Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000776.1 Hibiscus syriacus cultivar Beakdansim tig00001509_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: 304350
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 1 of 2
Found at i:798 original size:30 final size:30
Alignment explanation
Indices: 764--827 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
754 AATCCCTCCA
* * *
764 TTTTCCAAAATTTACGAATTGATCTCCAAC
1 TTTTCCAAAACTTACGAAATGATCCCCAAC
*
794 TTTT-CAAAACTTACGAAATGATCCCCAAT
1 TTTTCCAAAACTTACGAAATGATCCCCAAC
823 TTTTC
1 TTTTC
828 TAAGACTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (30 bp):
TTTTCCAAAACTTACGAAATGATCCCCAAC
Found at i:1998 original size:40 final size:40
Alignment explanation
Indices: 1943--2019 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
1933 GGACTCTCTG
1943 GAGAAATCTCTCCCTTATCCTACCCATTTCCACGTGTCTA
1 GAGAAATCTCTCCCTTATCCTACCCATTTCCACGTGTCTA
*
1983 GAGAAATCTCTCCCTTATCCTGCCCATTTCCACGTGT
1 GAGAAATCTCTCCCTTATCCTACCCATTTCCACGTGT
2020 TTTATATCCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.32
Consensus pattern (40 bp):
GAGAAATCTCTCCCTTATCCTACCCATTTCCACGTGTCTA
Found at i:3900 original size:13 final size:13
Alignment explanation
Indices: 3870--3900 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
3860 AAATAATAGA
3870 TAAAATATTAATT
1 TAAAATATTAATT
3883 T-AAATATTAATT
1 TAAAATATTAATT
3895 TAAAAT
1 TAAAAT
3901 TTTTAAGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAAATATTAATT
Found at i:4599 original size:60 final size:59
Alignment explanation
Indices: 4429--4604 Score: 226
Period size: 60 Copynumber: 2.9 Consensus size: 59
4419 AAGTATGATA
* * * * *
4429 TTCATTTTATATTGATCCCCAAACTTTTAAATATTTCAATTTCATCCCTAAACTATGATT
1 TTCATTCTAAATTGGTCCCCAAACTTTTTAATATTTCAATTTCATCCC-AAACTATGACT
* **
4489 TTCATTCTAAATTAGTCCTTAAACTTTTTAATATTTCAATTTCATCCCCAAACTATGACT
1 TTCATTCTAAATTGGTCCCCAAACTTTTTAATATTTCAATTTCAT-CCCAAACTATGACT
* * *
4549 TTCATTCTAAATTGGTCCCCAAACTTTTTGAATATTCCAATTTTATCCCAAGCTAT
1 TTCATTCTAAATTGGTCCCCAAACTTTTT-AATATTTCAATTTCATCCCAAACTAT
4605 ACCTATGCAC
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
60 83 0.83
61 17 0.17
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.43
Consensus pattern (59 bp):
TTCATTCTAAATTGGTCCCCAAACTTTTTAATATTTCAATTTCATCCCAAACTATGACT
Found at i:8370 original size:20 final size:20
Alignment explanation
Indices: 8334--8386 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
8324 ATACATTAAA
*
8334 TCAACTGAAAGTCAAATCCAT
1 TCAACTG-AAGTTAAATCCAT
8355 TCAACTGAAGTTAAATCCAT
1 TCAACTGAAGTTAAATCCAT
8375 TCAACTGAAGTT
1 TCAACTGAAGTT
8387 TGTAAAGGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 24 0.77
21 7 0.23
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (20 bp):
TCAACTGAAGTTAAATCCAT
Found at i:15273 original size:116 final size:115
Alignment explanation
Indices: 15057--15380 Score: 411
Period size: 116 Copynumber: 2.8 Consensus size: 115
15047 ACTGTCACGA
* * * * * * *
15057 GTTTATTTTGAAATTCAAATTTTTTATATTAATTATTTATTTTACTGAAGAAGCTTA-ATTTAAA
1 GTTTATTCTGAAATTCAAA-TTTTTATATTAATT-GTCATTTTACTGATGATGCCTACA-CTAAA
* * * *
15121 ATTTTATTTGTATTTATCCTATATGATTTTTTTTATTATTAATACATATTTGT
63 ATTTTATTTGTATTTATCCTATACGAATTTTATTATTATTAATACATATGTGT
* *
15174 GTTTATTCTAAAATTCAAATTTTTATATTAATTGTGCATTTTATTGATGATGCCTACACTAAAAT
1 GTTTATTCTGAAATTCAAATTTTTATATTAATTGT-CATTTTACTGATGATGCCTACACTAAAAT
*
15239 TTTATTTGTATTTACCCTATACGAATTTTATTATTATTAATACATATGTGT
65 TTTATTTGTATTTATCCTATACGAATTTTATTATTATTAATACATATGTGT
* *
15290 GTCTATTCTGAAATTCAATTTTTTTTATATTAATTGTCAATTTTACTGATGATGCCTAC-CTTAA
1 GTTTATTCTGAAATTCAA--ATTTTTATATTAATTGTC-ATTTTACTGATGATGCCTACAC-TAA
15354 AATTTTATTTGT-TTTATCCTATACGAA
62 AATTTTATTTGTATTTATCCTATACGAA
15381 AATACATATG
Statistics
Matches: 182, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
115 1 0.01
116 97 0.53
117 34 0.19
118 50 0.27
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.52
Consensus pattern (115 bp):
GTTTATTCTGAAATTCAAATTTTTATATTAATTGTCATTTTACTGATGATGCCTACACTAAAATT
TTATTTGTATTTATCCTATACGAATTTTATTATTATTAATACATATGTGT
Found at i:16489 original size:18 final size:18
Alignment explanation
Indices: 16466--16501 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16456 GACAATATGA
*
16466 AAATTTCATCTTGGTTGG
1 AAATTTCATCTTAGTTGG
16484 AAATTTCATCTTAGTTGG
1 AAATTTCATCTTAGTTGG
16502 TGGCCAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.44
Consensus pattern (18 bp):
AAATTTCATCTTAGTTGG
Found at i:25864 original size:30 final size:30
Alignment explanation
Indices: 25830--26071 Score: 160
Period size: 30 Copynumber: 8.2 Consensus size: 30
25820 CTTGAAGGGT
* * *
25830 TAAAATAGCAAAAATAGAAATTTAAGGGAC
1 TAAAATAACAAAAATAGAAACTTAAAGGAC
* *
25860 TAAAATAGA-AAAAATAGAAACTTAAAAGAT
1 TAAAATA-ACAAAAATAGAAACTTAAAGGAC
* * * *
25890 TAACACAACAAAACA-A-AAATTTAAAGGAA
1 TAAAATAACAAAA-ATAGAAACTTAAAGGAC
** *
25919 TAAAAT-GGAAAAATAGAAACTTAAAGGTC
1 TAAAATAACAAAAATAGAAACTTAAAGGAC
** * * *
25948 TAAAATAGTAAAAATTGAAACTTAAGGGTC
1 TAAAATAACAAAAATAGAAACTTAAAGGAC
*
25978 T-AAATAAC--AAATACAAACATTTAAAGGAC
1 TAAAATAACAAAAATAGAAAC--TTAAAGGAC
* * *
26007 TAAAATAACAAAAACA-AACATTTAAAGGAA
1 TAAAATAACAAAAATAGAA-ACTTAAAGGAC
* * *
26037 TAAAATAAC-AAAACACAAACTTAAGGGAC
1 TAAAATAACAAAAATAGAAACTTAAAGGAC
26066 TAAAAT
1 TAAAAT
26072 GGTATTAACA
Statistics
Matches: 167, Mismatches: 32, Indels: 27
0.74 0.14 0.12
Matches are distributed among these distances:
27 9 0.05
28 5 0.03
29 64 0.38
30 81 0.49
31 3 0.02
32 5 0.03
ACGTcount: A:0.60, C:0.10, G:0.11, T:0.19
Consensus pattern (30 bp):
TAAAATAACAAAAATAGAAACTTAAAGGAC
Found at i:25951 original size:88 final size:89
Alignment explanation
Indices: 25830--26060 Score: 238
Period size: 88 Copynumber: 2.6 Consensus size: 89
25820 CTTGAAGGGT
* *
25830 TAAAATAGCAAAAATAGAAATTTAAGGGACTAAAATAGAAAAAATAGAAACTTAAAAGAT-TAAC
1 TAAAATAGCAAAAATAGAAACTTAAAGGACTAAAATAGAAAAAATAGAAACTT-AAAGATCTAA-
25894 ACAACAAA-ACAAAAATTTAAAGGAA
64 ACAACAAATACAAAAATTTAAAGGAA
* * * * * * *
25919 TAAAAT-GGAAAAATAGAAACTTAAAGGTCTAAAATAGTAAAAATTGAAACTTAAGGGTCTAAAT
1 TAAAATAGCAAAAATAGAAACTTAAAGGACTAAAATAGAAAAAATAGAAACTTAAAGATCTAAAC
* *
25983 AACAAATACAAACATTTAAAGGAC
66 AACAAATACAAAAATTTAAAGGAA
* * * * * * *
26007 TAAAATAACAAAAACA-AACATTTAAAGGAATAAAATA-ACAAAACACAAACTTAA
1 TAAAATAGCAAAAATAGAA-ACTTAAAGGACTAAAATAGAAAAAATAGAAACTTAA
26061 GGGACTAAAA
Statistics
Matches: 116, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
87 11 0.09
88 78 0.67
89 27 0.23
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.19
Consensus pattern (89 bp):
TAAAATAGCAAAAATAGAAACTTAAAGGACTAAAATAGAAAAAATAGAAACTTAAAGATCTAAAC
AACAAATACAAAAATTTAAAGGAA
Found at i:25983 original size:29 final size:30
Alignment explanation
Indices: 25791--25981 Score: 122
Period size: 30 Copynumber: 6.4 Consensus size: 30
25781 CATATATGAT
* * * * *
25791 TTAAAGGACTTAAATAGTAAAAACATAATC
1 TTAAAGGTCTAAAATAGTAAAAATAGAAAC
* * *
25821 TTGAAGGGT-TAAAATAGCAAAAATAGAAAT
1 TT-AAAGGTCTAAAATAGTAAAAATAGAAAC
* * *
25851 TTAAGGGACTAAAATAGAAAAAATAGAAAC
1 TTAAAGGTCTAAAATAGTAAAAATAGAAAC
* * * * * *
25881 TTAAAAGAT-TAACACA--ACAAAACAAAAAT
1 TT-AAAGGTCTAAAATAGTA-AAAATAGAAAC
** *
25910 TTAAAGGAATAAAAT-GGAAAAATAGAAAC
1 TTAAAGGTCTAAAATAGTAAAAATAGAAAC
*
25939 TTAAAGGTCTAAAATAGTAAAAATTGAAAC
1 TTAAAGGTCTAAAATAGTAAAAATAGAAAC
*
25969 TTAAGGGTCTAAA
1 TTAAAGGTCTAAA
25982 TAACAAATAC
Statistics
Matches: 122, Mismatches: 31, Indels: 16
0.72 0.18 0.09
Matches are distributed among these distances:
28 5 0.04
29 40 0.33
30 70 0.57
31 7 0.06
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.22
Consensus pattern (30 bp):
TTAAAGGTCTAAAATAGTAAAAATAGAAAC
Found at i:26057 original size:118 final size:117
Alignment explanation
Indices: 25789--26071 Score: 275
Period size: 118 Copynumber: 2.4 Consensus size: 117
25779 ATCATATATG
* * * * * * ** *
25789 ATTTAAAGGACTTAAATAGTAAAAACATAATCTTGAAGGGTTAAAATAGCAAAAATAGAAATTTA
1 ATTTAAAGGAATAAAAT-GAAAAAACACAAACTTAAAGGACTAAAATAGCAAAAATAGAAACTTA
* * *
25854 AGGGACTAAAATAGAAAAAATAGAAACTTAAAAGATTAACACAACAAAACAAAA
65 AGGGACTAAAATA-AAAAAATACAAACTTAAAAGACTAAAACAACAAAACAAAA
* * * * * *
25908 ATTTAAAGGAATAAAATGGAAAAATAGAAACTTAAAGGTCTAAAATAGTAAAAATTGAAACTTAA
1 ATTTAAAGGAATAAAATGAAAAAACACAAACTTAAAGGACTAAAATAGCAAAAATAGAAACTTAA
* * * * *
25973 GGGTCT-AAAT-AACAAATACAAACATTTAAAGGACTAAAATAACAAAAACAAAC
66 GGGACTAAAATAAAAAAATACAAAC--TTAAAAGACTAAAACAAC-AAAACAAAA
*
26026 ATTTAAAGGAATAAAAT-AACAAAACACAAACTTAAGGGACTAAAAT
1 ATTTAAAGGAATAAAATGAA-AAAACACAAACTTAAAGGACTAAAAT
26072 GGTATTAACA
Statistics
Matches: 135, Mismatches: 25, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
115 11 0.08
117 19 0.14
118 90 0.67
119 15 0.11
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (117 bp):
ATTTAAAGGAATAAAATGAAAAAACACAAACTTAAAGGACTAAAATAGCAAAAATAGAAACTTAA
GGGACTAAAATAAAAAAATACAAACTTAAAAGACTAAAACAACAAAACAAAA
Found at i:26389 original size:14 final size:15
Alignment explanation
Indices: 26370--26398 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
26360 AAGTCAAATA
26370 TTAACATA-AATAAC
1 TTAACATACAATAAC
26384 TTAACATACAATAAC
1 TTAACATACAATAAC
26399 AAGACTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (15 bp):
TTAACATACAATAAC
Found at i:27469 original size:3 final size:3
Alignment explanation
Indices: 27461--27511 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
27451 AAATGTAATT
*
27461 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TATA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
27506 TAA TAA
1 TAA TAA
27512 GATAATATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:27521 original size:21 final size:20
Alignment explanation
Indices: 27461--27521 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 20
27451 AAATGTAATT
27461 TAATAATAAT-AATAATA-A
1 TAATAATAATAAATAATATA
*
27479 TAATAATAAT-ATTATATAATA
1 TAATAATAATAAATA-AT-ATA
27500 TAATAATAATAAGATAATATA
1 TAATAATAATAA-ATAATATA
27521 T
1 T
27522 TTGTTGACCC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
18 13 0.36
19 2 0.06
20 1 0.03
21 15 0.42
22 3 0.08
23 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TAATAATAATAAATAATATA
Found at i:27768 original size:40 final size:42
Alignment explanation
Indices: 27670--27783 Score: 133
Period size: 40 Copynumber: 2.7 Consensus size: 42
27660 GGTGGGGGAC
* * *
27670 GACACGTCTCATACGTGATGAAGAGGTCTGGTCGTCTAAGGGT
1 GACACGACTCATACGTGATGAAGAGATCTGGTCGTCT-AGGAT
* * * *
27713 GACACGGCTCCTACGTGATGAGGAGATCTGGTCG-GT-GGAT
1 GACACGACTCATACGTGATGAAGAGATCTGGTCGTCTAGGAT
*
27753 GACACGACTCATACGTGATGAAGAGTTCTGG
1 GACACGACTCATACGTGATGAAGAGATCTGG
27784 ACATCTTTAG
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
40 30 0.49
42 1 0.02
43 30 0.49
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (42 bp):
GACACGACTCATACGTGATGAAGAGATCTGGTCGTCTAGGAT
Found at i:27923 original size:134 final size:134
Alignment explanation
Indices: 27708--28013 Score: 348
Period size: 134 Copynumber: 2.3 Consensus size: 134
27698 TGGTCGTCTA
* * * * * *
27708 AGGG-TGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACGACTCATACGTGAT
1 AGGGATGACAGGGCTCCTACGTGATGAGGAGGTATGGTCAGTGGATAACACGACTCATACATGAT
* * * * * *
27772 GAAGAGTTCTGGACATCTTTAGGAAGGGAGATAACACGGTTCCTAGATGATGTGGACGGCTGGTT
66 GAAGAGTGCTGGACATCTTTAGGAAAGGAGATAACACGGTTCCTACACGATGAGGACGACTGGTT
*
27837 ATTT
131 ATCT
* ** *
27841 AGGGATGATAGGGCTCCTACGTGATGAGGAGGTATGGTCAGTGGATAACACGGTTCTTACATGAT
1 AGGGATGACAGGGCTCCTACGTGATGAGGAGGTATGGTCAGTGGATAACACGACTCATACATGAT
* * * *
27906 GAGGACG-GCAT-GCCATCTTTAGGAAAGGTGATAACACGGTTCCTACACGATGAGGACGATTGG
66 GAAGA-GTGC-TGGACATCTTTAGGAAAGGAGATAACACGGTTCCTACACGATGAGGACGACTGG
27969 TTATCT
129 TTATCT
* ** *
27975 AGGGGTGACATTGCTCCTACGTGATTAGGAGGTATGGTC
1 AGGGATGACAGGGCTCCTACGTGATGAGGAGGTATGGTC
28014 GTCTTTAGGA
Statistics
Matches: 144, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
133 4 0.03
134 138 0.96
135 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.26
Consensus pattern (134 bp):
AGGGATGACAGGGCTCCTACGTGATGAGGAGGTATGGTCAGTGGATAACACGACTCATACATGAT
GAAGAGTGCTGGACATCTTTAGGAAAGGAGATAACACGGTTCCTACACGATGAGGACGACTGGTT
ATCT
Found at i:28041 original size:94 final size:94
Alignment explanation
Indices: 27921--28108 Score: 288
Period size: 94 Copynumber: 2.0 Consensus size: 94
27911 CGGCATGCCA
*
27921 TCTTTAGGAAAGGTGATAACACGGTTCCTACACGATGAGGACGATTGGTTATCTAGGGGTGACAT
1 TCTTTAGGAAAGGTGATAACACGGTTCCTACACGATGAGGACGACTGGTTATCTAGGGGTGACAT
* *
27986 TGCTCCTACGTGATTAGGAGGTATGGTCG
66 GGCTCCTACGTGATGAGGAGGTATGGTCG
* * * *
28015 TCTTTAGG-AAGAGTGATAACATGGTTCCTACGCGATGAGGATGACTGGTTGTCTAGGGGTGACA
1 TCTTTAGGAAAG-GTGATAACACGGTTCCTACACGATGAGGACGACTGGTTATCTAGGGGTGACA
*
28079 TGGCTCCTACGTGATGAGGAGGTTTGGTCG
65 TGGCTCCTACGTGATGAGGAGGTATGGTCG
28109 GGGGGATGAC
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
93 3 0.04
94 82 0.96
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.29
Consensus pattern (94 bp):
TCTTTAGGAAAGGTGATAACACGGTTCCTACACGATGAGGACGACTGGTTATCTAGGGGTGACAT
GGCTCCTACGTGATGAGGAGGTATGGTCG
Found at i:28095 original size:43 final size:42
Alignment explanation
Indices: 27954--28098 Score: 119
Period size: 43 Copynumber: 3.2 Consensus size: 42
27944 GTTCCTACAC
* *
27954 GATGAGGACGATTGGTTATCTAGGGGTGACATTGCTCCTACGT
1 GATGAGGACGA-TGGTTGTCTAGGGGTGACATGGCTCCTACGT
* * * * *
27997 GATTAGGAGGTATGGTCGTCTTTAGGAAGAGTGATAACATGGTTCCTACGC
1 GATGAGGACG-ATGGTTGTC--TAGG--G-GTG---ACATGGCTCCTACGT
*
28048 GATGAGGATGACTGGTTGTCTAGGGGTGACATGGCTCCTACGT
1 GATGAGGACGA-TGGTTGTCTAGGGGTGACATGGCTCCTACGT
28091 GATGAGGA
1 GATGAGGA
28099 GGTTTGGTCG
Statistics
Matches: 80, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
43 35 0.44
44 1 0.01
45 4 0.05
46 3 0.04
47 2 0.03
48 3 0.04
49 4 0.05
50 1 0.01
51 27 0.34
ACGTcount: A:0.23, C:0.14, G:0.34, T:0.28
Consensus pattern (42 bp):
GATGAGGACGATGGTTGTCTAGGGGTGACATGGCTCCTACGT
Found at i:28506 original size:36 final size:36
Alignment explanation
Indices: 28465--28573 Score: 130
Period size: 36 Copynumber: 3.0 Consensus size: 36
28455 TTTTTATTCC
* *
28465 GAGAGAAAATATCTCAAGTAAGACAAAATTTGTTTT
1 GAGAGAAAATGTCTCAAGCAAGACAAAATTTGTTTT
* * * *
28501 GAGAGAAATTGTCTCAAGCGAGACACAATTCGTTTT
1 GAGAGAAAATGTCTCAAGCAAGACAAAATTTGTTTT
*
28537 TA-AGAAAACTGTCTCAAGCAAGACAAAATTTGATTTT
1 GAGAGAAAA-TGTCTCAAGCAAGACAAAATTTG-TTTT
28574 TTAAAAGAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
35 5 0.08
36 51 0.85
37 4 0.07
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (36 bp):
GAGAGAAAATGTCTCAAGCAAGACAAAATTTGTTTT
Found at i:30411 original size:81 final size:81
Alignment explanation
Indices: 30270--30911 Score: 882
Period size: 81 Copynumber: 8.0 Consensus size: 81
30260 TTCATTTATG
* * * * *
30270 TCAAAGGTATATAGCCTTTCATCTAACTTGCATGATTGACACC-TTCTTGTCCAATACACAGCTA
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTC-TGTCAAATGCACAGCTA
30334 GGCCATTAATCTTTTAC
65 GGCCATTAATCTTTTAC
* * *
30351 TCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAAAGCACAGCTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
*
30416 GCTATTAATCTTTTAC
66 GCCATTAATCTTTTAC
* * **
30432 TCAAAGGTATTTAACCTTTTATCTAACTGGCATAATTGGTACCTTTCTGTCAAATGCACAG--AG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
*
30495 GCTATTAATCTTTTAC
66 GCCATTAATCTTTTAC
* * * * *
30511 TTAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTATCAAATGCACAACTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
**
30576 GCTTTTAA---TTTAC
66 GCCATTAATCTTTTAC
* ** *
30589 TCAAAGGTATTTAACCTTTCACCTAACTGGCATGATTGGGATCTTTCTGTCAAATGCACAGCTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
* *
30654 GCTATTAGTCTTTTAC
66 GCCATTAATCTTTTAC
* * * * *
30670 TGAAAGGTATTTAACCTTTCATCTAACTGGAATGATTGACACCTTTCTGTCAAATACAAAGTTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
30735 GCCATTAATCTTTTAC
66 GCCATTAATCTTTTAC
* *
30751 TCAAAGGTATTTAACCTTTTATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGTTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
30816 GCCATTAATCTTTTAC
66 GCCATTAATCTTTTAC
* * * * *
30832 TCAATGGTATTTAACCTTTTATATAACTGGCATGATTGACACCTTTATGTCAAATGCACAACTAG
1 TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
30897 GCCATTAATCTTTTA
66 GCCATTAATCTTTTA
30912 TTTTAGAACA
Statistics
Matches: 501, Mismatches: 54, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
78 67 0.13
79 72 0.14
81 359 0.72
82 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (81 bp):
TCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAG
GCCATTAATCTTTTAC
Found at i:31117 original size:54 final size:54
Alignment explanation
Indices: 31051--31176 Score: 155
Period size: 54 Copynumber: 2.3 Consensus size: 54
31041 TTTATCAAGA
* * * *
31051 TGCACACGTAGTGCCTATACGGTCGTTCATCAACACATGAT-ACATTTCGTGGGT
1 TGCACACATAGTGCCTATACGGTCGTCCATCAACACATGATGA-ATTCCGTGGAT
* * * *
31105 TGCACACATAGTGCATGTACGGTTGTCCATCAACTCATGATGAATTCCGTGGAT
1 TGCACACATAGTGCCTATACGGTCGTCCATCAACACATGATGAATTCCGTGGAT
*
31159 TGAACACATAGTGCCTAT
1 TGCACACATAGTGCCTAT
31177 TTGGTAATCA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 59 0.98
55 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (54 bp):
TGCACACATAGTGCCTATACGGTCGTCCATCAACACATGATGAATTCCGTGGAT
Found at i:31632 original size:18 final size:19
Alignment explanation
Indices: 31592--31659 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 19
31582 TTATCAATGC
31592 TATCGATACCATCCTCATAG
1 TATCGATACCA-CCTCATAG
* *
31612 TATCGATACC-CCTCTTGG
1 TATCGATACCACCTCATAG
* *
31630 TATCGATACTACTTGCATTAG
1 TATCGATACCACCT-CA-TAG
31651 TATCGATAC
1 TATCGATAC
31660 TACTCAGCTG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
18 15 0.38
19 2 0.05
20 11 0.28
21 11 0.28
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (19 bp):
TATCGATACCACCTCATAG
Found at i:33770 original size:2 final size:2
Alignment explanation
Indices: 33765--33809 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
33755 CCAAAAAAGC
* *
33765 TA TA TA TA TA TA TA TT TA TT TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33807 TA T
1 TA T
33810 GTTTTGACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:36385 original size:81 final size:81
Alignment explanation
Indices: 36259--36665 Score: 571
Period size: 81 Copynumber: 5.0 Consensus size: 81
36249 GGCATATAGT
* * * * * * *
36259 CTTTCATCTAACTTGCATGATAGATACCTTTCTGTCTAATACACAACTAGGCCATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
36324 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * *
36340 CTTTCATCTAGCTGGCATAATTGACACCTTTCTGTCAAATGCACAACTGGGCTATTAATATTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
36405 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * * *
36421 CTGTCATATAACTGACGTAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
36486 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * *
36502 CTTTCATCTAACTGGCATAATTAACACCTTTTTGTTAAATGCACAACTAGGCTATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
*
36567 TTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* * * * * ** * *
36583 ATTTCATCTAACTGGCATGATTGAAACCCTTATGTCAAATGCACAGTTAGACCATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
36648 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
36664 CT
1 CT
36666 GTAACATCTC
Statistics
Matches: 288, Mismatches: 38, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 288 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (81 bp):
CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
CTCAAAGGTATTTAAC
Found at i:37358 original size:45 final size:46
Alignment explanation
Indices: 37301--37548 Score: 330
Period size: 45 Copynumber: 5.5 Consensus size: 46
37291 TCGTTTTTAA
* * * *
37301 CATCTTTTCATA-CTGATAATGCACCTATATGTATTTCAATTATGG
1 CATCATTTCATACCCGATAATGCACCCATATGCATTTCAATTATGG
*
37346 CATCATTTCATA-CCTATAATGCACCCATATGCATTTCAATTATGG
1 CATCATTTCATACCCGATAATGCACCCATATGCATTTCAATTATGG
*
37391 CAT-ACTTTCAT-GCCGATAATGCACCCATATGCATTTCAATTATGG
1 CATCA-TTTCATACCCGATAATGCACCCATATGCATTTCAATTATGG
* *
37436 CATCCTTTCA-AGCCGATAATGCACCCATATGCATTTCAATTATGG
1 CATCATTTCATACCCGATAATGCACCCATATGCATTTCAATTATGG
* *
37481 CATCATTTCAT-GCCGATAATGCACCCATATGCATTTCAATTATGA
1 CATCATTTCATACCCGATAATGCACCCATATGCATTTCAATTATGG
* *
37526 CATCCTTTCATA-CCTATAATGCA
1 CATCATTTCATACCCGATAATGCA
37549 TTGTTGTATA
Statistics
Matches: 186, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
44 1 0.01
45 185 0.99
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (46 bp):
CATCATTTCATACCCGATAATGCACCCATATGCATTTCAATTATGG
Found at i:37421 original size:90 final size:90
Alignment explanation
Indices: 37301--37548 Score: 392
Period size: 90 Copynumber: 2.8 Consensus size: 90
37291 TCGTTTTTAA
* * * * * *
37301 CATCTTTTCATACTGATAATGCACCTATATGTATTTCAATTATGGCATCATTTCATACCTATAAT
1 CATCATTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATACCTATAAT
37366 GCACCCATATGCATTTCAATTATGG
66 GCACCCATATGCATTTCAATTATGG
*
37391 CAT-ACTTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCA-AGCCGATA
1 CATCA-TTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATA-CCTATA
37454 ATGCACCCATATGCATTTCAATTATGG
64 ATGCACCCATATGCATTTCAATTATGG
*
37481 CATCATTTCATGCCGATAATGCACCCATATGCATTTCAATTATGACATCCTTTCATACCTATAAT
1 CATCATTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATACCTATAAT
37546 GCA
66 GCA
37549 TTGTTGTATA
Statistics
Matches: 145, Mismatches: 9, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
89 1 0.01
90 142 0.98
91 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (90 bp):
CATCATTTCATGCCGATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATACCTATAAT
GCACCCATATGCATTTCAATTATGG
Found at i:38006 original size:135 final size:134
Alignment explanation
Indices: 37809--38399 Score: 884
Period size: 135 Copynumber: 4.4 Consensus size: 134
37799 TCTTTAACCG
*
37809 TTCATCTAACTGGCATAATTGACACATTTCT-TCCAAATGCACA-TCTAGGCCTCAAAGGCACTT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGT-C-AATGCACAGT-TAGGCCTCAAAGGCACTT
* * * **
37872 AGCCTTTCATCTAACAGGCACAATTAACACCTTTCT-TCCAAATGCACAACTAGGCCTCAAAGGC
63 AGCCTTTCATCTAACTGGCACAATTGACACCTTTATGT-C-AATGCACAGTTAGGCCTCAAAGGC
37936 ACTTAGCCT
126 ACTTAGCCT
* * *
37945 TTCATCTAACTGGCACAATTAACACCTTTCTGTCAATGCACAGTTAGGCCTTAAAGGCACTTAGC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
* * * *
38010 CTTTCATCTAACTGGAACAATTGACACCATTCTATCAATGCACAGTTAGGCCTCAAAGGCACTTA
66 CTTTCATCTAACTGGCACAATTGACACCTTTATGTCAATGCACAGTTAGGCCTCAAAGGCACTTA
38075 GCCT
131 GCCT
* * * *
38079 TTCATCTAACTGGCACAATTGACACATTTCTGCCAAATGCACAGTTAGGCCCCAAAGGCACTTAG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTC-AATGCACAGTTAGGCCTCAAAGGCACTTAG
*
38144 ACTTTCATCTAACTGGCACAATTGACACCTTTATGTCAATGCACAGTTAGGCCTCAAAGGCACTT
65 CCTTTCATCTAACTGGCACAATTGACACCTTTATGTCAATGCACAGTTAGGCCTCAAAGGCACTT
38209 AGCCT
130 AGCCT
* * * * *
38214 TTCATCTAACT-GCATAACTAACATCTTTTTGTCAATGCACAGTTAGGCCTCAAAGGAACTTAGC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
*
38278 CTTTCATCTTACTGGCACAATTGACACCTTTATGTCAATGCACAGTTAGGCCTCAAAGGCACTTA
66 CTTTCATCTAACTGGCACAATTGACACCTTTATGTCAATGCACAGTTAGGCCTCAAAGGCACTTA
38343 GCCT
131 GCCT
38347 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCA
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCA
38400 TAATTTTTTA
Statistics
Matches: 415, Mismatches: 35, Indels: 12
0.90 0.08 0.03
Matches are distributed among these distances:
133 107 0.26
134 114 0.27
135 162 0.39
136 31 0.07
137 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (134 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
CTTTCATCTAACTGGCACAATTGACACCTTTATGTCAATGCACAGTTAGGCCTCAAAGGCACTTA
GCCT
Found at i:38020 original size:67 final size:67
Alignment explanation
Indices: 37809--38399 Score: 875
Period size: 67 Copynumber: 8.8 Consensus size: 67
37799 TCTTTAACCG
* *
37809 TTCATCTAACTGGCATAATTGACACATTTCT-TCCAAATGCACA-TCTAGGCCTCAAAGGCACTT
1 TTCATCTAACTGGCACAATTGACACCTTTCTGT-C-AATGCACAGT-TAGGCCTCAAAGGCACTT
37872 AGCCT
63 AGCCT
* * **
37877 TTCATCTAACAGGCACAATTAACACCTTTCT-TCCAAATGCACAACTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCACAATTGACACCTTTCTGT-C-AATGCACAGTTAGGCCTCAAAGGCACTTA
37941 GCCT
64 GCCT
* *
37945 TTCATCTAACTGGCACAATTAACACCTTTCTGTCAATGCACAGTTAGGCCTTAAAGGCACTTAGC
1 TTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
38010 CT
66 CT
* * *
38012 TTCATCTAACTGGAACAATTGACACCATTCTATCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
1 TTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
38077 CT
66 CT
* * *
38079 TTCATCTAACTGGCACAATTGACACATTTCTGCCAAATGCACAGTTAGGCCCCAAAGGCACTTAG
1 TTCATCTAACTGGCACAATTGACACCTTTCTGTC-AATGCACAGTTAGGCCTCAAAGGCACTTAG
*
38144 ACT
65 CCT
*
38147 TTCATCTAACTGGCACAATTGACACCTTTATGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
1 TTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
38212 CT
66 CT
* * * * * *
38214 TTCATCTAACT-GCATAACTAACATCTTTTTGTCAATGCACAGTTAGGCCTCAAAGGAACTTAGC
1 TTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
38278 CT
66 CT
* *
38280 TTCATCTTACTGGCACAATTGACACCTTTATGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
1 TTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
38345 CT
66 CT
*
38347 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCA
1 TTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCA
38400 TAATTTTTTA
Statistics
Matches: 477, Mismatches: 42, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
66 59 0.12
67 262 0.55
68 155 0.32
69 1 0.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (67 bp):
TTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
CT
Found at i:38156 original size:202 final size:200
Alignment explanation
Indices: 37809--38399 Score: 891
Period size: 202 Copynumber: 2.9 Consensus size: 200
37799 TCTTTAACCG
37809 TTCATCTAACTGGCATAATTGACACATTTCTTCCAAATGCACA-TCTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAATTGACACA-TTCTT-C-AATGCACAGT-TAGGCCTCAAAGGCACTTA
* * * **
37873 GCCTTTCATCTAACAGGCACAATTAACACCTTTCTTCCAAATGCACAACTAGGCCTCAAAGGCAC
62 GCCTTTCATCTAACTGGCACAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCTCAAAGGCAC
* *
37938 TTAGCCTTTCATCTAACTGGCACAATTAACACCTTTCTGTCAATGCACAGTTAGGCCTTAAAGGC
127 TTAGCCTTTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGC
38003 ACTTAGCCT
192 ACTTAGCCT
* *
38012 TTCATCTAACTGGAACAATTGACACCATTCTATCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
1 TTCATCTAACTGGCATAATTGACA-CATTCT-TCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
* *
38077 CTTTCATCTAACTGGCACAATTGACACATTTCTGCCAAATGCACAGTTAGGCCCCAAAGGCACTT
64 CTTTCATCTAACTGGCACAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCTCAAAGGCACTT
* *
38142 AGACTTTCATCTAACTGGCACAATTGACACCTTTATGTCAATGCACAGTTAGGCCTCAAAGGCAC
129 AGCCTTTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCAC
38207 TTAGCCT
194 TTAGCCT
* * * * *
38214 TTCATCTAACT-GCATAACTAACATCTTTTTGTCAATGCACAGTTAGGCCTCAAAGGAACTTAGC
1 TTCATCTAACTGGCATAATTGACA-CATTCT-TCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
* * *
38278 CTTTCATCTTACTGGCACAATTGACACCTTTATGTC-AATGCACAGTTAGGCCTCAAAGGCACTT
64 CTTTCATCTAACTGGCACAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCTCAAAGGCACTT
*
38342 AGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCA
129 AGCCTTTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCA
38400 TAATTTTTTA
Statistics
Matches: 355, Mismatches: 30, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
200 82 0.23
201 76 0.21
202 166 0.47
203 28 0.08
204 3 0.01
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (200 bp):
TTCATCTAACTGGCATAATTGACACATTCTTCAATGCACAGTTAGGCCTCAAAGGCACTTAGCCT
TTCATCTAACTGGCACAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
CCTTTCATCTAACTGGCACAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTT
AGCCT
Found at i:38778 original size:55 final size:55
Alignment explanation
Indices: 38600--38912 Score: 456
Period size: 54 Copynumber: 5.7 Consensus size: 55
38590 GATAATTTCA
*
38600 CATATAGAAATTCATACACTTAGTATGGATTTCTTA-TTTCGCACACATAGTGCC
1 CATACAGAAATTCATACACTTAGTATGGATTTCTTAGTTTCGCACACATAGTGCC
38654 CATAC-GAAAATTCATACACTTAGTATGGATTTCTTAG-TTCGCACACATAGTGCC
1 CATACAG-AAATTCATACACTTAGTATGGATTTCTTAGTTTCGCACACATAGTGCC
** * *
38708 CATAC-GAAAATTCATACACTTAGTATAAATTTCTTAGTTTTGCACACAAAGTGCC
1 CATACAG-AAATTCATACACTTAGTATGGATTTCTTAGTTTCGCACACATAGTGCC
*
38763 CATACAGAAATTCATACACTTAGTATGGATTTCTTAG-TTCGCACACTTAGTGCC
1 CATACAGAAATTCATACACTTAGTATGGATTTCTTAGTTTCGCACACATAGTGCC
* * * *
38817 CATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACTCAAAGTGCC
1 CATACAGAAATTCATACACTTAGTATGGATTTCTTAGTTTCGCACACATAGTGCC
* *
38872 CATACATAAATTCATACACCTAGTATGGATTTCTTAAGTTT
1 CATACAGAAATTCATACACTTAGTATGGATTTCTT-AGTTT
38913 TTGCACACTC
Statistics
Matches: 235, Mismatches: 18, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
53 1 0.00
54 135 0.57
55 93 0.40
56 6 0.03
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (55 bp):
CATACAGAAATTCATACACTTAGTATGGATTTCTTAGTTTCGCACACATAGTGCC
Found at i:38797 original size:109 final size:109
Alignment explanation
Indices: 38600--38907 Score: 496
Period size: 109 Copynumber: 2.8 Consensus size: 109
38590 GATAATTTCA
* * * *
38600 CATATAGAAATTCATACACTTAGTATGGATTTCTTA-TTTCGCACACATAGTGCCCATAC-GAAA
1 CATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAG-AA
38663 ATTCATACACTTAGTATGGATTTCTTAGTTCGCACACATAGTGCC
65 ATTCATACACTTAGTATGGATTTCTTAGTTCGCACACATAGTGCC
*
38708 CATAC-GAAAATTCATACACTTAGTATAAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAA
1 CATACAG-AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAA
*
38772 ATTCATACACTTAGTATGGATTTCTTAGTTCGCACACTTAGTGCC
65 ATTCATACACTTAGTATGGATTTCTTAGTTCGCACACATAGTGCC
* *
38817 CATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACTCAAAGTGCCCATACATAAA
1 CATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAAA
*
38882 TTCATACACCTAGTATGGATTTCTTA
66 TTCATACACTTAGTATGGATTTCTTA
38908 AGTTTTTGCA
Statistics
Matches: 186, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
107 1 0.01
108 31 0.17
109 152 0.82
110 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.34
Consensus pattern (109 bp):
CATACAGAAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAAAGTGCCCATACAGAAA
TTCATACACTTAGTATGGATTTCTTAGTTCGCACACATAGTGCC
Found at i:40959 original size:20 final size:22
Alignment explanation
Indices: 40929--40985 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
40919 ATTTCTGGCT
40929 CATGAGTATCGATACCA-T-TAC
1 CATG-GTATCGATACCACTATAC
*
40950 CATGGTATCGATACTACTATAC
1 CATGGTATCGATACCACTATAC
*
40972 CATGGTACCGATAC
1 CATGGTATCGATAC
40986 TTTATTACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 11 0.34
21 5 0.16
22 16 0.50
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (22 bp):
CATGGTATCGATACCACTATAC
Found at i:42171 original size:2 final size:2
Alignment explanation
Indices: 42164--42188 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42154 AGCTTTATTG
42164 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
42189 TTGTTTACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:44101 original size:17 final size:17
Alignment explanation
Indices: 44079--44133 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
44069 AATAATTACG
44079 AAAAATAAAACCCTTTC
1 AAAAATAAAACCCTTTC
*
44096 AAAAAT--AA---TTAC
1 AAAAATAAAACCCTTTC
44108 GAAAAATAAAACCCTTTC
1 -AAAAATAAAACCCTTTC
44126 AAAAATAA
1 AAAAATAA
44134 TTACGAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
12 3 0.10
13 6 0.20
15 4 0.13
17 14 0.47
18 3 0.10
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (17 bp):
AAAAATAAAACCCTTTC
Found at i:44102 original size:30 final size:29
Alignment explanation
Indices: 43989--44263 Score: 234
Period size: 29 Copynumber: 9.5 Consensus size: 29
43979 ATAAATTTAT
* * *
43989 TTACGAAACTATCACCCTTTTAAAAATAT
1 TTACGAAAATAACACCCTTTTAAAAATAA
*
44018 TTACGAAAATAACACCATTTT-AAAATAA
1 TTACGAAAATAACACCCTTTTAAAAATAA
* *
44046 TTACGAAAATAGCA-TCTTTTAAAAATAA
1 TTACGAAAATAACACCCTTTTAAAAATAA
* *
44074 TTACGAAAAATAAAACCCTTTCAAAAATAA
1 TTACG-AAAATAACACCCTTTTAAAAATAA
* *
44104 TTACGAAAAATAAAACCCTTTCAAAAATAA
1 TTACG-AAAATAACACCCTTTTAAAAATAA
*
44134 TTACGAAAATAGCACCCTTTTAAAAATAA
1 TTACGAAAATAACACCCTTTTAAAAATAA
* * *** *
44163 TTAC-AAAATAGCACCGTTACCGAAATTAA
1 TTACGAAAATAACACCCTT-TTAAAAATAA
* * * *
44192 TTAC-AAAACTAACATCATTTTAAACATAT
1 TTACGAAAA-TAACACCCTTTTAAAAATAA
* * * * *
44221 TTATGAAACTAGCACACTTTTAAAAATAT
1 TTACGAAAATAACACCCTTTTAAAAATAA
* *
44250 TTACAAAAACAACA
1 TTACGAAAATAACA
44264 TCAAACAGAA
Statistics
Matches: 200, Mismatches: 40, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
27 4 0.02
28 44 0.22
29 95 0.47
30 57 0.28
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.28
Consensus pattern (29 bp):
TTACGAAAATAACACCCTTTTAAAAATAA
Found at i:44241 original size:87 final size:85
Alignment explanation
Indices: 44010--44257 Score: 266
Period size: 87 Copynumber: 2.9 Consensus size: 85
44000 TCACCCTTTT
* *
44010 AAAAATATTTACGAAAATAACACCATTTTAAAATAATTACGAAAATAGCA-TCTTTTAAAAATAA
1 AAAAATAATTACGAAAATAACACCATTTTAAAATAATTACGAAAATAGCACACTTTTAAAAATAA
*
44074 TTACGAAAAATAAAACCCTTTC
66 TTAC--AAAATAAAACCCTTCC
* * * *
44096 AAAAATAATTACGAAAAATAAAACCCTTTCAAAAATAATTACGAAAATAGCACCCTTTTAAAAAT
1 AAAAATAATTACG-AAAATAACACCATTT-TAAAATAATTACGAAAATAGCACACTTTTAAAAAT
** *
44161 AATTACAAAATAGCACCGTTACC
64 AATTACAAAATAAAACCCTT-CC
* * * * * *
44184 GAAATTAATTAC-AAAACTAACATCATTTTAAACATATTTATGAAACTAGCACACTTTTAAAAAT
1 AAAAATAATTACGAAAA-TAACACCATTTTAAA-ATAATTACGAAAATAGCACACTTTTAAAAAT
*
44248 ATTTACAAAA
64 AATTACAAAA
44258 ACAACATCAA
Statistics
Matches: 136, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
86 19 0.14
87 68 0.50
88 32 0.24
89 17 0.12
ACGTcount: A:0.52, C:0.15, G:0.05, T:0.28
Consensus pattern (85 bp):
AAAAATAATTACGAAAATAACACCATTTTAAAATAATTACGAAAATAGCACACTTTTAAAAATAA
TTACAAAATAAAACCCTTCC
Found at i:44246 original size:116 final size:115
Alignment explanation
Indices: 43986--44263 Score: 292
Period size: 116 Copynumber: 2.4 Consensus size: 115
43976 ATCATAAATT
*
43986 TATTTACGAAACTATCACCCTTTTAAAAATATTTACGAAAATAACACCATTTTAAAATAATTACG
1 TATTTACGAAACTAACACCCTTTTAAAAATATTTACGAAAATAACACCATTTTAAAATAATTACG
** *
44051 AAAATAGCATCTTTTAAAAATAATTACGAAAAATAAAACCCTTTCAAAAA
66 AAAATAGCATCCGTTAAAAATAATTACGAAAAATAAAACCATTTCAAAAA
* * * * * * *
44101 TAATTACGAAAAATAAAACCCTTTCAAAAATAATTACGAAAATAGCACCCTTTTAAAAATAATTA
1 TATTTACG-AAACTAACACCCTTTTAAAAATATTTACGAAAATAACACCATTTT-AAAATAATTA
* * * * * *
44166 C-AAAATAGCA-CCGTTACCGAAATTAATTAC-AAAACTAACATCATTTTAAACA
64 CGAAAATAGCATCCGTTA---AAAATAATTACGAAAAATAAAACCATTTCAAAAA
* * * * *
44218 TATTTATGAAACTAGCACACTTTTAAAAATATTTACAAAAACAACA
1 TATTTACGAAACTAACACCCTTTTAAAAATATTTACGAAAATAACA
44264 TCAAACAGAA
Statistics
Matches: 130, Mismatches: 28, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
115 11 0.08
116 76 0.58
117 33 0.25
118 10 0.08
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.29
Consensus pattern (115 bp):
TATTTACGAAACTAACACCCTTTTAAAAATATTTACGAAAATAACACCATTTTAAAATAATTACG
AAAATAGCATCCGTTAAAAATAATTACGAAAAATAAAACCATTTCAAAAA
Found at i:44337 original size:58 final size:58
Alignment explanation
Indices: 44232--44345 Score: 142
Period size: 58 Copynumber: 2.0 Consensus size: 58
44222 TATGAAACTA
* *
44232 GCACACTTTTAAAAATATTTACAAAAACAACATCAAACAGAATTTAATTACGTATTAG
1 GCACACTTTTAAAAATATTCACAAAAACAACATCAAACAGAAATTAATTACGTATTAG
* * * *
44290 GCACTCTTTTAAAAATATTCCCAGAATAACACCAT-AACCA-AAATTAATTACGTATT
1 GCACACTTTTAAAAATATTCACA-AA-AACAACATCAAACAGAAATTAATTACGTATT
44346 TATCACCCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 35 0.73
59 6 0.12
60 7 0.15
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (58 bp):
GCACACTTTTAAAAATATTCACAAAAACAACATCAAACAGAAATTAATTACGTATTAG
Found at i:44853 original size:20 final size:20
Alignment explanation
Indices: 44828--44865 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
44818 CACTTCATTT
44828 TTTTATTCT-TAGTGCTATTA
1 TTTTATT-TATAGTGCTATTA
44848 TTTTATTTATAGTGCTAT
1 TTTTATTTATAGTGCTAT
44866 AGGATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.21, C:0.08, G:0.11, T:0.61
Consensus pattern (20 bp):
TTTTATTTATAGTGCTATTA
Found at i:51538 original size:28 final size:29
Alignment explanation
Indices: 51456--51686 Score: 202
Period size: 29 Copynumber: 8.1 Consensus size: 29
51446 ATGAAACTAT
* *
51456 CACCCTTTTAAAAATATTTACGAAAATAG
1 CACCTTTTTAAAAATAATTACGAAAATAG
*
51485 CACCTTTTTTAAAATAATTACGAAAATAG
1 CACCTTTTTAAAAATAATTACGAAAATAG
** * *
51514 CATTTTTTTAAAAATAATTACAAAAATAA
1 CACCTTTTTAAAAATAATTACGAAAATAG
*
51543 AACCTTTTTAAAAATAATTAC-AAAATAG
1 CACCTTTTTAAAAATAATTACGAAAATAG
* *
51571 TACCCTTTT-AAAATAATTACGAAAATAG
1 CACCTTTTTAAAAATAATTACGAAAATAG
*** * *
51599 CACCTTACCAAAATTAATTAC-AAAACTAA
1 CACCTTTTTAAAAATAATTACGAAAA-TAG
* * * * *
51628 CATCATTTTAAACATATTTACGAAACTAG
1 CACCTTTTTAAAAATAATTACGAAAATAG
* * *
51657 TACAC-TTTT-AAAATATTTACAAAAATAG
1 CAC-CTTTTTAAAAATAATTACGAAAATAG
51685 CA
1 CA
51687 TCGAACAGAA
Statistics
Matches: 160, Mismatches: 37, Indels: 11
0.77 0.18 0.05
Matches are distributed among these distances:
27 11 0.07
28 45 0.28
29 100 0.62
30 4 0.03
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.32
Consensus pattern (29 bp):
CACCTTTTTAAAAATAATTACGAAAATAG
Found at i:51592 original size:85 final size:86
Alignment explanation
Indices: 51461--51688 Score: 278
Period size: 85 Copynumber: 2.7 Consensus size: 86
51451 ACTATCACCC
* * * ***
51461 TTTTAAAAATATTTACGAAAATAGCACCTTTTTTAAAATAATTACGAAAATAGCATTTTTTTAAA
1 TTTTAAAAATATTTACGAAAATAGTACC-CTTTTAAAATAATTACGAAAATAGCATCTTACCAAA
*
51526 AATAATTACAAAAATAAAACCT
65 AATAATTACAAAAATAAAACCA
* *
51548 TTTTAAAAATAATTAC-AAAATAGTACCCTTTTAAAATAATTACGAAAATAGCACCTTACCAAAA
1 TTTTAAAAATATTTACGAAAATAGTACCCTTTTAAAATAATTACGAAAATAGCATCTTACCAAAA
* * * *
51612 TTAATTACAAAACTAACATCA
66 ATAATTACAAAAATAAAACCA
* * * * *
51633 TTTTAAACATATTTACGAAACTAGTACACTTTTAAAATATTTACAAAAATAGCATC
1 TTTTAAAAATATTTACGAAAATAGTACCCTTTTAAAATAATTACGAAAATAGCATC
51689 GAACAGAAAT
Statistics
Matches: 120, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
85 61 0.51
86 44 0.37
87 15 0.12
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (86 bp):
TTTTAAAAATATTTACGAAAATAGTACCCTTTTAAAATAATTACGAAAATAGCATCTTACCAAAA
ATAATTACAAAAATAAAACCA
Found at i:51666 original size:114 final size:114
Alignment explanation
Indices: 51457--51680 Score: 258
Period size: 114 Copynumber: 2.0 Consensus size: 114
51447 TGAAACTATC
* *** * **
51457 ACCCTTTTAAAAATATTTACGAAAATAGCACCTTTTTTAAAATAATTACGAAAATAGCATTTTTT
1 ACCCTTTTAAAAATAATTACGAAAATAGCACCTTTACCAAAATAATTACGAAAATAACATCATTT
51522 TAAAAATAATTACAAAAATAAAACCTTTTTAAAAATAATTACAAAATAGT
66 TAAAAATAATTACAAAAATAAAACCTTTTT-AAAATAATTACAAAATAGT
51572 ACCCTTTT-AAAATAATTACGAAAATAGCACC-TTACCAAAATTAATTAC-AAAACTAACATCAT
1 ACCCTTTTAAAAATAATTACGAAAATAGCACCTTTACCAAAA-TAATTACGAAAA-TAACATCAT
* * * * ** *
51634 TTTAAACATATTTACGAAACTAGTACAC-TTTTAAAATATTTACAAAA
64 TTTAAAAATAATTACAAAAATAAAAC-CTTTTTAAAATAATTACAAAA
51681 ATAGCATCGA
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
113 24 0.26
114 59 0.64
115 9 0.10
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (114 bp):
ACCCTTTTAAAAATAATTACGAAAATAGCACCTTTACCAAAATAATTACGAAAATAACATCATTT
TAAAAATAATTACAAAAATAAAACCTTTTTAAAATAATTACAAAATAGT
Found at i:56228 original size:30 final size:28
Alignment explanation
Indices: 56194--56463 Score: 130
Period size: 30 Copynumber: 9.1 Consensus size: 28
56184 CATATTAGAT
*
56194 TTAAAGGACTTAAATAGTAATAACATAAAC
1 TTAAAGGACTAAAATAGTAA-AA-ATAAAC
* *
56224 TTAAAGGGCTAAAATAGTAAAAATAGCAAT
1 TTAAAGGACTAAAATAGTAAAAATA--AAC
* *
56254 TTAAGGGACTAAAATAGCAAAAATAGAAAC
1 TTAAAGGACTAAAATAGTAAAAAT--AAAC
* * * ** * *
56284 TTAAAGGATTAACACAACAAAATAGAAAT
1 TTAAAGGACTAAAATAGTAAAA-ATAAAC
* * * *
56313 TTAAAGGAATAAAATGGCAAAAACAAAAAC
1 TTAAAGGACTAAAATAG-TAAAA-ATAAAC
* *
56343 TTAAAGGTCTAAAATAGTAAAAACCAAAAC
1 TTAAAGGACTAAAATAGTAAAAA--TAAAC
* * * *
56373 TTAAGGGTCT-AAATAGCAAATACA-AATAT
1 TTAAAGGACTAAAATAGTAAA-A-ATAA-AC
** *
56402 TTAAAGGACTAAAATAACAAAAATAGACAT
1 TTAAAGGACTAAAATAGTAAAAATA-A-AC
* * *
56432 TTAAAGGACTAAAATAGCAAATAGAAAC
1 TTAAAGGACTAAAATAGTAAAAATAAAC
56460 TTAA
1 TTAA
56464 GCAACTAAAA
Statistics
Matches: 188, Mismatches: 38, Indels: 30
0.73 0.15 0.12
Matches are distributed among these distances:
28 12 0.06
29 42 0.22
30 131 0.70
31 2 0.01
32 1 0.01
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (28 bp):
TTAAAGGACTAAAATAGTAAAAATAAAC
Found at i:56335 original size:89 final size:89
Alignment explanation
Indices: 56224--56463 Score: 233
Period size: 89 Copynumber: 2.7 Consensus size: 89
56214 TAACATAAAC
* * *
56224 TTAAAGGGCTAAAATAGTAAAAATAGCAATTTAAGGGACTAAAATAGCAAAAATAGAAACTTAAA
1 TTAAAGGACTAAAATAGCAAAAATAG-AATTTAAAGGACTAAAATAGCAAAAATAGAAACTTAAA
*
56289 GGAT-TAACACAACAAAATA-GAA-AT
65 GGATCTAA-ACAAC-AAATACAAATAT
* * * * * * * *
56313 TTAAAGGAATAAAATGGCAAAAACAAAAACTTAAAGGTCTAAAATAGTAAAAACCA-AAACTT-A
1 TTAAAGGACTAAAATAGCAAAAA-TAGAATTTAAAGGACTAAAATAGCAAAAA-TAGAAACTTAA
* * *
56376 AGGGTCTAAATAGCAAATACAAATAT
64 AGGATCTAAACAACAAATACAAATAT
*
56402 TTAAAGGACTAAAATAACAAAAATAGACATTTAAAGGACTAAAATAGC--AAATAGAAACTTAA
1 TTAAAGGACTAAAATAGCAAAAATAGA-ATTTAAAGGACTAAAATAGCAAAAATAGAAACTTAA
56464 GCAACTAAAA
Statistics
Matches: 119, Mismatches: 24, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
86 1 0.01
87 14 0.12
88 13 0.11
89 89 0.75
90 2 0.02
ACGTcount: A:0.57, C:0.10, G:0.13, T:0.20
Consensus pattern (89 bp):
TTAAAGGACTAAAATAGCAAAAATAGAATTTAAAGGACTAAAATAGCAAAAATAGAAACTTAAAG
GATCTAAACAACAAATACAAATAT
Found at i:56444 original size:59 final size:60
Alignment explanation
Indices: 56192--56463 Score: 234
Period size: 59 Copynumber: 4.6 Consensus size: 60
56182 ATCATATTAG
* * * * ** *
56192 ATTTAAAGGACTTAAATAG-TAATAACATAAACTTAAAGGGCTAAAATAGTAAAAATAGCA
1 ATTTAAAGGACTAAAATAGCAAAT-ACAGAAACTTAAAGGACTAAAATAACAAAAATAGAA
* * * * * *
56252 ATTTAAGGGACTAAAATAGCAAAAATAGAAACTTAAAGGATTAACACAAC-AAAATAGAA
1 ATTTAAAGGACTAAAATAGCAAATACAGAAACTTAAAGGACTAAAATAACAAAAATAGAA
* * * * * ** *
56311 ATTTAAAGGAATAAAATGGCAAAAACAAAAACTTAAAGGTCTAAAATAGTAAAAACCA-AA
1 ATTTAAAGGACTAAAATAGCAAATACAGAAACTTAAAGGACTAAAATAACAAAAA-TAGAA
* * * * *
56371 ACTTAAGGGTCT-AAATAGCAAATACA-AATATTTAAAGGACTAAAATAACAAAAATAGAC
1 ATTTAAAGGACTAAAATAGCAAATACAGAA-ACTTAAAGGACTAAAATAACAAAAATAGAA
56430 ATTTAAAGGACTAAAATAGCAAAT--AGAAACTTAA
1 ATTTAAAGGACTAAAATAGCAAATACAGAAACTTAA
56464 GCAACTAAAA
Statistics
Matches: 164, Mismatches: 41, Indels: 16
0.74 0.19 0.07
Matches are distributed among these distances:
58 9 0.05
59 92 0.56
60 60 0.37
61 3 0.02
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.21
Consensus pattern (60 bp):
ATTTAAAGGACTAAAATAGCAAATACAGAAACTTAAAGGACTAAAATAACAAAAATAGAA
Found at i:57813 original size:3 final size:3
Alignment explanation
Indices: 57805--57873 Score: 129
Period size: 3 Copynumber: 22.7 Consensus size: 3
57795 AAATGTAATT
57805 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57853 TAA TAA TAA TAA TAGA TAA TA
1 TAA TAA TAA TAA TA-A TAA TA
57874 TTTTTGTAGA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 62 0.95
4 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:60730 original size:19 final size:19
Alignment explanation
Indices: 60706--60752 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
60696 CCAGCCTATA
60706 ACTCGATTCGAGACTCGTG
1 ACTCGATTCGAGACTCGTG
* *
60725 ACTCGATTCGAGATTTGTG
1 ACTCGATTCGAGACTCGTG
*
60744 ACCCGATTC
1 ACTCGATTC
60753 AAGATTTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (19 bp):
ACTCGATTCGAGACTCGTG
Found at i:60757 original size:19 final size:19
Alignment explanation
Indices: 60722--60770 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
60712 TTCGAGACTC
* *
60722 GTGACTCGATTCGAGATTT
1 GTGACCCGATTCAAGATTT
60741 GTGACCCGATTCAAGATTT
1 GTGACCCGATTCAAGATTT
*
60760 GTGACCTGATT
1 GTGACCCGATT
60771 TATTACTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (19 bp):
GTGACCCGATTCAAGATTT
Found at i:61772 original size:29 final size:29
Alignment explanation
Indices: 61739--61809 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
61729 TTGGTTCGTG
61739 AGTTTGAGTCGAGTTGAGCTTACTTTTAA
1 AGTTTGAGTCGAGTTGAGCTTACTTTTAA
*
61768 AGTTTGAGTCGAGTTGAGCTTATTTTTAA
1 AGTTTGAGTCGAGTTGAGCTTACTTTTAA
61797 AGTTTGAGTCGAG
1 AGTTTGAGTCGAG
61810 CTCAGCAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (29 bp):
AGTTTGAGTCGAGTTGAGCTTACTTTTAA
Found at i:63392 original size:28 final size:28
Alignment explanation
Indices: 63360--63415 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
63350 GATCAATGTA
63360 ACCTTATAGATTTGGCTATAACATTTAG
1 ACCTTATAGATTTGGCTATAACATTTAG
*
63388 ACCTTCTAGATTTGGCTATAACATTTAG
1 ACCTTATAGATTTGGCTATAACATTTAG
63416 GTCAGGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (28 bp):
ACCTTATAGATTTGGCTATAACATTTAG
Found at i:64472 original size:17 final size:17
Alignment explanation
Indices: 64450--64511 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
64440 AGACGAAAAC
* *
64450 GAAAATGAACAAAATAA
1 GAAAATAAAAAAAATAA
64467 GAAAATAAAAAAAAT-A
1 GAAAATAAAAAAAATAA
64483 -AAAATAATAAAAAATAA
1 GAAAATAA-AAAAAATAA
*
64500 AAATAATAAAAA
1 GAA-AATAAAAA
64512 TTGAAGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.18
16 8 0.21
17 14 0.36
18 5 0.13
19 5 0.13
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.15
Consensus pattern (17 bp):
GAAAATAAAAAAAATAA
Found at i:64494 original size:16 final size:16
Alignment explanation
Indices: 64468--64511 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
64458 ACAAAATAAG
64468 AAAATAA-AAAAAATA
1 AAAATAATAAAAAATA
64483 AAAATAATAAAAAATA
1 AAAATAATAAAAAATA
64499 AAAATAATAAAAA
1 AAAATAATAAAAA
64512 TTGAAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 7 0.25
16 21 0.75
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAATAATAAAAAATA
Found at i:64496 original size:25 final size:26
Alignment explanation
Indices: 64462--64512 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 26
64452 AAATGAACAA
64462 AATAAGAAAATAAAAAAAATAAAAAT
1 AATAAGAAAATAAAAAAAATAAAAAT
*
64488 AATAA-AAAATAAAAATAATAAAAAT
1 AATAAGAAAATAAAAAAAATAAAAAT
64513 TGAAGAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (26 bp):
AATAAGAAAATAAAAAAAATAAAAAT
Found at i:64512 original size:9 final size:9
Alignment explanation
Indices: 64470--64512 Score: 63
Period size: 9 Copynumber: 5.0 Consensus size: 9
64460 AAAATAAGAA
*
64470 AATAAAAAA
1 AATAAAAAT
64479 AATAAAAAT
1 AATAAAAAT
64488 AAT-AAAA-
1 AATAAAAAT
64495 AATAAAAAT
1 AATAAAAAT
64504 AATAAAAAT
1 AATAAAAAT
64513 TGAAGAAAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 3 0.10
8 8 0.26
9 20 0.65
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AATAAAAAT
Found at i:64521 original size:25 final size:25
Alignment explanation
Indices: 64463--64531 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 25
64453 AATGAACAAA
64463 ATAAGAAAATAAAAAAAATAAAAAT
1 ATAAGAAAATAAAAAAAATAAAAAT
*
64488 AATAA-AAAATAAAAATAATAAAAAT
1 -ATAAGAAAATAAAAAAAATAAAAAT
*
64513 -TGAAGAAAAGTAAATAAAA
1 AT-AAGAAAA-TAAAAAAAA
64532 GAAACAAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 1 0.03
24 2 0.05
25 23 0.62
26 11 0.30
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (25 bp):
ATAAGAAAATAAAAAAAATAAAAAT
Found at i:64542 original size:18 final size:18
Alignment explanation
Indices: 64518--64566 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
64508 AAAATTGAAG
64518 AAAAGTAAATAAAAGAAA
1 AAAAGTAAATAAAAGAAA
*
64536 CAAAGTAAA-ATAAAGAAA
1 AAAAGTAAATA-AAAGAAA
*
64554 AAAACTAAATAAA
1 AAAAGTAAATAAA
64567 TAAATAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 24 0.92
19 1 0.04
ACGTcount: A:0.76, C:0.04, G:0.08, T:0.12
Consensus pattern (18 bp):
AAAAGTAAATAAAAGAAA
Found at i:64662 original size:22 final size:22
Alignment explanation
Indices: 64637--64678 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
64627 AAAGATATAT
64637 AAAGATAAAATAAAATAAAATA
1 AAAGATAAAATAAAATAAAATA
64659 AAAGATAAAATAAAATAAAA
1 AAAGATAAAATAAAATAAAA
64679 GGATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (22 bp):
AAAGATAAAATAAAATAAAATA
Found at i:64734 original size:17 final size:17
Alignment explanation
Indices: 64626--64735 Score: 93
Period size: 17 Copynumber: 6.2 Consensus size: 17
64616 ATGTAAAAGA
*
64626 AAAAGAT-ATATAAAGAT
1 AAAAGATAAAATAAA-AT
64643 -AAA-ATAAAATAAAAT
1 AAAAGATAAAATAAAAT
64658 AAAAGATAAAATAAAAT
1 AAAAGATAAAATAAAAT
64675 AAAAGGAT-AAATAAAAT
1 AAAA-GATAAAATAAAAT
*
64692 GCATAAATAATAATAATAATAAT
1 --A-AAA-GATAA-AATAA-AAT
*
64715 AAAAGATAAAACAAAAT
1 AAAAGATAAAATAAAAT
64732 AAAA
1 AAAA
64736 CATGATGATG
Statistics
Matches: 78, Mismatches: 5, Indels: 20
0.76 0.05 0.19
Matches are distributed among these distances:
15 4 0.05
16 12 0.15
17 32 0.41
18 7 0.09
19 5 0.06
20 8 0.10
21 2 0.03
22 5 0.06
23 3 0.04
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (17 bp):
AAAAGATAAAATAAAAT
Found at i:64803 original size:16 final size:16
Alignment explanation
Indices: 64782--64818 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
64772 GTAACAATAA
*
64782 AAAAATAAAATAAAAT
1 AAAAATAAAAGAAAAT
*
64798 AAAAATAAAAGAAACT
1 AAAAATAAAAGAAAAT
64814 AAAAA
1 AAAAA
64819 GAATTATAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.81, C:0.03, G:0.03, T:0.14
Consensus pattern (16 bp):
AAAAATAAAAGAAAAT
Found at i:64946 original size:20 final size:20
Alignment explanation
Indices: 64895--64946 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
64885 ATATATATAT
64895 ATATATAATAAAAAAAAAAAA
1 ATATAT-ATAAAAAAAAAAAA
* *
64916 ATACTAT-TAAAAAATAATAA
1 ATA-TATATAAAAAAAAAAAA
64936 ATATATATAAA
1 ATATATATAAA
64947 TGGATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.11
20 18 0.67
21 3 0.11
22 3 0.11
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
ATATATATAAAAAAAAAAAA
Found at i:66424 original size:59 final size:59
Alignment explanation
Indices: 66325--66444 Score: 177
Period size: 59 Copynumber: 2.0 Consensus size: 59
66315 ATCGAACTCA
* * * *
66325 GAGTACTAGGAAGTAGCTCTTGGATCGTCTTATGGTTCAAGATACTTCTTCCTGAAGGT
1 GAGTACTAGGAAGTAGCTCCTGGATCATCTTATGGCTCAAGATACTTCATCCTGAAGGT
* * *
66384 GAGTATTAGGAAGTAGCTCCTGGATCATCTTCTGGCTCAAGATACTTCATCGTGAAGGT
1 GAGTACTAGGAAGTAGCTCCTGGATCATCTTATGGCTCAAGATACTTCATCCTGAAGGT
66443 GA
1 GA
66445 AACTTTCCTG
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 54 1.00
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (59 bp):
GAGTACTAGGAAGTAGCTCCTGGATCATCTTATGGCTCAAGATACTTCATCCTGAAGGT
Found at i:77939 original size:8 final size:7
Alignment explanation
Indices: 77915--77977 Score: 58
Period size: 7 Copynumber: 8.7 Consensus size: 7
77905 AAAATACTAG
77915 AAAAAAT
1 AAAAAAT
77922 GAATAAAAT
1 -AA-AAAAT
77931 AAGAAAAT
1 AA-AAAAT
77939 AAAAAAT
1 AAAAAAT
77946 AAGAAAAT
1 AA-AAAAT
77954 -AAAAA-
1 AAAAAAT
*
77959 AAATAAT
1 AAAAAAT
*
77966 AAATAAT
1 AAAAAAT
77973 AAAAA
1 AAAAA
77978 CTGAAGAAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
6 8 0.17
7 19 0.40
8 16 0.33
9 5 0.10
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (7 bp):
AAAAAAT
Found at i:77942 original size:24 final size:24
Alignment explanation
Indices: 77915--77976 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
77905 AAAATACTAG
*
77915 AAAAAATGAATAAAAT-AAGAAAAT
1 AAAAAAT-AATAAAATAAAAAAAAT
*
77939 AAAAAATAAGAAAATAAAAAAAAT
1 AAAAAATAATAAAATAAAAAAAAT
*
77963 AATAAATAATAAAA
1 AAAAAATAATAAAA
77977 ACTGAAGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 7 0.21
24 26 0.79
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (24 bp):
AAAAAATAATAAAATAAAAAAAAT
Found at i:77946 original size:15 final size:15
Alignment explanation
Indices: 77926--77959 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
77916 AAAAATGAAT
77926 AAAATAAGAAAATAA
1 AAAATAAGAAAATAA
77941 AAAATAAGAAAATAA
1 AAAATAAGAAAATAA
77956 AAAA
1 AAAA
77960 AATAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (15 bp):
AAAATAAGAAAATAA
Found at i:77976 original size:15 final size:17
Alignment explanation
Indices: 77917--77976 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 17
77907 AATACTAGAA
*
77917 AAAATGAATAAAATAAG
1 AAAATAAATAAAATAAG
77934 AAAAT-AA-AAAATAAG
1 AAAATAAATAAAATAAG
*
77949 AAAATAAAAAAAATAA-
1 AAAATAAATAAAATAAG
*
77965 TAAAT-AATAAAA
1 AAAATAAATAAAA
77977 ACTGAAGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
15 19 0.49
16 8 0.21
17 12 0.31
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (17 bp):
AAAATAAATAAAATAAG
Found at i:78012 original size:19 final size:19
Alignment explanation
Indices: 77990--78033 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
77980 GAAGAAAGGT
*
77990 AAATAAAAGAAACAAAGA-A
1 AAATAAAAGAAA-AAAAACA
78009 AAAT-AAAGAAAAAAAACA
1 AAATAAAAGAAAAAAAACA
78027 AAATAAA
1 AAATAAA
78034 TAAATAAGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.18
18 12 0.55
19 6 0.27
ACGTcount: A:0.82, C:0.05, G:0.07, T:0.07
Consensus pattern (19 bp):
AAATAAAAGAAAAAAAACA
Found at i:78015 original size:23 final size:22
Alignment explanation
Indices: 77916--78040 Score: 69
Period size: 24 Copynumber: 5.5 Consensus size: 22
77906 AAATACTAGA
* * *
77916 AAAAATGAATAAAATAAGAAA-
1 AAAAATAAATAAAAAAACAAAG
* *
77937 ATAAA-AAATAAGAAAATA-AAAA
1 AAAAATAAATAA-AAAA-ACAAAG
*
77959 AAATAATAAATAATAAAAACTGAAG
1 AAA-AATAAATAA-AAAAAC-AAAG
**
77984 AAAGGTAAATAAAAGAAACAAAG
1 AAAAATAAATAAAA-AAACAAAG
*
78007 AAAAATAAAGAAAAAAAACAAA-
1 AAAAATAAA-TAAAAAAACAAAG
*
78029 ATAAATAAATAA
1 AAAAATAAATAA
78041 GGAAAAGAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
20 5 0.06
21 12 0.15
22 11 0.14
23 22 0.28
24 25 0.31
25 5 0.06
ACGTcount: A:0.76, C:0.02, G:0.08, T:0.14
Consensus pattern (22 bp):
AAAAATAAATAAAAAAACAAAG
Found at i:78172 original size:17 final size:17
Alignment explanation
Indices: 78150--78182 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
78140 ATAAAAAATA
78150 ATAAAA-AAAGATAAAAG
1 ATAAAACAAA-ATAAAAG
78167 ATAAAACAAAATAAAA
1 ATAAAACAAAATAAAA
78183 CATGATGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.12
Consensus pattern (17 bp):
ATAAAACAAAATAAAAG
Found at i:78338 original size:21 final size:20
Alignment explanation
Indices: 78314--78374 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
78304 TAACGTGTAA
78314 AAATAATATATATATATAAAT
1 AAATAATA-ATATATATAAAT
*
78335 AAATAA-AATACTAT-TAAAA
1 AAATAATAATA-TATATAAAT
*
78354 AAATAATAAATTTATATAAAT
1 AAATAAT-AATATATATAAAT
78375 GGATAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
19 13 0.39
20 7 0.21
21 13 0.39
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATAATAATATATATAAAT
Found at i:80664 original size:19 final size:17
Alignment explanation
Indices: 80636--80677 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
80626 TTTTTTAATG
*
80636 ATAATGATGATAATTCATT
1 ATAATAATGATAA-T-ATT
80655 ATAATAATGATAATATT
1 ATAATAATGATAATATT
80672 ATAATA
1 ATAATA
80678 TGAAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 1 0.05
19 12 0.55
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (17 bp):
ATAATAATGATAATATT
Found at i:82168 original size:24 final size:24
Alignment explanation
Indices: 82141--82198 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
82131 TGCTGGCTAG
82141 AGAAGAGAAAGGAAATGAGAAGAA
1 AGAAGAGAAAGGAAATGAGAAGAA
82165 AGAAGAGAAAGGAAATGAGAAGAA
1 AGAAGAGAAAGGAAATGAGAAGAA
82189 AGAAGAGAAA
1 AGAAGAGAAA
82199 AGAGAAAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (24 bp):
AGAAGAGAAAGGAAATGAGAAGAA
Found at i:82654 original size:14 final size:14
Alignment explanation
Indices: 82635--82670 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
82625 GTACGAAGAT
82635 TGAATAGAGATGCA
1 TGAATAGAGATGCA
82649 TGAATAGAGATGCA
1 TGAATAGAGATGCA
82663 TGAATAGA
1 TGAATAGA
82671 TATTGCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.44, C:0.06, G:0.28, T:0.22
Consensus pattern (14 bp):
TGAATAGAGATGCA
Found at i:83957 original size:10 final size:10
Alignment explanation
Indices: 83942--83979 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
83932 GTATATAATA
83942 TAATGTAACG
1 TAATGTAACG
83952 TAATGTAACG
1 TAATGTAACG
*
83962 TAATGCAACG
1 TAATGTAACG
83972 TAATGTAA
1 TAATGTAA
83980 TATAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.29
Consensus pattern (10 bp):
TAATGTAACG
Found at i:83985 original size:20 final size:20
Alignment explanation
Indices: 83937--83985 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
83927 AGAAGGTATA
*
83937 TAATATAATGTAACGTAATG
1 TAATATAATGCAACGTAATG
**
83957 TAACGTAATGCAACGTAATG
1 TAATATAATGCAACGTAATG
83977 TAATATAAT
1 TAATATAAT
83986 ATTATATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.33
Consensus pattern (20 bp):
TAATATAATGCAACGTAATG
Found at i:84742 original size:21 final size:21
Alignment explanation
Indices: 84718--84770 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
84708 ATTCTGACTA
*
84718 TCGCATTGTGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
84739 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
84760 TCGCAATGCGA
1 TCGCATTGCGA
84771 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:85425 original size:33 final size:34
Alignment explanation
Indices: 85375--85447 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
85365 ACTATCGCAA
** *
85375 TGCGATTCTGTCATTGCGATTTTC-ATTTCGCGT
1 TGCGATTCTGTCATTGCGATAGTCAAATTCGCGT
*
85408 TGCGATTCT-TGCGTTGCGATAGTCAAATTCGCGT
1 TGCGATTCTGT-CATTGCGATAGTCAAATTCGCGT
85442 TGCGAT
1 TGCGAT
85448 AGTCATTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 1 0.03
33 19 0.56
34 14 0.41
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (34 bp):
TGCGATTCTGTCATTGCGATAGTCAAATTCGCGT
Found at i:85443 original size:20 final size:20
Alignment explanation
Indices: 85418--85467 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
85408 TGCGATTCTT
85418 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
85438 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
85458 GTGTTGCGAT
1 GCGTTGCGAT
85468 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:85473 original size:20 final size:20
Alignment explanation
Indices: 85435--85489 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
85425 GATAGTCAAA
* **
85435 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
85455 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
85475 TTCGTGTTGTGATTT
1 TTCGTGTTGCGATTT
85490 AAAGTTTCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.15, G:0.24, T:0.51
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:85497 original size:20 final size:20
Alignment explanation
Indices: 85454--85497 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
85444 CGATAGTCAT
** *
85454 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
*
85474 TTTCGTGTTGTGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
85494 TTTC
1 TTTC
85498 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:87401 original size:20 final size:20
Alignment explanation
Indices: 87376--87465 Score: 162
Period size: 20 Copynumber: 4.5 Consensus size: 20
87366 AGAATAGTTT
87376 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
87396 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
87416 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
87436 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
87456 ACTATCGCAA
1 ACTATCGCAA
87466 CGAAAGAATC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:87431 original size:40 final size:40
Alignment explanation
Indices: 87376--87503 Score: 162
Period size: 40 Copynumber: 3.4 Consensus size: 40
87366 AGAATAGTTT
87376 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
**
87416 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
87456 ACTATCGCAA--CG-AAA-GA--ATCGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
** *
87489 AAAATCGCATTGCGA
1 ACTATCGCAATGCGA
87504 TTCTCTCGTT
Statistics
Matches: 78, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
33 10 0.13
34 11 0.14
35 2 0.03
36 2 0.03
37 3 0.04
38 2 0.03
40 48 0.62
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (40 bp):
ACTATCGCAATGCGAAAATGACTATCGCAATGCGAAAATG
Found at i:87555 original size:20 final size:20
Alignment explanation
Indices: 87510--87558 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
87500 GCGATTCTCT
87510 CGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTTG
* *
87530 CATTGCGATAGTC-ATTTTCG
1 CGTTGCGATAGTCAAATTT-G
87550 CGTTGCGAT
1 CGTTGCGAT
87559 TTTGTTGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTTG
Found at i:87592 original size:33 final size:34
Alignment explanation
Indices: 87532--87628 Score: 124
Period size: 33 Copynumber: 2.9 Consensus size: 34
87522 CAAATTTGCA
* *
87532 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCGTTGCGATTTTCTCG
** * * *
87566 TTGCGATTTTCA-TTTCGCATTACGATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCGATTTTCTCG
87599 TTGCGATAGTCATTTTCGCGTTGCGATTTT
1 TTGCGATAGTCATTTTCGCGTTGCGATTTT
87629 ATGTTTCAGA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
33 26 0.52
34 24 0.48
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.46
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCGATTTTCTCG
Found at i:88196 original size:41 final size:42
Alignment explanation
Indices: 88109--88215 Score: 114
Period size: 41 Copynumber: 2.6 Consensus size: 42
88099 AACTCACCTG
* * *
88109 TCATCGTTCAAGAGG--CCTCCCCTATCATTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGTCCCT-CCC-ACCGTTCAAGAGGCCACTA
*
88151 TCATC-TCTCAAGA-GTCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATCGT-TCAAGAGGTCCCTCCCACCGTTCAAGAGGCCACTA
*
88192 TCATCGTTGAAGAGGTCCCTCCCA
1 TCATCGTTCAAGAGGTCCCTCCCA
88216 ACATTCTAGA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
41 27 0.49
42 25 0.45
43 3 0.05
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:89589 original size:14 final size:14
Alignment explanation
Indices: 89570--89605 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
89560 ATTGTTTAAT
89570 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
89584 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
89598 TGATTTGT
1 TGATTTGT
89606 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:89770 original size:19 final size:19
Alignment explanation
Indices: 89742--89792 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
89732 AACGAGAGAA
*
89742 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
89761 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
89780 TCGCATTACGATT
1 TCGCATTGCGATT
89793 CTCTCGTTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:89807 original size:14 final size:14
Alignment explanation
Indices: 89788--89819 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
89778 TTTCGCATTA
89788 CGATTCTCTCGTTG
1 CGATTCTCTCGTTG
89802 CGATTCTCTCGTTG
1 CGATTCTCTCGTTG
89816 CGAT
1 CGAT
89820 AGTCATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.09, C:0.28, G:0.22, T:0.41
Consensus pattern (14 bp):
CGATTCTCTCGTTG
Found at i:89838 original size:20 final size:20
Alignment explanation
Indices: 89813--89885 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
89803 GATTCTCTCG
*
89813 TTGCGATAGTCATTTCTGCT
1 TTGCGATAGTCATTTCCGCT
* *
89833 TTGCGATAGTCAATTCCGCA
1 TTGCGATAGTCATTTCCGCT
89853 TTGCGATAGTCATTTCCG-T
1 TTGCGATAGTCATTTCCGCT
89872 GTTGCGATAGTCAT
1 -TTGCGATAGTCAT
89886 ATTCACGTTG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCT
Found at i:89868 original size:40 final size:41
Alignment explanation
Indices: 89813--89889 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 41
89803 GATTCTCTCG
*
89813 TTGCGATAGTCATTTCTGCT-TTGCGATAGTCA-ATTCCGCA
1 TTGCGATAGTCATTTCCG-TGTTGCGATAGTCATATTCCGCA
89853 TTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTC
1 TTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTC
89890 ACGTTGCGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
39 1 0.03
40 29 0.85
41 4 0.12
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTCCGCA
Found at i:89895 original size:20 final size:18
Alignment explanation
Indices: 89811--89899 Score: 88
Period size: 20 Copynumber: 4.5 Consensus size: 18
89801 GCGATTCTCT
89811 CGTTGCGATAGTCATTTC
1 CGTTGCGATAGTCATTTC
* *
89829 TGCTTTGCGATAGTCAATTC
1 --CGTTGCGATAGTCATTTC
89849 CGCATTGCGATAGTCATTTC
1 CG--TTGCGATAGTCATTTC
89869 CGTGTTGCGATAGTCATATTC
1 C--GTTGCGATAGTCAT-TTC
89890 ACGTTGCGAT
1 -CGTTGCGAT
89900 TTCCGCGTTG
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.02
20 53 0.90
21 3 0.05
22 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (18 bp):
CGTTGCGATAGTCATTTC
Found at i:89897 original size:40 final size:38
Alignment explanation
Indices: 89811--89899 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 38
89801 GCGATTCTCT
*
89811 CGTTGCGATAGTCATTTCTGCTTTGCGATAGTCAATTC
1 CGTTGCGATAGTCATTTCCGCTTTGCGATAGTCAATTC
89849 CGCATTGCGATAGTCATTTCCG-TGTTGCGATAGTCATATTC
1 CG--TTGCGATAGTCATTTCCGCT-TTGCGATAGTCA-ATTC
89890 ACGTTGCGAT
1 -CGTTGCGAT
89900 TTCCGCGTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
38 2 0.04
39 1 0.02
40 36 0.80
41 4 0.09
42 2 0.04
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.37
Consensus pattern (38 bp):
CGTTGCGATAGTCATTTCCGCTTTGCGATAGTCAATTC
Found at i:93287 original size:40 final size:40
Alignment explanation
Indices: 93243--93369 Score: 175
Period size: 40 Copynumber: 3.1 Consensus size: 40
93233 CAGAATCTCG
*
93243 TTGCGATTTACAGGTTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTACAGATTCGCATTGCGATTTACGTAATCGCA
93283 TTGCGATTTAC-GTATTCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTACAG-ATTCGCATTGCGATTTACGTAATCGCA
* * * * *
93323 TTGCGATTTTCCAAATTCGCGTTGCGATTTACGTATTCGCT
1 TTGCGA-TTTACAGATTCGCATTGCGATTTACGTAATCGCA
93364 TTGCGA
1 TTGCGA
93370 ATTAGGAAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
39 1 0.01
40 43 0.55
41 34 0.44
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.38
Consensus pattern (40 bp):
TTGCGATTTACAGATTCGCATTGCGATTTACGTAATCGCA
Found at i:93362 original size:20 final size:20
Alignment explanation
Indices: 93243--93369 Score: 157
Period size: 20 Copynumber: 6.3 Consensus size: 20
93233 CAGAATCTCG
*
93243 TTGCGATTTACAG-GTTCGCA
1 TTGCGATTTAC-GTATTCGCA
*
93263 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
93283 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
93303 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
93323 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
*
93344 TTGCGATTTACGTATTCGCT
1 TTGCGATTTACGTATTCGCA
93364 TTGCGA
1 TTGCGA
93370 ATTAGGAAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 1 0.01
20 76 0.83
21 15 0.16
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:93390 original size:21 final size:21
Alignment explanation
Indices: 93366--93411 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
93356 TATTCGCTTT
93366 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
93387 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
93408 GCGA
1 GCGA
93412 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:93871 original size:21 final size:21
Alignment explanation
Indices: 93845--93886 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
93835 TCCAGCAGAT
93845 ATGGGAGAGCAAAGTGGTGGG
1 ATGGGAGAGCAAAGTGGTGGG
*
93866 ATGGGAGAGCATAGTGGTGGG
1 ATGGGAGAGCAAAGTGGTGGG
93887 CATATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.52, T:0.17
Consensus pattern (21 bp):
ATGGGAGAGCAAAGTGGTGGG
Found at i:94605 original size:52 final size:50
Alignment explanation
Indices: 94549--94655 Score: 162
Period size: 52 Copynumber: 2.1 Consensus size: 50
94539 TGTATCAACT
*
94549 TTAAATTATACATTTTCAATTACAAAATCCAATAAAAAAATTAATTAAAATA
1 TTAAATTATACATTTTCAACTACAAAATCCAAT--AAAAATTAATTAAAATA
* *
94601 TTAAATTATACATTTTGAACTACACAATCCAATAAAAATTAATTAAAATA
1 TTAAATTATACATTTTCAACTACAAAATCCAATAAAAATTAATTAAAATA
94651 -TAAAT
1 TTAAAT
94656 AAATTGTATA
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
49 5 0.10
50 17 0.33
52 30 0.58
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.35
Consensus pattern (50 bp):
TTAAATTATACATTTTCAACTACAAAATCCAATAAAAATTAATTAAAATA
Found at i:97782 original size:167 final size:165
Alignment explanation
Indices: 97571--97871 Score: 487
Period size: 167 Copynumber: 1.8 Consensus size: 165
97561 TTAGCATAAC
* * *
97571 AACAATAAATCCAGAAAAAGGTAAAATACATCTACAAATATTTATAAAAATAATACAAACATAAT
1 AACAATAAATCCAAAAAAAGATAAAATACAACTACAAATATTTATAAAAATAATACAAACATAAT
* *
97636 AATCAATAGTAAAATACTTCAAATAAATTTTCTTCAAACTTAATTCATCGT-TTTTTTATCTGCA
66 AATCAATAGTAAAATACCTCAAATAAAATTTCTTCAAACTTAATTCA-C-TATTTTTT-TCTGCA
97700 AAAAAAAAACATACTAAATAAATAAATTGAGACAAAAT
128 AAAAAAAAACATACTAAATAAATAAATTGAGACAAAAT
* ** *
97738 AACAATAAATCCAAAAAAAGATAAAATACAACTACAAGTATTTATAAAAATAATATTAATATAAT
1 AACAATAAATCCAAAAAAAGATAAAATACAACTACAAATATTTATAAAAATAATACAAACATAAT
97803 AATCAATAGTAAAATACCTCAAATAAAATTTCTTCAAACTTAATTCACTATTTTTTTCTGCAAAA
66 AATCAATAGTAAAATACCTCAAATAAAATTTCTTCAAACTTAATTCACTATTTTTTTCTGCAAAA
97868 AAAA
131 AAAA
97872 CTAAATAGAA
Statistics
Matches: 124, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
165 14 0.11
166 7 0.06
167 103 0.83
ACGTcount: A:0.53, C:0.13, G:0.04, T:0.30
Consensus pattern (165 bp):
AACAATAAATCCAAAAAAAGATAAAATACAACTACAAATATTTATAAAAATAATACAAACATAAT
AATCAATAGTAAAATACCTCAAATAAAATTTCTTCAAACTTAATTCACTATTTTTTTCTGCAAAA
AAAAAACATACTAAATAAATAAATTGAGACAAAAT
Found at i:106836 original size:13 final size:13
Alignment explanation
Indices: 106818--106882 Score: 85
Period size: 13 Copynumber: 5.0 Consensus size: 13
106808 ATCATAAATC
106818 TATGACGCGCATT
1 TATGACGCGCATT
* *
106831 TATGACACGTATT
1 TATGACGCGCATT
* *
106844 TATGACACACATT
1 TATGACGCGCATT
106857 TATGACGCGCATT
1 TATGACGCGCATT
*
106870 TATGACGCACATT
1 TATGACGCGCATT
106883 GAGAGCCATT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:106856 original size:26 final size:26
Alignment explanation
Indices: 106818--106882 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
106808 ATCATAAATC
* *
106818 TATGACGCGCATTTATGACACGTATT
1 TATGACGCACATTTATGACACGCATT
* *
106844 TATGACACACATTTATGACGCGCATT
1 TATGACGCACATTTATGACACGCATT
106870 TATGACGCACATT
1 TATGACGCACATT
106883 GAGAGCCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (26 bp):
TATGACGCACATTTATGACACGCATT
Found at i:127400 original size:33 final size:33
Alignment explanation
Indices: 127363--127425 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
127353 CTTCTATTTC
127363 AGTTGCATTTCCTAGAAATTCTATTAAATATTG
1 AGTTGCATTTCCTAGAAATTCTATTAAATATTG
127396 AGTTGCATTTCCTAGAAATTCTATTAAATA
1 AGTTGCATTTCCTAGAAATTCTATTAAATA
127426 AATGGTAGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (33 bp):
AGTTGCATTTCCTAGAAATTCTATTAAATATTG
Found at i:138870 original size:21 final size:21
Alignment explanation
Indices: 138844--138886 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
138834 GTTTCCCTCT
*
138844 GACATACGTAGTGTGGTTGGA
1 GACATACGCAGTGTGGTTGGA
138865 GACATACGCAGTGTGGTTGGA
1 GACATACGCAGTGTGGTTGGA
138886 G
1 G
138887 GGGTCTTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.26
Consensus pattern (21 bp):
GACATACGCAGTGTGGTTGGA
Found at i:149367 original size:97 final size:98
Alignment explanation
Indices: 149200--149386 Score: 268
Period size: 97 Copynumber: 1.9 Consensus size: 98
149190 GTCATCGTCG
* * ** *
149200 ATAGGTAAGGATGCTTTTATTCCATACACCAAAGAAAAAAAGGCATTGCCCCCATTGAAGTACAT
1 ATAGGTAAGGATGATTTAATTCCATACACCAAAGAAAAAAAGAAATTACCCCCATTGAAGTACAT
*
149265 ACTGAATTCAGACATGCATACATGATGAATGGC
66 ACTGAAGTCAGACATGCATACATGATGAATGGC
* * * *
149298 ATAGGTAAGGTTGATTTAATTCTATACACTAAAG-AGAAAAGAAATTACCCCCATTGAAGTACAT
1 ATAGGTAAGGATGATTTAATTCCATACACCAAAGAAAAAAAGAAATTACCCCCATTGAAGTACAT
*
149362 ACTGAAGTCTGACATGCATACATGA
66 ACTGAAGTCAGACATGCATACATGA
149387 CGAAGGGAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
97 49 0.63
98 29 0.37
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.26
Consensus pattern (98 bp):
ATAGGTAAGGATGATTTAATTCCATACACCAAAGAAAAAAAGAAATTACCCCCATTGAAGTACAT
ACTGAAGTCAGACATGCATACATGATGAATGGC
Found at i:152191 original size:19 final size:19
Alignment explanation
Indices: 152155--152191 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
152145 GAACCGGGTC
**
152155 TGGTTAACCCGATGGAGTA
1 TGGTTAACCCGACCGAGTA
152174 TGGTTAACCCGACCGAGT
1 TGGTTAACCCGACCGAGT
152192 CAACTCGGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (19 bp):
TGGTTAACCCGACCGAGTA
Found at i:152226 original size:14 final size:14
Alignment explanation
Indices: 152188--152266 Score: 86
Period size: 14 Copynumber: 5.6 Consensus size: 14
152178 TAACCCGACC
*
152188 GAGTCAACTCGGACT
1 GAGTCAACTC-GTCT
*
152203 GAGTCCACTCGTCT
1 GAGTCAACTCGTCT
*
152217 GATTCAACTCGTCT
1 GAGTCAACTCGTCT
* *
152231 AAGTCAACTCGCCT
1 GAGTCAACTCGTCT
* *
152245 GAGTCAACTTGTCC
1 GAGTCAACTCGTCT
152259 GAGTCAAC
1 GAGTCAAC
152267 CCGTTGACTT
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
14 44 0.83
15 9 0.17
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.25
Consensus pattern (14 bp):
GAGTCAACTCGTCT
Found at i:154465 original size:23 final size:23
Alignment explanation
Indices: 154434--154483 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
154424 GTAGGCTCTG
*
154434 AGGCCCCGAAAACTTTCTTGGGT
1 AGGCACCGAAAACTTTCTTGGGT
*
154457 AGGCACCGAGAACTTTCTTGGGT
1 AGGCACCGAAAACTTTCTTGGGT
154480 AGGC
1 AGGC
154484 TCTCAAGTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.24, G:0.30, T:0.24
Consensus pattern (23 bp):
AGGCACCGAAAACTTTCTTGGGT
Found at i:158424 original size:2 final size:2
Alignment explanation
Indices: 158417--158460 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
158407 ATTATAATGC
158417 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
158459 AT
1 AT
158461 TATTGTTTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:159565 original size:60 final size:60
Alignment explanation
Indices: 159436--159550 Score: 146
Period size: 60 Copynumber: 1.9 Consensus size: 60
159426 AATATAACCC
* * *
159436 TCATTTTAAATTGGTCTCTAAACTTTTAGATATCTCAAATTTATCCCTATACTATATCTA
1 TCATTTTAAATTAGTCTCTAAACTTTTAGATATCTCAAATTTATCCCCAAACTATATCTA
*
159496 TCATTTTAAATTAGTC-CTCAAACTTTTTA-ATATTTC-AATTTCATCCCCAAACTAT
1 TCATTTTAAATTAGTCTCT-AAAC-TTTTAGATATCTCAAATTT-ATCCCCAAACTAT
159551 GACATTCATT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
59 7 0.15
60 36 0.75
61 5 0.10
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.44
Consensus pattern (60 bp):
TCATTTTAAATTAGTCTCTAAACTTTTAGATATCTCAAATTTATCCCCAAACTATATCTA
Found at i:161068 original size:25 final size:25
Alignment explanation
Indices: 161019--161100 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
161009 AGGTGGCTTA
*
161019 TTTAATTTTTAAA-ATAAAAATTAAT
1 TTTAAATTTTAAATATAAAAA-TAAT
161044 TTTAAATTTTAAATATAAAAATAAT
1 TTTAAATTTTAAATATAAAAATAAT
* * ** * *
161069 CTAAAAAATTAAATATAATAATATT
1 TTTAAATTTTAAATATAAAAATAAT
161094 ATTTAAA
1 -TTTAAA
161101 AAATTTAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
25 35 0.76
26 11 0.24
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (25 bp):
TTTAAATTTTAAATATAAAAATAAT
Found at i:161077 original size:27 final size:29
Alignment explanation
Indices: 161047--161106 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
161037 AATTAATTTT
161047 AAATTTTAAATATAA-AA-ATAATCTAAA
1 AAATTTTAAATATAATAATATAATCTAAA
* *
161074 AAA--TTAAATATAATAATATTATTTAAA
1 AAATTTTAAATATAATAATATAATCTAAA
161101 AAATTT
1 AAATTT
161107 AAAAACTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
25 10 0.37
26 2 0.07
27 14 0.52
29 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (29 bp):
AAATTTTAAATATAATAATATAATCTAAA
Found at i:161782 original size:2 final size:2
Alignment explanation
Indices: 161775--161824 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
161765 ATGTGGGTGA
*
161775 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
161817 GT AT AT AT
1 AT AT AT AT
161825 TTTTATAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:162088 original size:20 final size:20
Alignment explanation
Indices: 162063--162100 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
162053 ATCAACACTT
162063 ATACAAAGTATTCTTATTAA
1 ATACAAAGTATTCTTATTAA
162083 ATACAAAGTATTCTTATT
1 ATACAAAGTATTCTTATT
162101 GGATAATCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (20 bp):
ATACAAAGTATTCTTATTAA
Found at i:162555 original size:21 final size:21
Alignment explanation
Indices: 162515--162554 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
162505 TATATTTAAT
*
162515 TTTTTATTAATTTAATTTTTA
1 TTTTTAGTAATTTAATTTTTA
162536 TTTTTAGT-ATTTAATTTTT
1 TTTTTAGTAATTTAATTTTT
162555 TGACTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (21 bp):
TTTTTAGTAATTTAATTTTTA
Found at i:162586 original size:17 final size:17
Alignment explanation
Indices: 162536--162582 Score: 62
Period size: 16 Copynumber: 2.9 Consensus size: 17
162526 TTAATTTTTA
*
162536 TTTTTAGTATTT-AATT
1 TTTTTACTATTTGAATT
*
162552 TTTTGACTATTTGAATT
1 TTTTTACTATTTGAATT
162569 TTTTTA-TATTTGAA
1 TTTTTACTATTTGAA
162583 ATTTAACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.26, C:0.02, G:0.09, T:0.64
Consensus pattern (17 bp):
TTTTTACTATTTGAATT
Found at i:163144 original size:20 final size:17
Alignment explanation
Indices: 163104--163146 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
163094 CGATTATGTT
*
163104 ATATTATTTAATCAAAA
1 ATATTATTAAATCAAAA
163121 ATATTATTAAATACAATAA
1 ATATTATTAAAT-CAA-AA
163140 CATATTA
1 -ATATTA
163147 GGTAACGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 11 0.50
18 3 0.14
19 2 0.09
20 6 0.27
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATTATTAAATCAAAA
Found at i:163643 original size:197 final size:196
Alignment explanation
Indices: 163201--163900 Score: 718
Period size: 197 Copynumber: 3.5 Consensus size: 196
163191 TTTTATAAGT
* * ** * *
163201 AAACCGGTATATTTATACCGGTAACATTACAAAATTACCTATTACATTATAATTATCGGTTTCGA
1 AAACCGGTATATTTATACCGGTTACTTTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
* * * * *
163266 TGTTTTTTGGATCGATACTTTTTATAAATGTATCGACACTATATGCGTTCACCCTTTTGGGCATT
66 TGTTTTTGGGATCGATAC-TTTTAAAAATGTATCGACACTTTATGCGTGCACCCGTTT-GGCATT
* * * *
163331 CATTCTGGA-AAAAAGTATCGACACAACATTAAAAAGTGTCAACACATTAT-ATAAACTTATTCT
129 CATTCTGGACAAAAA-TATCGACACAA-ATTAAAAAGTGTCGATACATTATGAT-GACATATTCT
*
163394 CACATA
191 CTCATA
** ** * * *
163400 AAACCGGTATAAATATACCGGTTA-TATTACAAAATTATC-GATTACATTATAATTATGGGTTTC
1 AAACCGGTATATTTATACCGGTTACT-TTGTAAATTTA-CATATTACATTATAATTATCGGTTTC
* * *
163463 G-TGTTTTTGGGATCGATACTTTTTAAAAATGCATCGACACTTTATGAGTGCACCCGTCT-GCAT
64 GATGTTTTTGGGATCGATAC-TTTTAAAAATGTATCGACACTTTATGCGTGCACCCGTTTGGCAT
* * * *
163526 TCATTATGGACAAAATATATCGACACAAATTTAATAAGTGTCGATACTTTATGATGACATATTTT
128 TCATTCTGGACAAAA-ATATCGACACAAA-TTAAAAAGTGTCGATACATTATGATGACATATTCT
163591 CTCATA
191 CTCATA
* **
163597 AAACTGGTATATTTATATAGGTTACTTTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
1 AAACCGGTATATTTATACCGGTTACTTTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
* *
163662 T-TTTATTGTGATCGATACTTTTAATAATTGTATCGACACTTTATGCGTGCACCCCGTTTGGGCA
66 TGTTT-TTGGGATCGATACTTTTAA-AAATGTATCGACACTTTATGCGTGCA-CCCGTTT-GGCA
* * * * *
163726 TTTATTCTGGACAATAAGTATCGACACAAATTACACAAA-TGTCGATAAATTATGTTGACATGTT
127 TTCATTCTGGACAA-AAATATCGACACAAATTA-A-AAAGTGTCGATACATTATGATGACATATT
* *
163790 GTCTAAT-
189 CTCTCATA
* * * * **
163797 TAACCGATATATTTATACCGGTTACATTGTTAATTTACATATTACATTATAATTATTAGTTTCGA
1 AAACCGGTATATTTATACCGGTTACTTTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
*
163862 TGTTTTTTGGG-TTGATACTTTTAGAAAATGTATCGACAC
66 TG-TTTTTGGGATCGATACTTTTA-AAAATGTATCGACAC
163901 ATATTTAGGT
Statistics
Matches: 421, Mismatches: 60, Indels: 39
0.81 0.12 0.08
Matches are distributed among these distances:
196 15 0.04
197 104 0.25
198 90 0.21
199 61 0.14
200 85 0.20
201 59 0.14
202 7 0.02
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (196 bp):
AAACCGGTATATTTATACCGGTTACTTTGTAAATTTACATATTACATTATAATTATCGGTTTCGA
TGTTTTTGGGATCGATACTTTTAAAAATGTATCGACACTTTATGCGTGCACCCGTTTGGCATTCA
TTCTGGACAAAAATATCGACACAAATTAAAAAGTGTCGATACATTATGATGACATATTCTCTCAT
A
Found at i:167481 original size:199 final size:198
Alignment explanation
Indices: 167118--168262 Score: 1102
Period size: 199 Copynumber: 5.8 Consensus size: 198
167108 TGTTATTTAC
* * * * ** * * ** *
167118 AAGTATTGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTTATAAAATCAGT
1 AAGTATCGACACACATTTAAAA-GTGTCGACACATTATGTAGATCTATTCTCACATAAAATCGGT
* * * ** *
167183 ACATTTATACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
65 ATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
167248 GGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTTCACCCTTTTGGGCATTTATTATGG
130 GGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTTCACCCTTTTGGGCATTTATTATGG
167313 CAAA
195 CAAA
* *
167317 AAGTATCGACACATCATTTAAAAGTGTCGACAAATTATGTAGATCTATTCTGACATAAAATCGGT
1 AAGTATCGACACA-CATTTAAAAGTGTCGACACATTATGTAGATCTATTCTCACATAAAATCGGT
* * * * *
167382 ATATTTATATCGGTTATATTACAAAATTACATATTACATTATAATTATGGGTTTTGATGTTTTAG
65 ATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
* * * * * * *
167447 GGATCGATACTATTTAAAAATGTATCGACACTTTATGGGTGCAACCTTTTTGG-ATTTTCCTTAT
130 GGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTTCACCCTTTTGGGCA-TTT-ATTAT
167511 GG-ATCAA
193 GGCA--AA
* * * ** * * * *
167518 AAGTATCGACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTCAAAAAATCGGT
1 AAGTATCGACACACATTTAAAA-GTGTCGACACATTATGTAGATCTATTCTCACATAAAATCGGT
* ** * *
167583 ACATTTATACCGG-TATCATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTT
65 ATATTTATACCGGTTAT-ATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
* *
167647 GGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTTCACCCTTTTGGGCATTCATTCTG
129 GGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTTCACCCTTTTGGGCATTTATTATG
167712 GCAAA
194 GCAAA
* * * *
167717 AAGTATCGACACCACATTCAAAAGTGTCGACACATTATGTAGAACTATTCTAACATAAAATTGGT
1 AAGTATCGACA-CACATTTAAAAGTGTCGACACATTATGTAGATCTATTCTCACATAAAATCGGT
* * * * **
167782 ATGTTTATACCGGTTATATTACAAAATTACCTATTACATTATATTTATAGATTTTAATGTTTTTG
65 ATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
* ** * * **
167847 GGATCGACAC--TTTATGGATG-ATC--C-CTTT-T-TG--GA---TTTT--AC-TTGT-GGAT-
130 GGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTTCACCCTTTTGGGCATT-TATTATG
167894 -C-AA
194 GCAAA
* * * * * * * * * * *
167897 AAGTATCAACACAAATTCTACAAGTGTCGATACATTATATATATTTATTTTCTCAAAAAACCGGT
1 AAGTATCGACACACATT-TAAAAGTGTCGACACATTATGTAGATCTATTCTCACATAAAATCGGT
* * ** * * **
167962 TTATTTATACCGGTTACATTGTAAATTTACCAATTACATTATAATTATCGGTTTCGATAATTTTG
65 ATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTG
* **
168027 GGATCGATACTTTTTATAATTGTATCGACACTTTATGCCATTCACCCTTTTGGGCATTTATTATG
130 GGATCGATACTTTTTATAAATGTATCGACACTTTATG-TGTTCACCCTTTTGGGCATTTATTATG
168092 GCAAA
194 GCAAA
**
168097 AAGTATCGACACAACA-TTAACAAGTGTTAACACATTATGTAGA-CATATTCTCACA-AAAATCG
1 AAGTATCGACAC-ACATTTAA-AAGTGTCGACACATTATGTAGATC-TATTCTCACATAAAATCG
* * * * * * *
168159 GTATATTTATATCGGTTATATTACAAAATTACCTATTACATTGTATTTATTGATTTTGATGTTTC
63 GTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTT
168224 TGGGATCGATACTTTTTA-AAACTGTATCGACACTTTATG
128 TGGGATCGATACTTTTTATAAA-TGTATCGACACTTTATG
168263 GGAAACTTTA
Statistics
Matches: 748, Mismatches: 160, Indels: 76
0.76 0.16 0.08
Matches are distributed among these distances:
179 5 0.01
180 106 0.14
181 1 0.00
182 7 0.01
183 6 0.01
184 1 0.00
185 1 0.00
186 8 0.01
187 1 0.00
189 1 0.00
191 3 0.00
192 1 0.00
193 4 0.01
194 5 0.01
196 5 0.01
197 12 0.02
198 3 0.00
199 348 0.47
200 78 0.10
201 151 0.20
202 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (198 bp):
AAGTATCGACACACATTTAAAAGTGTCGACACATTATGTAGATCTATTCTCACATAAAATCGGTA
TATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
GATCGATACTTTTTATAAATGTATCGACACTTTATGTGTTCACCCTTTTGGGCATTTATTATGGC
AAA
Found at i:168177 original size:379 final size:384
Alignment explanation
Indices: 167126--168238 Score: 1521
Period size: 400 Copynumber: 2.9 Consensus size: 384
167116 ACAAGTATTG
* * * * *
167126 ACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTTATAAAATCAGTACATTTAT
1 ACACAAATCTAAAACGTGTCGATACATTATATTCACCTATTTTCTCAAAAAACCGGTACATTTAT
* *
167191 ACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGAT
66 ACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATCGAT
167256 ACTTTTTATAAATGTATCGACACTTTATGTGTTCACCCTTTTGGGCATTTATTATGGCAAAAAGT
131 ACTTTTTATAAATGTATCGACACTTTATGTGTTCACCCTTTTGGGCATTTATTATGGCAAAAAGT
* * *
167321 ATCGACACATCATTTAAAAGTGTCGACAAATTATGTAGATC-TATTCTGACATAAAATCGGTATA
196 ATCGACACAACA-TTAAAAGTGTCGACACATTATGTAGA-CATATTCTAACATAAAATCGGTATA
* * * * *
167385 TTTATATCGGTTATATTACAAAATTACATATTACATTATAATTATGGGTTTTGATGTTTTAGGGA
259 TTTATATCGGTTATATTACAAAATTACCTATTACATTATATTTATAGATTTTGATGTTTTTGGGA
* *
167450 TCGATACTATTTAAAAATGTATCGACACTTTATGGGTGCAACCTTTTTGGATTTTCCTTATGGAT
324 TCGATAC--TTT---AATG--T-G------TATGGATGC-ACCTTTTTGGATTTTACTTATGGAT
*
167515 CAAAAGTATCG
374 CAAAAGTATCA
* *
167526 ACACAAATCTAAAACGTGTCGATACATTATGTTCACCTATTTTCTCAAAAAATCGGTACATTTAT
1 ACACAAATCTAAAACGTGTCGATACATTATATTCACCTATTTTCTCAAAAAACCGGTACATTTAT
167591 ACCGG-TATCATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATCGA
66 ACCGGTTA-CATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATCGA
* *
167655 TACTTTTTATAAATGTATCGACACTTTATGTGTTCACCCTTTTGGGCATTCATTCTGGCAAAAAG
130 TACTTTTTATAAATGTATCGACACTTTATGTGTTCACCCTTTTGGGCATTTATTATGGCAAAAAG
* *
167720 TATCGACACCACATTCAAAAGTGTCGACACATTATGTAGA-ACTATTCTAACATAAAATTGGTAT
195 TATCGACACAACATT-AAAAGTGTCGACACATTATGTAGACA-TATTCTAACATAAAATCGGTAT
* * *
167784 GTTTATACCGGTTATATTACAAAATTACCTATTACATTATATTTATAGATTTTAATGTTTTTGGG
258 ATTTATATCGGTTATATTACAAAATTACCTATTACATTATATTTATAGATTTTGATGTTTTTGGG
* *
167849 ATCGACACTTT-ATG-G-AT-GAT-C-CCTTTTTGGATTTTACTTGTGGATCAAAAGTATCA
323 ATCGATACTTTAATGTGTATGGATGCACCTTTTTGGATTTTACTTATGGATCAAAAGTATCA
* ** **
167905 ACACAAATTCTACAA-GTGTCGATACATTATATAT-ATTTATTTTCTCAAAAAACCGGTTTATTT
1 ACACAAA-TCTAAAACGTGTCGATACATTATAT-TCACCTATTTTCTCAAAAAACCGGTACATTT
* *
167968 ATACCGGTTACATTGTAAATTTACCAATTACATTATAATTATCGGTTTCGATAATTTTGGGATCG
64 ATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATCG
* **
168033 ATACTTTTTATAATTGTATCGACACTTTATGCCATTCACCCTTTTGGGCATTTATTATGGCAAAA
129 ATACTTTTTATAAATGTATCGACACTTTATG-TGTTCACCCTTTTGGGCATTTATTATGGCAAAA
** *
168098 AGTATCGACACAACATTAACAAGTGTTAACACATTATGTAGACATATTCTCACA-AAAATCGGTA
193 AGTATCGACACAACATTAA-AAGTGTCGACACATTATGTAGACATATTCTAACATAAAATCGGTA
* * *
168162 TATTTATATCGGTTATATTACAAAATTACCTATTACATTGTATTTATTGATTTTGATGTTTCTGG
257 TATTTATATCGGTTATATTACAAAATTACCTATTACATTATATTTATAGATTTTGATGTTTTTGG
168227 GATCGATACTTT
322 GATCGATACTTT
168239 TTAAAACTGT
Statistics
Matches: 652, Mismatches: 51, Indels: 41
0.88 0.07 0.06
Matches are distributed among these distances:
379 250 0.38
380 83 0.13
381 2 0.00
382 2 0.00
383 2 0.00
390 1 0.00
394 3 0.00
398 3 0.00
399 4 0.01
400 302 0.46
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (384 bp):
ACACAAATCTAAAACGTGTCGATACATTATATTCACCTATTTTCTCAAAAAACCGGTACATTTAT
ACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTTTGGGATCGAT
ACTTTTTATAAATGTATCGACACTTTATGTGTTCACCCTTTTGGGCATTTATTATGGCAAAAAGT
ATCGACACAACATTAAAAGTGTCGACACATTATGTAGACATATTCTAACATAAAATCGGTATATT
TATATCGGTTATATTACAAAATTACCTATTACATTATATTTATAGATTTTGATGTTTTTGGGATC
GATACTTTAATGTGTATGGATGCACCTTTTTGGATTTTACTTATGGATCAAAAGTATCA
Found at i:168283 original size:15 final size:15
Alignment explanation
Indices: 168263--168301 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
168253 ACACTTTATG
*
168263 GGAAACTTTAAGTTT
1 GGAAACTTTAAGTAT
*
168278 GGAAACTTTATGTAT
1 GGAAACTTTAAGTAT
*
168293 GAAAACTTT
1 GGAAACTTT
168302 GTTGTGGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (15 bp):
GGAAACTTTAAGTAT
Found at i:168589 original size:11 final size:11
Alignment explanation
Indices: 168573--168597 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
168563 TATACATAAC
168573 AATGTTCAAAT
1 AATGTTCAAAT
168584 AATGTTCAAAT
1 AATGTTCAAAT
168595 AAT
1 AAT
168598 ATACCCACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (11 bp):
AATGTTCAAAT
Found at i:169589 original size:3 final size:3
Alignment explanation
Indices: 169574--169606 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
169564 ACTTATTTGG
*
169574 ATC ATC ATA ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
169607 TTTATCTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Done.