Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008645.1 Hibiscus syriacus cultivar Beakdansim tig00111621_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: 4138222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 22
Found at i:190554 original size:6 final size:6
Alignment explanation
Indices: 190530--190567 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
190520 GTTAAATAAT
*
190530 AAAAT- AAAAT- AAAACG AAAATG AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
190568 ATAAATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 9 0.30
6 21 0.70
ACGTcount: A:0.74, C:0.03, G:0.11, T:0.13
Consensus pattern (6 bp):
AAAATG
Found at i:191659 original size:39 final size:39
Alignment explanation
Indices: 191616--191695 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 39
191606 GCAGACGGGC
*
191616 TTGGGCCTTACCGAGTTTAATGGGTCAGGCTTGCTTCGG
1 TTGGGCCTTACCGAGTTTAATGGGTCAGACTTGCTTCGG
*** * **
191655 TTGGGCCTTGTTGGGTTTGCTGGGTCAGACTTGCTTCGG
1 TTGGGCCTTACCGAGTTTAATGGGTCAGACTTGCTTCGG
191694 TT
1 TT
191696 AGACTTCATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.09, C:0.19, G:0.35, T:0.38
Consensus pattern (39 bp):
TTGGGCCTTACCGAGTTTAATGGGTCAGACTTGCTTCGG
Found at i:191805 original size:22 final size:22
Alignment explanation
Indices: 191727--191917 Score: 97
Period size: 22 Copynumber: 8.7 Consensus size: 22
191717 AAAAACCGAA
*
191727 ATAGTAATAATAATAATATAATAA
1 ATAGTAATAAT-AT-ATATAATAC
**
191751 ATAACAA-AATATAATATTAAT--
1 ATAGTAATAATAT-ATA-TAATAC
*
191772 ATAATAAATAATATATACTAA-AC
1 ATAGT-AATAATATATA-TAATAC
191795 ATAGTAATAATAATATATAATAC
1 ATAGTAATAAT-ATATATAATAC
*
191818 -TA-T-ATAATATA-ATAATAT
1 ATAGTAATAATATATATAATAC
*
191836 ATAGTATATAATATACATATATAC
1 ATAGTA-ATAATATATATA-ATAC
191860 ATA-T-ATAATATATAATAATA-
1 ATAGTAATAATATAT-ATAATAC
191880 ATA-TATACTAAATATATATATATA-
1 ATAGTA-A-T-AATATATATA-ATAC
191904 ATA-T-ATAATATATA
1 ATAGTAATAATATATA
191918 CTATATACTA
Statistics
Matches: 140, Mismatches: 8, Indels: 42
0.74 0.04 0.22
Matches are distributed among these distances:
18 6 0.04
19 5 0.04
20 18 0.13
21 17 0.12
22 38 0.27
23 31 0.22
24 25 0.18
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.37
Consensus pattern (22 bp):
ATAGTAATAATATATATAATAC
Found at i:191823 original size:2 final size:2
Alignment explanation
Indices: 191807--191933 Score: 105
Period size: 2 Copynumber: 66.5 Consensus size: 2
191797 AGTAATAATA
191807 AT AT AT A- AT ACT AT AT A- AT AT A- AT A- AT AT AT AGT AT AT A-
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* *
191846 AT AT AC AT AT AT AC AT AT AT A- AT AT AT A- AT A- AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
191884 AT ACT AA AT AT AT AT AT AT A- AT AT AT A- AT AT AT ACT AT AT ACT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
191927 AT AT AT A
1 AT AT AT A
191934 CTAAAAGTGT
Statistics
Matches: 103, Mismatches: 6, Indels: 32
0.73 0.04 0.23
Matches are distributed among these distances:
1 11 0.11
2 82 0.80
3 10 0.10
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:191862 original size:65 final size:66
Alignment explanation
Indices: 191733--191934 Score: 191
Period size: 65 Copynumber: 2.9 Consensus size: 66
191723 CGAAATAGTA
* * *
191733 ATAATAATAATATAATAAATAAC-AA-AATATAATATTAATATAATAAATAATAT--ATACTAAA
1 ATAATAATAATATAAT-AAT-ACTAATAATATAATAAT-ATATAATATATAATATACATA-TATA
191794 CATA-
62 CATAT
* *
191798 GTAATAATAATAT-ATAATACTATATAATATAATAATATATAGTATATAATATACATATATACAT
1 ATAATAATAATATAATAATACTA-ATAATATAATAATATATAATATATAATATACATATATACAT
191862 AT
65 AT
191864 ATAATATATAATAATAATATATACTAAATATATATATATAATATATAATATATACTATATACTAT
1 ATAATA-ATAAT-ATAATA-ATACT-AATA-ATATA-ATAATATATAATATATA--ATATAC-AT
191929 ATATAC
57 ATATAC
191935 TAAAAGTGTC
Statistics
Matches: 114, Mismatches: 7, Indels: 22
0.80 0.05 0.15
Matches are distributed among these distances:
62 2 0.02
63 4 0.04
64 17 0.15
65 29 0.25
66 8 0.07
67 5 0.04
68 2 0.02
69 3 0.03
70 8 0.07
71 6 0.05
72 16 0.14
74 6 0.05
75 8 0.07
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (66 bp):
ATAATAATAATATAATAATACTAATAATATAATAATATATAATATATAATATACATATATACATA
T
Found at i:191914 original size:7 final size:7
Alignment explanation
Indices: 191733--191931 Score: 135
Period size: 7 Copynumber: 27.4 Consensus size: 7
191723 CGAAATAGTA
191733 ATAATA-
1 ATAATAT
191739 ATAATAT
1 ATAATAT
191746 AATAA-AT
1 -ATAATAT
* *
191753 AACAAAAT
1 -ATAATAT
191761 ATAATAT
1 ATAATAT
191768 -TAATAT
1 ATAATAT
191774 AATAA-AT
1 -ATAATAT
191781 A-ATATAT
1 ATA-ATAT
*
191788 ACTAAACAT
1 A-T-AATAT
191797 AGTAATA-
1 A-TAATAT
191804 ATAATAT
1 ATAATAT
191811 ATAATACTAT
1 AT-A-A-TAT
191821 ATAATAT
1 ATAATAT
191828 AATAATAT
1 -ATAATAT
*
191836 ATAGTAT
1 ATAATAT
191843 ATAATAT
1 ATAATAT
*
191850 A-CATAT
1 ATAATAT
191856 ATACATAT
1 ATA-ATAT
191864 ATAATAT
1 ATAATAT
191871 ATAATA-
1 ATAATAT
191877 ATAATAT
1 ATAATAT
*
191884 ATACTAAAT
1 ATA--ATAT
191893 ATATATAT
1 ATA-ATAT
191901 ATAATAT
1 ATAATAT
191908 ATAATAT
1 ATAATAT
*
191915 ATACTAT
1 ATAATAT
*
191922 ATACTAT
1 ATAATAT
191929 ATA
1 ATA
191932 TACTAAAAGT
Statistics
Matches: 160, Mismatches: 13, Indels: 39
0.75 0.06 0.18
Matches are distributed among these distances:
5 1 0.01
6 30 0.19
7 75 0.47
8 35 0.22
9 13 0.08
10 6 0.04
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.38
Consensus pattern (7 bp):
ATAATAT
Found at i:193549 original size:21 final size:21
Alignment explanation
Indices: 193525--193565 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
193515 TAAATAAAGT
*
193525 ATGAA-AAAATGCTAGGATTAA
1 ATGAATAAAAT-CTAAGATTAA
193546 ATGAATAAAATCTAAGATTA
1 ATGAATAAAATCTAAGATTA
193566 TATACTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.27
Consensus pattern (21 bp):
ATGAATAAAATCTAAGATTAA
Found at i:196548 original size:3 final size:3
Alignment explanation
Indices: 196542--196589 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
196532 TCAACATCTT
196542 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -AA G-A GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
196588 GA
1 GA
196590 GTGATAATCC
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:199453 original size:16 final size:16
Alignment explanation
Indices: 199434--199489 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 16
199424 CTTTCATGTC
199434 TTTTTTTTTCGAACAG
1 TTTTTTTTTCGAACAG
*
199450 TTTTTTTTTCGAACTG
1 TTTTTTTTTCGAACAG
199466 CTATTTTTTTTTC-AACA-
1 ---TTTTTTTTTCGAACAG
199483 TTTTTTT
1 TTTTTTT
199490 GTGATGGAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 7 0.20
16 15 0.43
18 3 0.09
19 10 0.29
ACGTcount: A:0.16, C:0.12, G:0.07, T:0.64
Consensus pattern (16 bp):
TTTTTTTTTCGAACAG
Found at i:208853 original size:15 final size:15
Alignment explanation
Indices: 208833--208871 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
208823 TCCTATTGTA
208833 GAAGAAGAGTAAGAT
1 GAAGAAGAGTAAGAT
*
208848 GAAGAAGAGTCAGAT
1 GAAGAAGAGTAAGAT
208863 GAAGAAGAG
1 GAAGAAGAG
208872 GTTCAGACCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.51, C:0.03, G:0.36, T:0.10
Consensus pattern (15 bp):
GAAGAAGAGTAAGAT
Found at i:213076 original size:9 final size:9
Alignment explanation
Indices: 213062--213095 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
213052 GAAATCGGTT
213062 AATTAACCG
1 AATTAACCG
*
213071 AATTAACCA
1 AATTAACCG
213080 AATTAACCG
1 AATTAACCG
213089 AAATTAA
1 -AATTAA
213096 TTATTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.53, C:0.18, G:0.06, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:224208 original size:21 final size:21
Alignment explanation
Indices: 224182--224338 Score: 205
Period size: 21 Copynumber: 7.5 Consensus size: 21
224172 GTTTCCTGAT
224182 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
224203 TCGCAATGCAAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
224224 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
224245 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
224265 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
*
224286 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
224307 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
224328 TCGCAATGCGA
1 TCGCAATGCGA
224339 TTTACATATT
Statistics
Matches: 120, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
20 17 0.14
21 103 0.86
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:224268 original size:62 final size:62
Alignment explanation
Indices: 224202--224318 Score: 182
Period size: 62 Copynumber: 1.9 Consensus size: 62
224192 AACTTCGACT
* * *
224202 ATCGCAATGC-AAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAAA-GTCGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAA
*
224264 ATCGCAATGCGATAGTCGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAA
1 ATCGCAATGCGAAAGTCGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAA
224319 CTTGGACTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
62 48 0.96
63 2 0.04
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (62 bp):
ATCGCAATGCGAAAGTCGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGTAA
Found at i:224270 original size:83 final size:83
Alignment explanation
Indices: 224182--224338 Score: 271
Period size: 83 Copynumber: 1.9 Consensus size: 83
224172 GTTTCCTGAT
* *
224182 TCGCAATGCGA-ACTTCGACTATCGCAATGCAAACTTCGACTATCGCAATGCGAACTTGGACTAT
1 TCGCAATGCGATA-GTCGACTATCGCAACGCAAACTTCGACTATCGCAATGCGAACTTGGACTAT
224246 CGCAATGCGAATATGTAAA
65 CGCAATGCGAATATGTAAA
*
224265 TCGCAATGCGATAGTCGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATC
1 TCGCAATGCGATAGTCGACTATCGCAACGCAAACTTCGACTATCGCAATGCGAACTTGGACTATC
224330 GCAATGCGA
66 GCAATGCGA
224339 TTTACATATT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
83 69 0.99
84 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (83 bp):
TCGCAATGCGATAGTCGACTATCGCAACGCAAACTTCGACTATCGCAATGCGAACTTGGACTATC
GCAATGCGAATATGTAAA
Found at i:224488 original size:6 final size:6
Alignment explanation
Indices: 224477--224518 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
224467 GACACGTATT
224477 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
224519 CGAGATGAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 15 0.42
6 21 0.58
ACGTcount: A:0.29, C:0.55, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:224509 original size:5 final size:5
Alignment explanation
Indices: 224481--224521 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
224471 CGTATTACCA
224481 CGACC ACGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
224522 GATGAGACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.51
6 17 0.49
ACGTcount: A:0.27, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:225039 original size:6 final size:6
Alignment explanation
Indices: 225028--225060 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
225018 TCTCGTCTCG
225028 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
225061 AATACGTGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:225195 original size:21 final size:21
Alignment explanation
Indices: 225146--225195 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
225136 CAGTCGATAA
* *
225146 ATCGCAACGCGAACTTGGACT
1 ATCGCAATGAGAACTTGGACT
225167 ATCGCAATGAGAACTTGGACT
1 ATCGCAATGAGAACTTGGACT
225188 ATCGCAAT
1 ATCGCAAT
225196 ATTCGCACTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (21 bp):
ATCGCAATGAGAACTTGGACT
Found at i:226905 original size:18 final size:18
Alignment explanation
Indices: 226882--226924 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
226872 AACTGGATCT
226882 ACCAAACCAGAATCCAAG
1 ACCAAACCAGAATCCAAG
226900 ACCAAACCAGAATCCAAG
1 ACCAAACCAGAATCCAAG
226918 ACCAAAC
1 ACCAAAC
226925 AATGTTGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.51, C:0.35, G:0.09, T:0.05
Consensus pattern (18 bp):
ACCAAACCAGAATCCAAG
Found at i:229734 original size:21 final size:21
Alignment explanation
Indices: 229710--229783 Score: 121
Period size: 21 Copynumber: 3.5 Consensus size: 21
229700 TAGTCGGCTA
* *
229710 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
229731 TCGCTTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
229752 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
229773 TCGCGTTGCGA
1 TCGCGTTGCGA
229784 ATCTAGAAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:229741 original size:42 final size:41
Alignment explanation
Indices: 229695--229783 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 41
229685 ATATTCGCAC
*
229695 TGCGATAGTCG-GCTATCGCATTGCGATAGTCCAAGTTCGCTT
1 TGCGATAGTCGAG-T-TCGCATTGCGATAGTCCAAGTTCGCGT
* *
229737 TGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCG-AGTTCGCATTGCGATAGTCCAAGTTCGCGT
229779 TGCGA
1 TGCGA
229784 ATCTAGAAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
42 40 0.95
43 1 0.02
44 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.29
Consensus pattern (41 bp):
TGCGATAGTCGAGTTCGCATTGCGATAGTCCAAGTTCGCGT
Found at i:233399 original size:114 final size:114
Alignment explanation
Indices: 233209--233419 Score: 318
Period size: 114 Copynumber: 1.9 Consensus size: 114
233199 GCTTATCCTG
233209 AATTTCCTGCACAAGCTGCGGCAAATTAGGATCAATCTCCTTCCTCACAGCAACATGATTCGTAC
1 AATTTCCTGCACAAGCTGCGGCAAATTAGGATCAATCTCCTTCCTCACAGCAACATGATTCGTAC
* *
233274 TCCTTTCCTTTTTCCTATCTCTCCTATGGTTGATGGACTGCTTATGGAT
66 TCCTTTCCTTTTCCCCATCTCTCCTATGGTTGATGGACTGCTTATGGAT
* ** * *
233323 AATTTCCTGCAGAAGCTGCGGCAAATTAGGATGGATCTCCTTCCTCACGGCCACATGATTC-TCA
1 AATTTCCTGCACAAGCTGCGGCAAATTAGGATCAATCTCCTTCCTCACAGCAACATGATTCGT-A
*
233387 GC-CCTTTCCTTTTCCCCATTTCTCCTATGGTTG
65 -CTCCTTTCCTTTTCCCCATCTCTCCTATGGTTG
233420 GTGGGCAGAC
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
113 1 0.01
114 85 0.98
115 1 0.01
ACGTcount: A:0.20, C:0.29, G:0.17, T:0.34
Consensus pattern (114 bp):
AATTTCCTGCACAAGCTGCGGCAAATTAGGATCAATCTCCTTCCTCACAGCAACATGATTCGTAC
TCCTTTCCTTTTCCCCATCTCTCCTATGGTTGATGGACTGCTTATGGAT
Found at i:234236 original size:22 final size:22
Alignment explanation
Indices: 234211--234254 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
234201 AAATATTATT
234211 TTTATTCAATAAA-ATATAGAGA
1 TTTATTCAA-AAATATATAGAGA
*
234233 TTTATTTAAAAATATATAGAGA
1 TTTATTCAAAAATATATAGAGA
234255 AAAAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (22 bp):
TTTATTCAAAAATATATAGAGA
Found at i:234931 original size:20 final size:20
Alignment explanation
Indices: 234904--234976 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
234894 TAGTTGAAAA
234904 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * * *
234924 TTGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
*
234945 TCGCGTTGCGATTTTCCGTT
1 TCGCGTTGCGATTTTCCATT
234965 TCGCGTTGCGAT
1 TCGCGTTGCGAT
234977 AGTCTACAGT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 3 0.07
20 23 0.56
21 11 0.27
22 4 0.10
ACGTcount: A:0.11, C:0.23, G:0.26, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:234932 original size:41 final size:41
Alignment explanation
Indices: 234877--235004 Score: 168
Period size: 41 Copynumber: 3.1 Consensus size: 41
234867 CGATCTCTAA
234877 TCCATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTT
1 TCCATTTCGCGTTGCGATAGTCT-AAAATCGCGTTGCGATTT
* * *
234918 TCCATTTTGCGTTGCGATAGTCTACAGTCGCGTTGCGATTT
1 TCCATTTCGCGTTGCGATAGTCTAAAATCGCGTTGCGATTT
* * * *
234959 TCCGTTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTT
1 TCCATTTCGCGTTGCGATAGTCTAAAATCG-CGTTGCGATTT
235001 TCCA
1 TCCA
235005 AATTCGTTGT
Statistics
Matches: 78, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
41 63 0.81
42 15 0.19
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (41 bp):
TCCATTTCGCGTTGCGATAGTCTAAAATCGCGTTGCGATTT
Found at i:235013 original size:41 final size:41
Alignment explanation
Indices: 234880--235020 Score: 162
Period size: 41 Copynumber: 3.4 Consensus size: 41
234870 TCTCTAATCC
* *
234880 ATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTCCA
1 ATTT-GCGTTGCGATAGTCT-ACAGTCGCGTTGCGATTTTCCA
*
234922 TTTTGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCC-
1 ATTTGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCA
* *
234962 GTTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCA
1 ATTT-GCGTTGCGATAGTCTACAGTCG-CGTTGCGATTTTCCA
* *
235005 AATT-CGTTGTGATAGT
1 ATTTGCGTTGCGATAGT
235021 TAAAAAAAGA
Statistics
Matches: 87, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
40 3 0.03
41 64 0.74
42 18 0.21
43 2 0.02
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (41 bp):
ATTTGCGTTGCGATAGTCTACAGTCGCGTTGCGATTTTCCA
Found at i:235188 original size:20 final size:20
Alignment explanation
Indices: 235165--235270 Score: 63
Period size: 20 Copynumber: 5.2 Consensus size: 20
235155 AGATCGCGTT
*
235165 GCGATTTCAACTATCGCAAC
1 GCGATTGCAACTATCGCAAC
* * *
235185 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTGCAACTATCGCAAC
*
235205 GCGATCTCCAACTATCGCAAC
1 GCGAT-TGCAACTATCGCAAC
* * * *
235226 GCGAAATGGAA-AAACGCAAC
1 GCG-ATTGCAACTATCGCAAC
* *
235246 GCGATTTTCAACTATCGCAAT
1 GCGA-TTGCAACTATCGCAAC
235267 GCGA
1 GCGA
235271 AATGCAACGT
Statistics
Matches: 61, Mismatches: 19, Indels: 11
0.67 0.21 0.12
Matches are distributed among these distances:
19 2 0.03
20 30 0.49
21 28 0.46
22 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (20 bp):
GCGATTGCAACTATCGCAAC
Found at i:235222 original size:41 final size:41
Alignment explanation
Indices: 235172--235274 Score: 170
Period size: 41 Copynumber: 2.5 Consensus size: 41
235162 GTTGCGATTT
*
235172 CAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
* *
235213 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
*
235254 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
235275 CAACGTGAAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.17
Consensus pattern (41 bp):
CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
Found at i:235278 original size:21 final size:21
Alignment explanation
Indices: 235172--235278 Score: 92
Period size: 21 Copynumber: 5.2 Consensus size: 21
235162 GTTGCGATTT
235172 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
235193 GAA-AATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATG
235213 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
235234 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
235254 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
235275 CAAC
1 CAAC
235279 GTGAATTTGC
Statistics
Matches: 61, Mismatches: 23, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
20 29 0.48
21 32 0.52
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:237199 original size:16 final size:18
Alignment explanation
Indices: 237180--237217 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
237170 TTCATTCGAA
237180 AAAATAACAAAA-AAAG-
1 AAAATAACAAAAGAAAGT
237196 AAAATAACAAAAGAAAGT
1 AAAATAACAAAAGAAAGT
237214 AAAA
1 AAAA
237218 AAAACCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.60
17 4 0.20
18 4 0.20
ACGTcount: A:0.79, C:0.05, G:0.08, T:0.08
Consensus pattern (18 bp):
AAAATAACAAAAGAAAGT
Found at i:238996 original size:5 final size:5
Alignment explanation
Indices: 238981--239024 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
238971 AAGTAATATC
* *
238981 TTTATT TTTAT TTTAT TTTAT TTTAT TTTAT TTCAT TCTAT TTT
1 TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
239025 TATGTTGTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:242575 original size:37 final size:32
Alignment explanation
Indices: 242497--242557 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
242487 AGTCGACGGT
* *
242497 TTACTTATGTCTTTCAGGACATATGGACAAGA
1 TTACCTATGTCTTTCGGGACATATGGACAAGA
242529 TTACCTATGTCTTTCGGGACATATGGACA
1 TTACCTATGTCTTTCGGGACATATGGACA
242558 GTTATAGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGACAAGA
Found at i:242610 original size:31 final size:31
Alignment explanation
Indices: 242566--242626 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
242556 CAGTTATAGC
242566 TTACCTATGTTCTTCGGAATATATGGACTGA
1 TTACCTATGTTCTTCGGAATATATGGACTGA
* *
242597 TTACCTA-GATTCTTCGGGATCTATGGACTG
1 TTACCTATG-TTCTTCGGAATATATGGACTG
242627 GTCCTTCGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAATATATGGACTGA
Found at i:243974 original size:22 final size:22
Alignment explanation
Indices: 243949--243993 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
243939 AATTTTTAAA
*
243949 AATTGAGAAAGAACTGCAA-GAG
1 AATTGACAAAGAA-TGCAACGAG
*
243971 AATTTACAAAGAATGCAACGAG
1 AATTGACAAAGAATGCAACGAG
243993 A
1 A
243994 CTAGAAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.51, C:0.11, G:0.22, T:0.16
Consensus pattern (22 bp):
AATTGACAAAGAATGCAACGAG
Found at i:246779 original size:23 final size:23
Alignment explanation
Indices: 246746--246812 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
246736 AAGTCGATGG
* *
246746 TCTACGCGGTCCTTCGGGACAAT
1 TCTACGTGGTCCTTCAGGACAAT
* *
246769 TCTACGTGGTCTTTTAGGACAAT
1 TCTACGTGGTCCTTCAGGACAAT
246792 TCTACGTGGTCCTTCAGGACA
1 TCTACGTGGTCCTTCAGGACA
246813 TATATGTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.31
Consensus pattern (23 bp):
TCTACGTGGTCCTTCAGGACAAT
Found at i:246962 original size:23 final size:23
Alignment explanation
Indices: 246936--246993 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
246926 GGCACTATTA
246936 TGCATTTCTACGCAGCACTTCGG
1 TGCATTTCTACGCAGCACTTCGG
* ** *
246959 TGCAATTCTACGTGGCACTTTGG
1 TGCATTTCTACGCAGCACTTCGG
*
246982 TGCATTTATACG
1 TGCATTTCTACG
246994 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.34
Consensus pattern (23 bp):
TGCATTTCTACGCAGCACTTCGG
Found at i:247722 original size:21 final size:21
Alignment explanation
Indices: 247680--247723 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
247670 AGTACTATAA
*
247680 CAGGGTATCAGTACACTGTAG
1 CAGGGTATCAGTACACTCTAG
*
247701 CAGGGTATC-GATACCCTCTAG
1 CAGGGTATCAG-TACACTCTAG
247722 CA
1 CA
247724 TTCTGCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (21 bp):
CAGGGTATCAGTACACTCTAG
Found at i:247773 original size:22 final size:22
Alignment explanation
Indices: 247747--247790 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
247737 TAGCATTCGA
*
247747 TACTGTTCACGGCATTGTTCAT
1 TACTGTTCACGGCACTGTTCAT
*
247769 TACTGTTCACGGTACTGTTCAT
1 TACTGTTCACGGCACTGTTCAT
247791 ACCATATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (22 bp):
TACTGTTCACGGCACTGTTCAT
Found at i:252003 original size:67 final size:66
Alignment explanation
Indices: 251817--252004 Score: 201
Period size: 65 Copynumber: 2.9 Consensus size: 66
251807 AAGTCGATCT
* * * *
251817 CACTTGAGATTGTTTTTCTCAAT-ATAAATTGTC--TCACTTGAGACAATATTCCTTAAGACATG
1 CACTTGAGATTGTTTTTCTTAATAACAAATT-TCATTCACTTGAGATAGTATTCCTTAAGACATG
251879 AA
65 AA
* * * *
251881 CACTTGATATTGTTTCTCTTAAAAAC-AATTT-ATCTCACTTGAGATAGTCTTCCTTAAGACACT
1 CACTTGAGATTGTTTTTCTTAATAACAAATTTCAT-TCACTTGAGATAGTATTCCTTAAGACA-T
251944 -AA
64 GAA
*
251946 CATTTGAGATTGTTTTTCTTAATAACAAATTTCATTTCACTTGAGATAGT-TTCCCTTAA
1 CACTTGAGATTGTTTTTCTTAATAACAAATTTCA-TTCACTTGAGATAGTATT-CCTTAA
252005 AACGCAGATT
Statistics
Matches: 103, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
63 1 0.01
64 23 0.22
65 49 0.48
66 8 0.08
67 21 0.20
68 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (66 bp):
CACTTGAGATTGTTTTTCTTAATAACAAATTTCATTCACTTGAGATAGTATTCCTTAAGACATGA
A
Found at i:252753 original size:104 final size:104
Alignment explanation
Indices: 252573--252811 Score: 295
Period size: 104 Copynumber: 2.3 Consensus size: 104
252563 AATTATCCAA
* * * * * *
252573 ATTGACTCGATTTCCTCAACGAGAAGGGACAACATCATATGAACGCGGCTAAGACTCTTTAACAT
1 ATTGACTCGACTTCCTCAACAAGAAGGAACAACATCATATGAAAGCGGCCAAGACTCTTCAACAT
*
252638 GGATGAGCAGAGTCGTCTTCAACACCAGATTATCTCTAG
66 GGATGAACAGAGTCGTCTTCAACACCAGATTATCTCTAG
* *
252677 ATTGACTCGACTTCCTCAATAAGAAGGAACAACGTCATATGAAAGCGGCCATA-ACTCTTCAACA
1 ATTGACTCGACTTCCTCAACAAGAAGGAACAACATCATATGAAAGCGGCCA-AGACTCTTCAACA
* * *
252741 TGGATGAACAGAGTCGTCTTCAACACTATATTATCTC-CG
65 TGGATGAACAGAGTCGTCTTCAACACCAGATTATCTCTAG
* * *
252780 AATTGAC-CTAATTTCCTCAACGAGAAGGAACA
1 -ATTGACTC-GACTTCCTCAACAAGAAGGAACA
252812 TCTTCATCTT
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
103 2 0.02
104 113 0.97
105 1 0.01
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (104 bp):
ATTGACTCGACTTCCTCAACAAGAAGGAACAACATCATATGAAAGCGGCCAAGACTCTTCAACAT
GGATGAACAGAGTCGTCTTCAACACCAGATTATCTCTAG
Found at i:253161 original size:3 final size:3
Alignment explanation
Indices: 253153--253201 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
253143 TATTTTTTAA
*
253153 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT CTCT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
253199 ATT
1 ATT
253202 TTACAGGTCC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 41 0.95
4 2 0.05
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:255092 original size:21 final size:19
Alignment explanation
Indices: 255062--255114 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
255052 TATCTTTATT
*
255062 TTTA-TTTTATTTTATTTC
1 TTTATTTTTATTTTATTAC
255080 ATTCTATTTTTATGTTTTATTAC
1 -TT-TATTTTTA--TTTTATTAC
255103 TTTATTTTTATT
1 TTTATTTTTATT
255115 ATGTTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
19 4 0.14
20 2 0.07
21 13 0.45
22 2 0.07
23 8 0.28
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTATTTTTATTTTATTAC
Found at i:257880 original size:24 final size:24
Alignment explanation
Indices: 257790--257919 Score: 106
Period size: 24 Copynumber: 5.4 Consensus size: 24
257780 AAGTCGAGGG
* * *
257790 TTCTACGCGATCATTCGTGACAAA
1 TTCTACGTGGTCATTCGGGACAAA
* * *
257814 TTTCTACGTGGTCCTT-GAGATAAA
1 -TTCTACGTGGTCATTCGGGACAAA
*
257838 TTTCTACGTGGTCCTTCGGGACAAA
1 -TTCTACGTGGTCATTCGGGACAAA
257863 TTCTACGTGGTCATTCGGGA-AAA
1 TTCTACGTGGTCATTCGGGACAAA
* * *
257886 ATCTATGTGG-CACTTCGGTG-CATA
1 TTCTACGTGGTCA-TTCGG-GACAAA
257910 TTCTACGTGG
1 TTCTACGTGG
257920 CACTTCAATG
Statistics
Matches: 88, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
22 2 0.02
23 16 0.18
24 52 0.59
25 18 0.20
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (24 bp):
TTCTACGTGGTCATTCGGGACAAA
Found at i:259167 original size:24 final size:26
Alignment explanation
Indices: 259111--259179 Score: 70
Period size: 24 Copynumber: 2.7 Consensus size: 26
259101 ATATATATAT
* *
259111 AATATAATACATAATATGATACATGATA
1 AATATAATA-ATAATA-AAAACATGATA
259139 AATATAATAAT-ATAAAAACAT-ATA
1 AATATAATAATAATAAAAACATGATA
* *
259163 CATATATTAATAATAAA
1 AATATAATAATAATAAA
259180 TACAAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 12 0.33
25 10 0.28
26 3 0.08
27 2 0.06
28 9 0.25
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (26 bp):
AATATAATAATAATAAAAACATGATA
Found at i:259271 original size:18 final size:18
Alignment explanation
Indices: 259246--259294 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
259236 GTATATATAA
*
259246 ATATAATATAAATAATTCT
1 ATATAATATAAA-AATTAT
259265 A-ATAATATAAAAA-TAT
1 ATATAATATAAAAATTAT
259281 ATATAATATAAAAA
1 ATATAATATAAAAA
259295 ATTAAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 3 0.11
17 14 0.50
18 10 0.36
19 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
ATATAATATAAAAATTAT
Found at i:259296 original size:18 final size:17
Alignment explanation
Indices: 259246--259306 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
259236 GTATATATAA
*
259246 ATATAATATAAATAATT
1 ATATAATATAAAAAATT
*
259263 CTAATAATAT-AAAAATAT
1 AT-ATAATATAAAAAAT-T
259281 ATATAATATAAAAAATT
1 ATATAATATAAAAAATT
259298 A-A-AATATAA
1 ATATAATATAA
259307 GGGATAAGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 7 0.18
16 1 0.03
17 15 0.39
18 15 0.39
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAATATAAAAAATT
Found at i:259304 original size:20 final size:19
Alignment explanation
Indices: 259243--259306 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 19
259233 TGTGTATATA
*
259243 TAAATATAATATAAATAAT
1 TAAATATAATATAAAAAAT
**
259262 TCTA-ATAATAT-AAAAA-
1 TAAATATAATATAAAAAAT
*
259278 TATATATAATATAAAAAAT
1 TAAATATAATATAAAAAAT
259297 TAAAATATAA
1 T-AAATATAA
259307 GGGATAAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
16 3 0.08
17 11 0.31
18 12 0.33
19 3 0.08
20 7 0.19
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAATATAATATAAAAAAT
Found at i:260341 original size:25 final size:26
Alignment explanation
Indices: 260298--260350 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
260288 CTGTAATGAC
260298 ATCATATAAAGAAACCATA-AAACAT
1 ATCATATAAAGAAACCATATAAACAT
* *
260323 ATCATATAACA-AAAGCATATATACAT
1 ATCATATAA-AGAAACCATATAAACAT
260349 AT
1 AT
260351 TTATACATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 16 0.67
26 8 0.33
ACGTcount: A:0.57, C:0.15, G:0.04, T:0.25
Consensus pattern (26 bp):
ATCATATAAAGAAACCATATAAACAT
Found at i:260544 original size:24 final size:24
Alignment explanation
Indices: 260507--260556 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
260497 CGGCTCGTAT
* * *
260507 AAATTGCACTGAAGTGCCTCATAG
1 AAATTACACCGAAGTGCCACATAG
260531 AAATTACACCGAAGTGCCACATAG
1 AAATTACACCGAAGTGCCACATAG
260555 AA
1 AA
260557 TGTCCCGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (24 bp):
AAATTACACCGAAGTGCCACATAG
Found at i:260610 original size:24 final size:23
Alignment explanation
Indices: 260539--260638 Score: 127
Period size: 21 Copynumber: 4.4 Consensus size: 23
260529 AGAAATTACA
260539 CCGAAGTG-CCACATAGAA-TGTC
1 CCGAAG-GACCACATAGAATTGTC
260561 CCGAAGGACCACATAG-A-TGTC
1 CCGAAGGACCACATAGAATTGTC
260582 CCGAAGGACCACATAGAAATTGTC
1 CCGAAGGACCACATAG-AATTGTC
* *
260606 CCGAATGACCACATAGATTTGTC
1 CCGAAGGACCACATAGAATTGTC
*
260629 CCGAATGACC
1 CCGAAGGACC
260639 TCCTAGAAAC
Statistics
Matches: 72, Mismatches: 2, Indels: 7
0.89 0.02 0.09
Matches are distributed among these distances:
21 22 0.31
22 14 0.19
23 17 0.24
24 19 0.26
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (23 bp):
CCGAAGGACCACATAGAATTGTC
Found at i:260618 original size:45 final size:45
Alignment explanation
Indices: 260539--260647 Score: 134
Period size: 45 Copynumber: 2.4 Consensus size: 45
260529 AGAAATTACA
260539 CCGAAGTG-CCACATAG-AATGTCCCGAAGGACCACATAGA-TGTC
1 CCGAAG-GACCACATAGAAATGTCCCGAAGGACCACATAGATTGTC
*
260582 CCGAAGGACCACATAGAAATTGTCCCGAATGACCACATAGATTTGTC
1 CCGAAGGACCACATAGAAA-TGTCCCGAAGGACCACATAGA-TTGTC
* * *
260629 CCGAATGACCTCCTAGAAA
1 CCGAAGGACCACATAGAAA
260648 CCTCGACTCT
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
42 1 0.02
43 14 0.25
44 2 0.04
45 20 0.35
47 20 0.35
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (45 bp):
CCGAAGGACCACATAGAAATGTCCCGAAGGACCACATAGATTGTC
Found at i:270295 original size:3 final size:3
Alignment explanation
Indices: 270287--270318 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
270277 TTTGCTTTTG
270287 CTT CTT CTT CTT CTT CTT CTT CTT CTCT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CT-T CTT C
270319 ATTTTCTCCT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:270854 original size:2 final size:2
Alignment explanation
Indices: 270847--270888 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
270837 AAACATCTTT
*
270847 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
270888 T
1 T
270889 GTTTTTTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:281820 original size:41 final size:42
Alignment explanation
Indices: 281775--281861 Score: 97
Period size: 42 Copynumber: 2.1 Consensus size: 42
281765 GCCCGAAGGT
* * * * *
281775 CTTATGGATGGCCC-AAATGACTT-ATCATCTTGCTCGAAAGA
1 CTTATAGATGACCCGAAA-GACTTAAGCATCATGCTCAAAAGA
*
281816 CTTATAGATGACCCGAAAGATTTAAGCATCATGCTCAAAAGA
1 CTTATAGATGACCCGAAAGACTTAAGCATCATGCTCAAAAGA
281858 CTTA
1 CTTA
281862 CTGATGGTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 16 0.42
42 22 0.58
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (42 bp):
CTTATAGATGACCCGAAAGACTTAAGCATCATGCTCAAAAGA
Found at i:283899 original size:4 final size:4
Alignment explanation
Indices: 283855--283959 Score: 53
Period size: 4 Copynumber: 26.8 Consensus size: 4
283845 ATCTGTCTAT
* * *
283855 TTTC -TTC TTTC -TTC TTT- TTT- TTCC TATTT TTTC TCTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC
* * * *
283900 TCTT- TTT- TTTG TTTT TTTC TTTC TTTTC TATA TTTC TTTCC TTTTC
1 T-TTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC TTTC TTT-C -TTTC
283946 TTT- TTTC TTTC TTT
1 TTTC TTTC TTTC TTT
283960 TTGTGTGTGT
Statistics
Matches: 79, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
3 19 0.24
4 47 0.59
5 10 0.13
6 3 0.04
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:283915 original size:40 final size:40
Alignment explanation
Indices: 283862--283949 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
283852 TATTTTCTTC
* *
283862 TTTCTTCTT-TTTTTTCCTATT-TTTTCTCTCTTTCTTTCTCT
1 TTTCTT-TTGTTTTTTCCT-TTCTTTTCTATATTTCTTTC-CT
*
283903 TTT-TTTTGTTTTTTTCTTTCTTTTCTATATTTCTTTCCT
1 TTTCTTTTGTTTTTTCCTTTCTTTTCTATATTTCTTTCCT
283942 TTTCTTTT
1 TTTCTTTT
283950 TTCTTTCTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
39 9 0.22
40 29 0.71
41 3 0.07
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.76
Consensus pattern (40 bp):
TTTCTTTTGTTTTTTCCTTTCTTTTCTATATTTCTTTCCT
Found at i:283916 original size:31 final size:34
Alignment explanation
Indices: 283859--283925 Score: 95
Period size: 31 Copynumber: 2.1 Consensus size: 34
283849 GTCTATTTTC
283859 TTCTTTCTTCTTTTTTTTCCTATTTTTTCTCTCT
1 TTCTTTCTTCTTTTTTTTCCTATTTTTTCTCTCT
* *
283893 TTCTTTC-TCTTTTTTTT-GT-TTTTTTCTTTCT
1 TTCTTTCTTCTTTTTTTTCCTATTTTTTCTCTCT
283924 TT
1 TT
283926 TCTATATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 13 0.42
32 1 0.03
33 10 0.32
34 7 0.23
ACGTcount: A:0.01, C:0.19, G:0.01, T:0.78
Consensus pattern (34 bp):
TTCTTTCTTCTTTTTTTTCCTATTTTTTCTCTCT
Found at i:283926 original size:17 final size:16
Alignment explanation
Indices: 283900--283961 Score: 61
Period size: 17 Copynumber: 3.7 Consensus size: 16
283890 TCTTTCTTTC
*
283900 TCTTTTTTTTGTTTTTT
1 TCTTTCTTTT-TTTTTT
* *
283917 TCTTTCTTTTCTATATT
1 TCTTTCTTTT-TTTTTT
*
283934 TCTTTCCTTTTCTTTTT
1 TCTTT-CTTTTTTTTTT
283951 TCTTTCTTTTT
1 TCTTTCTTTTT
283962 GTGTGTGTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
16 5 0.14
17 26 0.72
18 5 0.14
ACGTcount: A:0.03, C:0.16, G:0.02, T:0.79
Consensus pattern (16 bp):
TCTTTCTTTTTTTTTT
Found at i:283938 original size:34 final size:31
Alignment explanation
Indices: 283859--283960 Score: 89
Period size: 34 Copynumber: 3.1 Consensus size: 31
283849 GTCTATTTTC
*
283859 TTCTTTCTTCTTTTTTTTCCTATTTTTTCTCTC-T
1 TTCTTT-TTCTTTTTTTT--T-TTTTTTCTTTCTT
*
283893 TTCTTTCTCTTTTTTTTGTTTTTTTCTTTCTT
1 TTCTTTTTCTTTTTTTT-TTTTTTTCTTTCTT
* *
283925 TTCTATATTTCTTTCCTTTTCTTTTTTCTTTCTT
1 TTCT-T-TTTCTTT-TTTTTTTTTTTTCTTTCTT
283959 TT
1 TT
283961 TGTGTGTGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 10 0.17
32 6 0.10
33 11 0.19
34 27 0.47
35 4 0.07
ACGTcount: A:0.03, C:0.20, G:0.01, T:0.76
Consensus pattern (31 bp):
TTCTTTTTCTTTTTTTTTTTTTTTCTTTCTT
Found at i:283960 original size:10 final size:9
Alignment explanation
Indices: 283854--283961 Score: 58
Period size: 9 Copynumber: 11.1 Consensus size: 9
283844 GATCTGTCTA
283854 TTTTCTTCTT
1 TTTTCTT-TT
*
283864 TCTTCTTTT
1 TTTTCTTTT
283873 TTTTCCTATTT
1 TTTT-CT-TTT
283884 TTTCTCTCTTT
1 TTT-TCT-TTT
283895 CTTTCTCTTTT
1 -TTT-TCTTTT
*
283906 TTTT-GTTT
1 TTTTCTTTT
*
283914 TTTTCTTTC
1 TTTTCTTTT
283923 TTTTCTATATT
1 TTTTCT-T-TT
*
283934 TCTTTCCTTT
1 T-TTTCTTTT
*
283944 TCTT-TTTT
1 TTTTCTTTT
*
283952 CTTTCTTTT
1 TTTTCTTTT
283961 T
1 T
283962 GTGTGTGTTT
Statistics
Matches: 76, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
8 12 0.16
9 20 0.26
10 15 0.20
11 17 0.22
12 12 0.16
ACGTcount: A:0.03, C:0.19, G:0.01, T:0.77
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:285769 original size:149 final size:149
Alignment explanation
Indices: 285493--285800 Score: 401
Period size: 149 Copynumber: 2.1 Consensus size: 149
285483 TCGTCTTCAA
*
285493 AGCTTCTACTTCATCTCCTACTTTCAAAAGTCTTTCGAGCTGGTAGGTGATCTTCAACTGTTGGA
1 AGCTTCTACTTCATCTCCTACTTTCAAAAGTCTTTCGAGCTGGTACGTGATCTTCAACTGTTGGA
* * * * *
285558 TATTGTGTTGAACCTTCTTGAATCCAACTTGTTACCTCAACAGACAGATGTATGGCTTGTCTCCT
66 TATAGTGTCGAACCATCTCGAATCCAACTTGTTACCTCAACAGACAGATGTATAGCTTGTCTCCT
*
285623 TGGTAGGTAGACTCCTTCT
131 TGGTAGGTAGACTCCCTCT
*
285642 AGCTTCTACTTCATCTCCTAC-TTCTAGAAA-TCTTTCGAGCTGGTTCGTGATCTTCAACTGTTG
1 AGCTTCTACTTCATCTCCTACTTTC-A-AAAGTCTTTCGAGCTGGTACGTGATCTTCAACTGTTG
* * * * *
285705 GCT-TCAGTGTCGAATCATCTCGAGTCCAACTTGTTACCTCAGCAGGA-AGATGTCTAG-TTCGT
64 GATAT-AGTGTCGAACCATCTCGAATCCAACTTGTTACCTCAACA-GACAGATGTATAGCTT-GT
285767 CTCCTTGGTAGGTAGACTCCCTCT
126 CTCCTTGGTAGGTAGACTCCCTCT
* *
285791 TGATTCTACT
1 AGCTTCTACT
285801 CGATCTACGT
Statistics
Matches: 139, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
148 6 0.04
149 128 0.92
150 5 0.04
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.36
Consensus pattern (149 bp):
AGCTTCTACTTCATCTCCTACTTTCAAAAGTCTTTCGAGCTGGTACGTGATCTTCAACTGTTGGA
TATAGTGTCGAACCATCTCGAATCCAACTTGTTACCTCAACAGACAGATGTATAGCTTGTCTCCT
TGGTAGGTAGACTCCCTCT
Found at i:288848 original size:14 final size:13
Alignment explanation
Indices: 288831--288861 Score: 53
Period size: 13 Copynumber: 2.3 Consensus size: 13
288821 AAAAAGGATA
288831 AAAAAATATAAAAG
1 AAAAAAT-TAAAAG
288845 AAAAAATTAAAAG
1 AAAAAATTAAAAG
288858 AAAA
1 AAAA
288862 CAAGGGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (13 bp):
AAAAAATTAAAAG
Found at i:291061 original size:113 final size:112
Alignment explanation
Indices: 290859--291085 Score: 384
Period size: 113 Copynumber: 2.0 Consensus size: 112
290849 AGAATGCGAA
290859 CAAAATATCTCAAAACTAGTCTCATCGGACGATCATTGGAAGAGATCAAAGTATCAACACGTTGA
1 CAAAATATCTCAAAACTAGTCTCATCGGACGATCATTGGAAGAGATCAAAGTATCAACACGTTGA
290924 ACTTTTAAATGAATTTTCATTAATTTTGAATGTGATTCATGGAAAAT
66 ACTTTTAAATGAATTTTCATTAATTTTGAATGTGATTCATGGAAAAT
*
290971 CAAACATATCTCAAAACTAGTCTCATCGGACGATCATTGGAAGAGATCAAAGTATCAACATGTTG
1 CAAA-ATATCTCAAAACTAGTCTCATCGGACGATCATTGGAAGAGATCAAAGTATCAACACGTTG
* ** *
291036 AACTTTTAAAT-ATTGTTTTGTTAATTTTGAATGTGATTCATGGAATAT
65 AACTTTTAAATGAAT-TTTCATTAATTTTGAATGTGATTCATGGAAAAT
291084 CA
1 CA
291086 GTGACAGACG
Statistics
Matches: 108, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
112 6 0.06
113 102 0.94
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.33
Consensus pattern (112 bp):
CAAAATATCTCAAAACTAGTCTCATCGGACGATCATTGGAAGAGATCAAAGTATCAACACGTTGA
ACTTTTAAATGAATTTTCATTAATTTTGAATGTGATTCATGGAAAAT
Found at i:292413 original size:29 final size:28
Alignment explanation
Indices: 292381--292457 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 28
292371 TGAAATTATT
*
292381 AAAATTCCCAAAAACACCTTAAATTCCAG
1 AAAATTCCCAAAAAAACC-TAAATTCCAG
* * *
292410 AAAATTCCAAAAAAAATCTAAATTCCTG
1 AAAATTCCCAAAAAAACCTAAATTCCAG
*
292438 AAAA-TCCCAAAAAACCCTAA
1 AAAATTCCCAAAAAAACCTAA
292458 CTCTAAATCA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
27 13 0.32
28 13 0.32
29 15 0.37
ACGTcount: A:0.53, C:0.25, G:0.03, T:0.19
Consensus pattern (28 bp):
AAAATTCCCAAAAAAACCTAAATTCCAG
Found at i:292419 original size:28 final size:28
Alignment explanation
Indices: 292381--292451 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
292371 TGAAATTATT
* * *
292381 AAAATTCCCAAAAACACCTTAAATTCCAG
1 AAAATTCCAAAAAAAATC-TAAATTCCAG
*
292410 AAAATTCCAAAAAAAATCTAAATTCCTG
1 AAAATTCCAAAAAAAATCTAAATTCCAG
*
292438 AAAATCCCAAAAAA
1 AAAATTCCAAAAAA
292452 CCCTAACTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 22 0.59
29 15 0.41
ACGTcount: A:0.55, C:0.23, G:0.03, T:0.20
Consensus pattern (28 bp):
AAAATTCCAAAAAAAATCTAAATTCCAG
Found at i:296997 original size:2 final size:2
Alignment explanation
Indices: 296990--297043 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
296980 TAAACACGTG
296990 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
297032 TA TA TA TA TA TA
1 TA TA TA TA TA TA
297044 ATACTAAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:299403 original size:18 final size:17
Alignment explanation
Indices: 299368--299406 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
299358 TTTTAGTAAA
299368 AAAATACATAAAAATTT
1 AAAATACATAAAAATTT
* *
299385 AAAATATATAATAATTT
1 AAAATACATAAAAATTT
*
299402 TAAAT
1 AAAAT
299407 TTCTAAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAATACATAAAAATTT
Found at i:304141 original size:36 final size:36
Alignment explanation
Indices: 304096--304172 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
304086 TAAATTTCGG
*
304096 TTAACCGACCGATTAATC-GAACTTTATTCGGTTCAA
1 TTAATCGACCGATTAA-CAGAACTTTATTCGGTTCAA
* * *
304132 TTAATCGACCGATTAACATAACTTTTTTCGGTTTAA
1 TTAATCGACCGATTAACAGAACTTTATTCGGTTCAA
304168 TTAAT
1 TTAAT
304173 TGTTTTTATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
35 1 0.03
36 35 0.97
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.39
Consensus pattern (36 bp):
TTAATCGACCGATTAACAGAACTTTATTCGGTTCAA
Found at i:304817 original size:2 final size:2
Alignment explanation
Indices: 304810--304835 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
304800 AGACTATTCA
304810 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
304836 CAAACTGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:305551 original size:30 final size:30
Alignment explanation
Indices: 305515--305591 Score: 129
Period size: 30 Copynumber: 2.6 Consensus size: 30
305505 AAATAAATCA
*
305515 AACTTAAATTCATAACTTTTTATCTATCTT
1 AACTTAAATTCATAACTTTTTATATATCTT
*
305545 AACTTAAATTCATAACATTTTATATATCTT
1 AACTTAAATTCATAACTTTTTATATATCTT
305575 AACTT-AATTCATAACTT
1 AACTTAAATTCATAACTT
305592 ATTAAAAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 11 0.25
30 33 0.75
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (30 bp):
AACTTAAATTCATAACTTTTTATATATCTT
Found at i:305641 original size:29 final size:29
Alignment explanation
Indices: 305593--305697 Score: 108
Period size: 29 Copynumber: 3.6 Consensus size: 29
305583 TCATAACTTA
* * *
305593 TTAAAAAT--ATTTTATGCTTATTTTAAG
1 TTAAAAATAAATTTTATTCTTATTTGAAC
*
305620 TTAGAAATAAATTTTATTCTTATTTGAAC
1 TTAAAAATAAATTTTATTCTTATTTGAAC
*
305649 TTAAAAATAAATTTTATTCTTATACT-AAC
1 TTAAAAATAAATTTTATTCTTAT-TTGAAC
*
305678 TTCAAAATATATATTTTATT
1 TT-AAAA-ATAAATTTTATT
305698 TATATTTTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
27 7 0.11
29 43 0.65
30 5 0.08
31 11 0.17
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.50
Consensus pattern (29 bp):
TTAAAAATAAATTTTATTCTTATTTGAAC
Found at i:305738 original size:2 final size:2
Alignment explanation
Indices: 305733--305757 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
305723 TATATTAACT
305733 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
305758 TATTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:305879 original size:30 final size:29
Alignment explanation
Indices: 305801--305983 Score: 160
Period size: 29 Copynumber: 6.1 Consensus size: 29
305791 TTTAAGTTAA
*
305801 AAAATATATTTTTAAGTTAAGATACATATAT
1 AAAATATATTTTTAAGTTAAGATA-AGA-AT
* *
305832 ACATGTATATATTTTTAAGTTAAGATAATAAT
1 A-A--AATATATTTTTAAGTTAAGATAAGAAT
* * *
305864 AAAATACACTTTTTAAG-TAAAACTAAGTAT
1 AAAATATA-TTTTTAAGTTAAGA-TAAGAAT
*
305894 AAAATATATTTTTAAGTTAA-ACTAAGAAG
1 AAAATATATTTTTAAGTTAAGA-TAAGAAT
*
305923 AAAATATATATTTTGAAGTTAATATAAG-A-
1 AAAATATAT-TTTT-AAGTTAAGATAAGAAT
*
305952 AAAA-ATATTTTTAAGTTAAGATAAAAAT
1 AAAATATATTTTTAAGTTAAGATAAGAAT
305980 AAAA
1 AAAA
305984 AAAAATATTT
Statistics
Matches: 130, Mismatches: 11, Indels: 25
0.78 0.07 0.15
Matches are distributed among these distances:
26 11 0.08
27 5 0.04
28 8 0.06
29 36 0.28
30 28 0.22
31 13 0.10
32 5 0.04
33 3 0.02
34 21 0.16
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.37
Consensus pattern (29 bp):
AAAATATATTTTTAAGTTAAGATAAGAAT
Found at i:305904 original size:59 final size:58
Alignment explanation
Indices: 305838--305983 Score: 167
Period size: 59 Copynumber: 2.5 Consensus size: 58
305828 ATATACATGT
*
305838 ATATATTTTTAAGTTAAGATAATAATAAAATACACT-TTTT-AAG-TAAAACTAAGTATAAA
1 ATATATTTTTAAGTTAAGATAAAAATAAAATACA-TATTTTGAAGTTAAAA-TAAG-A-AAA
* * * *
305897 ATATATTTTTAAGTTAA-ACTAAGAAGAAAATATATATTTTGAAGTTAATATAAGAAAA
1 ATATATTTTTAAGTTAAGA-TAAAAATAAAATACATATTTTGAAGTTAAAATAAGAAAA
305955 A-ATATTTTTAAGTTAAGATAAAAATAAAA
1 ATATATTTTTAAGTTAAGATAAAAATAAAA
305984 AAAAATATTT
Statistics
Matches: 76, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
57 24 0.32
58 7 0.09
59 34 0.45
60 7 0.09
61 4 0.05
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (58 bp):
ATATATTTTTAAGTTAAGATAAAAATAAAATACATATTTTGAAGTTAAAATAAGAAAA
Found at i:305989 original size:32 final size:33
Alignment explanation
Indices: 305946--306007 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
305936 TGAAGTTAAT
* *
305946 ATAAGAAAAAATA-TTTTTAAGTTAAGATAAAA
1 ATAAAAAAAAATATTTTTTAAATTAAGATAAAA
305978 ATAAAAAAAAATATTTTTTAAATTAAGATA
1 ATAAAAAAAAATATTTTTTAAATTAAGATA
306008 TATAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 12 0.44
33 15 0.56
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (33 bp):
ATAAAAAAAAATATTTTTTAAATTAAGATAAAA
Found at i:308659 original size:18 final size:18
Alignment explanation
Indices: 308638--308726 Score: 74
Period size: 18 Copynumber: 4.8 Consensus size: 18
308628 TTAAAATATT
308638 TTAAAATTATAAAAAA-A
1 TTAAAATTATAAAAAATA
**
308655 CTTAAAAAAATAAAAAATA
1 -TTAAAATTATAAAAAATA
*
308674 TTAAGATTATAAAAAATA
1 TTAAAATTATAAAAAATA
* *
308692 TTGAAAAGTTAT-ACAAATGT
1 TT-AAAA-TTATAAAAAAT-A
308712 TTAAAAATTATAAAA
1 TT-AAAATTATAAAA
308727 TATTATAGAA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
18 31 0.55
19 13 0.23
20 12 0.21
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (18 bp):
TTAAAATTATAAAAAATA
Found at i:308748 original size:21 final size:21
Alignment explanation
Indices: 308722--308762 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
308712 TTAAAAATTA
*
308722 TAAAATATTATAGAATTATTC
1 TAAAATATTACAGAATTATTC
308743 TAAAATATTACAGAATTATT
1 TAAAATATTACAGAATTATT
308763 TTATAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (21 bp):
TAAAATATTACAGAATTATTC
Found at i:308751 original size:10 final size:10
Alignment explanation
Indices: 308700--308802 Score: 59
Period size: 11 Copynumber: 10.1 Consensus size: 10
308690 TATTGAAAAG
*
308700 TTATACAAATG
1 TTATA-AAATA
308711 TT-TAAAA-A
1 TTATAAAATA
308719 TTATAAAATA
1 TTATAAAATA
*
308729 TTATAGAATTA
1 TTATA-AAATA
*
308740 TTCTAAAATA
1 TTATAAAATA
* *
308750 TTACAGAATTA
1 TTATA-AAATA
* *
308761 TTTTATAA-A
1 TTATAAAATA
308770 TTATACAAATA
1 TTATA-AAATA
*
308781 TTACAAAAGTA
1 TTATAAAA-TA
*
308792 TTCTAAAATA
1 TTATAAAATA
308802 T
1 T
308803 AATAGAGTTA
Statistics
Matches: 69, Mismatches: 16, Indels: 15
0.69 0.16 0.15
Matches are distributed among these distances:
8 2 0.03
9 13 0.19
10 24 0.35
11 30 0.43
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (10 bp):
TTATAAAATA
Found at i:311182 original size:13 final size:12
Alignment explanation
Indices: 311158--311191 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
311148 ACCAACTACA
311158 AAATCAATATTAG
1 AAATCAA-ATTAG
311171 AAATTCAAATTAG
1 AAA-TCAAATTAG
311184 AAATCAAA
1 AAATCAAA
311192 CAAACCCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 11 0.55
14 4 0.20
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.26
Consensus pattern (12 bp):
AAATCAAATTAG
Found at i:312921 original size:37 final size:36
Alignment explanation
Indices: 312871--312969 Score: 119
Period size: 37 Copynumber: 2.7 Consensus size: 36
312861 TACAGAAGTG
*
312871 ATCTAATTATCGATTCGTTCATCCA-TTGGCATGATAA
1 ATCTAATTATCGATT-GTTCATCCACTAGG-ATGATAA
312908 ATCTAATTATCGATTGGTTCATCCACTAGGATGATAA
1 ATCTAATTATCGATT-GTTCATCCACTAGGATGATAA
* * *
312945 ATCCAACTATCAATTGATTCATCCA
1 ATCTAATTATCGATTG-TTCATCCA
312970 ACCGGGATGG
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
36 1 0.02
37 51 0.93
38 3 0.05
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.35
Consensus pattern (36 bp):
ATCTAATTATCGATTGTTCATCCACTAGGATGATAA
Found at i:313258 original size:3 final size:3
Alignment explanation
Indices: 313250--313300 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
313240 GGCCATTTCA
313250 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
313298 TAT
1 TAT
313301 ATTTTATGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:313731 original size:28 final size:28
Alignment explanation
Indices: 313678--313734 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
313668 CCATTATTGC
* **
313678 TTTCAAGCACTAGCTCGATGACATAATA
1 TTTCAAGCACTAACTCGAAAACATAATA
*
313706 TTTCAAGCACTAACTCGAAAATATAATA
1 TTTCAAGCACTAACTCGAAAACATAATA
313734 T
1 T
313735 AAACGGAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (28 bp):
TTTCAAGCACTAACTCGAAAACATAATA
Found at i:315431 original size:2 final size:2
Alignment explanation
Indices: 315424--315502 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
315414 TCATCCTAGT
315424 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
315466 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
315503 CAAATTGGAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:316210 original size:30 final size:30
Alignment explanation
Indices: 316174--316259 Score: 129
Period size: 30 Copynumber: 2.9 Consensus size: 30
316164 AAATAAATCA
*
316174 AACTTAAATTCATAACTTTTTATCTATCTT
1 AACTTAAATTCATAACTTTTTATATATCTT
*
316204 AACTTAAATTCATAACATTTTATATATCTT
1 AACTTAAATTCATAACTTTTTATATATCTT
* *
316234 AACTT-AATTCATAACTTATTAAATAT
1 AACTTAAATTCATAACTTTTTATATAT
316260 ATTTTATGGT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 18 0.35
30 33 0.65
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.47
Consensus pattern (30 bp):
AACTTAAATTCATAACTTTTTATATATCTT
Found at i:316395 original size:29 final size:28
Alignment explanation
Indices: 316254--316395 Score: 122
Period size: 29 Copynumber: 4.8 Consensus size: 28
316244 ATAACTTATT
* * *
316254 AAATATATTTTATGGTTATTTTAAGTTAG
1 AAATATATTTTAT-TTTATTTTAATTTAA
* * *
316283 AAATATATTTTATTCTTATTTGAACTTCA
1 AAATATATTTTATT-TTATTTTAATTTAA
* ** *
316312 AAATATATTTTATTCATATACTAACTTCAA
1 AAATATATTTTATT-TTATTTTAA-TTTAA
*
316342 AATATATATTTTATTTTTATCTTAATTTAA
1 AA-ATATATTTTA-TTTTATTTTAATTTAA
316372 AAATATATTTTATTTATATTTTAA
1 AAATATATTTTATTT-TATTTTAA
316396 CAAAAACATT
Statistics
Matches: 91, Mismatches: 17, Indels: 10
0.77 0.14 0.08
Matches are distributed among these distances:
28 3 0.03
29 60 0.66
30 10 0.11
31 16 0.18
32 2 0.02
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.53
Consensus pattern (28 bp):
AAATATATTTTATTTTATTTTAATTTAA
Found at i:316429 original size:2 final size:2
Alignment explanation
Indices: 316424--316452 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
316414 ATTAACTTTA
316424 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
316453 ATTATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:316526 original size:20 final size:20
Alignment explanation
Indices: 316485--316526 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
316475 CTTAACTTAA
*
316485 ATTTTTAAGTTAAAATATAT
1 ATTTTTAAGTTAAAATACAT
316505 ATTTTTAAG-TAAAGATACAT
1 ATTTTTAAGTTAAA-ATACAT
316525 AT
1 AT
316527 ATACATGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (20 bp):
ATTTTTAAGTTAAAATACAT
Found at i:316657 original size:61 final size:57
Alignment explanation
Indices: 316544--316699 Score: 163
Period size: 61 Copynumber: 2.6 Consensus size: 57
316534 TATATATGTA
* * * * *
316544 TAAGTTATGATAATAATAAAATACACTTTTTAAG-TAAAACTAAGTATAAAATATATTTTT
1 TAAGTTAAGATAA-AAAAAAATATA--TTTTAAGTTAATA-TAAGAATAAAATATATTTTT
316604 TAAGTTAA-ACTAAGAAGAAAATATATATTTTGAAGTTAATATAAGAATAAAATATATTTTT
1 TAAGTTAAGA-TAA-AA-AAAA-ATATATTTT-AAGTTAATATAAGAATAAAATATATTTTT
*
316665 TAAGTTAAGATAAAAAAAAATATGTTTTAAGTTAA
1 TAAGTTAAGATAAAAAAAAATATATTTTAAGTTAA
316700 GATATATAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
57 7 0.08
58 8 0.10
59 5 0.06
60 18 0.22
61 36 0.43
62 9 0.11
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.38
Consensus pattern (57 bp):
TAAGTTAAGATAAAAAAAAATATATTTTAAGTTAATATAAGAATAAAATATATTTTT
Found at i:316672 original size:30 final size:30
Alignment explanation
Indices: 316544--316699 Score: 153
Period size: 30 Copynumber: 5.3 Consensus size: 30
316534 TATATATGTA
* * *
316544 TAAGTT-ATGATAATAATAAAATACACTTTT
1 TAAGTTAAT-ATAAGAATAAAATATATTTTT
* *
316574 TAAG-TAAAACTAAGTATAAAATATATTTTT
1 TAAGTTAATA-TAAGAATAAAATATATTTTT
*
316604 TAAGTTAA-ACTAAGAAGAAAATATATATTTT
1 TAAGTTAATA-TAAGAATAAAATATAT-TTTT
*
316635 GAAGTTAATATAAGAATAAAATATATTTTT
1 TAAGTTAATATAAGAATAAAATATATTTTT
* *
316665 TAAGTTAAGATAA-AA-AAAA-ATATGTTT
1 TAAGTTAATATAAGAATAAAATATATTTTT
316692 TAAGTTAA
1 TAAGTTAA
316700 GATATATAAA
Statistics
Matches: 109, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
27 15 0.14
28 4 0.04
29 4 0.04
30 56 0.51
31 29 0.27
32 1 0.01
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.38
Consensus pattern (30 bp):
TAAGTTAATATAAGAATAAAATATATTTTT
Found at i:316708 original size:61 final size:61
Alignment explanation
Indices: 316584--316699 Score: 170
Period size: 61 Copynumber: 2.0 Consensus size: 61
316574 TAAGTAAAAC
*
316584 TAAGTATAAAATATATTTTTTAAGTTAAACTAAGAAGAAAATATATATTTTGAAGTTAATA
1 TAAGAATAAAATATATTTTTTAAGTTAAACTAAGAAGAAAATATATATTTTGAAGTTAATA
*
316645 TAAGAATAAAATATATTTTTTAAGTTAAGA-TAA-AA-AAAA-ATATGTTTT-AAGTTAA
1 TAAGAATAAAATATATTTTTTAAGTTAA-ACTAAGAAGAAAATATATATTTTGAAGTTAA
316700 GATATATAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
57 7 0.13
58 8 0.15
59 4 0.08
60 2 0.04
61 30 0.58
62 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (61 bp):
TAAGAATAAAATATATTTTTTAAGTTAAACTAAGAAGAAAATATATATTTTGAAGTTAATA
Found at i:322945 original size:13 final size:13
Alignment explanation
Indices: 322905--322947 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
322895 ACCGTTGACC
322905 TAACCTGACCCGT
1 TAACCTGACCCGT
* * *
322918 TGACCCGACCTGT
1 TAACCTGACCCGT
*
322931 TAACCTAACCCGT
1 TAACCTGACCCGT
322944 TAAC
1 TAAC
322948 TTTGACTCGT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.26, C:0.37, G:0.14, T:0.23
Consensus pattern (13 bp):
TAACCTGACCCGT
Found at i:323731 original size:37 final size:37
Alignment explanation
Indices: 323681--323775 Score: 118
Period size: 37 Copynumber: 2.6 Consensus size: 37
323671 GAAGTGATCA
* * * * *
323681 AATTATTGATTGGTTCATCCATTGGGATGATATATCT
1 AATTATCGATTGGTTCATCCACTAGGATGATAAATCC
323718 AATTATCGATTGGTTCATCCACTAGGATGATAAATCC
1 AATTATCGATTGGTTCATCCACTAGGATGATAAATCC
* * *
323755 AACTATCAATTGATTCATCCA
1 AATTATCGATTGGTTCATCCA
323776 ACCGGGATGG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (37 bp):
AATTATCGATTGGTTCATCCACTAGGATGATAAATCC
Found at i:324065 original size:3 final size:3
Alignment explanation
Indices: 324057--324105 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
324047 GACCATTTCA
324057 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
324105 T
1 T
324106 TACGTTTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:325325 original size:66 final size:66
Alignment explanation
Indices: 325249--325394 Score: 229
Period size: 66 Copynumber: 2.2 Consensus size: 66
325239 CTTATAAATT
* *
325249 ATGAAGTTGAAATTATGGATGGCCCCTTCGTTGTGAAGTTGAGCCTCAAATTAGATATCCTTCAT
1 ATGAAGTTGAAATCATGGATGGCCCCTTCGTTATGAAGTTGAGCCTCAAATTAGATATCCTTCAT
325314 C
66 C
* * * *
325315 ATGAAGTTGAAATCGTGGATGGCCCCTTCGTTATGAAGTTGAGCCTCGAATTGGATATCCTTCGT
1 ATGAAGTTGAAATCATGGATGGCCCCTTCGTTATGAAGTTGAGCCTCAAATTAGATATCCTTCAT
325380 C
66 C
*
325381 GTGAAGTTGAAATC
1 ATGAAGTTGAAATC
325395 TAATCTTGAG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 73 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (66 bp):
ATGAAGTTGAAATCATGGATGGCCCCTTCGTTATGAAGTTGAGCCTCAAATTAGATATCCTTCAT
C
Found at i:325386 original size:34 final size:34
Alignment explanation
Indices: 325273--325390 Score: 91
Period size: 34 Copynumber: 3.5 Consensus size: 34
325263 ATGGATGGCC
** * *
325273 CCTTCGTTGTGAAGTTGAGCCTCAAATTAGATAT
1 CCTTCGTCATGAAGTTGAGCCTCGAATTGGATAT
* ** **
325307 CCTTCATCATGAAGTTGA-AATCG---TGGATGGCC
1 CCTTCGTCATGAAGTTGAGCCTCGAATTGGAT--AT
*
325339 CCTTCGTTATGAAGTTGAGCCTCGAATTGGATAT
1 CCTTCGTCATGAAGTTGAGCCTCGAATTGGATAT
*
325373 CCTTCGTCGTGAAGTTGA
1 CCTTCGTCATGAAGTTGA
325391 AATCTAATCT
Statistics
Matches: 61, Mismatches: 17, Indels: 12
0.68 0.19 0.13
Matches are distributed among these distances:
30 4 0.07
32 16 0.26
33 5 0.08
34 31 0.51
36 5 0.08
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (34 bp):
CCTTCGTCATGAAGTTGAGCCTCGAATTGGATAT
Found at i:325438 original size:58 final size:58
Alignment explanation
Indices: 325368--325699 Score: 185
Period size: 58 Copynumber: 5.4 Consensus size: 58
325358 CCTCGAATTG
325368 GATATCCTTCGTCGTGAAGTTGAAATCTAATCTTGAGATGAATGTTGCTGGTGGGCAC
1 GATATCCTTCGTCGTGAAGTTGAAATCTAATCTTGAGATGAATGTTGCTGGTGGGCAC
*
325426 GATATCCTTCGTCGTGAAGTTGAAAT-TATGGATGACCCCTTCGTTG-TGAA-GTTGAGCCT--T
1 GATATCCTTCGTCGTGAAGTTGAAATCTA---AT-----CTT-G-AGATGAATGTT--G-CTGGT
*****
325486 GAATTG
53 GGGCAC
* * * ** *
325492 GATATCTTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGTTGGTGGGCAC
1 GATATCCTTCGTCGTGAAGTTGAAATCTAATCTTGAGATGAATGTTGCTGGTGGGCAC
* * * ** * *
325550 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCTTTCATTG-TGAA-GTTGATCCT-CGA
1 GATATCCTTCGTCGTGAAGTTGAAATC-T-AAT----C-TTGA--GATGAATGTTGCTGGTGGGC
*
325612 ATTG
57 A--C
* *
325616 GATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGATGAATGTTGCTGGTGGGCAT
1 GATATCCTTCGTCGTGAAGTTGAAATCTAATCTTGAGATGAATGTTGCTGGTGGGCAC
*
325674 GATATCATTCGTCGTGAAGTTGAAAT
1 GATATCCTTCGTCGTGAAGTTGAAAT
325700 TATGGATGGT
Statistics
Matches: 202, Mismatches: 40, Indels: 64
0.66 0.13 0.21
Matches are distributed among these distances:
56 1 0.00
57 5 0.02
58 86 0.43
59 14 0.07
60 7 0.03
64 7 0.03
65 14 0.07
66 62 0.31
67 4 0.02
68 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.34
Consensus pattern (58 bp):
GATATCCTTCGTCGTGAAGTTGAAATCTAATCTTGAGATGAATGTTGCTGGTGGGCAC
Found at i:325524 original size:124 final size:124
Alignment explanation
Indices: 325302--325724 Score: 648
Period size: 124 Copynumber: 3.4 Consensus size: 124
325292 CCTCAAATTA
* * * * *
325302 GATATCCTTCATCATGAAGTTGAAATCGTGGATGGCCCCTTCGTTATGAAGTTGAGCCTCGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCCCCTTCATTGTGAAGTTGAGCCTCGAATT
*
325367 GGATATCCTTCGTCGTGAAGTTGAAATCTAATCTTGAGATGAATGTTGCTGGTGGGCAC
66 GGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGATGAATGTTGCTGGTGGGCAC
* * * *
325426 GATATCCTTCGTCGTGAAGTTGAAATTATGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCCCCTTCATTGTGAAGTTGAGCCTCGAATT
* * ** *
325491 GGATATCTTTCATCGTGAAGTTGAAATCCAATCTAAAGATGAATGTTGTTGGTGGGCAC
66 GGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGATGAATGTTGCTGGTGGGCAC
* * *
325550 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCTTTCATTGTGAAGTTGATCCTCGAATT
1 GATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCCCCTTCATTGTGAAGTTGAGCCTCGAATT
*
325615 GGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGATGAATGTTGCTGGTGGGCAT
66 GGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGATGAATGTTGCTGGTGGGCAC
* * *
325674 GATATCATTCGTCGTGAAGTTGAAATTATGGATGGTCCCTTCATTGTGAAG
1 GATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCCCCTTCATTGTGAAG
325725 ATGAAATCCA
Statistics
Matches: 268, Mismatches: 31, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
124 268 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (124 bp):
GATATCCTTCGTCGTGAAGTTGAAATCATGGATGGCCCCTTCATTGTGAAGTTGAGCCTCGAATT
GGATATCCTTCGTCGTGAAGTTGAAATCCAATCTTGAGATGAATGTTGCTGGTGGGCAC
Found at i:325741 original size:90 final size:90
Alignment explanation
Indices: 325629--325814 Score: 264
Period size: 90 Copynumber: 2.1 Consensus size: 90
325619 ATCCTTCGTC
* * *
325629 GTGAAGTTGAAATCCAATCTTGAGATGAATGTTGCTGGTGGGCATGATATCATTCGTCGTGAAGT
1 GTGAAGATGAAATCCAATCTTGAGATGAATGTTGCTGGTAGGCACGATATCATTCGTCGTGAAGT
* ***
325694 TGAAATTATGGATGGTCCCTTCATT
66 TGAAATCATGGATAACCCCTTCATT
* * * *
325719 GTGAAGATGAAATCCAATCTTGAGATGAATTTTGTTGGTAGGCACGATATCTTTCTTCGTGAAGT
1 GTGAAGATGAAATCCAATCTTGAGATGAATGTTGCTGGTAGGCACGATATCATTCGTCGTGAAGT
*
325784 TGAAATCATGGATAACCCCTTCGTT
66 TGAAATCATGGATAACCCCTTCATT
325809 GTGAAG
1 GTGAAG
325815 TTGAGCCTTG
Statistics
Matches: 84, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 84 1.00
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (90 bp):
GTGAAGATGAAATCCAATCTTGAGATGAATGTTGCTGGTAGGCACGATATCATTCGTCGTGAAGT
TGAAATCATGGATAACCCCTTCATT
Found at i:325975 original size:66 final size:65
Alignment explanation
Indices: 325865--325995 Score: 183
Period size: 66 Copynumber: 2.0 Consensus size: 65
325855 TCCAAGAATT
* * * *
325865 GTTTTACCAAATTGGTTTCGAGCTGGATATTCTTCGTCGTGAAGTTGAAATCCAATTCTTGAGTA
1 GTTTTACCAAATTGCTTTCGAGCTGGATATCCTTCGTCGCGAAGTTGAAATCCAA-TCTCGAGTA
325930 A
65 A
* *
325931 GTTTTACCAAATTAGCTTT-GAGTTGGATATCCTTCGTTGCGAAGTTGAAATCCAATCTCGAGTA
1 GTTTTACCAAATT-GCTTTCGAGCTGGATATCCTTCGTCGCGAAGTTGAAATCCAATCTCGAGTA
325995 A
65 A
325996 ATTGTGTCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
65 9 0.16
66 45 0.78
67 4 0.07
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.37
Consensus pattern (65 bp):
GTTTTACCAAATTGCTTTCGAGCTGGATATCCTTCGTCGCGAAGTTGAAATCCAATCTCGAGTAA
Found at i:326115 original size:64 final size:64
Alignment explanation
Indices: 326009--326175 Score: 271
Period size: 64 Copynumber: 2.6 Consensus size: 64
325999 GTGTCGCTTC
*
326009 GAGTTCAATATCATTTGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCATTTGTT
1 GAGTCCAATATCATTTGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCATTTGTT
* * * *
326073 GAGTCCAATATCTTTTGCTGTAAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCGTTTGTT
1 GAGTCCAATATCATTTGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCATTTGTT
* *
326137 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
1 GAGTCCAATATCATTTGTTGTGAAGTTGAAATTGACTCT
326176 AAAAGCTGCA
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 94 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.37
Consensus pattern (64 bp):
GAGTCCAATATCATTTGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTCATTTGTT
Found at i:331226 original size:22 final size:22
Alignment explanation
Indices: 331199--331249 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
331189 GGTGGGGTAA
331199 TGGGTTGTTGTTGAGATAATGG
1 TGGGTTGTTGTTGAGATAATGG
331221 TGGGTTGTTGTTGAGATAATGG
1 TGGGTTGTTGTTGAGATAATGG
331243 TGGGTTG
1 TGGGTTG
331250 AACATGTGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.16, C:0.00, G:0.43, T:0.41
Consensus pattern (22 bp):
TGGGTTGTTGTTGAGATAATGG
Found at i:331313 original size:14 final size:14
Alignment explanation
Indices: 331294--331333 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
331284 TATTAATAGT
*
331294 AATAATAATAAATA
1 AATAATTATAAATA
331308 AATAATTATAAATA
1 AATAATTATAAATA
331322 AATAATTATAAA
1 AATAATTATAAA
331334 GTTTGGTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATTATAAATA
Found at i:332467 original size:32 final size:32
Alignment explanation
Indices: 332420--332550 Score: 149
Period size: 32 Copynumber: 4.1 Consensus size: 32
332410 GTAAGTTTCA
*
332420 ACCTAAGAGAA-TATCTTGGGGCCTGAGAGCCT
1 ACCTAAG-GAAGTATCTTGGGGCCTAAGAGCCT
*
332452 ACCTAATGG-AGTATCTTAGGGCCTAAGAGCCT
1 ACCTAA-GGAAGTATCTTGGGGCCTAAGAGCCT
* *
332484 ACCCAAGGAAGTATCTTGGGGCCTTAGAGCCT
1 ACCTAAGGAAGTATCTTGGGGCCTAAGAGCCT
* ** * *
332516 ACCTAAGGAAATGCCTTGGGGCCTCAGAGTCT
1 ACCTAAGGAAGTATCTTGGGGCCTAAGAGCCT
332548 ACC
1 ACC
332551 CAATTTCACC
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
31 3 0.04
32 81 0.95
33 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (32 bp):
ACCTAAGGAAGTATCTTGGGGCCTAAGAGCCT
Found at i:332538 original size:64 final size:64
Alignment explanation
Indices: 332431--332553 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 64
332421 CCTAAGAGAA
*
332431 TATCTTGGGGCCTGAGAGCCTACCTAATGGAGTATCTTAGGGCCTAAGAGCCTACCCAAGGAAG
1 TATCTTGGGGCCTGAGAGCCTACCTAATGGAGAATCTTAGGGCCTAAGAGCCTACCCAAGGAAG
* * * *
332495 TATCTTGGGGCCTTAGAGCCTACCTAA-GGA-AATGCCTTGGGGCCTCAGAGTCTACCCAA
1 TATCTTGGGGCCTGAGAGCCTACCTAATGGAGAAT--CTTAGGGCCTAAGAGCCTACCCAA
332554 TTTCACCCTA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
62 2 0.04
63 3 0.06
64 47 0.90
ACGTcount: A:0.25, C:0.25, G:0.27, T:0.23
Consensus pattern (64 bp):
TATCTTGGGGCCTGAGAGCCTACCTAATGGAGAATCTTAGGGCCTAAGAGCCTACCCAAGGAAG
Found at i:333591 original size:26 final size:26
Alignment explanation
Indices: 333556--333611 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
333546 TTCGAAGTTG
* *
333556 ATTTATTCATTTCGA-AGCTTGAGGGT
1 ATTTAGTCA-TTCGAGAGCTTGAAGGT
*
333582 ATTTAGTCATTCTAGAGCTTGAAGGT
1 ATTTAGTCATTCGAGAGCTTGAAGGT
333608 ATTT
1 ATTT
333612 TGGGTCATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (26 bp):
ATTTAGTCATTCGAGAGCTTGAAGGT
Found at i:335075 original size:16 final size:16
Alignment explanation
Indices: 335054--335112 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
335044 TGAAATTTTG
*
335054 GTCAAAGTCAACGCTA
1 GTCAAAGTCAACACTA
335070 GTCAAAGTCAACACTA
1 GTCAAAGTCAACACTA
*
335086 GTCAAAGTCAACTCTA
1 GTCAAAGTCAACACTA
* *
335102 ATTAAAGTCAA
1 GTCAAAGTCAA
335113 AGTCATGTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.22
Consensus pattern (16 bp):
GTCAAAGTCAACACTA
Found at i:336332 original size:60 final size:60
Alignment explanation
Indices: 336257--336379 Score: 185
Period size: 60 Copynumber: 2.0 Consensus size: 60
336247 GTCCCTCGAG
* * *
336257 TATAGGATATTATTTTGTTGAGTCTATCGACTATTAAAAGTTATAAAATGGTCATCTGAC
1 TATAGGATATTATTTTGTTGAGTCCATCAACTATTAAAAGTTATAAAATGATCATCTGAC
* *
336317 TATAGGGA-ATTATTTTGTTGAGTCCCTCAACTATTAAAAGTTATAAAATGATCATTTGAC
1 TATA-GGATATTATTTTGTTGAGTCCATCAACTATTAAAAGTTATAAAATGATCATCTGAC
336377 TAT
1 TAT
336380 TCACTATGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 54 0.95
61 3 0.05
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (60 bp):
TATAGGATATTATTTTGTTGAGTCCATCAACTATTAAAAGTTATAAAATGATCATCTGAC
Found at i:337171 original size:28 final size:28
Alignment explanation
Indices: 337131--337197 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
337121 TCCGGTTTAA
*
337131 CCGGTTCAATCGGGAATCGCTGCGTAGT
1 CCGGTTCAATCGGGAACCGCTGCGTAGT
*
337159 CCGGTTCAATCGGGAACCGTTGCGTAGT
1 CCGGTTCAATCGGGAACCGCTGCGTAGT
337187 CCGGTTCAATC
1 CCGGTTCAATC
337198 TACACCGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.18, C:0.27, G:0.30, T:0.25
Consensus pattern (28 bp):
CCGGTTCAATCGGGAACCGCTGCGTAGT
Found at i:338613 original size:7 final size:7
Alignment explanation
Indices: 338601--338635 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
338591 TAAATATAAA
338601 AATTATT
1 AATTATT
338608 AATTATT
1 AATTATT
338615 -ATTATT
1 AATTATT
338621 ATATTATT
1 A-ATTATT
338629 AATTATT
1 AATTATT
338636 TATCATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.23
7 13 0.50
8 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
AATTATT
Found at i:339426 original size:23 final size:23
Alignment explanation
Indices: 339389--339437 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
339379 ATAAATACAA
* *
339389 ATTTAATTGATGTTTAATATGTT
1 ATTTAATCGAAGTTTAATATGTT
339412 ATTTAATCGAAGTTTAATATGTT
1 ATTTAATCGAAGTTTAATATGTT
339435 ATT
1 ATT
339438 GATTTTCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (23 bp):
ATTTAATCGAAGTTTAATATGTT
Found at i:342846 original size:12 final size:13
Alignment explanation
Indices: 342818--342850 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
342808 CGGGTTTTGC
342818 TTCCCCGTCCCCG
1 TTCCCCGTCCCCG
342831 -TCCCC-TCCCCG
1 TTCCCCGTCCCCG
342842 TTCCCCGTC
1 TTCCCCGTC
342851 GGGTTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.33
12 10 0.56
13 2 0.11
ACGTcount: A:0.00, C:0.64, G:0.12, T:0.24
Consensus pattern (13 bp):
TTCCCCGTCCCCG
Found at i:343265 original size:2 final size:2
Alignment explanation
Indices: 343254--343283 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
343244 AAAATATAAA
343254 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
343284 ATCGGGGACG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:345009 original size:17 final size:17
Alignment explanation
Indices: 344987--345024 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
344977 GAACCGGTCC
344987 GACCCGACCCGATC-GTT
1 GACCCGACCCGA-CAGTT
345004 GACCCGACCCGACAGTT
1 GACCCGACCCGACAGTT
345021 GACC
1 GACC
345025 GTTGACCGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.21, C:0.42, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACAGTT
Found at i:345163 original size:27 final size:29
Alignment explanation
Indices: 345133--345213 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 29
345123 ATATGCTAGG
*
345133 AATTAATTAG-AAA-TATGCTATTTTGGT
1 AATTAATTAGAAAAGGATGCTATTTTGGT
*
345160 AATTAATTTGAAAAGGATGCTATTTTGGT
1 AATTAATTAGAAAAGGATGCTATTTTGGT
* * *
345189 TATTATTTTA-AAAAGGGTGCTATTT
1 AATTA-ATTAGAAAAGGATGCTATTT
345214 ATGTAAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 9 0.20
28 3 0.07
29 31 0.69
30 2 0.04
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (29 bp):
AATTAATTAGAAAAGGATGCTATTTTGGT
Found at i:345187 original size:29 final size:29
Alignment explanation
Indices: 345147--345213 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
345137 AATTAGAAAT
*
345147 ATGCTATTTTGGTAATTAATTTGAAAAGG
1 ATGCTATTTTGGTAATTAATTTAAAAAGG
* *
345176 ATGCTATTTTGGTTATTATTTTAAAAAGG
1 ATGCTATTTTGGTAATTAATTTAAAAAGG
*
345205 GTGCTATTT
1 ATGCTATTT
345214 ATGTAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.46
Consensus pattern (29 bp):
ATGCTATTTTGGTAATTAATTTAAAAAGG
Found at i:345963 original size:15 final size:15
Alignment explanation
Indices: 345943--345975 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
345933 TGATACGTGA
345943 TTCCTGAATAT-TGAT
1 TTCCTG-ATATCTGAT
345958 TTCCTGATATCTGAT
1 TTCCTGATATCTGAT
345973 TTC
1 TTC
345976 TGTATTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.18, G:0.12, T:0.48
Consensus pattern (15 bp):
TTCCTGATATCTGAT
Found at i:346471 original size:19 final size:18
Alignment explanation
Indices: 346432--346465 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
346422 ATTTGCTGTC
346432 GTTTTGGATATATATTTT
1 GTTTTGGATATATATTTT
*
346450 GTTTTGTAT-TATATTT
1 GTTTTGGATATATATTT
346466 AATGTTCTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.65
Consensus pattern (18 bp):
GTTTTGGATATATATTTT
Found at i:347373 original size:29 final size:29
Alignment explanation
Indices: 347340--347409 Score: 117
Period size: 28 Copynumber: 2.5 Consensus size: 29
347330 ATAATATTTT
*
347340 AACTCCTGACATTTTATTTTAAGATAAAA
1 AACTCCTGACATTTTATTTTAAGACAAAA
347369 AACT-CTGACATTTTATTTTAAGACAAAA
1 AACTCCTGACATTTTATTTTAAGACAAAA
347397 AAC-CCTGACATTT
1 AACTCCTGACATTT
347410 GATTGGATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
28 35 0.90
29 4 0.10
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (29 bp):
AACTCCTGACATTTTATTTTAAGACAAAA
Found at i:347969 original size:12 final size:12
Alignment explanation
Indices: 347954--347996 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
347944 TCATTTCGTT
*
347954 TTATTATTATTA
1 TTATTAATATTA
*
347966 TTATCAATATTA
1 TTATTAATATTA
* *
347978 GTATTAGTATTA
1 TTATTAATATTA
347990 TTATTAA
1 TTATTAA
347997 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (12 bp):
TTATTAATATTA
Found at i:349289 original size:16 final size:16
Alignment explanation
Indices: 349268--349316 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
349258 TTCAACACTA
349268 TATTTTTAAT-TTATCT
1 TATTTTTAATATTAT-T
349284 TA-TTTTAATCATTATT
1 TATTTTTAAT-ATTATT
*
349300 TATTTTCAATATTATT
1 TATTTTTAATATTATT
349316 T
1 T
349317 TATTATTACT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 7 0.24
16 12 0.41
17 10 0.34
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTTTAATATTATT
Done.