Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009568.1 Kokia drynarioides strain JFW-HI SEQ_124282, 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: 87108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:3502 original size:25 final size:23
Alignment explanation
Indices: 3474--3519 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
3464 GTTGGATCCA
3474 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAATT-TAAAAA-ATAATTAG
*
3499 AATTAAATTTAAACAATAATT
1 AATTAAATTTAAAAAATAATT
3520 CCCTAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 5 0.25
25 9 0.45
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
AATTAAATTTAAAAAATAATTAG
Found at i:4916 original size:6 final size:6
Alignment explanation
Indices: 4907--4972 Score: 66
Period size: 6 Copynumber: 11.3 Consensus size: 6
4897 TCAATTTGGG
* * *
4907 TTTAAA TTT-AG TTTAAG TTTAAA TTTAAA -TTAAG TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
4952 TTTGAA TTTAAAA TTTAAA TT
1 TTTAAA TTT-AAA TTTAAA TT
4973 AATTAAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
5 13 0.25
6 33 0.65
7 5 0.10
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:4920 original size:11 final size:11
Alignment explanation
Indices: 4906--4961 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
4896 TTCAATTTGG
4906 GTTTAAATTTA
1 GTTTAAATTTA
*
4917 GTTTAAGTTTAA
1 GTTTAAATTT-A
* *
4929 ATTTAAATTAA
1 GTTTAAATTTA
4940 GTTTAAATTTA
1 GTTTAAATTTA
* *
4951 ATTTGAATTTA
1 GTTTAAATTTA
4962 AAATTTAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
11 28 0.78
12 8 0.22
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (11 bp):
GTTTAAATTTA
Found at i:4926 original size:17 final size:17
Alignment explanation
Indices: 4906--4974 Score: 86
Period size: 17 Copynumber: 4.0 Consensus size: 17
4896 TTCAATTTGG
*
4906 GTTTAAATTTAGTTTAA
1 GTTTAAATTTAATTTAA
*
4923 GTTTAAATTTAAATTAA
1 GTTTAAATTTAATTTAA
4940 GTTTAAATTTAATTTGAA
1 GTTTAAATTTAATTT-AA
*
4958 -TTTAAAATTTAAATTAA
1 GTTT-AAATTTAATTTAA
4975 TTAAAAAAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
17 34 0.74
18 12 0.26
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.49
Consensus pattern (17 bp):
GTTTAAATTTAATTTAA
Found at i:4962 original size:23 final size:22
Alignment explanation
Indices: 4911--4976 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
4901 TTTGGGTTTA
*
4911 AATTT-AGTTTAAGTTTAAATTT
1 AATTTAAGTTTAAATTT-AATTT
*
4933 AAATTAAGTTTAAATTTAATTT
1 AATTTAAGTTTAAATTTAATTT
*
4955 GAATTTAAAATTTAAA-TTAATT
1 -AATTT-AAGTTTAAATTTAATT
4977 AAAAAAGTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 9 0.24
23 20 0.54
24 8 0.22
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (22 bp):
AATTTAAGTTTAAATTTAATTT
Found at i:4976 original size:17 final size:17
Alignment explanation
Indices: 4927--4980 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
4917 GTTTAAGTTT
4927 AAATTTAAATTAAGTTT-
1 AAATTTAAATTAA-TTTA
*
4944 AAATTTAATTTGAATTTA
1 AAATTTAAATT-AATTTA
4962 AAATTTAAATTAA-TTA
1 AAATTTAAATTAATTTA
4978 AAA
1 AAA
4981 AAGTCCAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 6 0.18
17 15 0.45
18 12 0.36
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (17 bp):
AAATTTAAATTAATTTA
Found at i:4981 original size:17 final size:16
Alignment explanation
Indices: 4927--4980 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 16
4917 GTTTAAGTTT
*
4927 AAATTTAAATTAAGTTT
1 AAATTTAAATTAA-TTA
*
4944 AAATTTAATTTGAATTTA
1 AAATTTAAATT-AA-TTA
4962 AAATTTAAATTAATTA
1 AAATTTAAATTAATTA
4978 AAA
1 AAA
4981 AAGTCCAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 6 0.19
17 12 0.38
18 14 0.44
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (16 bp):
AAATTTAAATTAATTA
Found at i:6735 original size:30 final size:30
Alignment explanation
Indices: 6652--7068 Score: 298
Period size: 29 Copynumber: 14.2 Consensus size: 30
6642 CTAATATTAT
* *
6652 ATTTTTGACCCCGAAACTTTCAAAAATTAC
1 ATTTTTGACCCCGAAACTTCCAAAAATTCC
6682 ATTTTT-ACCCTCG-AACTTCCAAAAATTCC
1 ATTTTTGACCC-CGAAACTTCCAAAAATTCC
* * * *
6711 ATTTTTGATCTCGAAACTTGCAAAAATTAC
1 ATTTTTGACCCCGAAACTTCCAAAAATTCC
6741 ATTTTT-AGCCCCG-AACTTCC-AAAATTCC
1 ATTTTTGA-CCCCGAAACTTCCAAAAATTCC
** *
6769 ATTTTTG-CCTTGAAACTTCCAAAAATTAC
1 ATTTTTGACCCCGAAACTTCCAAAAATTCC
* *
6798 A-TTTTCATCCCCG-AACTTCCAAAAGTTCC
1 ATTTTTGA-CCCCGAAACTTCCAAAAATTCC
* **
6827 GTTTTTGACCCCGAAACTTCCAAAAATTAT
1 ATTTTTGACCCCGAAACTTCCAAAAATTCC
* * *
6857 ATTTTT-ACCTTCG-AACTTTCAAAAATCCC
1 ATTTTTGACC-CCGAAACTTCCAAAAATTCC
* * * * *
6886 AATTTTAACCTCAAAACTCCCAAAAATTACC
1 ATTTTTGACCCCGAAACTTCCAAAAATT-CC
*
6917 A--TTTAACCCCTG-AACTTCCAAAAATTCC
1 ATTTTTGACCCC-GAAACTTCCAAAAATTCC
* *
6945 ATTTTTAACCCCAAAACTTCCAAAAATTACC
1 ATTTTTGACCCCGAAACTTCCAAAAATT-CC
* * * *
6976 A-TTTTGCCCCCG-TA-TGACCAAAAATTCA
1 ATTTTTGACCCCGAAACT-TCCAAAAATTCC
* * *
7004 ATTTTTAACCCCAAAACTTTCAAAAATTACC
1 ATTTTTGACCCCGAAACTTCCAAAAATT-CC
*
7035 -CTTTT-ACCCTC-AAA-TGTCCAAAAATTCC
1 ATTTTTGACCC-CGAAACT-TCCAAAAATTCC
7063 ATTTTT
1 ATTTTT
7069 TATCCAAATT
Statistics
Matches: 305, Mismatches: 54, Indels: 57
0.73 0.13 0.14
Matches are distributed among these distances:
27 3 0.01
28 33 0.11
29 141 0.46
30 120 0.39
31 8 0.03
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (30 bp):
ATTTTTGACCCCGAAACTTCCAAAAATTCC
Found at i:6744 original size:59 final size:58
Alignment explanation
Indices: 6652--7068 Score: 421
Period size: 59 Copynumber: 7.1 Consensus size: 58
6642 CTAATATTAT
*
6652 ATTTTTGACCCCGAAACTTTCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCC
1 ATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACCC-CGAACTTCCAAAAATTCC
* * *
6711 ATTTTTGATCTCGAAACTTGCAAAAATTACATTTTTAGCCCCGAACTTCC-AAAATTCC
1 ATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTA-CCCCGAACTTCCAAAAATTCC
** * *
6769 ATTTTTG-CCTTGAAACTTCCAAAAATTACATTTTCATCCCCGAACTTCCAAAAGTTCC
1 ATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTA-CCCCGAACTTCCAAAAATTCC
* * * * *
6827 GTTTTTGACCCCGAAACTTCCAAAAATTATATTTTTACCTTCGAACTTTCAAAAATCCC
1 ATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACC-CCGAACTTCCAAAAATTCC
* * * * * *
6886 AATTTTAACCTCAAAACTCCCAAAAATTACCA-TTTAACCCCTGAACTTCCAAAAATTCC
1 ATTTTTGACCCCGAAACTTCCAAAAATTA-CATTTTTACCCC-GAACTTCCAAAAATTCC
* * ** * * *
6945 ATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTGCCCCCGTA-TGACCAAAAATTCA
1 ATTTTTGACCCCGAAACTTCCAAAAATTA-CATTTTTACCCCGAACT-TCCAAAAATTCC
* * * ** *
7004 ATTTTTAACCCCAAAACTTTCAAAAATTACCCTTTTACCCTC-AAATGTCCAAAAATTCC
1 ATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACCC-CGAACT-TCCAAAAATTCC
7063 ATTTTT
1 ATTTTT
7069 TATCCAAATT
Statistics
Matches: 303, Mismatches: 45, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
57 37 0.12
58 40 0.13
59 215 0.71
60 11 0.04
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.33
Consensus pattern (58 bp):
ATTTTTGACCCCGAAACTTCCAAAAATTACATTTTTACCCCGAACTTCCAAAAATTCC
Found at i:7093 original size:60 final size:60
Alignment explanation
Indices: 6652--7128 Score: 294
Period size: 59 Copynumber: 8.1 Consensus size: 60
6642 CTAATATTAT
* * *
6652 ATTTTTGACCCCGAAACTT-TCAAAAATTA-CATTTTTACCCTCGAACT-TCCAAAAATTCC
1 ATTTTTAACCCCAAAACTTCTCAAAAATTACCA-TTTTACCCTC-AAATGTCCAAAAATTCC
* * * * * *
6711 ATTTTTGATCTCGAAACTT-GCAAAAATTA-CATTTTTAGCCC-CGAACT-TCC-AAAATTCC
1 ATTTTTAACCCCAAAACTTCTCAAAAATTACCA-TTTTA-CCCTC-AAATGTCCAAAAATTCC
* *** * *
6769 ATTTTT-GCCTTGAAACTTC-CAAAAATTA-CATTTTCATCCC-CGAACT-TCCAAAAGTTCC
1 ATTTTTAACCCCAAAACTTCTCAAAAATTACCATTTT-A-CCCTC-AAATGTCCAAAAATTCC
* * * * * * * *
6827 GTTTTTGACCCCGAAACTTC-CAAAAATTA-TATTTTTACCTTCGAACT-TTCAAAAATCCC
1 ATTTTTAACCCCAAAACTTCTCAAAAATTACCA-TTTTACCCTC-AAATGTCCAAAAATTCC
* * * * * *
6886 AATTTTAACCTCAAAAC-TCCCAAAAATTACCATTTAACCCCTGAACT-TCCAAAAATTCC
1 ATTTTTAACCCCAAAACTTCTCAAAAATTACCATTTTA-CCCTCAAATGTCCAAAAATTCC
* * ** * *
6945 ATTTTTAACCCCAAAACTTC-CAAAAATTACCATTTTGCCCCCGTATGACCAAAAATTCA
1 ATTTTTAACCCCAAAACTTCTCAAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCC
*
7004 ATTTTTAACCCCAAAACTT-TCAAAAATTACCCTTTTACCCTCAAATGTCCAAAAATTCC
1 ATTTTTAACCCCAAAACTTCTCAAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCC
* * ** * ** *
7063 ATTTTTTA-TCCAAATTTTCCTCAAAAATTACCATTTTACACTCGGATGTCCAAAAGTTCC
1 ATTTTTAACCCCAAAACTT-CTCAAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCC
*
7123 CTTTTT
1 ATTTTT
7129 TATCCCGATT
Statistics
Matches: 347, Mismatches: 56, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
56 4 0.01
57 33 0.10
58 41 0.12
59 216 0.62
60 53 0.15
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (60 bp):
ATTTTTAACCCCAAAACTTCTCAAAAATTACCATTTTACCCTCAAATGTCCAAAAATTCC
Found at i:15740 original size:201 final size:201
Alignment explanation
Indices: 15393--15777 Score: 590
Period size: 201 Copynumber: 1.9 Consensus size: 201
15383 CAAAAAAAAA
* * *
15393 AGGCGGTCATCTTCCTGATGAGATGCAGAGAAGTAAACCAACTCGACGCTCGACATGAGCAAATC
1 AGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAAACCAACTCGACGCTCAACACGAGCAAATC
* * * **
15458 TTCGAACCCCAGCTTTCTGATGAGATACTGAGAAGCAGGTCGAAGAAATAAAATGGTTAGTTTTT
66 TTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGAAATAAAATGGTTAGCTTCC
* *
15523 TGATGAGATGCTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATATAGAGAAGCGAATTGAAA
131 TGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGAATTGAAA
15588 CATGTG
196 CATGTG
* * * * *
15594 AGGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACGAACTCGAGGCTCAATACGAGCAAATC
1 AGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAAACCAACTCGACGCTCAACACGAGCAAATC
* * *
15659 TTTGAACCCCAACTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAATGGTTAGCTTCC
66 TTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGAAATAAAATGGTTAGCTTCC
**
15724 TGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTGATGAGATACAGAGAA
131 TGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAA
15778 ACCAACTTGA
Statistics
Matches: 164, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
201 164 1.00
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (201 bp):
AGGCGGTCATCTTCCTGATGAGATACAGAGAAGTAAACCAACTCGACGCTCAACACGAGCAAATC
TTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGAAATAAAATGGTTAGCTTCC
TGATGAGATACTGAGAAGTGGACCAAATTCATCTTCCTGATGAGATACAGAGAAGCGAATTGAAA
CATGTG
Found at i:15814 original size:148 final size:149
Alignment explanation
Indices: 15603--15925 Score: 504
Period size: 148 Copynumber: 2.2 Consensus size: 149
15593 GAGGCGGTCA
* * * *
15603 TCTTCCTGATGAGATATAGAGAAGTATACGAACTCGAGGCTCAATACGAGCAAATCTTTGAACCC
1 TCTTCCTGATGAGATACAGAG-A--ATACCAACTCGAGGCTCAAGACGAGCAAATCTTCGAACCC
*
15668 CAACTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGAT
63 CAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGAT
*
15733 ACTGAGAAGTGGACCAAATTTG
128 ACTGAGAAGTGGACCAAATTCG
* * *
15755 TCTTCCTGATGAGATACAGAGAA-ACCAACTTGAGGCTCAAGGCGAGCAAATCTTCGAACCCCAG
1 TCTTCCTGATGAGATACAGAGAATACCAACTCGAGGCTCAAGACGAGCAAATCTTCGAACCCCAA
*
15819 CTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACT
66 CTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACT
*
15884 GAGAAGTGGACCCAATTCG
131 GAGAAGTGGACCAAATTCG
*
15903 TCTTCTTGATGAGATACAGAGAA
1 TCTTCCTGATGAGATACAGAGAA
15926 GCGGATTGAA
Statistics
Matches: 159, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
148 137 0.86
149 1 0.01
151 1 0.01
152 20 0.13
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (149 bp):
TCTTCCTGATGAGATACAGAGAATACCAACTCGAGGCTCAAGACGAGCAAATCTTCGAACCCCAA
CTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACT
GAGAAGTGGACCAAATTCG
Found at i:16072 original size:134 final size:134
Alignment explanation
Indices: 15819--16109 Score: 420
Period size: 134 Copynumber: 2.2 Consensus size: 134
15809 CGAACCCCAG
* * * *
15819 CTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACT
1 CTTCCTGATGAGATACTGAGAAGCAGGTCAAAGAAATAAAATGGTTAGCTTCCTGATGAGATACA
* * * * * * ** *
15884 GAGAAGTGGACCCAATTCGTCTTCTTGATGAGATACAGAGAAGCGGATTGAAACAAATGATGCGG
66 GAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGAGAAGCGGATCAAAACAAATGATGCAG
15949 TCAT
131 TCAT
* * *
15953 CTTCCTGATGAGATATTGAGAATCAGGTCAAAGAAATAAAGTGGTTAGCTTCCTGATGAGATACA
1 CTTCCTGATGAGATACTGAGAAGCAGGTCAAAGAAATAAAATGGTTAGCTTCCTGATGAGATACA
* *
16018 GAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGAGAAGTGGATCAAAACAAGTGATGCAG
66 GAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGAGAAGCGGATCAAAACAAATGATGCAG
16083 TCAT
131 TCAT
16087 CTTCCTGATGAGATACTGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
16110 AAGGCCAAGT
Statistics
Matches: 137, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
134 137 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (134 bp):
CTTCCTGATGAGATACTGAGAAGCAGGTCAAAGAAATAAAATGGTTAGCTTCCTGATGAGATACA
GAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAGAGAAGCGGATCAAAACAAATGATGCAG
TCAT
Found at i:16525 original size:17 final size:17
Alignment explanation
Indices: 16503--16569 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
16493 TTTTGGGTTT
**
16503 TTAAATTTAGTTTAAGA
1 TTAAATTTAAATTAAGA
*
16520 TTAAATTTAAATTAAGT
1 TTAAATTTAAATTAAGA
* *
16537 TTAAATTTAATTTGAA-T
1 TTAAATTTAAATT-AAGA
16554 TTAAAATTTAAATTAA
1 TT-AAATTTAAATTAA
16570 TTAAAAAAGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
17 31 0.72
18 12 0.28
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
TTAAATTTAAATTAAGA
Found at i:16557 original size:23 final size:22
Alignment explanation
Indices: 16506--16571 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
16496 TGGGTTTTTA
*
16506 AATTT-AGTTTAAGATTAAATTT
1 AATTTAAGTTTAA-ATTTAATTT
*
16528 AAATTAAGTTTAAATTTAATTT
1 AATTTAAGTTTAAATTTAATTT
*
16550 GAATTTAAAATTTAAA-TTAATT
1 -AATTT-AAGTTTAAATTTAATT
16572 AAAAAAGTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 12 0.32
23 17 0.46
24 8 0.22
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (22 bp):
AATTTAAGTTTAAATTTAATTT
Found at i:16571 original size:17 final size:17
Alignment explanation
Indices: 16522--16575 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
16512 GTTTAAGATT
16522 AAATTTAAATTAAGTTT-
1 AAATTTAAATTAA-TTTA
*
16539 AAATTTAATTTGAATTTA
1 AAATTTAAATT-AATTTA
16557 AAATTTAAATTAA-TTA
1 AAATTTAAATTAATTTA
16573 AAA
1 AAA
16576 AAGTCCAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 6 0.18
17 15 0.45
18 12 0.36
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (17 bp):
AAATTTAAATTAATTTA
Found at i:16576 original size:17 final size:16
Alignment explanation
Indices: 16522--16575 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 16
16512 GTTTAAGATT
*
16522 AAATTTAAATTAAGTTT
1 AAATTTAAATTAA-TTA
*
16539 AAATTTAATTTGAATTTA
1 AAATTTAAATT-AA-TTA
16557 AAATTTAAATTAATTA
1 AAATTTAAATTAATTA
16573 AAA
1 AAA
16576 AAGTCCAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 6 0.19
17 12 0.38
18 14 0.44
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (16 bp):
AAATTTAAATTAATTA
Found at i:18646 original size:59 final size:59
Alignment explanation
Indices: 18459--18923 Score: 434
Period size: 59 Copynumber: 7.9 Consensus size: 59
18449 TTTGACCTCA
* *
18459 AAACTTCCAAAAATTACATTTTTACCCT-GAACTTCCAAAAAATCCATTTTTAACACCG
1 AAACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCG
* * *
18517 AAACTTCCAAAAATTATATTTTTACCCTCAAACTTCC-AAAATTCCATTTTTAACCTCG
1 AAACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCG
* * * * *
18575 AAACTTTCAAAAATTATATTTTCACCCTCGAACTTCCAAAAATTCCATTTTTTACCCCT
1 AAACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCG
* * * * * *
18634 AAACTTCTAAAAATTACATTTTTA-CCTCCGAACTTTCAAAAA-TCTTAATTTTGACCTCG
1 AAACTTCCAAAAATTACATTTTTACCCT-CGAACTTCCAAAAATTC-CATTTTTAACCCCG
*
18693 AAAC-TCACAAAAATTACCA-TTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCA
1 AAACTTC-CAAAAATTA-CATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCG
* * * * *
18752 AAACTTCCAAAAATTACCA-TTTTGCCCCCGTA-TGTCCCAAAAAATCCA-TTTTAACCCCA
1 AAACTTCCAAAAATTA-CATTTTTACCCTCGAACT-T-CCAAAAATTCCATTTTTAACCCCG
* ** * * * *
18811 AAACTTTCAAAAATTACCCTTTTACCCTCGTA-TGTCCAAAAATTCCATTTTTTATCTCG
1 AAACTTCCAAAAATTACATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTTAACCCCG
** *
18870 -ATTTTCCTAAAAAAATTACCA-TTTTACCCTCGGA-TATCCAAAAATTCCATTTTT
1 AAACTTCC---AAAAATTA-CATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTT
18924 GATCTCGATT
Statistics
Matches: 343, Mismatches: 47, Indels: 31
0.81 0.11 0.07
Matches are distributed among these distances:
58 103 0.30
59 180 0.52
60 20 0.06
61 39 0.11
62 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.34
Consensus pattern (59 bp):
AAACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCG
Found at i:18821 original size:29 final size:28
Alignment explanation
Indices: 18459--18861 Score: 242
Period size: 29 Copynumber: 13.8 Consensus size: 28
18449 TTTGACCTCA
* * *
18459 AAACTTCCAAAAATTACATTTTTACCCT
1 AAACTTCCAAAAATTCCATTTTAACCCC
* * *
18487 GAACTTCCAAAAAATCCATTTTTAACACCG
1 AAACTTCCAAAAATTCCA-TTTTAAC-CCC
** *
18517 AAACTTCCAAAAATTATATTTTTACCCTC
1 AAACTTCCAAAAATTCCATTTTAACCC-C
*
18546 AAACTTCC-AAAATTCCATTTTTAACCTCG
1 AAACTTCCAAAAATTCCA-TTTTAACC-CC
* ** *
18575 AAACTTTCAAAAATTATATTTTCACCCTC
1 AAACTTCCAAAAATTCCATTTTAACCC-C
* *
18604 GAACTTCCAAAAATTCCATTTTTTACCCC
1 AAACTTCCAAAAATTCCA-TTTTAACCCC
* * *
18633 TAAACTTCTAAAAATTACATTTTTACCTCC
1 -AAACTTCCAAAAATTCCATTTTAACC-CC
* * ** * *
18663 GAACTTTCAAAAATCTTAATTTTGACCTCG
1 AAACTTCCAAAAAT-TCCATTTTAACC-CC
18693 AAAC-TCACAAAAATTACCATTTT-ACCCTC
1 AAACTTC-CAAAAATT-CCATTTTAACCC-C
*
18722 GAACTTCCAAAAATTCCATTTTTAACCCC
1 AAACTTCCAAAAATTCCA-TTTTAACCCC
**
18751 AAAACTTCCAAAAATTACCATTTTGCCCCC
1 -AAACTTCCAAAAATT-CCATTTTAACCCC
** *
18781 GTA-TGTCCCAAAAAATCCATTTTAACCCC
1 AAACT-T-CCAAAAATTCCATTTTAACCCC
* *
18810 AAAACTTTCAAAAATTACCCTTTT-ACCCTC
1 -AAACTTCCAAAAATT-CCATTTTAACCC-C
**
18840 GTA-TGTCCAAAAATTCCATTTT
1 AAACT-TCCAAAAATTCCATTTT
18862 TTATCTCGAT
Statistics
Matches: 291, Mismatches: 58, Indels: 52
0.73 0.14 0.13
Matches are distributed among these distances:
28 37 0.13
29 130 0.45
30 120 0.41
31 4 0.01
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (28 bp):
AAACTTCCAAAAATTCCATTTTAACCCC
Found at i:18862 original size:29 final size:30
Alignment explanation
Indices: 18460--18923 Score: 295
Period size: 30 Copynumber: 15.8 Consensus size: 30
18450 TTGACCTCAA
18460 AACTTCCAAAAATTA-CATTTTTACCCT-G
1 AACTTCCAAAAATTACCATTTTTACCCTCG
* *
18488 AACTTCCAAAAAAT-CCATTTTTAACAC-CG
1 AACTTCCAAAAATTACCATTTTT-ACCCTCG
* *
18517 AAACTTCCAAAAATTA-TATTTTTACCCTCA
1 -AACTTCCAAAAATTACCATTTTTACCCTCG
*
18547 AACTTCC-AAAATT-CCATTTTTAACCTCG
1 AACTTCCAAAAATTACCATTTTTACCCTCG
* * *
18575 AAACTTTCAAAAATTA-TATTTTCACCCTCG
1 -AACTTCCAAAAATTACCATTTTTACCCTCG
*
18605 AACTTCCAAAAATT-CCATTTTTTACCC-CTA
1 AACTTCCAAAAATTACCA-TTTTTACCCTC-G
*
18635 AACTTCTAAAAATTA-CATTTTTA-CCTCCG
1 AACTTCCAAAAATTACCATTTTTACCCT-CG
* *
18664 AACTTTCAAAAATCTTA--ATTTTGA-CCTCG
1 AACTTCCAAAAA--TTACCATTTTTACCCTCG
18693 AAAC-TCACAAAAATTACCA-TTTTACCCTCG
1 -AACTTC-CAAAAATTACCATTTTTACCCTCG
*
18723 AACTTCCAAAAATT-CCATTTTTAACCC-CAA
1 AACTTCCAAAAATTACCATTTTT-ACCCTC-G
* *
18753 AACTTCCAAAAATTACCA-TTTTGCCCCCG
1 AACTTCCAAAAATTACCATTTTTACCCTCG
* * * *
18782 TA-TGTCCCAAAAAAT-CCATTTTAACCC-CAA
1 AACT-T-CCAAAAATTACCATTTTTACCCTC-G
* *
18812 AACTTTCAAAAATTACC-CTTTTACCCTCG
1 AACTTCCAAAAATTACCATTTTTACCCTCG
* *
18841 TA-TGTCCAAAAATT-CCATTTTTTA-TCTCG
1 AACT-TCCAAAAATTACCA-TTTTTACCCTCG
**
18870 ATTTTCCTAAAAAAATTACCA-TTTTACCCTCG
1 AACTTCC---AAAAATTACCATTTTTACCCTCG
*
18902 GA-TATCCAAAAATT-CCATTTTT
1 AACT-TCCAAAAATTACCATTTTT
18924 GATCTCGATT
Statistics
Matches: 342, Mismatches: 47, Indels: 93
0.71 0.10 0.19
Matches are distributed among these distances:
28 52 0.15
29 125 0.37
30 135 0.39
31 13 0.04
32 14 0.04
33 3 0.01
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (30 bp):
AACTTCCAAAAATTACCATTTTTACCCTCG
Found at i:18895 original size:61 final size:61
Alignment explanation
Indices: 18819--18935 Score: 198
Period size: 61 Copynumber: 1.9 Consensus size: 61
18809 CAAAACTTTC
* * * *
18819 AAAAATTACCCTTTTACCCTCGTATGTCCAAAAATTCCATTTTTTATCTCGATTTTCCTAA
1 AAAAATTACCATTTTACCCTCGGATATCCAAAAATTCCATTTTTGATCTCGATTTTCCTAA
18880 AAAAATTACCATTTTACCCTCGGATATCCAAAAATTCCATTTTTGATCTCGATTTT
1 AAAAATTACCATTTTACCCTCGGATATCCAAAAATTCCATTTTTGATCTCGATTTT
18936 TTGAAAGTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (61 bp):
AAAAATTACCATTTTACCCTCGGATATCCAAAAATTCCATTTTTGATCTCGATTTTCCTAA
Found at i:18930 original size:29 final size:29
Alignment explanation
Indices: 18845--18930 Score: 70
Period size: 29 Copynumber: 2.8 Consensus size: 29
18835 CCCTCGTATG
*
18845 TCCAAAAATTCCATTTTTTATCTC-GATTT
1 TCCAAAAATTCCA-TTTTTATCTCGGATTA
*
18874 TCCTAAAAAAATTACCA-TTTTACCCTCGGA-TA
1 TCC---AAAAATT-CCATTTTTA-TCTCGGATTA
18906 TCCAAAAATTCCATTTTTGATCTCG
1 TCCAAAAATTCCATTTTT-ATCTCG
18931 ATTTTTTGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 16
0.71 0.05 0.25
Matches are distributed among these distances:
28 3 0.07
29 18 0.39
30 1 0.02
31 5 0.11
32 14 0.30
33 5 0.11
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTATCTCGGATTA
Found at i:20656 original size:54 final size:54
Alignment explanation
Indices: 20593--20700 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
20583 TGGACGGTGA
*
20593 TTGAAATTTATATCGAGTAAAATATGTTATAATGGTAATTTTGTAATTAAATTG
1 TTGAAATTTATATCAAGTAAAATATGTTATAATGGTAATTTTGTAATTAAATTG
20647 TTGAAATTTATATCAAGTAAAATATGTTATAATGGTAATTTTGTAATTAAATTG
1 TTGAAATTTATATCAAGTAAAATATGTTATAATGGTAATTTTGTAATTAAATTG
20701 AAGTTAAGTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (54 bp):
TTGAAATTTATATCAAGTAAAATATGTTATAATGGTAATTTTGTAATTAAATTG
Found at i:20692 original size:26 final size:26
Alignment explanation
Indices: 20609--20692 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
20599 TTTATATCGA
20609 GTAAAATATGTTATAATGGTAATTTT
1 GTAAAATATGTTATAATGGTAATTTT
* ***
20635 GTAATTAA-ATTGTTGA-AAT-TTATATCAA
1 GTAA--AATA-TGTT-ATAATGGTA-ATTTT
20663 GTAAAATATGTTATAATGGTAATTTT
1 GTAAAATATGTTATAATGGTAATTTT
20689 GTAA
1 GTAA
20693 TTAAATTGAA
Statistics
Matches: 42, Mismatches: 8, Indels: 16
0.64 0.12 0.24
Matches are distributed among these distances:
25 1 0.02
26 19 0.45
27 6 0.14
28 15 0.36
29 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.44
Consensus pattern (26 bp):
GTAAAATATGTTATAATGGTAATTTT
Found at i:22012 original size:20 final size:20
Alignment explanation
Indices: 21985--22116 Score: 117
Period size: 20 Copynumber: 6.5 Consensus size: 20
21975 GAAATGAAGA
21985 GGTGCCCCTGTTTGCACTTC
1 GGTGCCCCTGTTTGCACTTC
* ** *
22005 GATGCCCCTGAATGCACTTT
1 GGTGCCCCTGTTTGCACTTC
22025 GGTGCCCCTGTTTGCACTTC
1 GGTGCCCCTGTTTGCACTTC
** *
22045 GGTGCCATTGAATT-CAC-TC
1 GGTGCCCCTG-TTTGCACTTC
**
22064 TGGTGCCCCTGAATGCAC-TC
1 -GGTGCCCCTGTTTGCACTTC
*
22084 TGGTGCCCCTATATTGCACTTC
1 -GGTGCCCCTGT-TTGCACTTC
22106 GGTGCCCCTGT
1 GGTGCCCCTGT
22117 GTGTCTAATC
Statistics
Matches: 89, Mismatches: 18, Indels: 9
0.77 0.16 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.74
21 17 0.19
22 2 0.02
ACGTcount: A:0.12, C:0.33, G:0.23, T:0.32
Consensus pattern (20 bp):
GGTGCCCCTGTTTGCACTTC
Found at i:22040 original size:40 final size:40
Alignment explanation
Indices: 21985--22116 Score: 151
Period size: 40 Copynumber: 3.3 Consensus size: 40
21975 GAAATGAAGA
*
21985 GGTGCCCCTGTTTGCACTTCGATGCCCCTGAATGCACTTT
1 GGTGCCCCTGTTTGCACTTCGGTGCCCCTGAATGCACTTT
** * *
22025 GGTGCCCCTGTTTGCACTTCGGTGCCATTGAATTCACTCT
1 GGTGCCCCTGTTTGCACTTCGGTGCCCCTGAATGCACTTT
** *
22065 GGTGCCCCTGAATGCAC-TCTGGTGCCCCT-ATATTGCACTTC
1 GGTGCCCCTGTTTGCACTTC-GGTGCCCCTGA-A-TGCACTTT
22106 GGTGCCCCTGT
1 GGTGCCCCTGT
22117 GTGTCTAATC
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
39 3 0.04
40 58 0.76
41 15 0.20
ACGTcount: A:0.12, C:0.33, G:0.23, T:0.32
Consensus pattern (40 bp):
GGTGCCCCTGTTTGCACTTCGGTGCCCCTGAATGCACTTT
Found at i:23443 original size:321 final size:321
Alignment explanation
Indices: 22861--23496 Score: 1056
Period size: 321 Copynumber: 2.0 Consensus size: 321
22851 ATGACACGGG
* * * *
22861 TTGTCACACGGTCGTGTGTGTGTTTTAGGGTGCAGTACAGTCTATTCGAATAGACACATGGGCTG
1 TTGTCACACGGCCGTGTGTGTGTTTTAGGGTGCAGTACAATCTATTCGAATAGACACACGGGCTA
* ** *
22926 AGCCACAGTCCAAAGCATAGGTGTGTAATGTAAGTCAGTAAGGTCTTTTCGAGCTTGAACACAAG
66 AGACACAGTCCAAAGCATAGGCATGTAATGTAAGTCAATAAGGTCTTTTCGAGCTTGAACACAAG
* * *
22991 CGGGCACACATGTTGTTACACGATCGTGTGACCTTATTTCGAAGGTACACACAGGCGAGAACACG
131 CGGGCACACATGCTGTTACACGACCGTGTGACCTTATTTCGAAGGTACACACAGGCGAGAACACA
* * *
23056 GGCTGGCACATGACTGTGTGCCCTTGTTTCGTATGATTTTCTAACTTTTCCTTGGACTTTCTGAT
196 GGCTGGCACATGACCGTGTGCCCCTGTTTCATATGATTTTCTAACTTTTCCTTGGACTTTCTGAT
*
23121 TGTTTGCAAATTAGTTTCTAGTCGTATTTAAACTACTCTTAAGTGAATGAATGTATGTTGA
261 TGTTTGCAAATTAGTTTCTAGTCATATTTAAACTACTCTTAAGTGAATGAATGTATGTTGA
23182 TTGTCACACGGCCGTGTGTGTGTTTTAGGGTGCAGTACAATCTATTCGAATAGACACACGGGCTA
1 TTGTCACACGGCCGTGTGTGTGTTTTAGGGTGCAGTACAATCTATTCGAATAGACACACGGGCTA
* * * *
23247 AGACACGGTCCAAAGCATGGGCATGTGATGTAAGTCAATAAGGTCTTTTCGAGCTTGAACACAGG
66 AGACACAGTCCAAAGCATAGGCATGTAATGTAAGTCAATAAGGTCTTTTCGAGCTTGAACACAAG
* *
23312 CGGGCACACGTGCTGTTACACGACCGTGTGACCTTATTTCGAAGGTACACACGGGCGAGAACACA
131 CGGGCACACATGCTGTTACACGACCGTGTGACCTTATTTCGAAGGTACACACAGGCGAGAACACA
*
23377 GGCTGGCACATGGCCGTGTGCCCCTGTTTCATATGATTTTCTAACTTTTCCTTGGACTTTCTGAT
196 GGCTGGCACATGACCGTGTGCCCCTGTTTCATATGATTTTCTAACTTTTCCTTGGACTTTCTGAT
* *
23442 TGTTTGCAAATTAGTTTCTATTCATATTTAAACTAGTCTTAAGTGAATGAATGTA
261 TGTTTGCAAATTAGTTTCTAGTCATATTTAAACTACTCTTAAGTGAATGAATGTA
23497 CGTTTTGAGA
Statistics
Matches: 291, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
321 291 1.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (321 bp):
TTGTCACACGGCCGTGTGTGTGTTTTAGGGTGCAGTACAATCTATTCGAATAGACACACGGGCTA
AGACACAGTCCAAAGCATAGGCATGTAATGTAAGTCAATAAGGTCTTTTCGAGCTTGAACACAAG
CGGGCACACATGCTGTTACACGACCGTGTGACCTTATTTCGAAGGTACACACAGGCGAGAACACA
GGCTGGCACATGACCGTGTGCCCCTGTTTCATATGATTTTCTAACTTTTCCTTGGACTTTCTGAT
TGTTTGCAAATTAGTTTCTAGTCATATTTAAACTACTCTTAAGTGAATGAATGTATGTTGA
Found at i:29394 original size:22 final size:22
Alignment explanation
Indices: 29369--29412 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29359 ATTTAATAAA
29369 AAGAAATTAAATTGTTAACAAT
1 AAGAAATTAAATTGTTAACAAT
29391 AAGAAATTAAATTGTTAACAAT
1 AAGAAATTAAATTGTTAACAAT
29413 TTTGTGAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.32
Consensus pattern (22 bp):
AAGAAATTAAATTGTTAACAAT
Found at i:29878 original size:108 final size:111
Alignment explanation
Indices: 29750--29964 Score: 337
Period size: 108 Copynumber: 2.0 Consensus size: 111
29740 TTGAAGCGAT
* *
29750 GAAAAGTCATAATAAAATTAAAATTTGAAAACTTAAAATTAAAATTTACATTTATTTTGTTTTGA
1 GAAAAGTCATAATAAAATTAAAATTTGAAAACTTAAAATTAAAACTTAAATTTATTTTGTTTTGA
*
29815 AAACTTAAA-A-GATAAATTTTGGAGAAAC-AAATTTTTGATGGAA
66 AAACTTAAAGATAATAAATTTTGGAGAAACGAAATTTTTGATGGAA
** * *
29858 GAAAAGTTGTAATAAAATTAAATTTTGAAAATTTAAAATTAAAACTTAAATTTATTTTGTTTTGA
1 GAAAAGTCATAATAAAATTAAAATTTGAAAACTTAAAATTAAAACTTAAATTTATTTTGTTTTGA
*
29923 TAACTTAAAGATAATAAATTTTGGAGAAACGAAATTTTTGAT
66 AAACTTAAAGATAATAAATTTTGGAGAAACGAAATTTTTGAT
29965 ATATTAGATG
Statistics
Matches: 96, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
108 67 0.70
109 1 0.01
110 17 0.18
111 11 0.11
ACGTcount: A:0.47, C:0.04, G:0.11, T:0.38
Consensus pattern (111 bp):
GAAAAGTCATAATAAAATTAAAATTTGAAAACTTAAAATTAAAACTTAAATTTATTTTGTTTTGA
AAACTTAAAGATAATAAATTTTGGAGAAACGAAATTTTTGATGGAA
Found at i:31445 original size:26 final size:30
Alignment explanation
Indices: 31415--31478 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
31405 ATAAATATAA
* *
31415 ATATAAAT-ATATATTTATTATT-TAACAT
1 ATATAATTGATATAATTATTATTATAACAT
*
31443 ATATAATTGATATAATTATTTTTATAACAT
1 ATATAATTGATATAATTATTATTATAACAT
31473 AATATA
1 -ATATA
31479 TTTGGGCTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 7 0.23
29 12 0.40
30 6 0.20
31 5 0.17
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (30 bp):
ATATAATTGATATAATTATTATTATAACAT
Found at i:37449 original size:18 final size:19
Alignment explanation
Indices: 37426--37467 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
37416 CCCTCGTGTA
*
37426 TTTTATG-TTTTTTTTAAT
1 TTTTATGATTTTTTATAAT
37444 TTTTATGAATTTTTTATAAT
1 TTTTATG-ATTTTTTATAAT
37464 TTTT
1 TTTT
37468 TAAATTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTATGATTTTTTATAAT
Found at i:37469 original size:10 final size:10
Alignment explanation
Indices: 37433--37475 Score: 54
Period size: 9 Copynumber: 4.4 Consensus size: 10
37423 GTATTTTATG
*
37433 TTTTTTTTAA
1 TTTTTTATAA
37443 -TTTTTATGAA
1 TTTTTTAT-AA
37453 TTTTTTATAA
1 TTTTTTATAA
37463 TTTTTTA-AA
1 TTTTTTATAA
37472 TTTT
1 TTTT
37476 GATTTTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 12 0.40
10 11 0.37
11 7 0.23
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:38599 original size:16 final size:16
Alignment explanation
Indices: 38578--38611 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
38568 TTTATAATAA
38578 TAATAATTTCATAT-TT
1 TAATAATTT-ATATCTT
38594 TAATAATTTATATCTT
1 TAATAATTTATATCTT
38610 TA
1 TA
38612 TTATTTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
TAATAATTTATATCTT
Found at i:51517 original size:160 final size:158
Alignment explanation
Indices: 51217--51542 Score: 526
Period size: 160 Copynumber: 2.1 Consensus size: 158
51207 ACCAAAAAAC
* *
51217 ACTTTAAAGAGTAAAATTTATGATGTTTTGAGTTTTGATCTCATTATGCACATATATTTTCTCTC
1 ACTTTAAAGAGTAAAATTTATGATGTTTTAAGTTTGGATCTCATTATGCACATATATTTTCTCTC
* * **
51282 AAAATAATATTTACCTATTTGTAAAACTAGAAGAGTTTTAGTAAATTCACAATTGCGTTGCGACT
66 AAAATAATATTTACCTATTTGTAAAAATAAAAGAGTTTTAGTAAATTCACAATTGAATTGCGACT
*
51347 CATCGAGGGTGACATCAACTCGGTCAAA
131 CATAGAGGGTGACATCAACTCGGTCAAA
51375 ACTTTAAAGAGTAAAATTTATGATGTTTTAAGTTTGGATCTCATTATGCACATATATTTTATCTC
1 ACTTTAAAGAGTAAAATTTATGATGTTTTAAGTTTGGATCTCATTATGCACATATA-TTT-TCTC
* * *
51440 TCAAAATAATATTTACCTCTTTGTAAAAATAAAAGGGTTTTAGTAAATTCACAATTGAATTGGGA
64 TCAAAATAATATTTACCTATTTGTAAAAATAAAAGAGTTTTAGTAAATTCACAATTGAATTGCGA
*
51505 TTCATAGAGGGTGACATCAACTCGGTCAAA
129 CTCATAGAGGGTGACATCAACTCGGTCAAA
*
51535 ATTTTAAA
1 ACTTTAAA
51543 TGTTTACTAG
Statistics
Matches: 154, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
158 54 0.35
159 3 0.02
160 97 0.63
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (158 bp):
ACTTTAAAGAGTAAAATTTATGATGTTTTAAGTTTGGATCTCATTATGCACATATATTTTCTCTC
AAAATAATATTTACCTATTTGTAAAAATAAAAGAGTTTTAGTAAATTCACAATTGAATTGCGACT
CATAGAGGGTGACATCAACTCGGTCAAA
Found at i:51616 original size:15 final size:16
Alignment explanation
Indices: 51580--51615 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
51570 ATGTGGGTGA
51580 AAAAATATTTTATGTT
1 AAAAATATTTTATGTT
*
51596 AAAAATATTTTATTTT
1 AAAAATATTTTATGTT
51612 AAAA
1 AAAA
51616 TTTATTCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
AAAAATATTTTATGTT
Found at i:52030 original size:97 final size:97
Alignment explanation
Indices: 51896--52110 Score: 285
Period size: 100 Copynumber: 2.2 Consensus size: 97
51886 AACTAAAAAA
* * *
51896 ATAAATTATTTGTATAGAATTAGACATATTGAAAAG-TTGTGTT-TTTTATTAGTTTTGATGGAG
1 ATAAATTATTAG-ATAGAATTAGACATATTGAAAAGTTTATGTTATTTTATTAGTTTTAATGGAG
51959 TCTTAAATAATTAAT-TTTTGTAATTAATTGTAAT
65 TCTTAAATAATT--TCTTTTGTAATTAATTGTAAT
* *
51993 ATAAATTATTAGATAGAATTAGA-ACTATTTGAAAAGTTTTTATTTTATTTTATTAGTTTTAATT
1 ATAAATTATTAGATAGAATTAGACA-TA-TTGAAAAG--TTTATGTTATTTTATTAGTTTTAATG
52057 GAGTCTTAAATAATTTCTTTTGTAATTAATTGTAAT
62 GAGTCTTAAATAATTTCTTTTGTAATTAATTGTAAT
*
52093 ATAAATTATTACATAGAA
1 ATAAATTATTAGATAGAA
52111 CTAGGCTTTC
Statistics
Matches: 105, Mismatches: 6, Indels: 11
0.86 0.05 0.09
Matches are distributed among these distances:
95 1 0.01
96 13 0.12
97 19 0.18
99 1 0.01
100 41 0.39
101 30 0.29
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.48
Consensus pattern (97 bp):
ATAAATTATTAGATAGAATTAGACATATTGAAAAGTTTATGTTATTTTATTAGTTTTAATGGAGT
CTTAAATAATTTCTTTTGTAATTAATTGTAAT
Found at i:58243 original size:21 final size:22
Alignment explanation
Indices: 58204--58244 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
58194 ACCGACTGAA
58204 TCGATCTAATTCGATTAATTAG
1 TCGATCTAATTCGATTAATTAG
58226 TCGAT-TAATT-GATCTAATT
1 TCGATCTAATTCGAT-TAATT
58245 CGGTCGGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 10 0.56
22 5 0.28
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (22 bp):
TCGATCTAATTCGATTAATTAG
Found at i:67560 original size:21 final size:21
Alignment explanation
Indices: 67517--67587 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
67507 GAATTATGGG
* * **
67517 TTGTATCGATAGTACCTATAC
1 TTGTATCGATAGAACTTCCAC
67538 TTGTATCGATAGAACTTCCAC
1 TTGTATCGATAGAACTTCCAC
* *
67559 TTTTATCGGTAGAACTTCCAC
1 TTGTATCGATAGAACTTCCAC
*
67580 TTCTATCG
1 TTGTATCG
67588 GTAGGAAACT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (21 bp):
TTGTATCGATAGAACTTCCAC
Found at i:67588 original size:21 final size:21
Alignment explanation
Indices: 67536--67591 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
67526 TAGTACCTAT
* *
67536 ACTTGTATCGATAGAACTTCC
1 ACTTCTATCGGTAGAACTTCC
*
67557 ACTTTTATCGGTAGAACTTCC
1 ACTTCTATCGGTAGAACTTCC
67578 ACTTCTATCGGTAG
1 ACTTCTATCGGTAG
67592 GAAACTGCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (21 bp):
ACTTCTATCGGTAGAACTTCC
Found at i:67946 original size:6 final size:6
Alignment explanation
Indices: 67937--68043 Score: 78
Period size: 6 Copynumber: 18.0 Consensus size: 6
67927 GATTTATTTC
* ** **
67937 TAAATT TAAATT TAAATT TAAATT CATTTT TAAATT TAAATT T-GTTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* * *
67984 TAAATT TAAATT T-AGTT TAAATT TGAAA-- TAATTT TAAAACT TAAACTT
1 TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT T-AAATT TAAA-TT
*
68032 TAAAAT TAAATT
1 TAAATT TAAATT
68044 CAAAGTCCAT
Statistics
Matches: 76, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
4 2 0.03
5 8 0.11
6 54 0.71
7 12 0.16
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:67949 original size:18 final size:17
Alignment explanation
Indices: 67937--68021 Score: 91
Period size: 17 Copynumber: 4.9 Consensus size: 17
67927 GATTTATTTC
*
67937 TAAATTTAAATTTAAATT
1 TAAATTT-ATTTTAAATT
*
67955 TAAATTCATTTTTAAATT
1 TAAATTTA-TTTTAAATT
*
67973 TAAATTTGTTTTAAATT
1 TAAATTTATTTTAAATT
*
67990 TAAATTTAGTTTAAATT
1 TAAATTTATTTTAAATT
*
68007 TGAAA-TAATTTTAAA
1 T-AAATTTATTTTAAA
68022 ACTTAAACTT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
17 34 0.60
18 23 0.40
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (17 bp):
TAAATTTATTTTAAATT
Found at i:69995 original size:59 final size:58
Alignment explanation
Indices: 69882--70258 Score: 281
Period size: 59 Copynumber: 6.4 Consensus size: 58
69872 GAAGGTTCCT
*
69882 AAACTGTCCAAAAATT--ATGTTTTGACCCCT-GAAC-TTCCAAAACTTCCATTTTTTACCCCG
1 AAACT-TCCAAAAATTCCAT-TTTTG-CCCCTAAAACTTTCCAAAA-TTCCA--TTTTACCCCG
** * *
69942 AAACTTCCAAAAATTCCATTTTTGCCCCTAAAACTTTTGAAATTTACCATTTTACCCCC
1 AAACTTCCAAAAATTCCATTTTTGCCCCTAAAACTTTCCAAAATT-CCATTTTACCCCG
* * * * **
70001 AAACTTCCAAAAATTCCATTCTTGACCTTGAAACTTTCCAAAATTTTATTTTTACCCC-
1 AAACTTCCAAAAATTCCATTTTTGCCCCTAAAACTTTCCAAAATTCCA-TTTTACCCCG
* * * **
70059 TAACTTTCC-AAAATTCTATTTTTACCCCTAAAACTTTCCAAAATTCCAATTTTACCATTG
1 AAAC-TTCCAAAAATTCCATTTTTGCCCCTAAAACTTTCCAAAATTCC-ATTTTACC-CCG
* *
70119 -AATTTCCAAAAATTCCATTTTTGACCCC-AAAACTTTCCAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTG-CCCCTAAAACTTTCCAAAATTCCA-TTTT-ACCCCG
** ** *
70178 AAACTTTCC-AAAATTCCATTTTT-ATCCTTGAAC-TTCCAAAAATTCCATTTTTTACCCAG
1 AAAC-TTCCAAAAATTCCATTTTTGCCCCTAAAACTTTCC-AAAATTCCA--TTTTACCCCG
* *
70237 AAGCTTTCAAAAATTACCATTT
1 AAACTTCCAAAAATT-CCATTT
70259 ATCCCCGGAT
Statistics
Matches: 256, Mismatches: 40, Indels: 42
0.76 0.12 0.12
Matches are distributed among these distances:
58 55 0.21
59 138 0.54
60 49 0.19
61 14 0.05
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (58 bp):
AAACTTCCAAAAATTCCATTTTTGCCCCTAAAACTTTCCAAAATTCCATTTTACCCCG
Found at i:70092 original size:117 final size:118
Alignment explanation
Indices: 69882--70201 Score: 346
Period size: 117 Copynumber: 2.7 Consensus size: 118
69872 GAAGGTTCCT
* ** *
69882 AAACTGTCCAAAAATT--ATGTTTTGACCCCTGAAC-TTCCAAAACTTCCATTTTTTACCCCGAA
1 AAACT-TCCAAAAATTCCAT-TCTTGACCCCAAAACTTTCCAAAA-TTCCA-TTTTTACCCCAAA
* ** * *
69944 AC-TTCCAAAAATTCCATTTTTGCCCCTAAAACTTTTGAAATTTACC-ATTTTACCCCC
62 ACTTTCC-AAAATTCCATTTTTACCCCTAAAACTTTCCAAAATT-CCAATTTTACCACC
*** ** *
70001 AAACTTCCAAAAATTCCATTCTTGACCTTGAAACTTTCCAAAATTTTATTTTTACCCC-TAACTT
1 AAACTTCCAAAAATTCCATTCTTGACCCCAAAACTTTCCAAAATTCCATTTTTACCCCAAAACTT
* **
70065 TCCAAAATTCTATTTTTACCCCTAAAACTTTCCAAAATTCCAATTTTACCATT
66 TCCAAAATTCCATTTTTACCCCTAAAACTTTCCAAAATTCCAATTTTACCACC
* * *
70118 GAATTTCCAAAAATTCCATTTTTGACCCCAAAACTTTCCAAAATTCCATTTTTGACCCCAAAACT
1 AAACTTCCAAAAATTCCATTCTTGACCCCAAAACTTTCCAAAATTCCATTTTT-ACCCCAAAACT
70183 TTCCAAAATTCCATTTTTA
65 TTCCAAAATTCCATTTTTA
70202 TCCTTGAACT
Statistics
Matches: 168, Mismatches: 26, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
116 2 0.01
117 87 0.52
118 29 0.17
119 40 0.24
120 10 0.06
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (118 bp):
AAACTTCCAAAAATTCCATTCTTGACCCCAAAACTTTCCAAAATTCCATTTTTACCCCAAAACTT
TCCAAAATTCCATTTTTACCCCTAAAACTTTCCAAAATTCCAATTTTACCACC
Found at i:70244 original size:89 final size:87
Alignment explanation
Indices: 69913--70258 Score: 355
Period size: 89 Copynumber: 3.9 Consensus size: 87
69903 TTGACCCCTG
** *
69913 AACTTCCAAAACTTCCATTTTTTACCCCGAAACTTCCAAAAATTCCATTTTTGCCCCTAAAACTT
1 AACTTCCAAAA-TTCCA-TTTTTACCTTGAAACTTCCAAAAATTCCATTTTTGACCC-AAAACTT
** * *
69978 TTGAAATTTACCA-TTTTACCCCCA
63 TCCAAAATTACCATTTTTACCCCAA
* ** **
70002 AACTTCCAAAAATTCCATTCTTGACCTTGAAACTTTCC-AAAATTTTATTTTT-ACCCCTAACTT
1 AACTTCC-AAAATTCCATT-TTTACCTTGAAAC-TTCCAAAAATTCCATTTTTGACCCAAAACTT
*
70065 TCCAAAATT-CTATTTTTACCCCTAA
63 TCCAAAATTACCATTTTTACCCC-AA
* *
70090 AACTTTCCAAAATTCCAATTTTACCATTG-AATTTCCAAAAATTCCATTTTTGACCCCAAAACTT
1 AAC-TTCCAAAATTCCATTTTTACC-TTGAAACTTCCAAAAATTCCATTTTTGA-CCCAAAACTT
70154 TCCAAAATT-CCATTTTTGACCCCAA
63 TCCAAAATTACCATTTTT-ACCCCAA
* *
70179 AACTTTCCAAAATTCCATTTTTATCCTTG-AACTTCCAAAAATTCCATTTTTTACCCAGAAGCTT
1 AAC-TTCCAAAATTCCATTTTTA-CCTTGAAACTTCCAAAAATTCCATTTTTGACCCA-AAACTT
*
70243 TCAAAAATTACCATTT
63 TCCAAAATTACCATTT
70259 ATCCCCGGAT
Statistics
Matches: 217, Mismatches: 26, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
86 6 0.03
87 39 0.18
88 27 0.12
89 124 0.57
90 21 0.10
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (87 bp):
AACTTCCAAAATTCCATTTTTACCTTGAAACTTCCAAAAATTCCATTTTTGACCCAAAACTTTCC
AAAATTACCATTTTTACCCCAA
Found at i:70248 original size:29 final size:31
Alignment explanation
Indices: 69882--70258 Score: 278
Period size: 30 Copynumber: 12.7 Consensus size: 31
69872 GAAGGTTCCT
* *
69882 AAACTGTCCAAAAATT--ATGTTTTGACCCCT
1 AAACTTTCCAAAAATTCCAT-TTTTGACCCCA
* * * *
69912 GAAC-TTCCAAAACTTCCATTTTTTACCCCG
1 AAACTTTCCAAAAATTCCATTTTTGACCCCA
69942 AAAC-TTCCAAAAATTCCATTTTTG-CCCCTA
1 AAACTTTCCAAAAATTCCATTTTTGACCCC-A
** * *
69972 AAACTTT-TGAAATTTACCA-TTTT-ACCCCC
1 AAACTTTCCAAAAATT-CCATTTTTGACCCCA
* ***
70001 AAAC-TTCCAAAAATTCCATTCTTGACCTTG
1 AAACTTTCCAAAAATTCCATTTTTGACCCCA
**
70031 AAACTTTCC-AAAATTTTATTTTT-ACCCC-
1 AAACTTTCCAAAAATTCCATTTTTGACCCCA
* *
70059 TAACTTTCC-AAAATTCTATTTTT-ACCCCTA
1 AAACTTTCCAAAAATTCCATTTTTGACCCC-A
* ***
70089 AAACTTTCC-AAAATTCCAATTTT-ACCATT
1 AAACTTTCCAAAAATTCCATTTTTGACCCCA
*
70118 GAA-TTTCCAAAAATTCCATTTTTGACCCCA
1 AAACTTTCCAAAAATTCCATTTTTGACCCCA
70148 AAACTTTCC-AAAATTCCATTTTTGACCCCA
1 AAACTTTCCAAAAATTCCATTTTTGACCCCA
* **
70178 AAACTTTCC-AAAATTCCATTTTT-ATCCTT
1 AAACTTTCCAAAAATTCCATTTTTGACCCCA
* *
70207 GAAC-TTCCAAAAATTCCATTTTTTA-CCCA
1 AAACTTTCCAAAAATTCCATTTTTGACCCCA
*
70236 GAAGCTTT-CAAAAATTACCATTT
1 -AAACTTTCCAAAAATT-CCATTT
70259 ATCCCCGGAT
Statistics
Matches: 280, Mismatches: 47, Indels: 39
0.77 0.13 0.11
Matches are distributed among these distances:
28 40 0.14
29 65 0.23
30 151 0.54
31 24 0.09
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (31 bp):
AAACTTTCCAAAAATTCCATTTTTGACCCCA
Found at i:80580 original size:20 final size:20
Alignment explanation
Indices: 80555--80596 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
80545 AAATTTATAT
80555 GTTTGTTCATTGGATTCTTG
1 GTTTGTTCATTGGATTCTTG
80575 GTTTGTTCATTGGATTCTTG
1 GTTTGTTCATTGGATTCTTG
80595 GT
1 GT
80597 CATAATATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.10, C:0.10, G:0.26, T:0.55
Consensus pattern (20 bp):
GTTTGTTCATTGGATTCTTG
Done.