Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008056.1 Hibiscus syriacus cultivar Beakdansim tig00110551_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: 2370532
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 13
Found at i:24883 original size:21 final size:22
Alignment explanation
Indices: 24853--24893 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
24843 ACAAGTGTCG
24853 TAATTATCAA-ATAAATAAACT
1 TAATTATCAATATAAATAAACT
* *
24874 TAATTTTCAATTTAAATAAA
1 TAATTATCAATATAAATAAA
24894 TAAAATAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (22 bp):
TAATTATCAATATAAATAAACT
Found at i:36535 original size:259 final size:260
Alignment explanation
Indices: 36044--36582 Score: 770
Period size: 259 Copynumber: 2.1 Consensus size: 260
36034 TGATTAAATT
* *
36044 CTTCGGGCAAGATGTTTTCACATGATGTTTTAAAAAATGAGGAAAACAATTTTTAAAGTTTCTCA
1 CTTCGGGCAAGATGTTTTCACATGATGTTTAAAAAAATGA-GAAAACAATTTTCAAAGTTTCTCA
* * * *
36109 TTTAATATTTTCTAAAAATGAAATTTTTAAAAAGTAAGAAAACGATTTCCAAAGTTTTTTACCCA
65 TTTAATATTTTCTAAAAATGAAATCTTTAAAAAGTAAGAAAACAATTTCCAAAGTTTCTAACCCA
* *
36174 GTAAACTATTTCCAAAATTAGTAAGTCCTTCTGGCCATCAATAAATCTTTCGAGCATGATGATTA
130 GTAAACTATTTCCAAAATTAGTAAGTCATTCTGGCCATCAATAAATCTTTCAAGCATGATGATTA
* * *
36239 AATCCTTCAGGTTATCTTTCAGTCTTTCAAGCAAGATGATAAGTCCTTTAGGCCATCTATAAGA-
195 AATCCTTCAGGTCATCTTTCAGTCTTTCAAGCAAGATGATAAATCCTTTAGGCCATCTATAACAC
36303 C
260 C
36304 CTTCGGGCAAGATGTTTTCACATGAT-TTTAAAAAAATGA-AAAAGGCAATTTTCAAAGTTTCTC
1 CTTCGGGCAAGATGTTTTCACATGATGTTTAAAAAAATGAGAAAA--CAATTTTCAAAGTTTCTC
* * *
36367 ATTTAATATTTT-TAGAAAATGAAATCTTTGAAAAGTAAGAAAATAATTTCCATAGTTTCTAACC
64 ATTTAATATTTTCTA-AAAATGAAATCTTTAAAAAGTAAGAAAACAATTTCCAAAGTTTCTAACC
* * *
36431 CAGTAAACTTTTTCCAAAATTGGTAAGTCATTC-GGTCCATCAATAAGTCTTTCAAGCATGATGA
128 CAGTAAACTATTTCCAAAATTAGTAAGTCATTCTGG-CCATCAATAAATCTTTCAAGCATGATGA
* * *
36495 TTAAATCCTTCGGGTCAT-TTGTCAGTCTTTCGAA-CAAGATGATAAATTCTTTGGGCCATCTAT
192 TTAAATCCTTCAGGTCATCTT-TCAGTCTTTC-AAGCAAGATGATAAATCCTTTAGGCCATCTAT
36558 AACACC
255 AACACC
*
36564 CTT-GGGCAAGATGCTTTCA
1 CTTCGGGCAAGATGTTTTCA
36583 TATGGACCAT
Statistics
Matches: 251, Mismatches: 21, Indels: 15
0.87 0.07 0.05
Matches are distributed among these distances:
257 4 0.02
258 6 0.02
259 209 0.83
260 32 0.13
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (260 bp):
CTTCGGGCAAGATGTTTTCACATGATGTTTAAAAAAATGAGAAAACAATTTTCAAAGTTTCTCAT
TTAATATTTTCTAAAAATGAAATCTTTAAAAAGTAAGAAAACAATTTCCAAAGTTTCTAACCCAG
TAAACTATTTCCAAAATTAGTAAGTCATTCTGGCCATCAATAAATCTTTCAAGCATGATGATTAA
ATCCTTCAGGTCATCTTTCAGTCTTTCAAGCAAGATGATAAATCCTTTAGGCCATCTATAACACC
Found at i:36975 original size:20 final size:20
Alignment explanation
Indices: 36950--37016 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
36940 GCCCACACAG
*
36950 CAGCACCAAATTCGCGGCAA
1 CAGCACCAAATTCGCAGCAA
* *
36970 CAGCACCAAATCCGTAGCAA
1 CAGCACCAAATTCGCAGCAA
* *
36990 CA-CTACCAAATTAGCAACAA
1 CAGC-ACCAAATTCGCAGCAA
37010 CAGCACC
1 CAGCACC
37017 TCTAGCACGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 1 0.03
20 36 0.95
21 1 0.03
ACGTcount: A:0.40, C:0.36, G:0.13, T:0.10
Consensus pattern (20 bp):
CAGCACCAAATTCGCAGCAA
Found at i:40638 original size:7 final size:7
Alignment explanation
Indices: 40626--40655 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
40616 ACAAACTTAC
40626 AATTATA
1 AATTATA
40633 AATTATA
1 AATTATA
40640 AATTATA
1 AATTATA
*
40647 AATTTTA
1 AATTATA
40654 AA
1 AA
40656 GTAATTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AATTATA
Found at i:49065 original size:31 final size:31
Alignment explanation
Indices: 48983--49066 Score: 107
Period size: 30 Copynumber: 2.7 Consensus size: 31
48973 GGGCTAGATG
* *
48983 AAAACTGATCGATTTGATATTGATTCGACCC
1 AAAATTGATCGATTTGATATTGATTAGACCC
* * * *
49014 -AAATCGAACGGTATGATATTGATTAGACCC
1 AAAATTGATCGATTTGATATTGATTAGACCC
49044 AAAATTGATCGATTTGATATTGA
1 AAAATTGATCGATTTGATATTGA
49067 CTCGACTAGA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
30 24 0.57
31 18 0.43
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (31 bp):
AAAATTGATCGATTTGATATTGATTAGACCC
Found at i:49709 original size:19 final size:20
Alignment explanation
Indices: 49685--49729 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
49675 AATGCGGTCT
*
49685 GATGCGATCCGATG-CGGCC
1 GATGCGATCCGATGTAGGCC
*
49704 GATGCGATCTGATGTAGGCC
1 GATGCGATCCGATGTAGGCC
49724 GATGCG
1 GATGCG
49730 TTTAGTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.18, C:0.24, G:0.38, T:0.20
Consensus pattern (20 bp):
GATGCGATCCGATGTAGGCC
Found at i:50691 original size:29 final size:30
Alignment explanation
Indices: 50635--50703 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
50625 ATTTTAATTC
*
50635 AAACTCCAAAATATTGAAAGATGATATTAT
1 AAACTCAAAAATATTGAAAGATGATATTAT
*
50665 AAACTCAAAAATATTGAAA-ATGGTATTAT
1 AAACTCAAAAATATTGAAAGATGATATTAT
50694 AAACTTCAAA
1 AAAC-TCAAA
50704 GTTAATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 13 0.36
30 23 0.64
ACGTcount: A:0.52, C:0.10, G:0.09, T:0.29
Consensus pattern (30 bp):
AAACTCAAAAATATTGAAAGATGATATTAT
Found at i:54048 original size:27 final size:27
Alignment explanation
Indices: 54015--54085 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
54005 CAGCCAATAG
*
54015 AACCAAACCAGTCAGCAACACTGAACC
1 AACCAAACCAGCCAGCAACACTGAACC
* * *
54042 AATCAAACTAGCCAACAACACTGAACC
1 AACCAAACCAGCCAGCAACACTGAACC
*
54069 AACCGAACCAGCCAGCA
1 AACCAAACCAGCCAGCA
54086 TAACCAGTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.45, C:0.37, G:0.11, T:0.07
Consensus pattern (27 bp):
AACCAAACCAGCCAGCAACACTGAACC
Found at i:55366 original size:2 final size:2
Alignment explanation
Indices: 55312--55351 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
55302 GCAACATTAC
55312 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55352 TATGGTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59274 original size:12 final size:12
Alignment explanation
Indices: 59257--59326 Score: 65
Period size: 12 Copynumber: 5.8 Consensus size: 12
59247 GGGAAATAGA
*
59257 AAAAAAACAAGG
1 AAAAAAAGAAGG
59269 -AAAAAAGAAGAG
1 AAAAAAAGAAG-G
*
59281 AAAAAAATAAGG
1 AAAAAAAGAAGG
59293 AAAAAAAGAA-G
1 AAAAAAAGAAGG
*
59304 AAAAAGAA-AAAG
1 AAAAA-AAGAAGG
59316 AAAAAAGAGAA
1 AAAAAA-AGAA
59327 CAGATTAAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
11 18 0.37
12 20 0.41
13 11 0.22
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.01
Consensus pattern (12 bp):
AAAAAAAGAAGG
Found at i:59282 original size:25 final size:24
Alignment explanation
Indices: 59254--59323 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 24
59244 AGAGGGAAAT
59254 AGAAAAAAAACAAGGAAAAAAGAAG
1 AGAAAAAAAA-AAGGAAAAAAGAAG
*
59279 AGAAAAAAATAAGGAAAAAAAGAAG
1 AGAAAAAAAAAAGG-AAAAAAGAAG
*
59304 A-AAAAGAAAAA-GAAAAAAGA
1 AGAAAAAAAAAAGGAAAAAAGA
59324 GAACAGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 8 0.20
23 1 0.02
24 12 0.29
25 20 0.49
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.01
Consensus pattern (24 bp):
AGAAAAAAAAAAGGAAAAAAGAAG
Found at i:59284 original size:24 final size:22
Alignment explanation
Indices: 59254--59323 Score: 88
Period size: 24 Copynumber: 3.0 Consensus size: 22
59244 AGAGGGAAAT
59254 AGAAAAAAAACAAGGAAAAAAGA
1 AGAAAAAAAA-AAGGAAAAAAGA
59277 AGAGAAAAAAATAAGGAAAAAAAGA
1 AGA-AAAAAAA-AAGG-AAAAAAGA
59302 AGAAAAAGAAAAA-GAAAAAAGA
1 AGAAAAA-AAAAAGGAAAAAAGA
59324 GAACAGATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
22 8 0.19
23 4 0.09
24 17 0.40
25 14 0.33
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.01
Consensus pattern (22 bp):
AGAAAAAAAAAAGGAAAAAAGA
Found at i:59326 original size:24 final size:23
Alignment explanation
Indices: 59254--59326 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 23
59244 AGAGGGAAAT
59254 AGAAAAAAAACAAGGAAAAAAGA-A
1 AGAAAAAAAA-AA-GAAAAAAGAGA
*
59278 GAGAAAAAAATAAGGAAAAAA-AGA
1 -AGAAAAAAA-AAAGAAAAAAGAGA
59302 AGAAAAAGAAAAAGAAAAAAGAGA
1 AGAAAAA-AAAAAGAAAAAAGAGA
59326 A
1 A
59327 CAGATTAAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
23 17 0.40
24 14 0.33
25 10 0.24
26 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (23 bp):
AGAAAAAAAAAAGAAAAAAGAGA
Found at i:62591 original size:12 final size:12
Alignment explanation
Indices: 62574--62603 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
62564 GATACCATCA
62574 AATTTCAGACAT
1 AATTTCAGACAT
*
62586 AATTTCAGACCT
1 AATTTCAGACAT
62598 AATTTC
1 AATTTC
62604 GGTATCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (12 bp):
AATTTCAGACAT
Found at i:63435 original size:18 final size:18
Alignment explanation
Indices: 63412--63446 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
63402 AGGGTTCTAC
63412 GTGGTCCTTCGAGACATA
1 GTGGTCCTTCGAGACATA
*
63430 GTGGTCCTTCGGGACAT
1 GTGGTCCTTCGAGACAT
63447 TTCATAGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (18 bp):
GTGGTCCTTCGAGACATA
Found at i:64647 original size:36 final size:37
Alignment explanation
Indices: 64600--64687 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 37
64590 CAAAGTTTCG
* * *
64600 TCTCATTTGAGACAGTTTTTCTT-GAAACAAAATTGA
1 TCTCACTTGAGACAGTTTTTCTTAAAAACAAAATTCA
** *
64636 TCTCACTTGAGATTG-TTTTCTTAAAAACAAATTTCA
1 TCTCACTTGAGACAGTTTTTCTTAAAAACAAAATTCA
64672 TCT-ATCTTGAGACAGT
1 TCTCA-CTTGAGACAGT
64688 ATTCCCTCGA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
35 8 0.20
36 33 0.80
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (37 bp):
TCTCACTTGAGACAGTTTTTCTTAAAAACAAAATTCA
Found at i:64700 original size:73 final size:74
Alignment explanation
Indices: 64569--64707 Score: 169
Period size: 73 Copynumber: 1.9 Consensus size: 74
64559 TCTGTCACCT
** * ** *
64569 TTGAGATTGTTTCTCTCGAAACAAAGTTTCGTCTCATTTGAGACAGTTTTTCTTGAAACA-AAAT
1 TTGAGATTGTTTCTCTAAAAACAAAGTTTCATCTCATTTGAGACAGTTTCCCTCGAAACATAAAT
64633 TGATCTCAC
66 TGATCTCAC
64642 TTGAGATTGTTT-TCTTAAAAACAAA-TTTCATCT-ATCTTGAGACAGTATTCCCTCGAAACATA
1 TTGAGATTGTTTCTC-TAAAAACAAAGTTTCATCTCAT-TTGAGACAGT-TTCCCTCGAAACATA
64704 AATT
63 AATT
64708 TTGAAATTGT
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
71 2 0.04
72 19 0.34
73 30 0.54
74 5 0.09
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (74 bp):
TTGAGATTGTTTCTCTAAAAACAAAGTTTCATCTCATTTGAGACAGTTTCCCTCGAAACATAAAT
TGATCTCAC
Found at i:64739 original size:102 final size:102
Alignment explanation
Indices: 64620--64837 Score: 330
Period size: 102 Copynumber: 2.1 Consensus size: 102
64610 GACAGTTTTT
* * *
64620 CTTGAAACAAAATTGATCTCACTTGAGATTGTTTTCTTAAAAACAAATTTCATCTATCTTGAGAC
1 CTTGAAACAAAATTGATCTCACTTGAGATTATTTTCCTAAAAACAAATTTCATCTAGCTTGAGAC
*
64685 AGTATTCCCTCGAAACAT-AAATTTTGAAATTGTTTCA
66 AATATTCCCTCGAAAC-TCAAATTTTGAAATTGTTTCA
* * *
64722 CTTGAAACAAAATTGATCTCACTTGAGATTATTTTCCTAAAAGCAAATTTCATCTCGCTTGAGAT
1 CTTGAAACAAAATTGATCTCACTTGAGATTATTTTCCTAAAAACAAATTTCATCTAGCTTGAGAC
* *
64787 AATTTTCCCTTGAAACTCAAATTTTGAAATTGTTTCA
66 AATATTCCCTCGAAACTCAAATTTTGAAATTGTTTCA
*
64824 CTCGAAACAAAATT
1 CTTGAAACAAAATT
64838 TTATTTCACC
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
101 1 0.01
102 104 0.99
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (102 bp):
CTTGAAACAAAATTGATCTCACTTGAGATTATTTTCCTAAAAACAAATTTCATCTAGCTTGAGAC
AATATTCCCTCGAAACTCAAATTTTGAAATTGTTTCA
Found at i:65607 original size:104 final size:103
Alignment explanation
Indices: 65463--65831 Score: 445
Period size: 104 Copynumber: 3.6 Consensus size: 103
65453 GAGCATTATT
* ** * * *
65463 ATCTTCAACACTATTTTATCTCTAGATTGAC-CTGATTTCCTCAACGAGAAGGAACAACATCATA
1 ATCTTCAACACCAGATTATCTCCAGATTGACTC-GACTTCCTCAACGAGAAGGAACAACGTCATA
* * *
65527 TGAAAGCGACCAAAACTCTTTAGAAAGGATGAAAAGTGTC
65 TGAAAGTGACCAAGACTCTTTA-AAAGGATGAACAGTGTC
*
65567 ATCTTCAACACCAGATTATCTCCAGATTGACTCGACTTCCTCAACAAGAAGGAACAACGTCATAT
1 ATCTTCAACACCAGATTATCTCCAGATTGACTCGACTTCCTCAACGAGAAGGAACAACGTCATAT
* * * * *
65632 GAAAATGGCCAAGACTCTTCAACATGGATGAGCAGTGTC
66 GAAAGTGACCAAGACTCTTTAA-AAGGATGAACAGTGTC
* * * * *
65671 ATCTTCAACACTAGATTATCTCCATATTGACTTGACATCCTCAACGAGAAGGAACAACGTCATAC
1 ATCTTCAACACCAGATTATCTCCAGATTGACTCGACTTCCTCAACGAGAAGGAACAACGTCATAT
*
65736 GAAAGTGACCAAGACT-TTTCAAAATGGATGATCAGTGTC
66 GAAAGTGACCAAGACTCTTT-AAAA-GGATGAACAGTGTC
* * * * *
65775 GTCTTCAACACCATATTATCTTCAGATTGACTCGATTTCCTCAACTAGAAGGAACAA
1 ATCTTCAACACCAGATTATCTCCAGATTGACTCGACTTCCTCAACGAGAAGGAACAA
65832 TGCCATCTTC
Statistics
Matches: 226, Mismatches: 35, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
103 4 0.02
104 221 0.98
105 1 0.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.26
Consensus pattern (103 bp):
ATCTTCAACACCAGATTATCTCCAGATTGACTCGACTTCCTCAACGAGAAGGAACAACGTCATAT
GAAAGTGACCAAGACTCTTTAAAAGGATGAACAGTGTC
Found at i:65795 original size:208 final size:208
Alignment explanation
Indices: 65437--65831 Score: 551
Period size: 208 Copynumber: 1.9 Consensus size: 208
65427 AGCAAACATA
* * * ** * **
65437 ACTCTTCGACATGAATGAGCATTATTATCTTCAACACTATTTTATCTCTAGATTGACCTGATTTC
1 ACTCTTCAACATGAATGAGCAGTATCATCTTCAACACTAGATTATCTCCAGATTGACCTGACATC
*
65502 CTCAACGAGAAGGAACAACATCATATGAAAGCGACCAAAACTCTTTAGAAAGGATGAAAAGTGTC
66 CTCAACGAGAAGGAACAACATCATACGAAAGCGACCAAAACTCTTTAGAAAGGATGAAAAGTGTC
65567 ATCTTCAACACCAGATTATCTCCAGATTGACTCGACTTCCTCAACAAGAAGGAACAACGTCATAT
131 ATCTTCAACACCAGATTATCTCCAGATTGACTCGACTTCCTCAACAAGAAGGAACAACGTCATAT
65632 GAAAATGGCCAAG
196 GAAAATGGCCAAG
* * * *
65645 ACTCTTCAACATGGATGAGCAGTGTCATCTTCAACACTAGATTATCTCCATATTGACTTGACATC
1 ACTCTTCAACATGAATGAGCAGTATCATCTTCAACACTAGATTATCTCCAGATTGACCTGACATC
* * * **
65710 CTCAACGAGAAGGAACAACGTCATACGAAAGTGACCAAGACT-TTTCA-AAATGGATGATCAGTG
66 CTCAACGAGAAGGAACAACATCATACGAAAGCGACCAAAACTCTTT-AGAAA-GGATGAAAAGTG
* * * * *
65773 TCGTCTTCAACACCATATTATCTTCAGATTGACTCGATTTCCTCAACTAGAAGGAACAA
129 TCATCTTCAACACCAGATTATCTCCAGATTGACTCGACTTCCTCAACAAGAAGGAACAA
65832 TGCCATCTTC
Statistics
Matches: 162, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
207 6 0.04
208 156 0.96
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (208 bp):
ACTCTTCAACATGAATGAGCAGTATCATCTTCAACACTAGATTATCTCCAGATTGACCTGACATC
CTCAACGAGAAGGAACAACATCATACGAAAGCGACCAAAACTCTTTAGAAAGGATGAAAAGTGTC
ATCTTCAACACCAGATTATCTCCAGATTGACTCGACTTCCTCAACAAGAAGGAACAACGTCATAT
GAAAATGGCCAAG
Found at i:66044 original size:3 final size:3
Alignment explanation
Indices: 66036--66083 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
66026 GGTTTAATTT
66036 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
66084 CAGACCAAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:67628 original size:2 final size:2
Alignment explanation
Indices: 67621--67655 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
67611 TACGCACCGA
67621 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
67656 CTCATAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:70528 original size:30 final size:30
Alignment explanation
Indices: 70494--70553 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
70484 TTCTTGAAAC
*
70494 ATTTTAGCCCGTAATGTTTCAATTTAAAGT
1 ATTTTAGCCCGTAATATTTCAATTTAAAGT
*
70524 ATTTTAGCCCGTAATATTTCAATTTGAAGT
1 ATTTTAGCCCGTAATATTTCAATTTAAAGT
70554 CATAATAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (30 bp):
ATTTTAGCCCGTAATATTTCAATTTAAAGT
Found at i:78784 original size:57 final size:56
Alignment explanation
Indices: 78637--78797 Score: 168
Period size: 57 Copynumber: 2.9 Consensus size: 56
78627 CCTACAGGCT
* * *
78637 TAAGGTAAGTCCTTATGAACCTAAGGCA--CCCTTAAGTTGGCTCATACACTTCGGA
1 TAAGGTAAGTCCTTATGAA-CTAAGGTATTCCCTTAGGTTGGCTCCTACACTTCGGA
* * *
78692 TAAGGTAAGTCCTTATGAACTCAATGTGTTCCCTTAGGTTGGCTCCTA-ATCTTCGGC
1 TAAGGTAAGTCCTTATGAACT-AAGGTATTCCCTTAGGTTGGCTCCTACA-CTTCGGA
* * *
78749 T-AGGATAAGTCCTTATGAATCTAAGGTATTTCCTTAGGTAGGATCCTAC
1 TAAGG-TAAGTCCTTATGAA-CTAAGGTATTCCCTTAGGTTGGCTCCTAC
78798 GTTCAATAGA
Statistics
Matches: 88, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
54 2 0.02
55 22 0.25
56 4 0.05
57 58 0.66
58 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (56 bp):
TAAGGTAAGTCCTTATGAACTAAGGTATTCCCTTAGGTTGGCTCCTACACTTCGGA
Found at i:80320 original size:26 final size:26
Alignment explanation
Indices: 80285--80353 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
80275 ACAAGCTAGA
*
80285 AGGAG-TGGCGAGCTAGGTGTTCGAG
1 AGGAGCTGGCGAGCTAGGCGTTCGAG
*
80310 AGGAGCTGGCGAGCTAGGCGTTCGAT
1 AGGAGCTGGCGAGCTAGGCGTTCGAG
* *
80336 AGGAGCTAGCGACCTAGG
1 AGGAGCTGGCGAGCTAGG
80354 GCAGTTCGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 5 0.13
26 34 0.87
ACGTcount: A:0.22, C:0.17, G:0.43, T:0.17
Consensus pattern (26 bp):
AGGAGCTGGCGAGCTAGGCGTTCGAG
Found at i:80597 original size:21 final size:20
Alignment explanation
Indices: 80564--80602 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
80554 TAATGGATGA
80564 TTGTTTTTTTATGATGTTGT
1 TTGTTTTTTTATGATGTTGT
80584 TTGTTTTGTTTATGATGTT
1 TTGTTTT-TTTATGATGTT
80603 TAATGGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.10, C:0.00, G:0.21, T:0.69
Consensus pattern (20 bp):
TTGTTTTTTTATGATGTTGT
Found at i:83460 original size:30 final size:31
Alignment explanation
Indices: 83384--83461 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
83374 AACCATTCAC
* * *
83384 AACTTTTCTAAAATTACCGAATTTGTCTTCT
1 AACTTTTCAAAAATTACCGAATTGGTCTCCT
**
83415 AACTTTTCAAAAATTATTGAATTGGTCTCCT
1 AACTTTTCAAAAATTACCGAATTGGTCTCCT
83446 AACTTTTC-AAAATTAC
1 AACTTTTCAAAAATTAC
83462 AAAATAATCC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 7 0.17
31 34 0.83
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (31 bp):
AACTTTTCAAAAATTACCGAATTGGTCTCCT
Found at i:84471 original size:29 final size:30
Alignment explanation
Indices: 84419--84476 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
84409 TTTGGTCCCT
* *
84419 AAACTTTTCAAAGTTTATACTTTGATCACC
1 AAACTTTACAAAGTTTATAATTTGATCACC
*
84449 AAACTTTACAAA-TTTATAATTTGGTCAC
1 AAACTTTACAAAGTTTATAATTTGATCAC
84477 TAACTAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (30 bp):
AAACTTTACAAAGTTTATAATTTGATCACC
Found at i:84710 original size:24 final size:24
Alignment explanation
Indices: 84682--84739 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
84672 AACGCCAAAT
* *
84682 AAACATGTTCATGAATATATAAAC
1 AAACATGTTCACGAACATATAAAC
* *
84706 AAACATGATCGCGAACATATAAAC
1 AAACATGTTCACGAACATATAAAC
* *
84730 GAATATGTTC
1 AAACATGTTC
84740 GCAAATGCTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.26
Consensus pattern (24 bp):
AAACATGTTCACGAACATATAAAC
Found at i:93405 original size:20 final size:23
Alignment explanation
Indices: 93360--93408 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
93350 GCATGGGTAG
93360 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCACATGTT-AAGAA
93384 TGCATCGATGCAC-TG-T-AGAA
1 TGCATCGATGCACATGTTAAGAA
93404 TGCAT
1 TGCAT
93409 AACTTCAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 9 0.36
22 1 0.04
23 2 0.08
24 13 0.52
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (23 bp):
TGCATCGATGCACATGTTAAGAA
Found at i:94400 original size:2 final size:2
Alignment explanation
Indices: 94387--94416 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
94377 GAATACAATG
94387 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
94417 GTTTTGTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:94448 original size:12 final size:12
Alignment explanation
Indices: 94387--94450 Score: 55
Period size: 10 Copynumber: 5.5 Consensus size: 12
94377 GAATACAATG
94387 TATATGATAT-A
1 TATATGATATGA
94398 TATAT-ATAT-A
1 TATATGATATGA
*
94408 TATAT-ATATGT
1 TATATGATATGA
* *
94419 TTTGTGATATGAA
1 TATATGATATG-A
94432 TTATATGATATGA
1 -TATATGATATGA
94445 TATATG
1 TATATG
94451 TGTGTGTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
10 14 0.33
11 8 0.19
12 11 0.26
13 1 0.02
14 9 0.21
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (12 bp):
TATATGATATGA
Found at i:94475 original size:32 final size:34
Alignment explanation
Indices: 94400--94480 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 34
94390 ATGATATATA
* *
94400 TATATATATAT-ATATATGTTTTGTGATATGAAT
1 TATATGTATATGATATATGTTGTGTGATATGAAT
*
94433 TATATG-ATATGATATATG-TGTGTGTTAATG-AT
1 TATATGTATATGATATATGTTGTGTGAT-ATGAAT
*
94465 TAT-TGTATATGTTATA
1 TATATGTATATGATATA
94481 AGATATATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 2 0.05
32 24 0.59
33 15 0.37
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (34 bp):
TATATGTATATGATATATGTTGTGTGATATGAAT
Found at i:96145 original size:44 final size:44
Alignment explanation
Indices: 96063--96165 Score: 136
Period size: 44 Copynumber: 2.4 Consensus size: 44
96053 TTGTGCAACA
* *
96063 TGCATCGATACACTA-AAGAGTGTACCGATGCATCCCTTGAATG
1 TGCATCGATACACCATAAGAGTGCACCGATGCATCCCTTGAATG
* *
96106 TGCATCGATACACCATAAGGGTGCACCGATGCATTCCTTGAATG
1 TGCATCGATACACCATAAGAGTGCACCGATGCATCCCTTGAATG
* * *
96150 TGAATCAATGCACCAT
1 TGCATCGATACACCAT
96166 GCTATGCATC
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
43 14 0.27
44 38 0.73
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (44 bp):
TGCATCGATACACCATAAGAGTGCACCGATGCATCCCTTGAATG
Found at i:98511 original size:13 final size:12
Alignment explanation
Indices: 98482--98509 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
98472 AGGGGGAGTA
98482 ATTTCAAAAATG
1 ATTTCAAAAATG
98494 ATTTCAAAAATG
1 ATTTCAAAAATG
98506 ATTT
1 ATTT
98510 TCCAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (12 bp):
ATTTCAAAAATG
Found at i:98960 original size:19 final size:19
Alignment explanation
Indices: 98936--99000 Score: 103
Period size: 19 Copynumber: 3.4 Consensus size: 19
98926 CATTTTGTGT
*
98936 ATCGATGCACAGACCAGGC
1 ATCGATGCACAGACCATGC
* *
98955 ATCGATGCACAAACCATGA
1 ATCGATGCACAGACCATGC
98974 ATCGATGCACAGACCATGC
1 ATCGATGCACAGACCATGC
98993 ATCGATGC
1 ATCGATGC
99001 TCTCCTGGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.34, C:0.29, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGATGCACAGACCATGC
Found at i:101620 original size:2 final size:2
Alignment explanation
Indices: 101613--101668 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
101603 CAACAAAGAA
101613 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
101655 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
101669 CTGAAACTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102340 original size:15 final size:16
Alignment explanation
Indices: 102296--102345 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
102286 TGTTACTTTG
*
102296 AAATCAACCAGAATCGA
1 AAATCAACCCGAA-CGA
*
102313 AAAT-AATCCGAAC-A
1 AAATCAACCCGAACGA
102327 AAATCAACCCGAACCGA
1 AAATCAACCCGAA-CGA
102344 AA
1 AA
102346 GCAATCCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
14 5 0.19
15 8 0.30
16 7 0.26
17 7 0.26
ACGTcount: A:0.54, C:0.26, G:0.10, T:0.10
Consensus pattern (16 bp):
AAATCAACCCGAACGA
Found at i:104841 original size:14 final size:14
Alignment explanation
Indices: 104824--104851 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
104814 ATATATATAT
104824 ATATATATAACTGC
1 ATATATATAACTGC
104838 ATATATATAACTGC
1 ATATATATAACTGC
104852 TTTCAGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
ATATATATAACTGC
Found at i:108881 original size:37 final size:36
Alignment explanation
Indices: 108806--108881 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
108796 TTTTTATATT
108806 TTTAATTTTGTAAAAAAATTATATAAATATTATAAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATAAA
*
108842 TTTAACTTTT-TAAAGAAAA-TATATAAATATTTTACAA
1 TTTAA-TTTTGTAAA-AAAATTATATAAATATTATA-AA
108879 TTT
1 TTT
108882 GTAATATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 23 0.64
37 13 0.36
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATAAA
Found at i:109044 original size:18 final size:19
Alignment explanation
Indices: 109021--109064 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
109011 CCAGTAATCC
*
109021 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
109039 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
109059 TATTCC
1 TATTCC
109065 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:109052 original size:20 final size:20
Alignment explanation
Indices: 109027--109064 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
109017 ATCCTATTCC
*
109027 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
109047 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
109065 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:109262 original size:24 final size:25
Alignment explanation
Indices: 109226--109276 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
109216 AAGAATAAAA
**
109226 ATATTTTTCATTT-TAATTTTAGAT
1 ATATTTTAAATTTATAATTTTAGAT
* *
109250 ATATTTTAAATTTATATTTTTATAT
1 ATATTTTAAATTTATAATTTTAGAT
109275 AT
1 AT
109277 TGTAATTGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (25 bp):
ATATTTTAAATTTATAATTTTAGAT
Found at i:110111 original size:10 final size:10
Alignment explanation
Indices: 110071--110105 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
110061 TTCATCACAC
110071 CAAATTCTCT
1 CAAATTCTCT
* *
110081 TAATTTCTCT
1 CAAATTCTCT
110091 CAAATTCTCT
1 CAAATTCTCT
110101 CAAAT
1 CAAAT
110106 ATTCTCTCTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.31, C:0.26, G:0.00, T:0.43
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:110188 original size:17 final size:18
Alignment explanation
Indices: 110153--110193 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
110143 ATATTATGTA
*
110153 TTTAATTTATTTAATTAT
1 TTTACTTTATTTAATTAT
110171 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAATTAT
110188 TTTACT
1 TTTACT
110194 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTACTTTATTTAATTAT
Found at i:112218 original size:3 final size:3
Alignment explanation
Indices: 112205--112260 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
112195 ACCTGCTCAG
* * * * *
112205 GAC GGC GAC GAC GAC GAC GAT GAC AAC GAC GAC GAC AAC GAC GAC GAT
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
112253 GAC GAC GA
1 GAC GAC GA
112261 TGATGATGAC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.36, C:0.29, G:0.32, T:0.04
Consensus pattern (3 bp):
GAC
Found at i:112233 original size:15 final size:15
Alignment explanation
Indices: 112215--112271 Score: 66
Period size: 15 Copynumber: 4.0 Consensus size: 15
112205 GACGGCGACG
112215 ACGACGACGATGACA
1 ACGACGACGATGACA
112230 ACGACGAC---GACA
1 ACGACGACGATGACA
*
112242 ACGACGACGATGACG
1 ACGACGACGATGACA
* *
112257 ACGATGATGATGACA
1 ACGACGACGATGACA
112272 GCGAGGAGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
12 12 0.34
15 23 0.66
ACGTcount: A:0.39, C:0.25, G:0.28, T:0.09
Consensus pattern (15 bp):
ACGACGACGATGACA
Found at i:112453 original size:26 final size:24
Alignment explanation
Indices: 112383--112454 Score: 69
Period size: 26 Copynumber: 3.0 Consensus size: 24
112373 TTATATTTGT
*
112383 ATTTACTTTATTTTGTTTAATTATA
1 ATTTACTTTATTTTGTTAAATT-TA
*
112408 ATTT--TTTATTGTT-TTGAATTTA
1 ATTTACTTTATT-TTGTTAAATTTA
112430 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
112455 GTTGGACTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
22 4 0.10
23 12 0.31
24 4 0.10
25 6 0.15
26 13 0.33
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:116184 original size:41 final size:41
Alignment explanation
Indices: 116139--116238 Score: 164
Period size: 41 Copynumber: 2.4 Consensus size: 41
116129 AATATAATTC
* *
116139 ACCCCTACGTGGCGTATAGTGCGCCCCCTGATCCGCGCTAT
1 ACCCCTACGTGGCGTATAGCGCACCCCCTGATCCGCGCTAT
* *
116180 ACCCCTACGTGACGTATAGCGCACCCCCTGATCCGTGCTAT
1 ACCCCTACGTGGCGTATAGCGCACCCCCTGATCCGCGCTAT
116221 ACCCCTACGTGGCGTATA
1 ACCCCTACGTGGCGTATA
116239 ACGCGGATCA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.18, C:0.38, G:0.22, T:0.22
Consensus pattern (41 bp):
ACCCCTACGTGGCGTATAGCGCACCCCCTGATCCGCGCTAT
Found at i:117116 original size:21 final size:21
Alignment explanation
Indices: 117091--117133 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
117081 TCATTTTTCT
117091 TTTATATTTTGCTTATGCTAC
1 TTTATATTTTGCTTATGCTAC
117112 TTTATATTTTGCTTATGCTAC
1 TTTATATTTTGCTTATGCTAC
117133 T
1 T
117134 GACATGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.09, T:0.58
Consensus pattern (21 bp):
TTTATATTTTGCTTATGCTAC
Found at i:120360 original size:12 final size:12
Alignment explanation
Indices: 120337--120370 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
120327 GATTTTTAAA
120337 AATATTTATTATT
1 AATATTT-TTATT
*
120350 ATTATTTTTATT
1 AATATTTTTATT
120362 AATATTTTT
1 AATATTTTT
120371 TTCTTTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 13 0.68
13 6 0.32
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
AATATTTTTATT
Found at i:125858 original size:73 final size:71
Alignment explanation
Indices: 125708--125997 Score: 291
Period size: 73 Copynumber: 4.0 Consensus size: 71
125698 TTTTGGAACT
* * * * * **
125708 AAGTTTTCTCTCTCTTGAGACAATT-TCTTTTGGAACTAAGCTTTTTCTCCCTTGAGACAATTTC
1 AAGTTTTGTCTCTCTTGAGACAGTTCTC-TTT-AAAC-AA-ATTTTTCTCTCTTGAGACGGTTTC
** *
125772 TTTTG-AACT
62 CCTTGAAACA
*
125781 AAGTTTTTTCTCTCTTGAGACAAGTTCTCTTTAAACAAATTTGTTCTCTCTTGAGACGGTTTCCC
1 AAGTTTTGTCTCTCTTGAGAC-AGTTCTCTTTAAACAAATTT-TTCTCTCTTGAGACGGTTTCCC
*
125846 TTAAAACA
64 TTGAAACA
125854 AAGTTTTGTCTCTCTTGAGACAGTT-TCTTTTGAAACAAATTTTGTCTCTCTTGAGACGGTTTCC
1 AAGTTTTGTCTCTCTTGAGACAGTTCTC-TTT-AAACAAATTTT-TCTCTCTTGAGACGGTTTCC
*
125918 TTTGAAACA
63 CTTGAAACA
* * * * *
125927 AA-TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAGATTTTTTCCCTCTTGAGACAGTTTCCC
1 AAGTTTTGTCTCTCTTGAGACAG-TTCTCTTTAAACA-AATTTTTCTCTCTTGAGACGGTTTCCC
125991 TTGAAAC
64 TTGAAAC
125998 GAAATCTTTG
Statistics
Matches: 187, Mismatches: 20, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
71 5 0.03
72 79 0.42
73 94 0.50
74 7 0.04
75 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (71 bp):
AAGTTTTGTCTCTCTTGAGACAGTTCTCTTTAAACAAATTTTTCTCTCTTGAGACGGTTTCCCTT
GAAACA
Found at i:125907 original size:109 final size:108
Alignment explanation
Indices: 125749--126007 Score: 312
Period size: 109 Copynumber: 2.4 Consensus size: 108
125739 GGAACTAAGC
* * * * *
125749 TTTTTCTCCCTTGAGACAATTTCTTTTG-AACTAAGTTTTTTCTCTCTTGAGACAAG-TTCTCTT
1 TTTTTCTCTCTTGAGACAGTTTCTTTTGAAACGAAATTTTGTCTCTCTTGAGAC-AGTTTC-CTT
*
125812 T-AAACAAA-TTTGTTCTCTCTTGAGACGGTTTCCCTTAAAACAAA
64 TGAAACAAATTTTG-TCTCTCTTGAGACAGTTTCCCTTAAAACAAA
*
125856 GTTTTGTCTCTCTTGAGACAGTTTCTTTTGAAAC-AAATTTTGTCTCTCTTGAGACGGTTTCCTT
1 -TTTT-TCTCTCTTGAGACAGTTTCTTTTGAAACGAAATTTTGTCTCTCTTGAGACAGTTTCCTT
* *
125920 TGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAGAT
64 TGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACA-AA
* **
125966 TTTTTCCCTCTTGAGACAGTTTCCCTTGAAACGAAATCTTTG
1 TTTTTCTCTCTTGAGACAGTTTCTTTTGAAACGAAAT-TTTG
126008 AATATGTTTT
Statistics
Matches: 132, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
108 34 0.26
109 86 0.65
110 12 0.09
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (108 bp):
TTTTTCTCTCTTGAGACAGTTTCTTTTGAAACGAAATTTTGTCTCTCTTGAGACAGTTTCCTTTG
AAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA
Found at i:125943 original size:21 final size:21
Alignment explanation
Indices: 125883--125943 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
125873 ACAGTTTCTT
125883 TTGAAACAAATTTTGTCTCTC
1 TTGAAACAAATTTTGTCTCTC
* **
125904 TTGAGAC---GGTT-TC-CT-
1 TTGAAACAAATTTTGTCTCTC
125919 TTGAAACAAATTTTGTCTCTC
1 TTGAAACAAATTTTGTCTCTC
125940 TTGA
1 TTGA
125944 GACAGTTTCC
Statistics
Matches: 28, Mismatches: 6, Indels: 12
0.61 0.13 0.26
Matches are distributed among these distances:
15 6 0.21
16 2 0.07
17 2 0.07
18 4 0.14
19 2 0.07
20 2 0.07
21 10 0.36
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.43
Consensus pattern (21 bp):
TTGAAACAAATTTTGTCTCTC
Found at i:125989 original size:36 final size:36
Alignment explanation
Indices: 125711--126007 Score: 287
Period size: 36 Copynumber: 8.1 Consensus size: 36
125701 TGGAACTAAG
* * ** * *
125711 TTTTCTCTCTCTTGAGACAATTTCTTTTGGAACTAAGC
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AA-A
* * ** *
125749 TTTT-TCTCCCTTGAGACAATTTCTTTTG-AACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
* * *
125784 TTTTTTCTCTCTTGAGACAAG-TTCTCTTTAAACAAA
1 TTTTGTCTCTCTTGAGAC-AGTTTCCCTTGAAACAAA
* *
125820 -TTTGTTCTCTCTTGAGACGGTTTCCCTTAAAACAAA
1 TTTTG-TCTCTCTTGAGACAGTTTCCCTTGAAACAAA
**
125856 GTTTTGTCTCTCTTGAGACAGTTTCTTTTGAAACAAA
1 -TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
125893 TTTTGTCTCTCTTGAGACGGTTTCCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
125929 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAGA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
125965 TTTTTTCCCTCTTGAGACAGTTTCCCTTGAAACGAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
126002 TCTTTG
1 T-TTTG
126008 AATATGTTTT
Statistics
Matches: 226, Mismatches: 24, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
35 8 0.04
36 150 0.66
37 57 0.25
38 11 0.05
ACGTcount: A:0.23, C:0.21, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:125990 original size:17 final size:17
Alignment explanation
Indices: 125937--125991 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 17
125927 AATTTTGTCT
125937 CTCTTGAGACAGTTT-C
1 CTCTTGAGACAGTTTCC
*
125953 C-CTTGAAACAGATTTTTTCC
1 CTCTTGAGACAG----TTTCC
125973 CTCTTGAGACAGTTTCC
1 CTCTTGAGACAGTTTCC
125990 CT
1 CT
125992 TGAAACGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
15 9 0.29
16 1 0.03
17 7 0.23
19 3 0.10
20 2 0.06
21 9 0.29
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.38
Consensus pattern (17 bp):
CTCTTGAGACAGTTTCC
Found at i:126109 original size:174 final size:175
Alignment explanation
Indices: 125868--126243 Score: 510
Period size: 174 Copynumber: 2.1 Consensus size: 175
125858 TTTGTCTCTC
*
125868 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCTCTCTTGAGACGGTTTCCTTTGAAACAAATTTT
1 TTGAGACAGTTTCTTTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCTTTGAAACAAATTTT
* * *
125933 GTCTCTCTTGAGACAGTTTCCCTTG-AAACAGA-TTTTTTCCCTCTTGAGACAGTTTCCCTTGAA
66 GTCTCTCTTGAGACAGTTTCCCTTGAAAAAAAAGTTTTGTCCCTCTTGAGACAGTTTCCCTTGAA
*
125996 ACGA-AATCTTTGAATATGTTTTTCTTGAAACAGATTTCGTCTCCA
131 AC-ACAATCTTTGAATATGTTTATCTTGAAACAGATTTCGTCTCCA
* * * *
126041 TTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTTTTGAGATAGTTT-CTCTTGAAACAAATT
1 TTGAGACAGTTTCTTTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCT-TTGAAACAAATT
* *
126105 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
64 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAAAAGTTTTGTCCCTCTTGAGACAGTTTCCCTTG
* * * * *
126170 AAACACCAGTCTTTGAATATGTTTATCTTGAAACAAAATTTTGCCTCCC
129 AAACA-CAATCTTTGAATATGTTTATCTTGAAAC-AGATTTCGTCTCCA
*
126219 TGGAGACAGTTT-TTCTTGAAACAAA
1 TTGAGACAGTTTCTT-TTGAAACAAA
126244 AAACCTTTGA
Statistics
Matches: 176, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
173 23 0.13
174 61 0.35
175 6 0.03
176 30 0.17
177 29 0.16
178 27 0.15
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (175 bp):
TTGAGACAGTTTCTTTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCTTTGAAACAAATTTT
GTCTCTCTTGAGACAGTTTCCCTTGAAAAAAAAGTTTTGTCCCTCTTGAGACAGTTTCCCTTGAA
ACACAATCTTTGAATATGTTTATCTTGAAACAGATTTCGTCTCCA
Found at i:126118 original size:36 final size:36
Alignment explanation
Indices: 126013--126174 Score: 191
Period size: 36 Copynumber: 4.4 Consensus size: 36
126003 CTTTGAATAT
* * *
126013 GTTTTTCTTGAAACAGATTTCGTCTC-CATTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTC-TTGAGACA
* * * * *
126049 GTTTCTTTTGGAACTAAGTTTTGTCTCTTTTGAGATA
1 GTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
126086 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
126122 GTTTCCCTTGAAAAAAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCTCTTG-AAACAAA-TTTTGTCTCTCTTGAGACA
126160 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
126175 CCAGTCTTTG
Statistics
Matches: 105, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
36 39 0.37
37 38 0.36
38 28 0.27
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (36 bp):
GTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:126123 original size:73 final size:74
Alignment explanation
Indices: 126004--126174 Score: 213
Period size: 73 Copynumber: 2.3 Consensus size: 74
125994 AAACGAAATC
* * ** * **
126004 TTTGA-ATATGTTTTTCTTGAAACAGATTTCGTCTCCATTGAGACAGTTTCTTTTG-GAACTAAG
1 TTTGAGATA-GTTTCTCTTGAAACAAATTTCGTCTCCATTGAGACAGTTTCCCTTGAAAAAAAAG
126067 TTTTGTCTCT
65 TTTTGTCTCT
*
126077 TTTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCTC-TTGAGACAGTTTCCCTTGAAAAAAAAG
1 TTTGAGATAGTTTCTCTTGAAACAAATTTCGTCTC-CATTGAGACAGTTTCCCTTGAAAAAAAAG
126141 TTTTGTCTCT
65 TTTTGTCTCT
* *
126151 CTTGAGACAGTTTCTCTTGAAACA
1 TTTGAGATAGTTTCTCTTGAAACA
126175 CCAGTCTTTG
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
73 44 0.52
74 41 0.48
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (74 bp):
TTTGAGATAGTTTCTCTTGAAACAAATTTCGTCTCCATTGAGACAGTTTCCCTTGAAAAAAAAGT
TTTGTCTCT
Found at i:126145 original size:38 final size:38
Alignment explanation
Indices: 126041--126172 Score: 171
Period size: 38 Copynumber: 3.6 Consensus size: 38
126031 TTCGTCTCCA
* * ** *
126041 TTGAGACAGTTTCTTTTG-GAACTAAGTTTTGTCTCTT
1 TTGAGACAGTTTCTCTTGAAAAAAAAGTTTTGTCTCTC
* *
126078 TTGAGATAGTTTCTCTTG-AAACAAA-TTTTGTCTCTC
1 TTGAGACAGTTTCTCTTGAAAAAAAAGTTTTGTCTCTC
*
126114 TTGAGACAGTTTCCCTTGAAAAAAAAGTTTTGTCTCTC
1 TTGAGACAGTTTCTCTTGAAAAAAAAGTTTTGTCTCTC
126152 TTGAGACAGTTTCTCTTGAAA
1 TTGAGACAGTTTCTCTTGAAA
126173 CACCAGTCTT
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
36 26 0.31
37 27 0.32
38 31 0.37
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (38 bp):
TTGAGACAGTTTCTCTTGAAAAAAAAGTTTTGTCTCTC
Found at i:126635 original size:3 final size:3
Alignment explanation
Indices: 126627--126674 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
126617 TTGAAAATAT
* *
126627 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
126675 ATATATTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:133094 original size:16 final size:18
Alignment explanation
Indices: 133073--133115 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
133063 TTTTAAAAAC
133073 TTAAAATTA-TT-TTTTT
1 TTAAAATTACTTATTTTT
133089 TTAAAA-TACTTATTTTT
1 TTAAAATTACTTATTTTT
133106 TTAAATATTA
1 TTAAA-ATTA
133116 GAAAAACTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.09
16 8 0.35
17 10 0.43
18 1 0.04
19 2 0.09
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAAAATTACTTATTTTT
Found at i:134170 original size:10 final size:10
Alignment explanation
Indices: 134142--134203 Score: 61
Period size: 11 Copynumber: 5.9 Consensus size: 10
134132 AATTATAAAA
*
134142 AATATAAAATA
1 AATA-AAAATG
134153 AATAAAAATG
1 AATAAAAATG
*
134163 CAATAAAAAAG
1 -AATAAAAATG
134174 AATTAAAAATG
1 AA-TAAAAATG
* *
134185 AATAAAATTC
1 AATAAAAATG
134195 AATAAAAAT
1 AATAAAAAT
134204 ATAATGTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
10 21 0.49
11 22 0.51
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (10 bp):
AATAAAAATG
Found at i:134282 original size:23 final size:24
Alignment explanation
Indices: 134253--134313 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
134243 TATTATTTAT
134253 AATATTAATTTTAAA-AAATATAA
1 AATATTAATTTTAAATAAATATAA
* **
134276 AATATTAAATATTAAATAAATATTG
1 AATATT-AATTTTAAATAAATATAA
*
134301 AATTTTAATTTTA
1 AATATTAATTTTA
134314 TTAAAAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 6 0.19
24 14 0.45
25 11 0.35
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
AATATTAATTTTAAATAAATATAA
Found at i:134855 original size:10 final size:10
Alignment explanation
Indices: 134842--134870 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
134832 TAAAAGTTAA
134842 TAAATATTAT
1 TAAATATTAT
134852 TAAATATTAT
1 TAAATATTAT
134862 TAAATATTA
1 TAAATATTA
134871 AAAAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TAAATATTAT
Found at i:135349 original size:23 final size:23
Alignment explanation
Indices: 135323--135398 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
135313 GGAATTTAGG
135323 GAATTTGGGTATCAAAGATTTAA
1 GAATTTGGGTATCAAAGATTTAA
** * *
135346 GAATTTAAGT-T-TAAGAATTTAGG
1 GAATTTGGGTATCAAAG-ATTTA-A
*
135369 GAATTTGGGTATCAAAGATTTTA
1 GAATTTGGGTATCAAAGATTTAA
135392 GAGATTT
1 GA-ATTT
135399 AGGAATTTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
21 3 0.08
22 6 0.15
23 18 0.46
24 9 0.23
25 3 0.08
ACGTcount: A:0.37, C:0.03, G:0.22, T:0.38
Consensus pattern (23 bp):
GAATTTGGGTATCAAAGATTTAA
Found at i:135420 original size:46 final size:45
Alignment explanation
Indices: 135324--135420 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 45
135314 GAATTTAGGG
* **
135324 AATTTGGGTATCAAAGATTTAAGAATTTAAGTTTAAGAATTTAGGG
1 AATTTGGGTATCAAAGATTTAAGAATTTAAATTTAAG-ATTTAGAA
*
135370 AATTTGGGTATCAAAGATTTTAGAGATTTAGGAATTTAAG-TTTA-AA
1 AATTTGGGTATCAAAGATTTAAGA-ATTTA--AATTTAAGATTTAGAA
135416 AATTT
1 AATTT
135421 ATGGATTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
46 28 0.64
47 9 0.20
49 7 0.16
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (45 bp):
AATTTGGGTATCAAAGATTTAAGAATTTAAATTTAAGATTTAGAA
Found at i:136025 original size:27 final size:28
Alignment explanation
Indices: 135958--136026 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
135948 TTAAAAAAAA
**
135958 ATTAATTGTTAAAAAACCTTAAACGTATT
1 ATTAATT-TTAAAAAACCTTAAACAAATT
135987 ATT-ATTTTAAAAAACCTTAAA-AAATT
1 ATTAATTTTAAAAAACCTTAAACAAATT
*
136013 -TTAATTTTGAAAAA
1 ATTAATTTTAAAAAA
136027 GTAACTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 2 0.06
26 13 0.36
27 15 0.42
28 3 0.08
29 3 0.08
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.39
Consensus pattern (28 bp):
ATTAATTTTAAAAAACCTTAAACAAATT
Found at i:136416 original size:17 final size:18
Alignment explanation
Indices: 136396--136439 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
136386 GATTTTAGAA
136396 AATATATTTTTTTAAA-T
1 AATATATTTTTTTAAATT
*
136413 AATA-ATATTTTTAAATT
1 AATATATTTTTTTAAATT
*
136430 AAAATATTTT
1 AATATATTTT
136440 AAAAAATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 10 0.45
17 8 0.36
18 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
AATATATTTTTTTAAATT
Found at i:142534 original size:6 final size:6
Alignment explanation
Indices: 142499--142565 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
142489 AAAAATAATT
* * * *
142499 TATAAA -ATAAA TACAAA TA-AAA TTTTAA TATAAA TATTAA TAATAAA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA T-ATAAA
*
142546 -ATAAA TAATTAA TATAAA TA
1 TATAAA T-ATAAA TATAAA TA
142566 AATTCGAATT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
5 14 0.30
6 24 0.51
7 9 0.19
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (6 bp):
TATAAA
Found at i:143529 original size:9 final size:9
Alignment explanation
Indices: 143500--143540 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
143490 GACCGGTCAG
143500 ACCGATTTG-
1 ACCGA-TTGA
*
143509 ACCGATTTA
1 ACCGATTGA
143518 ACCGATTGA
1 ACCGATTGA
143527 ACCGA-TGA
1 ACCGATTGA
143535 ACCGAT
1 ACCGAT
143541 AGCATGACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 10 0.36
9 18 0.64
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (9 bp):
ACCGATTGA
Found at i:144723 original size:15 final size:16
Alignment explanation
Indices: 144703--144735 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
144693 TATCATTTAA
144703 AATAA-TTTAAAAAAT
1 AATAATTTTAAAAAAT
*
144718 AATAATTTTAAAAGAT
1 AATAATTTTAAAAAAT
144734 AA
1 AA
144736 AAAGTGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
AATAATTTTAAAAAAT
Found at i:147462 original size:3 final size:3
Alignment explanation
Indices: 147454--147509 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
147444 AATTATTTAT
* * *
147454 TAA TAA TAA T-A CAA TAA TAA T-A TAA TAA TAA TAA TAT TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
147500 TAA TAA TAA T
1 TAA TAA TAA T
147510 TTTAAAATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 3 0.07
3 42 0.93
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:147469 original size:11 final size:11
Alignment explanation
Indices: 147455--147486 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
147445 ATTATTTATT
147455 AATAATAATAC
1 AATAATAATAC
*
147466 AATAATAATAT
1 AATAATAATAC
147477 AATAATAATA
1 AATAATAATA
147487 ATATTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (11 bp):
AATAATAATAC
Found at i:147946 original size:22 final size:23
Alignment explanation
Indices: 147885--147947 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 23
147875 TTTTTGAAAA
*
147885 CATCCTGCACTGTAGGTCTTATG
1 CATCTTGCACTGTAGGTCTTATG
* * *
147908 GA--TGGCCCTG-AGGTCTTAT-
1 CATCTTGCACTGTAGGTCTTATG
147927 CATCTTGCACTGTAGGTCTTA
1 CATCTTGCACTGTAGGTCTTA
147948 CAGATGACCC
Statistics
Matches: 30, Mismatches: 7, Indels: 7
0.68 0.16 0.16
Matches are distributed among these distances:
19 1 0.03
20 9 0.30
21 11 0.37
22 8 0.27
23 1 0.03
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (23 bp):
CATCTTGCACTGTAGGTCTTATG
Found at i:147965 original size:116 final size:117
Alignment explanation
Indices: 147761--148022 Score: 463
Period size: 116 Copynumber: 2.2 Consensus size: 117
147751 TAAAATCTCA
* *
147761 TTTGAAAACATCCTGTACTGGAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTATAG
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTATAG
147826 GTCTTACAGATGACCCAAAGGCTTTAAATATCAAAAAGCTCCCGAAGG-CTT
66 GTCTTACAGATGACCCAAAGGCTTTAAATATCAAAAAGCTCCCGAAGGTCTT
*
147877 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAG
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTATAG
* *
147942 GTCTTACAGATGACCCGAAGGCTTTAAATATCAAAAAGCTCCCGAAGGTTTT
66 GTCTTACAGATGACCCAAAGGCTTTAAATATCAAAAAGCTCCCGAAGGTCTT
*
147994 TTTGAAAACATCATGCACTGTAGGTCTTA
1 TTTGAAAACATCCTGCACTGTAGGTCTTA
148023 CAGATGTGGG
Statistics
Matches: 139, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
116 109 0.78
117 30 0.22
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (117 bp):
TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTATAG
GTCTTACAGATGACCCAAAGGCTTTAAATATCAAAAAGCTCCCGAAGGTCTT
Found at i:149129 original size:54 final size:54
Alignment explanation
Indices: 149048--149322 Score: 318
Period size: 54 Copynumber: 5.1 Consensus size: 54
149038 ATAATCACTG
* * * *
149048 GTTCGTAAAACATTTGAGAACACATTCATCATTTCCTGTAGCTTCTGTC-CAGAG
1 GTTCGTAATACATTTGACAACACATTCATCATTTCCTGTGGCTTCTG-CACAGAT
* * * * * *
149102 GTTCGTAAAATATTTGACAACACATTCATCATTTCATGTGGCTTCTCCCCTGAT
1 GTTCGTAATACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCACAGAT
* * * * * *
149156 GTTCGTAATACATTTGACAATACGTTAATCCTTTCCTGTGGCTCCAGCACAGAT
1 GTTCGTAATACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCACAGAT
* * * * * *
149210 GTTCGTAATATATTTGATAATACATTCACCATTTTCTGTGTCTTCTGCACAGAT
1 GTTCGTAATACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCACAGAT
* *
149264 GTTCGTAATACATTTGACAACACGTTCATCCTTTCCTGTGGCTTCTGCACAGAT
1 GTTCGTAATACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCACAGAT
149318 GTTCG
1 GTTCG
149323 CCAGTGAAGT
Statistics
Matches: 183, Mismatches: 37, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
53 1 0.01
54 182 0.99
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (54 bp):
GTTCGTAATACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCACAGAT
Found at i:149237 original size:108 final size:108
Alignment explanation
Indices: 149048--149322 Score: 356
Period size: 108 Copynumber: 2.5 Consensus size: 108
149038 ATAATCACTG
* * * * * *
149048 GTTCGTAAAACATTTGAGAACACATTCATCATTTCCTGTAGCTTCTGTC-CAGAGGTTCGTAAAA
1 GTTCGTAATACATTTGACAACACGTTCATCCTTTCCTGTGGCTTCTG-CACAGATGTTCGTAAAA
* * *
149112 TATTTGACAACACATTCATCA-TTTCATGTGGCTTCTCCCCTGAT
65 TATTTGACAACACATTCACCATTTTC-TGTGGCTTCTCCACAGAT
* * * * *
149156 GTTCGTAATACATTTGACAATACGTTAATCCTTTCCTGTGGCTCCAGCACAGATGTTCGTAATAT
1 GTTCGTAATACATTTGACAACACGTTCATCCTTTCCTGTGGCTTCTGCACAGATGTTCGTAAAAT
* * * *
149221 ATTTGATAATACATTCACCATTTTCTGTGTCTTCTGCACAGAT
66 ATTTGACAACACATTCACCATTTTCTGTGGCTTCTCCACAGAT
149264 GTTCGTAATACATTTGACAACACGTTCATCCTTTCCTGTGGCTTCTGCACAGATGTTCG
1 GTTCGTAATACATTTGACAACACGTTCATCCTTTCCTGTGGCTTCTGCACAGATGTTCG
149323 CCAGTGAAGT
Statistics
Matches: 143, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
107 1 0.01
108 138 0.97
109 4 0.03
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (108 bp):
GTTCGTAATACATTTGACAACACGTTCATCCTTTCCTGTGGCTTCTGCACAGATGTTCGTAAAAT
ATTTGACAACACATTCACCATTTTCTGTGGCTTCTCCACAGAT
Found at i:152056 original size:22 final size:21
Alignment explanation
Indices: 152026--152069 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
152016 CAATTTATCA
* *
152026 TCTTTTTTCTTGTTTTTCTTCT
1 TCTTCTTTCTTCTTTTT-TTCT
152048 TCTTCTTTCTTCTTTTTTTCT
1 TCTTCTTTCTTCTTTTTTTCT
152069 T
1 T
152070 ATAATGAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.77
Consensus pattern (21 bp):
TCTTCTTTCTTCTTTTTTTCT
Found at i:156278 original size:15 final size:16
Alignment explanation
Indices: 156237--156279 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
156227 AAGTTGGAGC
*
156237 AAAATAAAATGTACAA
1 AAAATAAAATGAACAA
*
156253 AAAATAAAAAT-AAGAA
1 AAAAT-AAAATGAACAA
156269 AAAATAAAATG
1 AAAATAAAATG
156280 GTTAGTACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 5 0.22
16 13 0.57
17 5 0.22
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.16
Consensus pattern (16 bp):
AAAATAAAATGAACAA
Found at i:157718 original size:37 final size:36
Alignment explanation
Indices: 157647--157718 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
157637 TTGTTTGATA
157647 TTAAAAATAAATAAATAAAGAATATAATAATTTTTC
1 TTAAAAATAAATAAATAAAGAATATAATAATTTTTC
*
157683 TTAAAAAT-AATAAA-AATGAAGTATATATATATTTTT
1 TTAAAAATAAATAAATAAAGAA-TATA-ATA-ATTTTT
157719 AAATAAGATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
34 5 0.16
35 10 0.31
36 11 0.34
37 6 0.19
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (36 bp):
TTAAAAATAAATAAATAAAGAATATAATAATTTTTC
Found at i:157835 original size:24 final size:23
Alignment explanation
Indices: 157791--157836 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 23
157781 AATTTCTTAA
157791 TATTTAAAAATAAATAAACATTAT
1 TATTTAAAAATAAAT-AACATTAT
157815 TATTTAATCAAATAAAT-ACATT
1 TATTTAA--AAATAAATAACATT
157837 TATATGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
24 12 0.60
26 8 0.40
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (23 bp):
TATTTAAAAATAAATAACATTAT
Found at i:159185 original size:3 final size:3
Alignment explanation
Indices: 159179--159211 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
159169 ATTATTTTTT
*
159179 TAA TAA TAA TAA T-A CAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
159212 TTAAAATGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 1 0.04
3 26 0.96
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:159199 original size:14 final size:14
Alignment explanation
Indices: 159180--159206 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
159170 TTATTTTTTT
159180 AATAATAATAATAC
1 AATAATAATAATAC
159194 AATAATAATAATA
1 AATAATAATAATA
159207 ATAATTTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAATAATAATAC
Found at i:160636 original size:3 final size:3
Alignment explanation
Indices: 160628--160724 Score: 59
Period size: 3 Copynumber: 30.7 Consensus size: 3
160618 TGTAACAATA
* * * *
160628 AAT AAT AAT AAT AAT AATT AAT AAT AAT ATT ATT AAAT ATT AAAT ATT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT -AAT AAT -AAT AAT
* * * * * *
160676 AAAT AAA AAT AAT AAG AAT AAG AAT AAT ATT AAAT ATT AAT AAT GAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
160723 AA
1 AA
160725 CCTGGCAAAA
Statistics
Matches: 71, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
3 60 0.85
4 11 0.15
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:160649 original size:16 final size:16
Alignment explanation
Indices: 160624--160724 Score: 73
Period size: 16 Copynumber: 6.3 Consensus size: 16
160614 AATTTGTAAC
160624 AATAAATAATAATAAT
1 AATAAATAATAATAAT
*
160640 AATAATTAATAATAAT
1 AATAAATAATAATAAT
*
160656 ATTATTAAAT-ATTA-AAT
1 A--A-TAAATAATAATAAT
* *
160673 ATTAAATAAAAATAAT
1 AATAAATAATAATAAT
* *
160689 AA-GAATAAGAATAAT
1 AATAAATAATAATAAT
* *
160704 ATTAAATATTAATAAT
1 AATAAATAATAATAAT
*
160720 GATAA
1 AATAA
160725 CCTGGCAAAA
Statistics
Matches: 64, Mismatches: 15, Indels: 12
0.70 0.16 0.13
Matches are distributed among these distances:
14 5 0.08
15 14 0.22
16 33 0.52
17 4 0.06
18 4 0.06
19 4 0.06
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
AATAAATAATAATAAT
Found at i:161144 original size:42 final size:40
Alignment explanation
Indices: 161072--161173 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 40
161062 AACGTCTTAT
*
161072 AGATGAACCGAAGGACTTATCATCTTGCTCGAAAGACTGAC
1 AGATG-ACCGAAGGACTTATCATCATGCTCGAAAGACTGAC
* *
161113 AGATGACCTGAAGGATTTAATCATCATGCTCGAAAGACTTAC
1 AGATGACC-GAAGGACTT-ATCATCATGCTCGAAAGACTGAC
* *
161155 TGATGGCCCGAAGGACTTA
1 AGAT-GACCGAAGGACTTA
161174 CCAATTTTGG
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
40 3 0.06
41 14 0.27
42 32 0.62
43 3 0.06
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (40 bp):
AGATGACCGAAGGACTTATCATCATGCTCGAAAGACTGAC
Found at i:161615 original size:260 final size:261
Alignment explanation
Indices: 160864--161816 Score: 1418
Period size: 260 Copynumber: 3.7 Consensus size: 261
160854 AATAACCCGG
* * * *
160864 AGGATTTAATCATCATGCTCGAAAGACTTACTGATGACTCGAAGGACTTGCCAATTTTAGAAATA
1 AGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATA
* * *
160929 GTCTACTAGGTAAGAAACTTTGGAAATTAG-TTTCTTACTTTTCAAAAATTTCA-TTTCTGAAAA
66 GTTTACTAGGTAAGAAACTTT-GAAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAA
160992 TATTAAATGAGAAACTTTGAAAATT-CATTTTCTCATTTTTCATAAACATCATATG-AAATCATC
130 TATTAAATGAGAAACTTTGAAAATTAC-TTTTCTCATTTTTCATAAACATCATATGAAAAT-ATC
* *
161055 TTGCCCAAACGTCTTATAGATGAACCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGA-
193 TTGCCCAAAGGTCTTATAGATGGACCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGAT
*
161119 CCTGA
258 TC-GA
161124 AGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATA
1 AGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATA
* * *
161189 GTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACATTTCAAAATTTTCATTTTCTGAAAAA
66 GTTTACTAGGTAAGAAACTTTGAAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTG-AAAA
* *
161254 TATTAAATGAGAAACTTTGAAAATTACTTTTCTCATTTTTCATAAATATCATATGAAAACATCTT
130 TATTAAATGAGAAACTTTGAAAATTACTTTTCTCATTTTTCATAAACATCATATGAAAATATCTT
* * * *
161319 ACCCAAAGGTCTTATAGATAGTCCGAAGGGCTTATCATCTTGCTCGAAAGACTGACAGATGATTC
195 GCCCAAAGGTCTTATAGATGGACCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGATTC
161384 GA
260 GA
* * *
161386 ATGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACGAAGGACTTACCAA-TTTGGAAATT
1 AGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATA
* * *
161450 GTTTACTAGGTAAGAAACTTTGAAAATCGCTTTCTTACTTTTCAAATATTTTATTTTATGAAAAT
66 GTTTACTAGGTAAGAAACTTTGAAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAT
* *
161515 ATTAAATAAGAAACTTTGAAAATTACTTTTCTCATTTTTCACAAACATCATATGAAAATATCTTG
131 ATTAAATGAGAAACTTTGAAAATTACTTTTCTCATTTTTCATAAACATCATATGAAAATATCTTG
* * * * *
161580 CCCAAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTT-CTTCAAAAGACTAATAGAT-TTCT
196 CCCAAAGGTCTTATAGATGGACCGAAGGACTTATCATCTTGC-TCGAAAGACTGACAGATGAT-T
161643 CGA
259 CGA
* * *
161646 AGGATTTAATCATCATGCTTGAAAGACTTACTGATTGCCCGAATGACTTACCAATTTTGGAAATA
1 AGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATA
* * *
161711 GTTTACTAGGCAAGAAACTTTGAAAATTGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAC
66 GTTTACTAGGTAAGAAACTTTGAAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAT
* * *
161776 ATTAAAGGAGAAACTTTGAAAATTGCTTTTCACATTTTTCA
131 ATTAAATGAGAAACTTTGAAAATTACTTTTCTCATTTTTCA
161817 AATTATATAA
Statistics
Matches: 628, Mismatches: 56, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
259 7 0.01
260 271 0.43
261 174 0.28
262 171 0.27
263 5 0.01
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (261 bp):
AGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATA
GTTTACTAGGTAAGAAACTTTGAAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAAT
ATTAAATGAGAAACTTTGAAAATTACTTTTCTCATTTTTCATAAACATCATATGAAAATATCTTG
CCCAAAGGTCTTATAGATGGACCGAAGGACTTATCATCTTGCTCGAAAGACTGACAGATGATTCG
A
Found at i:163761 original size:16 final size:16
Alignment explanation
Indices: 163700--163775 Score: 64
Period size: 16 Copynumber: 4.6 Consensus size: 16
163690 TGATTTGTTC
*
163700 TCTTCTTCTTTC-TTT
1 TCTTCTTTTTTCTTTT
*
163715 TCTTTCCTTTTTCTTTT
1 TC-TTCTTTTTTCTTTT
* * *
163732 TGTTGTTTTATCTTTT
1 TCTTCTTTTTTCTTTT
163748 TCTTCTTTTTTCTTATCT
1 TCTTCTTTTTTCTT-T-T
*
163766 TTTTCTTTTT
1 TCTTCTTTTT
163776 ATCTCTCCTT
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
15 2 0.04
16 30 0.64
17 5 0.11
18 10 0.21
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (16 bp):
TCTTCTTTTTTCTTTT
Found at i:163763 original size:21 final size:21
Alignment explanation
Indices: 163702--163772 Score: 74
Period size: 21 Copynumber: 3.2 Consensus size: 21
163692 ATTTGTTCTC
163702 TTCTTCTTTCTTTTCTT-TCCTTT
1 TTCTTC-TT-TTTTCTTAT-CTTT
*
163725 TTCTT-TTTGTTGTTTTATCTTT
1 TTCTTCTTT-TT-TCTTATCTTT
163747 TTCTTCTTTTTTCTTATCTTT
1 TTCTTCTTTTTTCTTATCTTT
163768 TTCTT
1 TTCTT
163773 TTTATCTCTC
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
20 1 0.02
21 18 0.43
22 14 0.33
23 9 0.21
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TTCTTCTTTTTTCTTATCTTT
Found at i:163768 original size:11 final size:11
Alignment explanation
Indices: 163739--163772 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
163729 TTTTGTTGTT
163739 TTATCTTTTTC
1 TTATCTTTTTC
*
163750 TTCT-TTTTTC
1 TTATCTTTTTC
163760 TTATCTTTTTC
1 TTATCTTTTTC
163771 TT
1 TT
163773 TTTATCTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATCTTTTTC
Found at i:179661 original size:235 final size:235
Alignment explanation
Indices: 179250--179719 Score: 940
Period size: 235 Copynumber: 2.0 Consensus size: 235
179240 TAGAGCCAAA
179250 ACCCATCATATAATAAAACTTAGAACTGGAGTTTAGGTGAAACCTAACGTAAATAAGTTTTGTAA
1 ACCCATCATATAATAAAACTTAGAACTGGAGTTTAGGTGAAACCTAACGTAAATAAGTTTTGTAA
179315 GGTTAACACAAGGAAAAGCATGTTGAGTCTTTCATTTTATTTAGCATTATTTTATTTTCTGAATA
66 GGTTAACACAAGGAAAAGCATGTTGAGTCTTTCATTTTATTTAGCATTATTTTATTTTCTGAATA
179380 AATGCATTCGAACTAGAAATCATGTGATTAGTTTATTTTTCCAAACAAAGCATGGAACTAGAAAG
131 AATGCATTCGAACTAGAAATCATGTGATTAGTTTATTTTTCCAAACAAAGCATGGAACTAGAAAG
179445 CATGAGGTTAGGATATGATTTGTTTCTTACTAACCAGTTT
196 CATGAGGTTAGGATATGATTTGTTTCTTACTAACCAGTTT
179485 ACCCATCATATAATAAAACTTAGAACTGGAGTTTAGGTGAAACCTAACGTAAATAAGTTTTGTAA
1 ACCCATCATATAATAAAACTTAGAACTGGAGTTTAGGTGAAACCTAACGTAAATAAGTTTTGTAA
179550 GGTTAACACAAGGAAAAGCATGTTGAGTCTTTCATTTTATTTAGCATTATTTTATTTTCTGAATA
66 GGTTAACACAAGGAAAAGCATGTTGAGTCTTTCATTTTATTTAGCATTATTTTATTTTCTGAATA
179615 AATGCATTCGAACTAGAAATCATGTGATTAGTTTATTTTTCCAAACAAAGCATGGAACTAGAAAG
131 AATGCATTCGAACTAGAAATCATGTGATTAGTTTATTTTTCCAAACAAAGCATGGAACTAGAAAG
179680 CATGAGGTTAGGATATGATTTGTTTCTTACTAACCAGTTT
196 CATGAGGTTAGGATATGATTTGTTTCTTACTAACCAGTTT
179720 TTCTATATAT
Statistics
Matches: 235, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
235 235 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (235 bp):
ACCCATCATATAATAAAACTTAGAACTGGAGTTTAGGTGAAACCTAACGTAAATAAGTTTTGTAA
GGTTAACACAAGGAAAAGCATGTTGAGTCTTTCATTTTATTTAGCATTATTTTATTTTCTGAATA
AATGCATTCGAACTAGAAATCATGTGATTAGTTTATTTTTCCAAACAAAGCATGGAACTAGAAAG
CATGAGGTTAGGATATGATTTGTTTCTTACTAACCAGTTT
Found at i:184164 original size:42 final size:42
Alignment explanation
Indices: 184083--184164 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
184073 CTTGCAATGT
* **
184083 TGGGGCATGCTGAAGGTCCATTTCAATCAGGAATAATCCATG
1 TGGGGCATGCTGAAGGCCCATTTCAATCAAAAATAATCCATG
* *
184125 TGGGGCATGCTGAAGGCCCATTTTAGA-CAAAAATGATCCA
1 TGGGGCATGCTGAAGGCCCATTTCA-ATCAAAAATAATCCA
184165 AGTAGGATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (42 bp):
TGGGGCATGCTGAAGGCCCATTTCAATCAAAAATAATCCATG
Found at i:185975 original size:20 final size:20
Alignment explanation
Indices: 185950--186013 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
185940 TCTAGAAAAT
185950 TAAAGCATTCGGGTCATTTG
1 TAAAGCATTCGGGTCATTTG
185970 TAAAGCCA-TCGGGTCATTTG
1 TAAAG-CATTCGGGTCATTTG
* *
185990 TAAATCCTTCGGGTCATTTG
1 TAAAGCATTCGGGTCATTTG
186010 TAAA
1 TAAA
186014 TCTTTTGTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.03
20 37 0.93
21 2 0.05
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (20 bp):
TAAAGCATTCGGGTCATTTG
Found at i:186026 original size:20 final size:20
Alignment explanation
Indices: 185957--186015 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
185947 AATTAAAGCA
*
185957 TTCGGGTCATTTGTAAAGCC
1 TTCGGGTCATTTGTAAATCC
*
185977 ATCGGGTCATTTGTAAATCC
1 TTCGGGTCATTTGTAAATCC
185997 TTCGGGTCATTTGTAAATC
1 TTCGGGTCATTTGTAAATC
186016 TTTTGTGTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
TTCGGGTCATTTGTAAATCC
Found at i:189083 original size:20 final size:20
Alignment explanation
Indices: 189058--189115 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 20
189048 GTTATGAGAT
189058 GGGGGAATCGGTACCCCTTG
1 GGGGGAATCGGTACCCCTTG
*
189078 GGGGGAATCGGTTCCCTCCTTG
1 GGGGGAATCGG-TACC-CCTTG
189100 GGGAGG-ATCGGTACCC
1 GGG-GGAATCGGTACCC
189116 TCTGAGTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 12 0.36
21 6 0.18
22 13 0.39
23 2 0.06
ACGTcount: A:0.14, C:0.26, G:0.40, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCTTG
Found at i:189321 original size:18 final size:19
Alignment explanation
Indices: 189298--189336 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
189288 AATTTAATCA
*
189298 AATATATAA-TTAAAATTC
1 AATATAAAACTTAAAATTC
189316 AATATAAAATCTTAAAATTC
1 AATATAAAA-CTTAAAATTC
189336 A
1 A
189337 TTAACACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATAAAACTTAAAATTC
Found at i:189754 original size:2 final size:2
Alignment explanation
Indices: 189747--189771 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
189737 AAAAGACCAA
189747 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 A
189772 ATAAGTTCAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:191722 original size:23 final size:23
Alignment explanation
Indices: 191691--191800 Score: 134
Period size: 23 Copynumber: 4.8 Consensus size: 23
191681 TCAATTCCCT
191691 AAAGGGGGAATCGATTCCCATTC
1 AAAGGGGGAATCGATTCCCATTC
*
191714 AAAGAGGGAATC-AGTTCCCATTC
1 AAAGGGGGAATCGA-TTCCCATTC
*
191737 AAAGGGGGAATCGGTTCCCCATTC
1 AAAGGGGGAATCGATT-CCCATTC
* * *
191761 AAAGGGGGAATCGGTTCCCCTGC
1 AAAGGGGGAATCGATTCCCATTC
*
191784 -AAGGGGGTATCGATTCC
1 AAAGGGGGAATCGATTCC
191801 TCCTGCACTA
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
22 16 0.21
23 38 0.49
24 23 0.30
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (23 bp):
AAAGGGGGAATCGATTCCCATTC
Found at i:191772 original size:47 final size:46
Alignment explanation
Indices: 191691--191800 Score: 150
Period size: 46 Copynumber: 2.4 Consensus size: 46
191681 TCAATTCCCT
191691 AAAGGGGGAATCGATTCCCATTCAAAGAGGGAATCAGTTCCCATTC
1 AAAGGGGGAATCGATTCCCATTCAAAGAGGGAATCAGTTCCCATTC
* * * * *
191737 AAAGGGGGAATCGGTTCCCCATTCAAAGGGGGAATCGGTTCCCCTGC
1 AAAGGGGGAATCGATT-CCCATTCAAAGAGGGAATCAGTTCCCATTC
*
191784 -AAGGGGGTATCGATTCC
1 AAAGGGGGAATCGATTCC
191801 TCCTGCACTA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
45 2 0.04
46 28 0.50
47 26 0.46
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (46 bp):
AAAGGGGGAATCGATTCCCATTCAAAGAGGGAATCAGTTCCCATTC
Found at i:191780 original size:24 final size:23
Alignment explanation
Indices: 191691--191779 Score: 142
Period size: 23 Copynumber: 3.8 Consensus size: 23
191681 TCAATTCCCT
*
191691 AAAGGGGGAATCGATTCCCATTC
1 AAAGGGGGAATCGGTTCCCATTC
* *
191714 AAAGAGGGAATCAGTTCCCATTC
1 AAAGGGGGAATCGGTTCCCATTC
191737 AAAGGGGGAATCGGTTCCCCATTC
1 AAAGGGGGAATCGGTT-CCCATTC
191761 AAAGGGGGAATCGGTTCCC
1 AAAGGGGGAATCGGTTCCC
191780 CTGCAAGGGG
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 37 0.62
24 23 0.38
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.20
Consensus pattern (23 bp):
AAAGGGGGAATCGGTTCCCATTC
Found at i:197715 original size:18 final size:19
Alignment explanation
Indices: 197692--197730 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
197682 AATTTAATCG
*
197692 AATATATAA-TTAAAATTC
1 AATATAAAACTTAAAATTC
197710 AATATAAAATCTTAAAATTC
1 AATATAAAA-CTTAAAATTC
197730 A
1 A
197731 TTAACACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATAAAACTTAAAATTC
Found at i:199350 original size:3 final size:3
Alignment explanation
Indices: 199328--199386 Score: 64
Period size: 3 Copynumber: 18.7 Consensus size: 3
199318 TGTAACCAAA
* * *
199328 AAT ATAT AAC AAT AAAT AAT AAT AAT AAT AAT ATT AAAT ATT AAT AAT
1 AAT A-AT AAT AAT -AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
199376 AAT AAT AAT AA
1 AAT AAT AAT AA
199387 ATATTAAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 39 0.83
4 8 0.17
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:199360 original size:19 final size:19
Alignment explanation
Indices: 199345--199383 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
199335 AACAATAAAT
*
199345 AATAATAATAATAATATTA
1 AATAATAATAATAATAATA
*
199364 AATATTAATAATAATAATA
1 AATAATAATAATAATAATA
199383 A
1 A
199384 TAAATATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAATAATAATAATAATA
Found at i:199390 original size:22 final size:22
Alignment explanation
Indices: 199328--199393 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
199318 TGTAACCAAA
* *
199328 AATATATAACAATAAATAATAAT
1 AATA-ATAATAATAAATATTAAT
*
199351 AATAATAATATTAAATATTAAT
1 AATAATAATAATAAATATTAAT
199373 AATAATAATAATAAATATTAA
1 AATAATAATAATAAATATTAA
199394 ATGATAACCC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAATAATAATAAATATTAAT
Found at i:199684 original size:21 final size:22
Alignment explanation
Indices: 199638--199684 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
199628 AATATTTGAT
* * *
199638 AAATTAATGTATAATATGATTA
1 AAATAAATGTATAATACGAATA
199660 AAATAAATGTATAA-ACGAATA
1 AAATAAATGTATAATACGAATA
199681 AAAT
1 AAAT
199685 TTTTATGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (22 bp):
AAATAAATGTATAATACGAATA
Found at i:200888 original size:2 final size:2
Alignment explanation
Indices: 200877--200958 Score: 150
Period size: 2 Copynumber: 42.0 Consensus size: 2
200867 TATACTTCAA
200877 AT AT -T AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
200917 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
200959 TTGATTATTT
Statistics
Matches: 78, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 76 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:201571 original size:26 final size:27
Alignment explanation
Indices: 201541--201603 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 27
201531 GTTTTCGCCC
*
201541 ATAAAATTTTATAAAAATTCATCCTCT
1 ATAAAATTTTATAAAAATTCATCCCCT
201568 -TAAAA-TTT-TAAAAATTCATCCCCT
1 ATAAAATTTTATAAAAATTCATCCCCT
201592 AATAAAATTTTA
1 -ATAAAATTTTA
201604 AGTTCGTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
24 15 0.48
25 3 0.10
26 10 0.32
27 3 0.10
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.40
Consensus pattern (27 bp):
ATAAAATTTTATAAAAATTCATCCCCT
Found at i:201604 original size:26 final size:25
Alignment explanation
Indices: 201541--201604 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 25
201531 GTTTTCGCCC
*
201541 ATAAAATTTTATAAAAATTCATCCTCT
1 ATAAAA-TTT-TAAAAATTCATCCCCT
201568 -TAAAATTTTAAAAATTCATCCCCT
1 ATAAAATTTTAAAAATTCATCCCCT
201592 AATAAAATTTTAA
1 -ATAAAATTTTAA
201605 GTTCGTGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
24 15 0.44
25 3 0.09
26 16 0.47
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAAAATTTTAAAAATTCATCCCCT
Found at i:205720 original size:23 final size:21
Alignment explanation
Indices: 205664--205726 Score: 56
Period size: 24 Copynumber: 2.9 Consensus size: 21
205654 TTTGTTATAG
205664 TTTTATAA-AATTTAATAATA
1 TTTTATAATAATTTAATAATA
* * *
205684 TTTTTTGATAAATTATAATGATTA
1 TTTTATAAT-AATT-TAAT-AATA
*
205708 TTTTATAATAATTCAATAA
1 TTTTATAATAATTTAATAA
205727 ATGTAACGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
20 6 0.19
21 1 0.03
22 7 0.22
23 8 0.25
24 10 0.31
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.51
Consensus pattern (21 bp):
TTTTATAATAATTTAATAATA
Found at i:206989 original size:58 final size:58
Alignment explanation
Indices: 206883--207027 Score: 159
Period size: 59 Copynumber: 2.4 Consensus size: 58
206873 GAACATATGA
* *
206883 ATAGTCGAGTGATCATTTTGTAACTTTTAATAATCGGGAGACTCAACAAA-ATAACA-CCT
1 ATAGTCGAG-GATCA-TTTGTAACTTTTAATAATAGAGAGACTCAACAAAGA-AACACCCT
* * *
206942 ATAGTCGAGAGATCATTTGTAACTTTTAATAGTAGAGAGGCTTAACAAAGAAACACCCT
1 ATAGTCGAG-GATCATTTGTAACTTTTAATAATAGAGAGACTCAACAAAGAAACACCCT
* *
207001 AGAGTCAATGGATCATTTGTATACTTT
1 ATAGTCGA-GGATCATTTGTA-ACTTT
207028 ACCCTCTTGT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
58 33 0.45
59 35 0.47
60 6 0.08
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (58 bp):
ATAGTCGAGGATCATTTGTAACTTTTAATAATAGAGAGACTCAACAAAGAAACACCCT
Found at i:210594 original size:11 final size:11
Alignment explanation
Indices: 210578--210603 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
210568 GTTTGATGCT
210578 TTCTCTCTTGA
1 TTCTCTCTTGA
210589 TTCTCTCTTGA
1 TTCTCTCTTGA
210600 TTCT
1 TTCT
210604 AGCTTGATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.27, G:0.08, T:0.58
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:211275 original size:30 final size:30
Alignment explanation
Indices: 211215--211274 Score: 113
Period size: 29 Copynumber: 2.0 Consensus size: 30
211205 TAATTTTAAG
211215 ATTTTGAAATCAAGTTTTGAAATTAGAAAA
1 ATTTTGAAATCAAGTTTTGAAATTAGAAAA
211245 ATTTTGAAATCAAG-TTTGAAATTAGAAAA
1 ATTTTGAAATCAAGTTTTGAAATTAGAAAA
211274 A
1 A
211275 AATGAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.48, C:0.03, G:0.13, T:0.35
Consensus pattern (30 bp):
ATTTTGAAATCAAGTTTTGAAATTAGAAAA
Found at i:213597 original size:22 final size:21
Alignment explanation
Indices: 213549--213608 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
213539 ATTCCCCTGT
213549 GGGGGGAATCGGTTCCCTTCA
1 GGGGGGAATCGGTTCCCTTCA
**
213570 AAGGGGAATCGGTTTCCC-TCA
1 GGGGGGAATCGG-TTCCCTTCA
* *
213591 GGGGGGGATCGATTCCCT
1 GGGGGGAATCGGTTCCCT
213609 CTGCACCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 5 0.16
21 21 0.68
22 5 0.16
ACGTcount: A:0.17, C:0.23, G:0.37, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCTTCA
Found at i:221448 original size:257 final size:257
Alignment explanation
Indices: 220966--221841 Score: 1222
Period size: 263 Copynumber: 3.4 Consensus size: 257
220956 CTTATTCATA
* * * *
220966 TATTGAATAAAAATATTTTTTTTATTATTTTGGATCAGGTCGGGTTTCTAATTCATATATTTGGG
1 TATTGAATAAAAATA-TTTTTTTATTATTTCGGGTCAGGTCGGATTTCTAATTCATATATTCGGG
**
221031 TACGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTC
65 TTTGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTC
* * * *
221096 GGGTCGAATTCGGGTTTAGGGT-TAAAATACCCGACCCAAAAATATATATAATTTTACCTTATAT
130 GGGTCGAGTTCGGGTTTAGGGTGAAAAATAACCGACCCGAAAATATATATAATTTTACCTTATAT
* *
221160 ATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTTACTATTTT
195 ATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCACTGTTTT
221223 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCAGGTCGGATTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCAGGTCGGATTTCTAATTCATATATTCGGGT
* * *
221288 TTGGTCGGGTGAAATTTTATTTTGGTCCGGTCGGGTCGGTTTTTCTAAGTGTGATATTCGGGTCG
66 TTGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCG
* *
221353 GGTCGAGTTCGGGATTAGGGTGAAAAATAACCAACCCGAAAATATATATAATTTTACCTTATATA
131 GGTCGAGTTCGGGTTTAGGGTGAAAAATAACCGACCCGAAAATATATATAATTTTACCTTATATA
*
221418 TTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTTCAATCAATTAAGTCATTGTT
196 TTTAGGAATAATTACAATAATACCCCTCTATATATAA--TTTTTT---TCAATTAAGTCACTGTT
221483 TT
256 TT
* * *
221485 TATTGAATAAAAATAATTTTTTTATTATTTCAGGTCGGGTTGGATTTCTAATTCATATATTCGGG
1 TATTGAATAAAAAT-ATTTTTTTATTATTTCGGGTCAGGTCGGATTTCTAATTCATATATTCGGG
**
221550 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTC
65 TTTGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTC
* * * *
221615 TGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGATCCGACCCGACCCAAGAAATATATAATATT
130 GGGTCGAGTTCGGGTTTAGGGTGAAAAATA----A-CCGACCCGA---AA-ATATATATAATTTT
* *
221680 ACATTATATATTTAGGAATAATTACAATAATACCCCTCTATGTAT--TTTTTTT-AATTAAGTCA
186 ACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCA
221742 CTGTTTT
251 CTGTTTT
*
221749 TATTGAATAAAAATTATTTTTTTATTATTTCGGGTC--G--GG-TTTATAATTCATATATTC-GG
1 TATTGAATAAAAA-TATTTTTTTATTATTTCGGGTCAGGTCGGATTTCTAATTCATATATTCGGG
*
221808 -TT--T-GGGTGAAACTTTATTTTGGTCGGGTCAGGTC
65 TTTGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTC
221842 TCGGATGGAG
Statistics
Matches: 562, Mismatches: 40, Indels: 37
0.88 0.06 0.06
Matches are distributed among these distances:
254 30 0.05
255 1 0.00
256 125 0.22
257 91 0.16
258 2 0.00
259 23 0.04
260 2 0.00
262 31 0.06
263 134 0.24
264 49 0.09
265 2 0.00
267 1 0.00
268 14 0.02
271 2 0.00
272 55 0.10
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (257 bp):
TATTGAATAAAAATATTTTTTTATTATTTCGGGTCAGGTCGGATTTCTAATTCATATATTCGGGT
TTGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCG
GGTCGAGTTCGGGTTTAGGGTGAAAAATAACCGACCCGAAAATATATATAATTTTACCTTATATA
TTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCACTGTTTT
Found at i:222117 original size:21 final size:20
Alignment explanation
Indices: 222050--222186 Score: 71
Period size: 21 Copynumber: 6.8 Consensus size: 20
222040 AAATGACCAA
***
222050 CAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
222070 CAGAATCGCAAATC-AGTTT
1 CAAAATCGCAACGCGATTTT
*
222089 CCAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
222110 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
222131 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
222151 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
222172 -GAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
222187 ACACATAAAT
Statistics
Matches: 85, Mismatches: 28, Indels: 9
0.70 0.23 0.07
Matches are distributed among these distances:
19 25 0.29
20 14 0.16
21 46 0.54
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:222217 original size:40 final size:40
Alignment explanation
Indices: 222154--222305 Score: 179
Period size: 39 Copynumber: 3.9 Consensus size: 40
222144 CGATTTTCCA
* **
222154 AAATCGCAACGCGAATATG-AAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
222193 AAATCGCAACGCGTATCCGTAAATCGC-ACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
*
222232 AAATCGCAACGCGTATCCGTAAATCGCAA--CGATATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGA-ACACAT
222271 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
222306 TATTTTAAAG
Statistics
Matches: 95, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
39 51 0.54
40 39 0.41
42 3 0.03
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:222280 original size:79 final size:77
Alignment explanation
Indices: 222154--222299 Score: 213
Period size: 79 Copynumber: 1.9 Consensus size: 77
222144 CGATTTTCCA
*
222154 AAATCGCAACGCGAATATGAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCG
1 AAATCGCAACGCGAATACGAAATCGCAAC-CGAACACATAAATCGCAACGCGTATCCGTAAATCG
222219 CACGTGTATCCGT
65 CACGTGTATCCGT
* * *
222232 AAATCGCAACGCGTATCCGTAAATCGCAA-CGATATACATAAAATCGCAACGCGTATCCGTAAAT
1 AAATCGCAACGCGAATACG-AAATCGCAACCGA-ACACAT-AAATCGCAACGCGTATCCGTAAAT
222296 CGCA
63 CGCA
222300 ACGCGATATT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
77 3 0.05
78 21 0.34
79 37 0.61
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (77 bp):
AAATCGCAACGCGAATACGAAATCGCAACCGAACACATAAATCGCAACGCGTATCCGTAAATCGC
ACGTGTATCCGT
Found at i:222314 original size:20 final size:20
Alignment explanation
Indices: 222154--222304 Score: 175
Period size: 20 Copynumber: 7.7 Consensus size: 20
222144 CGATTTTCCA
* **
222154 AAATCGCAACGCGAATATG-
1 AAATCGCAACGCGTATCCGT
* *
222173 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
222193 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
222213 AAATCGC-ACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
222232 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
222252 AAATCGCAACG-ATATACAT
1 AAATCGCAACGCGTATCCGT
222271 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
222292 AAATCGCAACGCG
1 AAATCGCAACGCG
222305 ATATTTTAAA
Statistics
Matches: 112, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
18 1 0.01
19 36 0.32
20 68 0.61
21 7 0.06
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:222725 original size:33 final size:33
Alignment explanation
Indices: 222686--222756 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
222676 TTCACTTAGA
*
222686 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
222719 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
222752 TTTCA
1 TTTCA
222757 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Done.