Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 15 of 310
Found at i:3841765 original size:38 final size:39
Alignment explanation
Indices: 3841716--3841792 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 39
3841706 TTCTTTAAAT
* *
3841716 TTTCCAATATGATACCATAACCCACCAGTTATGGTCTTA
1 TTTCCAATATGATACCATAACCAACCAGTTACGGTCTTA
**
3841755 TTTCC-ATATGATGTCATAACCAACCAGTTACGGTCTTA
1 TTTCCAATATGATACCATAACCAACCAGTTACGGTCTTA
3841793 CACGATATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
38 29 0.85
39 5 0.15
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.34
Consensus pattern (39 bp):
TTTCCAATATGATACCATAACCAACCAGTTACGGTCTTA
Found at i:3841828 original size:53 final size:53
Alignment explanation
Indices: 3841745--3841853 Score: 155
Period size: 53 Copynumber: 2.1 Consensus size: 53
3841735 ACCCACCAGT
* **
3841745 TATGGTCTTATTTCCATATGATGTCATAACCAACCAGTTACGGTCTTACACGA
1 TATGGTCTTATTTCCATATGATATCATAACCAACCAGTTACAATCTTACACGA
* * * *
3841798 TATGGTCTTTTTTCCATATGATATCGTAACCCACTAGTTACAATCTTACACGA
1 TATGGTCTTATTTCCATATGATATCATAACCAACCAGTTACAATCTTACACGA
3841851 TAT
1 TAT
3841854 AGTTCTTCAG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (53 bp):
TATGGTCTTATTTCCATATGATATCATAACCAACCAGTTACAATCTTACACGA
Found at i:3847802 original size:17 final size:17
Alignment explanation
Indices: 3847757--3847806 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
3847747 CTAAAATTTC
*
3847757 TCTTCACCTTTT-TTATT
1 TCTTCTCCTTTTCTT-TT
*
3847774 TCTTCTCTTTTTCTTTT
1 TCTTCTCCTTTTCTTTT
*
3847791 TCTTTTCCTTTTCTTT
1 TCTTCTCCTTTTCTTT
3847807 ACGCCATACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 26 0.93
18 2 0.07
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (17 bp):
TCTTCTCCTTTTCTTTT
Found at i:3848055 original size:20 final size:20
Alignment explanation
Indices: 3848030--3848068 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3848020 CTTTTACAAT
3848030 TCTTG-TCAAATCCTTGATAA
1 TCTTGTTCAAAT-CTTGATAA
*
3848050 TCTTGTTGAAATCTTGATA
1 TCTTGTTCAAATCTTGATA
3848069 CCAATCGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (20 bp):
TCTTGTTCAAATCTTGATAA
Found at i:3848968 original size:26 final size:26
Alignment explanation
Indices: 3848938--3848999 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
3848928 CATTTGCTAA
*
3848938 GAAAACTTTAAAATCCATCATTTTTG
1 GAAAATTTTAAAATCCATCATTTTTG
3848964 GAAAATTTTAAAATCCATCATTTTTG
1 GAAAATTTTAAAATCCATCATTTTTG
3848990 GAAAATTTTA
1 GAAAATTTTA
3849000 CTCTTTAGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.40
Consensus pattern (26 bp):
GAAAATTTTAAAATCCATCATTTTTG
Found at i:3854500 original size:18 final size:17
Alignment explanation
Indices: 3854457--3854500 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3854447 AATTTCTTAA
3854457 AAATAGGCCCACACAGCC
1 AAAT-GGCCCACACAGCC
* *
3854475 ATATGGCCCACACGGCC
1 AAATGGCCCACACAGCC
3854492 TAAATGGCC
1 -AAATGGCC
3854501 AGCCCGTGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.32, C:0.36, G:0.20, T:0.11
Consensus pattern (17 bp):
AAATGGCCCACACAGCC
Found at i:3858476 original size:11 final size:11
Alignment explanation
Indices: 3858460--3858493 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3858450 GGGCATGTGG
*
3858460 ACCACACCGCC
1 ACCACACGGCC
*
3858471 ACCACAAGGCC
1 ACCACACGGCC
3858482 ACCACACGGCC
1 ACCACACGGCC
3858493 A
1 A
3858494 TGTGCCTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.32, C:0.53, G:0.15, T:0.00
Consensus pattern (11 bp):
ACCACACGGCC
Found at i:3859213 original size:13 final size:13
Alignment explanation
Indices: 3859178--3859219 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
3859168 TTAAGCCCTT
3859178 TACAGATCAGATA
1 TACAGATCAGATA
*
3859191 -ACAGAACAGATA
1 TACAGATCAGATA
*
3859203 TACAGATCAGAAA
1 TACAGATCAGATA
3859216 TACA
1 TACA
3859220 AAATCCTACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.52, C:0.17, G:0.14, T:0.17
Consensus pattern (13 bp):
TACAGATCAGATA
Found at i:3868498 original size:16 final size:17
Alignment explanation
Indices: 3868477--3868510 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3868467 CTTTGAGAAG
3868477 CTCAAG-TCTGTTCTGA
1 CTCAAGCTCTGTTCTGA
3868493 CTCAAGCTTCTGTTCTGA
1 CTCAAGC-TCTGTTCTGA
3868511 TTCAGCCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.18, C:0.26, G:0.18, T:0.38
Consensus pattern (17 bp):
CTCAAGCTCTGTTCTGA
Found at i:3874015 original size:14 final size:15
Alignment explanation
Indices: 3873985--3874018 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3873975 TGACCTTTTT
3873985 AATTTTGTTTAATTG
1 AATTTTGTTTAATTG
*
3874000 AATTTT-TTTCATTG
1 AATTTTGTTTAATTG
3874014 AATTT
1 AATTT
3874019 GACTATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.26, C:0.03, G:0.09, T:0.62
Consensus pattern (15 bp):
AATTTTGTTTAATTG
Found at i:3874451 original size:16 final size:18
Alignment explanation
Indices: 3874422--3874517 Score: 71
Period size: 15 Copynumber: 5.6 Consensus size: 18
3874412 CATTTATCAA
*
3874422 TAAGTCTAAT-TATTT-T
1 TAAGTCAAATCTATTTAT
3874438 T-AGTCAAATCTATTTAT
1 TAAGTCAAATCTATTTAT
* *
3874455 TAAGTAAAAAC-ATTTAT
1 TAAGTCAAATCTATTTAT
*
3874472 CAATAAGTCTAAT-TATTT-T
1 ---TAAGTCAAATCTATTTAT
3874491 T-AGTCAAATCTATTTAT
1 TAAGTCAAATCTATTTAT
*
3874508 TAAGTAAAAT
1 TAAGTCAAAT
3874518 TTAAATAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
15 14 0.23
16 12 0.19
17 10 0.16
18 14 0.23
19 1 0.02
20 11 0.18
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (18 bp):
TAAGTCAAATCTATTTAT
Found at i:3874473 original size:53 final size:53
Alignment explanation
Indices: 3874411--3874516 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
3874401 TTTAAAAATT
3874411 ACATTTATCAATAAGTCTAATTATTTTTAGTCAAATCTATTTATTAAGTAAAA
1 ACATTTATCAATAAGTCTAATTATTTTTAGTCAAATCTATTTATTAAGTAAAA
3874464 ACATTTATCAATAAGTCTAATTATTTTTAGTCAAATCTATTTATTAAGTAAAA
1 ACATTTATCAATAAGTCTAATTATTTTTAGTCAAATCTATTTATTAAGTAAAA
3874517 TTTAAATAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (53 bp):
ACATTTATCAATAAGTCTAATTATTTTTAGTCAAATCTATTTATTAAGTAAAA
Found at i:3875206 original size:33 final size:34
Alignment explanation
Indices: 3875169--3875234 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
3875159 TGTAATGAAA
*
3875169 TTTA-TAATTTAATTTAAAAATAATT-AAAATAAT
1 TTTATTAATTTAATTGAAAAAT-ATTGAAAATAAT
*
3875202 TTTATTATTTTAATTGAAAAATATTGAAAATAA
1 TTTATTAATTTAATTGAAAAATATTGAAAATAA
3875235 AATATAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (34 bp):
TTTATTAATTTAATTGAAAAATATTGAAAATAAT
Found at i:3889792 original size:29 final size:29
Alignment explanation
Indices: 3889750--3889805 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
3889740 TGATTTAGAA
3889750 CCACACGGCCAAGGACATGGACGTGTGAG
1 CCACACGGCCAAGGACATGGACGTGTGAG
* *
3889779 CCACACGGGCAAGGACATGGGCGTGTG
1 CCACACGGCCAAGGACATGGACGTGTG
3889806 TCTAGGCCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.25, C:0.27, G:0.38, T:0.11
Consensus pattern (29 bp):
CCACACGGCCAAGGACATGGACGTGTGAG
Found at i:3893837 original size:5 final size:5
Alignment explanation
Indices: 3893827--3893854 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3893817 TTATAAAAAT
3893827 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
3893855 TTATAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:3894124 original size:17 final size:17
Alignment explanation
Indices: 3894087--3894128 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
3894077 ATTATTAATT
* *
3894087 TAATAAATTCTTTTTAG
1 TAATAAATTCTTATTAA
3894104 TAATTAAATT-TTATTAA
1 TAA-TAAATTCTTATTAA
3894121 TAATAAAT
1 TAATAAAT
3894129 ATCAGATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 11 0.50
18 6 0.27
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
TAATAAATTCTTATTAA
Found at i:3898886 original size:8 final size:7
Alignment explanation
Indices: 3898854--3899043 Score: 53
Period size: 7 Copynumber: 25.1 Consensus size: 7
3898844 GAAATATCAC
3898854 ATAATAA
1 ATAATAA
3898861 ATAGATAA
1 ATA-ATAA
*
3898869 ATAATTA
1 ATAATAA
3898876 ATAATGAA
1 ATAAT-AA
* *
3898884 ATATGTAT
1 ATA-ATAA
3898892 ATAATATA
1 ATAATA-A
*
3898900 A-ATTAA
1 ATAATAA
*
3898906 AT-ATGTA
1 ATAAT-AA
3898913 ATAATAA
1 ATAATAA
* * *
3898920 TTTACAA
1 ATAATAA
**
3898927 ATCTTAAA
1 ATAATA-A
*
3898935 ATTATAA
1 ATAATAA
3898942 ATAATATA
1 ATAATA-A
3898950 ATGAATAA
1 AT-AATAA
*
3898958 TATAA-AC
1 -ATAATAA
3898965 ATAAATAA
1 AT-AATAA
3898973 TATAATAA
1 -ATAATAA
*
3898981 ATAATAT
1 ATAATAA
*
3898988 ATGATATAC
1 AT-A-ATAA
*
3898997 ATAATAT
1 ATAATAA
3899004 ATAATAAA
1 ATAAT-AA
*
3899012 AAAATAA
1 ATAATAA
3899019 TATAATAA
1 -ATAATAA
*
3899027 GTAATATA
1 ATAATA-A
3899035 TATAATAA
1 -ATAATAA
3899043 A
1 A
3899044 AGTAAAAATA
Statistics
Matches: 133, Mismatches: 30, Indels: 40
0.66 0.15 0.20
Matches are distributed among these distances:
6 5 0.04
7 59 0.44
8 50 0.38
9 19 0.14
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (7 bp):
ATAATAA
Found at i:3898921 original size:18 final size:19
Alignment explanation
Indices: 3898874--3898921 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
3898864 GATAAATAAT
*
3898874 TAATAATGAAATATGTATA
1 TAATAATTAAATATGTATA
3898893 TAATATAAATTAAATATGTA-A
1 T-A-AT-AATTAAATATGTATA
3898914 TAATAATT
1 TAATAATT
3898922 TACAAATCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 4 0.16
19 3 0.12
20 2 0.08
21 4 0.16
22 12 0.48
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (19 bp):
TAATAATTAAATATGTATA
Found at i:3898958 original size:12 final size:12
Alignment explanation
Indices: 3898938--3899061 Score: 91
Period size: 12 Copynumber: 10.5 Consensus size: 12
3898928 TCTTAAAATT
3898938 ATAAATAATATA
1 ATAAATAATATA
*
3898950 ATGAATAATATAAA
1 ATAAATAATAT--A
3898964 CATAAATAATATA
1 -ATAAATAATATA
3898977 ATAAATAATAT-
1 ATAAATAATATA
* *
3898988 AT-GATATACATA
1 ATAAATA-ATATA
*
3899000 ATATATAATA-A
1 ATAAATAATATA
*
3899011 AAAAATAATATA
1 ATAAATAATATA
*
3899023 ATAAGTAATAT-
1 ATAAATAATATA
3899034 ATATAATAA-A-A
1 ATA-AATAATATA
*
3899045 GTAAA-AATATA
1 ATAAATAATATA
3899056 ATAAAT
1 ATAAAT
3899062 GCTATATAAT
Statistics
Matches: 87, Mismatches: 13, Indels: 24
0.70 0.10 0.19
Matches are distributed among these distances:
9 2 0.02
10 6 0.07
11 25 0.29
12 39 0.45
13 4 0.05
14 1 0.01
15 10 0.11
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (12 bp):
ATAAATAATATA
Found at i:3899007 original size:27 final size:27
Alignment explanation
Indices: 3898937--3899094 Score: 95
Period size: 27 Copynumber: 5.9 Consensus size: 27
3898927 ATCTTAAAAT
*
3898937 TATAAATAATATAATGAATAATATAAA
1 TATAAATAATATAATAAATAATATAAA
* *
3898964 CATAAATAATATAATAAATAATATATGA
1 TATAAATAATATAATAAATAATATA-AA
*
3898992 TATACATAATAT-AT-AATAA-A-AAA
1 TATAAATAATATAATAAATAATATAAA
3899015 -ATAATATAATAAGTAATATATATAATA-AAA
1 TATAA-ATAAT-A-TAATA-A-ATAATATAAA
* **
3899045 -GTAAA-AATATAATAAATGCTATATAA
1 TATAAATAATATAATAAATAATATA-AA
3899071 TA-AAATACA-AT-ATAAATATATATA
1 TATAAATA-ATATAATAAATA-ATATA
3899095 GGAGAATAAA
Statistics
Matches: 103, Mismatches: 13, Indels: 30
0.71 0.09 0.21
Matches are distributed among these distances:
22 3 0.03
23 6 0.06
24 6 0.06
25 4 0.04
26 23 0.22
27 33 0.32
28 16 0.16
29 5 0.05
30 7 0.07
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (27 bp):
TATAAATAATATAATAAATAATATAAA
Found at i:3899032 original size:30 final size:30
Alignment explanation
Indices: 3898997--3899075 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 30
3898987 TATGATATAC
3898997 ATAATATATAATAAAA-AAATAATATAATAA
1 ATAATATATAATAAAAGAAA-AATATAATAA
*
3899027 GTAATATATATAATAAAAGTAAAAATATAATAA
1 AT-A-ATATATAATAAAAG-AAAAATATAATAA
**
3899060 ATGCTATATAATAAAA
1 ATAATATATAATAAAA
3899076 TACAATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
30 1 0.02
31 13 0.32
32 13 0.32
33 11 0.27
34 3 0.07
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (30 bp):
ATAATATATAATAAAAGAAAAATATAATAA
Found at i:3899069 original size:33 final size:32
Alignment explanation
Indices: 3898969--3899061 Score: 91
Period size: 34 Copynumber: 2.8 Consensus size: 32
3898959 ATAAACATAA
* *
3898969 ATAATATAATAAATAATAT-ATGATATACATAATAT
1 ATAATA-AAAAAATAATATAAT-AAATA-AT-ATAT
*
3899004 ATAATAAAAAAATAATATAATAAGTAATATAT
1 ATAATAAAAAAATAATATAATAAATAATATAT
3899036 ATAATAAAAGTAAA-AATATAATAAAT
1 ATAATAAAA--AAATAATATAATAAAT
3899062 GCTATATAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
32 13 0.25
33 13 0.25
34 17 0.33
35 8 0.16
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (32 bp):
ATAATAAAAAAATAATATAATAAATAATATAT
Found at i:3901150 original size:119 final size:119
Alignment explanation
Indices: 3900877--3901351 Score: 698
Period size: 119 Copynumber: 4.0 Consensus size: 119
3900867 TGAGTCTGTT
* * * * ***
3900877 TGAGAACATCTAAGAGTCAAATCTGCTATGTCCTTGATTTGTTTCTTGTAAACATAAGAATGTTA
1 TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCA
* * * * *
3900942 AATCATCTTGGATCTTGCTTCAGTATAAACCTCTGAACGCTAGATCTGCCATGTC
66 AATCATCTTGGATC-TGCTTCAGTATAAACATCTAAAAGCTAGATCTGCTATATC
* * * *
3900997 TAATAACATCTGAGAGTCAAATCTGCTATGTCCTCGGTTTGTTCCTTGTGAACACAAGAATACCA
1 TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCA
*
3901062 AATCATCTTGGATCTGCTTCAGTATAAACATCTAAAAGCTAGATCTGCTATATT
66 AATCATCTTGGATCTGCTTCAGTATAAACATCTAAAAGCTAGATCTGCTATATC
* * * *
3901116 TGAGAACATTTGAGAGTTAAATCTGCTATGTCCTCGATTTGCTCCTTGTAACCACAAGAATACCA
1 TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCA
* *
3901181 AATCATCTTGGATCTGCTTCAGTATAAACATCTGAAAGTTAGATCTGCTATATC
66 AATCATCTTGGATCTGCTTCAGTATAAACATCTAAAAGCTAGATCTGCTATATC
* * * *
3901235 TGGGAACGTCTGAGAGTCAAATCTGCTATGTCCCCGATTTGTTCCTTGTAAACACAAAAATACCA
1 TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCA
3901300 AATCATCTTGGATCTGCTTCAGTATAAACATCTAAAAGCTAGATCTGCTATA
66 AATCATCTTGGATCTGCTTCAGTATAAACATCTAAAAGCTAGATCTGCTATA
3901352 CTGCGGCCTA
Statistics
Matches: 317, Mismatches: 38, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
119 249 0.79
120 68 0.21
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (119 bp):
TGAGAACATCTGAGAGTCAAATCTGCTATGTCCTCGATTTGTTCCTTGTAAACACAAGAATACCA
AATCATCTTGGATCTGCTTCAGTATAAACATCTAAAAGCTAGATCTGCTATATC
Found at i:3909403 original size:15 final size:15
Alignment explanation
Indices: 3909362--3909409 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
3909352 ATAACTTTAA
*
3909362 ATGCAAATG-ATGTG
1 ATGCAAATGCATGAG
3909376 ATG-AAATGCCATGAG
1 ATGCAAATG-CATGAG
3909391 ATGCAAATGCATGA-
1 ATGCAAATGCATGAG
3909405 ATGCA
1 ATGCA
3909410 TAAAGAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 5 0.17
14 8 0.27
15 12 0.40
16 5 0.17
ACGTcount: A:0.40, C:0.12, G:0.25, T:0.23
Consensus pattern (15 bp):
ATGCAAATGCATGAG
Found at i:3913420 original size:12 final size:12
Alignment explanation
Indices: 3913400--3913523 Score: 82
Period size: 12 Copynumber: 10.5 Consensus size: 12
3913390 TCTTAAAATT
3913400 ATAAATAATATA
1 ATAAATAATATA
*
3913412 ATGAATAATATAAA
1 ATAAATAATAT--A
3913426 CATAAATAATATA
1 -ATAAATAATATA
3913439 ATAAATAATAT-
1 ATAAATAATATA
* *
3913450 AT-GATATACATA
1 ATAAATA-ATATA
*
3913462 ATATATAATA-A
1 ATAAATAATATA
*
3913473 AAAAATAATATA
1 ATAAATAATATA
* *
3913485 GTAAGTAATAT-
1 ATAAATAATATA
3913496 ATATAATAA-A-A
1 ATA-AATAATATA
*
3913507 GTAAA-AATATA
1 ATAAATAATATA
3913518 ATAAAT
1 ATAAAT
3913524 GCTATATAAT
Statistics
Matches: 85, Mismatches: 15, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
9 2 0.02
10 6 0.07
11 24 0.28
12 38 0.45
13 4 0.05
14 1 0.01
15 10 0.12
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (12 bp):
ATAAATAATATA
Found at i:3913469 original size:27 final size:27
Alignment explanation
Indices: 3913399--3913556 Score: 93
Period size: 27 Copynumber: 5.9 Consensus size: 27
3913389 ATCTTAAAAT
*
3913399 TATAAATAATATAATGAATAATATAAA
1 TATAAATAATATAATAAATAATATAAA
* *
3913426 CATAAATAATATAATAAATAATATATGA
1 TATAAATAATATAATAAATAATATA-AA
* *
3913454 TATACATAATATATAATAAA-AAAATAATA
1 TATAAAT-A-ATATAATAAATAATATAA-A
*
3913483 TAGTAAGTAATAT-AT--ATAATA-AAA
1 TA-TAAATAATATAATAAATAATATAAA
* **
3913507 -GTAAA-AATATAATAAATGCTATATAA
1 TATAAATAATATAATAAATAATATA-AA
3913533 TA-AAATACA-AT-ATAAATATATATA
1 TATAAATA-ATATAATAAATA-ATATA
3913557 GGAGAATAAA
Statistics
Matches: 99, Mismatches: 17, Indels: 30
0.68 0.12 0.21
Matches are distributed among these distances:
21 5 0.05
22 5 0.05
24 5 0.05
25 4 0.04
26 14 0.14
27 32 0.32
28 11 0.11
29 10 0.10
30 13 0.13
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (27 bp):
TATAAATAATATAATAAATAATATAAA
Found at i:3913531 original size:33 final size:32
Alignment explanation
Indices: 3913431--3913523 Score: 82
Period size: 34 Copynumber: 2.8 Consensus size: 32
3913421 ATAAACATAA
* *
3913431 ATAATATAATAAATAATAT-ATGATATACATAATAT
1 ATAATA-AAAAAATAATATAAT-AAATA-AT-ATAT
* *
3913466 ATAATAAAAAAATAATATAGTAAGTAATATAT
1 ATAATAAAAAAATAATATAATAAATAATATAT
3913498 ATAATAAAAGTAAA-AATATAATAAAT
1 ATAATAAAA--AAATAATATAATAAAT
3913524 GCTATATAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
32 13 0.27
33 12 0.24
34 17 0.35
35 7 0.14
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (32 bp):
ATAATAAAAAAATAATATAATAAATAATATAT
Found at i:3916018 original size:127 final size:124
Alignment explanation
Indices: 3915821--3916286 Score: 485
Period size: 127 Copynumber: 3.7 Consensus size: 124
3915811 TGAGAAAACA
* ** * * *
3915821 TGGATGGAATTTCAAAAGGATATTCTGTATTTTAGTCGTATGAAAAATTGAAACTCAGCACAATT
1 TGGATGAAATTTCAAAAGGATATTCCATATTTTAGTCGAATGAAAAATTGAAACCCAGCACGATT
*
3915886 GGGCACGACCTCCCTAACTTCCAAGA-ACGAAATATTACCTCGTTTTATTTTAAGAAAGC
66 GGGCACGACCTCCCAAACTTCCAA-ACACGAAATATTACCTCGTTTTATTTTAAGAAAGC
* * * * *
3915945 GTGGATGAAATTTCAAAAAAGGATATTTCATATTTTAGTCGAGTGGAAAATTGAAGCCCAACACG
1 -TGGATGAAATTTC--AAAAGGATATTCCATATTTTAGTCGAATGAAAAATTGAAACCCAGCACG
* *
3916010 ATTGGGCACGACTTCCCAAACTTCCAAACATGAAATATTACCTCGTTTTATTTTAAGTAAATGC
63 ATTGGGCACGACCTCCCAAACTTCCAAACACGAAATATTACCTCGTTTTATTTTAAG-AAA-GC
*** *
3916074 -GGATG-AATAAAAAAAGGATATTCCATA-TTTAGTCGAATGAACAAAATGAAACCCAGCACGAT
1 TGGATGAAATTTCAAAAGGATATTCCATATTTTAGTCGAATGAA-AAATTGAAACCCAGCACGAT
** * * * * * * *
3916136 TGGGCATAATCTCTCAAACTCCCCAAATACAAAATATTGCCTCCTTTTAATTTTTTAA-AAAGC
65 TGGGCACGACCTCCCAAACT-TCCAAACACGAAATATTACCTCGTTTT-A--TTTTAAGAAAGC
* * * * *
3916199 ATGGACGAAATTTCCAAAGGATATTCCGTATTTTAGCCGAATGGAAAATT-AAAGCCCAGCACGA
1 -TGGATGAAATTTCAAAAGGATATTCCATATTTTAGTCGAATGAAAAATTGAAA-CCCAGCACGA
3916263 TTGGGCACGACCTCCCAAACTTCC
64 TTGGGCACGACCTCCCAAACTTCC
3916287 CAAGACGATT
Statistics
Matches: 278, Mismatches: 48, Indels: 28
0.79 0.14 0.08
Matches are distributed among these distances:
123 12 0.04
124 47 0.17
125 35 0.13
126 8 0.03
127 105 0.38
128 57 0.21
129 14 0.05
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (124 bp):
TGGATGAAATTTCAAAAGGATATTCCATATTTTAGTCGAATGAAAAATTGAAACCCAGCACGATT
GGGCACGACCTCCCAAACTTCCAAACACGAAATATTACCTCGTTTTATTTTAAGAAAGC
Found at i:3916220 original size:252 final size:250
Alignment explanation
Indices: 3915834--3916286 Score: 590
Period size: 252 Copynumber: 1.8 Consensus size: 250
3915824 ATGGAATTTC
** * * * *
3915834 AAAAGGATATTCTGTATTTTAGTCGTATGAAAAATTGAAACTCAGCACAATTGGGCACGACCTCC
1 AAAAGGATATTCCATATTTTAGTCGAATGAAAAAATGAAACCCAGCACAATTGGGCACAACCTCC
* * * * * *
3915899 CTAACTTCCAAGAACGAAATATTACCTCGTTTTATTTTAAGAAAGCGTGGATGAAATTTCAAAAA
66 CAAACTCCCAAGAACAAAATATTACCTCCTTTTATTTTAAGAAAGCATGGACGAAATTTC-AAAA
* * * * *
3915964 AGGATATTTCATATTTTAGTCGAGTGGAAAATTGAAGCCCAACACGATTGGGCACGACTTCCCAA
130 AGGATATTCCATATTTTAGCCGAATGGAAAATTAAAGCCCAACACGATTGGGCACGACCTCCCAA
3916029 ACTTCCAAACATGAAATATTACCTCGTTTTATTTTAAGTAAATGCGGATGAATAAA
195 ACTTCCAAACATGAAATATTACCTCGTTTTATTTTAAGTAAATGCGGATGAATAAA
* * *
3916085 AAAAGGATATTCCATA-TTTAGTCGAATGAACAAAATGAAACCCAGCACGATTGGGCATAATCTC
1 AAAAGGATATTCCATATTTTAGTCGAATGAA-AAAATGAAACCCAGCACAATTGGGCACAACCTC
* *
3916149 TCAAACTCCCCAA-ATACAAAATATTGCCTCCTTTTAATTTTTTAA-AAAGCATGGACGAAATTT
65 CCAAACT-CCCAAGA-ACAAAATATTACCTCCTTTT-A--TTTTAAGAAAGCATGGACGAAATTT
* * *
3916212 C-CAAAGGATATTCCGTATTTTAGCCGAATGGAAAATTAAAGCCCAGCACGATTGGGCACGACCT
125 CAAAAAGGATATTCCATATTTTAGCCGAATGGAAAATTAAAGCCCAACACGATTGGGCACGACCT
3916276 CCCAAACTTCC
190 CCCAAACTTCC
3916287 CAAGACGATT
Statistics
Matches: 171, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
250 13 0.08
251 47 0.27
252 87 0.51
253 1 0.01
254 17 0.10
255 6 0.04
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (250 bp):
AAAAGGATATTCCATATTTTAGTCGAATGAAAAAATGAAACCCAGCACAATTGGGCACAACCTCC
CAAACTCCCAAGAACAAAATATTACCTCCTTTTATTTTAAGAAAGCATGGACGAAATTTCAAAAA
GGATATTCCATATTTTAGCCGAATGGAAAATTAAAGCCCAACACGATTGGGCACGACCTCCCAAA
CTTCCAAACATGAAATATTACCTCGTTTTATTTTAAGTAAATGCGGATGAATAAA
Found at i:3916784 original size:64 final size:64
Alignment explanation
Indices: 3916670--3916793 Score: 162
Period size: 64 Copynumber: 1.9 Consensus size: 64
3916660 TCATGTATCT
* *
3916670 ATGCTTATGCCAAATAACTAGGATGCTATGATCAAAATAATCCAAATGCTCCTAGCTAGACGTG
1 ATGCTTATACCAAATAACTAAGATGCTATGATCAAAATAATCCAAATGCTCCTAGCTAGACGTG
* * * *
3916734 ATGCTTATATCAAATAATTAAGATGCTATGA-CTAGAATGAAT-CAAGTGCTCCTAGCTAGA
1 ATGCTTATACCAAATAACTAAGATGCTATGATC-AAAAT-AATCCAAATGCTCCTAGCTAGA
3916794 TGTATTATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 1 0.02
64 48 0.92
65 3 0.06
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (64 bp):
ATGCTTATACCAAATAACTAAGATGCTATGATCAAAATAATCCAAATGCTCCTAGCTAGACGTG
Found at i:3921989 original size:30 final size:30
Alignment explanation
Indices: 3921954--3922014 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
3921944 CCAGTAAACA
* * *
3921954 ATTATAAGTAGGCTTGATGTCTATCACGAG
1 ATTATAAGAAGGCCTGATGTCCATCACGAG
3921984 ATTATAAGAAGGCCTGATGTCCATCACGAG
1 ATTATAAGAAGGCCTGATGTCCATCACGAG
3922014 A
1 A
3922015 AAGTCTACCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.28
Consensus pattern (30 bp):
ATTATAAGAAGGCCTGATGTCCATCACGAG
Found at i:3928236 original size:127 final size:127
Alignment explanation
Indices: 3927962--3928525 Score: 559
Period size: 127 Copynumber: 4.4 Consensus size: 127
3927952 AACGGTAAGC
** ** * * * * * * *
3927962 CGAAACCCAGCACGATTGGGCACGATTTATCGAATTTCCAAATACGAAACATTGCCACATTTTAA
1 CGAAACCCAGCACGATTGGGCACGACCTCCCAAACTTCCAAACACGAAATATTGCCTCGTTTTAT
* * * * * **
3928027 ATTGAGAAAACATGAATGGAATTTC--AAAAGGATATTCTGTATTTTAGTCGAATGAAAAAT
66 TTTAAGAAAGCATGGATGAAATTTCAAAAAAGGATATTCCATATTTTAGTCGAATGAAAAAT
* *
3928087 CGAAACCCAGCACGATTGGGCACGACCTCCCAAACTTCCAAGCACGAAATATTACCTCGTTTTAT
1 CGAAACCCAGCACGATTGGGCACGACCTCCCAAACTTCCAAACACGAAATATTGCCTCGTTTTAT
* * * *
3928152 TTTAAGAAAGCGTGGATGAAATTTCAAAAAAGGATATTTCATATTTTAGTCGAGTGGAAAAT
66 TTTAAGAAAGCATGGATGAAATTTCAAAAAAGGATATTCCATATTTTAGTCGAATGAAAAAT
* * * * *
3928214 TGAAGCCCAGCACGATTGGGCACGACTTCCCAAACTTCCAAACCCGAAATATTGCCTTGTTTTAT
1 CGAAACCCAGCACGATTGGGCACGACCTCCCAAACTTCCAAACACGAAATATTGCCTCGTTTTAT
* * *
3928279 TTTAAGTAAA-CACGGATG-AATTTAAAAAAAAGGATATTCCATA-TTTAGTCGAATGAACAAAA
66 TTTAAG-AAAGCATGGATGAAATTT-CAAAAAAGGATATTCCATATTTTAGTCGAATGAA-AAAT
* * * * * *
3928341 CAAAACCCAGCACGATTGGGCACGATCTCTCAAACTCCCTAAATACGAAATATTGCCTCCTTTTA
1 CGAAACCCAGCACGATTGGGCACGACCTCCCAAACTTCC-AAACACGAAATATTGCCTCGTTTT-
* * * * * *
3928406 ATTTTTTCA-AAAGCATGGACGAAATTTC--CAAAGGATATTCCGTATTTTAGCCGAATGGAAAA
64 A--TTTTAAGAAAGCATGGATGAAATTTCAAAAAAGGATATTCCATATTTTAGTCGAATGAAAAA
3928468 T
127 T
* * * * * *
3928469 TGAAGCCCAGCACGATTGGGCATGACCTTCAAAACTTCCCAACACGAAATATTGCCT
1 CGAAACCCAGCACGATTGGGCACGACCTCCCAAACTTCCAAACACGAAATATTGCCT
3928526 TCTGCTGAGA
Statistics
Matches: 358, Mismatches: 69, Indels: 22
0.80 0.15 0.05
Matches are distributed among these distances:
125 71 0.20
126 17 0.05
127 168 0.47
128 70 0.20
129 16 0.04
130 6 0.02
131 10 0.03
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (127 bp):
CGAAACCCAGCACGATTGGGCACGACCTCCCAAACTTCCAAACACGAAATATTGCCTCGTTTTAT
TTTAAGAAAGCATGGATGAAATTTCAAAAAAGGATATTCCATATTTTAGTCGAATGAAAAAT
Found at i:3928467 original size:255 final size:253
Alignment explanation
Indices: 3928052--3928526 Score: 652
Period size: 255 Copynumber: 1.9 Consensus size: 253
3928042 ATGGAATTTC
** * *
3928052 AAAAGGATATTCTGTATTTTAGTCGAATGAAAAATCGAAACCCAGCACGATTGGGCACGACCTCC
1 AAAAGGATATTCCATATTTTAGTCGAATGAAAAAACAAAACCCAGCACGATTGGGCACGACCTCC
* * * * *
3928117 CAAACTTCCAAGCACGAAATATTACCTCGTTTTATTTTAAGAAAGCGTGGATGAAATTTCAAAAA
66 CAAACTCCCAAACACGAAATATTACCTCCTTTTATTTTAAGAAAGCATGGACGAAATTTC-AAAA
* * * *
3928182 AGGATATTTCATATTTTAGTCGAGTGGAAAATTGAAGCCCAGCACGATTGGGCACGA-CTTCCCA
130 AGGATATTCCATATTTTAGCCGAATGGAAAATTGAAGCCCAGCACGATTGGGCACGACCTT-CAA
*
3928246 AACTTCCAAACCCGAAATATTGCCTTGTTTTATTTTAAGTAAACACGGATGAATTTAAAA
194 AACTTCCAAACACGAAATATTGCCTTGTTTTATTTTAAGTAAACACGGATGAATTTAAAA
*
3928306 AAAAGGATATTCCATA-TTTAGTCGAATGAACAAAACAAAACCCAGCACGATTGGGCACGATCTC
1 AAAAGGATATTCCATATTTTAGTCGAATGAA-AAAACAAAACCCAGCACGATTGGGCACGACCTC
* * * *
3928370 TCAAACTCCCTAAATACGAAATATTGCCTCCTTTTAATTTTTTCA-AAAGCATGGACGAAATTTC
65 CCAAACTCCC-AAACACGAAATATTACCTCCTTTT-A--TTTTAAGAAAGCATGGACGAAATTTC
* * *
3928434 -CAAAGGATATTCCGTATTTTAGCCGAATGGAAAATTGAAGCCCAGCACGATTGGGCATGACCTT
126 AAAAAGGATATTCCATATTTTAGCCGAATGGAAAATTGAAGCCCAGCACGATTGGGCACGACCTT
*
3928498 CAAAACTTCCCAACACGAAATATTGCCTT
191 CAAAACTTCCAAACACGAAATATTGCCTT
3928527 CTGCTGAGAG
Statistics
Matches: 192, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
253 14 0.07
254 52 0.27
255 100 0.52
256 4 0.02
257 17 0.09
258 5 0.03
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (253 bp):
AAAAGGATATTCCATATTTTAGTCGAATGAAAAAACAAAACCCAGCACGATTGGGCACGACCTCC
CAAACTCCCAAACACGAAATATTACCTCCTTTTATTTTAAGAAAGCATGGACGAAATTTCAAAAA
GGATATTCCATATTTTAGCCGAATGGAAAATTGAAGCCCAGCACGATTGGGCACGACCTTCAAAA
CTTCCAAACACGAAATATTGCCTTGTTTTATTTTAAGTAAACACGGATGAATTTAAAA
Found at i:3931606 original size:5 final size:5
Alignment explanation
Indices: 3931596--3931620 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3931586 TGTACTAACG
3931596 TGTTT TGTTT TGTTT TGTTT TGTTT
1 TGTTT TGTTT TGTTT TGTTT TGTTT
3931621 ATGACTGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
TGTTT
Found at i:3932741 original size:38 final size:38
Alignment explanation
Indices: 3932691--3932766 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
3932681 GGTTGGAGGA
*
3932691 AAAATTTAAGGCAATGGAGAATGTTGACTACTATTATG
1 AAAAGTTAAGGCAATGGAGAATGTTGACTACTATTATG
3932729 AAAAGTTAAGGCAATGGAGAATGTTGACTACTATTATG
1 AAAAGTTAAGGCAATGGAGAATGTTGACTACTATTATG
3932767 GGGTTGACGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.30
Consensus pattern (38 bp):
AAAAGTTAAGGCAATGGAGAATGTTGACTACTATTATG
Found at i:3936704 original size:220 final size:220
Alignment explanation
Indices: 3936319--3936768 Score: 686
Period size: 220 Copynumber: 2.0 Consensus size: 220
3936309 AGGTTTGACT
* *
3936319 ATCCTATCACCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGTAAATCTTGCCTCCCTGAAGTTGT
1 ATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAAATCTTGCCTCCCTGAAGTTGT
** * * *
3936384 AGGGGAGCAGATCGAAGACGATGAGCCTTAACCCCCTAAGCAGTAGGGCAACAGGCTAGAAATTA
66 AGGGGAGCAGATAAAAAACAATAAGCCTTAACCCCCTAAGCAGTAGGGCAACAGGCTAGAAATTA
* * * *
3936449 CAGATCTTGTCTCCCTGAAGCTGCAGTGGAACAGATCGAAGACGATGAATCTTGTCT-CTCTAAC
131 CAGATCTTATCTCCCTGAAGCTACAGTGAAACAGATCGAAGACGATGAATCTTATCTCCT-TAAC
*
3936513 CAGTAGTGGAGCATATTTAAGCCACC
195 CAGTAGTGGAGCAGATTTAAGCCACC
*
3936539 ATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAGATCTTGCCTCCCTGAAGTTGT
1 ATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAAATCTTGCCTCCCTGAAGTTGT
* * * *
3936604 AGTGGAGTAGATAAAAAACAATAAGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAGAAATTG
66 AGGGGAGCAGATAAAAAACAATAAGCCTTAACCCCCTAAGCAGTAGGGCAACAGGCTAGAAATTA
* * *
3936669 CAGATCTTATCTCCCTGAAGTTACAGTGAAACAGATTGAAGACGGTGAATCTTATCTCCTTAACC
131 CAGATCTTATCTCCCTGAAGCTACAGTGAAACAGATCGAAGACGATGAATCTTATCTCCTTAACC
* *
3936734 AGTAGTGGAGCAGATTTAAGCTACT
196 AGTAGTGGAGCAGATTTAAGCCACC
3936759 ATCCTATCTC
1 ATCCTATCTC
3936769 TCTGAAGTTG
Statistics
Matches: 207, Mismatches: 22, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
220 205 0.99
221 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.25
Consensus pattern (220 bp):
ATCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAAATTGCAAATCTTGCCTCCCTGAAGTTGT
AGGGGAGCAGATAAAAAACAATAAGCCTTAACCCCCTAAGCAGTAGGGCAACAGGCTAGAAATTA
CAGATCTTATCTCCCTGAAGCTACAGTGAAACAGATCGAAGACGATGAATCTTATCTCCTTAACC
AGTAGTGGAGCAGATTTAAGCCACC
Found at i:3936814 original size:46 final size:46
Alignment explanation
Indices: 3936763--3936880 Score: 136
Period size: 45 Copynumber: 2.6 Consensus size: 46
3936753 GCTACTATCC
* *
3936763 TATCTCTCTGAAGTTGTAGTAGAGCAGGA-TAAAATTACCCA-AGTCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGGACTAAAATTA-CCAGA-TCT
* * *
3936809 TATCTC-CTTGAAGTTGCAGTGGAGCA-GACTGAAGTTAGCAGATCT
1 TATCTCTC-TGAAGTTGCAGTGGAGCAGGACTAAAATTACCAGATCT
3936854 TATCTCTCTGAAGTTGCAGTGGAGCAG
1 TATCTCTCTGAAGTTGCAGTGGAGCAG
3936881 ATCGAAGCCA
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
45 32 0.52
46 30 0.48
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (46 bp):
TATCTCTCTGAAGTTGCAGTGGAGCAGGACTAAAATTACCAGATCT
Found at i:3936866 original size:45 final size:45
Alignment explanation
Indices: 3936763--3936969 Score: 140
Period size: 46 Copynumber: 4.6 Consensus size: 45
3936753 GCTACTATCC
* *
3936763 TATCTCTCTGAAGTTGTAGTAGAGCAGGATAAAATTACCCAAGTCT
1 TATCTCTCTGAAGTTGCAGTGGAGCA-GATAAAATTACCCAAGTCT
* * *
3936809 TATCTC-CTTGAAGTTGCAGTGGAGCAGACTGAAGTTA-GC-AGATCT
1 TATCTCTC-TGAAGTTGCAGTGGAGCAGA-TAAAATTACCCAAG-TCT
** *
3936854 TATCTCTCTGAAGTTGCAGTGGAGCAGATCGAA--GCCACAA-TCCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATAAAATTACC-CAAGT-CT
* * * * * * * *
3936898 TATCTTTCTGAAGTTACAGTAGAACAGGATAAAAATACACGAA-CCG
1 TATCTCTCTGAAGTTGCAGTGGAGCA-GATAAAATTAC-CCAAGTCT
*
3936944 TATCTCCCTGAAGTTGCAGTGGAGCA
1 TATCTCTCTGAAGTTGCAGTGGAGCA
3936970 ATTACAATAG
Statistics
Matches: 124, Mismatches: 25, Indels: 24
0.72 0.14 0.14
Matches are distributed among these distances:
43 1 0.01
44 29 0.23
45 39 0.31
46 51 0.41
47 3 0.02
48 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (45 bp):
TATCTCTCTGAAGTTGCAGTGGAGCAGATAAAATTACCCAAGTCT
Found at i:3937225 original size:45 final size:45
Alignment explanation
Indices: 3937161--3937281 Score: 188
Period size: 45 Copynumber: 2.7 Consensus size: 45
3937151 ATCACCCAAG
* * *
3937161 TCTCATCTCCCTAAAGTTGCACTGGAGTAGACTGAAGTTAGCAGA
1 TCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTTAGCAGA
*
3937206 TCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTGGAGTTAGCAGA
1 TCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTTAGCAGA
* *
3937251 TCTTACCTCCCTGAAGTTGCAGTGGAGCAGA
1 TCTCATCTCCCTGAAGTTGCAGTGGAGCAGA
3937282 TCGAAGCCAC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 70 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (45 bp):
TCTCATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGTTAGCAGA
Found at i:3945910 original size:25 final size:22
Alignment explanation
Indices: 3945852--3945911 Score: 57
Period size: 25 Copynumber: 2.5 Consensus size: 22
3945842 ACAACCACTT
3945852 TTTTATATTAAAATATATTTTTA
1 TTTT-TATTAAAATATATTTTTA
* * *
3945875 CTTTAAATAAAATATTATTATTTTA
1 TTTTTATTAAAATA-TA-T-TTTTA
3945900 TTTTTATTAAAA
1 TTTTTATTAAAA
3945912 ACATTTAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
22 8 0.29
23 5 0.18
24 1 0.04
25 14 0.50
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTTATTAAAATATATTTTTA
Found at i:3946342 original size:23 final size:21
Alignment explanation
Indices: 3946316--3946357 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
3946306 TTTGGGTTAA
3946316 TATTTTGTATGAATTTATTTTTT
1 TATTTTGTAT-AA-TTATTTTTT
*
3946339 TATTTTTTATAATTATTTT
1 TATTTTGTATAATTATTTT
3946358 AAAATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 2 0.11
23 9 0.50
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTGTATAATTATTTTTT
Found at i:3946441 original size:60 final size:60
Alignment explanation
Indices: 3946348--3946466 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 60
3946338 TTATTTTTTA
* *
3946348 TAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTGTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATGATGTTATAAATTGTTGTGTTTG
3946408 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATGATGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATGATGTTATAAATTGTTGTGTTT
3946467 AGTTTAGTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATGATGTTATAAATTGTTGTGTTTG
Found at i:3946584 original size:60 final size:60
Alignment explanation
Indices: 3946515--3946702 Score: 234
Period size: 60 Copynumber: 3.0 Consensus size: 60
3946505 TTTTATTAAA
3946515 TATTTTGTTAGTAATTTATTATAAATTGTTGTGTTTTGTGAGTTTTTAGTAATGTAAAAT
1 TATTTTGTTAGTAATTTATTATAAATTGTTGTGTTTTGTGAGTTTTTAGTAATGTAAAAT
* * *
3946575 TATTTTGTTAGTAATTTATTATAAATTATTGTGTTTTATGAGTTTTTATTAATGTAAAAT
1 TATTTTGTTAGTAATTTATTATAAATTGTTGTGTTTTGTGAGTTTTTAGTAATGTAAAAT
*
3946635 TATTTTGATAATTTTTTTTAAG-AATTTATTATAAATTGTTTTGTTTTGTGAGTTTTTAGTAATG
1 TATTTTG----------TT-AGTAATTTATTATAAATTGTTGTGTTTTGTGAGTTTTTAGTAATG
3946699 TAAA
55 TAAA
3946703 TTTCTTAAAA
Statistics
Matches: 110, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
60 64 0.58
70 44 0.40
71 2 0.02
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (60 bp):
TATTTTGTTAGTAATTTATTATAAATTGTTGTGTTTTGTGAGTTTTTAGTAATGTAAAAT
Found at i:3946720 original size:130 final size:132
Alignment explanation
Indices: 3946480--3946721 Score: 330
Period size: 130 Copynumber: 1.8 Consensus size: 132
3946470 TTAGTATTTG
3946480 ATGAGTTTTTAGTAATGTAAAATAATTTTATTAAATATTTTGTTAGTAATTTATTATAAATTGTT
1 ATGAGTTTTTAGTAATGTAAAATAATTTTATTAAATATTTTGTTAGTAATTTATTATAAATTGTT
***** *
3946545 GTGTTTTGTGAGTTTTTAGTAATGTAAAATTATTTTGTTAGTAATTTATTATAAATTATTGTGTT
66 GTGTTTTGTGAGTTTTTAGTAATGTAAAATTATTAAAAAAATAATTTATTATAAATTATTGTGTT
3946610 TT
131 TT
* * *
3946612 ATGAGTTTTTATTAATGTAAAATTATTTTGA-T-AAT-TTTTTTTAAG-AATTTATTATAAATTG
1 ATGAGTTTTTAGTAATGTAAAATAATTTT-ATTAAATATTTTGTT-AGTAATTTATTATAAATTG
* * *
3946673 TTTTGTTTTGTGAGTTTTTAGTAATGTAAATTTCTTAAAAAAATAATTT
64 TTGTGTTTTGTGAGTTTTTAGTAATGTAAAATTATTAAAAAAATAATTT
3946722 TATAGTTATT
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
130 62 0.65
131 5 0.05
132 28 0.29
133 1 0.01
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (132 bp):
ATGAGTTTTTAGTAATGTAAAATAATTTTATTAAATATTTTGTTAGTAATTTATTATAAATTGTT
GTGTTTTGTGAGTTTTTAGTAATGTAAAATTATTAAAAAAATAATTTATTATAAATTATTGTGTT
TT
Found at i:3946784 original size:18 final size:19
Alignment explanation
Indices: 3946761--3946805 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
3946751 AGGTTATAAA
* *
3946761 TTGTTAGT-GTTTTTTGTT
1 TTGTTAGTAGTTATTTATT
3946779 TTGTTA-TAGTTATTTATT
1 TTGTTAGTAGTTATTTATT
3946797 TTGTTAGTA
1 TTGTTAGTA
3946806 ATTTATGGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 20 0.87
19 2 0.09
ACGTcount: A:0.16, C:0.00, G:0.18, T:0.67
Consensus pattern (19 bp):
TTGTTAGTAGTTATTTATT
Found at i:3949060 original size:33 final size:33
Alignment explanation
Indices: 3949009--3949082 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
3948999 CAGTACTCTG
* * * *
3949009 CTCCTTTCGGCCCGTATCCACCATCGTACTCCA
1 CTCCTCTCTGCCCATATCCACCATCATACTCCA
* * *
3949042 TTCCTCTCTGCCCATATCCATCGTCATACTCCA
1 CTCCTCTCTGCCCATATCCACCATCATACTCCA
3949075 CTCCTCTC
1 CTCCTCTC
3949083 GGCTCGTATC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.15, C:0.46, G:0.08, T:0.31
Consensus pattern (33 bp):
CTCCTCTCTGCCCATATCCACCATCATACTCCA
Found at i:3949138 original size:66 final size:66
Alignment explanation
Indices: 3949009--3949162 Score: 150
Period size: 66 Copynumber: 2.3 Consensus size: 66
3948999 CAGTACTCTG
* * * *
3949009 CTCCTTTCGGCCCGTATCCACCATCGTACTCCATTCCTCTCTGCCCATATCCATCGTCATACTCC
1 CTCCTCTCGGCCCGTATCCACCATCGTACTCCATTCCTCTCAGCCCATATCCACCGCCATACTCC
3949074 A
66 A
* * * * *
3949075 CTCCTCTCGGCTCGTATCGACCA-CTGTACTCCACTT-CTCTCAGTCTATATCCACCGCCGTACT
1 CTCCTCTCGGCCCGTATCCACCATC-GTACTCCA-TTCCTCTCAGCCCATATCCACCGCCATACT
**
3949138 CTG
64 CCA
* * *
3949141 CTCTTCCCAGCCCGTATCCACC
1 CTCCTCTCGGCCCGTATCCACC
3949163 GCCGAACTCC
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
65 1 0.01
66 67 0.96
67 2 0.03
ACGTcount: A:0.16, C:0.44, G:0.11, T:0.29
Consensus pattern (66 bp):
CTCCTCTCGGCCCGTATCCACCATCGTACTCCATTCCTCTCAGCCCATATCCACCGCCATACTCC
A
Found at i:3952119 original size:174 final size:174
Alignment explanation
Indices: 3951822--3952170 Score: 637
Period size: 174 Copynumber: 2.0 Consensus size: 174
3951812 CTTAAAAATT
* *
3951822 AGCAAGCGGCAATCCAAGGTCTCGAGACTCAAATAGGTCAGGTTGCTAAGCTGATCTCAGAAAGA
1 AGCAAGCGGCAATCCAAGGTCTCGAGACTCAAATAGGTCAGGTTGCTAAGCTAATCTCAAAAAGA
3951887 CCACAAGGTAGCTTGCCTAGCAACACCACAACTAACCCAAGAGAGCAACTCCATGCGATTACTGT
66 CCACAAGGTAGCTTGCCTAGCAACACCACAACTAACCCAAGAGAGCAACTCCATGCGATTACTGT
3951952 TCGAGATGAAA-AAGGGTTAGTTGAGTTCAAACCAGAACCAAGGA
131 TCGAGAT-AAAGAAGGGTTAGTTGAGTTCAAACCAGAACCAAGGA
3951996 AGCAAGCGGCAATCCAAGGTCTCGAGACTCAAATAGGTCAGGTTGCTAAGCTAATCTCAAAAAGA
1 AGCAAGCGGCAATCCAAGGTCTCGAGACTCAAATAGGTCAGGTTGCTAAGCTAATCTCAAAAAGA
* *
3952061 CCACAAGGTAGCTTGCCTAGCAACACCACGACTAACCCAAGAGAGCAACTCTATGCGATTACTGT
66 CCACAAGGTAGCTTGCCTAGCAACACCACAACTAACCCAAGAGAGCAACTCCATGCGATTACTGT
*
3952126 TCGAGATAAAGAAGGGTTAGTTGAGTTTAAACCAGAACCAAGGA
131 TCGAGATAAAGAAGGGTTAGTTGAGTTCAAACCAGAACCAAGGA
3952170 A
1 A
3952171 AGAAACTGTG
Statistics
Matches: 169, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
173 3 0.02
174 166 0.98
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (174 bp):
AGCAAGCGGCAATCCAAGGTCTCGAGACTCAAATAGGTCAGGTTGCTAAGCTAATCTCAAAAAGA
CCACAAGGTAGCTTGCCTAGCAACACCACAACTAACCCAAGAGAGCAACTCCATGCGATTACTGT
TCGAGATAAAGAAGGGTTAGTTGAGTTCAAACCAGAACCAAGGA
Found at i:3956996 original size:30 final size:30
Alignment explanation
Indices: 3956962--3957018 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
3956952 TAGACACTTC
*
3956962 CACACAGGTAATCCACACACCCGTGTGAGA
1 CACACAGGTAAGCCACACACCCGTGTGAGA
* * *
3956992 CACACGGGTAGGCCACACGCCCGTGTG
1 CACACAGGTAAGCCACACACCCGTGTG
3957019 TCATAGCCGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.26, C:0.35, G:0.26, T:0.12
Consensus pattern (30 bp):
CACACAGGTAAGCCACACACCCGTGTGAGA
Found at i:3962447 original size:17 final size:16
Alignment explanation
Indices: 3962419--3962471 Score: 97
Period size: 16 Copynumber: 3.2 Consensus size: 16
3962409 TTTGGTTCGC
3962419 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3962435 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
3962452 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3962468 TGTA
1 TGTA
3962472 ATAGCTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
16 20 0.56
17 16 0.44
ACGTcount: A:0.25, C:0.00, G:0.38, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:3962536 original size:44 final size:45
Alignment explanation
Indices: 3962452--3962542 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
3962442 GGATTAGAGG
* * *
3962452 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
3962497 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
3962541 TG
1 TG
3962543 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:3972284 original size:64 final size:64
Alignment explanation
Indices: 3972180--3972304 Score: 160
Period size: 64 Copynumber: 2.0 Consensus size: 64
3972170 TCTTTCGAGC
* * * * * *
3972180 AATTAATCTAATTGTTGAGCCATATTCCTATGCTAATAATGTCGACCAAATTGATTAAGAATTA
1 AATTAATCTAACTATGGAGCCATATTCCTATGCCAATAATGTCAACCAAATTAATTAAGAATTA
* ** *
3972244 AATTAATCTAACTATGGAGCTATATTCCTATGCCGGTAATGTTAACCAAATTAATTAAGAA
1 AATTAATCTAACTATGGAGCCATATTCCTATGCCAATAATGTCAACCAAATTAATTAAGAA
3972305 CTATCCCAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.34
Consensus pattern (64 bp):
AATTAATCTAACTATGGAGCCATATTCCTATGCCAATAATGTCAACCAAATTAATTAAGAATTA
Found at i:3976992 original size:17 final size:17
Alignment explanation
Indices: 3976970--3977004 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3976960 AAACTAAAAT
3976970 TTACTTGTGGCCACCAC
1 TTACTTGTGGCCACCAC
3976987 TTACTTGTGGCCACCAC
1 TTACTTGTGGCCACCAC
3977004 T
1 T
3977005 GAGCCCTCCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.34, G:0.17, T:0.31
Consensus pattern (17 bp):
TTACTTGTGGCCACCAC
Found at i:3993310 original size:19 final size:19
Alignment explanation
Indices: 3993286--3993325 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
3993276 AATGTATATG
3993286 AATGCAGTCAAGTATTAAA
1 AATGCAGTCAAGTATTAAA
3993305 AATGCAGTCAAGTATTAAA
1 AATGCAGTCAAGTATTAAA
3993324 AA
1 AA
3993326 AACTACCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (19 bp):
AATGCAGTCAAGTATTAAA
Found at i:3998464 original size:25 final size:25
Alignment explanation
Indices: 3998430--3998481 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
3998420 ATTGGTTACT
*
3998430 TAGTGTCCAAGAAACTACTAATTGG
1 TAGTGTCCAAGAAACTACAAATTGG
3998455 TAGTGTCCAAGAAACTACAAATTGG
1 TAGTGTCCAAGAAACTACAAATTGG
3998480 TA
1 TA
3998482 AACTTGAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (25 bp):
TAGTGTCCAAGAAACTACAAATTGG
Found at i:4001651 original size:63 final size:63
Alignment explanation
Indices: 4001578--4001753 Score: 185
Period size: 63 Copynumber: 2.8 Consensus size: 63
4001568 CACATGCCTA
* * *
4001578 TGTCTCCAGCCCGTGTACCTTTGATTCTAAAACAGTAAGTTACACT-GCTTAGACACACACCCG
1 TGTCTCCAGCCCGTGTACCTTTAATTCTAAAACAGTGAGTTACA-TAGCCTAGACACACACCCG
* * * * * * * **
4001641 TTTCTCCAGCCCATGTGCCTCTAATTCCAAAACAGTGAGTTACATAGCCTGGACACACGCTTG
1 TGTCTCCAGCCCGTGTACCTTTAATTCTAAAACAGTGAGTTACATAGCCTAGACACACACCCG
* * * *
4001704 TGTCTCTAGCCCGTATACCTTTTATTCTAAAACAATGAGTTACATA-CCTA
1 TGTCTCCAGCCCGTGTACCTTTAATTCTAAAACAGTGAGTTACATAGCCTA
4001754 TGTCTTTAGC
Statistics
Matches: 90, Mismatches: 22, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
62 4 0.04
63 86 0.96
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (63 bp):
TGTCTCCAGCCCGTGTACCTTTAATTCTAAAACAGTGAGTTACATAGCCTAGACACACACCCG
Found at i:4009921 original size:46 final size:46
Alignment explanation
Indices: 4009869--4010827 Score: 1641
Period size: 46 Copynumber: 20.8 Consensus size: 46
4009859 AGTGTGCTCT
* *
4009869 CTGATATGGAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
4009915 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
4009961 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
4010007 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
4010053 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
4010099 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
4010145 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
4010191 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
4010237 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
4010283 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
4010329 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
4010375 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
4010421 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAT
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* **
4010467 GTGATATGAAATGAAAAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
4010513 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** * *
4010559 ATGACGGGAAAATGAATAAGACCATAGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
4010606 GTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
4010652 GTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
4010698 CTGACATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** * *
4010744 ATGACGGGAAAATGAATAAGACAATGGTTGAAAGATACCATGGCAAC
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * *
4010791 ATGATA-GAAAATGAGTAAAACCATAGTTGAAAGATAC
1 CTGATATG-AAATGAGTAAGACCATGGTTGAAAGATAC
4010828 TATGACATCA
Statistics
Matches: 872, Mismatches: 39, Indels: 4
0.95 0.04 0.00
Matches are distributed among these distances:
46 792 0.91
47 80 0.09
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
CTGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:4016933 original size:17 final size:17
Alignment explanation
Indices: 4016911--4016948 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
4016901 AGAGTTCGAT
4016911 GTTCCTGGAATGGTCCA
1 GTTCCTGGAATGGTCCA
4016928 GTTCCTGGAATGGTCCA
1 GTTCCTGGAATGGTCCA
4016945 GTTC
1 GTTC
4016949 TGTCTCGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.32
Consensus pattern (17 bp):
GTTCCTGGAATGGTCCA
Found at i:4020741 original size:13 final size:13
Alignment explanation
Indices: 4020723--4020749 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4020713 TTTGTGCATT
4020723 ATTAGTTTAGTTA
1 ATTAGTTTAGTTA
4020736 ATTAGTTTAGTTA
1 ATTAGTTTAGTTA
4020749 A
1 A
4020750 AACAAATCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (13 bp):
ATTAGTTTAGTTA
Found at i:4022898 original size:18 final size:18
Alignment explanation
Indices: 4022860--4022899 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
4022850 TACAAAAAAA
*
4022860 AAAATTAAAATATTTTTT
1 AAAATTAAAATATTTTAT
4022878 AAAATTAAAA-ATATTTAT
1 AAAATTAAAATAT-TTTAT
4022896 AAAA
1 AAAA
4022900 ATATCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTAAAATATTTTAT
Found at i:4022900 original size:19 final size:18
Alignment explanation
Indices: 4022859--4022914 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
4022849 TTACAAAAAA
*
4022859 AAAAATTAAAATATTTTT
1 AAAAATTAAAATATTTAT
*
4022877 TAAAATTAAAAATATTTAT
1 AAAAATT-AAAATATTTAT
*
4022896 AAAAATATCAAA-ATTTAT
1 AAAAAT-TAAAATATTTAT
4022914 A
1 A
4022915 TTTTTAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 13 0.41
19 18 0.56
20 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATTAAAATATTTAT
Found at i:4024192 original size:36 final size:36
Alignment explanation
Indices: 4024124--4024198 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
4024114 TTTGATTCTC
* * *
4024124 AAACACATATAATTAAATATAGATATAGTTATATTT
1 AAACACATATAATTAAATATAGATAAAATTATATGT
* *
4024160 AAACACATATAATTAAATCTTGATAAAATTATATGT
1 AAACACATATAATTAAATATAGATAAAATTATATGT
4024196 AAA
1 AAA
4024199 TTTACAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (36 bp):
AAACACATATAATTAAATATAGATAAAATTATATGT
Found at i:4024239 original size:15 final size:17
Alignment explanation
Indices: 4024219--4024253 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
4024209 TGATAAGCCC
4024219 AAAAACT-AGAACC-CA
1 AAAAACTCAGAACCTCA
4024234 AAAAACTCAGAACCTCA
1 AAAAACTCAGAACCTCA
4024251 AAA
1 AAA
4024254 CTTAGTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 6 0.33
17 5 0.28
ACGTcount: A:0.60, C:0.26, G:0.06, T:0.09
Consensus pattern (17 bp):
AAAAACTCAGAACCTCA
Found at i:4024613 original size:19 final size:19
Alignment explanation
Indices: 4024589--4024625 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4024579 ATGCATATAT
*
4024589 TTTTATAATTTATAATTTC
1 TTTTATAATTTAAAATTTC
*
4024608 TTTTATATTTTAAAATTT
1 TTTTATAATTTAAAATTT
4024626 TGGCTAAAGG
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:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATAATTTAAAATTTC
Found at i:4024976 original size:15 final size:14
Alignment explanation
Indices: 4024940--4024987 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
4024930 TTATTTTTTT
*
4024940 AATTAATTTTAAAA
1 AATTAATTTTTAAA
*
4024954 AAATAATTTTTAAA
1 AATTAATTTTTAAA
*
4024968 AATTAAATTTTATAA
1 AATTAATTTTTA-AA
4024983 AATTA
1 AATTA
4024988 TTAAATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.76
15 7 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATTAATTTTTAAA
Found at i:4025676 original size:15 final size:15
Alignment explanation
Indices: 4025656--4025687 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
4025646 ATAATTTATA
4025656 TTTAATTATATGTGT
1 TTTAATTATATGTGT
4025671 TTTAATTATATGTGT
1 TTTAATTATATGTGT
4025686 TT
1 TT
4025688 GAGAATAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (15 bp):
TTTAATTATATGTGT
Found at i:4025900 original size:21 final size:21
Alignment explanation
Indices: 4025875--4025914 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4025865 AAAACGTTCT
4025875 AAAATGTTAATAATTAAATTG
1 AAAATGTTAATAATTAAATTG
* * *
4025896 AAAATTTTTATAGTTAAAT
1 AAAATGTTAATAATTAAAT
4025915 AAAAAAATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.42
Consensus pattern (21 bp):
AAAATGTTAATAATTAAATTG
Found at i:4046438 original size:15 final size:14
Alignment explanation
Indices: 4046415--4046445 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
4046405 GCCCTTTACC
4046415 AAAAAAAAAAAGAA
1 AAAAAAAAAAAGAA
4046429 AAAAAGAAAAAAGAA
1 AAAAA-AAAAAAGAA
4046444 AA
1 AA
4046446 CCTTGATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAA
Found at i:4059182 original size:24 final size:24
Alignment explanation
Indices: 4059131--4059196 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 24
4059121 TAACGAATTC
*
4059131 AAATAATTTTAAATTTTGTAAGTTAT
1 AAAT-ATTTT-AATTTTGTAAGTAAT
4059157 AAATATTTTAATTTTG-AATGTAAT
1 AAATATTTTAATTTTGTAA-GTAAT
* *
4059181 AATTTATTTTACTTTT
1 AA-ATATTTTAATTTT
4059197 TTACAATGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 2 0.06
24 13 0.37
25 16 0.46
26 4 0.11
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (24 bp):
AAATATTTTAATTTTGTAAGTAAT
Found at i:4059929 original size:42 final size:43
Alignment explanation
Indices: 4059882--4060086 Score: 172
Period size: 42 Copynumber: 4.8 Consensus size: 43
4059872 TAGTGGCGTT
4059882 TTTGTACAAAAACGCCGCTAAAGAATATGTTCTTTAGCGGC-A
1 TTTGTACAAAAACGCCGCTAAAGAATATGTTCTTTAGCGGCGA
* * * * *
4059924 TTTGTAAAAAAAGCGCGGCTAAAGAACATGGTCTTTAGCGGCGT
1 TTTGTACAAAAA-CGCCGCTAAAGAATATGTTCTTTAGCGGCGA
* * ** *
4059968 TTTCTAC-AAAGCGCCATTAAAGAACATGTTCTTTAGCGGCGCA
1 TTTGTACAAAAACGCCGCTAAAGAATATGTTCTTTAGCGGCG-A
* * * * *
4060011 TAT-T-CACAAACGCCACTAAAG-ATCATGTCCTTTAGCGGCGC
1 TTTGTACAAAAACGCCGCTAAAGAAT-ATGTTCTTTAGCGGCGA
* *
4060052 TTTGTA-GAAATCGCCGCTAAAG-ATCATGTTCTTTA
1 TTTGTACAAAAACGCCGCTAAAGAAT-ATGTTCTTTA
4060087 ACGACGTTCT
Statistics
Matches: 130, Mismatches: 26, Indels: 14
0.76 0.15 0.08
Matches are distributed among these distances:
41 4 0.03
42 90 0.69
43 31 0.24
44 5 0.04
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (43 bp):
TTTGTACAAAAACGCCGCTAAAGAATATGTTCTTTAGCGGCGA
Found at i:4059959 original size:43 final size:43
Alignment explanation
Indices: 4059882--4060230 Score: 157
Period size: 42 Copynumber: 8.0 Consensus size: 43
4059872 TAGTGGCGTT
* *
4059882 TTTGTACAAAAA-CGCCGCTAAAGAATATGTTCTTTAGCGGCA
1 TTTGTAAAAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCA
* * *
4059924 TTTGTAAAAAAAGCGCGGCTAAAGAACATGGTCTTTAGCGGCG
1 TTTGTAAAAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCA
** * **
4059967 TTT-TCTACAAAGCGCCATTAAAGAACATGTTCTTTAGCGGCGCA
1 TTTGTAAAAAAAGCGCCGCTAAAGAACATGTTCTTTAGC-G-GCA
* * * * * * *
4060011 TAT-T-CACAAA-CGCCACTAAAGATCATGTCCTTTAGCGGCGC
1 TTTGTAAAAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC-A
* * * *
4060052 TTTGT--AGAAATCGCCGCTAAAGATCATGTTCTTTAACGACGTTC-
1 TTTGTAAAAAAAGCGCCGCTAAAGAACATGTTCTTT-A-G-CG-GCA
* * * *
4060096 TTTAGCGGCGCTTAGAAAAAAACGCTGCTAAAGATCATGTTCTTTAGCGGCG
1 TTT------G--TA-AAAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCA
* * *
4060148 TTTAG-AAACAAAA--GCCGCTAAAGATCATATTCTTTAGCGGCGC
1 TTT-GTAAA-AAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC-A
* * *
4060191 TTAG-AAAAAAA-CGCCACTAAAGAACATGATCTTTAGCGGC
1 TTTGTAAAAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGC
4060231 GTTTTTGTTT
Statistics
Matches: 245, Mismatches: 37, Indels: 50
0.74 0.11 0.15
Matches are distributed among these distances:
40 2 0.01
41 11 0.04
42 138 0.56
43 40 0.16
44 14 0.06
45 2 0.01
46 1 0.00
47 1 0.00
50 1 0.00
51 1 0.00
52 6 0.02
53 1 0.00
54 1 0.00
55 26 0.11
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (43 bp):
TTTGTAAAAAAAGCGCCGCTAAAGAACATGTTCTTTAGCGGCA
Found at i:4060073 original size:84 final size:85
Alignment explanation
Indices: 4059894--4060086 Score: 205
Period size: 84 Copynumber: 2.3 Consensus size: 85
4059884 TGTACAAAAA
* * **
4059894 CGCCGCTAAAGAATATGTTCTTTAGCGGCATTTGTAAAAAAAGCGCGGCTAAAGAACATGGTCTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCATATGTAAAAAAAGCGCCACTAAAGAACATGGTCTT
*
4059959 TAGCGGCGTTTTCTACAAAG
66 TAGCGGCGCTTTCTACAAAG
** * * *
4059979 CGCCATTAAAGAACATGTTCTTTAGCGGCGCATAT-T-CACAAA-CGCCACTAAAGATCAT-GTC
1 CGCCGCTAAAGAACATGTTCTTTAGC-G-GCATATGTAAAAAAAGCGCCACTAAAGAACATGGT-
* * *
4060040 CTTTAGCGGCGCTTTGTAGAAAT
63 CTTTAGCGGCGCTTTCTACAAAG
*
4060063 CGCCGCTAAAGATCATGTTCTTTA
1 CGCCGCTAAAGAACATGTTCTTTA
4060087 ACGACGTTCT
Statistics
Matches: 89, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
83 2 0.02
84 53 0.60
85 27 0.30
86 2 0.02
87 5 0.06
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.28
Consensus pattern (85 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCATATGTAAAAAAAGCGCCACTAAAGAACATGGTCTT
TAGCGGCGCTTTCTACAAAG
Found at i:4060153 original size:42 final size:42
Alignment explanation
Indices: 4060092--4060231 Score: 210
Period size: 42 Copynumber: 3.3 Consensus size: 42
4060082 CTTTAACGAC
*
4060092 GTTCTTTAGCGGCGCTTAGAAAAAAACGCTGCTAAAGATCAT
1 GTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCAT
*
4060134 GTTCTTTAGCGGCGTTTAGAAACAAAA-GCCGCTAAAGATCAT
1 GTTCTTTAGCGGCGCTTAGAAA-AAAACGCCGCTAAAGATCAT
* * *
4060176 ATTCTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAGAACAT
1 GTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCAT
*
4060218 GATCTTTAGCGGCG
1 GTTCTTTAGCGGCG
4060232 TTTTTGTTTA
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
41 4 0.05
42 80 0.91
43 4 0.05
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (42 bp):
GTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCAT
Found at i:4060448 original size:20 final size:20
Alignment explanation
Indices: 4060425--4060464 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4060415 TCTTAAAGCT
4060425 TCAAATGTAAATTAATCATG
1 TCAAATGTAAATTAATCATG
4060445 TCAAATGTAAATTAATCATG
1 TCAAATGTAAATTAATCATG
4060465 GGATTCAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
TCAAATGTAAATTAATCATG
Found at i:4061355 original size:17 final size:19
Alignment explanation
Indices: 4061333--4061370 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4061323 AACAATTAAT
4061333 TAAAAA-TTA-AAAATATA
1 TAAAAATTTAGAAAATATA
4061350 TAAAAATTTAGAAAATATA
1 TAAAAATTTAGAAAATATA
4061369 TA
1 TA
4061371 TTTAGTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
19 10 0.53
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATTTAGAAAATATA
Found at i:4061539 original size:15 final size:16
Alignment explanation
Indices: 4061503--4061532 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4061493 GTAATTAATT
4061503 AAAATTGAAAAATATA
1 AAAATTGAAAAATATA
4061519 AAAATT-AAAAATAT
1 AAAATTGAAAAATAT
4061533 TGAAATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
AAAATTGAAAAATATA
Found at i:4063248 original size:11 final size:11
Alignment explanation
Indices: 4063232--4063306 Score: 87
Period size: 11 Copynumber: 6.8 Consensus size: 11
4063222 CACAAAAAGT
4063232 AGCACCAAAAC
1 AGCACCAAAAC
* *
4063243 AACACCAAAAT
1 AGCACCAAAAC
4063254 AGCACCAAAAC
1 AGCACCAAAAC
* *
4063265 AGCAACAAAAT
1 AGCACCAAAAC
*
4063276 AGCAACAAAAC
1 AGCACCAAAAC
* *
4063287 AGCACAAAAAT
1 AGCACCAAAAC
4063298 AGCACCAAA
1 AGCACCAAA
4063307 CAACGGCAGT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 53 1.00
ACGTcount: A:0.60, C:0.28, G:0.08, T:0.04
Consensus pattern (11 bp):
AGCACCAAAAC
Found at i:4063259 original size:22 final size:22
Alignment explanation
Indices: 4063215--4063310 Score: 115
Period size: 22 Copynumber: 4.4 Consensus size: 22
4063205 AAAGAACAAT
*
4063215 AAAACACCACAAAAAGTAGCACC
1 AAAACAACACAAAAA-TAGCACC
*
4063238 AAAACAACACCAAAATAGCACC
1 AAAACAACACAAAAATAGCACC
* *
4063260 AAAACAGCA-ACAAAATAGCAAC
1 AAAACAACACA-AAAATAGCACC
*
4063282 AAAACAGCACAAAAATAGCACC
1 AAAACAACACAAAAATAGCACC
4063304 -AAACAAC
1 AAAACAAC
4063311 GGCAGTGAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
21 6 0.09
22 44 0.69
23 14 0.22
ACGTcount: A:0.60, C:0.28, G:0.07, T:0.04
Consensus pattern (22 bp):
AAAACAACACAAAAATAGCACC
Found at i:4063511 original size:18 final size:18
Alignment explanation
Indices: 4063488--4063523 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4063478 ATCGAAGAAA
*
4063488 CATCATCCTTATCGTCCT
1 CATCATCCTCATCGTCCT
4063506 CATCATCCTCATCGTCCT
1 CATCATCCTCATCGTCCT
4063524 TGCAACCAAT
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:0.17, C:0.42, G:0.06, T:0.36
Consensus pattern (18 bp):
CATCATCCTCATCGTCCT
Found at i:4069670 original size:11 final size:11
Alignment explanation
Indices: 4069654--4069689 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
4069644 TAAGTATCAT
4069654 AAATATAAGAA
1 AAATATAAGAA
4069665 AAATATAAG-A
1 AAATATAAGAA
*
4069675 AAATATAAGAT
1 AAATATAAGAA
4069686 AAAT
1 AAAT
4069690 GTGAAAGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (11 bp):
AAATATAAGAA
Found at i:4069829 original size:3 final size:3
Alignment explanation
Indices: 4069823--4069850 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4069813 ATGCAGCAGT
4069823 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
4069851 CTTACCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:4072275 original size:44 final size:44
Alignment explanation
Indices: 4072216--4072343 Score: 159
Period size: 44 Copynumber: 2.9 Consensus size: 44
4072206 AGATTCACAT
* * *
4072216 CTTCAGTCTGTTCCACTGCAATTTCAAGGAGATAAGATTTGTGG
1 CTTCAATCTGCTCCACTGCAATTTCAGGGAGATAAGATTTGTGG
** *
4072260 CTTCAATCTGCTCCACTATAACTTT-AGGGAGATAAGATTAGTGG
1 CTTCAATCTGCTCCACTGCAA-TTTCAGGGAGATAAGATTTGTGG
* * *
4072304 CTTCAATCTGCTCTACTGCAACTTCAGGGAGATGAGATTT
1 CTTCAATCTGCTCCACTGCAATTTCAGGGAGATAAGATTT
4072344 ACCATGGTAG
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 2 0.03
44 65 0.93
45 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.33
Consensus pattern (44 bp):
CTTCAATCTGCTCCACTGCAATTTCAGGGAGATAAGATTTGTGG
Found at i:4072335 original size:88 final size:89
Alignment explanation
Indices: 4072170--4072343 Score: 219
Period size: 88 Copynumber: 2.0 Consensus size: 89
4072160 AGATTCGCAT
* *
4072170 CTTCAATCTGCTCCACTACAACTTGGTAGGGAAATAAGATTCACATCTTCAGTCTGTTCCACTGC
1 CTTCAATCTGCTCCACTACAACTT-GTAGGGAAATAAGATTCACATCTTCAATCTGCTCCACTGC
*
4072235 AATTTCAAGGAGATAAGATTTGTGG
65 AACTTCAAGGAGATAAGATTTGTGG
* * * *
4072260 CTTCAATCTGCTCCACTATAACTT-TAGGGAGATAAGATT-A-GTGGCTTCAATCTGCTCTACTG
1 CTTCAATCTGCTCCACTACAACTTGTAGGGAAATAAGATTCACAT--CTTCAATCTGCTCCACTG
* *
4072322 CAACTTCAGGGAGATGAGATTT
64 CAACTTCAAGGAGATAAGATTT
4072344 ACCATGGTAG
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
86 1 0.01
87 1 0.01
88 48 0.66
90 23 0.32
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (89 bp):
CTTCAATCTGCTCCACTACAACTTGTAGGGAAATAAGATTCACATCTTCAATCTGCTCCACTGCA
ACTTCAAGGAGATAAGATTTGTGG
Found at i:4072473 original size:45 final size:44
Alignment explanation
Indices: 4072409--4072576 Score: 138
Period size: 44 Copynumber: 3.8 Consensus size: 44
4072399 TTGTAGCTTT
* * * * * *
4072409 AATCTGTTCTACTGCAACTTTAGGGAAATGAGATTCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATT-GATAACTTC
* ** *
4072454 AATCTGCTCCACTGCAACTTCAAGGAGCTAAGATTTATAACTTC
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTGATAACTTC
* * * * ** *
4072498 AACCTGCTCCACTGCAACTTCAGGGAGATAAGATAGTTGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTGATAACTTC
* * * *
4072542 AATCTGCTCCACTGTAACTCCAAGGAGATAAGATT
1 AATCTGCTCCACTGCAACTTCAGGGAAATAAGATT
4072577 CGCCACGATG
Statistics
Matches: 99, Mismatches: 24, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
44 71 0.72
45 28 0.28
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAAATAAGATTGATAACTTC
Found at i:4072509 original size:44 final size:43
Alignment explanation
Indices: 4072450--4072576 Score: 155
Period size: 44 Copynumber: 2.9 Consensus size: 43
4072440 GATTCGCTAT
*
4072450 CTTCAATCTGCTCCACTGCAACTTCAAGGAGCTAAGATTTATAA
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTT-TAA
* * * **
4072494 CTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGATAGTTGG
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGAT-TTTAA
* * *
4072538 CTTTAATCTGCTCCACTGTAACTCCAAGGAGATAAGATT
1 CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT
4072577 CGCCACGATG
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
44 69 0.99
45 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (43 bp):
CTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTTAA
Found at i:4073994 original size:24 final size:24
Alignment explanation
Indices: 4073966--4074013 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
4073956 GGTAACTTCT
4073966 CATGCCAATCTTTATAAGTCTCAA
1 CATGCCAATCTTTATAAGTCTCAA
4073990 CATGCCAATCTTTATAAGTCTCAA
1 CATGCCAATCTTTATAAGTCTCAA
4074014 TCATTTTCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.33
Consensus pattern (24 bp):
CATGCCAATCTTTATAAGTCTCAA
Found at i:4083955 original size:22 final size:22
Alignment explanation
Indices: 4083927--4083968 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
4083917 ATTAAAGAAG
4083927 ATAGTGACGTGCCTTTGATTTT
1 ATAGTGACGTGCCTTTGATTTT
*
4083949 ATAGTGATGTGCCTTTGATT
1 ATAGTGACGTGCCTTTGATT
4083969 CTAGGACGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (22 bp):
ATAGTGACGTGCCTTTGATTTT
Found at i:4085271 original size:20 final size:19
Alignment explanation
Indices: 4085243--4085297 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
4085233 CCCATTCTCC
*
4085243 TCTTCCTTTCCCTTCCACTT
1 TCTTTCTTTCCCTTCC-CTT
*
4085263 TCTTTCTTTCCCAT-CCTT
1 TCTTTCTTTCCCTTCCCTT
4085281 TCTTCTCTTCTCCCTTC
1 TCTT-TCTT-TCCCTTC
4085298 ACCCAGCGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 7 0.24
19 5 0.17
20 17 0.59
ACGTcount: A:0.04, C:0.44, G:0.00, T:0.53
Consensus pattern (19 bp):
TCTTTCTTTCCCTTCCCTT
Found at i:4085468 original size:6 final size:6
Alignment explanation
Indices: 4085445--4085484 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
4085435 CTTTCTCATA
*
4085445 TTTTAT TTTT-T TAATTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT T-TTTAT TTTTAT TTTTAT TTTTAT TTTT
4085485 CTTATCATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 2 0.07
6 26 0.87
7 2 0.07
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:4091596 original size:19 final size:20
Alignment explanation
Indices: 4091580--4091624 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
4091570 TTATGAAACT
*
4091580 TAATGCATATG-ATGAAATG
1 TAATGCAGATGAATGAAATG
4091599 TAATGCAGATGAATGAAATG
1 TAATGCAGATGAATGAAATG
4091619 -AATGCA
1 TAATGCA
4091625 AAAAGAGGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.27
Consensus pattern (20 bp):
TAATGCAGATGAATGAAATG
Found at i:4096409 original size:6 final size:6
Alignment explanation
Indices: 4096398--4096428 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
4096388 TTGCAGGTGA
4096398 CAGTGG CAGTGG CAGTGG CAGTGG CAGTGG C
1 CAGTGG CAGTGG CAGTGG CAGTGG CAGTGG C
4096429 TGATGGTGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (6 bp):
CAGTGG
Found at i:4105955 original size:24 final size:24
Alignment explanation
Indices: 4105907--4105955 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
4105897 TTTTGAGCAA
* *
4105907 TTTAATTTTTTTTCATTTATGTTT
1 TTTAATTTTTTTTCATTCATCTTT
4105931 TTTAACTTTTTTTTCATTCA-CTTT
1 TTTAA-TTTTTTTTCATTCATCTTT
4105955 T
1 T
4105956 GTTTCTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.16, C:0.10, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTAATTTTTTTTCATTCATCTTT
Found at i:4108098 original size:47 final size:47
Alignment explanation
Indices: 4108047--4108144 Score: 126
Period size: 47 Copynumber: 2.1 Consensus size: 47
4108037 TTTAGGATTT
* *
4108047 AATGTGATGAATGT-GAACATGCATATATGTGATAAGGCCGAATGGCC
1 AATGTGATGAACGTGGAA-ATGCATATATGTGATAAAGCCGAATGGCC
* * * *
4108094 AATGTGATGAACGTGGAAGTGTATATATGTGGTAAAGCCGAATGGCT
1 AATGTGATGAACGTGGAAATGCATATATGTGATAAAGCCGAATGGCC
4108141 AATG
1 AATG
4108145 CGAAATGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
47 41 0.93
48 3 0.07
ACGTcount: A:0.34, C:0.10, G:0.30, T:0.27
Consensus pattern (47 bp):
AATGTGATGAACGTGGAAATGCATATATGTGATAAAGCCGAATGGCC
Found at i:4108174 original size:46 final size:46
Alignment explanation
Indices: 4108118--4108300 Score: 276
Period size: 46 Copynumber: 4.0 Consensus size: 46
4108108 GGAAGTGTAT
* **
4108118 ATATGTGGTAAAGCCGAATGGCTAATGCGAAATGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG
*
4108164 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACGTGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG
4108210 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG
** * * * *
4108256 ATATGTCGTAAAGCCAAATGGCTAATGTGAGATATGTATGAGATG
1 ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATG
4108301 TGTATATATA
Statistics
Matches: 128, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 128 1.00
ACGTcount: A:0.35, C:0.10, G:0.31, T:0.25
Consensus pattern (46 bp):
ATATGAGGTAAAGCCGAATGGCTAATGCGAAACATGTATGAGATGG
Found at i:4110527 original size:17 final size:17
Alignment explanation
Indices: 4110505--4110539 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4110495 CATCAAGTTA
4110505 TTTTA-TTATATATATAT
1 TTTTATTTAT-TATATAT
4110522 TTTTATTTATTATATAT
1 TTTTATTTATTATATAT
4110539 T
1 T
4110540 ATCTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTATTTATTATATAT
Found at i:4110530 original size:21 final size:21
Alignment explanation
Indices: 4110506--4110548 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
4110496 ATCAAGTTAT
4110506 TTTATTATATATATAT-TTTTA
1 TTTATTATATAT-TATCTTTTA
4110527 TTTATTATATATTATCTTTTA
1 TTTATTATATATTATCTTTTA
4110548 T
1 T
4110549 ATTCTTTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTATTATATATTATCTTTTA
Found at i:4110789 original size:24 final size:22
Alignment explanation
Indices: 4110737--4110804 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 22
4110727 TTCAATATTA
*
4110737 TTTTACATTTTTATATATATAT
1 TTTTAAATTTTTATATATATAT
* * *
4110759 ATATAAATTTTTATATATCATCT
1 TTTTAAATTTTTATATAT-ATAT
* *
4110782 GTTTTAAATTGTTGTATAT-TAT
1 -TTTTAAATTTTTATATATATAT
4110804 T
1 T
4110805 GATTCTTAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
21 1 0.03
22 17 0.49
23 3 0.09
24 14 0.40
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.59
Consensus pattern (22 bp):
TTTTAAATTTTTATATATATAT
Found at i:4111772 original size:16 final size:18
Alignment explanation
Indices: 4111741--4111773 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
4111731 GAAAACAGAG
4111741 GGAAAAGTAGAAGAGAAT
1 GGAAAAGTAGAAGAGAAT
4111759 GGAAAA-TA-AAGAGAA
1 GGAAAAGTAGAAGAGAA
4111774 AAAAGAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.30, T:0.09
Consensus pattern (18 bp):
GGAAAAGTAGAAGAGAAT
Found at i:4117143 original size:30 final size:30
Alignment explanation
Indices: 4117085--4117143 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
4117075 GTTATGTTGG
* *
4117085 TGAAAAGTTAATTGCTTAATAGATTAGCTA
1 TGAAAAGTTAATAGCTTAATAGACTAGCTA
*
4117115 TGAAAAGCTT-ATAGCTTAATAGCCTAGCT
1 TGAAAAG-TTAATAGCTTAATAGACTAGCT
4117144 TTCAAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (30 bp):
TGAAAAGTTAATAGCTTAATAGACTAGCTA
Found at i:4119991 original size:41 final size:41
Alignment explanation
Indices: 4119896--4119984 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
4119886 CGGCGTTTTG
* * * *
4119896 AACTGAGCAATTGTGGCGTTTTCATGCAAAACGCCGCTAAA
1 AACTGAGCAATAGTAGTGTTTTCATGCAAAACGCCGCAAAA
4119937 AACTGAGCAATAGTAGTGTTTTCATGCAAAACGCCGCAAAA
1 AACTGAGCAATAGTAGTGTTTTCATGCAAAACGCCGCAAAA
4119978 AACTGAG
1 AACTGAG
4119985 ATATAGTGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.22
Consensus pattern (41 bp):
AACTGAGCAATAGTAGTGTTTTCATGCAAAACGCCGCAAAA
Found at i:4120010 original size:41 final size:41
Alignment explanation
Indices: 4119896--4120018 Score: 115
Period size: 41 Copynumber: 3.0 Consensus size: 41
4119886 CGGCGTTTTG
* * * * * *
4119896 AACTGAGCAATTGTGGCGTTTTCATGCAAAACGCCGCTAAA
1 AACTGAGCAATAGTAGTGCTTTCAGGCAAAACGCCGCAAAA
* *
4119937 AACTGAGCAATAGTAGTGTTTTCATGCAAAACGCCGCAAAA
1 AACTGAGCAATAGTAGTGCTTTCAGGCAAAACGCCGCAAAA
* * *
4119978 AACTGAG-ATATAGTGGTGCTTT-AGGTCCAAACGCCACAAAA
1 AACTGAGCA-ATAGTAGTGCTTTCAGG-CAAAACGCCGCAAAA
4120019 GGTTGAGCTA
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
40 3 0.04
41 68 0.96
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (41 bp):
AACTGAGCAATAGTAGTGCTTTCAGGCAAAACGCCGCAAAA
Found at i:4123968 original size:26 final size:26
Alignment explanation
Indices: 4123932--4124015 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
4123922 CATGAAATTC
4123932 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
4123958 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
4123984 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
4124010 TTATCA
1 TTATCA
4124016 ATTTGTATCA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:4124911 original size:19 final size:20
Alignment explanation
Indices: 4124886--4124936 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
4124876 CCCCACCCAA
4124886 ATTTCCCCAAATACCTA-ACT
1 ATTTCCCCAAATACCTACA-T
* *
4124906 -TTTCCCCTAATCCCTACAT
1 ATTTCCCCAAATACCTACAT
4124925 ATTTCCCCAAAT
1 ATTTCCCCAAAT
4124937 CAAAATCGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.29, C:0.37, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTTCCCCAAATACCTACAT
Found at i:4124977 original size:19 final size:19
Alignment explanation
Indices: 4124955--4124992 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4124945 AAATATCCTT
4124955 CTGCCGTTGAAAACTCCGA
1 CTGCCGTTGAAAACTCCGA
*
4124974 CTGCCGTTGAAGACTCCGA
1 CTGCCGTTGAAAACTCCGA
4124993 GTGGACGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.24, T:0.21
Consensus pattern (19 bp):
CTGCCGTTGAAAACTCCGA
Found at i:4126503 original size:14 final size:13
Alignment explanation
Indices: 4126480--4126509 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
4126470 ATTACTATAA
4126480 TAATTATATGAAG
1 TAATTATATGAAG
4126493 TAATATATATGAAG
1 TAAT-TATATGAAG
4126507 TAA
1 TAA
4126510 AATTATATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (13 bp):
TAATTATATGAAG
Found at i:4127309 original size:27 final size:27
Alignment explanation
Indices: 4127276--4127341 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
4127266 ATTTACTTGT
4127276 GTATATGAAATTTCAGCATGATTTATA
1 GTATATGAAATTTCAGCATGATTTATA
4127303 GTATATGAAATTTCAGCATGATTTATA
1 GTATATGAAATTTCAGCATGATTTATA
4127330 GTATATGAAATT
1 GTATATGAAATT
4127342 GACATGTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (27 bp):
GTATATGAAATTTCAGCATGATTTATA
Found at i:4127607 original size:23 final size:23
Alignment explanation
Indices: 4127577--4127626 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
4127567 AACATTAATC
4127577 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
4127600 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
4127623 AAAT
1 AAAT
4127627 AAACTTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (23 bp):
AAATGTATGAATTGCAGCCCTTT
Found at i:4128172 original size:241 final size:242
Alignment explanation
Indices: 4127749--4128202 Score: 865
Period size: 241 Copynumber: 1.9 Consensus size: 242
4127739 ATGAATTAAT
4127749 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACTTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACTTT
* *
4127814 ATTTTAAATATTTTAAAGATTCAAAGTATATTGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGAGTTGCCTTATATCGAG
*
4127879 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACATATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAACGGATCCTCCCTAGGTGTAACAACGCCACATATGATGAATCTTAAAAAATTC
4127944 AAAAAGACTT-GAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
196 AAAAAGACTTGGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
4127990 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACTTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACTTT
4128055 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGAGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGAGTTGCCTTATATCGAG
*
4128120 CTGTAAGATATAACGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAACGGATCCTCCCTAGGTGTAACAACGCCACATATGATGAATCTTAAAAAATTC
4128185 AAAAAGACTTGGAAAAAA
196 AAAAAGACTTGGAAAAAA
4128203 CATATATCAT
Statistics
Matches: 208, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
241 201 0.97
242 7 0.03
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (242 bp):
TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACTTT
ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGAGTTGCCTTATATCGAG
CTGTAAGATATAACGGATCCTCCCTAGGTGTAACAACGCCACATATGATGAATCTTAAAAAATTC
AAAAAGACTTGGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
Found at i:4128238 original size:9 final size:9
Alignment explanation
Indices: 4128224--4128313 Score: 81
Period size: 9 Copynumber: 9.3 Consensus size: 9
4128214 TAGTTTAAAG
*
4128224 TTACATAAT
1 TTACATAAC
4128233 TTACATAACAAC
1 TTACAT-A--AC
4128245 TTACATAAC
1 TTACATAAC
*
4128254 TCACATAAC
1 TTACATAAC
*
4128263 TTACATAAT
1 TTACATAAC
4128272 TTACATAAC
1 TTACATAAC
*
4128281 TCACATAAC
1 TTACATAAC
*
4128290 GTACATAACAAC
1 TTACAT---AAC
4128302 TTACATAAC
1 TTACATAAC
4128311 TTA
1 TTA
4128314 ACTAATACAT
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
9 49 0.74
10 1 0.02
11 1 0.02
12 15 0.23
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.31
Consensus pattern (9 bp):
TTACATAAC
Found at i:4128283 original size:27 final size:27
Alignment explanation
Indices: 4128245--4128297 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
4128235 ACATAACAAC
*
4128245 TTACATAACTCACATAACTTACATAAT
1 TTACATAACTCACATAACGTACATAAT
4128272 TTACATAACTCACATAACGTACATAA
1 TTACATAACTCACATAACGTACATAA
4128298 CAACTTACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (27 bp):
TTACATAACTCACATAACGTACATAAT
Found at i:4133888 original size:21 final size:21
Alignment explanation
Indices: 4133862--4133908 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
4133852 CAACTTAGAA
*
4133862 CGGAGGCAGCAGCGCGGGAGG
1 CGGAGGCAGCAGCGAGGGAGG
4133883 CGGAGGCAGCAGCGAGGGAGG
1 CGGAGGCAGCAGCGAGGGAGG
4133904 CGGAG
1 CGGAG
4133909 CAGAACAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.57, T:0.00
Consensus pattern (21 bp):
CGGAGGCAGCAGCGAGGGAGG
Found at i:4135382 original size:17 final size:17
Alignment explanation
Indices: 4135352--4135386 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4135342 GGAGTTGGGA
*
4135352 TTTTAGTTTGAATTTTT
1 TTTTAATTTGAATTTTT
*
4135369 TTTTAATTTTAATTTTT
1 TTTTAATTTGAATTTTT
4135386 T
1 T
4135387 CCAAAAATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTAATTTGAATTTTT
Found at i:4138377 original size:19 final size:19
Alignment explanation
Indices: 4138353--4138442 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
4138343 AAATTAAATC
4138353 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
4138372 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
4138391 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
*
4138408 TCTAAGATTGTATATCATA
1 TCTAAGATTGCATATCATA
4138427 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
4138443 CTTAAAGATT
Statistics
Matches: 68, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
17 17 0.25
19 51 0.75
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:4138410 original size:36 final size:37
Alignment explanation
Indices: 4138353--4138442 Score: 146
Period size: 36 Copynumber: 2.4 Consensus size: 37
4138343 AAATTAAATC
4138353 TCTAAGATTGCATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTG-ATATCATATCTAAGATTGCATATCATA
*
4138391 TCTAAGATTG-TATCATATCTAAGATTGTATATCATA
1 TCTAAGATTGATATCATATCTAAGATTGCATATCATA
4138427 TCTAAGATTGCATATC
1 TCTAAGATTG-ATATC
4138443 CTTAAAGATT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
36 35 0.71
38 14 0.29
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (37 bp):
TCTAAGATTGATATCATATCTAAGATTGCATATCATA
Found at i:4140286 original size:25 final size:25
Alignment explanation
Indices: 4140254--4140303 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
4140244 CCAATATTTG
4140254 ATAGTACAAAAAATTAGTTGAAAGC
1 ATAGTACAAAAAATTAGTTGAAAGC
4140279 ATAGTACAAAAAATTAGTTGAAAGC
1 ATAGTACAAAAAATTAGTTGAAAGC
4140304 TCCAGAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (25 bp):
ATAGTACAAAAAATTAGTTGAAAGC
Found at i:4144582 original size:28 final size:28
Alignment explanation
Indices: 4144511--4144598 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 28
4144501 CTTTATACAT
* *
4144511 ATATACATTATTT-GTTTTAAAT-TTTT
1 ATATACATTATTTATTTTTAAATCTTTC
* *
4144537 ATATA-TTTACTGTCATTTTTAAATCTTTC
1 ATATACATTA-T-TTATTTTTAAATCTTTC
4144566 ATATACATTATTTATTTCTTAAATCTTTAC
1 ATATACATTATTTATTT-TTAAATCTTT-C
4144596 ATA
1 ATA
4144599 CTGTTATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
25 3 0.06
26 6 0.12
27 1 0.02
28 13 0.27
29 19 0.39
30 7 0.14
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (28 bp):
ATATACATTATTTATTTTTAAATCTTTC
Found at i:4144866 original size:26 final size:23
Alignment explanation
Indices: 4144833--4144898 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 23
4144823 ATTTTTGCTT
4144833 TATT-TTATTTTAAATTATGTTATA
1 TATTATTATTTTAAATTAT-TT-TA
4144857 TATTAATTATTTTAAATTATTTTA
1 TATT-ATTATTTTAAATTATTTTA
*
4144881 TATTATCTACTTTAAATT
1 TATTAT-TATTTTAAATT
4144899 GCTTCATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
23 2 0.05
24 20 0.53
25 2 0.05
26 14 0.37
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (23 bp):
TATTATTATTTTAAATTATTTTA
Found at i:4149484 original size:9 final size:9
Alignment explanation
Indices: 4149470--4149494 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
4149460 ACAGTCATGA
4149470 AAAAAAAAC
1 AAAAAAAAC
4149479 AAAAAAAAC
1 AAAAAAAAC
4149488 AAAAAAA
1 AAAAAAA
4149495 GAGATCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:4150102 original size:14 final size:15
Alignment explanation
Indices: 4150074--4150115 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
4150064 CATTCATTCA
4150074 AAAGCAAAA-AAAAAG
1 AAAG-AAAAGAAAAAG
4150089 AAAG-AAAGAAAAAG
1 AAAGAAAAGAAAAAG
4150103 AAAGAAAAGAAAA
1 AAAGAAAAGAAAA
4150116 TGGAGAGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.12
14 10 0.40
15 12 0.48
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:4151999 original size:46 final size:45
Alignment explanation
Indices: 4151946--4152121 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
4151936 TATTTGGGCA
4151946 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
4151992 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
4152039 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
4152085 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
4152122 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Done.