Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008973.1 Hibiscus syriacus cultivar Beakdansim tig00112319_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: 2070395
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 11
Found at i:1340619 original size:54 final size:55
Alignment explanation
Indices: 1340503--1340751 Score: 313
Period size: 55 Copynumber: 4.5 Consensus size: 55
1340493 GTTTTTTAGG
* * * * * * * * *
1340503 AACTAAGTATGATTTTCATAAGTTTCTTTATGATTTTTAAATGAGATTTTAAAGA
1 AACTAAGTCTAATTTTTAGAAGTTTCTTGACGATTTTTAAACGAGCTTTCAAAGA
*
1340558 AACTAAGTCCAATTTTTAGAAGTTTCTTGACGA-TTTTAAACGAGCTTTCAAAGA
1 AACTAAGTCTAATTTTTAGAAGTTTCTTGACGATTTTTAAACGAGCTTTCAAAGA
* * * * *
1340612 AACTAAGTCTTATTTTCAAAAGTTACTTGACGATTTTTAAACGAGTTTTCAAAGA
1 AACTAAGTCTAATTTTTAGAAGTTTCTTGACGATTTTTAAACGAGCTTTCAAAGA
*
1340667 AACTAAGTCTAATTTTTAGAAGTTTCTTGATGATTTTTAAACGAGCTTTCAAAGA
1 AACTAAGTCTAATTTTTAGAAGTTTCTTGACGATTTTTAAACGAGCTTTCAAAGA
* *
1340722 AATTAAGTCTGATTTTTAG-AGATTTCTTGA
1 AACTAAGTCTAATTTTTAGAAG-TTTCTTGA
1340752 GAAAATGAAT
Statistics
Matches: 168, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
54 48 0.29
55 120 0.71
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (55 bp):
AACTAAGTCTAATTTTTAGAAGTTTCTTGACGATTTTTAAACGAGCTTTCAAAGA
Found at i:1340694 original size:109 final size:110
Alignment explanation
Indices: 1340503--1340737 Score: 357
Period size: 109 Copynumber: 2.1 Consensus size: 110
1340493 GTTTTTTAGG
* * * * * *
1340503 AACTAAGTATGATTTTCATAAGTTTCTTTATGATTTTTAAATGAGATTTTAAAGAAACTAAGTCC
1 AACTAAGTCTGATTTTCAAAAGTTACTTGACGATTTTTAAACGAGATTTTAAAGAAACTAAGTCC
1340568 AATTTTTAGAAGTTTCTTGACGA-TTTTAAACGAGCTTTCAAAGA
66 AATTTTTAGAAGTTTCTTGACGATTTTTAAACGAGCTTTCAAAGA
*
1340612 AACTAAGTCTTATTTTCAAAAGTTACTTGACGATTTTTAAACGAG-TTTTCAAAGAAACTAAGTC
1 AACTAAGTCTGATTTTCAAAAGTTACTTGACGATTTTTAAACGAGATTTT-AAAGAAACTAAGTC
* *
1340676 TAATTTTTAGAAGTTTCTTGATGATTTTTAAACGAGCTTTCAAAGA
65 CAATTTTTAGAAGTTTCTTGACGATTTTTAAACGAGCTTTCAAAGA
*
1340722 AATTAAGTCTGATTTT
1 AACTAAGTCTGATTTT
1340738 TAGAGATTTC
Statistics
Matches: 113, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
108 4 0.04
109 74 0.65
110 35 0.31
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (110 bp):
AACTAAGTCTGATTTTCAAAAGTTACTTGACGATTTTTAAACGAGATTTTAAAGAAACTAAGTCC
AATTTTTAGAAGTTTCTTGACGATTTTTAAACGAGCTTTCAAAGA
Found at i:1340888 original size:53 final size:52
Alignment explanation
Indices: 1340524--1341010 Score: 219
Period size: 55 Copynumber: 9.2 Consensus size: 52
1340514 ATTTTCATAA
* * **
1340524 GTTTCTTTATGATTTTTAAATGAGATTTTAAAGAAACTAAGTCC-AATTTTTAGAA
1 GTTTCTTGATG-TTTTCAAATGA-A-TTTAAAGAAACTAAG-CCTAATTTTTAGGG
* * * * * * ***
1340579 GTTTCTTGACGATTTT-AAACGAGCTTTCAAAGAAACTAAGTCTTATTTTCAAAA
1 GTTTCTTGATG-TTTTCAAATGA-ATTT-AAAGAAACTAAGCCTAATTTTTAGGG
* * * * * * **
1340633 GTTACTTGACGATTTTTAAACGAGTTTTCAAAGAAACTAAGTCTAATTTTTAGAA
1 GTTTCTTGATG-TTTTCAAATGA-ATTT-AAAGAAACTAAGCCTAATTTTTAGGG
* * * * * * *
1340688 GTTTCTTGATGATTTTTAAACGAGCTTTCAAAGAAATTAAGTCTGATTTTTAGAG
1 GTTTCTTGATG-TTTTCAAATGA-ATTT-AAAGAAACTAAGCCTAATTTTTAGGG
* * *
1340743 ATTTCTTGA-G----AAAATGAATTTGAAAGAAGCTGAA-CCTAATTTTTAGGG
1 GTTTCTTGATGTTTTCAAATGAATTT-AAAGAAACT-AAGCCTAATTTTTAGGG
* * * * * *
1340791 GGTTATTGATGTTTGCAAATGAATATGAAAGAAGCAAAGCCTAATTTTTAGGG
1 GTTTCTTGATGTTTTCAAATGAAT-TTAAAGAAACTAAGCCTAATTTTTAGGG
* * *
1340844 GTTTCTTGATGTTTTCAAATTAATTTAAATGAAACTATA-TCTAATTTTT-GGAA
1 GTTTCTTGATGTTTTCAAATGAATTTAAA-GAAACTA-AGCCTAATTTTTAGG-G
* ** * * *
1340897 GTTTCTTGAT-TATTT--GATCTA-TCAAAGAAATTAAGCCTAATTTTCAGGG
1 GTTTCTTGATGT-TTTCAAATGAATTTAAAGAAACTAAGCCTAATTTTTAGGG
* * * *
1340946 GTTTCTTGATATTTTCAAATGAACTTTTATAGAATCTAATCCTAATTTTTAGGG
1 GTTTCTTGATGTTTTCAAATGAA--TTTAAAGAAACTAAGCCTAATTTTTAGGG
*
1341000 GTTTCATGATG
1 GTTTCTTGATG
1341011 ATAACTGTAA
Statistics
Matches: 346, Mismatches: 63, Indels: 47
0.76 0.14 0.10
Matches are distributed among these distances:
48 28 0.08
49 35 0.10
50 7 0.02
51 6 0.02
52 9 0.03
53 81 0.23
54 75 0.22
55 105 0.30
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (52 bp):
GTTTCTTGATGTTTTCAAATGAATTTAAAGAAACTAAGCCTAATTTTTAGGG
Found at i:1341000 original size:54 final size:53
Alignment explanation
Indices: 1340754--1341010 Score: 185
Period size: 53 Copynumber: 4.9 Consensus size: 53
1340744 TTTCTTGAGA
* * * *
1340754 AAATGAAT-TTGAAAGAAGCTGAA-CCTAATTTTTAGGGGGTTATTGATGTTTGC
1 AAATGAATATT-AAAGAATCT-AAGCCTAATTTTTAGGGGTTTCTTGATGTTTTC
* * *
1340807 AAATGAATATGAAAGAAGCAAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTC
1 AAATGAATATTAAAGAATCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTC
* * * * *
1340860 AAATTAAT-TTAAATGAAACTATA-TCTAATTTTT-GGAAGTTTCTTGAT-TATT-
1 AAATGAATATTAAA-GAATCTA-AGCCTAATTTTTAGG-GGTTTCTTGATGTTTTC
* * * *
1340911 ---TGATCTATCAAAGAAAT-TAAGCCTAATTTTCAGGGGTTTCTTGATATTTTC
1 AAATGA-ATATTAAAG-AATCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTC
* * * *
1340962 AAATGAACTTTTATAGAATCTAATCCTAATTTTTAGGGGTTTCATGATG
1 AAATGAA-TATTAAAGAATCTAAGCCTAATTTTTAGGGGTTTCTTGATG
1341011 ATAACTGTAA
Statistics
Matches: 159, Mismatches: 28, Indels: 33
0.72 0.13 0.15
Matches are distributed among these distances:
48 3 0.02
49 22 0.14
50 11 0.07
52 11 0.07
53 77 0.48
54 35 0.22
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (53 bp):
AAATGAATATTAAAGAATCTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTC
Found at i:1341100 original size:20 final size:20
Alignment explanation
Indices: 1341071--1341142 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1341061 CTTGATGAGG
*
1341071 AAGTCCTTCGGGCCATTAGT
1 AAGTCTTTCGGGCCATTAGT
*
1341091 AAGTCTTTCGAG-CATTATGATT
1 AAGTCTTTCGGGCCATTA-G--T
* *
1341113 AAATCTTTCGGGCCATCAGT
1 AAGTCTTTCGGGCCATTAGT
1341133 AAGTCTTTCG
1 AAGTCTTTCG
1341143 AGCATGATGA
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 5 0.12
20 21 0.50
22 12 0.29
23 4 0.10
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (20 bp):
AAGTCTTTCGGGCCATTAGT
Found at i:1341120 original size:22 final size:22
Alignment explanation
Indices: 1341094--1341164 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
1341084 CATTAGTAAG
*
1341094 TCTTTCGAGCATTATGATTAAA
1 TCTTTCGAGCATCATGATTAAA
* *
1341116 TCTTTCGGGCCATCA-G--TAAG
1 TCTTTCGAG-CATCATGATTAAA
*
1341136 TCTTTCGAGCATGATGATTAAA
1 TCTTTCGAGCATCATGATTAAA
*
1341158 TCCTTCG
1 TCTTTCG
1341165 GGTCATCTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 4 0.11
20 12 0.32
22 18 0.47
23 4 0.11
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (22 bp):
TCTTTCGAGCATCATGATTAAA
Found at i:1341136 original size:42 final size:42
Alignment explanation
Indices: 1341074--1341207 Score: 189
Period size: 42 Copynumber: 3.2 Consensus size: 42
1341064 GATGAGGAAG
* *
1341074 TCCTTCGGGCCATTAGTAAGTCTTTCGAGCATTATGATTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
*
1341116 TCTTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
* * * * *
1341158 TCCTTCGGGTCATCTGTAAGTTTTTCGAGCAAGATGA-TAAG
1 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1341199 TCCTTCGGG
1 TCCTTCGGG
1341208 GAAATCCATA
Statistics
Matches: 83, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 12 0.14
42 71 0.86
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.34
Consensus pattern (42 bp):
TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
Found at i:1341432 original size:73 final size:73
Alignment explanation
Indices: 1341321--1341591 Score: 325
Period size: 73 Copynumber: 3.7 Consensus size: 73
1341311 TGAGATTGTT
* *
1341321 TTTCACACGAAACAAAATTT-ATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTAGTCTAGCT
1 TTTCACTCGAAACAAAATTTCATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTAGTCTCGCT
1341385 TGAGATAA
66 TGAGATAA
* * * *
1341393 TTTCGCTCGAAACAAAATTTCATCTCACTTGTGACTGTTTTTCTTAAAACAAACTTCGTCTCGCT
1 TTTCACTCGAAACAAAATTTCATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTAGTCTCGCT
1341458 TGAAGCAT--
66 TG-AG-ATAA
* * *
1341466 TTTCACTCGAAACAAAATTTCACCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTGTCGCT
1 TTTCACTCGAAACAAAATTTCATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTAGTCTCGCT
*
1341531 TGAGACAA
66 TGAGATAA
* * * * * * * *
1341539 TTCTTACTCAAAAC-AAATTTTATCTCACCTGGGATAGTTTCTCTTCAAACAAA
1 TT-TCACTCGAAACAAAATTTCATCTCACTTGAGATTGTTTTTCTTAAAACAAA
1341592 TTTCTTTTGA
Statistics
Matches: 171, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
71 1 0.01
72 20 0.12
73 137 0.80
74 11 0.06
75 2 0.01
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (73 bp):
TTTCACTCGAAACAAAATTTCATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTAGTCTCGCT
TGAGATAA
Found at i:1341516 original size:37 final size:37
Alignment explanation
Indices: 1341309--1341518 Score: 146
Period size: 36 Copynumber: 5.7 Consensus size: 37
1341299 TAACATCACG
*
1341309 CTTGAGATTGTTTTTCACACGAAACAAAATTT-ATCTCA
1 CTTGAGATTGTTTTTCTCA--AAACAAAATTTCATCTCA
* *
1341347 CTTGAGATTGTTTTTCTTAAAAC-AAACTT-AGTCT-A
1 CTTGAGATTGTTTTTCTCAAAACAAAATTTCA-TCTCA
** ** *
1341382 GCTTGAGATAATTTCGCTCGAAACAAAATTTCATCTCA
1 -CTTGAGATTGTTTTTCTCAAAACAAAATTTCATCTCA
* * * * * *
1341420 CTTGTGACTGTTTTTCTTAAAAC-AAACTTCGTCTCG
1 CTTGAGATTGTTTTTCTCAAAACAAAATTTCATCTCA
** * *
1341456 CTTGAAGCA-T-TTTCACTCGAAACAAAATTTCACCTCA
1 CTTG-AG-ATTGTTTTTCTCAAAACAAAATTTCATCTCA
*
1341493 CTTGAGATTGTTTTTCTTAAAACAAA
1 CTTGAGATTGTTTTTCTCAAAACAAA
1341519 CTTTGTGTCG
Statistics
Matches: 128, Mismatches: 34, Indels: 21
0.70 0.19 0.11
Matches are distributed among these distances:
35 8 0.06
36 50 0.39
37 50 0.39
38 20 0.16
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (37 bp):
CTTGAGATTGTTTTTCTCAAAACAAAATTTCATCTCA
Found at i:1341535 original size:36 final size:36
Alignment explanation
Indices: 1341307--1341564 Score: 144
Period size: 37 Copynumber: 7.0 Consensus size: 36
1341297 ATTAACATCA
*
1341307 CGCTTGAGATTGTTTTTCACACGAAACAAAATTTATCT
1 CGCTTGAGATTGTTTTTCTCA--AAACAAAATTTATCT
* * *
1341345 CACTTGAGATTGTTTTTCTTAAAAC-AAACTTAGTCT
1 CGCTTGAGATTGTTTTTCTCAAAACAAAATTTA-TCT
* ** ** *
1341381 AGCTTGAGATAATTTCGCTCGAAACAAAATTTCATCT
1 CGCTTGAGATTGTTTTTCTCAAAACAAAATTT-ATCT
* * * * * **
1341418 CACTTGTGACTGTTTTTCTTAAAACAAACTTCGTCT
1 CGCTTGAGATTGTTTTTCTCAAAACAAAATTTATCT
** * *
1341454 CGCTTGAAGCA-T-TTTCACTCGAAACAAAATTTCACCT
1 CGCTTG-AG-ATTGTTTTTCTCAAAACAAAATTT-ATCT
* * * * *
1341491 CACTTGAGATTGTTTTTCTTAAAACAAACTTTGTGT
1 CGCTTGAGATTGTTTTTCTCAAAACAAAATTTATCT
*** * *
1341527 CGCTTGAGACAATTCTTACTCAAAACAAATTTTATCT
1 CGCTTGAGATTGTT-TTTCTCAAAACAAAATTTATCT
1341564 C
1 C
1341565 ACCTGGGATA
Statistics
Matches: 157, Mismatches: 54, Indels: 19
0.68 0.23 0.08
Matches are distributed among these distances:
35 7 0.04
36 60 0.38
37 70 0.45
38 20 0.13
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (36 bp):
CGCTTGAGATTGTTTTTCTCAAAACAAAATTTATCT
Found at i:1341589 original size:146 final size:145
Alignment explanation
Indices: 1341320--1341591 Score: 377
Period size: 146 Copynumber: 1.9 Consensus size: 145
1341310 TTGAGATTGT
*
1341320 TTTTCACACGAAACAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTTAGTCTAGCT
1 TTTTCACACGAAACAAAATTTACCTCACTTGAGATTGTTTTTCTTAAAACAAACTTAGTCTAGCT
* * * * * *
1341385 TGAGATAATTTCGCTCGAAACAAAATTTCATCTCACTTGTGACTGTTTTTCTTAAAACAAACTTC
66 TGAGACAATTTCACTCAAAACAAAATTTCATCTCACCTGGGACTGTTTCTCTTAAAACAAACTTC
1341450 GTCTCGCTTGAAGCA
131 GTCTCGCTTGAAGCA
* * * *
1341465 TTTTCACTCGAAACAAAATTTCACCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTGTGTCGC
1 TTTTCACACGAAACAAAATTT-ACCTCACTTGAGATTGTTTTTCTTAAAACAAACTTAGTCTAGC
* * *
1341530 TTGAGACAATTCTTACTCAAAAC-AAATTTTATCTCACCTGGGA-TAGTTTCTCTTCAAACAAA
65 TTGAGACAATT-TCACTCAAAACAAAATTTCATCTCACCTGGGACT-GTTTCTCTTAAAACAAA
1341592 TTTCTTTTGA
Statistics
Matches: 110, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
145 21 0.19
146 81 0.74
147 8 0.07
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (145 bp):
TTTTCACACGAAACAAAATTTACCTCACTTGAGATTGTTTTTCTTAAAACAAACTTAGTCTAGCT
TGAGACAATTTCACTCAAAACAAAATTTCATCTCACCTGGGACTGTTTCTCTTAAAACAAACTTC
GTCTCGCTTGAAGCA
Found at i:1342108 original size:139 final size:138
Alignment explanation
Indices: 1341855--1342258 Score: 598
Period size: 139 Copynumber: 2.9 Consensus size: 138
1341845 AAGATAAACC
* *
1341855 GATCAACATTTCCAATGGAGAGTTCATAATGAGAAAAACTCATCCAACAGAGGGAGAAGAAGTTC
1 GATCAACATTT-CAATGGAGAGTTCATAATGAGAAAAACTCATCCGA-TGAGGGAGAAGAAGTTC
* * *
1341920 ATAATGAGAAGAACTTGTTC-ATCATAGCTCT-ATTCATCACATATGGAGTTGAATCAGCAACAC
64 ATAATGAGAAGAACTTGTTCAACCTTAGCT-TAATTCATCACATATGGAGTTGAATCAACAACAC
1341983 CTCACTCGAGG
128 CTCACTCGAGG
*
1341994 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCA
1 GATCAACATTTCAA-TGGAGAGTTCATAATGAGAAAAACTCATCCGATGAGGGAGAAGAAGTTCA
*
1342059 TAATGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATTGAGTTGAATCATA-AACACC
65 TAATGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGGAGTTGAATCA-ACAACACC
1342123 TCACTCGAGG
129 TCACTCGAGG
* * * * * * *
1342133 TATCAACATTTCAAATGGAAAGTTTATAATGAGAAGAACTAATTCGATGATGGAGAAGAAGTTCA
1 GATCAACATTTC-AATGGAGAGTTCATAATGAGAAAAACTCATCCGATGAGGGAGAAGAAGTTCA
*
1342198 TAATGAGAATAACTTGTTCAACCTTAGCTTAATTCATCACATATGGAGTTGAATCAACAAC
65 TAATGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGGAGTTGAATCAACAAC
1342259 TTGTTCAACC
Statistics
Matches: 243, Mismatches: 16, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
138 41 0.17
139 200 0.82
140 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (138 bp):
GATCAACATTTCAATGGAGAGTTCATAATGAGAAAAACTCATCCGATGAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTAGCTTAATTCATCACATATGGAGTTGAATCAACAACACCTC
ACTCGAGG
Found at i:1342280 original size:48 final size:48
Alignment explanation
Indices: 1342208--1342299 Score: 175
Period size: 48 Copynumber: 1.9 Consensus size: 48
1342198 TAATGAGAAT
*
1342208 AACTTGTTCAACCTTAGCTTAATTCATCACATATGGAGTTGAATCAAC
1 AACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAATCAAC
1342256 AACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAAT
1 AACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAAT
1342300 TGACAATACC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.34
Consensus pattern (48 bp):
AACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAATCAAC
Found at i:1342330 original size:187 final size:183
Alignment explanation
Indices: 1342069--1342437 Score: 569
Period size: 187 Copynumber: 2.0 Consensus size: 183
1342059 TAATGAGAAG
* * *
1342069 AACTTGTTCAACCTTAGCTTAATTCATCACATATTGAGTTGAATCATAAACACCTCACTCGAGGT
1 AACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAAT-ATAAACACCTCACTCGAGGG
* *
1342134 ATCAACATTTCAAATGGAAAGTTTATAATGAGAAGAACTAATTCGATGATGGAGAAGAAGTTCAT
65 ATAAACATTTCAAATGGAAAGTTCATAATGAGAAGAACTAATTCGATG-TGG-G-AGAAGTTCAT
* *
1342199 AATGAGAATAACTTGTTCAACCTTAGCTTAATTCATCACATATGGAGTTGAATCAAC
127 AATGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAATCAAC
* *
1342256 AACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAAT-TGACAATACCTCACTTGAGG
1 AACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAATAT-A-AACACCTCACTCGAGG
* *
1342320 GATAAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATTCGATGTGGGAGAAGTTCATAA
64 GATAAACATTTCAAATGGAAAGTTCATAATGAGAAGAACTAATTCGATGTGGGAGAAGTTCATAA
*
1342385 TGAGAAGAACTTGTTCAACTTTAGCTCAATTCATCACATATGGAGTTGAATCA
129 TGAGAAGAACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAATCA
1342438 GTAAACACCT
Statistics
Matches: 168, Mismatches: 12, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
184 62 0.37
185 2 0.01
186 4 0.02
187 100 0.60
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (183 bp):
AACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAATATAAACACCTCACTCGAGGGA
TAAACATTTCAAATGGAAAGTTCATAATGAGAAGAACTAATTCGATGTGGGAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAATCAAC
Found at i:1342511 original size:137 final size:137
Alignment explanation
Indices: 1342256--1342536 Score: 386
Period size: 137 Copynumber: 2.0 Consensus size: 137
1342246 TTGAATCAAC
* * *
1342256 AACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAATTGACAATACCTCACTTGAGGG
1 AACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAATAGACAACACCTCACTCGAGGG
* * **
1342321 ATAAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATTCGATGTGGGAG-AAGTTCATAA
66 ATAAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAAGTTCATAA
*
1342385 TGAGAAG
131 TAAGAAG
*
1342392 AACTTGTTCAACTTTAGCTCAATTCATCACATATGGAGTTGAATCAGTA-AACACCTCACTCGAG
1 AACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAAT-AG-ACAACACCTCACTCGAG
** * * *
1342456 GGATCTACATTTCCAGTAGATAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAATAAGTTC
64 GGATAAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAG-A-AAGTTC
1342521 ATAATAAGAAG
127 ATAATAAGAAG
1342532 AACTT
1 AACTT
1342537 TAGCTGGTTT
Statistics
Matches: 126, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
136 43 0.34
137 61 0.48
138 1 0.01
140 21 0.17
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (137 bp):
AACTTGTTCAACCTTAGCTCAATTCATCACATATGGAGTTGAATAGACAACACCTCACTCGAGGG
ATAAACATTTCAAATAGAGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAGAAAGTTCATAA
TAAGAAG
Found at i:1342693 original size:41 final size:42
Alignment explanation
Indices: 1342591--1342699 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
1342581 TTCTCTTCCT
* * *
1342591 TCACATAAGGAGTTGGATCAACATTATCATTTCGCTAGTCTA
1 TCACATAAGGAGTTGGATCAACATCATCATTTCGCTAATCCA
*
1342633 TCACATAAGGAGTTGGATCAACATCATCATTTTGCTAATCCA
1 TCACATAAGGAGTTGGATCAACATCATCATTTCGCTAATCCA
* * * *
1342675 -CACATAAAGATTTAGATCAGCATCA
1 TCACATAAGGAGTTGGATCAACATCA
1342700 CCTTGGATCA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 21 0.36
42 38 0.64
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (42 bp):
TCACATAAGGAGTTGGATCAACATCATCATTTCGCTAATCCA
Found at i:1342942 original size:12 final size:12
Alignment explanation
Indices: 1342892--1342939 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 12
1342882 TTTTTTTATA
1342892 TATTATTATAAT
1 TATTATTATAAT
1342904 TATTATTAATAAT
1 TATTATT-ATAAT
1342917 AATATTATTATTTAAT
1 --TATTATTA--TAAT
1342933 TATTATT
1 TATTATT
1342940 TTATTTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 7 0.23
13 5 0.16
14 8 0.26
15 7 0.23
16 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATTATAAT
Found at i:1342943 original size:19 final size:18
Alignment explanation
Indices: 1342893--1342944 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
1342883 TTTTTTATAT
1342893 ATTATTATAATTATTATTA
1 ATTATTAT-ATTATTATTA
* *
1342912 ATAATAATATTATTATTTA
1 ATTATTATATTATTA-TTA
*
1342931 ATTATTATTTTATT
1 ATTATTATATTATT
1342945 TTCTTACAGA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTATTATATTATTATTA
Found at i:1343188 original size:53 final size:53
Alignment explanation
Indices: 1343098--1343214 Score: 180
Period size: 53 Copynumber: 2.2 Consensus size: 53
1343088 CAAGTCATTA
* * * *
1343098 CCATGCCCTGCCATCTCCAGTACCCCACGTGAAGCACCACAAATTGAGCAGAT
1 CCATGCCCTACCATCTCCAATACCCCACGTGAAGCACCACAAACTGAGCAGAC
* *
1343151 CCATACCCTACCATCTCCAATACCCCACGTGAAGCACCACCAACTGAGCAGAC
1 CCATGCCCTACCATCTCCAATACCCCACGTGAAGCACCACAAACTGAGCAGAC
1343204 CCATGCCCTAC
1 CCATGCCCTAC
1343215 TCCACAGTAC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.29, C:0.42, G:0.14, T:0.15
Consensus pattern (53 bp):
CCATGCCCTACCATCTCCAATACCCCACGTGAAGCACCACAAACTGAGCAGAC
Found at i:1344013 original size:14 final size:13
Alignment explanation
Indices: 1343987--1344011 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1343977 AAATCTAATA
1343987 TAAAAAAATAAAT
1 TAAAAAAATAAAT
1344000 TAAAAAAATAAA
1 TAAAAAAATAAA
1344012 ATATTGACAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
TAAAAAAATAAAT
Found at i:1346289 original size:11 final size:11
Alignment explanation
Indices: 1346275--1346305 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1346265 GATAACTAAA
1346275 GGAGCTGAACG
1 GGAGCTGAACG
1346286 GGAGCTGAACG
1 GGAGCTGAACG
1346297 GGAGCTGAA
1 GGAGCTGAA
1346306 AGTAGCTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.16, G:0.45, T:0.10
Consensus pattern (11 bp):
GGAGCTGAACG
Found at i:1347041 original size:20 final size:21
Alignment explanation
Indices: 1347005--1347043 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1346995 ATTAAAGCTA
1347005 TTTTCTTTTATCTTTCTTTAG
1 TTTTCTTTTATCTTTCTTTAG
1347026 TTTTCTTTTA-CTTTCTTT
1 TTTTCTTTTATCTTTCTTT
1347044 TTAAACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.08, C:0.15, G:0.03, T:0.74
Consensus pattern (21 bp):
TTTTCTTTTATCTTTCTTTAG
Found at i:1349774 original size:15 final size:15
Alignment explanation
Indices: 1349750--1349792 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1349740 AATCTGATCC
*
1349750 GAATAACACATTTAT
1 GAATAACACATATAT
*
1349765 GAATAGCACATATAT
1 GAATAACACATATAT
*
1349780 GAATAACATATAT
1 GAATAACACATAT
1349793 CCAAATAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.49, C:0.12, G:0.09, T:0.30
Consensus pattern (15 bp):
GAATAACACATATAT
Found at i:1354503 original size:19 final size:18
Alignment explanation
Indices: 1354469--1354504 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1354459 ATTAATTTTT
*
1354469 TAATTAAAAATATATTTC
1 TAATTAAAAAAATATTTC
1354487 TAATTAAAAAAATTATTT
1 TAATTAAAAAAA-TATTT
1354505 TTTAAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAATTAAAAAAATATTTC
Found at i:1359264 original size:114 final size:114
Alignment explanation
Indices: 1359065--1360122 Score: 903
Period size: 114 Copynumber: 9.4 Consensus size: 114
1359055 CTTAAGTCAA
* * * * * *
1359065 AATTTCTTTTATATTAAATAAAAAATCTTATTTG-CACAATAATAATTGCAAATGACAT-AGAAT
1 AATTTCTTTCATATTGAATGAAAAATCTTATTTGATACAATAATTATTTCAAATGAC-TGAGAAT
* * * ** ** * *
1359128 TTTAACTATTCAAATCATTTTCTTTTTGGTGATATATTGCCTCAAATTAG
65 CTTAACTATTCAAGTCGTTTTCTTTTCAGTGATATATCACCTCATATCAG
* * * *
1359178 AATTTCTTTCATATTGAATAAAAAATATTATTTGATACAATCATAATTTCAAATGACTGAGAAT-
1 AATTTCTTTCATATTGAATGAAAAATCTTATTTGATACAATAATTATTTCAAATGACTGAGAATC
* * * **
1359242 TGTAATTGTTCACGTTTTTTTCTTTTCAGTGATATATCACCTCATATC-G
66 T-TAACTATTCAAGTCGTTTTCTTTTCAGTGATATATCACCTCATATCAG
* ** * * *
1359291 AATGTTCTCTCATATTGAATG-AAAATGGTATTT-AGTACAATAATTATTCCAAATGGCAGAGAA
1 AAT-TTCTTTCATATTGAATGAAAAATCTTATTTGA-TACAATAATTATTTCAAATGACTGAGAA
* * * *
1359354 TCTTAGCTATTCAAGT--TCTT-TTTTCAGTGATATATTACCTCATATCAT
64 TCTTAACTATTCAAGTCGTTTTCTTTTCAGTGATATATCACCTCATATCAG
* * * *
1359402 AAATTCTTTGATATTGAATGAAAAATCTTATTTGATACAATATTTATTTCAAATGACGGAGAATC
1 AATTTCTTTCATATTGAATGAAAAATCTTATTTGATACAATAATTATTTCAAATGACTGAGAATC
* * * *
1359467 TTAACTATTCAGGTCGTTTTCTTTTCAATGATATATCACCTTATATCAT
66 TTAACTATTCAAGTCGTTTTCTTTTCAGTGATATATCACCTCATATCAG
* * * * *
1359516 AACTTCTTTCATATTGAATGAAAAATCTTATTTGGTACAATAATTATTTCAAATAAATAAGAATC
1 AATTTCTTTCATATTGAATGAAAAATCTTATTTGATACAATAATTATTTCAAATGACTGAGAATC
* * * *
1359581 TTAACTATTCACA-TTGTTTTCTTTTCATTGATATATCAGCTCATATAAG
66 TTAACTATTCA-AGTCGTTTTCTTTTCAGTGATATATCACCTCATATCAG
* * * * * * *
1359630 AACTTCTTTCATATTGGATGAAAAATCTTATTTGATACGATAATTATTTTAAAGGACCGTGAATC
1 AATTTCTTTCATATTGAATGAAAAATCTTATTTGATACAATAATTATTTCAAATGACTGAGAATC
* * * * * * *
1359695 GTAACTATTTATGTCAG--TT-TTTTCATTGTTATATCACCTTATATAAG
66 TTAACTATTCAAGTC-GTTTTCTTTTCAGTGATATATCACCTCATATCAG
* * * * * * **
1359742 AACTTCTTTCATATTGAATGAAAAATCTTA-TTCAGTATAATAATTATTGCACATAACAAAGAAT
1 AATTTCTTTCATATTGAATGAAAAATCTTATTTGA-TACAATAATTATTTCAAATGACTGAGAAT
* * * ** *
1359806 CTTAACTATTAAAGTCTTTTTCTTTTTAGCAATATATCACCTCATATCAA
65 CTTAACTATTCAAGTCGTTTTCTTTTCAGTGATATATCACCTCATATCAG
* * * * *
1359856 AACTTATTTCATATAGAATGAAAAATCTTATCTGATACAATAATAATTTCAAATGA-TAGAGAAT
1 AATTTCTTTCATATTGAATGAAAAATCTTATTTGATACAATAATTATTTCAAATGACT-GAGAAT
* * *
1359920 TTTAACTATT-ATTA-TC-TTTT-TTTCCAGTGATATAGCACCTCATATCAG
65 CTTAACTATTCA--AGTCGTTTTCTTTTCAGTGATATATCACCTCATATCAG
* * * * ** * * ***
1359968 TACTTCTTTCATATTGAATGACAAATGTTATCCGATACAATAATAATTTCAAATTAAAAAGAATC
1 AATTTCTTTCATATTGAATGAAAAATCTTATTTGATACAATAATTATTTCAAATGACTGAGAATC
* * * * * * *
1360033 TTAACTATTTAGGTCATTTTCTTTTCAATGATTTATCTCCTCAAAATCAG
66 TTAACTATTCAAGTCGTTTTCTTTTCAGTGATATATCACCTC-ATATCAG
* * * *
1360083 AACTTCTTTCATATGGAATGAAAAATCTTATCTGGTACAA
1 AATTTCTTTCATATTGAATGAAAAATCTTATTTGATACAA
1360123 ATCATAAGTT
Statistics
Matches: 770, Mismatches: 146, Indels: 56
0.79 0.15 0.06
Matches are distributed among these distances:
110 40 0.05
111 56 0.07
112 175 0.23
113 97 0.13
114 358 0.46
115 44 0.06
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (114 bp):
AATTTCTTTCATATTGAATGAAAAATCTTATTTGATACAATAATTATTTCAAATGACTGAGAATC
TTAACTATTCAAGTCGTTTTCTTTTCAGTGATATATCACCTCATATCAG
Found at i:1359644 original size:338 final size:335
Alignment explanation
Indices: 1359068--1360122 Score: 976
Period size: 338 Copynumber: 3.1 Consensus size: 335
1359058 AAGTCAAAAT
* * * * * * *
1359068 TTCTTTTATATTAAATAAAAAATCTTATTTG-CACAATAATAATTGCAAATGACATAGAATTTTA
1 TTCTTTCATATTGAATGAAAAATCTTATTTGATACAATAATTATTGCAAATGACAAAGAATCTTA
* * ** * * * *
1359132 ACTATTCAAATCATTTTCTTTTTGGTGATATATTGCCTCAAATTAGAATTTCTTTCATATTGAAT
66 ACTATTCAAGTCATTTTCTTTTTAGTGATATATCACCTCATATCAAAACTTCTTTCATATTGAAT
* * * * * * * * *
1359197 AAAAAATATTATTTGATACAATCATAATTTCAAATGACTGAGAATTGTAATTGTTCACGTTTTTT
131 GAAAAATCTTATTTGATACAATAATAATTTCAAAT-AATAAGAATT-TAACTATTCACATTATTT
* * *
1359262 TCTTTTCAGTGATATATCACCTCATATCGAATGTTCTCTCATATTGAATGAAAATGGTATTT-AG
194 TCTTTTCAGTGATATATCACCTCATATAGAA-CTTCTTTCATATTGAATGAAAATGGTATTTGA-
* *
1359326 TACAATAATTATTCCAAATGG-CAGAGAATCTTAGCTATTCAAGTTC-TTTTTTCAGTGATATAT
257 TACAATAATTATTCCAAA-GGACAGAGAATCGTAACTATTCAAG-TCATTTTTTCAGTGATATAT
* * *
1359389 TACCTCATATCATAAA
320 CACCTCATATAAGAAA
* * * **
1359405 TTCTTTGATATTGAATGAAAAATCTTATTTGATACAATATTTATTTCAAATGACGGAGAATCTTA
1 TTCTTTCATATTGAATGAAAAATCTTATTTGATACAATAATTATTGCAAATGACAAAGAATCTTA
* * * * * *
1359470 ACTATTCAGGTCGTTTTCTTTTCAATGATATATCACCTTATATCATAACTTCTTTCATATTGAAT
66 ACTATTCAAGTCATTTTCTTTTTAGTGATATATCACCTCATATCAAAACTTCTTTCATATTGAAT
* * *
1359535 GAAAAATCTTATTTGGTACAATAATTATTTCAAATAAATAAGAATCTTAACTATTCACATTGTTT
131 GAAAAATCTTATTTGATACAATAATAATTTCAAAT-AATAAGAAT-TTAACTATTCACATTATTT
* * * **
1359600 TCTTTTCATTGATATATCAGCTCATATAAGAACTTCTTTCATATTGGATGAAAAATCTTATTTGA
194 TCTTTTCAGTGATATATCACCTCATAT-AGAACTTCTTTCATATTGAATG-AAAATGGTATTTGA
* ** * * * * * *
1359665 TACGATAATTATTTTAAAGGACCGTGAATCGTAACTATTTATGTCAGTTTTTTCATTGTTATATC
257 TACAATAATTATTCCAAAGGACAGAGAATCGTAACTATTCAAGTCA-TTTTTTCAGTGATATATC
* *
1359730 ACCTTATATAAGAAC
321 ACCTCATATAAGAAA
* * * *
1359745 TTCTTTCATATTGAATGAAAAATCTTA-TTCAGTATAATAATTATTGCACATAACAAAGAATCTT
1 TTCTTTCATATTGAATGAAAAATCTTATTTGA-TACAATAATTATTGCAAATGACAAAGAATCTT
* * ** * *
1359809 AACTATTAAAGTCTTTTTCTTTTTAGCAATATATCACCTCATATCAAAACTTATTTCATATAGAA
65 AACTATTCAAGTCATTTTCTTTTTAGTGATATATCACCTCATATCAAAACTTCTTTCATATTGAA
* *
1359874 TGAAAAATCTTATCTGATACAATAATAATTTCAAATGATAGAGAATTTTAACTATT---ATTATC
130 TGAAAAATCTTATTTGATACAATAATAATTTCAAATAATA-AGAA-TTTAACTATTCACATTAT-
* * * *
1359936 TTT-TTTTCCAGTGATATAGCACCTCATATCAGTACTTCTTTCATATTGAATGACAAATGTTATC
192 TTTCTTTT-CAGTGATATATCACCTCATAT-AGAACTTCTTTCATATTGAATGA-AAATGGTATT
* * * ** * * * * * *
1360000 CGATACAATAATAATTTCAAATTAAAAAGAATCTTAACTATTTAGGTCATTTTCTTTTCAATGAT
254 TGATACAATAATTATTCCAAAGGACAGAGAATCGTAACTATTCAAGTCA--TT-TTTTCAGTGAT
* * * * *
1360065 TTATCTCCTCAAAATCAGAAC
316 ATATCACCTC-ATATAAGAAA
* * *
1360086 TTCTTTCATATGGAATGAAAAATCTTATCTGGTACAA
1 TTCTTTCATATTGAATGAAAAATCTTATTTGATACAA
1360123 ATCATAAGTT
Statistics
Matches: 583, Mismatches: 117, Indels: 32
0.80 0.16 0.04
Matches are distributed among these distances:
337 37 0.06
338 259 0.44
339 53 0.09
340 194 0.33
341 39 0.07
342 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (335 bp):
TTCTTTCATATTGAATGAAAAATCTTATTTGATACAATAATTATTGCAAATGACAAAGAATCTTA
ACTATTCAAGTCATTTTCTTTTTAGTGATATATCACCTCATATCAAAACTTCTTTCATATTGAAT
GAAAAATCTTATTTGATACAATAATAATTTCAAATAATAAGAATTTAACTATTCACATTATTTTC
TTTTCAGTGATATATCACCTCATATAGAACTTCTTTCATATTGAATGAAAATGGTATTTGATACA
ATAATTATTCCAAAGGACAGAGAATCGTAACTATTCAAGTCATTTTTTCAGTGATATATCACCTC
ATATAAGAAA
Found at i:1359770 original size:226 final size:225
Alignment explanation
Indices: 1359068--1360122 Score: 955
Period size: 226 Copynumber: 4.7 Consensus size: 225
1359058 AAGTCAAAAT
* * * * * * * *
1359068 TTCTTTTATATTAAATAAAAAATCTTATTT-GCACAATAATAATTGCAAATGACATAGAATTTTA
1 TTCTTTCATATTGAATGAAAAATCTTATTTAGTACAATAATTATTGCAAAT-AAAAAGAATCTTA
** ** * * *
1359132 ACTATTCAAATCATTTTCTTTTTGGTGATATATTGCCTCAAATTAGAATTTCTTTCATATTGAAT
65 ACTATTCAAATCATTTTCTTTTCAGTGATATATCACCTCATATAAGAACTTCTTTCATATTGAAT
* * * * * * * * **
1359197 AAAAAATATTATTTGATACAATCATAATTTCAAATGACTGAGAATTGTAATTGTTCACGTTTTTT
130 GAAAAATCTTATTTGATACAATAATAATTTCAAATGACAGAGAATCGTAACTATTCA--TGTCGT
*
1359262 TCTTTTCAGTGATATATCACCTCATATC-GAATG
193 TCTTTTCAGTGATATATCACCTCATATCAGAA-C
* ** * ** *
1359295 TTCTCTCATATTGAATG-AAAATGGTATTTAGTACAATAATTATTCCAAATGGCAGAGAATCTTA
1 TTCTTTCATATTGAATGAAAAATCTTATTTAGTACAATAATTATTGCAAAT-AAAAAGAATCTTA
* * * * * * * *
1359359 GCTATTCAAGT--TCTT-TTTTCAGTGATATATTACCTCATATCATAAATTCTTTGATATTGAAT
65 ACTATTCAAATCATTTTCTTTTCAGTGATATATCACCTCATATAAGAACTTCTTTCATATTGAAT
* * * * *
1359421 GAAAAATCTTATTTGATACAATATTTATTTCAAATGACGGAGAATCTTAACTATTCAGGTCGTTT
130 GAAAAATCTTATTTGATACAATAATAATTTCAAATGACAGAGAATCGTAACTATTCATGTCG--T
* * *
1359486 TCTTTTCAATGATATATCACCTTATATCATAAC
193 TCTTTTCAGTGATATATCACCTCATATCAGAAC
* *
1359519 TTCTTTCATATTGAATGAAAAATCTTATTTGGTACAATAATTATTTCAAATAAATAAGAATCTTA
1 TTCTTTCATATTGAATGAAAAATCTTATTTAGTACAATAATTATTGCAAATAAA-AAGAATCTTA
* ** * * *
1359584 ACTATTCACATTGTTTTCTTTTCATTGATATATCAGCTCATATAAGAACTTCTTTCATATTGGAT
65 ACTATTCAAATCATTTTCTTTTCAGTGATATATCACCTCATATAAGAACTTCTTTCATATTGAAT
* * * * * * *
1359649 GAAAAATCTTATTTGATACGATAATTATTTTAAAGGACCGTGAATCGTAACTATTTATGTCAGTT
130 GAAAAATCTTATTTGATACAATAATAATTTCAAATGACAGAGAATCGTAACTATTCATGTC-GTT
* * * *
1359714 -TTTTCATTGTTATATCACCTTATATAAGAAC
194 CTTTTCAGTGATATATCACCTCATATCAGAAC
* * *
1359745 TTCTTTCATATTGAATGAAAAATCTTATTCAGTATAATAATTATTGCACATAACAAAGAATCTTA
1 TTCTTTCATATTGAATGAAAAATCTTATTTAGTACAATAATTATTGCAAATAA-AAAGAATCTTA
* * ** * *
1359810 ACTATT-AAAGTCTTTTTCTTTTTAGCAATATATCACCTCATATCAA-AACTTATTTCATATAGA
65 ACTATTCAAA-TCATTTTCTTTTCAGTGATATATCACCTCATAT-AAGAACTTCTTTCATATTGA
* * ** *
1359873 ATGAAAAATCTTATCTGATACAATAATAATTTCAAATGATAGAGAATTTTAACTATT-ATTATC-
128 ATGAAAAATCTTATTTGATACAATAATAATTTCAAATGACAGAGAATCGTAACTATTCA-TGTCG
* * *
1359936 TTTTTTTCCAGTGATATAGCACCTCATATCAGTAC
192 TTCTTTT-CAGTGATATATCACCTCATATCAGAAC
* * ** * *
1359971 TTCTTTCATATTGAATGACAAATGTTA-TCCGATACAATAATAATTTCAAATTAAAAAGAATCTT
1 TTCTTTCATATTGAATGAAAAATCTTATTTAG-TACAATAATTATTGCAAA-TAAAAAGAATCTT
* ** * * * * * *
1360035 AACTATTTAGGTCATTTTCTTTTCAATGATTTATCTCCTCAAAATCAGAACTTCTTTCATATGGA
64 AACTATTCAAATCATTTTCTTTTCAGTGATATATCACCTC-ATATAAGAACTTCTTTCATATTGA
* *
1360100 ATGAAAAATCTTATCTGGTACAA
128 ATGAAAAATCTTATTTGATACAA
1360123 ATCATAAGTT
Statistics
Matches: 679, Mismatches: 128, Indels: 42
0.80 0.15 0.05
Matches are distributed among these distances:
222 1 0.00
224 132 0.19
225 61 0.09
226 291 0.43
227 102 0.15
228 91 0.13
229 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (225 bp):
TTCTTTCATATTGAATGAAAAATCTTATTTAGTACAATAATTATTGCAAATAAAAAGAATCTTAA
CTATTCAAATCATTTTCTTTTCAGTGATATATCACCTCATATAAGAACTTCTTTCATATTGAATG
AAAAATCTTATTTGATACAATAATAATTTCAAATGACAGAGAATCGTAACTATTCATGTCGTTCT
TTTCAGTGATATATCACCTCATATCAGAAC
Found at i:1361664 original size:22 final size:22
Alignment explanation
Indices: 1361639--1361688 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
1361629 CACTGGTGCT
*
1361639 AAAGTGCCTCAACATTGATACG
1 AAAGTGCATCAACATTGATACG
* *
1361661 AAAGTGCATTAACATTGATACT
1 AAAGTGCATCAACATTGATACG
1361683 AAAGTG
1 AAAGTG
1361689 TCTCGACACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (22 bp):
AAAGTGCATCAACATTGATACG
Found at i:1363521 original size:18 final size:18
Alignment explanation
Indices: 1363498--1363544 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
1363488 CAATACTATG
1363498 GTACCGATACCCCTTTTA
1 GTACCGATACCCCTTTTA
1363516 GTACCGATACCCCTTTTA
1 GTACCGATACCCCTTTTA
*
1363534 GTATCGATACC
1 GTACCGATACC
1363545 ATTTATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.23, C:0.32, G:0.13, T:0.32
Consensus pattern (18 bp):
GTACCGATACCCCTTTTA
Found at i:1366701 original size:53 final size:53
Alignment explanation
Indices: 1366638--1366778 Score: 176
Period size: 54 Copynumber: 2.6 Consensus size: 53
1366628 AGAGCCATGA
* * * * **
1366638 GTGTATCGATGCA-CCAGTTGTGTATCGGTACATAAAATTCGTTTGATGTTGGT
1 GTGTATCGATGCATCAAG-AGTGTATCGGTACATAAAATGCATTCAATGTTGGT
1366691 GTGTATCGATGCATTCAAGAGTGTATCGGTACATAAAATGCATTCAATGTTGGT
1 GTGTATCGATGCA-TCAAGAGTGTATCGGTACATAAAATGCATTCAATGTTGGT
* *
1366745 CTGTATCGATGTATTCAAGAGTGTATCGGTACAT
1 GTGTATCGATGCA-TCAAGAGTGTATCGGTACAT
1366779 CCCTTTGTAA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
53 13 0.17
54 62 0.79
55 3 0.04
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.35
Consensus pattern (53 bp):
GTGTATCGATGCATCAAGAGTGTATCGGTACATAAAATGCATTCAATGTTGGT
Found at i:1366723 original size:54 final size:54
Alignment explanation
Indices: 1366657--1366778 Score: 190
Period size: 54 Copynumber: 2.3 Consensus size: 54
1366647 TGCACCAGTT
* * ** *
1366657 GTGTATCGGTACATAAAATTCGTTTGATGTTGGTGTGTATCGATGCATTCAAGA
1 GTGTATCGGTACATAAAATGCATTCAATGTTGGTCTGTATCGATGCATTCAAGA
*
1366711 GTGTATCGGTACATAAAATGCATTCAATGTTGGTCTGTATCGATGTATTCAAGA
1 GTGTATCGGTACATAAAATGCATTCAATGTTGGTCTGTATCGATGCATTCAAGA
1366765 GTGTATCGGTACAT
1 GTGTATCGGTACAT
1366779 CCCTTTGTAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (54 bp):
GTGTATCGGTACATAAAATGCATTCAATGTTGGTCTGTATCGATGCATTCAAGA
Found at i:1375015 original size:21 final size:21
Alignment explanation
Indices: 1374989--1375048 Score: 111
Period size: 21 Copynumber: 2.9 Consensus size: 21
1374979 TTAGGAGCGT
1374989 AGGTGTATCGGTACACTCTCA
1 AGGTGTATCGGTACACTCTCA
*
1375010 AGGTGTATCGGTACACTCTTA
1 AGGTGTATCGGTACACTCTCA
1375031 AGGTGTATCGGTACACTC
1 AGGTGTATCGGTACACTC
1375049 AGTGTAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (21 bp):
AGGTGTATCGGTACACTCTCA
Found at i:1375362 original size:193 final size:191
Alignment explanation
Indices: 1375033--1375425 Score: 651
Period size: 193 Copynumber: 2.0 Consensus size: 191
1375023 CACTCTTAAG
*
1375033 GTGTATCGGTACACTCAGTGTAAAATTCAAATATTTCGACCGTTGGTTGACCTAGTGTATCAATA
1 GTGTATCGGTACACTCAGTGTAAAATTCAAATATTTCGACCGTTGGTTAACCTAGTGTATCAATA
* * *
1375098 TATCCCAGGTATATCGGTACACTAATTACATTCGATGTTTCTTGGAGCCAGGAGTGCATCGATGT
66 CATCCCAGGTATATCGGTACACTAATTACATTCGATGTTTCTTAGAGCCAGGAGTGCATCGATGC
1375163 ATCAGCTATGTATCGGTACATAAAATGCATTTGATGTTGGTGTGTATCGATGCAATCAAGA
131 ATCAGCTATGTATCGGTACATAAAATGCATTTGATGTTGGTGTGTATCGATGCAATCAAGA
* **
1375224 GTGTATCGGTACACTCAGTGTAAAATTCAAATATTTCGATCGTGCTGGTTAACCTAGTGTATCGG
1 GTGTATCGGTACACTCAGTGTAAAATTCAAATATTTCGACCGT--TGGTTAACCTAGTGTATCAA
* * * * *
1375289 TACATCTCAGGTGTATCGGTATACTAATTACATTTGATGTTTCTTAGAGCCAGGAGTGCATTGAT
64 TACATCCCAGGTATATCGGTACACTAATTACATTCGATGTTTCTTAGAGCCAGGAGTGCATCGAT
*
1375354 GCATCAGCTGTGTATCGGTACATAAAATGCATTTGATGTTGGTGTGTATCGATGCAATCAAGA
129 GCATCAGCTATGTATCGGTACATAAAATGCATTTGATGTTGGTGTGTATCGATGCAATCAAGA
1375417 GTGTATCGG
1 GTGTATCGG
1375426 AACATAAAAT
Statistics
Matches: 187, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
191 42 0.22
193 145 0.78
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (191 bp):
GTGTATCGGTACACTCAGTGTAAAATTCAAATATTTCGACCGTTGGTTAACCTAGTGTATCAATA
CATCCCAGGTATATCGGTACACTAATTACATTCGATGTTTCTTAGAGCCAGGAGTGCATCGATGC
ATCAGCTATGTATCGGTACATAAAATGCATTTGATGTTGGTGTGTATCGATGCAATCAAGA
Found at i:1375422 original size:54 final size:54
Alignment explanation
Indices: 1375363--1375484 Score: 190
Period size: 54 Copynumber: 2.3 Consensus size: 54
1375353 TGCATCAGCT
**
1375363 GTGTATCGGTACATAAAATGCATTTGATGTTGGTGTGTATCGATGCAATCAAGA
1 GTGTATCGGTACATAAAATGCATTCAATGTTGGTGTGTATCGATGCAATCAAGA
* * *
1375417 GTGTATCGGAACATAAAATGCATTCAATGTTGGTGTGTATCGATGTATTCAAGA
1 GTGTATCGGTACATAAAATGCATTCAATGTTGGTGTGTATCGATGCAATCAAGA
*
1375471 GTATATCGGTACAT
1 GTGTATCGGTACAT
1375485 CACTTTGTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 61 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (54 bp):
GTGTATCGGTACATAAAATGCATTCAATGTTGGTGTGTATCGATGCAATCAAGA
Found at i:1378058 original size:20 final size:20
Alignment explanation
Indices: 1378033--1378177 Score: 110
Period size: 20 Copynumber: 6.7 Consensus size: 20
1378023 TTAATTTATG
*
1378033 GCATCCTTCCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
1378053 GCATCCTTTCATGCTTTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
1378078 GGAATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
1378099 GCATCCTTTTATGCATATTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
* * *
1378124 GGATTCTTTTATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
1378144 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
1378164 GCATCGTTTCATGC
1 GCATCCTTTCATGC
1378178 ATTTTATTTA
Statistics
Matches: 100, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
20 57 0.57
21 2 0.02
22 6 0.06
23 3 0.03
24 3 0.03
25 16 0.16
26 13 0.13
ACGTcount: A:0.20, C:0.23, G:0.12, T:0.45
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:1378092 original size:46 final size:45
Alignment explanation
Indices: 1378026--1378157 Score: 192
Period size: 46 Copynumber: 2.9 Consensus size: 45
1378016 CGTTAATTTA
* * *
1378026 ATTTATGGCATCCTTCCATGCCTTAATGCATCCTTTCATGCTTTTT
1 ATTTATGG-ATCCTTTCATGCCTTAATGCATCCTTTCATGCATATT
*
1378072 ATTTATGGAATCCTTTCATGCCTTAATGCATCCTTTTATGCATATT
1 ATTTATGG-ATCCTTTCATGCCTTAATGCATCCTTTCATGCATATT
* *
1378118 ATTTATGGATTCTTTTATGCCTTAATGCATCCTTTCATGC
1 ATTTATGGATCCTTTCATGCCTTAATGCATCCTTTCATGC
1378158 CTTAATGCAT
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
45 29 0.37
46 49 0.63
ACGTcount: A:0.20, C:0.22, G:0.11, T:0.46
Consensus pattern (45 bp):
ATTTATGGATCCTTTCATGCCTTAATGCATCCTTTCATGCATATT
Found at i:1380849 original size:17 final size:18
Alignment explanation
Indices: 1380811--1380849 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
1380801 ATGCCCTTGC
1380811 ATCGATACCCTATAAAGAAT
1 ATCGATACCCTAT--AGAAT
1380831 ATCGATACCCTAT-GAAT
1 ATCGATACCCTATAGAAT
1380848 AT
1 AT
1380850 AGTAACGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
20 13 0.68
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (18 bp):
ATCGATACCCTATAGAAT
Found at i:1397340 original size:18 final size:18
Alignment explanation
Indices: 1397314--1397348 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1397304 TTGAAATGAC
*
1397314 TAAAGTAAATGATAAGAT
1 TAAAGTAAATAATAAGAT
*
1397332 TAAATTAAATAATAAGA
1 TAAAGTAAATAATAAGA
1397349 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.11, T:0.29
Consensus pattern (18 bp):
TAAAGTAAATAATAAGAT
Found at i:1397820 original size:2 final size:2
Alignment explanation
Indices: 1397813--1397844 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1397803 CAGAATTACA
1397813 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
1397845 GAAATTCAGA
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):
AT
Found at i:1398553 original size:48 final size:48
Alignment explanation
Indices: 1398501--1398592 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
1398491 TAACTTAAAC
* *
1398501 TCTGTTCTGATACATTACCTAAATTCTGTTACGATTTCTTATATGTAT
1 TCTGTTCTGATACATGACCTAAATTCTGTTACGATTTCTGATATGTAT
* * * **
1398549 TCTGTTCTGATATATGATCTGAATTCTGTTTTGATTTCTGATAT
1 TCTGTTCTGATACATGACCTAAATTCTGTTACGATTTCTGATAT
1398593 CTCCGTTTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.50
Consensus pattern (48 bp):
TCTGTTCTGATACATGACCTAAATTCTGTTACGATTTCTGATATGTAT
Found at i:1398590 original size:24 final size:24
Alignment explanation
Indices: 1398522--1398592 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 24
1398512 ACATTACCTA
* *
1398522 AATTCTGTTACGATTTCTTATATG
1 AATTCTGTTATGATTTCTGATATG
* * * * *
1398546 TATTCTGTTCTGATATATGATCTG
1 AATTCTGTTATGATTTCTGATATG
*
1398570 AATTCTGTTTTGATTTCTGATAT
1 AATTCTGTTATGATTTCTGATAT
1398593 CTCCGTTTAC
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.52
Consensus pattern (24 bp):
AATTCTGTTATGATTTCTGATATG
Found at i:1402691 original size:2 final size:2
Alignment explanation
Indices: 1402684--1402719 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1402674 CGGAATTACA
1402684 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
1402720 GAAATTCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1408628 original size:20 final size:20
Alignment explanation
Indices: 1408592--1408639 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1408582 TATTCATGAG
*
1408592 GTATCGATACCTGAAGGGCA
1 GTATCGATACCTGAAGGACA
1408612 GTATCGATACCAT-AAGGACA
1 GTATCGATACC-TGAAGGACA
*
1408632 ATATCGAT
1 GTATCGAT
1408640 TCTATTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (20 bp):
GTATCGATACCTGAAGGACA
Found at i:1409388 original size:23 final size:22
Alignment explanation
Indices: 1409340--1409390 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1409330 CCAAGAGTCT
** *
1409340 GGGACATATACATAGGTTGTTT
1 GGGACATATACATAGGTCCTTC
1409362 GGGACATATACATGAGGTCCTTC
1 GGGACATATACAT-AGGTCCTTC
1409385 GGGACA
1 GGGACA
1409391 AATTTCACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.27
Consensus pattern (22 bp):
GGGACATATACATAGGTCCTTC
Found at i:1410526 original size:21 final size:21
Alignment explanation
Indices: 1410480--1410537 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 21
1410470 TGTTTTTATA
*
1410480 TAATTTTATTATATTGTATATT
1 TAATTTT-TTATTTTGTATATT
*
1410502 TAATTTTTTATTTTTTAT-TT
1 TAATTTTTTATTTTGTATATT
1410522 CTAATATTTTTTATTT
1 -T-A-ATTTTTTATTT
1410538 ATGTTATAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 2 0.06
21 10 0.32
22 8 0.26
23 11 0.35
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (21 bp):
TAATTTTTTATTTTGTATATT
Found at i:1413950 original size:19 final size:19
Alignment explanation
Indices: 1413926--1413972 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1413916 AGTTGCTTTT
1413926 AGGTGTAGGAGATTCTACC
1 AGGTGTAGGAGATTCTACC
1413945 AGGTGTAGGAGATTCTACC
1 AGGTGTAGGAGATTCTACC
*
1413964 AGTTGTAGG
1 AGGTGTAGG
1413973 TATTTTGCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.26, C:0.13, G:0.34, T:0.28
Consensus pattern (19 bp):
AGGTGTAGGAGATTCTACC
Found at i:1415977 original size:33 final size:34
Alignment explanation
Indices: 1415918--1416007 Score: 164
Period size: 33 Copynumber: 2.7 Consensus size: 34
1415908 CCCATGTTCA
*
1415918 AAGTTGGCCACCTACCAAAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
1415952 AAGTTGGCCACCAACC-AAGATGAATTTTCCAAT
1 AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
1415985 AAGTTGGCCACCAACCAAAGATG
1 AAGTTGGCCACCAACCAAAGATG
1416008 TCAACTTTAC
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
33 33 0.61
34 21 0.39
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (34 bp):
AAGTTGGCCACCAACCAAAGATGAATTTTCCAAT
Found at i:1417913 original size:13 final size:13
Alignment explanation
Indices: 1417895--1417919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1417885 TCATCTTGTG
1417895 ATTCTTCTATTGC
1 ATTCTTCTATTGC
1417908 ATTCTTCTATTG
1 ATTCTTCTATTG
1417920 GATTTGAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.20, G:0.08, T:0.56
Consensus pattern (13 bp):
ATTCTTCTATTGC
Found at i:1420782 original size:16 final size:17
Alignment explanation
Indices: 1420758--1420802 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
1420748 AAGATGTCAT
*
1420758 CTTTACCAACTTTTA-A
1 CTTTGCCAACTTTTATA
1420774 CTTTGCCAAC-TTTATA
1 CTTTGCCAACTTTTATA
1420790 CTTTGCCAACTTT
1 CTTTGCCAACTTT
1420803 CAAGCCAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 4 0.15
16 20 0.77
17 2 0.08
ACGTcount: A:0.24, C:0.27, G:0.04, T:0.44
Consensus pattern (17 bp):
CTTTGCCAACTTTTATA
Found at i:1422983 original size:28 final size:29
Alignment explanation
Indices: 1422941--1423025 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 29
1422931 TCCCATCTTC
* * *
1422941 ATTCTGCATGGGATTATATCCTCGTCCTG
1 ATTCTACATGAGATTATATCCCCGTCCTG
* *
1422970 A-TCTACATGAGATTATATCCCCATCTTG
1 ATTCTACATGAGATTATATCCCCGTCCTG
* * *
1422998 ATTCTATATGTGATTATGTCCCCGTCCT
1 ATTCTACATGAGATTATATCCCCGTCCT
1423026 AATTTTGTAT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
28 23 0.51
29 22 0.49
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (29 bp):
ATTCTACATGAGATTATATCCCCGTCCTG
Found at i:1423013 original size:29 final size:29
Alignment explanation
Indices: 1422924--1423020 Score: 97
Period size: 29 Copynumber: 3.4 Consensus size: 29
1422914 TCTACTTGGA
* * * *
1422924 ATTATATTCCCATCTTCATTCTGCATGGG
1 ATTATATCCCCATCTTGATTCTACATGAG
* * *
1422953 ATTATATCCTCGTCCTGA-TCTACATGAG
1 ATTATATCCCCATCTTGATTCTACATGAG
* *
1422981 ATTATATCCCCATCTTGATTCTATATGTG
1 ATTATATCCCCATCTTGATTCTACATGAG
*
1423010 ATTATGTCCCC
1 ATTATATCCCC
1423021 GTCCTAATTT
Statistics
Matches: 54, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
28 23 0.43
29 31 0.57
ACGTcount: A:0.23, C:0.25, G:0.12, T:0.40
Consensus pattern (29 bp):
ATTATATCCCCATCTTGATTCTACATGAG
Found at i:1423845 original size:17 final size:18
Alignment explanation
Indices: 1423809--1423851 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1423799 TAAAAGTTAT
*
1423809 TTAAAT-AATAAAAATGA
1 TTAAATAAATAAAAATAA
1423826 TTAAATAAATAAAAA-AA
1 TTAAATAAATAAAAATAA
*
1423843 TTAAGTAAA
1 TTAAATAAA
1423852 AATAAGAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (18 bp):
TTAAATAAATAAAAATAA
Found at i:1423851 original size:21 final size:21
Alignment explanation
Indices: 1423810--1423851 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1423800 AAAAGTTATT
* *
1423810 TAAATAATAAAAATGATTAAA
1 TAAATAATAAAAATAAGTAAA
1423831 TAAATAA-AAAAATTAAGTAAA
1 TAAATAATAAAAA-TAAGTAAA
1423852 AATAAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (21 bp):
TAAATAATAAAAATAAGTAAA
Found at i:1427198 original size:7 final size:6
Alignment explanation
Indices: 1427178--1427242 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
1427168 TTGTTCCTAT
* ** *
1427178 AAAATA AAAATA AAAAT- TAAAT- AAAATA AAATATGA TCAATC AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAA-AT-A AAAATA AAAATA
*
1427226 AAAACA AAAATA AAAAT
1 AAAATA AAAATA AAAAT
1427243 GTAACAAAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
5 8 0.17
6 32 0.70
7 4 0.09
8 2 0.04
ACGTcount: A:0.74, C:0.05, G:0.02, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:1430122 original size:17 final size:19
Alignment explanation
Indices: 1430090--1430130 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1430080 AGGGGTTTGG
*
1430090 TAAAAGTTATTTAAAT-AA
1 TAAAAGTGATTTAAATAAA
1430108 TAAAAGTGA-TTAAATAAA
1 TAAAAGTGATTTAAATAAA
1430126 TAAAA
1 TAAAA
1430131 TCAATTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (19 bp):
TAAAAGTGATTTAAATAAA
Found at i:1437064 original size:18 final size:18
Alignment explanation
Indices: 1437038--1437083 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
1437028 GCTATACAAG
*
1437038 TGTGACTATTCCAAGACT
1 TGTGCCTATTCCAAGACT
1437056 TGTGCCTATT-CAAGACT
1 TGTGCCTATTCCAAGACT
1437073 TGTGCCTATTC
1 TGTGCCTATTC
1437084 TAGATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 17 0.65
18 9 0.35
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTGCCTATTCCAAGACT
Found at i:1437476 original size:90 final size:89
Alignment explanation
Indices: 1437358--1437534 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 89
1437348 TAATCCCGAA
* * *
1437358 TATTTAATTTCAATTAATTAAAAATAGATTTAATTAATTTGAAATAATAAAATCTCTAATATGAT
1 TATTAAATTCCAATTAATTAAAAATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGAT
1437423 TAGGGTAACTTAGATATAAAAGGAT
65 TAGGGTAACTTAGATATAAAAGGAT
*
1437448 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAAAATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
* *
1437513 AGGGTAACTTGGCTATAAAAGG
66 AGGGTAACTTAGATATAAAAGG
1437535 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 32 0.40
90 49 0.60
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAAAATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
AGGGTAACTTAGATATAAAAGGAT
Found at i:1450142 original size:24 final size:24
Alignment explanation
Indices: 1450110--1450211 Score: 114
Period size: 24 Copynumber: 4.2 Consensus size: 24
1450100 CTGTTTTATA
* *
1450110 TGATTTCTTATTTGAATTCTGTTC
1 TGATTTCTTATCTGAATTCTGTTT
* *
1450134 TGATTTCTTATCTGAATTATGTTA
1 TGATTTCTTATCTGAATTCTGTTT
* * * *
1450158 TGATTTCTAATATGGACTCTGTTT
1 TGATTTCTTATCTGAATTCTGTTT
* *
1450182 TGATATCTGATCTGAATTCTGTTT
1 TGATTTCTTATCTGAATTCTGTTT
1450206 TGATTT
1 TGATTT
1450212 ATGATATATT
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.21, C:0.11, G:0.15, T:0.54
Consensus pattern (24 bp):
TGATTTCTTATCTGAATTCTGTTT
Found at i:1450164 original size:48 final size:48
Alignment explanation
Indices: 1450108--1450211 Score: 127
Period size: 48 Copynumber: 2.2 Consensus size: 48
1450098 GACTGTTTTA
* * * * *
1450108 TATGATTTCTTATTTGAATTCTGTTCTGATTTCTTATCTGAATTATGT
1 TATGATTTCTAATATGAACTCTGTTCTGATATCTGATCTGAATTATGT
* * *
1450156 TATGATTTCTAATATGGACTCTGTTTTGATATCTGATCTGAATTCTGT
1 TATGATTTCTAATATGAACTCTGTTCTGATATCTGATCTGAATTATGT
*
1450204 TTTGATTT
1 TATGATTT
1450212 ATGATATATT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.21, C:0.11, G:0.14, T:0.54
Consensus pattern (48 bp):
TATGATTTCTAATATGAACTCTGTTCTGATATCTGATCTGAATTATGT
Found at i:1452304 original size:19 final size:19
Alignment explanation
Indices: 1452267--1452304 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1452257 AGAAAATCGG
*
1452267 TTTGACCGGTTTGAACCGA
1 TTTGACCGGTCTGAACCGA
*
1452286 TTTGACCGGTCTGACCCGA
1 TTTGACCGGTCTGAACCGA
1452305 CTGACCAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (19 bp):
TTTGACCGGTCTGAACCGA
Found at i:1452341 original size:17 final size:17
Alignment explanation
Indices: 1452321--1452354 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1452311 AACCCGACCA
1452321 GTTGACCAACGTTGACT
1 GTTGACCAACGTTGACT
**
1452338 GTTGACCGGCGTTGACT
1 GTTGACCAACGTTGACT
1452355 TTCATTGACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (17 bp):
GTTGACCAACGTTGACT
Found at i:1454570 original size:24 final size:24
Alignment explanation
Indices: 1454542--1454629 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 24
1454532 GTTTTATCTG
* *
1454542 ATTTCGGATTTGAATTTTGTTCTA
1 ATTTCTGATATGAATTTTGTTCTA
*
1454566 ATTTCTGATATGAATTTTGTTCTG
1 ATTTCTGATATGAATTTTGTTCTA
* * * *
1454590 ATTTCTGATCTGGACTTTGTTCTG
1 ATTTCTGATATGAATTTTGTTCTA
* *
1454614 ATATCTGATCTGAATT
1 ATTTCTGATATGAATT
1454630 CTATTTTGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTTCTGATATGAATTTTGTTCTA
Found at i:1454591 original size:48 final size:48
Alignment explanation
Indices: 1454538--1454629 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
1454528 GAATGTTTTA
* * *
1454538 TCTGATTTCGGATTTGAATTTTGTTCTAATTTCTGATATGAATTTTGT
1 TCTGATTTCGGATCTGAACTTTGTTCTAATATCTGATATGAATTTTGT
* * * *
1454586 TCTGATTTCTGATCTGGACTTTGTTCTGATATCTGATCTGAATT
1 TCTGATTTCGGATCTGAACTTTGTTCTAATATCTGATATGAATT
1454630 CTATTTTGAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.20, C:0.12, G:0.17, T:0.51
Consensus pattern (48 bp):
TCTGATTTCGGATCTGAACTTTGTTCTAATATCTGATATGAATTTTGT
Found at i:1463298 original size:21 final size:21
Alignment explanation
Indices: 1463265--1463317 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1463255 ATTCTGACTA
1463265 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
1463286 TCGCGTTGTGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
1463307 TCGCAATGCGA
1 TCGCATTGCGA
1463318 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1463353 original size:41 final size:40
Alignment explanation
Indices: 1463307--1463408 Score: 123
Period size: 41 Copynumber: 2.5 Consensus size: 40
1463297 TTTTCCTAAT
* **
1463307 TCGCAATGCGAATACGTAAATCACAACGTGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCACAACGCGAA-TACGAAAA
* * * *
1463348 TCGCAATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAATCACAACGCGAATACGAAAA
*
1463388 TCGCAATGCGAATATGTAAAT
1 TCGCAATGCGAATACGTAAAT
1463409 GGCAATGCAA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
40 24 0.46
41 28 0.54
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.24
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCACAACGCGAATACGAAAA
Found at i:1463370 original size:20 final size:20
Alignment explanation
Indices: 1463307--1463416 Score: 130
Period size: 20 Copynumber: 5.5 Consensus size: 20
1463297 TTTTCCTAAT
1463307 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * * ** *
1463327 TCACAACGTGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
1463348 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
1463368 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1463388 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
1463408 TGGCAATGC
1 TCGCAATGC
1463417 AAATCTGACT
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
20 60 0.82
21 13 0.18
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1463433 original size:20 final size:20
Alignment explanation
Indices: 1463410--1463474 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
1463400 TATGTAAATG
1463410 GCAATGCAAATCTGACTATC
1 GCAATGCAAATCTGACTATC
*
1463430 GCAATGCGAATCTGACTATC
1 GCAATGCAAATCTGACTATC
* *
1463450 GCAACG-AGATTCTGACTATC
1 GCAATGCA-AATCTGACTATC
1463470 GCAAT
1 GCAAT
1463475 ACTGAATTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
GCAATGCAAATCTGACTATC
Found at i:1464543 original size:3 final size:3
Alignment explanation
Indices: 1464535--1464561 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1464525 ATATAACCCT
1464535 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1464562 ATCCCCAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1466239 original size:20 final size:20
Alignment explanation
Indices: 1466171--1466239 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
1466161 CAACGCGGAA
*
1466171 ATCGGAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
* *
1466191 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGGAAATGACT
1466211 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
1466231 ATTGCAACG
1 ATCGCAACG
1466240 AGAGAATCGC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:1466299 original size:34 final size:33
Alignment explanation
Indices: 1466234--1466306 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
1466224 AATGACTATT
* *
1466234 GCAACGAGAGAATCGCATTGCGAAATGAAAATC
1 GCAACGAGAGAATCGAAATGCGAAATGAAAATC
*
1466267 GCAACGAGTGAATCGAAATGCGAAAATGAAAATC
1 GCAACGAGAGAATCGAAATGCG-AAATGAAAATC
1466301 GCAACG
1 GCAACG
1466307 CGAATTTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 19 0.53
34 17 0.47
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (33 bp):
GCAACGAGAGAATCGAAATGCGAAATGAAAATC
Found at i:1466362 original size:14 final size:14
Alignment explanation
Indices: 1466343--1466396 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1466333 CATTTTCGCA
1466343 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1466357 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
1466374 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
1466390 TTGCGAT
1 TTGCGAT
1466397 AGTTATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 13 0.39
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1466378 original size:33 final size:34
Alignment explanation
Indices: 1466321--1466396 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 34
1466311 TTTAGTTTCG
*
1466321 CGTTGTGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1466355 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1466388 CGTTGCGAT
1 CGTTGCGAT
1466397 AGTTATTTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 28 0.68
34 13 0.32
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
Found at i:1466405 original size:33 final size:33
Alignment explanation
Indices: 1466321--1466416 Score: 122
Period size: 33 Copynumber: 2.8 Consensus size: 33
1466311 TTTAGTTTCG
* *
1466321 CGTTGTGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATGTTCA-TTTCGCATTGCGATTCTCT
*
1466355 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATGTTCATTTCGCATTGCGATTCTCT
*
1466388 CGTTGCGATAGTT-ATTTCCGCGTTGCGAT
1 CGTTGCGAT-GTTCATTT-CGCATTGCGAT
1466417 AGTATGTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 32 0.56
34 25 0.44
ACGTcount: A:0.12, C:0.22, G:0.21, T:0.45
Consensus pattern (33 bp):
CGTTGCGATGTTCATTTCGCATTGCGATTCTCT
Found at i:1468036 original size:42 final size:42
Alignment explanation
Indices: 1467938--1468049 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
1467928 TCTAGAATGT
* * * *
1467938 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGGA-CTCTTGAACGATGATAGGGGCCTCTTGAACGA
* **
1467980 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGACTCTTGAACGATGATAGGGGCCTCTTGAACGA
*
1468022 TAGGG-GAGGCCTCTTGAACGATGATAGG
1 T-GGGAGAGGACTCTTGAACGATGATAGG
1468050 TGAGTCGGGC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
42 52 0.90
43 6 0.10
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGACTCTTGAACGATGATAGGGGCCTCTTGAACGA
Found at i:1468552 original size:20 final size:20
Alignment explanation
Indices: 1468529--1468637 Score: 128
Period size: 20 Copynumber: 5.5 Consensus size: 20
1468519 GAAACTTAAA
1468529 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1468549 ATCGCAAAGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1468569 ATCACAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* * **
1468589 ATCGTAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
* ** *
1468609 ATCGCAATGCGAATTTAACT
1 ATCGCAACGCGAAAATGACT
1468629 ATCGCAACG
1 ATCGCAACG
1468638 AGAGAATCGC
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1468719 original size:20 final size:20
Alignment explanation
Indices: 1468696--1468802 Score: 120
Period size: 20 Copynumber: 5.7 Consensus size: 20
1468686 AATAATCAAA
1468696 TTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATAGTCATT
1468716 TTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATAGTCATT
* **
1468736 TTCGCGTTGCGATTTTCA-T
1 TTCGCATTGCGATAGTCATT
1468755 TTCGCATTGCGAT--TC--T
1 TTCGCATTGCGATAGTCATT
*
1468771 CTCG--TTGCGATAGTCATT
1 TTCGCATTGCGATAGTCATT
*
1468789 TTCCCATTGCGATA
1 TTCGCATTGCGATA
1468803 ATAAACTATT
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
14 7 0.09
16 6 0.08
17 2 0.03
18 3 0.04
19 13 0.18
20 43 0.58
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (20 bp):
TTCGCATTGCGATAGTCATT
Found at i:1470684 original size:20 final size:20
Alignment explanation
Indices: 1470661--1470715 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1470651 CTGAAACTTT
1470661 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
1470681 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
1470701 CTATCGCAACGCGAA
1 AAATCGCAACACGAA
1470716 TTTGACTATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:1470721 original size:20 final size:20
Alignment explanation
Indices: 1470663--1470732 Score: 77
Period size: 20 Copynumber: 3.5 Consensus size: 20
1470653 GAAACTTTAA
* **
1470663 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
1470683 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
1470703 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
1470723 ATCACAACGC
1 ATCGCAACGC
1470733 AAGAATCGCA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.43, C:0.26, G:0.16, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1471159 original size:22 final size:22
Alignment explanation
Indices: 1471100--1471175 Score: 80
Period size: 22 Copynumber: 3.5 Consensus size: 22
1471090 TAACCGTGAA
* *
1471100 TGATTTCGCAGGAGATGGAGAC
1 TGATTTCGCCGGAGATGGGGAC
* * *
1471122 TGATATCGTCGAAGATGGGGAC
1 TGATTTCGCCGGAGATGGGGAC
* *
1471144 TGATTTCACCGGAGATGTGGAC
1 TGATTTCGCCGGAGATGGGGAC
*
1471166 GGATTTCGCC
1 TGATTTCGCC
1471176 TTAGAGAGTA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (22 bp):
TGATTTCGCCGGAGATGGGGAC
Found at i:1471407 original size:40 final size:40
Alignment explanation
Indices: 1471345--1471496 Score: 191
Period size: 40 Copynumber: 3.8 Consensus size: 40
1471335 GCTATGTAAA
*
1471345 TCGCATTGCGATAGT-CAG-ATTCGCATTGCGATTTGCATAT
1 TCGCATTGCGATA-TAC-GTATTCGCATTGCGATTTACATAT
*
1471385 TCGCATTGCGATATACGTATTCGCATTGCGATTTACATAA
1 TCGCATTGCGATATACGTATTCGCATTGCGATTTACATAT
* * * *
1471425 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATATACGTATTCGCATTGCGA-TTTACATAT
* *
1471466 TCGCGTTGCGATTTACGTATTCGCATTGCGA
1 TCGCATTGCGATATACGTATTCGCATTGCGA
1471497 ATTAGGAAAA
Statistics
Matches: 100, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
39 2 0.02
40 63 0.63
41 35 0.35
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (40 bp):
TCGCATTGCGATATACGTATTCGCATTGCGATTTACATAT
Found at i:1471437 original size:20 final size:20
Alignment explanation
Indices: 1471343--1471496 Score: 150
Period size: 20 Copynumber: 7.7 Consensus size: 20
1471333 GTGCTATGTA
* *
1471343 AATCGCATTGCGATAGT-CAG
1 AATCGCATTGCGAT-TTACAT
* *
1471363 ATTCGCATTGCGATTTGCAT
1 AATCGCATTGCGATTTACAT
* * *
1471383 ATTCGCATTGCGATATACGT
1 AATCGCATTGCGATTTACAT
*
1471403 ATTCGCATTGCGATTTACAT
1 AATCGCATTGCGATTTACAT
*
1471423 AATCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACAT
*
1471443 AATCGCATTGCGATTTTCCA-
1 AATCGCATTGCGA-TTTACAT
* *
1471463 AATTCGCGTTGCGATTTACGT
1 AA-TCGCATTGCGATTTACAT
*
1471484 ATTCGCATTGCGA
1 AATCGCATTGCGA
1471497 ATTAGGAAAA
Statistics
Matches: 113, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.01
20 97 0.86
21 15 0.13
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (20 bp):
AATCGCATTGCGATTTACAT
Found at i:1471517 original size:21 final size:21
Alignment explanation
Indices: 1471493--1471538 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1471483 TATTCGCATT
1471493 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
1471514 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1471535 GCGA
1 GCGA
1471539 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1473877 original size:18 final size:18
Alignment explanation
Indices: 1473850--1473895 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
1473840 GGTTTTTAAT
*
1473850 TTTA-CTTTCTTTGATTC
1 TTTATCTTTCTTTGAATC
1473867 TTTATCTTTCTTTGAATC
1 TTTATCTTTCTTTGAATC
*
1473885 ATTAT-TTTCTT
1 TTTATCTTTCTT
1473896 ATTCAATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.15, C:0.15, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTATCTTTCTTTGAATC
Found at i:1475806 original size:28 final size:27
Alignment explanation
Indices: 1475739--1475812 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
1475729 TAGATGGAAG
* * *
1475739 GAAATGTCTAAAATACCCTTAAATTGT
1 GAAATGACTAAAATACCCCTAAAGTGT
* *
1475766 GAAATAACTAAAATGCCCCTAAAGTGT
1 GAAATGACTAAAATACCCCTAAAGTGT
1475793 GAAATGACTTAAAATACCCC
1 GAAATGAC-TAAAATACCCC
1475813 AAGCTCTGGA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 29 0.74
28 10 0.26
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (27 bp):
GAAATGACTAAAATACCCCTAAAGTGT
Found at i:1500308 original size:17 final size:17
Alignment explanation
Indices: 1500286--1500323 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1500276 GAATTTAACC
1500286 TTTTG-TGTTTGTCCTAA
1 TTTTGTTGTTTGTCC-AA
*
1500303 TTTTGTTGTTTTTCCAA
1 TTTTGTTGTTTGTCCAA
1500320 TTTT
1 TTTT
1500324 AATTTTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.11, C:0.11, G:0.13, T:0.66
Consensus pattern (17 bp):
TTTTGTTGTTTGTCCAA
Found at i:1502572 original size:55 final size:55
Alignment explanation
Indices: 1502507--1502634 Score: 181
Period size: 52 Copynumber: 2.4 Consensus size: 55
1502497 GCGTTCAGAT
*
1502507 GATTCATGAAGAAAGACATCCGATGAATGAAGAAATTTGAACCTGATTGAAGAAC
1 GATTCATGAAGAAAGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGAAC
**
1502562 GATTCATGAAG---GACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGATT
1 GATTCATGAAGAAAGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGAAC
* **
1502614 GATCCACAAAGAAAGACATCC
1 GATTCATGAAGAAAGACATCC
1502635 TGAAGATGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
52 46 0.72
55 18 0.28
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (55 bp):
GATTCATGAAGAAAGACATCCGATGAATGAAGAAATTTGAAACTGATTGAAGAAC
Found at i:1503394 original size:70 final size:68
Alignment explanation
Indices: 1503310--1503441 Score: 237
Period size: 70 Copynumber: 1.9 Consensus size: 68
1503300 AAATATGAAG
1503310 ACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAACCAATGTGATGATAGCAAATGATCAAGAACA
1 ACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAACCAA--TGATGATAGCAAATGATCAAGAACA
1503375 GATGA
64 GATGA
*
1503380 ACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAACCAATGATGATAGCAACTGATCAAGAAC
1 ACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAACCAATGATGATAGCAAATGATCAAGAAC
1503442 CTGTTAGGGG
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
68 23 0.38
70 38 0.62
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (68 bp):
ACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAACCAATGATGATAGCAAATGATCAAGAACAGA
TGA
Found at i:1507254 original size:17 final size:16
Alignment explanation
Indices: 1507223--1507256 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1507213 CACGTGAGGA
1507223 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1507239 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1507256 T
1 T
1507257 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1513629 original size:19 final size:21
Alignment explanation
Indices: 1513592--1513634 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1513582 TAACTTTTTC
1513592 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
1513612 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
1513632 TTT
1 TTT
1513635 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:1513640 original size:19 final size:20
Alignment explanation
Indices: 1513591--1513640 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1513581 TTAACTTTTT
*
1513591 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
1513611 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
1513630 CTTTTACCTTT
1 CTTTTACCTTT
1513641 TCTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:1516575 original size:17 final size:16
Alignment explanation
Indices: 1516544--1516577 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1516534 CACGTGAGGA
1516544 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1516560 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1516577 T
1 T
1516578 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:1518870 original size:42 final size:42
Alignment explanation
Indices: 1518824--1518906 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
1518814 TCCTTCGAGT
*
1518824 CATCAATAAGTCTTTCT-AGCATGATGCTTAAATCATTAGGGC
1 CATCAATAAGTCTTT-TGAGCATGATGATTAAATCATTAGGGC
* * *
1518866 CATCAGTAAGTCTTTTGAGCTTGATGATTAAATCCTTAGGG
1 CATCAATAAGTCTTTTGAGCATGATGATTAAATCATTAGGG
1518907 TAATTTGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 1 0.03
42 35 0.97
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (42 bp):
CATCAATAAGTCTTTTGAGCATGATGATTAAATCATTAGGGC
Found at i:1518963 original size:13 final size:13
Alignment explanation
Indices: 1518945--1518969 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1518935 TGAAGCAAAC
1518945 CCATCAGTAAGTG
1 CCATCAGTAAGTG
1518958 CCATCAGTAAGT
1 CCATCAGTAAGT
1518970 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:1519018 original size:42 final size:42
Alignment explanation
Indices: 1518959--1519361 Score: 373
Period size: 42 Copynumber: 9.4 Consensus size: 42
1518949 CAGTAAGTGC
* *
1518959 CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
1519001 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
* * ** * *
1519043 CATCAGTAAGTCTTTCGAGCATAATGATGATGTCCTTCAGGC
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
1519085 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
* ** * * ** * *
1519127 AATTTGTAAGCCTTCACCGAAG-A-GTAGTGAAGCAAATCCATCAGTAAGTGC
1 CATCAGTAAGTCTT--TCG-AGCATG-A-TG-ATTAAATCCTTC-G---G-GT
1519178 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
* * **
1519220 CATCATTAAGTCTTTCGAGCATGATGATTAAATCATTCGGAC
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
* * * * *
1519262 CATCATTAATTCTTTCGAGCATGATGATTAAATCATTTGAGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
*** * * *
1519304 CATTTTTGAGTCTTTCGAGCAAGAT-AATAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
*
1519345 CATCCA-TAAGTCCTTCG
1 CAT-CAGTAAGTCTTTCG
1519362 GGTAGGATGT
Statistics
Matches: 293, Mismatches: 54, Indels: 29
0.78 0.14 0.08
Matches are distributed among these distances:
41 24 0.08
42 218 0.74
43 2 0.01
44 4 0.01
45 4 0.01
46 10 0.03
47 10 0.03
48 4 0.01
49 4 0.01
50 2 0.01
51 11 0.04
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
Found at i:1519182 original size:13 final size:13
Alignment explanation
Indices: 1519164--1519188 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1519154 TGAAGCAAAT
1519164 CCATCAGTAAGTG
1 CCATCAGTAAGTG
1519177 CCATCAGTAAGT
1 CCATCAGTAAGT
1519189 CTTTCGAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:1519189 original size:219 final size:219
Alignment explanation
Indices: 1518810--1519298 Score: 755
Period size: 219 Copynumber: 2.2 Consensus size: 219
1518800 TCACGCTTAG
* * * *
1518810 TAAATCCTTCGAGTCATCAATAAGTCTTTCTAGCATGATGCTTAAATCATTAGGGCCATCAGTAA
1 TAAATCCTTCGGGTCATCAATAAGTCTTTCGAGCATGATGATGAAATCATTAGGGCCATCAGTAA
* * *
1518875 GTCTTTTGAGCTTGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACGGAAGAGTAGTGAAG
66 GTCTTTCGAGCATGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAG
*
1518940 CAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGTCATC
131 CAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATC
1519005 AGTAAGTCTTTCGAGCATGATGAT
196 AGTAAGTCTTTCGAGCATGATGAT
* * ** *
1519029 TAAATCCTTCGGGTCATCAGTAAGTCTTTCGAGCATAATGATGATGTCCTTCA-GGCCATCAGTA
1 TAAATCCTTCGGGTCATCAATAAGTCTTTCGAGCATGATGATGAAATCATT-AGGGCCATCAGTA
*
1519093 AGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAA
65 AGTCTTTCGAGCATGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAA
* *
1519158 GCAAATCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCAT
130 GCAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCAT
*
1519223 CATTAAGTCTTTCGAGCATGATGAT
195 CAGTAAGTCTTTCGAGCATGATGAT
* ** * * *
1519248 TAAATCATTCGGACCATCATTAATTCTTTCGAGCATGATGATTAAATCATT
1 TAAATCCTTCGGGTCATCAATAAGTCTTTCGAGCATGATGATGAAATCATT
1519299 TGAGTCATTT
Statistics
Matches: 242, Mismatches: 27, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
219 241 1.00
220 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (219 bp):
TAAATCCTTCGGGTCATCAATAAGTCTTTCGAGCATGATGATGAAATCATTAGGGCCATCAGTAA
GTCTTTCGAGCATGATGATTAAATCCTTAGGGTAATTTGTAAGCCTTCACCGAAGAGTAGTGAAG
CAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATC
AGTAAGTCTTTCGAGCATGATGAT
Found at i:1519249 original size:22 final size:22
Alignment explanation
Indices: 1519188--1519295 Score: 98
Period size: 22 Copynumber: 5.1 Consensus size: 22
1519178 CATCAGTAAG
1519188 TCTTTCGAGCATGATGATTAAA
1 TCTTTCGAGCATGATGATTAAA
* * * * *
1519210 TCCTTCG-G-GTCATCATTAAG
1 TCTTTCGAGCATGATGATTAAA
1519230 TCTTTCGAGCATGATGATTAAA
1 TCTTTCGAGCATGATGATTAAA
* ** * *
1519252 TCATTCG-G-ACCATCATTAAT
1 TCTTTCGAGCATGATGATTAAA
1519272 TCTTTCGAGCATGATGATTAAA
1 TCTTTCGAGCATGATGATTAAA
1519294 TC
1 TC
1519296 ATTTGAGTCA
Statistics
Matches: 62, Mismatches: 20, Indels: 8
0.69 0.22 0.09
Matches are distributed among these distances:
20 28 0.45
21 4 0.06
22 30 0.48
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (22 bp):
TCTTTCGAGCATGATGATTAAA
Found at i:1519849 original size:53 final size:53
Alignment explanation
Indices: 1519783--1520274 Score: 556
Period size: 53 Copynumber: 9.2 Consensus size: 53
1519773 AAAATTACAC
* *
1519783 CAGAAAATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGC
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * * * *
1519836 CAGAATATCGTTCGAGTTCTACTCCCAGAAGCAAGAGGGAGCAAACCCATAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * *
1519889 CAGAAGATTGTTCGAGTTCTACGCTCCATTAAGCAAGTGGGAGCGAACCCGTAAG
1 CAGAAGATTGTTCGAGTTCTA--CTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* **
1519944 CAGAAGATCGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAAA
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* ** * * ***
1519997 CAGAAGATTGTTCGAGTTCAACTCCCTGAAGCATTAGGGAGCGAACTCATTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * *
1520050 TAGAAGATTGTTCAAGTTCTACTCCCTGAAGCAAGAGGGGGCGAACCCATAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * * *
1520103 CAGAAGATTATTCGAGTTATACTCCTTAAAGCAAGAGGGAGTGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * **
1520156 CAGAAGATTGTTCGAGTTCTAC-CCCTTGAAACAAGAGGGAGCAAACCTATAGG
1 CAGAAGATTGTTCGAGTTCTACTCCC-TGAAGCAAGAGGGAGCGAACCCGTAGG
* * * *
1520209 CAGAAGATTATTCGAGTTCTACTCCTTGACGCAAGAAGGAGCGAACCCGCT-GG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG-TAGG
**
1520262 TTGAAGATTGTTC
1 CAGAAGATTGTTC
1520275 AAAGAAGAGG
Statistics
Matches: 366, Mismatches: 68, Indels: 10
0.82 0.15 0.02
Matches are distributed among these distances:
52 2 0.01
53 315 0.86
54 3 0.01
55 46 0.13
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:1523397 original size:43 final size:43
Alignment explanation
Indices: 1523327--1523415 Score: 142
Period size: 43 Copynumber: 2.1 Consensus size: 43
1523317 CACGTGGTCA
* *
1523327 CCTGTTTCTGCAGTCTTGTCTCAATTTCGACCATACCCTATCG
1 CCTGTTTCCGCAGTCTTCTCTCAATTTCGACCATACCCTATCG
* *
1523370 CCTGTTTCCGCAGTCTTCTCTCGATTTCGAGCATACCCTATCG
1 CCTGTTTCCGCAGTCTTCTCTCAATTTCGACCATACCCTATCG
1523413 CCT
1 CCT
1523416 ACCCATGCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.15, C:0.35, G:0.15, T:0.36
Consensus pattern (43 bp):
CCTGTTTCCGCAGTCTTCTCTCAATTTCGACCATACCCTATCG
Found at i:1533010 original size:35 final size:35
Alignment explanation
Indices: 1532966--1533033 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
1532956 AAACAAATGA
* *
1532966 AATTCCTTAAGAATTCCTAAATACAACAAGTGGAT
1 AATTACTTAAGAATTCCCAAATACAACAAGTGGAT
*
1533001 AATTACTTAAGAATTCCCAGATACAACAAGTGG
1 AATTACTTAAGAATTCCCAAATACAACAAGTGG
1533034 GAGAAGATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (35 bp):
AATTACTTAAGAATTCCCAAATACAACAAGTGGAT
Found at i:1536120 original size:2 final size:2
Alignment explanation
Indices: 1536113--1536142 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1536103 ATTATGAAGT
1536113 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
1536143 AGGGTGATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1543574 original size:20 final size:20
Alignment explanation
Indices: 1543538--1543577 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1543528 GATGTTACAA
*
1543538 ATTTGTTCATCATAAAATCC
1 ATTTGTTCACCATAAAATCC
1543558 ATTT-TTCACCATCAAAATCC
1 ATTTGTTCACCAT-AAAATCC
1543578 TTGTATCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.38
Consensus pattern (20 bp):
ATTTGTTCACCATAAAATCC
Found at i:1550939 original size:17 final size:17
Alignment explanation
Indices: 1550919--1550995 Score: 100
Period size: 17 Copynumber: 4.4 Consensus size: 17
1550909 GGAAGTCAAC
* *
1550919 GGTCAACGGTCGGGTCA
1 GGTCAACAGTCGGGTCG
1550936 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
1550953 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
**
1550970 GGTCGGGTCAGTCGGGTCG
1 GGTC--AACAGTCGGGTCG
1550989 GGTCAAC
1 GGTCAAC
1550996 CCGGTTCAGA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
17 37 0.71
19 15 0.29
ACGTcount: A:0.16, C:0.23, G:0.43, T:0.18
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:1550983 original size:19 final size:20
Alignment explanation
Indices: 1550944--1550992 Score: 73
Period size: 19 Copynumber: 2.4 Consensus size: 20
1550934 CAGGTCAACA
1550944 GTCGGGTCGGGTCAACAGTCGG
1 GTCGGGTCGGGT--ACAGTCGG
1550966 GTCGGGTCGGGT-CAGTCGG
1 GTCGGGTCGGGTACAGTCGG
1550985 GTCGGGTC
1 GTCGGGTC
1550993 AACCCGGTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.56
22 12 0.44
ACGTcount: A:0.08, C:0.22, G:0.49, T:0.20
Consensus pattern (20 bp):
GTCGGGTCGGGTACAGTCGG
Found at i:1550985 original size:14 final size:14
Alignment explanation
Indices: 1550966--1550993 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1550956 CAACAGTCGG
1550966 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
1550980 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
1550994 ACCCGGTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.50, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:1551011 original size:19 final size:19
Alignment explanation
Indices: 1550989--1551041 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
1550979 AGTCGGGTCG
*
1550989 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
1551008 GGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
1551027 GGTCAAACCGGTTCA
1 GGTCAAACCGGTTCA
1551042 AAACTGGTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:1551019 original size:9 final size:9
Alignment explanation
Indices: 1550989--1551058 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
1550979 AGTCGGGTCG
*
1550989 GGTCAACCC
1 GGTCAAACC
*
1550998 GGTTCAGACC
1 GG-TCAAACC
1551008 GGTCAAACC
1 GGTCAAACC
*
1551017 GGTTCAGACC
1 GG-TCAAACC
1551027 GGTCAAACC
1 GGTCAAACC
*
1551036 GGTTCAAAACT
1 GG-TC-AAACC
*
1551047 GGTCGAACC
1 GGTCAAACC
1551056 GGT
1 GGT
1551059 TTTCCAGCAG
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
9 24 0.49
10 19 0.39
11 6 0.12
ACGTcount: A:0.26, C:0.30, G:0.27, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1551027 original size:10 final size:10
Alignment explanation
Indices: 1550991--1551043 Score: 65
Period size: 10 Copynumber: 5.5 Consensus size: 10
1550981 TCGGGTCGGG
*
1550991 TCAACCCGGT
1 TCAAACCGGT
*
1551001 TCAGACCGG-
1 TCAAACCGGT
1551010 TCAAACCGGT
1 TCAAACCGGT
*
1551020 TCAGACCGG-
1 TCAAACCGGT
1551029 TCAAACCGGT
1 TCAAACCGGT
1551039 TCAAA
1 TCAAA
1551044 ACTGGTCGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
9 16 0.44
10 20 0.56
ACGTcount: A:0.28, C:0.32, G:0.23, T:0.17
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:1551669 original size:34 final size:34
Alignment explanation
Indices: 1551626--1551699 Score: 148
Period size: 34 Copynumber: 2.2 Consensus size: 34
1551616 ATCCTTACCT
1551626 AATTTTATTGGGTAAATTCAGGGCTTGGTCCCTG
1 AATTTTATTGGGTAAATTCAGGGCTTGGTCCCTG
1551660 AATTTTATTGGGTAAATTCAGGGCTTGGTCCCTG
1 AATTTTATTGGGTAAATTCAGGGCTTGGTCCCTG
1551694 AATTTT
1 AATTTT
1551700 CTTGAACTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.41
Consensus pattern (34 bp):
AATTTTATTGGGTAAATTCAGGGCTTGGTCCCTG
Found at i:1553192 original size:23 final size:23
Alignment explanation
Indices: 1553166--1553247 Score: 105
Period size: 23 Copynumber: 3.7 Consensus size: 23
1553156 GGTCCCTCAG
* *
1553166 GACAAAACTATATTGTCCTTTGA
1 GACAAAACTATGTGGTCCTTTGA
*
1553189 GACAAAACTATGTGGTCCTTTGG
1 GACAAAACTATGTGGTCCTTTGA
* *
1553212 GACAAACCTATGTGGTCATTTGA
1 GACAAAACTATGTGGTCCTTTGA
1553235 GAC-AAA-TATGTGG
1 GACAAAACTATGTGG
1553248 CACTTCGGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
21 7 0.13
22 2 0.04
23 43 0.83
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (23 bp):
GACAAAACTATGTGGTCCTTTGA
Found at i:1553203 original size:46 final size:45
Alignment explanation
Indices: 1553150--1553247 Score: 117
Period size: 46 Copynumber: 2.2 Consensus size: 45
1553140 GTCGAGGGTT
* *
1553150 CTATGTGGTCCCTCAGGACAAAACTATATTGTCCTTTGAGACAAAA
1 CTATGTGGTCCCTCAGGACAAAACTATATGGTCATTTGAGAC-AAA
* ** * *
1553196 CTATGTGGTCCTTTGGGACAAACCTATGTGGTCATTTGAGACAAA
1 CTATGTGGTCCCTCAGGACAAAACTATATGGTCATTTGAGACAAA
1553241 -TATGTGG
1 CTATGTGG
1553248 CACTTCGGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 7 0.16
45 3 0.07
46 35 0.78
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (45 bp):
CTATGTGGTCCCTCAGGACAAAACTATATGGTCATTTGAGACAAA
Found at i:1557704 original size:20 final size:21
Alignment explanation
Indices: 1557676--1557715 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1557666 ATAGTATGAA
*
1557676 CTGGATGAA-CAATATCGATT
1 CTGGATGAAGAAATATCGATT
*
1557696 CTGGTTGAAGAAATATCGAT
1 CTGGATGAAGAAATATCGAT
1557716 ACTAATGTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (21 bp):
CTGGATGAAGAAATATCGATT
Found at i:1558610 original size:23 final size:23
Alignment explanation
Indices: 1558570--1558704 Score: 159
Period size: 23 Copynumber: 6.0 Consensus size: 23
1558560 GTCGAGGGTT
* * *
1558570 CTATATGGTCCTTTGGGACAAAA
1 CTATGTGGTCATTCGGGACAAAA
* *
1558593 CTATGTGATCTTTCGGGACAAAA
1 CTATGTGGTCATTCGGGACAAAA
*
1558616 CTATGTGGTCATTCGGAACAAAA
1 CTATGTGGTCATTCGGGACAAAA
*
1558639 CTATGTGGTCATTCGGAACAAAA
1 CTATGTGGTCATTCGGGACAAAA
*
1558662 CTATGTGGTCCTTCGGGAC-AAA
1 CTATGTGGTCATTCGGGACAAAA
*
1558684 -TATGTGGT-ACTTCGGGGCAAA
1 CTATGTGGTCA-TTCGGGACAAA
1558705 TTATGTGAGT
Statistics
Matches: 99, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
21 15 0.15
22 5 0.05
23 79 0.80
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGACAAAA
Found at i:1561079 original size:31 final size:32
Alignment explanation
Indices: 1561044--1561108 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
1561034 TAAAAAAAAT
* *
1561044 ATATGGT-AATTTTTGTTTATATTTAATTAAG
1 ATATGGTCAATTTTTATTTATATTTAATAAAG
* *
1561075 ATATGGTCACTTTTTATTTTTATTTAATAAAG
1 ATATGGTCAATTTTTATTTATATTTAATAAAG
1561107 AT
1 AT
1561109 GTACTCATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 7 0.24
32 22 0.76
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.54
Consensus pattern (32 bp):
ATATGGTCAATTTTTATTTATATTTAATAAAG
Found at i:1561419 original size:31 final size:31
Alignment explanation
Indices: 1561381--1561440 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1561371 ATATATCACC
*
1561381 ATTCGATTGGAGGACTAACTTTATTTTAACA
1 ATTCGATTGGAGGACTAAATTTATTTTAACA
*
1561412 ATTCGATTGGAGGATTAAATTTATTTTAA
1 ATTCGATTGGAGGACTAAATTTATTTTAA
1561441 TTTACTACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (31 bp):
ATTCGATTGGAGGACTAAATTTATTTTAACA
Found at i:1562569 original size:21 final size:21
Alignment explanation
Indices: 1562530--1562569 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1562520 TATGTTGATG
**
1562530 CTCCACCTATTTTGGAGTACA
1 CTCCACCTATTTTAAAGTACA
*
1562551 CTCCACCTGTTTTAAAGTA
1 CTCCACCTATTTTAAAGTA
1562570 ATACTTGTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (21 bp):
CTCCACCTATTTTAAAGTACA
Found at i:1565555 original size:54 final size:55
Alignment explanation
Indices: 1565491--1565645 Score: 233
Period size: 55 Copynumber: 2.8 Consensus size: 55
1565481 TCGTAGGTTA
** *
1565491 TGCACACATAGTGCTGATAC-GACAATTCACAAACTCATTATGAATTCTGT-GGGT
1 TGCACACATAGTGCCAATACAGA-AATTCATAAACTCATTATGAATTCTGTGGGGT
* *
1565545 TGCACACATAGTGCCAATACAGAAATTCATAAATTCATTATGAATTTTGTGGGGT
1 TGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTCTGTGGGGT
*
1565600 TGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATT
1 TGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATT
1565646 AAGTACGAAT
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
54 42 0.46
55 50 0.54
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (55 bp):
TGCACACATAGTGCCAATACAGAAATTCATAAACTCATTATGAATTCTGTGGGGT
Found at i:1571803 original size:19 final size:19
Alignment explanation
Indices: 1571779--1571824 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1571769 TGTAAGGGTG
1571779 AATAAATGTTTTTAAATTC
1 AATAAATGTTTTTAAATTC
1571798 AATAAATGTTTTTAAATTC
1 AATAAATGTTTTTAAATTC
1571817 AATAAATG
1 AATAAATG
1571825 ATGCAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (19 bp):
AATAAATGTTTTTAAATTC
Found at i:1576980 original size:38 final size:37
Alignment explanation
Indices: 1576952--1577443 Score: 489
Period size: 38 Copynumber: 13.5 Consensus size: 37
1576942 TAATATATAT
1576952 AAAA-ATTTTCGAAAATATATATAATATATAGTTTTTG
1 AAAACATTTT-GAAAATATATATAATATATAGTTTTTG
*
1576989 AAAATATTTTGAAAATATATATAATATATAGTTTTTG
1 AAAACATTTTGAAAATATATATAATATATAGTTTTTG
1577026 AAAACATTTTGAAAACATATATATAATATATAGTTTTTG
1 AAAACATTTTG-AAA-ATATATATAATATATAGTTTTTG
1577065 -AAACATTTTGAAAACATATATATAATATATAG-TTTTG
1 AAAACATTTTG-AAA-ATATATATAATATATAGTTTTTG
*
1577102 AAAACATTTTGAAAATATATATAATATATAG-ATTTG
1 AAAACATTTTGAAAATATATATAATATATAGTTTTTG
* *
1577138 AAAATATTTTGAAAATGTATATATAATATTTAGTTTTTG
1 AAAACATTTTGAAAA--TATATATAATATATAGTTTTTG
*
1577177 ACAACATTTTGAAAACATATATATAATATATAGTTTTT-
1 AAAACATTTTG-AAA-ATATATATAATATATAGTTTTTG
* * *
1577215 AAAAGATTTTTAAAATATATATATAATATATAG-TTTTA
1 AAAACA-TTTTGAAA-ATATATATAATATATAGTTTTTG
* *
1577253 AAAATATTTTGAAATTTTATATACATAATATATAGTTTTTG
1 AAAACATTTTGAAA----ATATATATAATATATAGTTTTTG
*
1577294 ATAACATTTTGAAAACATATATATAATATATAGTTTTTG
1 AAAACATTTTG-AAA-ATATATATAATATATAGTTTTTG
*
1577333 AAAAC---------ATATATATAATATATTGTTTTTG
1 AAAACATTTTGAAAATATATATAATATATAGTTTTTG
*
1577361 AAAAC---------ATATATATAATATATTG-TTTTG
1 AAAACATTTTGAAAATATATATAATATATAGTTTTTG
*
1577388 AAAACATTTTGAAAATATATATAATATATA-ATTTT-
1 AAAACATTTTGAAAATATATATAATATATAGTTTTTG
**
1577423 AAAATGTTTTTGAAAATATAT
1 AAAA-CATTTTGAAAATATAT
1577444 CATATGTATA
Statistics
Matches: 403, Mismatches: 25, Indels: 55
0.83 0.05 0.11
Matches are distributed among these distances:
27 10 0.02
28 44 0.11
35 4 0.01
36 68 0.17
37 60 0.15
38 94 0.23
39 86 0.21
40 20 0.05
41 14 0.03
42 3 0.01
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (37 bp):
AAAACATTTTGAAAATATATATAATATATAGTTTTTG
Found at i:1577118 original size:27 final size:27
Alignment explanation
Indices: 1577070--1577122 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1577060 TTTTGAAACA
*
1577070 TTTTGAAAACATATATATAATATATAG
1 TTTTGAAAACATATATAAAATATATAG
*
1577097 TTTTGAAAACAT-TTTGAAAATATATA
1 TTTTGAAAACATATAT-AAAATATATA
1577123 TAATATATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.42
Consensus pattern (27 bp):
TTTTGAAAACATATATAAAATATATAG
Done.