Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008229.1 Hibiscus syriacus cultivar Beakdansim tig00110865_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: 3634043
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 17
Found at i:1667096 original size:167 final size:168
Alignment explanation
Indices: 1666798--1667114 Score: 557
Period size: 167 Copynumber: 1.9 Consensus size: 168
1666788 AAGATGATGC
*
1666798 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
*
1666863 GAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
1666928 GGAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
131 GGAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
*
1666966 TTCAAGAG-AAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
1 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
*
1667030 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAATG-GAGA
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAA-GAGAGA
**
1667094 CGGAATTTGTTTCAAGGGAAA
130 CGGAATTCATTTCAAGGGAAA
1667115 CTATCTCAAG
Statistics
Matches: 142, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
167 133 0.94
168 9 0.06
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (168 bp):
TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
GGAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
Found at i:1667115 original size:36 final size:35
Alignment explanation
Indices: 1666963--1667270 Score: 168
Period size: 36 Copynumber: 8.9 Consensus size: 35
1666953 TCAATGTTTA
* *
1666963 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAATGGAGAC-AAA-TT
*
1667000 TGTTTCAAGGGAAACTATCTCAA-GAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAATG-GAGAC-AAATT
** * *
1667036 CATTTCAAGGGAAA-TGTTTTCAAT---G----TTT
1 TGTTTCAAGGGAAACTG-TCTCAATGGAGACAAATT
* *
1667064 ATGTTTCAAGAGAAACTGTCTCAATGGAGACGGAATT
1 -TGTTTCAAGGGAAACTGTCTCAATGGAGAC-AAATT
* *
1667101 TGTTTCAAGGGAAACTATCTCAA-GAGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAATG-GAGAC-AAATT
** * *
1667137 CATTTCAAGGGAAA-TGTTTTCAAT---G----TTT
1 TGTTTCAAGGGAAACTG-TCTCAATGGAGACAAATT
* * *
1667165 ATGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAATGGAG-ACAAA-TT
**
1667203 TGTTTCAAGGGAAACTGTCTCAACAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAATGGAGACAAA-TT
1667239 TGTTTCAAGGGAAACTGTCTCAA-GAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAATG-GAGACAA
1667271 TGGTGAGCAC
Statistics
Matches: 208, Mismatches: 35, Indels: 57
0.69 0.12 0.19
Matches are distributed among these distances:
28 3 0.01
29 33 0.16
30 4 0.02
32 2 0.01
33 2 0.01
35 3 0.01
36 102 0.49
37 57 0.27
38 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGGGAAACTGTCTCAATGGAGACAAATT
Found at i:1667166 original size:101 final size:102
Alignment explanation
Indices: 1666898--1667252 Score: 586
Period size: 102 Copynumber: 3.5 Consensus size: 102
1666888 TCAATGTTTA
* **
1666898 TGTTTCAAGAGAAACTATCTCAAGAGAGACGGAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1666963 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1667000 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* **
1667065 TGTTTCAAGAGAAACTGTCTCAATGGAGACGGAA-TT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
1667101 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
1667166 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * * **
1667203 TGTTTCAAGGGAAACTGTCTCAACAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
1667253 CTGTCTCAAG
Statistics
Matches: 235, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
101 96 0.41
102 139 0.59
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:1668155 original size:22 final size:22
Alignment explanation
Indices: 1668130--1668180 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1668120 TTGTGTTTGG
1668130 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1668152 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1668174 TCAAAGG
1 TCAAAGG
1668181 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1668906 original size:40 final size:39
Alignment explanation
Indices: 1668819--1668908 Score: 101
Period size: 41 Copynumber: 2.3 Consensus size: 39
1668809 TTTTGTCCCT
* *
1668819 TTTTCTTTTTGATTTTTGTTTTTTTTCCTTTTGTTCTTG
1 TTTTCTTTTTCATTTTTGTTTTTTTTCCTTTTGTTCTTC
* * *
1668858 TTTCTCTTTTTCTTTGTTTTTTTTTTTTGCTTTT-TTGCTTC
1 TTT-TCTTTTTCATT-TTTGTTTTTTTTCCTTTTGTT-CTTC
1668899 TTTTCTTTTT
1 TTTTCTTTTT
1668909 TGTTCTTGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
39 3 0.07
40 18 0.42
41 22 0.51
ACGTcount: A:0.01, C:0.12, G:0.08, T:0.79
Consensus pattern (39 bp):
TTTTCTTTTTCATTTTTGTTTTTTTTCCTTTTGTTCTTC
Found at i:1668911 original size:37 final size:36
Alignment explanation
Indices: 1668831--1668912 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 36
1668821 TTCTTTTTGA
*
1668831 TTTTTGTTTTTTTTCCTTTTGTTCTTGTTTCTCTTTT
1 TTTTTGTTTTTTTT-CTTTTGTTCTTGCTTCTCTTTT
* *
1668868 TCTTTGTTTTTTTT-TTTTGCTTTTTTGCTTCT-TTTCT
1 TTTTTGTTTTTTTTCTTTTG--TTCTTGCTTCTCTTT-T
1668905 TTTTTGTT
1 TTTTTGTT
1668913 CTTGATTGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
35 5 0.13
36 3 0.08
37 30 0.79
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (36 bp):
TTTTTGTTTTTTTTCTTTTGTTCTTGCTTCTCTTTT
Found at i:1668914 original size:15 final size:16
Alignment explanation
Indices: 1668870--1668915 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1668860 TCTCTTTTTC
1668870 TTTG-TTTTTT-TT-T
1 TTTGCTTTTTTGTTCT
1668883 TTTGCTTTTTTGCTTCT
1 TTTGCTTTTTTG-TTCT
1668900 TTT-CTTTTTTGTTCT
1 TTTGCTTTTTTGTTCT
1668915 T
1 T
1668916 GATTGGATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 4 0.14
14 6 0.21
15 5 0.17
16 10 0.34
17 4 0.14
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.80
Consensus pattern (16 bp):
TTTGCTTTTTTGTTCT
Found at i:1670086 original size:8 final size:8
Alignment explanation
Indices: 1670070--1670108 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
1670060 AATATAGATG
1670070 AAAATGCA
1 AAAATGCA
*
1670078 AAAAGGCA
1 AAAATGCA
1670086 AAAATGC-
1 AAAATGCA
1670093 AAAATGCA
1 AAAATGCA
*
1670101 AGAATGCA
1 AAAATGCA
1670109 CGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:1670096 original size:15 final size:15
Alignment explanation
Indices: 1670070--1670108 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1670060 AATATAGATG
1670070 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
1670086 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
1670101 AGAATGCA
1 AAAATGCA
1670109 CGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:1670653 original size:18 final size:18
Alignment explanation
Indices: 1670630--1670668 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
1670620 TTAGTCTTTT
1670630 AGAAGTGGATGTGAATCC
1 AGAAGTGGATGTGAATCC
1670648 AGAAGTGGATGTGAATCC
1 AGAAGTGGATGTGAATCC
1670666 AGA
1 AGA
1670669 CTTGAAGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.33, T:0.21
Consensus pattern (18 bp):
AGAAGTGGATGTGAATCC
Found at i:1673244 original size:18 final size:17
Alignment explanation
Indices: 1673221--1673263 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1673211 ATATATACAT
1673221 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1673239 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1673256 ATAA-AATA
1 ATAATAATA
1673264 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1673729 original size:34 final size:34
Alignment explanation
Indices: 1673675--1673743 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
1673665 GAATCCTAGC
*
1673675 AAAATTCTATCATATCTTTAGGAGTTTGAATCCT
1 AAAATTATATCATATCTTTAGGAGTTTGAATCCT
* *
1673709 AAAATTATATCCTATTTTTAGGAGTTTGAATCCT
1 AAAATTATATCATATCTTTAGGAGTTTGAATCCT
1673743 A
1 A
1673744 GTAGGACGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (34 bp):
AAAATTATATCATATCTTTAGGAGTTTGAATCCT
Found at i:1674145 original size:15 final size:15
Alignment explanation
Indices: 1674127--1674161 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1674117 TATTTAAAAT
*
1674127 TAAAATAATAATTAA
1 TAAAAGAATAATTAA
*
1674142 TAAAGGAATAATTAA
1 TAAAAGAATAATTAA
1674157 TAAAA
1 TAAAA
1674162 AAAATAAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
TAAAAGAATAATTAA
Found at i:1676720 original size:19 final size:20
Alignment explanation
Indices: 1676683--1676720 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1676673 AAATATTAAG
1676683 TAAATTTTAGAAGAAAATAT
1 TAAATTTTAGAAGAAAATAT
1676703 TAAATTTTAGAA-AAAATA
1 TAAATTTTAGAAGAAAATA
1676721 ATTCAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (20 bp):
TAAATTTTAGAAGAAAATAT
Found at i:1677980 original size:14 final size:14
Alignment explanation
Indices: 1677942--1677973 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1677932 TTGGACCTGG
1677942 ATAAAAA-ATA-AA
1 ATAAAAATATATAA
1677954 ATAAAAATATATAA
1 ATAAAAATATATAA
1677968 ATAAAA
1 ATAAAA
1677974 TCATATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
ATAAAAATATATAA
Found at i:1678077 original size:37 final size:37
Alignment explanation
Indices: 1678011--1678417 Score: 456
Period size: 37 Copynumber: 11.3 Consensus size: 37
1678001 CTATATACAC
* *
1678011 ATTTTCGAAAACATTTTTTC-AAATTATATATTATATAT
1 ATTTTC-AAAA-ATGTTTTCAAAACTATATATTATATAT
* *
1678049 ATTTTTTAAAAACGTTTT-AAAAC----TA-TATATAT
1 A-TTTTCAAAAATGTTTTCAAAACTATATATTATATAT
*
1678081 AGTTT-AAAGAATGTTTTC---A--ATATATTATATAT
1 ATTTTCAAA-AATGTTTTCAAAACTATATATTATATAT
*
1678113 ATTTTCCAAAATGTTTTCAAAACTATATATTATATAT
1 ATTTTCAAAAATGTTTTCAAAACTATATATTATATAT
*
1678150 ATTTTCAAAAATGTTTTCAAGACTATATATTATATAT
1 ATTTTCAAAAATGTTTTCAAAACTATATATTATATAT
*
1678187 ATTTTCAAAAATATTTTCAAAACTATATA-T-TATAT
1 ATTTTCAAAAATGTTTTCAAAACTATATATTATATAT
* * *
1678222 ATTTTCGAAAATGCTTTCAAAACTATATATGATATAT
1 ATTTTCAAAAATGTTTTCAAAACTATATATTATATAT
*
1678259 ATTTTCAAAATTGTTTTCAAAACTATATATTATATAT
1 ATTTTCAAAAATGTTTTCAAAACTATATATTATATAT
1678296 ATTTTCAAAAATGTTTTCAAAA-T-TATA-TAT-TAT
1 ATTTTCAAAAATGTTTTCAAAACTATATATTATATAT
**
1678329 ATTTTTGAAAATGTTTTCAAAACTATATATTATATATTT
1 ATTTTCAAAAATGTTTTCAAAACTATATATTATATA--T
*
1678368 ATATATTCAAAAGATGTTTTCAAAATTATATATTATATAT
1 AT-T-TTCAAAA-ATGTTTTCAAAACTATATATTATATAT
*
1678408 GTTTTCAAAA
1 ATTTTCAAAA
1678418 CTATATATTA
Statistics
Matches: 317, Mismatches: 27, Indels: 50
0.80 0.07 0.13
Matches are distributed among these distances:
29 1 0.00
30 3 0.01
31 12 0.04
32 28 0.09
33 27 0.09
34 4 0.01
35 40 0.13
36 5 0.02
37 144 0.45
38 12 0.04
39 8 0.03
40 3 0.01
41 5 0.02
42 25 0.08
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (37 bp):
ATTTTCAAAAATGTTTTCAAAACTATATATTATATAT
Found at i:1678240 original size:109 final size:108
Alignment explanation
Indices: 1678011--1678417 Score: 505
Period size: 109 Copynumber: 3.8 Consensus size: 108
1678001 CTATATACAC
* * * *
1678011 ATTTTCGAAAACATTTTTTC-AAATTATATATTATATATATTTTTTAAAAACGTTTT-AAAAC--
1 ATTTTCG-AAA-ATGTTTTCAAAACTATATATTATATATA-TTTTCAAAAATGTTTTCAAAACTA
* *
1678072 --TA-TATATATAGTTT-AAAGAATGTTTTCAATATAT-TA-TATAT
63 TATATTATATATATTTTCAAA-AATGTTTTCAAAATATATATTATAT
* *
1678113 ATTTTCCAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAGACTATAT
1 ATTTTCGAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAACTATAT
*
1678178 ATTATATATATTTTCAAAAATATTTTCAAAACTATATATTATAT
66 ATTATATATATTTTCAAAAATGTTTTCAAAA-TATATATTATAT
* * *
1678222 ATTTTCGAAAATGCTTTCAAAACTATATATGATATATATTTTCAAAATTGTTTTCAAAACTATAT
1 ATTTTCGAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAACTATAT
1678287 ATTATATATATTTTCAAAAATGTTTTCAAAATTATATATTATAT
66 ATTATATATATTTTCAAAAATGTTTTCAAAA-TATATATTATAT
*
1678331 -TTTT-GAAAATGTTTTCAAAACTATATATTATATATTTATATATTCAAAAGATGTTTTCAAAAT
1 ATTTTCGAAAATGTTTTCAAAACTATATATTATATA--TAT-T-TTCAAAA-ATGTTTTCAAAAC
*
1678394 TATATATTATATATGTTTTCAAAA
61 TATATATTATATATATTTTCAAAA
1678418 CTATATATTA
Statistics
Matches: 268, Mismatches: 21, Indels: 22
0.86 0.07 0.07
Matches are distributed among these distances:
100 21 0.08
101 25 0.09
102 6 0.02
105 2 0.01
106 22 0.08
107 34 0.13
108 6 0.02
109 110 0.41
110 1 0.00
111 7 0.03
112 34 0.13
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (108 bp):
ATTTTCGAAAATGTTTTCAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAACTATAT
ATTATATATATTTTCAAAAATGTTTTCAAAATATATATTATAT
Found at i:1678399 original size:27 final size:25
Alignment explanation
Indices: 1678366--1678442 Score: 82
Period size: 25 Copynumber: 3.0 Consensus size: 25
1678356 TATTATATAT
1678366 TTATATATTCAAAAGATGTTTTCAAAA
1 TTATATATT--AAAGATGTTTTCAAAA
* *
1678393 TTATATATTATATATGTTTTCAAAA
1 TTATATATTAAAGATGTTTTCAAAA
* * * *
1678418 CTATATATTATATATATTTTCAAAA
1 TTATATATTAAAGATGTTTTCAAAA
1678443 ACTAATTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 37 0.80
27 9 0.20
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (25 bp):
TTATATATTAAAGATGTTTTCAAAA
Found at i:1678429 original size:23 final size:25
Alignment explanation
Indices: 1678381--1678442 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
1678371 TATTCAAAAG
*
1678381 ATGTTTTCAAAATTATATATTATAT
1 ATGTTTTCAAAACTATATATTATAT
1678406 ATGTTTTCAAAACTATATATTATAT
1 ATGTTTTCAAAACTATATATTATAT
*
1678431 ATATTTTCAAAA
1 ATGTTTTCAAAA
1678443 ACTAATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (25 bp):
ATGTTTTCAAAACTATATATTATAT
Found at i:1678479 original size:17 final size:17
Alignment explanation
Indices: 1678459--1678500 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
1678449 TTTTTTTAAA
*
1678459 AAAAAACTATATGTTTC
1 AAAAAACTATATATTTC
1678476 AAAAAA-TAT-TATTTC
1 AAAAAACTATATATTTC
1678491 -AAAAACTATA
1 AAAAAACTATA
1678501 CTATATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 5 0.23
15 8 0.36
16 3 0.14
17 6 0.27
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAAAACTATATATTTC
Found at i:1679191 original size:202 final size:202
Alignment explanation
Indices: 1678819--1679191 Score: 514
Period size: 202 Copynumber: 1.8 Consensus size: 202
1678809 AAGGTGGCTT
* * ** ** **
1678819 CTTGTTGCCAAATCGTAGTCAACCTTGGTCTTCTTCTCGGTTTAAAGACCTCGGTTTGAAAATTC
1 CTTGTTGCCAAATCGCAGCCAACCCAGGTCTTCTTCTCGACTTAAAGACCTCAATTTGAAAATTC
* * *
1678884 AACTGAAAAGTAGTTCCTCGATGCTACCATGTGATTAATATGCCCTCGAGCTGAATGGAATCGAA
66 AACTGAAAAGTAGTTACTCGATGCTACCATGAGATTAATATGCCATCGAGCTGAATGGAATCGAA
*
1678949 CTCGAAGGTTTTTGTTGATAGATAGCCCTTCTCGCCTTGAGTTATGCTATAAATTTGACTGGGAT
131 CTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTATAAATTTGACTGGGAT
1679014 ATAGTTC
196 ATAGTTC
* * **
1679021 CTTGTTGCTAAATCGCAGCCAACCCAGGTCTTCTTCTTGACTTAAAGACCTCAATTT-AAGCTTC
1 CTTGTTGCCAAATCGCAGCCAACCCAGGTCTTCTTCTCGACTTAAAGACCTCAATTTGAAAATTC
* * * * *
1679085 AACTGGAAAGTAGTTACTCGTTGCTACCATGAGGTTGATATGTCATCGAGCTGAATGGAATCGAA
66 AACTGAAAAGTAGTTACTCGATGCTACCATGAGATTAATATGCCATCGAGCTGAATGGAATCGAA
* * *
1679150 CTCGAAAGTTTTTTGTTGACAGATAGTCTTTCTCGCCTTGAG
131 CTCG-AAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAG
1679192 CTATCCTTTA
Statistics
Matches: 146, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
201 66 0.45
202 80 0.55
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (202 bp):
CTTGTTGCCAAATCGCAGCCAACCCAGGTCTTCTTCTCGACTTAAAGACCTCAATTTGAAAATTC
AACTGAAAAGTAGTTACTCGATGCTACCATGAGATTAATATGCCATCGAGCTGAATGGAATCGAA
CTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGTTATGCTATAAATTTGACTGGGAT
ATAGTTC
Found at i:1680196 original size:20 final size:19
Alignment explanation
Indices: 1680180--1680217 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1680170 AAAAAAAATT
*
1680180 AAGTAAATTTTATAAAAAA
1 AAGTAAATTTTAGAAAAAA
*
1680199 AATTAAATTTTAGAAAAAA
1 AAGTAAATTTTAGAAAAAA
1680218 TAAATCAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
AAGTAAATTTTAGAAAAAA
Found at i:1680907 original size:30 final size:30
Alignment explanation
Indices: 1680867--1680926 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1680857 AAATCCTCTA
*
1680867 AAACTATTCTCCCTGGCGTAGATCTAACTC
1 AAACTATTCTCCCTGGCATAGATCTAACTC
*
1680897 AAACTGTTCTCCCTGGCATAGATCTAACTC
1 AAACTATTCTCCCTGGCATAGATCTAACTC
1680927 GAAAGATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (30 bp):
AAACTATTCTCCCTGGCATAGATCTAACTC
Found at i:1681647 original size:30 final size:31
Alignment explanation
Indices: 1681611--1681684 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
1681601 CAAATTATAT
1681611 TATATATATATATTAAA-AACGTTTT-AAAA
1 TATATATATATATTAAAGAACGTTTTCAAAA
* *
1681640 CTATATATATATTTTAAAGAATGTTTTCAAAA
1 -TATATATATATATTAAAGAACGTTTTCAAAA
1681672 TAT-TATATATATT
1 TATATATATATATT
1681685 TTCAAAACTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 25 0.64
31 10 0.26
32 4 0.10
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (31 bp):
TATATATATATATTAAAGAACGTTTTCAAAA
Found at i:1681679 original size:32 final size:31
Alignment explanation
Indices: 1681597--1681815 Score: 112
Period size: 35 Copynumber: 6.7 Consensus size: 31
1681587 CGAAAACTTT
1681597 TTTTCAAATTATATTATATATATATATTAAAAACG
1 TTTTCAAA--ATATTATATATAT-T-TTAAAAACG
*
1681632 TTTT-AAAACTA-TATATATATTTTAAAGAATG
1 TTTTCAAAA-TATTATATATATTTTAAA-AACG
*
1681663 TTTTCAAAATATTATATATATTTTCAAAAC-
1 TTTTCAAAATATTATATATATTTTAAAAACG
* **
1681693 ---T--ATATATTATATATATTTTTAAAAATA
1 TTTTCAAAATATTATATATA-TTTTAAAAACG
**
1681720 TTTTCAAAACTATATATTATATATATATTCAAAAATA
1 TTTTCAAAA-TAT-TA-TATATAT-T-TT-AAAAACG
* *
1681757 TTTTCAAAACTATATATTATATATTTTCGAAAATG
1 TTTTCAAAA-TAT-TA-TATATATTTT-AAAAACG
*
1681792 CTTTCAAAACTATATATGATATAT
1 TTTTCAAAA-TAT-TAT-ATATAT
1681816 ATTTTCAAAA
Statistics
Matches: 156, Mismatches: 10, Indels: 36
0.77 0.05 0.18
Matches are distributed among these distances:
25 13 0.08
26 8 0.05
27 1 0.01
30 6 0.04
31 12 0.08
32 30 0.19
33 5 0.03
34 7 0.04
35 40 0.26
36 3 0.02
37 31 0.20
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.46
Consensus pattern (31 bp):
TTTTCAAAATATTATATATATTTTAAAAACG
Found at i:1681688 original size:20 final size:23
Alignment explanation
Indices: 1681663--1681706 Score: 67
Period size: 20 Copynumber: 2.0 Consensus size: 23
1681653 TTAAAGAATG
1681663 TTTTCAAAA-TAT-TA-TATATA
1 TTTTCAAAACTATATATTATATA
1681683 TTTTCAAAACTATATATTATATA
1 TTTTCAAAACTATATATTATATA
1681706 T
1 T
1681707 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 3 0.14
22 2 0.10
23 7 0.33
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTCAAAACTATATATTATATA
Found at i:1681697 original size:23 final size:24
Alignment explanation
Indices: 1681671--1681720 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
1681661 TGTTTTCAAA
1681671 ATATTATATATATTTTCAAAACTAT
1 ATATTATATATATTTTCAAAAC-AT
*
1681696 ATATTATATATATTTTTAAAA-AT
1 ATATTATATATATTTTCAAAACAT
1681719 AT
1 AT
1681721 TTTCAAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 4 0.17
25 20 0.83
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
ATATTATATATATTTTCAAAACAT
Found at i:1681721 original size:37 final size:37
Alignment explanation
Indices: 1681680--1681902 Score: 326
Period size: 37 Copynumber: 6.0 Consensus size: 37
1681670 AATATTATAT
*
1681680 ATATTTTCAAAACTATATATTATATATATTTTTAAAA
1 ATATTTTCAAAACTATATATTATATATATTTTCAAAA
*
1681717 ATATTTTCAAAACTATATATTATATATATATTCAAAA
1 ATATTTTCAAAACTATATATTATATATATTTTCAAAA
*
1681754 ATATTTTCAAAACTATATA-T-TATATATTTTCGAAA
1 ATATTTTCAAAACTATATATTATATATATTTTCAAAA
** *
1681789 ATGCTTTCAAAACTATATATGATATATATTTTCAAAA
1 ATATTTTCAAAACTATATATTATATATATTTTCAAAA
*
1681826 ATATTTTTCAAAACTATATATTATATATATTTTTAAAA
1 ATA-TTTTCAAAACTATATATTATATATATTTTCAAAA
*
1681864 ATA-TTTCAAAACTTTATACTATATATATATTTTCAAAA
1 ATATTTTCAAAACTATATA-T-TATATATATTTTCAAAA
1681902 A
1 A
1681903 ACTGATTTTT
Statistics
Matches: 167, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
35 30 0.18
36 15 0.09
37 71 0.43
38 51 0.31
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.45
Consensus pattern (37 bp):
ATATTTTCAAAACTATATATTATATATATTTTCAAAA
Found at i:1681722 original size:12 final size:12
Alignment explanation
Indices: 1681705--1681874 Score: 55
Period size: 12 Copynumber: 14.0 Consensus size: 12
1681695 TATATTATAT
*
1681705 ATATTTTTAAAA
1 ATATTTTCAAAA
1681717 ATATTTTCAAAA
1 ATATTTTCAAAA
* * *
1681729 CTATATATT-ATAT
1 --ATATTTTCAAAA
*
1681742 ATATATTCAAAA
1 ATATTTTCAAAA
1681754 ATATTTTCAAAA
1 ATATTTTCAAAA
* *
1681766 CTATATATT---AT
1 --ATATTTTCAAAA
*
1681777 ATATTTTCGAAA
1 ATATTTTCAAAA
**
1681789 ATGCTTTCAAAA
1 ATATTTTCAAAA
* * * * *
1681801 CTATATATGATAT
1 ATAT-TTTCAAAA
1681814 ATATTTTCAAAA
1 ATATTTTCAAAA
1681826 ATATTTTTCAAAA
1 ATA-TTTTCAAAA
* * *
1681839 CTATATATT-ATAT
1 --ATATTTTCAAAA
*
1681852 ATATTTTTAAAA
1 ATATTTTCAAAA
1681864 ATA-TTTCAAAA
1 ATATTTTCAAAA
1681875 CTTTATACTA
Statistics
Matches: 112, Mismatches: 33, Indels: 27
0.65 0.19 0.16
Matches are distributed among these distances:
9 6 0.05
11 21 0.19
12 47 0.42
13 20 0.18
14 15 0.13
15 3 0.03
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.45
Consensus pattern (12 bp):
ATATTTTCAAAA
Found at i:1681758 original size:74 final size:73
Alignment explanation
Indices: 1681680--1681894 Score: 326
Period size: 72 Copynumber: 2.9 Consensus size: 73
1681670 AATATTATAT
1681680 ATATTTTCAAAACTATATATTATATATATTTTTAAAAATATTTTCAAAACTATATATTATATATA
1 ATATTTTCAAAACTATATATTATATATATTTTTAAAAATA-TTTCAAAACTATATATTATATATA
1681745 TATTCAAAA
65 TATTCAAAA
** * *
1681754 ATATTTTCAAAACTATATA-T-TATATATTTTCGAAAATGCTTTCAAAACTATATATGATATATA
1 ATATTTTCAAAACTATATATTATATATATTTTTAAAAAT-ATTTCAAAACTATATATTATATATA
*
1681817 TTTTCAAAA
65 TATTCAAAA
* *
1681826 ATATTTTTCAAAACTATATATTATATATATTTTTAAAAATATTTCAAAACTTTATACTATATATA
1 ATA-TTTTCAAAACTATATATTATATATATTTTTAAAAATATTTCAAAACTATATATTATATATA
1681891 TATT
65 TATT
1681895 TTCAAAAAAC
Statistics
Matches: 125, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
72 49 0.39
73 17 0.14
74 44 0.35
75 15 0.12
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (73 bp):
ATATTTTCAAAACTATATATTATATATATTTTTAAAAATATTTCAAAACTATATATTATATATAT
ATTCAAAA
Found at i:1683782 original size:62 final size:63
Alignment explanation
Indices: 1683685--1683811 Score: 220
Period size: 62 Copynumber: 2.0 Consensus size: 63
1683675 CTCCCATATA
*
1683685 ATATTTGTAATTTGGAGTTTGGACAATCATCTTCTACCGATGCTTAGAT-AAAACATTTAATC
1 ATATTTGTAATTTGGAGTTTGGACAATCATCTTCTACCAATGCTTAGATAAAAACATTTAATC
* *
1683747 ATATTTGTAATTTGGAGTTTGGACAATGATCTTCTATCAATGCTTAGATAAAAACATTTAATC
1 ATATTTGTAATTTGGAGTTTGGACAATCATCTTCTACCAATGCTTAGATAAAAACATTTAATC
1683810 AT
1 AT
1683812 GTGTCACACT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
62 46 0.75
63 15 0.25
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (63 bp):
ATATTTGTAATTTGGAGTTTGGACAATCATCTTCTACCAATGCTTAGATAAAAACATTTAATC
Found at i:1687757 original size:26 final size:27
Alignment explanation
Indices: 1687720--1687779 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
1687710 TAATTAAAAT
*
1687720 AATATTATTTTA-TGTA-TTTAATATAA
1 AATATTATTTTAGTATATTTTAATA-AA
*
1687746 TATATTATTTTAGTATATTTTAATAAA
1 AATATTATTTTAGTATATTTTAATAAA
1687773 AATATTA
1 AATATTA
1687780 ATTATTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 11 0.38
27 11 0.38
28 7 0.24
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (27 bp):
AATATTATTTTAGTATATTTTAATAAA
Found at i:1687777 original size:29 final size:26
Alignment explanation
Indices: 1687714--1687779 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 26
1687704 TAAAAATAAT
*
1687714 TAAAATAATATTATTTTATGTATTTAA
1 TAAAAT-ATATTATTTTATATATTTAA
*
1687741 TATAATATATTATTTTAGTATATTTTAA
1 TAAAATATATTATTTTA-TATA-TTTAA
1687769 TAAAA-ATATTA
1 TAAAATATATTA
1687780 ATTATTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.32
27 14 0.41
28 9 0.26
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (26 bp):
TAAAATATATTATTTTATATATTTAA
Found at i:1687846 original size:31 final size:30
Alignment explanation
Indices: 1687788--1687877 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 30
1687778 TAATTATTAA
1687788 AATATATTTATTAATGATTTTAATAATATAATAT
1 AATATA-TT-TTAATG--TTTAATAATATAATAT
**
1687822 AATATATTTTAATGTTATAATAATATTTTAT
1 AATATATTTTAATGTT-TAATAATATAATAT
* * *
1687853 ATTAAATTTTTAT-TTTAATAATATA
1 AATATATTTTAATGTTTAATAATATA
1687878 TACTGAATTA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 9 0.18
30 4 0.08
31 22 0.45
32 6 0.12
33 2 0.04
34 6 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
AATATATTTTAATGTTTAATAATATAATAT
Found at i:1687971 original size:22 final size:23
Alignment explanation
Indices: 1687938--1688010 Score: 60
Period size: 27 Copynumber: 3.0 Consensus size: 23
1687928 ATTATTAAAA
1687938 TATTAA-ATATTTTAAATAT-ATT
1 TATTAATA-ATTTTAAATATAATT
1687960 TATTAATAATTTTTAAAATATAATT
1 TATTAATAA-TTTT-AAATATAATT
*
1687985 TACTATTATAATTTTAATATTATAAT
1 TA-T-TAATAATTTTAA-A-TATAAT
1688011 AATATTTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
22 7 0.17
23 5 0.12
24 6 0.14
25 7 0.17
26 6 0.14
27 11 0.26
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATAATTTTAAATATAATT
Found at i:1688000 original size:14 final size:14
Alignment explanation
Indices: 1687960--1688010 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1687950 TAAATATATT
1687960 TATTAATAATTTTTAA
1 TATT-ATAA-TTTTAA
* *
1687976 -AATATAA-TTTAC
1 TATTATAATTTTAA
1687988 TATTATAATTTTAA
1 TATTATAATTTTAA
1688002 TATTATAAT
1 TATTATAAT
1688011 AATATTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 4 0.14
13 6 0.21
14 17 0.59
15 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTATAATTTTAA
Found at i:1688119 original size:24 final size:24
Alignment explanation
Indices: 1688092--1688140 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1688082 TATTTTTTTA
1688092 TTTAAAAATAATAATATTAATTAT
1 TTTAAAAATAATAATATTAATTAT
* * *
1688116 TTTATAATTAATAATATTATTTAT
1 TTTAAAAATAATAATATTAATTAT
1688140 T
1 T
1688141 GTATTCATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTAAAAATAATAATATTAATTAT
Found at i:1688881 original size:103 final size:99
Alignment explanation
Indices: 1688715--1688925 Score: 223
Period size: 103 Copynumber: 2.1 Consensus size: 99
1688705 TAACCATTTG
* * *
1688715 TATTATAAT-ACTATATAATAAATTCAGTTGTGATGGTAACATAACATGTTCTGCATTGATTTTT
1 TATTATAATAAC-CTATAAGAAATTCAATTGTGATGGTAACAT-ACATGTTCTGCATTGATTTTT
*
1688779 TGTCCGAACCTG-TTAAATTATAAGGCTTTAACAGTTTA
64 T-T-CGAACC-GATTAAATTATAAGCCTTTAACAGTTTA
* *
1688817 TATTTATAATAACCTATAAGAAATTCAATTGTGATGGTAACGT-CATGGGTTGC-GCCTTGATTT
1 TA-TTATAATAACCTATAAGAAATTCAATTGTGATGGTAACATACAT--GTT-CTGCATTGATTT
** * *
1688880 TTTTTTAACCGATTAAGTTATAAGCCTTTAACTGTTTA
62 TTTTCGAACCGATTAAATTATAAGCCTTTAACAGTTTA
1688918 TATTATAA
1 TATTATAA
1688926 ATGTAACCCC
Statistics
Matches: 93, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
100 7 0.08
101 32 0.34
102 3 0.03
103 48 0.52
104 3 0.03
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (99 bp):
TATTATAATAACCTATAAGAAATTCAATTGTGATGGTAACATACATGTTCTGCATTGATTTTTTT
CGAACCGATTAAATTATAAGCCTTTAACAGTTTA
Found at i:1690408 original size:5 final size:5
Alignment explanation
Indices: 1690398--1690435 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
1690388 AACAGTCAAC
*
1690398 GGTCG GGTCG GGTCG GGTC- AGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1690436 AGACCGATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 27 0.90
ACGTcount: A:0.03, C:0.21, G:0.55, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:1690423 original size:14 final size:14
Alignment explanation
Indices: 1690404--1690430 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1690394 CAACGGTCGG
1690404 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
1690418 GTCGGGTCGGGTC
1 GTCGGGTCGGGTC
1690431 GGGTCAGACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.22, G:0.52, T:0.22
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:1690423 original size:19 final size:19
Alignment explanation
Indices: 1690399--1690437 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1690389 ACAGTCAACG
1690399 GTCGGGTCGGGTCGGGTCA
1 GTCGGGTCGGGTCGGGTCA
1690418 GTCGGGTCGGGTCGGGTCA
1 GTCGGGTCGGGTCGGGTCA
1690437 G
1 G
1690438 ACCGATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.21, G:0.54, T:0.21
Consensus pattern (19 bp):
GTCGGGTCGGGTCGGGTCA
Found at i:1690456 original size:19 final size:19
Alignment explanation
Indices: 1690434--1690491 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
1690424 TCGGGTCGGG
1690434 TCAGACCGATCAAACCGGT
1 TCAGACCGATCAAACCGGT
* *
1690453 TCAGACCGGTCAAACAGG-
1 TCAGACCGATCAAACCGGT
* *
1690471 TCGAAACCGATCAAATCGGT
1 TC-AGACCGATCAAACCGGT
1690491 T
1 T
1690492 TCCAGCCCTC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 2 0.06
19 28 0.90
20 1 0.03
ACGTcount: A:0.33, C:0.28, G:0.22, T:0.17
Consensus pattern (19 bp):
TCAGACCGATCAAACCGGT
Found at i:1697682 original size:20 final size:19
Alignment explanation
Indices: 1697632--1697684 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1697622 GTCGGGTCAG
*
1697632 ACCGGTCAAACCGGTTTGG
1 ACCGGTCAAACCGGTTTGA
1697651 ACCGGTCGAAACCGG-TTGAAA
1 ACCGGTC-AAACCGGTTTG--A
1697672 ACCGGTCAAACCG
1 ACCGGTCAAACCG
1697685 ATTTCCAGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.33
20 13 0.43
21 7 0.23
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.15
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTTGA
Found at i:1699463 original size:5 final size:5
Alignment explanation
Indices: 1699453--1699513 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
1699443 AAAAGTTAGC
*
1699453 TAAAA TAAAA TAAAA TAAAA TAAAA -ATAA TACAAA -AAGAA TAAAA -ATAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA-AAA TAA-AA TAAAA TA-AAA
1699503 TAAAAA TAAAA
1 T-AAAA TAAAA
1699514 CTAATTTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
4 5 0.11
5 33 0.70
6 8 0.17
7 1 0.02
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
TAAAA
Found at i:1699524 original size:16 final size:16
Alignment explanation
Indices: 1699455--1699513 Score: 54
Period size: 16 Copynumber: 3.9 Consensus size: 16
1699445 AAGTTAGCTA
1699455 AAAT-AAAAT-AAAAT
1 AAATAAAAATAAAAAT
* *
1699469 AAAATAAAAAT-AATAC
1 -AAATAAAAATAAAAAT
*
1699485 AAA-AAGAATAAAAAT
1 AAATAAAAATAAAAAT
1699500 AAATAAAAATAAAA
1 AAATAAAAATAAAA
1699514 CTAATTTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
14 5 0.14
15 13 0.37
16 17 0.49
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.17
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:1699525 original size:36 final size:37
Alignment explanation
Indices: 1699459--1699534 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
1699449 TAGCTAAAAT
*
1699459 AAAATAAAATAAAATAAAAATAATACAAAAA-GAATA
1 AAAATAAAATAAAATAAAAATAATACAAAAACCAATA
* **
1699495 AAAAT-AAATAAAAATAAAACTAATTTAAAAACCAATA
1 AAAATAAAAT-AAAATAAAAATAATACAAAAACCAATA
1699532 AAA
1 AAA
1699535 GAAGAAAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 4 0.12
36 23 0.68
37 7 0.21
ACGTcount: A:0.75, C:0.05, G:0.01, T:0.18
Consensus pattern (37 bp):
AAAATAAAATAAAATAAAAATAATACAAAAACCAATA
Found at i:1699611 original size:16 final size:16
Alignment explanation
Indices: 1699592--1699626 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1699582 TAAAGGAAAA
1699592 AAAAAGAAATAAAATT
1 AAAAAGAAATAAAATT
* *
1699608 AAAAATAATTAAAATT
1 AAAAAGAAATAAAATT
1699624 AAA
1 AAA
1699627 TTAAAAATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAAAGAAATAAAATT
Found at i:1713572 original size:38 final size:39
Alignment explanation
Indices: 1713540--1713641 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 39
1713530 TAAAATGTTA
1713540 AAAAAATA-AAAAAAAAGAAAAAATA-AAATAAAATAAAT
1 AAAAAA-ATAAAAAAAAGAAAAAATATAAATAAAATAAAT
* * * *
1713578 AAAACAATACAAAAAAGAAGAAATATAAATAAAAATAATT
1 AAAAAAATAAAAAAAAGAAAAAATATAAAT-AAAATAAAT
* *
1713618 TAAAAAATAATAAACGAAGAAAAA
1 AAAAAAATAA-AAA-AAAGAAAAA
1713642 GAAATAAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
37 1 0.02
38 20 0.40
39 4 0.08
40 15 0.30
41 3 0.06
42 7 0.14
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (39 bp):
AAAAAAATAAAAAAAAGAAAAAATATAAATAAAATAAAT
Found at i:1713592 original size:30 final size:27
Alignment explanation
Indices: 1713542--1713612 Score: 72
Period size: 30 Copynumber: 2.5 Consensus size: 27
1713532 AAATGTTAAA
*
1713542 AAAATAAA-AAAAAAGAAAAAATAAAAT
1 AAAATAAATAAAAAAGAAAAAA-AAAAG
* *
1713569 AAAATAAATAAAACAATACAAAAAAGAAG
1 AAAATAAATAAAA-AAGA-AAAAAAAAAG
1713598 AAATATAAATAAAAA
1 AAA-ATAAATAAAAA
1713613 TAATTTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 8 0.22
28 4 0.11
29 10 0.27
30 15 0.41
ACGTcount: A:0.80, C:0.03, G:0.04, T:0.13
Consensus pattern (27 bp):
AAAATAAATAAAAAAGAAAAAAAAAAG
Found at i:1713637 original size:39 final size:39
Alignment explanation
Indices: 1713550--1713650 Score: 109
Period size: 39 Copynumber: 2.6 Consensus size: 39
1713540 AAAAAATAAA
*
1713550 AAAAAAGAAAAAATAAAAT-AAAATAAATAAAACAATAC
1 AAAAAAGAAGAAATAAAATAAAAATAAATAAAACAATAC
*
1713588 AAAAAAGAAGAAATATAAATAAAAATAATTTAAAA-AATA-
1 AAAAAAGAAGAAATA-AAATAAAAATAA-ATAAAACAATAC
* * *
1713627 ATAAACGAAGAAAAAGAAATAAAA
1 AAAAAAGAAGAAATA-AAATAAAA
1713651 TGATAAGGAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
38 14 0.26
39 24 0.44
40 11 0.20
41 5 0.09
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (39 bp):
AAAAAAGAAGAAATAAAATAAAAATAAATAAAACAATAC
Found at i:1713706 original size:5 final size:5
Alignment explanation
Indices: 1713696--1713740 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
1713686 GGAAGAAAAA
*
1713696 TAAAT TAAAT TAAA- AAGAAT TAAAAT TAAAT TAAAT TAAAT TAAA
1 TAAAT TAAAT TAAAT TA-AAT T-AAAT TAAAT TAAAT TAAAT TAAA
1713741 AAACCATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
4 1 0.03
5 29 0.83
6 4 0.11
7 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (5 bp):
TAAAT
Found at i:1713720 original size:26 final size:25
Alignment explanation
Indices: 1713678--1713735 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 25
1713668 GATTAAAAAC
*
1713678 AATTAAAAGGAAGAAAAATAAATTA
1 AATTAAAAAGAAGAAAAATAAATTA
* *
1713703 AATTAAAAAGAATTAAAATTAAATTA
1 AATTAAAAAGAA-GAAAAATAAATTA
1713729 AATTAAA
1 AATTAAA
1713736 TTAAAAAACC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 11 0.38
26 18 0.62
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (25 bp):
AATTAAAAAGAAGAAAAATAAATTA
Found at i:1715139 original size:30 final size:30
Alignment explanation
Indices: 1715105--1715166 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1715095 TAACCATTCA
1715105 TATTATAATAACATATTACAAATCCAGTTG
1 TATTATAATAACATATTACAAATCCAGTTG
1715135 TATTATAATAACATATTACAAATCCAGTTG
1 TATTATAATAACATATTACAAATCCAGTTG
1715165 TA
1 TA
1715167 AGGGTGACGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (30 bp):
TATTATAATAACATATTACAAATCCAGTTG
Found at i:1718580 original size:11 final size:11
Alignment explanation
Indices: 1718564--1718589 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1718554 TATATAACTA
1718564 AAATAATAATT
1 AAATAATAATT
1718575 AAATAATAATT
1 AAATAATAATT
1718586 AAAT
1 AAAT
1718590 TACTAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAATAATAATT
Found at i:1719816 original size:23 final size:23
Alignment explanation
Indices: 1719775--1719818 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1719765 GGAGCTAGGG
* *
1719775 TTTAGAAACCTTAGCTGAAACGA
1 TTTAGAAACCCTAACTGAAACGA
*
1719798 TTTAGAAACCCTAATTGAAAC
1 TTTAGAAACCCTAACTGAAAC
1719819 CCTAAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (23 bp):
TTTAGAAACCCTAACTGAAACGA
Found at i:1719932 original size:3 final size:3
Alignment explanation
Indices: 1719917--1719983 Score: 107
Period size: 3 Copynumber: 22.0 Consensus size: 3
1719907 AATATTTATT
* *
1719917 TAA TAA TAC TAA TAA TAA TGTA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
1719963 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
1719984 AAGCAAACTG
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
3 57 0.97
4 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1720399 original size:74 final size:73
Alignment explanation
Indices: 1720163--1720398 Score: 373
Period size: 73 Copynumber: 3.2 Consensus size: 73
1720153 CTTATTATCT
* * *
1720163 TGCACTGTAGGTCTTACAGATGACCTTGAGGCTTTAAGATTAAAAAGCTCCCGAAGGCTTTTTGA
1 TGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTTTTTGA
1720228 AAACATCA
66 AAACATCA
*
1720236 TGCACTGTAGGTCTTACAGATGACCCTAAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTTTTTGA
1 TGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTTTTTGA
1720301 AAACATCA
66 AAACATCA
* * * * *
1720309 TGAACTGTATGTCTTATAGATGACCCTGAGGCTTTAAAATCAAAAAAGCTCCCTAAGGCTTTTTG
1 TGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATC-AAAAAGCTCCCAAAGGCTTTTTG
1720374 AAAACATCA
65 AAAACATCA
*
1720383 TGCACTGTAGGACTTA
1 TGCACTGTAGGTCTTA
1720399 TGATGTTGGA
Statistics
Matches: 149, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
73 105 0.70
74 44 0.30
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (73 bp):
TGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCAAAGGCTTTTTGA
AAACATCA
Found at i:1720428 original size:74 final size:72
Alignment explanation
Indices: 1720204--1720429 Score: 185
Period size: 73 Copynumber: 3.1 Consensus size: 72
1720194 CTTTAAGATT
* * **
1720204 AAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTA-CA-GATGACCCTAAGG
1 AAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGATGATGA-AAT-A-G
* *
1720267 CTT-TAAGATC
63 TTTATAAG-TA
* * **
1720277 AAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGAACTGTATGTCTTAT-A-GATGACCCTGAGG
1 AAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGATGATGA-AAT-A-G
*
1720340 CTTTA-AAATCA
63 -TTTATAAGT-A
* * *
1720351 AAAAAGCTCCCTAAGGCTTTTTGAAAACATCATGCACTGTAGGACTTATGATGTTGGAAATAGTT
1 AAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGATGAT-GAAATAGTT
1720416 TACTAAGTA
65 TA-TAAGTA
1720425 AAAAA
1 AAAAA
1720430 CTATGGAAAT
Statistics
Matches: 129, Mismatches: 15, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
73 63 0.49
74 56 0.43
75 5 0.04
76 3 0.02
77 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (72 bp):
AAAAAGCTCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGATGATGAAATAGTTT
ATAAGTA
Found at i:1722502 original size:182 final size:182
Alignment explanation
Indices: 1722195--1722550 Score: 658
Period size: 182 Copynumber: 2.0 Consensus size: 182
1722185 AAGATGATTA
* *
1722195 GGTATTTGAAACCTTACTTGCTGAGTAGATATTTGTTCAACAACAAGACCTTGATGCTGCCTGAT
1 GGTATTTGAAACCCTACTTGCTGAGTAGATATTTGTTCAACAACAAGACCTTGATACTGCCTGAT
1722260 GAACGAAGCAATTATGTATAGTCAGCTCGACTGTCACTGCTTCATTTTCATTCTTCATACTTTTC
66 GAACGAAGCAATTATGTATAGTCAGCTCGACTGTCACTGCTTCATTTTCATTCTTCATACTTTTC
1722325 TGCCTCATCAGAAGTATTTGCTCAAATCAATGATATTTAACACAGAATATTT
131 TGCCTCATCAGAAGTATTTGCTCAAATCAATGATATTTAACACAGAATATTT
*
1722377 GGTATTTGAAACCCTACTTGCTGAGTAGATATTTGTTCAACAACAAGACCTTGATACTGCTTGAT
1 GGTATTTGAAACCCTACTTGCTGAGTAGATATTTGTTCAACAACAAGACCTTGATACTGCCTGAT
*
1722442 GAACGAAGCAATTATGTATAGTCAGCTCGATTGTCACTGCTTCATTTTCATTCTTCATACTTTTC
66 GAACGAAGCAATTATGTATAGTCAGCTCGACTGTCACTGCTTCATTTTCATTCTTCATACTTTTC
* *
1722507 TGCCTCATCGGAAGTATTTGCTCAAATCCATGATATTTAACACA
131 TGCCTCATCAGAAGTATTTGCTCAAATCAATGATATTTAACACA
1722551 TGATGATGTG
Statistics
Matches: 168, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
182 168 1.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (182 bp):
GGTATTTGAAACCCTACTTGCTGAGTAGATATTTGTTCAACAACAAGACCTTGATACTGCCTGAT
GAACGAAGCAATTATGTATAGTCAGCTCGACTGTCACTGCTTCATTTTCATTCTTCATACTTTTC
TGCCTCATCAGAAGTATTTGCTCAAATCAATGATATTTAACACAGAATATTT
Found at i:1722731 original size:75 final size:75
Alignment explanation
Indices: 1722598--1722737 Score: 183
Period size: 75 Copynumber: 1.9 Consensus size: 75
1722588 GATATGAACA
* * *
1722598 TTCAAAATACATCAACATTCCTGATTCTGATTGAAATGGGCTTTCAGTATATCCCAACATTTGCT
1 TTCAAAATACATCAACATTCCTCATTCTGATTGAAATGGGCTTTCAGCATATCACAACATTTGCT
1722663 GATACAAACG
66 GATACAAACG
* * * * * *
1722673 TTCAAAATGCGTCAACATTCTTCTTTCTGATTGAAATGGGGTTTCAGCAT-GCTACAACATTTGC
1 TTCAAAATACATCAACATTCCTCATTCTGATTGAAATGGGCTTTCAGCATATC-ACAACATTTGC
1722737 T
65 T
1722738 TCTTGTTGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
74 1 0.02
75 54 0.98
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (75 bp):
TTCAAAATACATCAACATTCCTCATTCTGATTGAAATGGGCTTTCAGCATATCACAACATTTGCT
GATACAAACG
Found at i:1725568 original size:9 final size:9
Alignment explanation
Indices: 1725549--1725581 Score: 52
Period size: 8 Copynumber: 3.9 Consensus size: 9
1725539 ATTGGTTCAA
1725549 TTTTTCC-T
1 TTTTTCCTT
1725557 TTTTTCCTT
1 TTTTTCCTT
1725566 TTTTT-CTT
1 TTTTTCCTT
1725574 TTTTTCCT
1 TTTTTCCT
1725582 CCTTTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTCCTT
Found at i:1725587 original size:17 final size:17
Alignment explanation
Indices: 1725550--1725591 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1725540 TTGGTTCAAT
* **
1725550 TTTTCCTTTTTTCCTTT
1 TTTTCTTTTTTTCCTCC
1725567 TTTTCTTTTTTTCCTCC
1 TTTTCTTTTTTTCCTCC
1725584 TTTTCTTT
1 TTTTCTTT
1725592 AAAGTATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTCTTTTTTTCCTCC
Found at i:1732676 original size:3 final size:3
Alignment explanation
Indices: 1732661--1732723 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
1732651 AATATTTATT
* *
1732661 TAA TAA TAC TAA TAA TAA TGTA TAA TAA TAA TAA TAA TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
1732706 TAAA TAA TAA -AA TAA TAA
1 T-AA TAA TAA TAA TAA TAA
1732724 AAGCAAACTG
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
2 4 0.08
3 43 0.83
4 5 0.10
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:1741612 original size:21 final size:22
Alignment explanation
Indices: 1741586--1741628 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1741576 GATACCCTCA
1741586 TGAA-GGAACCGATTCCCCCTT
1 TGAAGGGAACCGATTCCCCCTT
1741607 TGAAGGGGAACCGATTCCCCCT
1 TGAA-GGGAACCGATTCCCCCT
1741629 AGGGGAATCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
23 16 0.80
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (22 bp):
TGAAGGGAACCGATTCCCCCTT
Found at i:1741634 original size:19 final size:21
Alignment explanation
Indices: 1741590--1741640 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 21
1741580 CCCTCATGAA
1741590 GGAACCGATTCCCCCTTTGAAGG
1 GGAACCGATTCCCCC-TT-AAGG
1741613 GGAACCGATTCCCCC-T-AGG
1 GGAACCGATTCCCCCTTAAGG
*
1741632 GGAATCGAT
1 GGAACCGAT
1741641 AGCCCCTGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 11 0.41
21 1 0.04
23 15 0.56
ACGTcount: A:0.24, C:0.29, G:0.27, T:0.20
Consensus pattern (21 bp):
GGAACCGATTCCCCCTTAAGG
Found at i:1741646 original size:19 final size:19
Alignment explanation
Indices: 1741610--1741651 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1741600 CCCCCTTTGA
*
1741610 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATACCCCCT
* *
1741629 AGGGGAATCGATAGCCCCT
1 AGGGGAACCGATACCCCCT
1741648 -GGGG
1 AGGGG
1741652 TTCTGGAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.21, C:0.29, G:0.36, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATACCCCCT
Found at i:1750759 original size:17 final size:17
Alignment explanation
Indices: 1750737--1750791 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
1750727 TTAATTGCTA
1750737 TATTTATATATTTTAAT
1 TATTTATATATTTTAAT
1750754 TATTTAT-TATATTTAAT
1 TATTTATATAT-TTTAAT
* *
1750771 AAATTA-ATATTATTAAT
1 TATTTATATATT-TTAAT
1750788 TATT
1 TATT
1750792 ATTATATTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 4 0.13
17 27 0.87
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTATATATTTTAAT
Found at i:1754628 original size:23 final size:21
Alignment explanation
Indices: 1754577--1754642 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 21
1754567 TATTTTATTC
*
1754577 TTTATTTTTACTATTTTATTTTTG
1 TTTA-TTTTA-TATCTTA-TTTTG
1754601 TTTATTATTATATCTTATTTTG
1 TTTATT-TTATATCTTATTTTG
*
1754623 TATTATTTTATTTCTCTATT
1 T-TTATTTTATATCT-TATT
1754643 ATTATTGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
22 13 0.35
23 17 0.46
24 7 0.19
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (21 bp):
TTTATTTTATATCTTATTTTG
Found at i:1754645 original size:39 final size:37
Alignment explanation
Indices: 1754565--1754648 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 37
1754555 TTTTCATATT
* *
1754565 TTTATT-TTATTCTTTATTTTTACTATTTTATTTTTG
1 TTTATTATTATTCTTTATTTTTACTATTTTATTTCTC
*
1754601 TTTATTATTATATC-TTATTTTGTATTATTTTATTTCTC
1 TTTATTATTAT-TCTTTATTTT-TACTATTTTATTTCTC
1754639 TATTATTATT
1 T-TTATTATT
1754649 GTATTTTTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
36 6 0.15
37 11 0.27
38 16 0.39
39 8 0.20
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.71
Consensus pattern (37 bp):
TTTATTATTATTCTTTATTTTTACTATTTTATTTCTC
Found at i:1754680 original size:2 final size:2
Alignment explanation
Indices: 1754673--1754717 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1754663 AGTATTTAAT
*
1754673 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1754715 TA T
1 TA T
1754718 TTCCATTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1755173 original size:30 final size:31
Alignment explanation
Indices: 1755138--1755201 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
1755128 TGTTTTAACC
1755138 TTACTTTATTAT-CATTTTTTATTTCTTT-TT
1 TTACTTTATT-TCCATTTTTTATTTCTTTATT
*
1755168 TTACTTTATTTCCATTTTTTATTTTTTTATT
1 TTACTTTATTTCCATTTTTTATTTCTTTATT
1755199 TTA
1 TTA
1755202 TTATTTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 1 0.03
30 25 0.81
31 5 0.16
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.73
Consensus pattern (31 bp):
TTACTTTATTTCCATTTTTTATTTCTTTATT
Found at i:1756289 original size:15 final size:15
Alignment explanation
Indices: 1756269--1756322 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
1756259 CCATGTTTTT
1756269 TTCTTTTACTTTTCA
1 TTCTTTTACTTTTCA
1756284 TTC-TTT-CTTTCATCA
1 TTCTTTTACTTT--TCA
*
1756299 TTTTTTTACTTTT-A
1 TTCTTTTACTTTTCA
*
1756313 TTATTTTACT
1 TTCTTTTACT
1756323 AACTTTTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
13 4 0.12
14 13 0.39
15 9 0.27
16 3 0.09
17 4 0.12
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.69
Consensus pattern (15 bp):
TTCTTTTACTTTTCA
Found at i:1765849 original size:8 final size:7
Alignment explanation
Indices: 1765830--1765880 Score: 57
Period size: 7 Copynumber: 6.9 Consensus size: 7
1765820 GCCCTAAATT
1765830 GAAAAAA
1 GAAAAAA
*
1765837 GAAAAAG
1 GAAAAAA
1765844 GAAAAAA
1 GAAAAAA
1765851 GAACAAAAA
1 G-A-AAAAA
1765860 GAATAAAA
1 GAA-AAAA
*
1765868 GAGAAAA
1 GAAAAAA
1765875 GAAAAA
1 GAAAAA
1765881 TAAGGTGGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 23 0.62
8 8 0.22
9 6 0.16
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (7 bp):
GAAAAAA
Found at i:1765874 original size:24 final size:23
Alignment explanation
Indices: 1765832--1765877 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1765822 CCTAAATTGA
*
1765832 AAAAAGAAAAAGGAAAAAAGAAC
1 AAAAAGAAAAAAGAAAAAAGAAC
*
1765855 AAAAAGAATAAAAGAGAAAAGAA
1 AAAAAGAA-AAAAGAAAAAAGAA
1765878 AAATAAGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.02
Consensus pattern (23 bp):
AAAAAGAAAAAAGAAAAAAGAAC
Found at i:1767183 original size:111 final size:108
Alignment explanation
Indices: 1766985--1767243 Score: 326
Period size: 111 Copynumber: 2.4 Consensus size: 108
1766975 GCTTTCCAAT
* *
1766985 TTTAGAGCTAATTTTAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTTAGAGC-AATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAACTCAACTTCA
**
1767050 CAACGAAGGGGCGACTGACTGTCAACAAACAACTTTTTCAGTTTC
65 CAACGAAGGGGCGACTGACTGTCAACAAACAA-TTTCCCAGTTTC
* * *
1767095 ATTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCAAGATAGCACAAACTCAACTTC
1 -TTTAGAG-CAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAACTCAACTTC
* * * *
1767160 ATAGCGAAGGGGCGTCTGGCTGTCAACAAACAATTTCCCAGTTTC
64 ACAACGAAGGGGCGACTGACTGTCAACAAACAATTTCCCAGTTTC
* * *
1767205 ---AGAGCCAATTTCAATTTCACGGCGGAGGATATTGGACTC
1 TTTAGAG-CAATTTCAACTTCACAGCGAAGGATATTGGACTC
1767244 GAAACAATAC
Statistics
Matches: 131, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
106 34 0.26
110 10 0.08
111 86 0.66
112 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (108 bp):
TTTAGAGCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAACTCAACTTCAC
AACGAAGGGGCGACTGACTGTCAACAAACAATTTCCCAGTTTC
Found at i:1769019 original size:6 final size:6
Alignment explanation
Indices: 1769010--1769076 Score: 57
Period size: 7 Copynumber: 10.7 Consensus size: 6
1769000 TATATTTTCA
1769010 TATTTT TA-TTT TATTCTT TATTCTT TATTTT TAATATTT TA-TTT TATTTT
1 TATTTT TATTTT TATT-TT TATT-TT TATTTT T-AT-TTT TATTTT TATTTT
* *
1769060 TGTTTAT TATTAT TATT
1 TATTT-T TATTTT TATT
1769077 ATATCTTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
5 10 0.19
6 18 0.35
7 20 0.38
8 4 0.08
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (6 bp):
TATTTT
Found at i:1769031 original size:12 final size:11
Alignment explanation
Indices: 1769010--1769102 Score: 61
Period size: 10 Copynumber: 8.5 Consensus size: 11
1769000 TATATTTTCA
1769010 TATTTTTATTT
1 TATTTTTATTT
1769021 TATTCTTTATTCTT
1 TATT-TTTA-T-TT
*
1769035 TATTTTTA--A
1 TATTTTTATTT
1769044 TA-TTTTATTT
1 TATTTTTATTT
*
1769054 TATTTTT-GTT
1 TATTTTTATTT
*
1769064 TATTATTATTAT
1 TATTTTTATT-T
*
1769076 TATATCTTATTT
1 TAT-TTTTATTT
*
1769088 T-TTATTATTT
1 TATTTTTATTT
1769098 TATTT
1 TATTT
1769103 CTCTATTATT
Statistics
Matches: 64, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
8 5 0.08
9 2 0.03
10 18 0.28
11 12 0.19
12 10 0.16
13 11 0.17
14 6 0.09
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:1769050 original size:14 final size:13
Alignment explanation
Indices: 1769000--1769102 Score: 58
Period size: 14 Copynumber: 7.9 Consensus size: 13
1768990 TCATTATACA
1769000 TATATTTTCATATTT
1 TATATTTT-AT-TTT
1769015 T-TATTTTATTCTT
1 TATATTTTATT-TT
1769028 TAT-TCTTTATTTT
1 TATAT-TTTATTTT
1769041 TAATATTTTA--TT
1 T-ATATTTTATTTT
*
1769053 T-TATTTT-TGTT
1 TATATTTTATTTT
* *
1769064 TAT-TATTATTAT
1 TATATTTTATTTT
*
1769076 TATATCTTATTTTT
1 TATATTTTA-TTTT
1769090 TATTATTTTATTT
1 TA-TATTTTATTT
1769103 CTCTATTATT
Statistics
Matches: 70, Mismatches: 6, Indels: 25
0.69 0.06 0.25
Matches are distributed among these distances:
10 6 0.09
11 6 0.09
12 10 0.14
13 13 0.19
14 27 0.39
15 8 0.11
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (13 bp):
TATATTTTATTTT
Found at i:1769076 original size:29 final size:28
Alignment explanation
Indices: 1769010--1769101 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 28
1769000 TATATTTTCA
* * *
1769010 TATTTTTATTTTATTCTT-TATTCTTTAT
1 TATTATTATTTTATT-TTATTTTTTTTAT
* *
1769038 TTTTAATATTTTATTTTATTTTTGTTTAT
1 TATTATTATTTTATTTTATTTTT-TTTAT
* *
1769067 TATTATTATTATATCTTATTTTTTATTAT
1 TATTATTATTTTATTTTATTTTTT-TTAT
1769096 T-TTATT
1 TATTATT
1769102 TCTCTATTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
27 2 0.04
28 21 0.40
29 29 0.56
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (28 bp):
TATTATTATTTTATTTTATTTTTTTTAT
Found at i:1769092 original size:7 final size:7
Alignment explanation
Indices: 1769018--1769102 Score: 55
Period size: 7 Copynumber: 11.1 Consensus size: 7
1769008 CATATTTTTA
1769018 TTTTATT
1 TTTTATT
*
1769025 CTTTATT
1 TTTTATT
*
1769032 CTTTATT
1 TTTTATT
* *
1769039 TTTAATA
1 TTTTATT
1769046 TTTTATT
1 TTTTATT
1769053 TTATT-TT
1 TT-TTATT
1769060 TGTTTATT
1 T-TTTATT
1769068 ATTATTATT
1 -TT-TTATT
1769077 ATATCTTATT
1 -T-T-TTATT
1769087 TTTTATT
1 TTTTATT
1769094 ATTTTATT
1 -TTTTATT
1769102 T
1 T
1769103 CTCTATTATT
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
7 35 0.55
8 14 0.22
9 9 0.14
10 6 0.09
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (7 bp):
TTTTATT
Found at i:1769147 original size:2 final size:2
Alignment explanation
Indices: 1769140--1769191 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
1769130 AGTATTTAAT
* * *
1769140 TA TA TA TA TG TA TC TA TA TA TT TA T- 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
1769181 TA TA TA TA TA T
1 TA TA TA TA TA T
1769192 TTCTATTTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1769166 original size:25 final size:26
Alignment explanation
Indices: 1769132--1769185 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
1769122 TTCCCTCTAG
* *
1769132 TATTTAATTATATATATGTATCTATA
1 TATTTAATTATATATATATATATATA
1769158 TATTT-ATTATATATATATATATATA
1 TATTTAATTATATATATATATATATA
1769183 TAT
1 TAT
1769186 ATATATTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (26 bp):
TATTTAATTATATATATATATATATA
Found at i:1769594 original size:19 final size:18
Alignment explanation
Indices: 1769572--1769609 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1769562 ATTCTTTAAA
*
1769572 TTTTT-ATTGTCTTTACCC
1 TTTTTAATTGT-TTTAACC
1769590 TTTTTAATTGTTTTAACC
1 TTTTTAATTGTTTTAACC
1769608 TT
1 TT
1769610 ACTTTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.16, C:0.16, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTTTAATTGTTTTAACC
Found at i:1769656 original size:18 final size:19
Alignment explanation
Indices: 1769625--1769719 Score: 56
Period size: 19 Copynumber: 5.2 Consensus size: 19
1769615 ATTATCATTT
* *
1769625 TTTATTT-CTTTTTTTTAC
1 TTTATTTCCATTTTATTAC
*
1769643 TTTATTTCCATTTTATTAT
1 TTTATTTCCATTTTATTAC
*
1769662 TTTA-TT--ATTTTATTAT
1 TTTATTTCCATTTTATTAC
** *
1769678 TTTATTAT-TTTTTTATTTTC
1 TTTATT-TCCATTTTA-TTAC
* *
1769698 TTGATTTTCATTTTATTAC
1 TTTATTTCCATTTTATTAC
1769717 TTT
1 TTT
1769720 CCTTCTTGTT
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
16 14 0.23
17 1 0.02
18 10 0.17
19 23 0.38
20 12 0.20
ACGTcount: A:0.18, C:0.07, G:0.01, T:0.74
Consensus pattern (19 bp):
TTTATTTCCATTTTATTAC
Found at i:1769665 original size:8 final size:8
Alignment explanation
Indices: 1769652--1769696 Score: 81
Period size: 8 Copynumber: 5.6 Consensus size: 8
1769642 CTTTATTTCC
1769652 ATTTTATT
1 ATTTTATT
1769660 ATTTTATT
1 ATTTTATT
1769668 ATTTTATT
1 ATTTTATT
1769676 ATTTTATT
1 ATTTTATT
*
1769684 ATTTTTTT
1 ATTTTATT
1769692 ATTTT
1 ATTTT
1769697 CTTGATTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
ATTTTATT
Found at i:1769679 original size:24 final size:25
Alignment explanation
Indices: 1769652--1769705 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 25
1769642 CTTTATTTCC
1769652 ATTTTATTATTTTATTATTTTATT-
1 ATTTTATTATTTTATTATTTTATTG
* *
1769676 ATTTTATTATTTTTTTATTTTCTTG
1 ATTTTATTATTTTATTATTTTATTG
1769701 ATTTT
1 ATTTT
1769706 CATTTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (25 bp):
ATTTTATTATTTTATTATTTTATTG
Found at i:1770504 original size:28 final size:29
Alignment explanation
Indices: 1770472--1770537 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
1770462 TAAATTAGAG
*
1770472 TTTATGTTAATTAAGA-TTAAATATTTTT
1 TTTATGTTAATTAAGATTTAAATATTTGT
*
1770500 TTTATGTTAA--AATATTTAAATATTTGT
1 TTTATGTTAATTAAGATTTAAATATTTGT
1770527 TTT-T-TTAATTA
1 TTTATGTTAATTA
1770538 TAAGTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
25 4 0.12
26 4 0.12
27 15 0.45
28 10 0.30
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (29 bp):
TTTATGTTAATTAAGATTTAAATATTTGT
Found at i:1771124 original size:14 final size:15
Alignment explanation
Indices: 1771105--1771137 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1771095 AACCTAATTT
1771105 AAATATTT-TCAACA
1 AAATATTTCTCAACA
*
1771119 AAATATTTCTTAACA
1 AAATATTTCTCAACA
1771134 AAAT
1 AAAT
1771138 TTAACACATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATATTTCTCAACA
Found at i:1773039 original size:20 final size:19
Alignment explanation
Indices: 1773006--1773044 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1772996 TGTTTTAAAA
*
1773006 AATATTTTTAAAATCATAT
1 AATATTTTTAAAATAATAT
*
1773025 AATATATTTTCAAATAATAT
1 AATAT-TTTTAAAATAATAT
1773045 TTTAAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
AATATTTTTAAAATAATAT
Found at i:1773191 original size:38 final size:36
Alignment explanation
Indices: 1773010--1773320 Score: 181
Period size: 36 Copynumber: 8.7 Consensus size: 36
1773000 TTAAAAAATA
* **
1773010 TTTTTAAAATCATATA--ATATATTTTC-AAATAAT
1 TTTTTAAAAACATATATTATATATTTTCAAAATGTT
* * *
1773043 ATTTT-AAAA-TTATA-TATATATTTTAAAAAATG--
1 TTTTTAAAAACATATATTATATATTTT-CAAAATGTT
* * *
1773075 TTTTCAAAATCATATACTATATAGTTTTCAAAATG--
1 TTTTTAAAAACATATATTATATA-TTTTCAAAATGTT
* *
1773110 TTTTTAAAAAC-TATATTCTATAATTATTTCTTCAAACTATT
1 TTTTTAAAAACATATA-T-TAT-A-TA-TT-TTCAAAATGTT
1773151 TTTTTAAAAATCATATATTATATATATTTCAAAATGTT
1 TTTTTAAAAA-CATATATTATATAT-TTTCAAAATGTT
* *
1773189 TTTTT-TAAACTATATAATATATATGTTTTCAAAAATG--
1 TTTTTAAAAAC-ATAT-AT-TATATATTTTC-AAAATGTT
*
1773226 TTTTCAAAAAC-TATA-TATATATTTTCAAAATGCTTT
1 TTTTTAAAAACATATATTATATATTTTCAAAATG--TT
* **
1773262 TTTTTAAAAAC-TATA-TATATGTTTTCAAAATGCC
1 TTTTTAAAAACATATATTATATATTTTCAAAATGTT
*
1773296 TTTTTAAACACTATATATTATATAT
1 TTTTTAAAAAC-ATATATTATATAT
1773321 CTATTTCAAA
Statistics
Matches: 220, Mismatches: 29, Indels: 54
0.73 0.10 0.18
Matches are distributed among these distances:
31 4 0.02
32 21 0.10
33 17 0.08
34 22 0.10
35 22 0.10
36 45 0.20
37 18 0.08
38 29 0.13
39 22 0.10
40 1 0.00
41 13 0.06
42 2 0.01
43 4 0.02
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (36 bp):
TTTTTAAAAACATATATTATATATTTTCAAAATGTT
Found at i:1773228 original size:12 final size:12
Alignment explanation
Indices: 1773211--1773235 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1773201 TATAATATAT
1773211 ATGTTTTCAAAA
1 ATGTTTTCAAAA
1773223 ATGTTTTCAAAA
1 ATGTTTTCAAAA
1773235 A
1 A
1773236 CTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:1774021 original size:84 final size:84
Alignment explanation
Indices: 1773920--1774927 Score: 1082
Period size: 84 Copynumber: 12.1 Consensus size: 84
1773910 TGCCTTGAGC
* * * *
1773920 TATGATGTAAATGATGTGCCTTGGAGCTAAGCGTAGCCGAACTCGAAGGTCTTTGGTTGGCAGAT
1 TATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
* *
1773985 AGCCCTTCTCGACTTAAGT
66 AACCCTTCTAGACTTAAGT
* * *
1774004 TATGCTGCAAATTATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGAT
1 TATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
* *
1774068 AACCCTTCTAGCCTTGAGT
66 AACCCTTCTAGACTTAAGT
* *** *
1774087 TATGTTGTAAATGATATGCCCTCAAAGCTGAGCGTAATCGAACTCG-A-G-CTTCT--TTGGCAG
1 TATGCTGTAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT-TGGTTGGCAG
* *
1774147 ATAACCCTTCTTGACTTAAGC
64 ATAACCCTTCTAGACTTAAGT
* *
1774168 TATGCTATAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGAT
1 TATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
*
1774232 AACCCTTCTAG-CATTGAGT
66 AACCCTTCTAGAC-TTAAGT
* * * * *
1774251 TATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGG-T---AGA
1 TATGCTGTAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGA
* * *
1774312 TAGCCCTTCTCGACTTAAGC
65 TAACCCTTCTAGACTTAAGT
* * * * *
1774332 TATGCTGCAAATGATGTACCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAGTTGGCAGAT
1 TATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
*
1774397 AACCCTTCTCGACTTAAGT
66 AACCCTTCTAGACTTAAGT
* * *
1774416 TATGCTGTAAATGATATGCCTTGGAGCTGAGGGTAGTCGAACTCGAAGGCCTTTGG-TGACAGAT
1 TATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
* * *
1774480 AGCCCTTCTAGGCTTGAGT
66 AACCCTTCTAGACTTAAGT
* *** ** * *
1774499 TATGCTGTAAATGATGTGCCCTCAAAGCTGAGTATAAT-GAAACTCGAGGGTC--T--TTGGCAG
1 TATGCTGTAAATGATATG-CCTTGGAGCTGAGCGTAGTCG-AACTCGAAGGTCTTTGGTTGGCAG
* * *
1774559 ATAACCCTTCTCGAATTAAGA
64 ATAACCCTTCTAGACTTAAGT
* * *
1774580 TATGCTGCAAATAATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
1 TATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
*
1774645 AACCCTTCTCGACTTAAGT
66 AACCCTTCTAGACTTAAGT
* * * * * **
1774664 TATGCTGAAAATGATATACCTTGGAGCTAAGCTTAGTCGAACTCGAAGTTCTTTCGG-TCACAGA
1 TATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GGTTGGCAGA
* *
1774728 TAACCCTTCTAGCCTTGAGT
65 TAACCCTTCTAGACTTAAGT
* * * * * *
1774748 TATGTTGTAAATGATGTTCCTTGGAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTTGGCATAT
1 TATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
* * *
1774813 AACCCTTCTTGATTTAAGC
66 AACCCTTCTAGACTTAAGT
* * * * *
1774832 TATGATGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGAT
1 TATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
* *
1774897 AACCCTTCTAGCCTTGAGT
66 AACCCTTCTAGACTTAAGT
*
1774916 TATGCTGCAAAT
1 TATGCTGTAAAT
1774928 AGTTTCTTCA
Statistics
Matches: 766, Mismatches: 134, Indels: 48
0.81 0.14 0.05
Matches are distributed among these distances:
80 79 0.10
81 113 0.15
82 8 0.01
83 123 0.16
84 441 0.58
85 2 0.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (84 bp):
TATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
AACCCTTCTAGACTTAAGT
Found at i:1774166 original size:164 final size:165
Alignment explanation
Indices: 1773903--1774927 Score: 1104
Period size: 164 Copynumber: 6.2 Consensus size: 165
1773893 TGATAAATAG
* * * * * *
1773903 CCCTTCTTGCCTTGAGCTATGATGTAAATGATGTGCCTTGGAGCTAAGCGTAGCCGAACTCGAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * *
1773968 GTCTT-TGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATTATGTGCCTTGGAGCT
66 G-CTTCT--TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
1774032 GAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAA
128 GAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAA
* *** *
1774070 CCCTTCTAGCCTTGAGTTATGTTGTAAATGATATGCCCTCAAAGCTGAGCGTAATCGAACTCG-A
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA
* ** *
1774134 -GCTTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATGCTATAAATGATATGCCTTGGAGCTGA
65 GGCTTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGA
* *
1774198 GCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAA
130 GCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAA
* * * * *
1774234 CCCTTCTAGCATTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCG-A
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAA
* * * * *
1774298 GG-GTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTACCTTAGAGCTGA
65 GGCTTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGA
1774362 GCGTAGTCGAACTCGAAGGTCTTTAGTTGGCAGATAA
130 GCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAA
* * * *
1774399 CCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGGGTAGTCGAACTCGAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * * * * * ***
1774464 GC--CTTTGGTGACAGATAGCCCTTCTAGGCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGC
66 GCTTCTTT-G-G-CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGC
** * *
1774527 TGAGTATAAT-GAAACTCGAGGGTC--T-TTGGCAGATAA
127 TGAGCGTAGTCG-AACTCGAAGGTCTTTGTTGGCAGATAA
* ** * * * * *
1774563 CCCTTCTCGAATTAAGATATGCTGCAAATAATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * * *
1774628 GTCTT-TGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGAAAATGATATACCTTGGAGCT
66 G-CTTCT--TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
* * * * **
1774692 AAGCTTAGTCGAACTCGAAGTTCTTTCGGTCACAGATAA
128 GAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAA
* * * * *
1774731 CCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTTCCTTGGAGCTGAGTGTAGTCAAACTCGAAG
1 CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
* * * * *
1774796 GTCTT-TGGTTGGCATATAACCCTTCTTGATTTAAGCTATGATGCAAATGATGTGCCTTTGAGCT
66 G-CTTCT--TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
1774860 GAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAA
128 GAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAA
*
1774899 CCCTTCTAGCCTTGAGTTATGCTGCAAAT
1 CCCTTCTAGCCTTGAGTTATGCTGTAAAT
1774928 AGTTTCTTCA
Statistics
Matches: 726, Mismatches: 110, Indels: 43
0.83 0.13 0.05
Matches are distributed among these distances:
164 342 0.47
165 86 0.12
166 7 0.01
167 69 0.10
168 219 0.30
169 3 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (165 bp):
CCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
GCTTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAG
CGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAA
Found at i:1774203 original size:248 final size:246
Alignment explanation
Indices: 1773903--1774905 Score: 1185
Period size: 248 Copynumber: 4.0 Consensus size: 246
1773893 TGATAAATAG
* * * * * * *
1773903 CCCTTCTTGCCTTGAGCTATGATGTAAATGATGTGCCTTGGAGCTAAGCGTAGCCGAACTCGAAG
1 CCCTTCTCGACTTAAGCTATGCTATAAATGATATGCCTTGGAGCTAAGCGTAGTCGAACTCGAAG
* * * * * * * *
1773968 GTCTTTGGTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATTATGTG-CCTTGGAGCT
66 GTCTTTGG-TGACAGATAACCCTTCTAG-CTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCT
* * * * * * * *
1774032 GAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGTTGTAA
129 GAGTGTAATCGAACTCGAAGGTC--T-TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAA
* * *
1774097 ATGATATGCCCTCAAAGCTGAGCGTAATCGAACTCG-A-G-CTTCT-TTGGCAGATAA
191 ATGATATG-CCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTT-TGTTGGCAGATAA
* *
1774151 CCCTTCTTGACTTAAGCTATGCTATAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGCTATGCTATAAATGATATGCCTTGGAGCTAAGCGTAGTCGAACTCGAAG
*
1774216 GTCTTTGGTGACAGATAACCCTTCTAGCATTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTG
66 GTCTTTGGTGACAGATAACCCTTCTAGC-TTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTG
* * *
1774281 AGTGTAATCGAACTCGAGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGA
130 AGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGA
* *
1774346 TGTACCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAGTTGGCAGATAA
195 TATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAA
* * * *
1774399 CCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGGGTAGTCGAACTCGAAG
1 CCCTTCTCGACTTAAGCTATGCTATAAATGATATGCCTTGGAGCTAAGCGTAGTCGAACTCGAAG
* * *
1774464 GCCTTTGGTGACAGATAGCCCTTCTAGGCTTGAGTTATGCTGTAAATGATGTGCCCTCAAAGCTG
66 GTCTTTGGTGACAGATAACCCTTCTA-GCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTG
* * * * *
1774529 AGTATAAT-GAAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGAATTAAGATATGCTGCAAATA
130 AGTGTAATCG-AACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATG
* *
1774593 ATATGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
194 ATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGATAA
* * *
1774647 CCCTTCTCGACTTAAGTTATGCTGA-AAATGATATACCTTGGAGCTAAGCTTAGTCGAACTCGAA
1 CCCTTCTCGACTTAAGCTATGCT-ATAAATGATATGCCTTGGAGCTAAGCGTAGTCGAACTCGAA
* * * * * *
1774711 GTTCTTTCGGTCACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGT-TCCTTGGAGC
65 GGTCTTT-GGTGACAGATAACCCTTCTAG-CTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGC
* * * * * *
1774775 TGAGTGTAGTCAAACTCGAAGGTCTTTGGTTGGCATATAACCCTTCTTGATTTAAGCTATGATGC
128 TGAGTGTAATCGAACTCGAAGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGC
* *
1774840 AAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAA
189 AAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGATAA
1774899 CCCTTCT
1 CCCTTCT
1774906 AGCCTTGAGT
Statistics
Matches: 659, Mismatches: 78, Indels: 32
0.86 0.10 0.04
Matches are distributed among these distances:
244 24 0.04
245 37 0.06
246 4 0.01
247 40 0.06
248 418 0.63
249 43 0.07
250 1 0.00
252 89 0.14
253 3 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (246 bp):
CCCTTCTCGACTTAAGCTATGCTATAAATGATATGCCTTGGAGCTAAGCGTAGTCGAACTCGAAG
GTCTTTGGTGACAGATAACCCTTCTAGCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGA
GTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGAT
ATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATAA
Found at i:1776255 original size:20 final size:20
Alignment explanation
Indices: 1776230--1776272 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1776220 TCTTAAGATT
*
1776230 GTCAAGAAGAACTTGTTATA
1 GTCAAGAAGAACCTGTTATA
1776250 GTCAAGAAGAACCTGTTATA
1 GTCAAGAAGAACCTGTTATA
1776270 GTC
1 GTC
1776273 TAGGTGTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (20 bp):
GTCAAGAAGAACCTGTTATA
Found at i:1781559 original size:70 final size:71
Alignment explanation
Indices: 1781473--1781638 Score: 187
Period size: 70 Copynumber: 2.3 Consensus size: 71
1781463 TAAAAATAAA
* *
1781473 AAAACATTTTAAAATTATATACCATATATATGTTTTTAAAAAA-AATT-AAAATCATATA-ATAT
1 AAAATATTTTAAAATTATATACCATATATAT-ATTTTAAAAAAGAATTCAAAATCATATACATAT
1781535 A-TTTTC
65 AGTTTTC
** **
1781541 AAATAATATTTTAAAATTATATATTATATATATATTTTAAAAAATGTTTTCAAAATCATATACTA
1 -AA-AATATTTTAAAATTATATACCATATATATATTTTAAAAAA-GAATTCAAAATCATATAC-A
1781606 TATAGTTTTC
62 TATAGTTTTC
1781616 AAAATATTTTTAAAATCTATATA
1 AAAATA-TTTTAAAAT-TATATA
1781639 TTATAAATAT
Statistics
Matches: 82, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
69 12 0.15
70 26 0.32
71 2 0.02
72 11 0.13
73 4 0.05
74 16 0.20
75 11 0.13
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (71 bp):
AAAATATTTTAAAATTATATACCATATATATATTTTAAAAAAGAATTCAAAATCATATACATATA
GTTTTC
Found at i:1781561 original size:26 final size:26
Alignment explanation
Indices: 1781532--1781582 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1781522 AATCATATAA
*
1781532 TATATTTTCAAATA-ATATTTTAAAAT
1 TATATATT-AAATATATATTTTAAAAT
*
1781558 TATATATTATATATATATTTTAAAA
1 TATATATTAAATATATATTTTAAAA
1781583 AATGTTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
TATATATTAAATATATATTTTAAAAT
Found at i:1781685 original size:77 final size:72
Alignment explanation
Indices: 1781479--1781769 Score: 258
Period size: 77 Copynumber: 4.0 Consensus size: 72
1781469 TAAAAAAACA
** * **
1781479 TTTTAAAATTATATACCATATATATGTTTTTAAAAAA--AATT-AAAATCATATA-ATATATTTT
1 TTTTAAAATTATATATTATATATAT-ATTTTAAAAAATGTTTTAAAAATCATATATATATATTTT
1781540 C-AAATAAT
65 CAAAAT-AT
*
1781548 ATTTTAAAATTATATATTATATATATATTTTAAAAAATGTTTTCAAAATCATATACTATATAGTT
1 -TTTTAAAATTATATATTATATATATATTTTAAAAAATGTTTTAAAAATCATATA-TATATA-TT
1781613 TTCAAAATAT
63 TTCAAAATAT
** *
1781623 TTTTAAAATCTATATATTATA-A-ATATTTCTTCAAACTGTTTTTTTAAAAATCATATATTATAT
1 TTTTAAAAT-TATATATTATATATATATTT-TAAAAAATG---TTTTAAAAATCATATA-TATAT
1781686 ATATTTCAAAATAT
60 AT-TTTCAAAATAT
** * * * *
1781700 TTTTAAAAAAACTATATAATATATATGTTTTCAAAAATATTTTCAAAAA-C-TATATATATATTT
1 TTTTAAAATTA-TATATTATATATATATTTTAAAAAATGTTTT-AAAAATCATATATATATATTT
1781763 TCAAAAT
64 TCAAAAT
1781770 GCTTTTTTAA
Statistics
Matches: 186, Mismatches: 18, Indels: 32
0.79 0.08 0.14
Matches are distributed among these distances:
69 10 0.05
70 23 0.12
71 2 0.01
72 20 0.11
73 13 0.07
74 25 0.13
75 23 0.12
76 11 0.06
77 48 0.26
78 6 0.03
79 5 0.03
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (72 bp):
TTTTAAAATTATATATTATATATATATTTTAAAAAATGTTTTAAAAATCATATATATATATTTTC
AAAATAT
Found at i:1781703 original size:38 final size:35
Alignment explanation
Indices: 1781520--1781805 Score: 194
Period size: 36 Copynumber: 7.8 Consensus size: 35
1781510 AAAAAAAATT
*
1781520 AAAATCATATA-ATATATTTTC-AAATAATATTTTA
1 AAAATCATATATATATATTTTCAAAAT-ATTTTTTA
* * * *
1781554 AAATTAT-ATATTATATATATATTTTAAAAAATGTTTTC
1 AAA--ATCATA-TATATATAT-TTTCAAAATATTTTTTA
1781592 AAAATCATATACTATATAGTTTTCAAAATA-TTTTT-
1 AAAATCATATA-TATATA-TTTTCAAAATATTTTTTA
* *
1781627 AAAATCTATATATTATAAATATTTCTTCAAACTGTTTTTTTA
1 AAAATC-ATATA-TAT--ATA-TT-TTCAAAAT-ATTTTTTA
*
1781669 AAAATCATATATTATATATATTTCAAAATATTTTTAA
1 AAAATCATATA-TATATAT-TTTCAAAATATTTTTTA
* *
1781706 AAAAACTATATAATATATATGTTTTCAAAA-ATATTTTCA
1 AAAATC-ATAT-ATATATA--TTTTCAAAATAT-TTTTTA
*
1781745 AAAA-C-TATATATATATTTTCAAAATGCTTTTTTA
1 AAAATCATATATATATATTTTCAAAAT-ATTTTTTA
*
1781779 AAAA-CACTATATATATGTTTTCAAAAT
1 AAAATCA-TATATATATATTTTCAAAAT
1781806 GCCCTGTTGA
Statistics
Matches: 207, Mismatches: 19, Indels: 50
0.75 0.07 0.18
Matches are distributed among these distances:
33 9 0.04
34 13 0.06
35 17 0.08
36 42 0.20
37 34 0.16
38 39 0.19
39 32 0.15
40 1 0.00
41 14 0.07
42 6 0.03
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (35 bp):
AAAATCATATATATATATTTTCAAAATATTTTTTA
Found at i:1781790 original size:34 final size:35
Alignment explanation
Indices: 1781565--1781807 Score: 112
Period size: 38 Copynumber: 6.7 Consensus size: 35
1781555 AATTATATAT
* *
1781565 TATATATATA-TTTTAAAAAATG--TTTTCAAAATC
1 TATATATATAGTTTT-CAAAATGCTTTTTCAAAAAC
* *
1781598 ATATACTATATAGTTTTCAAAAT-ATTTTT-AAAATC
1 -TATA-TATATAGTTTTCAAAATGCTTTTTCAAAAAC
* * * *
1781633 TATATATTATAAATATTTCTTCAAACTGTTTTTTTAAAAATC
1 --TATA-TAT--ATAGTT-TTCAAAATGCTTTTTCAAAAA-C
* *
1781675 ATATATTATATA-TATTTCAAAAT-ATTTTTAAAAAAAC
1 -TATA-TATATAGT-TTTCAAAATGCTTTTT-CAAAAAC
*
1781712 TATATAATATATATGTTTTCAAAAAT--ATTTTCAAAAAC
1 --TAT-ATATATA-GTTTTC-AAAATGCTTTTTCAAAAAC
*
1781750 TATATATATA-TTTTCAAAATGCTTTTTTAAAAAC
1 TATATATATAGTTTTCAAAATGCTTTTTCAAAAAC
1781784 -ACTATATATATGTTTTCAAAATGC
1 TA-TATATATA-GTTTTCAAAATGC
1781808 CCTGTTGAAC
Statistics
Matches: 173, Mismatches: 13, Indels: 44
0.75 0.06 0.19
Matches are distributed among these distances:
32 5 0.03
33 6 0.03
34 22 0.13
35 24 0.14
36 31 0.18
37 6 0.03
38 34 0.20
39 20 0.12
40 11 0.06
41 13 0.08
42 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (35 bp):
TATATATATAGTTTTCAAAATGCTTTTTCAAAAAC
Found at i:1781826 original size:36 final size:36
Alignment explanation
Indices: 1781744--1781831 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 36
1781734 AAATATTTTC
** *
1781744 AAAA-ACTATATATATATTTTCAAAATGCTTTTTTA
1 AAAACACTATATATATATTTTCAAAATGCCCTGTTA
*
1781779 AAAACACTATATATATGTTTTCAAAATGCCCTGTT-
1 AAAACACTATATATATATTTTCAAAATGCCCTGTTA
*
1781814 -GAACACTATATATTATAT
1 AAAACACTATATA-TATAT
1781832 ATCTATTTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
34 11 0.24
35 8 0.18
36 26 0.58
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (36 bp):
AAAACACTATATATATATTTTCAAAATGCCCTGTTA
Found at i:1783599 original size:12 final size:13
Alignment explanation
Indices: 1783577--1783605 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1783567 CGAATTGAAT
1783577 TTTTAAATTTTAA
1 TTTTAAATTTTAA
1783590 TTTT-AATTTTAA
1 TTTTAAATTTTAA
1783602 TTTT
1 TTTT
1783606 CGCAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:1784543 original size:3 final size:3
Alignment explanation
Indices: 1784535--1784574 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1784525 TTAGTGAGGC
1784535 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1784575 ATAAGACATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1787012 original size:14 final size:13
Alignment explanation
Indices: 1786995--1787028 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1786985 TTTTAATTTG
1786995 TTTTAAAGTATATT
1 TTTTAAA-TATATT
1787009 TTTTAAATATATT
1 TTTTAAATATATT
*
1787022 TTATAAA
1 TTTTAAA
1787029 AATTTGAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
TTTTAAATATATT
Found at i:1793088 original size:21 final size:21
Alignment explanation
Indices: 1793064--1793106 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1793054 TGTCATTGTC
* *
1793064 ATAACCATTTTTTTAAAAAAA
1 ATAAACATTATTTTAAAAAAA
* *
1793085 ATAAATATTATTTTAATAAAA
1 ATAAACATTATTTTAAAAAAA
1793106 A
1 A
1793107 CAATTATGAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAAACATTATTTTAAAAAAA
Found at i:1794103 original size:30 final size:30
Alignment explanation
Indices: 1794069--1794145 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
1794059 GCCAAAACAT
* *
1794069 AAACTTACATGGT-TAAAATAGTAAAAATAG
1 AAACTTA-AGGGTCTAAAATAGCAAAAATAG
1794099 AAACTTAAGGGTCTAAAATAGCAAAAATAG
1 AAACTTAAGGGTCTAAAATAGCAAAAATAG
* *
1794129 AAA-TTTAGGGCCTAAAA
1 AAACTTAAGGGTCTAAAA
1794146 CAGTTAAACA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.52, C:0.09, G:0.16, T:0.23
Consensus pattern (30 bp):
AAACTTAAGGGTCTAAAATAGCAAAAATAG
Found at i:1794232 original size:60 final size:58
Alignment explanation
Indices: 1794111--1794241 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 58
1794101 ACTTAAGGGT
* * * * *
1794111 CTAAAATAGCAAAAATAGAAATTTAGGGCCTAAAACAGTTAAACAGAAACCTAAAGGA
1 CTAAAATAGAAAAAATAGAAATTTAGGGACTAAAACAATAAAACAGAAACCTAAAGAA
* *
1794169 CTAAAATGGAAAAAAGTA-AAATATTAGGGACTAAAACAATAAAAACAGAAACCTAGAGAA
1 CTAAAATAGAAAAAA-TAGAAAT-TTAGGGACTAAAACAAT-AAAACAGAAACCTAAAGAA
1794229 CTAAAATA-AAAAA
1 CTAAAATAGAAAAA
1794242 CAAAAAATTA
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
58 17 0.27
59 22 0.35
60 23 0.37
ACGTcount: A:0.59, C:0.11, G:0.14, T:0.16
Consensus pattern (58 bp):
CTAAAATAGAAAAAATAGAAATTTAGGGACTAAAACAATAAAACAGAAACCTAAAGAA
Found at i:1794249 original size:59 final size:57
Alignment explanation
Indices: 1794111--1794250 Score: 138
Period size: 58 Copynumber: 2.4 Consensus size: 57
1794101 ACTTAAGGGT
* * * * * * *
1794111 CTAAAATAGCAAAAATAGAAATTTAGGGCCTAAAACAGTTAAACAGAAACCTAAAGGA
1 CTAAAAT-GAAAAAAAAAAAATTTAGGGACTAAAACAATAAAACAGAAACCTAAAGAA
** *
1794169 CTAAAATGGAAAAAAGTAAAATATTAGGGACTAAAACAATAAAAACAGAAACCTAGAGAA
1 CTAAAAT-GAAAAAAAAAAAAT-TTAGGGACTAAAACAAT-AAAACAGAAACCTAAAGAA
1794229 CTAAAAT-AAAAAACAAAAAATT
1 CTAAAATGAAAAAA-AAAAAATT
1794251 AAGGACCAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
58 24 0.36
59 20 0.30
60 23 0.34
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.16
Consensus pattern (57 bp):
CTAAAATGAAAAAAAAAAAATTTAGGGACTAAAACAATAAAACAGAAACCTAAAGAA
Found at i:1796236 original size:43 final size:42
Alignment explanation
Indices: 1796096--1796271 Score: 139
Period size: 40 Copynumber: 4.3 Consensus size: 42
1796086 GTTCCTATGC
*
1796096 GATGAGGACGGCTGGTTATCTAGGGTGACACGGCTCCTACGT
1 GATGAGGACGGCTGGTTATCTAGGATGACACGGCTCCTACGT
* * * ** * *
1796138 GATGAAGAAGTCTGG---TCGGGGGATGACACGGTTCCTACAT
1 GATGAGGACGGCTGGTTATC-TAGGATGACACGGCTCCTACGT
* *
1796178 GATAAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGT
1 GATGAGGACGGCTGGTTATCTA-GGATGACACGGCTCCTACGT
* * ** * *
1796221 TATGAGGA-GGTCTGGTCA--GGGGATGACACAGTTCCTACGT
1 GATGAGGACGG-CTGGTTATCTAGGATGACACGGCTCCTACGT
1796261 GATGAGGACGG
1 GATGAGGACGG
1796272 TTGACCATCT
Statistics
Matches: 101, Mismatches: 26, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
39 2 0.02
40 52 0.51
41 2 0.02
42 14 0.14
43 31 0.31
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (42 bp):
GATGAGGACGGCTGGTTATCTAGGATGACACGGCTCCTACGT
Found at i:1796237 original size:83 final size:82
Alignment explanation
Indices: 1796100--1796271 Score: 263
Period size: 83 Copynumber: 2.1 Consensus size: 82
1796090 CTATGCGATG
*
1796100 AGGACGGCTGGTTATCTAGGGTGACACGGCTCCTACGTGATGAAGAAGTCTGGTCGGGGGATGAC
1 AGGACGGCTGGTTATCTAGGGTGACACGGCTCCTACGTGATGAAGAAGTCTGGTCAGGGGATGAC
*
1796165 ACGGTTCCTACATGATA
66 ACAGTTCCTACATGATA
* * * *
1796182 AGGACGGCTGGTTATCTATGGTTGACACGGCTCCTACGTTATGAGGAGGTCTGGTCAGGGGATGA
1 AGGACGGCTGGTTATCTA-GGGTGACACGGCTCCTACGTGATGAAGAAGTCTGGTCAGGGGATGA
* *
1796247 CACAGTTCCTACGTGATG
65 CACAGTTCCTACATGATA
1796265 AGGACGG
1 AGGACGG
1796272 TTGACCATCT
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
82 18 0.22
83 63 0.78
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.24
Consensus pattern (82 bp):
AGGACGGCTGGTTATCTAGGGTGACACGGCTCCTACGTGATGAAGAAGTCTGGTCAGGGGATGAC
ACAGTTCCTACATGATA
Found at i:1796334 original size:28 final size:28
Alignment explanation
Indices: 1796294--1796375 Score: 105
Period size: 28 Copynumber: 2.9 Consensus size: 28
1796284 AGGGATTATA
*
1796294 GTTTCAAGAGAAACCAACTCAAAGATTT
1 GTTTCAAAAGAAACCAACTCAAAGATTT
1796322 GTTTCAAAAGAAA-CAGACTCAAAGATTT
1 GTTTCAAAAGAAACCA-ACTCAAAGATTT
* *
1796350 GTTTCCAGAA-AAACAAACTCAAAGAT
1 GTTT-CAAAAGAAACCAACTCAAAGAT
1796376 AATACATTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
27 2 0.04
28 41 0.85
29 5 0.10
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.23
Consensus pattern (28 bp):
GTTTCAAAAGAAACCAACTCAAAGATTT
Found at i:1796803 original size:66 final size:65
Alignment explanation
Indices: 1796733--1796889 Score: 165
Period size: 66 Copynumber: 2.3 Consensus size: 65
1796723 CAGGTTGGTT
*
1796733 TTTCATTAGAAAATGTCTCAAGAGAGACAAAATTTGTTTTCAA-ATAAATAGACTCAAAGATGA-
1 TTTCATTAGAAAA-GTCTCAAGAGAGACAAAATTTG-TTTCAAGAGAAA-AGACTCAAAGATGAT
1796796 TTG
63 TTG
* * * * *
1796799 TTTCAATAGAATCAGTCTTAAGAGAGACAAAATTTGTTTCAAGGGAAACGACTCAAAGATGATTT
1 TTTCATTAGAA-AAGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAAGACTCAAAGATGA--T
1796864 GTTG
63 -TTG
*
1796868 TTTCATGAGAAAAGGTCTCAAG
1 TTTCATTAGAAAA-GTCTCAAG
1796890 GAAAATAAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 11
0.78 0.11 0.12
Matches are distributed among these distances:
65 19 0.26
66 34 0.46
67 1 0.01
68 1 0.01
69 19 0.26
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.31
Consensus pattern (65 bp):
TTTCATTAGAAAAGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAAAGACTCAAAGATGATTTG
Found at i:1798092 original size:8 final size:8
Alignment explanation
Indices: 1797500--1798090 Score: 858
Period size: 8 Copynumber: 73.9 Consensus size: 8
1797490 GTATGCATAT
*
1797500 GTATGTAT
1 GTATGTAC
1797508 GTATGTAC
1 GTATGTAC
*
1797516 GTAGGTAC
1 GTATGTAC
1797524 GTATGTAC
1 GTATGTAC
1797532 GTATGTAC
1 GTATGTAC
1797540 GTATGTAC
1 GTATGTAC
1797548 GTATGTAC
1 GTATGTAC
1797556 GTATGTAC
1 GTATGTAC
1797564 GTATGTAC
1 GTATGTAC
1797572 GTATGTAC
1 GTATGTAC
1797580 GTATGTAC
1 GTATGTAC
1797588 GTATGTAC
1 GTATGTAC
1797596 GTATGTAC
1 GTATGTAC
*
1797604 GTGTGTAC
1 GTATGTAC
1797612 GTATGTAC
1 GTATGTAC
*
1797620 GTGTGTAC
1 GTATGTAC
1797628 GTATGTAC
1 GTATGTAC
*
1797636 GTGTGTAC
1 GTATGTAC
*
1797644 GTGTGTAC
1 GTATGTAC
*
1797652 GTGTGTAC
1 GTATGTAC
*
1797660 GTGTGTAC
1 GTATGTAC
*
1797668 GTGTGTAC
1 GTATGTAC
*
1797676 GTGTGTAC
1 GTATGTAC
*
1797684 GTGTGTAC
1 GTATGTAC
*
1797692 GTGTGTAC
1 GTATGTAC
*
1797700 GTGTGTAC
1 GTATGTAC
*
1797708 GTGTGTAC
1 GTATGTAC
1797716 GTATGTAC
1 GTATGTAC
*
1797724 GTGTGTAC
1 GTATGTAC
1797732 GTATGTAC
1 GTATGTAC
1797740 GTATGTAC
1 GTATGTAC
1797748 GTATGTAC
1 GTATGTAC
*
1797756 GTGTGTAC
1 GTATGTAC
1797764 GTATGTAC
1 GTATGTAC
*
1797772 GTGTGTAC
1 GTATGTAC
*
1797780 GTGTGTAC
1 GTATGTAC
*
1797788 GTGTGTAC
1 GTATGTAC
*
1797796 GTGTGTAC
1 GTATGTAC
*
1797804 GTGTGTAC
1 GTATGTAC
*
1797812 GTGTGTAC
1 GTATGTAC
*
1797820 GTGTGTAC
1 GTATGTAC
*
1797828 GTGTGTAC
1 GTATGTAC
1797836 GTATGTAC
1 GTATGTAC
*
1797844 GTGTGTAC
1 GTATGTAC
*
1797852 GTGTGTAC
1 GTATGTAC
1797860 GTATGTAC
1 GTATGTAC
*
1797868 GTGTGTAC
1 GTATGTAC
1797876 GTATGTAC
1 GTATGTAC
*
1797884 GTGTGTAC
1 GTATGTAC
1797892 GTATGTAC
1 GTATGTAC
*
1797900 GTGTGTAC
1 GTATGTAC
1797908 GTATGTAC
1 GTATGTAC
*
1797916 GTGTGTAC
1 GTATGTAC
1797924 GTATGTAC
1 GTATGTAC
1797932 GTATGTAC
1 GTATGTAC
1797940 GTATGTAC
1 GTATGTAC
1797948 GTATGTAC
1 GTATGTAC
1797956 GTATGTAC
1 GTATGTAC
1797964 GTATGTAC
1 GTATGTAC
1797972 GTATGTAC
1 GTATGTAC
1797980 GTATGTAC
1 GTATGTAC
1797988 GTATGTAC
1 GTATGTAC
1797996 GTATGTAC
1 GTATGTAC
1798004 GTATGTAC
1 GTATGTAC
1798012 GTATGTAC
1 GTATGTAC
1798020 GTATGTAC
1 GTATGTAC
1798028 GTATGTAC
1 GTATGTAC
*
1798036 GTATGTAT
1 GTATGTAC
*
1798044 GTATGTAT
1 GTATGTAC
*
1798052 GTATGTAT
1 GTATGTAC
*
1798060 GTATGTAT
1 GTATGTAC
*
1798068 GTATGTAT
1 GTATGTAC
*
1798076 GTATGTAT
1 GTATGTAC
1798084 GTATGTA
1 GTATGTA
1798091 TGATTTTCTC
Statistics
Matches: 557, Mismatches: 26, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 557 1.00
ACGTcount: A:0.20, C:0.11, G:0.30, T:0.39
Consensus pattern (8 bp):
GTATGTAC
Found at i:1801807 original size:210 final size:209
Alignment explanation
Indices: 1801424--1801809 Score: 513
Period size: 209 Copynumber: 1.8 Consensus size: 209
1801414 TTCTTGAAAT
* * * * * *
1801424 TGATGCCCCTCAAGCGTTCTGTAACCTAACTCGGTTGATGCCCCTGCGGTGCTGAAGTCAGTGCG
1 TGATGCCCCTCAAGCG-TCTGTAAACTAACTCCGTTAATACCCCGGCAGTGCTGAAGTCAGTGCG
* * * *
1801489 TCACTCCTTGGTGGTTAGCGTTGGAATGATCGTAGATAAGAATCTACTATTGGATTACTCATCGA
65 TCACTCCTTGATGGTTAGCGATGGAATAATCGTAGATAAGAATCTACTACTGGATTACTCATCGA
* * * *
1801554 ACAGTGGACTATCATATTAGTCTCGAATGTTGCATGATCTTTGAGCTCACTGTTTCGTCTCGGAT
130 ACAATGAACTATCATATCAGTCTCGAATGTTGCACGATCTTTGAGCTCACTGTTTCGTCTCGGAT
1801619 CTTTGTATTTGGAAC
195 CTTTGTATTTGGAAC
* * ** *
1801634 TGATGCCCCTCAATGC-TCTGTAAACTAACTCCGTTAATACCTCGGCAGTGTTGAAGTTTGTGCT
1 TGATGCCCCTCAA-GCGTCTGTAAACTAACTCCGTTAATACCCCGGCAGTGCTGAAGTCAGTGCG
* * * *
1801698 TCACTCCTTGATGGTTAGCGATGGAATAATCGTGGATGAGAATCTACTGCTGGATTACTCCTCGG
65 TCACTCCTTGATGGTTAGCGATGGAATAATCGTAGATAAGAATCTACTACTGGATTACTCATC-G
* *
1801763 ATCAATGAATTATCATATCAGTCTCGAATGTTGCACGATCTTTGAGC
129 AACAATGAACTATCATATCAGTCTCGAATGTTGCACGATCTTTGAGC
1801810 GAGTCTCATT
Statistics
Matches: 149, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
209 92 0.62
210 55 0.37
211 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.33
Consensus pattern (209 bp):
TGATGCCCCTCAAGCGTCTGTAAACTAACTCCGTTAATACCCCGGCAGTGCTGAAGTCAGTGCGT
CACTCCTTGATGGTTAGCGATGGAATAATCGTAGATAAGAATCTACTACTGGATTACTCATCGAA
CAATGAACTATCATATCAGTCTCGAATGTTGCACGATCTTTGAGCTCACTGTTTCGTCTCGGATC
TTTGTATTTGGAAC
Found at i:1803990 original size:29 final size:30
Alignment explanation
Indices: 1803927--1804021 Score: 79
Period size: 30 Copynumber: 3.2 Consensus size: 30
1803917 ACTTACATGG
* **
1803927 CTAAAATAGTAAAAATAGAAACTTAAGGGT
1 CTAAAATAGTAAAAACAGAAACTTAAGGAC
* *
1803957 CTAAAATAGTAAAAACATAAA-TTTAGGAC
1 CTAAAATAGTAAAAACAGAAACTTAAGGAC
* * * *
1803986 CTAAAACAAT-AAAACAAAAACCTAAAGGA-
1 CTAAAATAGTAAAAACAGAAA-CTTAAGGAC
1804015 CTAAAAT
1 CTAAAAT
1804022 GACAAAAAGT
Statistics
Matches: 52, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
28 9 0.17
29 19 0.37
30 24 0.46
ACGTcount: A:0.58, C:0.12, G:0.11, T:0.20
Consensus pattern (30 bp):
CTAAAATAGTAAAAACAGAAACTTAAGGAC
Found at i:1805673 original size:2 final size:2
Alignment explanation
Indices: 1805666--1805690 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1805656 AGCAATATTA
1805666 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1805691 ACACTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1806025 original size:27 final size:27
Alignment explanation
Indices: 1805965--1806026 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
1805955 CTACCACCGC
*
1805965 CATCACCACTTCGAACTTGAAACTCCA
1 CATCATCACTTCGAACTTGAAACTCCA
* * * *
1805992 TAGCATCACTTTGAACTTGAAAGTCCA
1 CATCATCACTTCGAACTTGAAACTCCA
1806019 CATCATCA
1 CATCATCA
1806027 AGATCTTCAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.31, G:0.10, T:0.26
Consensus pattern (27 bp):
CATCATCACTTCGAACTTGAAACTCCA
Found at i:1806341 original size:20 final size:21
Alignment explanation
Indices: 1806301--1806343 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1806291 TTTTGGATGC
1806301 TCCCAACCGGTTCACACCGGT
1 TCCCAACCGGTTCACACCGGT
* *
1806322 TCCCAGCCGGTTC-TACCGGT
1 TCCCAACCGGTTCACACCGGT
1806342 TC
1 TC
1806344 TTTAGCGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.14, C:0.42, G:0.21, T:0.23
Consensus pattern (21 bp):
TCCCAACCGGTTCACACCGGT
Found at i:1806621 original size:3 final size:3
Alignment explanation
Indices: 1806609--1806649 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1806599 CAAAATGATG
1806609 TAA T-A 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
1806650 ATGAAATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1807701 original size:29 final size:30
Alignment explanation
Indices: 1807632--1807703 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
1807622 AATCTAAGTA
*
1807632 TTTTTAA-CAAAATAAATATGTAAAATTAT
1 TTTTTAATCAAAATAAATATCTAAAATTAT
* * * *
1807661 TCTTT-GTTAAAATAAGTATCTAAAA-TAT
1 TTTTTAATCAAAATAAATATCTAAAATTAT
1807689 TTTTTAATCAAAATA
1 TTTTTAATCAAAATA
1807704 TGTACATATC
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
28 7 0.21
29 26 0.79
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (30 bp):
TTTTTAATCAAAATAAATATCTAAAATTAT
Done.