAAGAA
1103448 TTAGAATCT
1 TTAGAATCT
1103457 AATTCTATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
17 15 0.41
18 16 0.43
19 6 0.16
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (17 bp):
TTAGAATCTGTGAAGAA
Found at i:1104540 original size:2 final size:2
Alignment explanation
Indices: 1104533--1104564 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1104523 CACCTTACTT
1104533 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
1104565 ATTAAATTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1105739 original size:34 final size:34
Alignment explanation
Indices: 1105672--1105739 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
1105662 TTAAAAATTC
* *
1105672 AATTATTTATTTATTTGAAATAATATTATATTTA
1 AATTATCTATTTATTTGAAATAATATTAAATTTA
* *
1105706 AATTATCTATTTAATTTTAAATAA-CTTAAATTTA
1 AATTATCTATTT-ATTTGAAATAATATTAAATTTA
1105740 GGGTAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 19 0.66
35 10 0.34
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (34 bp):
AATTATCTATTTATTTGAAATAATATTAAATTTA
Found at i:1105849 original size:22 final size:22
Alignment explanation
Indices: 1105801--1105850 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1105791 TATTTAAGAT
*
1105801 TAAATAGATAATTTATTTCAAA
1 TAAATAGATAATTGATTTCAAA
* *
1105823 TAAATATATAATATGATTTTAAA
1 TAAATAGATAAT-TGATTTCAAA
1105846 -AAATA
1 TAAATA
1105851 AATATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (22 bp):
TAAATAGATAATTGATTTCAAA
Found at i:1108959 original size:20 final size:19
Alignment explanation
Indices: 1108934--1108996 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
1108924 TGTTTTGTAA
1108934 TTTTTTTGATTTTTTGATT
1 TTTTTTTGATTTTTTGATT
1108953 TTTTTTTGTATTTTTTCTGA-T
1 TTTTTTTG-A-TTTTT-TGATT
*
1108974 TTTTTCTGATTTTTT-ATT
1 TTTTTTTGATTTTTTGATT
1108992 TTTTT
1 TTTTT
1108997 AAATTCAAGT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
17 1 0.03
18 7 0.18
19 13 0.33
20 2 0.05
21 13 0.33
22 3 0.08
ACGTcount: A:0.10, C:0.03, G:0.08, T:0.79
Consensus pattern (19 bp):
TTTTTTTGATTTTTTGATT
Found at i:1108960 original size:30 final size:32
Alignment explanation
Indices: 1108926--1108988 Score: 96
Period size: 30 Copynumber: 2.0 Consensus size: 32
1108916 ATACTAATTG
1108926 TTTTGTAATTTTTT-TGA-TTTTT-TGATTTTT
1 TTTTGT-ATTTTTTCTGATTTTTTCTGATTTTT
1108956 TTTTGTATTTTTTCTGATTTTTTCTGATTTTT
1 TTTTGTATTTTTTCTGATTTTTTCTGATTTTT
1108988 T
1 T
1108989 ATTTTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 7 0.23
30 9 0.30
31 5 0.17
32 9 0.30
ACGTcount: A:0.11, C:0.03, G:0.10, T:0.76
Consensus pattern (32 bp):
TTTTGTATTTTTTCTGATTTTTTCTGATTTTT
Found at i:1108965 original size:12 final size:11
Alignment explanation
Indices: 1108943--1108988 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
1108933 ATTTTTTTGA
1108943 TTTTTTGATTT
1 TTTTTTGATTT
1108954 TTTTTTG-TATT
1 TTTTTTGAT-TT
*
1108965 TTTTCTGA-TT
1 TTTTTTGATTT
*
1108975 TTTTCTGATTT
1 TTTTTTGATTT
1108986 TTT
1 TTT
1108989 ATTTTTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
10 11 0.35
11 20 0.65
ACGTcount: A:0.09, C:0.04, G:0.09, T:0.78
Consensus pattern (11 bp):
TTTTTTGATTT
Found at i:1108996 original size:10 final size:10
Alignment explanation
Indices: 1108933--1108988 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
1108923 TTGTTTTGTA
1108933 ATTTTTT-TG
1 ATTTTTTCTG
1108942 A-TTTTT-TG
1 ATTTTTTCTG
*
1108950 ATTTTTTTTTG
1 A-TTTTTTCTG
1108961 TATTTTTTCTG
1 -ATTTTTTCTG
1108972 ATTTTTTCTG
1 ATTTTTTCTG
1108982 ATTTTTT
1 ATTTTTT
1108989 ATTTTTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
8 8 0.19
9 1 0.02
10 22 0.52
11 10 0.24
12 1 0.02
ACGTcount: A:0.11, C:0.04, G:0.09, T:0.77
Consensus pattern (10 bp):
ATTTTTTCTG
Found at i:1112158 original size:15 final size:16
Alignment explanation
Indices: 1112138--1112168 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1112128 TTTAAAAAAA
1112138 ATATTATAA-TTATTT
1 ATATTATAATTTATTT
1112153 ATATTATAATTTATTT
1 ATATTATAATTTATTT
1112169 TATAACATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATATTATAATTTATTT
Found at i:1122250 original size:42 final size:42
Alignment explanation
Indices: 1122149--1122235 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
1122139 GTCTGAAGCA
* * * *
1122149 ATGCCTCCTTTCATTCTATTTTAGGCGAGAATCGAAAGAGCG
1 ATGCCTCATTCCATTCTATTTTAGACGAGAATCAAAAGAGCG
* *
1122191 ATGCCTCATTCCATTCTATTTTAGACGAGAATTAAAAGTGCG
1 ATGCCTCATTCCATTCTATTTTAGACGAGAATCAAAAGAGCG
1122233 ATG
1 ATG
1122236 TTTTCTTCCG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (42 bp):
ATGCCTCATTCCATTCTATTTTAGACGAGAATCAAAAGAGCG
Found at i:1122271 original size:42 final size:42
Alignment explanation
Indices: 1122149--1122277 Score: 107
Period size: 42 Copynumber: 3.1 Consensus size: 42
1122139 GTCTGAAGCA
* * * * * *
1122149 ATGCCTCCTTTCATTCTATTTTAGGCGAGAATCGAAAGAGCG
1 ATGCCTCATTCCATTCTACTTTAGACAAGAATCGAAAGTGCG
* * **
1122191 ATGCCTCATTCCATTCTATTTTAGACGAGAATTAAAAGTGCG
1 ATGCCTCATTCCATTCTACTTTAGACAAGAATCGAAAGTGCG
** * * *
1122233 ATGTTTTC-TTCCGTTCTACTTTAGATAAGAATCGAAAGTACG
1 ATG-CCTCATTCCATTCTACTTTAGACAAGAATCGAAAGTGCG
1122275 ATG
1 ATG
1122278 ACGAGAATCA
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 69 0.97
43 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (42 bp):
ATGCCTCATTCCATTCTACTTTAGACAAGAATCGAAAGTGCG
Found at i:1122286 original size:21 final size:21
Alignment explanation
Indices: 1122260--1122299 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1122250 ACTTTAGATA
1122260 AGAATCGAAA-GTACGATGACG
1 AGAATC-AAATGTACGATGACG
*
1122281 AGAATCAAATGTGCGATGA
1 AGAATCAAATGTACGATGA
1122300 TTTCTTCCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.42, C:0.12, G:0.28, T:0.17
Consensus pattern (21 bp):
AGAATCAAATGTACGATGACG
Found at i:1122313 original size:63 final size:63
Alignment explanation
Indices: 1122214--1122340 Score: 200
Period size: 63 Copynumber: 2.0 Consensus size: 63
1122204 TTCTATTTTA
* * *
1122214 GACGAGAATTAAAAGTGCGATGTTTTCTTCCGTTCTACTTTAGATAAGAATCGAAAGTACGAT
1 GACGAGAATCAAAAGTGCGATGATTTCTTCCGTTCTACTTTAGACAAGAATCGAAAGTACGAT
* * *
1122277 GACGAGAATCAAATGTGCGATGATTTCTTCCGTTCTACTTTAGACGAGAATCGAAAGTGCGAT
1 GACGAGAATCAAAAGTGCGATGATTTCTTCCGTTCTACTTTAGACAAGAATCGAAAGTACGAT
1122340 G
1 G
1122341 CCTCATTCCA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (63 bp):
GACGAGAATCAAAAGTGCGATGATTTCTTCCGTTCTACTTTAGACAAGAATCGAAAGTACGAT
Found at i:1122337 original size:42 final size:42
Alignment explanation
Indices: 1122277--1122391 Score: 126
Period size: 42 Copynumber: 2.7 Consensus size: 42
1122267 AAAGTACGAT
** *
1122277 GACGAGAATC-AAATGTGCGATGATTTC-TTCCGTTCTACTTTA
1 GACGAGAATCGAAA-GTGCGATG-CCTCATTCCATTCTACTTTA
1122319 GACGAGAATCGAAAGTGCGATGCCTCATTCCATTCTACTTTA
1 GACGAGAATCGAAAGTGCGATGCCTCATTCCATTCTACTTTA
** * *
1122361 GATAAGAATCGAAAGAGCGATGTCTCCATTC
1 GACGAGAATCGAAAGTGCGATGCCT-CATTC
1122392 TATTTTATTC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
41 2 0.03
42 53 0.84
43 8 0.13
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (42 bp):
GACGAGAATCGAAAGTGCGATGCCTCATTCCATTCTACTTTA
Found at i:1124327 original size:37 final size:37
Alignment explanation
Indices: 1124242--1124327 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 37
1124232 ATTAAACTTT
*
1124242 TTTTATATTTTTAATTTTGTAAAAAAATTTATATAAATA
1 TTTTATA-ATTTAATTTTGTAAAAAAA-TTATATAAATA
*
1124281 --TTATGAATTTAATTTTTTAAAGAAAA-TATATAAATA
1 TTTTAT-AATTTAATTTTGTAAA-AAAATTATATAAATA
1124317 TTTTATAATTT
1 TTTTATAATTT
1124328 GTAATATTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
36 10 0.24
37 22 0.54
38 9 0.22
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (37 bp):
TTTTATAATTTAATTTTGTAAAAAAATTATATAAATA
Found at i:1124530 original size:20 final size:20
Alignment explanation
Indices: 1124471--1124523 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1124461 TAATCATATT
1124471 CACTGGTAATCTTTTATTCC
1 CACTGGTAATCTTTTATTCC
1124491 CACTGGTAATCTTTTATTCC
1 CACTGGTAATCTTTTATTCC
*
1124511 CACTGATAATCTT
1 CACTGGTAATCTT
1124524 ACATTCCGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.25, G:0.09, T:0.43
Consensus pattern (20 bp):
CACTGGTAATCTTTTATTCC
Found at i:1125765 original size:21 final size:21
Alignment explanation
Indices: 1125741--1125801 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
1125731 AAACATCTAC
1125741 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
*
1125762 CAAA----G--AAACATTTAT
1 CAAACTTTGAAAAACATTTTT
1125777 CAAACTTTGAAAAACATTTTT
1 CAAACTTTGAAAAACATTTTT
1125798 CAAA
1 CAAA
1125802 GTTGGTTGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
15 13 0.41
17 1 0.03
19 1 0.03
21 17 0.53
ACGTcount: A:0.48, C:0.15, G:0.05, T:0.33
Consensus pattern (21 bp):
CAAACTTTGAAAAACATTTTT
Found at i:1125781 original size:36 final size:36
Alignment explanation
Indices: 1125723--1125802 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
1125713 CCCATTCCTA
*
1125723 TTTTC-AACAAACATCTACCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
* *
1125758 TTTTCAAAGAAACATTTATCAAACTTTGAAAAACAT
1 TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
1125794 TTTTCAAAG
1 TTTTCAAAG
1125803 TTGGTTGCCA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 5 0.12
36 36 0.88
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (36 bp):
TTTTCAAAGAAACATCTACCAAACTTTGAAAAACAT
Found at i:1127163 original size:45 final size:46
Alignment explanation
Indices: 1127081--1127186 Score: 121
Period size: 45 Copynumber: 2.3 Consensus size: 46
1127071 GATGCACAGG
** *
1127081 TAGTGCATCGATGCACTCTTTTAAAATAAAAAGATCGAATGCA-AT
1 TAGTGCATCGATGCACTCCATTAAAATAAAAACATCGAATGCATAT
*
1127126 TAGTGCATCGATGCA-TCCCATTAATAAT-AAAACATCGAATGCATTT
1 TAGTGCATCGATGCACT-CCATTAA-AATAAAAACATCGAATGCATAT
*
1127172 TA-TGCACCGATGCAC
1 TAGTGCATCGATGCAC
1127187 AAGTAGTGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
44 1 0.02
45 45 0.87
46 6 0.12
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (46 bp):
TAGTGCATCGATGCACTCCATTAAAATAAAAACATCGAATGCATAT
Found at i:1127636 original size:29 final size:29
Alignment explanation
Indices: 1127593--1127702 Score: 161
Period size: 29 Copynumber: 3.8 Consensus size: 29
1127583 TATATGATAT
1127593 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
1127623 GAGAAATTG-CATGAGCTACATGATCACAA
1 GAGAAA-TGACATGAGCTACATGATCACAA
*
1127652 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
**
1127681 TTGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
1127703 ACATATAAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
28 9 0.12
29 58 0.78
30 7 0.09
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:1127816 original size:18 final size:18
Alignment explanation
Indices: 1127789--1127835 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
1127779 GGGTATAATA
* * *
1127789 GTCCTTCGGGACGTAGTG
1 GTCCTACGGGACATAGGG
1127807 GTCCTACGGGACATAGGG
1 GTCCTACGGGACATAGGG
1127825 GTCCTACGGGA
1 GTCCTACGGGA
1127836 TATATATGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.17, C:0.23, G:0.38, T:0.21
Consensus pattern (18 bp):
GTCCTACGGGACATAGGG
Found at i:1134597 original size:29 final size:29
Alignment explanation
Indices: 1134558--1134667 Score: 177
Period size: 29 Copynumber: 3.8 Consensus size: 29
1134548 TATATGATAT
1134558 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
*
1134588 GAGAAATGACATGAGCTACATGATCATAA
1 GAGAAATGACATGAGCTACATGATCACAA
* *
1134617 GAGAAATAACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
1134646 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
1134668 ACATATAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
28 7 0.09
29 62 0.84
30 5 0.07
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.18
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:1134796 original size:18 final size:18
Alignment explanation
Indices: 1134786--1134830 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1134776 GGGATATAGT
1134786 GGTCCTACGGGACGTAGG
1 GGTCCTACGGGACGTAGG
1134804 GGTCCTACGGGACGTAGG
1 GGTCCTACGGGACGTAGG
1134822 GGTCCTACG
1 GGTCCTACG
1134831 TGACATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.16, C:0.24, G:0.42, T:0.18
Consensus pattern (18 bp):
GGTCCTACGGGACGTAGG
Found at i:1139517 original size:21 final size:21
Alignment explanation
Indices: 1139462--1139511 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1139452 TATTTTCAAC
*
1139462 AAACATCTACCAAACTTTGAA
1 AAACATTTACCAAACTTTGAA
*
1139483 AAGCATTTACCAAACTTTGAA
1 AAACATTTACCAAACTTTGAA
1139504 AAACATTT
1 AAACATTT
1139512 TTCAAAGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.46, C:0.20, G:0.06, T:0.28
Consensus pattern (21 bp):
AAACATTTACCAAACTTTGAA
Found at i:1142007 original size:42 final size:42
Alignment explanation
Indices: 1141943--1142062 Score: 222
Period size: 42 Copynumber: 2.9 Consensus size: 42
1141933 TTTCCCCGAA
* *
1141943 TTCCAGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1141985 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1142027 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1142063 TGTAATTCAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:1142298 original size:22 final size:23
Alignment explanation
Indices: 1142251--1142364 Score: 74
Period size: 22 Copynumber: 4.8 Consensus size: 23
1142241 TAATTATTAA
* *
1142251 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
1142272 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
1142295 -ATATTTTTAATATTATATAAAATAATC
1 AATATTTATAATA--ATAT--AAT-ATT
*
1142322 AATTATATTATAATAATATAAGA-T
1 AA-TAT-TTATAATAATATAATATT
*
1142346 ATTATTTATTAATAATATA
1 AATATTTA-TAATAATATA
1142365 TAATAAATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 20
0.73 0.08 0.20
Matches are distributed among these distances:
21 11 0.15
22 18 0.24
23 17 0.23
24 5 0.07
25 1 0.01
26 5 0.07
27 2 0.03
28 5 0.07
29 3 0.04
30 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:1142327 original size:31 final size:32
Alignment explanation
Indices: 1142262--1142340 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 32
1142252 ATATTTAAAA
1142262 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTTATTAATATTTATAATAATATAATAT
*
1142294 TATATTT-TTAATA-TTAT-ATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAATATAAT--AT
*
1142325 TATATTATAATAATAT
1 TATATT-TATTAATAT
1142341 AAGATATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 9 0.22
30 4 0.10
31 14 0.35
32 8 0.20
33 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAATATAATAT
Found at i:1142393 original size:32 final size:28
Alignment explanation
Indices: 1142282--1142424 Score: 89
Period size: 29 Copynumber: 5.0 Consensus size: 28
1142272 AATATTTATA
* * *
1142282 ATAATATAATATTATATTTTTAATATTAT
1 ATAATATTAT-TTATATATTTAATAATAT
* * **
1142311 ATAAAATAATCAATTATATTATAATAATAT
1 ATAATATTATTTA-TATATT-TAATAATAT
*
1142341 A-AGATATTATTTAT-TA-ATAAT-ATAT
1 ATA-ATATTATTTATATATTTAATAATAT
* *
1142366 AATAAATTTTTTTTATATATTTAATAATGA-
1 -AT-AATATTATTTATATATTTAATAAT-AT
1142396 ATAATATTATTTATATATTTCAATAATAT
1 ATAATATTATTTATATATTT-AATAATAT
1142425 TTTAGTAAAG
Statistics
Matches: 87, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
25 4 0.05
26 5 0.06
27 9 0.10
28 23 0.26
29 28 0.32
30 17 0.20
31 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
ATAATATTATTTATATATTTAATAATAT
Found at i:1142398 original size:29 final size:27
Alignment explanation
Indices: 1142260--1142423 Score: 90
Period size: 28 Copynumber: 5.9 Consensus size: 27
1142250 AAATATTTAA
1142260 AATA-TATTTATTAATATTT-ATAATAAT
1 AATATTATTTA-T-ATATTTAATAATAAT
* * *
1142287 -ATAATA-TTATATTTTTAATATTATAT
1 AATATTATTTATATATTTAATAATA-AT
* * **
1142313 AAAATAATCAATTATATTATAATAAT-AT
1 AATATTATTTA-TATATT-TAATAATAAT
*
1142341 AAGATATTATTTAT-TA-ATAATATATAAT
1 -A-ATATTATTTATATATTTAATA-ATAAT
* *
1142369 AAATTTTTTTTATATATTTAATAATGAAT
1 -AATATTATTTATATATTTAATAAT-AAT
1142398 AATATTATTTATATATTTCAATAATA
1 AATATTATTTATATATTT-AATAATA
1142424 TTTTAGTAAA
Statistics
Matches: 103, Mismatches: 19, Indels: 29
0.68 0.13 0.19
Matches are distributed among these distances:
24 5 0.05
25 6 0.06
26 13 0.13
27 16 0.16
28 30 0.29
29 21 0.20
30 12 0.12
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (27 bp):
AATATTATTTATATATTTAATAATAAT
Found at i:1142615 original size:20 final size:20
Alignment explanation
Indices: 1142590--1142659 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
1142580 TTTTCAGATG
1142590 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1142610 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
1142630 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
1142650 TTTTTCAGAA
1 TTTTCCAGAA
1142660 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:1142663 original size:14 final size:15
Alignment explanation
Indices: 1142642--1142728 Score: 104
Period size: 15 Copynumber: 5.9 Consensus size: 15
1142632 TTACAGAAAT
*
1142642 GTAATTCATTTTTCA
1 GTAATTCATTTTCCA
**
1142657 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
1142671 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
1142686 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
**
1142701 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
1142716 GTAATTCATTTTC
1 GTAATTCATTTTC
1142729 TGGAAAACCA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 11 0.18
15 51 0.82
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:1142668 original size:40 final size:40
Alignment explanation
Indices: 1142590--1142668 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
1142580 TTTTCAGATG
* **
1142590 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
* *
1142630 TTTTACAGAAATGTAATTCATTTTTCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
1142669 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:1142678 original size:15 final size:15
Alignment explanation
Indices: 1142658--1142723 Score: 114
Period size: 15 Copynumber: 4.4 Consensus size: 15
1142648 CATTTTTCAG
1142658 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
**
1142673 AATTCATTTTCCAGT
1 AATTCAAATTCCAGT
1142688 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
1142703 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
1142718 AATTCA
1 AATTCA
1142724 TTTTCTGGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:1142694 original size:30 final size:30
Alignment explanation
Indices: 1142642--1142723 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
1142632 TTACAGAAAT
*
1142642 GTAATTCATTTTTCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
1142671 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
1142701 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
1142724 TTTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 15 0.31
30 34 0.69
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:1144964 original size:29 final size:29
Alignment explanation
Indices: 1144922--1145003 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
1144912 AAACTAAATT
* * * *
1144922 GATGTAATTACTTATATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
* *
1144951 GATGTCATTGCTTACATTATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
1144980 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
1145004 GTTAGGTGAG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 40 0.89
30 5 0.11
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:1149069 original size:24 final size:21
Alignment explanation
Indices: 1149042--1149091 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 21
1149032 TGCATCTTGT
1149042 TTACTGTATATAGGATATTTCTTC
1 TTACTGT-TATAGG--ATTTCTTC
*
1149066 TTACTGTTATAGGGTTTCTTC
1 TTACTGTTATAGGATTTCTTC
1149087 TTACT
1 TTACT
1149092 TTGCTATAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 12 0.48
23 6 0.24
24 7 0.28
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.52
Consensus pattern (21 bp):
TTACTGTTATAGGATTTCTTC
Found at i:1149099 original size:23 final size:21
Alignment explanation
Indices: 1149059--1149101 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1149049 ATATAGGATA
*
1149059 TTTCTTCTTACTGTTATAGGG
1 TTTCTTCTTACTGCTATAGGG
1149080 TTTCTTCTTACTTTGCTATAGG
1 TTTCTTCTTAC--TGCTATAGG
1149102 CTTTTAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.14, C:0.16, G:0.16, T:0.53
Consensus pattern (21 bp):
TTTCTTCTTACTGCTATAGGG
Found at i:1151542 original size:22 final size:22
Alignment explanation
Indices: 1151469--1151529 Score: 122
Period size: 22 Copynumber: 2.8 Consensus size: 22
1151459 AATAAACTGA
1151469 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1151491 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1151513 TTTAAAATAAATCAATC
1 TTTAAAATAAATCAATC
1151530 TATACTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1151551 original size:54 final size:54
Alignment explanation
Indices: 1151491--1152045 Score: 618
Period size: 54 Copynumber: 10.4 Consensus size: 54
1151481 CAATCCATAT
1151491 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTA
1151545 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTA
*
1151599 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTA
1151653 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-TCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCT-ATACTAATAAATTA
* *** * * * *
1151707 TTTAAAATAAATCAATCTATACAACTACAAT-AATAAATCAAT-C-CAT--A-T-
1 TTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCTATACTAATAAATTA
* ** * ** * * * **
1151755 TTTAAAATAAATAAATCCATACTAATAAATTATTTAAAAC-A-AATCAATCCA-TA
1 TTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCTATACT-AATAAATTA
** * * * * * ** * **
1151808 TTTTAAAATAAATCAATTTATA-CTAATAAATTATTTAAAATA-AATCAATCCA-TA
1 -TTTAAAATAAATCAATCCATATTTTA-AAATAAATCAATCTATACT-AATAAATTA
*
1151862 TTTTAAAATAAATCAATCCGTATTTTAAAATAAATCAATCTATACTAATAAATTA
1 -TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTA
*
1151917 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTA
1151971 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-TCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCT-ATACTAATAAATTA
1152025 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1152046 CTAATAAATT
Statistics
Matches: 436, Mismatches: 48, Indels: 34
0.84 0.09 0.07
Matches are distributed among these distances:
48 26 0.06
49 6 0.01
50 3 0.01
52 5 0.01
53 9 0.02
54 376 0.86
55 11 0.03
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTA
Found at i:1151552 original size:32 final size:32
Alignment explanation
Indices: 1151513--1152122 Score: 237
Period size: 32 Copynumber: 20.4 Consensus size: 32
1151503 CAATCCATAT
1151513 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
1151545 TTTAAAATAAATCAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
1151567 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
1151599 TTTAAAATAAATCAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
1151621 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
1151653 TTTAAAATAAATCAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
1151675 TTTAAAATAAATCAAT-TCATACTAATAAATTA
1 TTTAAAATAAATCAATCT-ATACTAATAAATTA
1151707 TTTAAAATAAATCAATCTATAC-AACTACAA-TA
1 TTTAAAATAAATCAATCTATACTAA-TA-AATTA
* * * * *
1151739 -AT-AAATCAATCCATAT-TTTA-AAATAAATAAA
1 TTTAAAATAAAT-CA-ATCTATACTAATAAAT-TA
* * * * * * *
1151770 TCCATACTAATAAAT-TATTTAAAACAAATCAATCCATA
1 T--TTA-AAATAAATCAATCT-ATACTAATAAAT---TA
*
1151808 TTTTAAAATAAATCAATTTATACTAATAAATTA
1 -TTTAAAATAAATCAATCTATACTAATAAATTA
1151841 TTTAAAATAAATCAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
** *
1151863 TTTAAAATAAATCAATCCGTATTTTAAAATAAATCAA
1 TTTAAAATAAATCAAT-C-TATACT--AATAAAT-TA
* * * * * *
1151900 TCTATACTAATAAAT-TATTTAAAATAAATCAATCCATA
1 T-T-TA-AAATAAATCAATCTATACT-AATAAAT---TA
*
1151938 TTTTAAAATAAATCAATCCATACTAATAAATTA
1 -TTTAAAATAAATCAATCTATACTAATAAATTA
1151971 TTTAAAATAAATCAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
1151993 TTTAAAATAAATCAAT-TCATACTAATAAATTA
1 TTTAAAATAAATCAATCT-ATACTAATAAATTA
*
1152025 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
1152057 TTTAAAATAAATCAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
1152079 TTTAAAATAAATCAAT-TCATACTAATAAATTA
1 TTTAAAATAAATCAATCT-ATACTAATAAATTA
1152111 TTTAAAATAAAT
1 TTTAAAATAAAT
1152123 TATTTTAAAA
Statistics
Matches: 445, Mismatches: 37, Indels: 192
0.66 0.05 0.28
Matches are distributed among these distances:
22 98 0.22
23 7 0.02
24 6 0.01
26 17 0.04
28 16 0.04
29 2 0.00
30 14 0.03
31 16 0.04
32 171 0.38
33 9 0.02
34 4 0.01
35 1 0.00
36 49 0.11
37 17 0.04
38 5 0.01
39 6 0.01
40 7 0.02
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCTATACTAATAAATTA
Found at i:1151596 original size:22 final size:22
Alignment explanation
Indices: 1151547--1151595 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1151537 ATAAATTATT
**
1151547 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
1151569 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
1151592 TAAA
1 TAAA
1151596 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1151625 original size:22 final size:22
Alignment explanation
Indices: 1151599--1151641 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1151589 TAATAAATTA
1151599 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1151621 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1151642 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1151650 original size:22 final size:22
Alignment explanation
Indices: 1151601--1151649 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1151591 ATAAATTATT
**
1151601 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1151623 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1151646 TAAA
1 TAAA
1151650 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1151679 original size:22 final size:22
Alignment explanation
Indices: 1151653--1151695 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1151643 TAATAAATTA
1151653 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
1151675 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
1151696 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1151704 original size:22 final size:22
Alignment explanation
Indices: 1151655--1151703 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1151645 ATAAATTATT
**
1151655 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
1151677 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1151700 TAAA
1 TAAA
1151704 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1151849 original size:14 final size:15
Alignment explanation
Indices: 1151809--1151856 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
1151799 CAATCCATAT
1151809 TTTAAAATAAATCAA
1 TTTAAAATAAATCAA
*
1151824 TTTATACTAATAAAT-TA
1 TTTA-A--AATAAATCAA
1151841 TTTAAAATAAATCAA
1 TTTAAAATAAATCAA
1151856 T
1 T
1151857 CCATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 2 0.07
17 5 0.19
18 7 0.26
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (15 bp):
TTTAAAATAAATCAA
Found at i:1151867 original size:22 final size:22
Alignment explanation
Indices: 1151841--1151901 Score: 113
Period size: 22 Copynumber: 2.8 Consensus size: 22
1151831 TAATAAATTA
1151841 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
1151863 TTTAAAATAAATCAATCCGTAT
1 TTTAAAATAAATCAATCCATAT
1151885 TTTAAAATAAATCAATC
1 TTTAAAATAAATCAATC
1151902 TATACTAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1151943 original size:22 final size:22
Alignment explanation
Indices: 1151917--1151959 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1151907 TAATAAATTA
1151917 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1151939 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1151960 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1151968 original size:22 final size:22
Alignment explanation
Indices: 1151919--1151967 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1151909 ATAAATTATT
**
1151919 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
1151941 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1151964 TAAA
1 TAAA
1151968 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1151997 original size:22 final size:22
Alignment explanation
Indices: 1151971--1152013 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1151961 TAATAAATTA
1151971 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
1151993 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
1152014 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1152022 original size:22 final size:22
Alignment explanation
Indices: 1151973--1152021 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1151963 ATAAATTATT
**
1151973 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
1151995 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1152018 TAAA
1 TAAA
1152022 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1152083 original size:22 final size:22
Alignment explanation
Indices: 1152057--1152099 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1152047 TAATAAATTA
1152057 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
1152079 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
1152100 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1152131 original size:15 final size:15
Alignment explanation
Indices: 1152102--1152249 Score: 172
Period size: 15 Copynumber: 9.5 Consensus size: 15
1152092 AATTCATACT
1152102 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
1152116 AATAAATTATTTTAAAATA
1 AATAAATTATTTT---A-A
*
1152135 AATAAATCCATATTTTAT
1 AATAAAT---TATTTTAA
*
1152153 AATAATTTATTTTAA
1 AATAAATTATTTTAA
* *
1152168 AGTAAATTATTTTAT
1 AATAAATTATTTTAA
1152183 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1152198 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
1152213 CATAAATTATTTTAA
1 AATAAATTATTTTAA
1152228 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1152243 AATAAAT
1 AATAAAT
1152250 AATCTTATTA
Statistics
Matches: 114, Mismatches: 12, Indels: 15
0.81 0.09 0.11
Matches are distributed among these distances:
14 9 0.08
15 83 0.73
18 7 0.06
19 9 0.08
22 6 0.05
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1152151 original size:22 final size:22
Alignment explanation
Indices: 1152057--1152157 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
1152047 TAATAAATTA
*
1152057 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATAAATCCATAT
* *
1152079 TTTAAAATAAATCAATTCATACT
1 TTTAAAATAAATAAATCCATA-T
** * ** **
1152102 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-AAATCCA-TAT
1152126 TTTAAAATAAATAAATCCATAT
1 TTTAAAATAAATAAATCCATAT
*
1152148 TTTATAATAA
1 TTTAAAATAA
1152158 TTTATTTTAA
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
22 32 0.54
23 13 0.22
24 12 0.20
25 2 0.03
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATAAATCCATAT
Found at i:1152161 original size:47 final size:49
Alignment explanation
Indices: 1151752--1152189 Score: 160
Period size: 54 Copynumber: 8.3 Consensus size: 49
1151742 AATCAATCCA
* * * *
1151752 TATTTTAAAATAAATAAATCCATACTAATAAATTATTTAAAACAAATCAAT
1 TATTTTAAAATAAATAAATCCATACTAATAAATAATTT-ATA-AAGTAAAT
* ** * *
1151803 CCATATTTTAAAATAAATCAATTTATACTAATAAATTATTTAAAATAAA-TCAAT
1 ---TATTTTAAAATAAATAAATCCATACTAATAAATAATTT---ATAAAGTAAAT
* ** *
1151857 CCATATTTTAAAATAAATCAATCCGTATTTTAAAATAAATCAATCTATACTAA-TAAAT
1 ---TATTTTAAAATAAATAAATCC--ATACT--AATAAAT-AATTTATA--AAGTAAAT
* * **
1151915 TA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAA-TAAAT
1 TATTTTAAAATAAATAAATCCATA--CT--AATAAAT-AATTTATA--AAGTAAAT
* * *
1151969 TA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAA-TAAAT
1 TATTTTAAAATAAATAAATCCATA--CT--AATAAAT-AATTTATA--AAGTAAAT
* * *
1152023 TA-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA-TCAAT
1 TATTTTAAAATAAATAAATCCATACTAATAAATAATTT---ATAAAGTAAAT
* * *
1152073 CCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTA-AAA-TAAAT
1 ---TATTTTAAAATAAATAAATCCATACTAATAAATAATTTATAAAGTAAAT
**
1152123 TATTTTAAAATAAATAAATCCATA-TTTTATAATAATTTATTTTAAAGTAAAT
1 TATTTTAAAATAAATAAATCCATACTAATA-AATAATTTA---TAAAGTAAAT
*
1152175 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
1152190 TATTTTAAAA
Statistics
Matches: 334, Mismatches: 26, Indels: 50
0.81 0.06 0.12
Matches are distributed among these distances:
46 3 0.01
47 30 0.09
49 3 0.01
50 20 0.06
51 4 0.01
52 25 0.07
53 2 0.01
54 218 0.65
55 4 0.01
56 9 0.03
58 13 0.04
59 3 0.01
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (49 bp):
TATTTTAAAATAAATAAATCCATACTAATAAATAATTTATAAAGTAAAT
Found at i:1152196 original size:45 final size:44
Alignment explanation
Indices: 1152102--1152267 Score: 172
Period size: 45 Copynumber: 3.6 Consensus size: 44
1152092 AATTCATACT
* *
1152102 AATAAATTATTTAAAATAAATTATTTTAAAATAAATAAATCCATATTTTAT
1 AATAAATTATTTTAAATAAATTATTTT---AT-AATAAAT---TATTTTAA
*
1152153 AATAATTTATTTTAAAGTAAATTATTTTATAATAAATTATTTTAA
1 AATAAATTATTTTAAA-TAAATTATTTTATAATAAATTATTTTAA
* *
1152198 AATAAATTATTTTATCATAAATTATTTTAAAATAAATTATTTTAA
1 AATAAATTATTTTA-AATAAATTATTTTATAATAAATTATTTTAA
* * *
1152243 AATAAATAATCTT-ATTAAATTATTT
1 AATAAATTATTTTAAATAAATTATTT
1152268 AAAATTATTT
Statistics
Matches: 103, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
43 10 0.10
45 58 0.56
46 1 0.01
48 7 0.07
49 2 0.02
51 14 0.14
52 11 0.11
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (44 bp):
AATAAATTATTTTAAATAAATTATTTTATAATAAATTATTTTAA
Found at i:1159058 original size:10 final size:10
Alignment explanation
Indices: 1159043--1159077 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
1159033 TTCATCACAC
1159043 CAAATTCTCT
1 CAAATTCTCT
*
1159053 CAAATTTTCT
1 CAAATTCTCT
*
1159063 CAATTTCTCT
1 CAAATTCTCT
1159073 CAAAT
1 CAAAT
1159078 ACTATATCTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1159162 original size:17 final size:18
Alignment explanation
Indices: 1159125--1159165 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1159115 ATATTATGTA
*
1159125 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
1159143 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
1159160 TTTACT
1 TTTACT
1159166 GATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:1161436 original size:26 final size:24
Alignment explanation
Indices: 1161365--1161436 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
1161355 TTATATTTGT
1161365 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
1161390 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
1161412 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
1161437 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:1169186 original size:38 final size:37
Alignment explanation
Indices: 1169130--1169221 Score: 139
Period size: 38 Copynumber: 2.5 Consensus size: 37
1169120 CCTAAACTTG
* *
1169130 AACCCGACCCGACCCGACCTGAATATCCCACTTAAAAA
1 AACCCGACCCGACCCGACCCGAATATCACACTT-AAAA
* *
1169168 AACCCGACTCGACTCGACCCGAATATCACACTTAAAA
1 AACCCGACCCGACCCGACCCGAATATCACACTTAAAA
1169205 AACCCGACCCGACCCGA
1 AACCCGACCCGACCCGA
1169222 ACAAAATAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 19 0.40
38 29 0.60
ACGTcount: A:0.36, C:0.40, G:0.12, T:0.12
Consensus pattern (37 bp):
AACCCGACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:1169281 original size:16 final size:16
Alignment explanation
Indices: 1169260--1169292 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1169250 TGAATATATG
1169260 AATTAGAAATCCGAAC
1 AATTAGAAATCCGAAC
1169276 AATTAGAAATCCGAAC
1 AATTAGAAATCCGAAC
1169292 A
1 A
1169293 GACCCGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (16 bp):
AATTAGAAATCCGAAC
Found at i:1169513 original size:211 final size:212
Alignment explanation
Indices: 1169276--1169661 Score: 630
Period size: 211 Copynumber: 1.8 Consensus size: 212
1169266 AAATCCGAAC
* *
1169276 AATTAGAAATCCGAACAGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTT
1 AATTAGAAATCCCAACAGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTT
1169341 AATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGA
66 AATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGA
* *
1169406 ACCCCACCCGACCCGAATATCACACTT-AAAAAACCCGTCCCGAACAAAATAAAGTTTCATCCGA
131 ACCCCACCCGACCCAAATATCACACTTAAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGA
1169470 CCCGACCCGAATATATG
196 CCCGACCCGAATATATG
* * * * *
1169487 AATTAGAAATCCCACCCGATCCGAAATAATAAAAAAATGTTTTTATTTAATAAAAATAGTGACTT
1 AATTAGAAATCCCAACAGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTT
* * *
1169552 AATCCGACCCGATCTGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTTACCCTAAACCCGA
66 AATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGA
* * *
1169617 ACCCGACTCGACCCAAATATCACGCTTAAAAAAACCCGACCCGAA
131 ACCCCACCCGACCCAAATATCACACTTAAAAAAACCCGACCCGAA
1169662 TATCACACTT
Statistics
Matches: 159, Mismatches: 15, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
211 143 0.90
212 16 0.10
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.26
Consensus pattern (212 bp):
AATTAGAAATCCCAACAGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTT
AATCCGACCCGACCCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGA
ACCCCACCCGACCCAAATATCACACTTAAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGA
CCCGACCCGAATATATG
Found at i:1169688 original size:27 final size:28
Alignment explanation
Indices: 1169632--1169688 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
1169622 ACTCGACCCA
* *
1169632 AATATCACGCTTAAAAAAACCCGACCCG
1 AATATCACACTTAAAAAAACCCGACACG
*
1169660 AATATCACACTT-AAAAAACCTGACACG
1 AATATCACACTTAAAAAAACCCGACACG
1169687 AA
1 AA
1169689 CAAAATAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.47, C:0.28, G:0.09, T:0.16
Consensus pattern (28 bp):
AATATCACACTTAAAAAAACCCGACACG
Found at i:1169706 original size:239 final size:241
Alignment explanation
Indices: 1169411--1169874 Score: 770
Period size: 244 Copynumber: 1.9 Consensus size: 241
1169401 CCCGAACCCC
* * *
1169411 ACCCGACCCGAATATCACACTTAAAAAACCCGTCCCGAACAAAATAAAGTTTCATCCGACCCGAC
1 ACCCGACCCGAATATCACACTTAAAAAACCCGACACGAACAAAATAAAGGTTCATCCGACCCGAC
* * * *
1169476 CCGAATATATGAATTAGAAAT-CCC-ACCCGATCCGAAATAATAAAAAAATGTTTTTATTTAATA
66 CCGAATATATGAATTAGAAATCCCCGACCCGACCCAAAATAATAAAAAAATATTTTTATATAATA
* * *
1169539 AAAATAGTGACTTAATCCGACCCGATCTGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTT
131 AAAACAGTGACTTAATCCGACCCGACCTGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTC
*
1169604 ACCCTAAACCCGAACCCGACTCGACCCAAATATCACGCTTAAAAAA
196 ACCCTAAACCCGAACCCGACCCGACCCAAATATCACGCTTAAAAAA
*
1169650 ACCCGACCCGAATATCACACTTAAAAAACCTGACACGAACAAAATAAAGGTTCATCCGACCCGAC
1 ACCCGACCCGAATATCACACTTAAAAAACCCGACACGAACAAAATAAAGGTTCATCCGACCCGAC
*
1169715 CCGAATATATGAATTAGAAATCCGACCCGACCCGACCCAAAATAATAAAAAATTATTTTTATATA
66 CCGAATATATGAATTAGAAAT-C--CCCGACCCGACCCAAAATAATAAAAAAATATTTTTATATA
1169780 ATAAAAACAGTGACTTAATCCGACCCGACCTGAATTATATATATTTTCGGGTCGGTCCGGTTTTT
128 ATAAAAACAGTGACTTAATCCGACCCGACCTGAATTATATATATTTTCGGGTCGGTCCGGTTTTT
1169845 TTCACCCTAAACCCGAACCCGACCCGACCC
193 TTCACCCTAAACCCGAACCCGACCCGACCC
1169875 GACCCGAATA
Statistics
Matches: 207, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
239 82 0.40
243 3 0.01
244 122 0.59
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (241 bp):
ACCCGACCCGAATATCACACTTAAAAAACCCGACACGAACAAAATAAAGGTTCATCCGACCCGAC
CCGAATATATGAATTAGAAATCCCCGACCCGACCCAAAATAATAAAAAAATATTTTTATATAATA
AAAACAGTGACTTAATCCGACCCGACCTGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTC
ACCCTAAACCCGAACCCGACCCGACCCAAATATCACGCTTAAAAAA
Found at i:1186949 original size:64 final size:64
Alignment explanation
Indices: 1186881--1187036 Score: 174
Period size: 64 Copynumber: 2.4 Consensus size: 64
1186871 TTGAAGGTGT
* ** *
1186881 ATCGATGCACATGTAGTGCATCGATGCACTCTTTTAA-AATATAAACATCGAATGCA-ATTAGTG
1 ATCGATGCACAAGTAGTGCATCGATGCACTCCATTAATAATA-AAAAATCGAATGCATATTA-TG
1186944 C
64 C
* * * *
1186945 ATCGATGCATAAGGCA-TGCATCGATGCATTCCATTAATAATAAAAAATCGAATGCATTTTATGC
1 ATCGATGCACAA-GTAGTGCATCGATGCACTCCATTAATAATAAAAAATCGAATGCATATTATGC
* *
1187009 ACCGATGCACAAGTAGTGCATCAATGCA
1 ATCGATGCACAAGTAGTGCATCGATGCA
1187037 TACCTTCATT
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
63 2 0.03
64 65 0.86
65 9 0.12
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (64 bp):
ATCGATGCACAAGTAGTGCATCGATGCACTCCATTAATAATAAAAAATCGAATGCATATTATGC
Found at i:1187454 original size:29 final size:29
Alignment explanation
Indices: 1187415--1187495 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
1187405 TATGTGATAT
1187415 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
1187445 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
1187474 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
1187496 ACATATGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 7 0.14
29 39 0.76
30 5 0.10
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:1194322 original size:29 final size:29
Alignment explanation
Indices: 1194283--1194363 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
1194273 CATGTGATAT
*
1194283 GAGAACATGACATGAGCTACGTGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
1194313 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
1194342 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
1194364 CCATATGAAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
28 7 0.14
29 38 0.76
30 5 0.10
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:1194465 original size:15 final size:15
Alignment explanation
Indices: 1194447--1194481 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1194437 CGAGGGTATA
1194447 ATAGTCCTTCGGGAT
1 ATAGTCCTTCGGGAT
1194462 ATAGTCCTTCGGGAT
1 ATAGTCCTTCGGGAT
*
1194477 GTAGT
1 ATAGT
1194482 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (15 bp):
ATAGTCCTTCGGGAT
Found at i:1197775 original size:15 final size:16
Alignment explanation
Indices: 1197747--1197785 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1197737 TTATTTTAAT
*
1197747 TTTTTAAAATTAAATA
1 TTTTTAATATTAAATA
*
1197763 TTTTTAATA-TAAATT
1 TTTTTAATATTAAATA
1197778 TTTTTAAT
1 TTTTTAAT
1197786 TTCTTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTAATATTAAATA
Found at i:1205137 original size:24 final size:24
Alignment explanation
Indices: 1205101--1205170 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
1205091 AATAAACACT
*
1205101 TCTCCTTCTCTCTCTCCCCCCCCC
1 TCTCCCTCTCTCTCTCCCCCCCCC
* * *
1205125 TCTCCCTCCCTCTCTCCCCCTCTC
1 TCTCCCTCTCTCTCTCCCCCCCCC
*
1205149 TCTCTCTCTCTCTCTCCCCCCC
1 TCTCCCTCTCTCTCTCCCCCCC
1205171 TTTATAAAAG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (24 bp):
TCTCCCTCTCTCTCTCCCCCCCCC
Found at i:1205145 original size:14 final size:14
Alignment explanation
Indices: 1205110--1205154 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
1205100 TTCTCCTTCT
1205110 CTCTCTCCCCC-CC
1 CTCTCTCCCCCTCC
1205123 C-CTCT--CCCTCC
1 CTCTCTCCCCCTCC
*
1205134 CTCTCTCCCCCTCT
1 CTCTCTCCCCCTCC
1205148 CTCTCTC
1 CTCTCTC
1205155 TCTCTCTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
10 3 0.11
11 3 0.11
12 8 0.30
13 1 0.04
14 12 0.44
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (14 bp):
CTCTCTCCCCCTCC
Found at i:1205145 original size:20 final size:20
Alignment explanation
Indices: 1205120--1205160 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1205110 CTCTCTCCCC
1205120 CCCCCTCTCCCTCCCTCTCT
1 CCCCCTCTCCCTCCCTCTCT
* *
1205140 CCCCCTCTCTCTCTCTCTCT
1 CCCCCTCTCCCTCCCTCTCT
1205160 C
1 C
1205161 TCTCCCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (20 bp):
CCCCCTCTCCCTCCCTCTCT
Found at i:1205164 original size:10 final size:10
Alignment explanation
Indices: 1205122--1205162 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
1205112 CTCTCCCCCC
*
1205122 CCCTCTCCCT
1 CCCTCTCTCT
*
1205132 CCCTCTCTCC
1 CCCTCTCTCT
1205142 CCCTCTCTCT
1 CCCTCTCTCT
*
1205152 CTCTCTCTCT
1 CCCTCTCTCT
1205162 C
1 C
1205163 TCCCCCCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (10 bp):
CCCTCTCTCT
Found at i:1207027 original size:45 final size:45
Alignment explanation
Indices: 1206978--1207072 Score: 190
Period size: 45 Copynumber: 2.1 Consensus size: 45
1206968 AGAAGTTGAG
1206978 TGTTGAAGAAAAGAAAGCTGAAGATAAAGCTGGAGAGGAGAAGGC
1 TGTTGAAGAAAAGAAAGCTGAAGATAAAGCTGGAGAGGAGAAGGC
1207023 TGTTGAAGAAAAGAAAGCTGAAGATAAAGCTGGAGAGGAGAAGGC
1 TGTTGAAGAAAAGAAAGCTGAAGATAAAGCTGGAGAGGAGAAGGC
1207068 TGTTG
1 TGTTG
1207073 CTACGAAGGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.42, C:0.06, G:0.36, T:0.16
Consensus pattern (45 bp):
TGTTGAAGAAAAGAAAGCTGAAGATAAAGCTGGAGAGGAGAAGGC
Found at i:1208480 original size:40 final size:41
Alignment explanation
Indices: 1208416--1208507 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 41
1208406 ATTTTCTCTT
* * * * *
1208416 GTTTTATTTCTCAATTTTATCAAGCA-ATAAATAAATAAAA
1 GTTTTTTTTATCATTTTTACCAAGCACATAAATAAACAAAA
* *
1208456 -TATTTTTTTATCATTTTTACCAAGCACATCAATATACAAAA
1 GT-TTTTTTTATCATTTTTACCAAGCACATAAATAAACAAAA
1208497 GTTTTTTTTAT
1 GTTTTTTTTAT
1208508 AAATACTTCT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
39 1 0.02
40 20 0.48
41 20 0.48
42 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (41 bp):
GTTTTTTTTATCATTTTTACCAAGCACATAAATAAACAAAA
Found at i:1213074 original size:12 final size:13
Alignment explanation
Indices: 1213040--1213072 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1213030 TAAATTAGGA
1213040 TTATCTTTTAGAT
1 TTATCTTTTAGAT
1213053 TTATCTTTTA-AT
1 TTATCTTTTAGAT
1213065 TT-TCTTTT
1 TTATCTTTT
1213073 TATCTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.30
12 4 0.20
13 10 0.50
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.70
Consensus pattern (13 bp):
TTATCTTTTAGAT
Found at i:1213126 original size:12 final size:13
Alignment explanation
Indices: 1213093--1213127 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1213083 GAATTATCCC
*
1213093 TTATCTTTTGGGAT
1 TTAT-TTTTAGGAT
1213107 TTATTTTTAGGAT
1 TTATTTTTAGGAT
1213120 TTATTTTT
1 TTATTTTT
1213128 GAACAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.17, C:0.03, G:0.14, T:0.66
Consensus pattern (13 bp):
TTATTTTTAGGAT
Found at i:1217349 original size:14 final size:14
Alignment explanation
Indices: 1217332--1217361 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1217322 AAATTAAAAA
*
1217332 TATTAAATTATTAT
1 TATTAAAATATTAT
1217346 TATTAAAATATTAT
1 TATTAAAATATTAT
1217360 TA
1 TA
1217362 CATCTATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTAAAATATTAT
Found at i:1221853 original size:21 final size:20
Alignment explanation
Indices: 1221823--1221862 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1221813 CCTTTCTCAA
1221823 AGAAGATTTGGGAGGATTTAT
1 AGAAGATTT-GGAGGATTTAT
* *
1221844 AGAAGCTTTGTAGGATTTA
1 AGAAGATTTGGAGGATTTA
1221863 GAGGGTTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.35
Consensus pattern (20 bp):
AGAAGATTTGGAGGATTTAT
Found at i:1235285 original size:24 final size:22
Alignment explanation
Indices: 1235243--1235291 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
1235233 TTTAAATAAT
*
1235243 ATTTGAAAAATTGAAAAATGTG
1 ATTTGAAAAATTGAAAAATATG
*
1235265 ATTTGTAAAAATTAGACAAATATG
1 ATTTG-AAAAATT-GAAAAATATG
1235289 ATT
1 ATT
1235292 AGATTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 7 0.30
24 11 0.48
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (22 bp):
ATTTGAAAAATTGAAAAATATG
Found at i:1235402 original size:44 final size:44
Alignment explanation
Indices: 1235354--1235616 Score: 253
Period size: 44 Copynumber: 6.0 Consensus size: 44
1235344 AATTTATGAA
* * *
1235354 ATTGAAAATACTTAGAGACCTTAATTATAAAGGTAGAAATTGAG
1 ATTGAAAAAACTTAGGGACCTCAATTATAAAGGTAGAAATTGAG
* ** * *
1235398 ATTGAAAAAA-ATAGGGGTCTCAATTATAAAGGTA-TAATTGGG
1 ATTGAAAAAACTTAGGGACCTCAATTATAAAGGTAGAAATTGAG
* * * * *
1235440 ATTTAAAAAACATAGGGGCCTCAATTATAAAAGTAAAAATTGAG
1 ATTGAAAAAACTTAGGGACCTCAATTATAAAGGTAGAAATTGAG
* * *
1235484 ATTGAAAAAACTTAGGGACCTTAATTATAAAGATAGAAAGTGAG
1 ATTGAAAAAACTTAGGGACCTCAATTATAAAGGTAGAAATTGAG
* * * * * *
1235528 ATTAAAAAATATTTAAGGACCTCAATTATAAAGTTAAAAATGTGGG
1 ATTGAAAAA-ACTTAGGGACCTCAATTATAAAGGTAGAAAT-TGAG
* * * *
1235574 ATT-AAAAAAATTAGGGGCTTCAATTATAAAGATAGAAATTGAG
1 ATTGAAAAAACTTAGGGACCTCAATTATAAAGGTAGAAATTGAG
1235617 GTTTGTTGAC
Statistics
Matches: 179, Mismatches: 36, Indels: 9
0.80 0.16 0.04
Matches are distributed among these distances:
42 15 0.08
43 44 0.25
44 84 0.47
45 30 0.17
46 6 0.03
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (44 bp):
ATTGAAAAAACTTAGGGACCTCAATTATAAAGGTAGAAATTGAG
Found at i:1240395 original size:44 final size:44
Alignment explanation
Indices: 1240317--1240541 Score: 168
Period size: 41 Copynumber: 5.2 Consensus size: 44
1240307 GAAAAGGTAG
* * *
1240317 AAAATGAGATTGAAAAAAAATTAAGGGCCACAATTATAAAGTTAAAA
1 AAAATGAGATT---AAAAAATTAAGGACCTCAATTATAAAGGTAAAA
1240364 AAAATGAGATTAAAAAATTAAGGACCTCAATTATAAAGGT--AA
1 AAAATGAGATTAAAAAATTAAGGACCTCAATTATAAAGGTAAAA
* * *
1240406 AAAAT--GATTAAGAAAATT-AGATACTTCAATTATAAA-G-ATAA
1 AAAATGAGATTAA-AAAATTAAG-GACCTCAATTATAAAGGTAAAA
* * *
1240447 AAAGTGAGATTGAATAAAATT-AGGACTTCACTTATAAAGGTAAAA
1 AAAATGAGATT-AA-AAAATTAAGGACCTCAATTATAAAGGTAAAA
* * * * *
1240492 ATAA-GA-TTTAAAAAATTAA-GAGCCT-AAATATAAAGATGAAA
1 AAAATGAGATTAAAAAATTAAGGA-CCTCAATTATAAAGGTAAAA
1240533 AAAATGAGA
1 AAAATGAGA
1240542 CCCTAATTAC
Statistics
Matches: 145, Mismatches: 20, Indels: 30
0.74 0.10 0.15
Matches are distributed among these distances:
40 9 0.06
41 48 0.33
42 14 0.10
43 19 0.13
44 39 0.27
45 5 0.03
47 11 0.08
ACGTcount: A:0.56, C:0.06, G:0.14, T:0.24
Consensus pattern (44 bp):
AAAATGAGATTAAAAAATTAAGGACCTCAATTATAAAGGTAAAA
Found at i:1240422 original size:41 final size:41
Alignment explanation
Indices: 1240331--1240511 Score: 163
Period size: 44 Copynumber: 4.3 Consensus size: 41
1240321 TGAGATTGAA
* * *
1240331 AAAAAATTAAGGGCCACAATTATAAAGTTAAAAAAAATGAGATT
1 AAAAAATTAAGGACCTCAATTATAAAGGT--AAAAAAT-AGATT
1240375 AAAAAATTAAGGACCTCAATTATAAAGGTAAAAAAT-GATT
1 AAAAAATTAAGGACCTCAATTATAAAGGTAAAAAATAGATT
* * * *
1240415 AAGAAAATT-AGATACTTCAATTATAAAGATAAAAAGTGAGATT
1 AA-AAAATTAAG-GACCTCAATTATAAAGGTAAAAAAT-AGATT
* *
1240458 GAATAAAATT-AGGACTTCACTTATAAAGGT-AAAAATAAGATTT
1 -AA-AAAATTAAGGACCTCAATTATAAAGGTAAAAAAT-AGA-TT
1240501 AAAAAATTAAG
1 AAAAAATTAAG
1240512 AGCCTAAATA
Statistics
Matches: 117, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
40 8 0.07
41 33 0.28
42 19 0.16
43 21 0.18
44 36 0.31
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.26
Consensus pattern (41 bp):
AAAAAATTAAGGACCTCAATTATAAAGGTAAAAAATAGATT
Found at i:1240438 original size:85 final size:85
Alignment explanation
Indices: 1240347--1240509 Score: 217
Period size: 85 Copynumber: 1.9 Consensus size: 85
1240337 TTAAGGGCCA
1240347 CAATTATAAAGTTAAAAAAAATGAGATT-AA-AAAATTAAGGACCTCAATTATAAAGGTAAAAA-
1 CAATTATAAAG--AAAAAAAATGAGATTGAATAAAATT-AGGACCTCAATTATAAAGGTAAAAAT
*
1240409 ATGA-TTAAGAAAATTAGATACTT
63 AAGATTTAA-AAAATTAGATACTT
* * * *
1240432 CAATTATAAAGATAAAAAGTGAGATTGAATAAAATTAGGACTTCACTTATAAAGGTAAAAATAAG
1 CAATTATAAAGAAAAAAAATGAGATTGAATAAAATTAGGACCTCAATTATAAAGGTAAAAATAAG
1240497 ATTTAAAAAATTA
66 ATTTAAAAAATTA
1240510 AGAGCCTAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
83 13 0.19
84 25 0.36
85 27 0.39
86 4 0.06
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.28
Consensus pattern (85 bp):
CAATTATAAAGAAAAAAAATGAGATTGAATAAAATTAGGACCTCAATTATAAAGGTAAAAATAAG
ATTTAAAAAATTAGATACTT
Found at i:1240525 original size:84 final size:81
Alignment explanation
Indices: 1240331--1240541 Score: 203
Period size: 84 Copynumber: 2.5 Consensus size: 81
1240321 TGAGATTGAA
* *
1240331 AAAAAATTAAGGGCC-ACAATTATAAAGTTAAAAAAAATGAGATTAAAAAATTAAGGACCTCAAT
1 AAAAAATTAAGAGCCTA-AA-TATAAAG--ATAAAAAATGAGATTAAAAAATTAAGGACCTCAAT
*
1240395 TATAAAGGTAAAAAATGATT
62 TATAAAGGTAAAAAAAGATT
* * * * * *
1240415 AAGAAAATT-AGATACTTCAATTATAAAGATAAAAAGTGAGATTGAATAAAATT-AGGACTTCAC
1 AA-AAAATTAAGA-GCCT-AAATATAAAGATAAAAAATGAGATT-AA-AAAATTAAGGACCTCAA
1240478 TTATAAAGGTAAAAATAAGATTT
61 TTATAAAGGTAAAAA-AAGA-TT
1240501 AAAAAATTAAGAGCCTAAATATAAAGATGAAAAAAATGAGA
1 AAAAAATTAAGAGCCTAAATATAAAGAT--AAAAAATGAGA
1240542 CCCTAATTAC
Statistics
Matches: 103, Mismatches: 13, Indels: 20
0.76 0.10 0.15
Matches are distributed among these distances:
83 13 0.13
84 40 0.39
85 31 0.30
86 18 0.17
87 1 0.01
ACGTcount: A:0.55, C:0.06, G:0.14, T:0.25
Consensus pattern (81 bp):
AAAAAATTAAGAGCCTAAATATAAAGATAAAAAATGAGATTAAAAAATTAAGGACCTCAATTATA
AAGGTAAAAAAAGATT
Found at i:1240533 original size:29 final size:29
Alignment explanation
Indices: 1240501--1240566 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
1240491 AATAAGATTT
* *
1240501 AAAAAATTAAGAGCCTAAATATAAAGATGA
1 AAAAAATTAAGACCCTAAATACAAAGAT-A
* *
1240531 AAAAAA-TGAGACCCTAATTACAAAGATA
1 AAAAAATTAAGACCCTAAATACAAAGATA
1240559 AAAAAATT
1 AAAAAATT
1240567 GGAGGCCCGG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 7 0.23
29 18 0.58
30 6 0.19
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.20
Consensus pattern (29 bp):
AAAAAATTAAGACCCTAAATACAAAGATA
Found at i:1247079 original size:28 final size:28
Alignment explanation
Indices: 1247013--1247079 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
1247003 TTGAGGTAAC
*
1247013 ATAT-TTAA-AAGAAATCAATAAAATAA
1 ATATATTAACAAGAAATCAATAAAACAA
* *
1247039 ATATAGTAGCAAGTAAAT-AATAAAACAA
1 ATATATTAACAAG-AAATCAATAAAACAA
1247067 ATATATTAACAAG
1 ATATATTAACAAG
1247080 GAAAGATACA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
26 4 0.12
27 2 0.06
28 23 0.70
29 4 0.12
ACGTcount: A:0.61, C:0.06, G:0.07, T:0.25
Consensus pattern (28 bp):
ATATATTAACAAGAAATCAATAAAACAA
Found at i:1260503 original size:28 final size:28
Alignment explanation
Indices: 1260447--1260506 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
1260437 GTTTTTCATT
* *
1260447 TTATAAAAAGTGAAACAAATTGCAGTAA
1 TTATAAAAAGTGAAACAAATCGCAATAA
*
1260475 TTATAAAAAGTGCAACAAA-CGACAATAA
1 TTATAAAAAGTGAAACAAATCG-CAATAA
1260503 TTAT
1 TTAT
1260507 GTTATTATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.53, C:0.10, G:0.12, T:0.25
Consensus pattern (28 bp):
TTATAAAAAGTGAAACAAATCGCAATAA
Found at i:1261652 original size:8 final size:8
Alignment explanation
Indices: 1261641--1261675 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
1261631 AGAAAATAAA
*
1261641 AAATATTT
1 AAATGTTT
1261649 AAATGTTT
1 AAATGTTT
1261657 AAATGTTT
1 AAATGTTT
1261665 AAATGTTT
1 AAATGTTT
1261673 AAA
1 AAA
1261676 ATCATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (8 bp):
AAATGTTT
Found at i:1262946 original size:21 final size:22
Alignment explanation
Indices: 1262908--1262951 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1262898 TAATTAGTTT
* * *
1262908 TTTATTTACATATTATTT-TGA
1 TTTATTTAAAAATAATTTATGA
1262929 TTTATTTAAAAATAATTTATGA
1 TTTATTTAAAAATAATTTATGA
1262951 T
1 T
1262952 GTTTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (22 bp):
TTTATTTAAAAATAATTTATGA
Found at i:1264433 original size:16 final size:16
Alignment explanation
Indices: 1264403--1264432 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1264393 ATATTTACAT
1264403 TTTATTTTTATTTTTA
1 TTTATTTTTATTTTTA
1264419 TTTA-TTTTATTTTT
1 TTTATTTTTATTTTT
1264433 TGTGTCAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTATTTTTATTTTTA
Done.