Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, 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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 18 of 117
Found at i:1963623 original size:21 final size:19
Alignment explanation
Indices: 1963585--1963623 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1963575 GATGATAGAG
1963585 TTTTTTAAAAATTTATTAA
1 TTTTTTAAAAATTTATTAA
*
1963604 TTTTTGTAAATATATTATTA
1 TTTTT-TAAAAAT-TTATTA
1963624 TAAAATACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTTTTAAAAATTTATTAA
Found at i:1964264 original size:17 final size:16
Alignment explanation
Indices: 1964242--1964291 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
1964232 ACACAAAATA
*
1964242 ATTAAATAAAAATATTT
1 ATTAAATAAAAATA-AT
*
1964259 ATTAAATTTAAAATAAT
1 ATTAAA-TAAAAATAAT
1964276 ATTAAATAAAAA-AAT
1 ATTAAATAAAAATAAT
1964291 A
1 A
1964292 AATAAAAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 4 0.14
16 5 0.17
17 13 0.45
18 7 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTAAATAAAAATAAT
Found at i:1965160 original size:21 final size:21
Alignment explanation
Indices: 1965135--1965187 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 21
1965125 TCTATCACTG
1965135 ATTTTAATC-TCATTAAAACTA
1 ATTTTAA-CATCATTAAAACTA
1965156 ATTTTAACATCATTAAAACTA
1 ATTTTAACATCATTAAAACTA
1965177 ATTTTAACATC
1 ATTTTAACATC
1965188 CAACCAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTTAACATCATTAAAACTA
Found at i:1965436 original size:17 final size:17
Alignment explanation
Indices: 1965414--1965446 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1965404 AAAAACATAT
1965414 ACTTAA-TAGAAATAAAC
1 ACTTAAGTA-AAATAAAC
1965431 ACTTAAGTAAAATAAA
1 ACTTAAGTAAAATAAA
1965447 TTACCATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.61, C:0.09, G:0.06, T:0.24
Consensus pattern (17 bp):
ACTTAAGTAAAATAAAC
Found at i:1967337 original size:89 final size:89
Alignment explanation
Indices: 1967233--1967414 Score: 330
Period size: 89 Copynumber: 2.0 Consensus size: 89
1967223 ACAAGTAGTA
1967233 TTAAGATTGTAACTTTTCAAATTTAAGTATT-AAAGAATTTTACTCTAATTCAAGTATCAAATGT
1 TTAAGATTGTAACTTTTCAAATTTAAGT-TTCAAAGAATTTTACTCTAATTCAAGTATCAAATGT
* *
1967297 GTAATTAATCTTTGAAGTTTAACAC
65 GTAATTAATCTTTAAAGCTTAACAC
1967322 TTAAGATTGTAACTTTTCAAATTTAAGTTTCAAAGAATTTTACTCTAATTCAAGTATCAAATGTG
1 TTAAGATTGTAACTTTTCAAATTTAAGTTTCAAAGAATTTTACTCTAATTCAAGTATCAAATGTG
1967387 TAATTAATCTTTAAAGCTTAACAC
66 TAATTAATCTTTAAAGCTTAACAC
1967411 TTAA
1 TTAA
1967415 TTTTTCAATA
Statistics
Matches: 90, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
88 2 0.02
89 88 0.98
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.41
Consensus pattern (89 bp):
TTAAGATTGTAACTTTTCAAATTTAAGTTTCAAAGAATTTTACTCTAATTCAAGTATCAAATGTG
TAATTAATCTTTAAAGCTTAACAC
Found at i:1968843 original size:9 final size:9
Alignment explanation
Indices: 1968829--1968853 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1968819 GTGTGGTGAG
1968829 CTTTTGACA
1 CTTTTGACA
1968838 CTTTTGACA
1 CTTTTGACA
1968847 CTTTTGA
1 CTTTTGA
1968854 TATTTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (9 bp):
CTTTTGACA
Found at i:1968985 original size:25 final size:27
Alignment explanation
Indices: 1968937--1969001 Score: 91
Period size: 25 Copynumber: 2.5 Consensus size: 27
1968927 TATAATAAAC
*
1968937 TTATAAATAAATAAAGTTATTATTATA
1 TTATAAATTAATAAAGTTATTATTATA
1968964 TTATAAATTAA-AAA-TTATTATTATA
1 TTATAAATTAATAAAGTTATTATTATA
*
1968989 -TAAAAATTAATAA
1 TTATAAATTAATAA
1969002 CTAAATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 9 0.26
25 13 0.37
26 3 0.09
27 10 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (27 bp):
TTATAAATTAATAAAGTTATTATTATA
Found at i:1969178 original size:19 final size:20
Alignment explanation
Indices: 1969156--1969198 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1969146 TTTTACATAA
*
1969156 AAATAATTTACTGATTTT-T
1 AAATAATTTACTAATTTTAT
* *
1969175 AAATTATTTATTAATTTTAT
1 AAATAATTTACTAATTTTAT
1969195 AAAT
1 AAAT
1969199 GTTAAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
AAATAATTTACTAATTTTAT
Found at i:1974454 original size:1 final size:1
Alignment explanation
Indices: 1974450--1974476 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
1974440 AGAGATTAGG
1974450 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1974477 ACATTTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1978129 original size:40 final size:40
Alignment explanation
Indices: 1978067--1978158 Score: 130
Period size: 40 Copynumber: 2.2 Consensus size: 40
1978057 AACAAGACTT
* *
1978067 GGAATGATATTAAGAAAGAAGCCATAATTTGTATAATTCAAA
1 GGAAT-ATA-TAAGAAAAAAGCCATAATTTGGATAATTCAAA
* *
1978109 GGAATATATAAGAAAAAAGCCATGATTTGGATAGTTCAAA
1 GGAATATATAAGAAAAAAGCCATAATTTGGATAATTCAAA
1978149 GGAATATATA
1 GGAATATATA
1978159 TTTTGTTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 38 0.83
41 3 0.07
42 5 0.11
ACGTcount: A:0.48, C:0.07, G:0.18, T:0.27
Consensus pattern (40 bp):
GGAATATATAAGAAAAAAGCCATAATTTGGATAATTCAAA
Found at i:1978808 original size:17 final size:17
Alignment explanation
Indices: 1978786--1978818 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1978776 TATAAATTAT
1978786 ATTAGCTAGCATGAATA
1 ATTAGCTAGCATGAATA
1978803 ATTAGCTAGCATGAAT
1 ATTAGCTAGCATGAAT
1978819 GTTCAGGCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (17 bp):
ATTAGCTAGCATGAATA
Found at i:1979296 original size:38 final size:39
Alignment explanation
Indices: 1979217--1979298 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 39
1979207 AAAAACAGAG
* ***
1979217 TTTTTTAATATTAGATTACGATTTTTTTAAAAATTGTAGT
1 TTTTTTAATATTAGA-TACGATTTTTTCAAAAATCAAAGT
*
1979257 TTTTTTAATATTAGA-CCGATTTTTTCAAAAATCAAAGT
1 TTTTTTAATATTAGATACGATTTTTTCAAAAATCAAAGT
1979295 TTTT
1 TTTT
1979299 AGGTATATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 22 0.59
40 15 0.41
ACGTcount: A:0.33, C:0.06, G:0.09, T:0.52
Consensus pattern (39 bp):
TTTTTTAATATTAGATACGATTTTTTCAAAAATCAAAGT
Found at i:1980211 original size:15 final size:15
Alignment explanation
Indices: 1980192--1980227 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1980182 TTAAAATTAA
1980192 ATTATAAATTATTATT
1 ATTATAAATT-TTATT
1980208 -TTATAAATTTTATT
1 ATTATAAATTTTATT
1980222 ATTATA
1 ATTATA
1980228 TAAAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTATAAATTTTATT
Found at i:1981980 original size:15 final size:15
Alignment explanation
Indices: 1981959--1981995 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1981949 TTAAAATTGA
1981959 ATTATAAATTATTATT
1 ATTATAAATT-TTATT
1981975 -TTATAAATTTTATT
1 ATTATAAATTTTATT
1981989 ATTATAA
1 ATTATAA
1981996 TTAATTAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTATAAATTTTATT
Found at i:1982174 original size:19 final size:20
Alignment explanation
Indices: 1982152--1982194 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
1982142 ATTTGACATA
*
1982152 AAATAATTTATTGATTTT-T
1 AAATAATTTATTAATTTTGT
1982171 AAATAATTTATTAATTTTGT
1 AAATAATTTATTAATTTTGT
1982191 AAAT
1 AAAT
1982195 TTTAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
AAATAATTTATTAATTTTGT
Found at i:1987303 original size:15 final size:12
Alignment explanation
Indices: 1987273--1987309 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1987263 CTATCTTTTT
1987273 CTACTACAGTGA
1 CTACTACAGTGA
1987285 CTACTACAGTGA
1 CTACTACAGTGA
*
1987297 CTGCTACAGTGA
1 CTACTACAGTGA
1987309 C
1 C
1987310 ATTTATCTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (12 bp):
CTACTACAGTGA
Found at i:1990532 original size:17 final size:17
Alignment explanation
Indices: 1990506--1990540 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1990496 AGATAATCCT
*
1990506 AAATTTTTCAAATAATA
1 AAATTATTCAAATAATA
*
1990523 AAATTATTCAAATTATA
1 AAATTATTCAAATAATA
1990540 A
1 A
1990541 TTGAAACTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATTATTCAAATAATA
Found at i:1999252 original size:5 final size:5
Alignment explanation
Indices: 1999244--1999271 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1999234 AATAAAATAA
1999244 TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TAT
1999272 AATTTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:2001727 original size:59 final size:59
Alignment explanation
Indices: 2001653--2001807 Score: 224
Period size: 59 Copynumber: 2.6 Consensus size: 59
2001643 TTAATTTTTT
*
2001653 GTTATAAATTTGTTGAAATTTGTTT-GGATTTTGGTTACCAATGTGTTAAGTTTTTGTTA
1 GTTATATATTTGTTGAAATTTGTTTAGG-TTTTGGTTACCAATGTGTTAAGTTTTTGTTA
* * *
2001712 GTTA-ATTATTTGTTGAAATTTTTTTAGGTTTTGGTTACCAATTTGTTGAGTTTTTGTTA
1 GTTATA-TATTTGTTGAAATTTGTTTAGGTTTTGGTTACCAATGTGTTAAGTTTTTGTTA
* *
2001771 GTTCTATGTTTGTTGAAATTTGTTTAGGTTTTGGTTA
1 GTTATATATTTGTTGAAATTTGTTTAGGTTTTGGTTA
2001808 TATATTTGTT
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
58 1 0.01
59 82 0.95
60 3 0.03
ACGTcount: A:0.21, C:0.03, G:0.21, T:0.55
Consensus pattern (59 bp):
GTTATATATTTGTTGAAATTTGTTTAGGTTTTGGTTACCAATGTGTTAAGTTTTTGTTA
Found at i:2001793 original size:36 final size:33
Alignment explanation
Indices: 2001751--2001828 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
2001741 TTTGGTTACC
* * * *
2001751 AATTTGTTGAGTTTTTGTTAGTTCTATGTTTGTTGA
1 AATTTGTTGAGGTTTTG---GTTATATATTTGTTAA
*
2001787 AATTTGTTTAGGTTTTGGTTATATATTTGTTAA
1 AATTTGTTGAGGTTTTGGTTATATATTTGTTAA
2001820 AATTTGTTG
1 AATTTGTTG
2001829 GTGATATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
33 21 0.58
36 15 0.42
ACGTcount: A:0.21, C:0.01, G:0.21, T:0.58
Consensus pattern (33 bp):
AATTTGTTGAGGTTTTGGTTATATATTTGTTAA
Found at i:2003233 original size:22 final size:22
Alignment explanation
Indices: 2003205--2003261 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
2003195 TCAAAAATTT
*
2003205 TGAATCTTTGAAATTTTGGATG
1 TGAATCTTTGAAATTTTGAATG
* *
2003227 TGAATCTCT-AATTTTTTGAATG
1 TGAATCTTTGAA-ATTTTGAATG
2003249 TGAATCTTTGAAA
1 TGAATCTTTGAAA
2003262 CTTCATATGA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
21 2 0.07
22 24 0.86
23 2 0.07
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.46
Consensus pattern (22 bp):
TGAATCTTTGAAATTTTGAATG
Found at i:2003390 original size:45 final size:45
Alignment explanation
Indices: 2003207--2003496 Score: 218
Period size: 44 Copynumber: 6.5 Consensus size: 45
2003197 AAAAATTTTG
**
2003207 AATCTTTGAAATTTTGGATGTGAATCTCT-AATTTTTTGAATGTG
1 AATCTTTGAAATTTTGGATGTGAATCTCTAAATTTTTTGAATGAA
* *** ** * *
2003251 AATCTTTGAAACTTCATATGAAAATTTCTTAAAATTTTTT-AAT-ATG
1 AATCTTTGAAATTTTGGATGTGAATCTC-T-AAATTTTTTGAATGA-A
* * * ** *
2003297 AATTTTTGAAATTTT-GATGTGAAT-TGCTAAAACTCTTCAAATGTA
1 AATCTTTGAAATTTTGGATGTGAATCT-CT-AAATTTTTTGAATGAA
** *
2003342 AATCTTTGAAATTTTTTATGTGAATCTCTAAGTTTTTTGAATGAA
1 AATCTTTGAAATTTTGGATGTGAATCTCTAAATTTTTTGAATGAA
* * * ** *
2003387 AATCTTT-AACTTTTGGATGTGAATCCCAAAATTTTTCAAATGAG
1 AATCTTTGAAATTTTGGATGTGAATCTCTAAATTTTTTGAATGAA
* *
2003431 AATCTTTGAAATTTGGGATGTGAA--TCTAAGTTTTTTGAATGAA
1 AATCTTTGAAATTTTGGATGTGAATCTCTAAATTTTTTGAATGAA
* *
2003474 AACCTTTGAAACTTTGGATGTGA
1 AATCTTTGAAATTTTGGATGTGA
2003497 GACCCTAAAA
Statistics
Matches: 189, Mismatches: 47, Indels: 21
0.74 0.18 0.08
Matches are distributed among these distances:
43 33 0.17
44 65 0.34
45 56 0.30
46 26 0.14
47 9 0.05
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (45 bp):
AATCTTTGAAATTTTGGATGTGAATCTCTAAATTTTTTGAATGAA
Found at i:2003401 original size:89 final size:87
Alignment explanation
Indices: 2003308--2003529 Score: 234
Period size: 89 Copynumber: 2.5 Consensus size: 87
2003298 ATTTTTGAAA
* * ***
2003308 TTTTGATGTGAATTGCTAAAACTCTTCAAATGTA-AATCTTTGAAATTTTTTATGTGAATCTCTA
1 TTTTGATGTGAA-TCCCAAAACTCTTCAAATG-AGAATCTTTGAAATTTGGGATGTGAA--TCTA
*
2003372 AGTTTTTTGAATGAAAATCTTT-AAC
62 AGTTTTTTGAATGAAAACCTTTAAAC
* *
2003397 TTTTGGATGTGAATCCCAAAATTTTTCAAATGAGAATCTTTGAAATTTGGGATGTGAATCTAAGT
1 TTTT-GATGTGAATCCCAAAACTCTTCAAATGAGAATCTTTGAAATTTGGGATGTGAATCTAAGT
2003462 TTTTTGAATGAAAACCTTTGAAAC
65 TTTTTGAATGAAAACCTTT-AAAC
* * * * *
2003486 TTTGGATGTGAGA-CCCTAAAATTTTTCAAATGATAATATTTGAA
1 TTTTGATGTGA-ATCCC-AAAACTCTTCAAATGAGAATCTTTGAA
2003530 TTTTTCTATA
Statistics
Matches: 116, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
87 25 0.22
88 11 0.09
89 72 0.62
90 8 0.07
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (87 bp):
TTTTGATGTGAATCCCAAAACTCTTCAAATGAGAATCTTTGAAATTTGGGATGTGAATCTAAGTT
TTTTGAATGAAAACCTTTAAAC
Found at i:2003481 original size:43 final size:43
Alignment explanation
Indices: 2003336--2003496 Score: 171
Period size: 43 Copynumber: 3.7 Consensus size: 43
2003326 AAACTCTTCA
* **
2003336 AATGTAAATCTTTGAAATTTTTTATGTGAATCTCTAAGTTTTTTG
1 AATGAAAATCTTTGAAATTTTGGATGTGAA--TCTAAGTTTTTTG
* * * **
2003381 AATGAAAATCTTT-AACTTTTGGATGTGAATCCCAAAATTTTTCA
1 AATGAAAATCTTTGAAATTTTGGATGTGAAT--CTAAGTTTTTTG
* *
2003425 AATGAGAATCTTTGAAATTTGGGATGTGAATCTAAGTTTTTTG
1 AATGAAAATCTTTGAAATTTTGGATGTGAATCTAAGTTTTTTG
* *
2003468 AATGAAAACCTTTGAAACTTTGGATGTGA
1 AATGAAAATCTTTGAAATTTTGGATGTGA
2003497 GACCCTAAAA
Statistics
Matches: 94, Mismatches: 19, Indels: 8
0.78 0.16 0.07
Matches are distributed among these distances:
42 1 0.01
43 33 0.35
44 33 0.35
45 27 0.29
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.42
Consensus pattern (43 bp):
AATGAAAATCTTTGAAATTTTGGATGTGAATCTAAGTTTTTTG
Found at i:2003809 original size:61 final size:61
Alignment explanation
Indices: 2003734--2003864 Score: 181
Period size: 61 Copynumber: 2.1 Consensus size: 61
2003724 AAGTTTTACG
* * ** * *
2003734 AATCTTTCAATTCTTGTGAATCTAAAACTCTTATGAATTTTTGCGAATCTCAATTCTTAAA
1 AATCTTCCAATTCTTGTGAATCTAAAACTCTTAAGAATTCCTGCAAATCTAAATTCTTAAA
* **
2003795 AATCTTCCCATTCTTGTGAATCTAAAACTCTTAAGAATTCCTGCAAATCTAAATTCTTATG
1 AATCTTCCAATTCTTGTGAATCTAAAACTCTTAAGAATTCCTGCAAATCTAAATTCTTAAA
2003856 AATCTTCCA
1 AATCTTCCA
2003865 CTCTGCGAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.40
Consensus pattern (61 bp):
AATCTTCCAATTCTTGTGAATCTAAAACTCTTAAGAATTCCTGCAAATCTAAATTCTTAAA
Found at i:2003937 original size:18 final size:18
Alignment explanation
Indices: 2003914--2003959 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
2003904 GAAAATCTTA
* *
2003914 AATCTTGGAACCTTTGCG
1 AATCTTGGAACCTCTACG
* *
2003932 AATCTTGAAACCTCTATG
1 AATCTTGGAACCTCTACG
2003950 AATCTTGGAA
1 AATCTTGGAA
2003960 TTTTTAATAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (18 bp):
AATCTTGGAACCTCTACG
Found at i:2004014 original size:18 final size:17
Alignment explanation
Indices: 2003991--2004025 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2003981 TCACAAACTT
*
2003991 TTGAAATTTTTGCGAAAC
1 TTGAAATTCTTGC-AAAC
2004009 TTGAAATTCTTGCAAAC
1 TTGAAATTCTTGCAAAC
2004026 CTTTGTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (17 bp):
TTGAAATTCTTGCAAAC
Found at i:2010634 original size:23 final size:25
Alignment explanation
Indices: 2010576--2010642 Score: 68
Period size: 27 Copynumber: 2.7 Consensus size: 25
2010566 AGTATATAAA
*
2010576 ATTTTATTAAATAATATAAATTATT
1 ATTTTATTAAATAAAATAAATTATT
* *
2010601 ATTTTAGATTAATTAAAATCAA-TA-T
1 ATTTT--ATTAAATAAAATAAATTATT
2010626 ATTTTATTAAA-AAAATA
1 ATTTTATTAAATAAAATA
2010643 TATATTAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
22 5 0.14
23 5 0.14
25 11 0.31
26 2 0.06
27 12 0.34
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (25 bp):
ATTTTATTAAATAAAATAAATTATT
Found at i:2018152 original size:17 final size:17
Alignment explanation
Indices: 2018130--2018165 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2018120 AGAAGTTAAA
*
2018130 AAAGAAAAAAATTATTT
1 AAAGAAAAAAATGATTT
2018147 AAAGAAAAAAATGATTT
1 AAAGAAAAAAATGATTT
2018164 AA
1 AA
2018166 TGATTTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (17 bp):
AAAGAAAAAAATGATTT
Found at i:2018898 original size:25 final size:25
Alignment explanation
Indices: 2018851--2018899 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2018841 TTCTTTAAAC
*
2018851 AAATAAAAACATATTTGACATATTA
1 AAATAAAAACATATTTCACATATTA
*
2018876 AAATAAAATAGATATTTCA-ATATT
1 AAATAAAA-ACATATTTCACATATT
2018900 CAACAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (25 bp):
AAATAAAAACATATTTCACATATTA
Found at i:2020089 original size:20 final size:22
Alignment explanation
Indices: 2020066--2020105 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2020056 TAAAATATAT
2020066 TTATT-AAATTAAA-AAATTAA
1 TTATTAAAATTAAATAAATTAA
2020086 TTATTAAAATTAAATAAATT
1 TTATTAAAATTAAATAAATT
2020106 CATGCCAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 8 0.44
22 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTATTAAAATTAAATAAATTAA
Found at i:2022667 original size:20 final size:19
Alignment explanation
Indices: 2022638--2022683 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
2022628 CTTCTTACAC
* *
2022638 TTTTTAATTATTTGGTGTTA
1 TTTTTTATTATTT-GTCTTA
*
2022658 TTTTTTATTATTTTTCTTA
1 TTTTTTATTATTTGTCTTA
2022677 TTTTTTA
1 TTTTTTA
2022684 AAATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (19 bp):
TTTTTTATTATTTGTCTTA
Found at i:2022829 original size:3 final size:3
Alignment explanation
Indices: 2022821--2022879 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
2022811 TATTGTTTTC
2022821 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2022869 ATT ATT ATT AT
1 ATT ATT ATT AT
2022880 ATAAAAACAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2024614 original size:84 final size:84
Alignment explanation
Indices: 2024486--2024707 Score: 232
Period size: 84 Copynumber: 2.7 Consensus size: 84
2024476 GAAACAAAGC
* * * * * ** *
2024486 AAATTCAACTTAAAAAATTTACGAATCCTATCTAAAAGACTTAGAGCTTATGCT-TAGAGCTCTT
1 AAATTCAACTCAGAAAACTTACGAATCTTACCCGAAAGACTTAGAGATTATGCTCTAGAGCTCTT
2024550 ACAAATCTCAAAACTAAAAT
66 ACAAATCT-AAAACTAAAAT
* * * * * * *
2024570 AAATTCAGCTCAGAAAACTTATGAATCTTGCCCGGAGGACTTAGAGATTATG-TCTAGGGGTCTT
1 AAATTCAACTCAGAAAACTTACGAATCTTACCCGAAAGACTTAGAGATTATGCTCTAGAGCTCTT
* *
2024634 ATAAATCTAGAACTAAAAT
66 ACAAATCTAAAACTAAAAT
* * * *
2024653 AGATTTAACTCAGAATACTTACGAATCTTACCCGAAAAACTTAGAGATTATGCTC
1 AAATTCAACTCAGAAAACTTACGAATCTTACCCGAAAGACTTAGAGATTATGCTC
2024708 AAAGGTTTTA
Statistics
Matches: 110, Mismatches: 26, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
83 54 0.49
84 56 0.51
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.29
Consensus pattern (84 bp):
AAATTCAACTCAGAAAACTTACGAATCTTACCCGAAAGACTTAGAGATTATGCTCTAGAGCTCTT
ACAAATCTAAAACTAAAAT
Found at i:2025175 original size:24 final size:24
Alignment explanation
Indices: 2025143--2025191 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2025133 AGCTTAGGTC
2025143 TTATCTTGCATCGTATTTCATTTT
1 TTATCTTGCATCGTATTTCATTTT
2025167 TTATCTTGCATCGTATTTCATTTT
1 TTATCTTGCATCGTATTTCATTTT
2025191 T
1 T
2025192 CTTACTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.59
Consensus pattern (24 bp):
TTATCTTGCATCGTATTTCATTTT
Found at i:2034350 original size:15 final size:15
Alignment explanation
Indices: 2034332--2034365 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2034322 AAACCACACA
*
2034332 ACAATGTCACAAGCC
1 ACAAAGTCACAAGCC
2034347 ACAAAGTCACAAGCC
1 ACAAAGTCACAAGCC
2034362 ACAA
1 ACAA
2034366 GAGAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.32, G:0.12, T:0.09
Consensus pattern (15 bp):
ACAAAGTCACAAGCC
Found at i:2041952 original size:21 final size:20
Alignment explanation
Indices: 2041928--2041980 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 20
2041918 TGCCTTACCC
2041928 GATCGATCCCTTGCTTTAGGG
1 GATCGATCCCTT-CTTTAGGG
* ** *
2041949 GATCAATCTGTTCTTTAGGT
1 GATCGATCCCTTCTTTAGGG
2041969 GATCGATTCCCT
1 GATCGA-TCCCT
2041981 ATGTGGGGGG
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
GATCGATCCCTTCTTTAGGG
Found at i:2043187 original size:60 final size:59
Alignment explanation
Indices: 2043060--2043266 Score: 199
Period size: 60 Copynumber: 3.5 Consensus size: 59
2043050 TTGTATAGGA
* * ** * * *
2043060 GAAAATTGATATTTTCAAC-TTCTC-CCCAAAATACTTTTTTAGAAACTTTAATTTCAAG
1 GAAAATTGATACTTTCAACTTTTTCTCAAAAAAAACTTTTTT-GAAAATTTATTTTCAAG
*
2043118 GAAAATTGATACTTTCAACTTTTTCTCAAAAAAAACCTTTTTTGAAAATTTATTTTTAAG
1 GAAAATTGATACTTTCAACTTTTTCTCAAAAAAAA-CTTTTTTGAAAATTTATTTTCAAG
* ** * * **
2043178 AAAAATTGATACTTTCAACTTTCCCTC-AAAAATA-TTTTTGGAAAGCTTATTTTCAAG
1 GAAAATTGATACTTTCAACTTTTTCTCAAAAAAAACTTTTTTGAAAATTTATTTTCAAG
* *
2043235 GAAAATTAACACTTTCAAC-TTTTCTTCAAAAA
1 GAAAATTGATACTTTCAACTTTTTC-TCAAAAA
2043267 TATTTTTTTT
Statistics
Matches: 123, Mismatches: 21, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
56 3 0.02
57 37 0.30
58 22 0.18
59 10 0.08
60 44 0.36
61 7 0.06
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (59 bp):
GAAAATTGATACTTTCAACTTTTTCTCAAAAAAAACTTTTTTGAAAATTTATTTTCAAG
Found at i:2043240 original size:57 final size:57
Alignment explanation
Indices: 2043060--2043274 Score: 211
Period size: 57 Copynumber: 3.7 Consensus size: 57
2043050 TTGTATAGGA
* *
2043060 GAAAATTGATATTTTCAACTTCTCCC-C-AAAATACTTTTTTAGAAACTTTAATTTCAAG
1 GAAAATTGATACTTTCAACTT-TCCCTCAAAAATAC-TTTTTAGAAAC-TTATTTTCAAG
** * * * *
2043118 GAAAATTGATACTTTCAACTTTTTCTCAAAAAAAACCTTTTTTGAAAATTTATTTTTAAG
1 GAAAATTGATACTTTCAACTTTCCCTC-AAAAATA-CTTTTTAG-AAACTTATTTTCAAG
* *
2043178 AAAAATTGATACTTTCAACTTTCCCTCAAAAATA-TTTTTGGAAAGCTTATTTTCAAG
1 GAAAATTGATACTTTCAACTTTCCCTCAAAAATACTTTTTAGAAA-CTTATTTTCAAG
* * * * *
2043235 GAAAATTAACACTTTCAACTTTTCTTCAAAAATATTTTTT
1 GAAAATTGATACTTTCAACTTTCCCTCAAAAATACTTTTT
2043275 TTTAATTTTA
Statistics
Matches: 130, Mismatches: 20, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
56 3 0.02
57 47 0.36
58 26 0.20
59 6 0.05
60 44 0.34
61 4 0.03
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (57 bp):
GAAAATTGATACTTTCAACTTTCCCTCAAAAATACTTTTTAGAAACTTATTTTCAAG
Found at i:2043328 original size:3 final size:3
Alignment explanation
Indices: 2043316--2043353 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
2043306 TAAACAATTC
2043316 TAA T-A 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
2043354 ATAAACAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2043608 original size:19 final size:17
Alignment explanation
Indices: 2043584--2043618 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 17
2043574 AGCAGAACCC
2043584 TCCTTCCCTCTCTCTCTCT
1 TCCTT-CCTCT-TCTCTCT
2043603 TCCTTCCTCTTCTCTC
1 TCCTTCCTCTTCTCTC
2043619 CTTTCTCTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (17 bp):
TCCTTCCTCTTCTCTCT
Found at i:2044148 original size:12 final size:12
Alignment explanation
Indices: 2044128--2044167 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
2044118 GGTAAAGGAT
* *
2044128 AAAAGAAAAGAA
1 AAAATAAAATAA
2044140 AAAATAAAATAA
1 AAAATAAAATAA
*
2044152 ATAATAAAATAA
1 AAAATAAAATAA
2044164 AAAA
1 AAAA
2044168 GATAATAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:2044160 original size:17 final size:16
Alignment explanation
Indices: 2044140--2044359 Score: 93
Period size: 17 Copynumber: 13.2 Consensus size: 16
2044130 AAGAAAAGAA
2044140 AAAATAAAATAAATAAT
1 AAAAT-AAATAAATAAT
*
2044157 AAAATAAA-AAA-GAT
1 AAAATAAATAAATAAT
*
2044171 AATAATAAGGATAATATATT
1 AA-AATAA--ATAA-ATAAT
*
2044191 AATTAATAGATAAATAAT
1 AA--AATAAATAAATAAT
*
2044209 AATAATAGATAAATAAT
1 AA-AATAAATAAATAAT
*
2044226 AATAATATATAAATAGAT
1 AA-AATAAATAAATA-AT
2044244 -AAAT-AATAATAATAAT
1 AAAATAAAT-A-AATAAT
2044260 AAAAATAAAATAATATATAT
1 -AAAAT-AAATAA-ATA-AT
* *
2044280 ATTAATAAATAGTATAAT
1 A-AAATAAATA-AATAAT
2044298 -AAATAAATAAATAAT
1 AAAATAAATAAATAAT
* *
2044313 -AAATACATAAA-ATAC
1 AAAATAAATAAATA-AT
*
2044328 AAAATAAA-GAA-AAT
1 AAAATAAATAAATAAT
*
2044342 AAAATCAA-AAAT-AT
1 AAAATAAATAAATAAT
2044356 AAAA
1 AAAA
2044360 ATATAAGAAA
Statistics
Matches: 164, Mismatches: 18, Indels: 45
0.72 0.08 0.20
Matches are distributed among these distances:
14 21 0.13
15 29 0.18
16 23 0.14
17 40 0.24
18 17 0.10
19 18 0.11
20 11 0.07
21 5 0.03
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (16 bp):
AAAATAAATAAATAAT
Found at i:2044175 original size:3 final size:3
Alignment explanation
Indices: 2044142--2044314 Score: 90
Period size: 3 Copynumber: 54.7 Consensus size: 3
2044132 GAAAAGAAAA
* * *
2044142 AAT AA- AAT AAAT AAT AA- AAT AA- AAA AGAT AAT AAT AAG GAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
*
2044186 -AT ATT AATT AAT AGAT AAAT AAT AAT AAT AGAT AAAT AAT AAT AAT
1 AAT AAT AA-T AAT A-AT -AAT AAT AAT AAT A-AT -AAT AAT AAT AAT
*
2044232 ATAT AAAT AGAT AAAT AAT AAT AAT AAT AAA AAT AA- AAT AAT -AT ATAT
1 A-AT -AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* *
2044280 ATT AAT AAAT AGT -AT AAT AAAT AAAT AAAT AAT AA
1 AAT AAT -AAT AAT AAT AAT -AAT -AAT -AAT AAT AA
2044315 ATACATAAAA
Statistics
Matches: 136, Mismatches: 13, Indels: 42
0.71 0.07 0.22
Matches are distributed among these distances:
2 13 0.10
3 78 0.57
4 41 0.30
5 4 0.03
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2044207 original size:4 final size:4
Alignment explanation
Indices: 2044195--2044323 Score: 57
Period size: 4 Copynumber: 34.5 Consensus size: 4
2044185 TATATTAATT
* * *
2044195 AATA GATA AAT- AAT- AAT- AATA GATA AAT- AAT- AAT- AATA TATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* * * * *
2044237 AATA GATA AAT- AAT- AAT- AATA ATAAA AATA AA-A TAATA TATA TATT
1 AATA AATA AATA AATA AATA AATA A-ATA AATA AATA -AATA AATA AATA
* *
2044283 AATA AAT- AGTA TAATA AATA AATA AAT- AATA AATA CATA AA
1 AATA AATA AATA -AATA AATA AATA AATA AATA AATA AATA AA
2044324 ATACAAAATA
Statistics
Matches: 98, Mismatches: 18, Indels: 18
0.73 0.13 0.13
Matches are distributed among these distances:
3 33 0.34
4 58 0.59
5 7 0.07
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (4 bp):
AATA
Found at i:2044250 original size:42 final size:41
Alignment explanation
Indices: 2044169--2044323 Score: 149
Period size: 42 Copynumber: 3.7 Consensus size: 41
2044159 AATAAAAAAG
* *
2044169 ATAATAATAAGGATAAT-ATATTA-ATTAATAGATAAATAATA
1 ATAATAATAA--ATAATAATAATATATAAATAGATAAATAATA
2044210 ATAATAGATAAATAATAATAATATATAAATAGATAAATAATA
1 ATAATA-ATAAATAATAATAATATATAAATAGATAAATAATA
* *
2044252 ATAATAATAAA-AATAAAATAATATATATATTA-ATAAATAGT-
1 ATAATAATAAATAAT--AATAATATATA-AATAGATAAATAATA
*
2044293 ATAATAAATAAATAAATAATAAATACATAAA
1 ATAAT-AATAAAT-AATAAT-AATATATAAA
2044324 ATACAAAATA
Statistics
Matches: 98, Mismatches: 6, Indels: 19
0.80 0.05 0.15
Matches are distributed among these distances:
40 8 0.08
41 21 0.21
42 56 0.57
43 10 0.10
44 3 0.03
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.32
Consensus pattern (41 bp):
ATAATAATAAATAATAATAATATATAAATAGATAAATAATA
Found at i:2044271 original size:20 final size:20
Alignment explanation
Indices: 2044139--2044354 Score: 94
Period size: 21 Copynumber: 10.3 Consensus size: 20
2044129 AAAGAAAAGA
2044139 AAAAATAAAAT-A-AATAAT
1 AAAAATAAAATAATAATAAT
*
2044157 -AAAATAAAAAAGATAATAAT
1 AAAAATAAAATA-ATAATAAT
** * *
2044177 AAGGATAATATATTAAT--T
1 AAAAATAAAATAATAATAAT
*
2044195 AATAGAT-AAATAATAATAAT
1 AA-AAATAAAATAATAATAAT
2044215 AGATAAAT--AATAATAATATAT
1 A-A-AAATAAAATAATAATA-AT
2044236 AAATAGATAAATAATAATAATAAT
1 AAA-A-AT-AA-AATAATAATAAT
2044260 AAAAATAAAATAATATATATATT
1 AAAAATAAAATAATA-ATA-A-T
**
2044283 AATAAATAGTATAATAAATAAAT
1 AA-AAATAAAATAAT-AAT-AAT
2044306 AAATAAT-AAATACATAA-AAT
1 AAA-AATAAAATA-ATAATAAT
*
2044326 ACAAAATAAAGAAAATAA-AAT
1 A-AAAATAAA-ATAATAATAAT
2044347 CAAAAATA
1 -AAAAATA
2044355 TAAAAATATA
Statistics
Matches: 156, Mismatches: 15, Indels: 51
0.70 0.07 0.23
Matches are distributed among these distances:
17 9 0.06
18 11 0.07
19 5 0.03
20 38 0.24
21 39 0.25
22 12 0.08
23 12 0.08
24 18 0.12
25 12 0.08
ACGTcount: A:0.68, C:0.01, G:0.04, T:0.27
Consensus pattern (20 bp):
AAAAATAAAATAATAATAAT
Found at i:2044352 original size:21 final size:20
Alignment explanation
Indices: 2044298--2044376 Score: 56
Period size: 21 Copynumber: 3.8 Consensus size: 20
2044288 ATAGTATAAT
*
2044298 AAAT-AAATA-AATAATAAAT
1 AAATAAAATACAA-AATAAAA
*
2044317 ACATAAAATACAAAATAAAGA
1 AAATAAAATACAAAATAAA-A
2044338 AAATAAAAT-CAAAAATATAAA
1 AAATAAAATAC-AAAATA-AAA
2044359 AATATAAGAAATACAAAA
1 AA-AT-A-AAATACAAAA
2044377 ATACAAAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 3 0.06
20 12 0.25
21 19 0.40
22 4 0.08
23 1 0.02
24 8 0.17
25 1 0.02
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (20 bp):
AAATAAAATACAAAATAAAA
Found at i:2044361 original size:8 final size:8
Alignment explanation
Indices: 2044313--2044384 Score: 55
Period size: 8 Copynumber: 9.2 Consensus size: 8
2044303 AATAAATAAT
2044313 AAATACATA
1 AAATACA-A
2044322 AAATAC-A
1 AAATACAA
2044329 AAATA-AA
1 AAATACAA
*
2044336 GAAA-A-TA
1 -AAATACAA
2044343 AAAT-CAA
1 AAATACAA
*
2044350 AAATATAA
1 AAATACAA
*
2044358 AAATATAA
1 AAATACAA
2044366 GAAATACAA
1 -AAATACAA
2044375 AAATACAA
1 AAATACAA
2044383 AA
1 AA
2044385 TAAAGTGGGC
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
6 3 0.06
7 14 0.26
8 23 0.43
9 13 0.25
ACGTcount: A:0.74, C:0.07, G:0.03, T:0.17
Consensus pattern (8 bp):
AAATACAA
Found at i:2044708 original size:41 final size:41
Alignment explanation
Indices: 2044571--2045120 Score: 421
Period size: 41 Copynumber: 13.1 Consensus size: 41
2044561 TTGATCAAAA
** * **
2044571 CTCCTCTAAGTAGAGGCTCAACGACTTTGAAAAACATAAACAAAG
1 CTCCTCTAAACAGAGGCTCAACGACTTTG-GAAA-AT-AA-ATGG
* * **
2044616 CTCTTCTAATCAGAGGCTCAACGACTTT-GAAAATGAATAAAG
1 CTCCTCTAAACAGAGGCTCAACGACTTTGGAAAAT-AA-ATGG
* *
2044658 CTCCTCTAAACAGAGGCTCAATGAATTTGGAAAATAAATGG
1 CTCCTCTAAACAGAGGCTCAACGACTTTGGAAAATAAATGG
* * *
2044699 CTCCTCTAAATAGAGGCTCAATGACTTTGAAAAATAAATGG
1 CTCCTCTAAACAGAGGCTCAACGACTTTGGAAAATAAATGG
* * * * *
2044740 CTCATTTAATCAGAGGCATC-ACAACTTTGGAAAATAAATAAAG
1 CTCCTCTAAACAGAGGC-TCAACGACTTTGGAAAATAAAT--GG
* * *
2044783 CTCCTCTAAACAGAGGCTCAATGAATTTGGAAAATAAACGG
1 CTCCTCTAAACAGAGGCTCAACGACTTTGGAAAATAAATGG
* ** * *
2044824 CTCCTTTAATTAGAGGCTCAGCGACTTTGAAAAATAAATGG
1 CTCCTCTAAACAGAGGCTCAACGACTTTGGAAAATAAATGG
* * *
2044865 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATAAAGT
1 CTCCTCTAAACAGAGGCTCAACGACTTTGGAAAATAAAT---GG
* * *
2044909 CTCCTCTAAACAGAGGCATC-ACAACTTTGAAAAATAAATAAAG
1 CTCCTCTAAACAGAGGC-TCAACGACTTTGGAAAATAAAT--GG
* * * * *
2044952 CTCCTCTAAAGAGAGGCACCACGA-TTTTGAAAAGTAAATTG
1 CTCCTCTAAACAGAGGCTCAACGACTTTGGAAAA-TAAATGG
* * * *
2044993 CTCTTCTAAGCAGAGGCATC-ACAACTTTGGAAAATAAATTG
1 CTCCTCTAAACAGAGGC-TCAACGACTTTGGAAAATAAATGG
* * * *
2045034 CTCCTCTAAATAGAGGCACCACGACTTT-GAAAAGTAAATTG
1 CTCCTCTAAACAGAGGCTCAACGACTTTGGAAAA-TAAATGG
* * * * *
2045075 TTCCTCTAAACAGAGGCACCATGACTTT-GAAAAGTAAATTG
1 CTCCTCTAAACAGAGGCTCAACGACTTTGGAAAA-TAAATGG
2045116 CTCCT
1 CTCCT
2045121 TGACAATCAT
Statistics
Matches: 422, Mismatches: 68, Indels: 34
0.81 0.13 0.06
Matches are distributed among these distances:
40 6 0.01
41 234 0.55
42 55 0.13
43 65 0.15
44 35 0.08
45 27 0.06
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.25
Consensus pattern (41 bp):
CTCCTCTAAACAGAGGCTCAACGACTTTGGAAAATAAATGG
Found at i:2044801 original size:125 final size:125
Alignment explanation
Indices: 2044571--2045118 Score: 583
Period size: 125 Copynumber: 4.4 Consensus size: 125
2044561 TTGATCAAAA
* **
2044571 CTCCTCTAAGTAGAGGCTCAACGACTTTGAAAAACATAAACAAAGCTCTTCTAATCAGAGGCTCA
1 CTCCTCTAAATAGAGGCTCAACGACTTTG-AAAA-AT-AA-ATGGCTCTTCTAATCAGAGGCTCA
* *
2044636 ACGACTTT-GAAAATGAATAAAGCTCCTCTAAACAGAGGCTCAATGAATTTGGAAAATAAATGG
62 ACAACTTTGGAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAATGAATTTGGAAAATAAATGG
*
2044699 CTCCTCTAAATAGAGGCTCAATGACTTTGAAAAATAAATGGCTCATT-TAATCAGAGGCATC-AC
1 CTCCTCTAAATAGAGGCTCAACGACTTTGAAAAATAAATGGCTC-TTCTAATCAGAGGC-TCAAC
*
2044762 AACTTTGGAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAATGAATTTGGAAAATAAACGG
64 AACTTTGGAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAATGAATTTGGAAAATAAATGG
* * * * *
2044824 CTCCTTTAATTAGAGGCTCAGCGACTTTGAAAAATAAATGGCTCCTCTAATCAGAGGCTCAACGA
1 CTCCTCTAAATAGAGGCTCAACGACTTTGAAAAATAAATGGCTCTTCTAATCAGAGGCTCAACAA
* * * *
2044889 CTTTGAAAAATAAATAAAGTCTCCTCTAAACAGAGGCATCACA--ACTTTGAAAAATAAATAAAG
66 CTTTGGAAAATAAATAAAG-CTCCTCTAAACAGAGGC-TCA-ATGAATTTGGAAAATAAAT--GG
* * * * * * *
2044952 CTCCTCTAAAGAGAGGCACCACGATTTTGAAAAGTAAATTGCTCTTCTAAGCAGAGGCATC-ACA
1 CTCCTCTAAATAGAGGCTCAACGACTTTGAAAAATAAATGGCTCTTCTAATCAGAGGC-TCAACA
* * * * * * *
2045016 ACTTTGGAAAATAAAT--TGCTCCTCTAAATAGAGGCACCACGACTTT-GAAAAGTAAATTG
65 ACTTTGGAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAATGAATTTGGAAAA-TAAATGG
* * * * * * *
2045075 TTCCTCTAAACAGAGGCACCATGACTTTGAAAAGTAAATTGCTC
1 CTCCTCTAAATAGAGGCTCAACGACTTTGAAAAATAAATGGCTC
2045119 CTTGACAATC
Statistics
Matches: 365, Mismatches: 41, Indels: 33
0.83 0.09 0.08
Matches are distributed among these distances:
123 42 0.12
124 31 0.08
125 157 0.43
126 33 0.09
127 7 0.02
128 93 0.25
129 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.25
Consensus pattern (125 bp):
CTCCTCTAAATAGAGGCTCAACGACTTTGAAAAATAAATGGCTCTTCTAATCAGAGGCTCAACAA
CTTTGGAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAATGAATTTGGAAAATAAATGG
Found at i:2045029 original size:169 final size:163
Alignment explanation
Indices: 2044571--2045113 Score: 558
Period size: 169 Copynumber: 3.2 Consensus size: 163
2044561 TTGATCAAAA
** * * * *
2044571 CTCCTCTAAGTAGAGGC-TCAACGACTTTGAAAAACATAAACAAAGCTCTTCTAATCAGAGGCTC
1 CTCCTCTAAACAGAGGCATC-ACAACTTTG-AAAA-ATAAATAAAGCTCCTCTAAACAGAGGCTC
* * *
2044635 AACGACTTTGAAAATGAATAAAGCTCCTCTAAACAGAGGCTCA-ATGAATTTGGAAAATAAATGG
63 AACGATTTTGAAAA-G--TAAAGCTCTTCTAAACAGAGGCTCACA--ACTTTGGAAAATAAATGG
* *
2044699 CTCCTCTAAATAGAGGCTCAATGACTTTGAAAAATAAATGG
123 CTCCTCTAAATAGAGGCTCAACGACTTTGAAAAATAAATGT
* * * * *
2044740 CTCATTTAATCAGAGGCATCACAACTTTGGAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAAT
1 CTCCTCTAAACAGAGGCATCACAACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAAC
* ** * *
2044805 GAATTTGGAAAA-TAAACGGCTCCTT-TAATTAGAGGCTCAGCGACTTTGAAAAATAAATGGCTC
66 G-ATTTTGAAAAGTAAA--GCT-CTTCTAAACAGAGGCTCA-CAACTTTGGAAAATAAATGGCTC
2044868 CTCT-AATCAGAGGCTCAACGACTTTGAAAAATAAATAAAGT
126 CTCTAAAT-AGAGGCTCAACGACTTTGAAAAATAAAT---GT
* * *
2044909 CTCCTCTAAACAGAGGCATCACAACTTTGAAAAATAAATAAAGCTCCTCTAAAGAGAGGCACCAC
1 CTCCTCTAAACAGAGGCATCACAACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAAC
* *
2044974 GATTTTGAAAAGTAAATTGCTCTTCTAAGCAGAGGCATCACAACTTTGGAAAATAAATTGCTCCT
66 GATTTTGAAAAGTAAA--GCTCTTCTAAACAGAGGC-TCACAACTTTGGAAAATAAATGGCTCCT
* * *
2045039 CTAAATAGAGGCACCACGACTTTGAAAAGTAAATTGT
128 CTAAATAGAGGCTCAACGACTTTGAAAAATAAA-TGT
* ** *
2045076 -TCCTCTAAACAGAGGCACCATGACTTTGAAAAGTAAAT
1 CTCCTCTAAACAGAGGCATCACAACTTTGAAAAATAAAT
2045114 TGCTCCTTGA
Statistics
Matches: 315, Mismatches: 43, Indels: 35
0.80 0.11 0.09
Matches are distributed among these distances:
164 4 0.01
165 3 0.01
166 99 0.31
167 33 0.10
168 23 0.07
169 144 0.46
170 9 0.03
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (163 bp):
CTCCTCTAAACAGAGGCATCACAACTTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAAC
GATTTTGAAAAGTAAAGCTCTTCTAAACAGAGGCTCACAACTTTGGAAAATAAATGGCTCCTCTA
AATAGAGGCTCAACGACTTTGAAAAATAAATGT
Found at i:2051012 original size:61 final size:59
Alignment explanation
Indices: 2050831--2051099 Score: 278
Period size: 60 Copynumber: 4.6 Consensus size: 59
2050821 TTTGTATAGG
* * * * * *
2050831 GAAAAATTGATACTTTCAACTTCTCC-C-CAAAATACTTTTTTAGAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAAACTTTTTT-GAAAATTTATTTTCAA
** * ** *
2050889 GGCAAATTGATACTTTCAACTTTTTCTCAAAAAAAACCTTTTTCAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAAA-CTTTTTTGAAAATTTATTTTCAA
*
2050949 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAAACCCTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAAA--CTTTTTTGAAAATTTATTTTCAA
* * * **
2051010 GAAAAATTAATACTTTCAAC-TTTCTCTC-AAAAATA-TTTTTGGAAAGCTTATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTC-CTCAAAAAAAACTTTTTTGAAAATTTATTTTCAA
* *
2051067 GGAAAATTGATACTTTTAACTTTTCCTCAAAAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAA
2051100 TATTTTTTTT
Statistics
Matches: 178, Mismatches: 26, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
57 38 0.21
58 30 0.17
59 1 0.01
60 59 0.33
61 50 0.28
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (59 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAAACTTTTTTGAAAATTTATTTTCAA
Found at i:2051134 original size:118 final size:119
Alignment explanation
Indices: 2050831--2051099 Score: 298
Period size: 118 Copynumber: 2.3 Consensus size: 119
2050821 TTTGTATAGG
* * * * ** **
2050831 GAAAAATTGATACTTTCAACTTCTCC-C-CAAAATA--CTTTTTTAGAAACTTTAATTTCGAGGC
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAAACCCTTTTTT-GAAA-TTTATTTTTAAGAA
* * * *
2050892 AAATTGATACTTTCAACTTTTTCTCAAAAAAAACCTTTTTCAAAAATTTATTTTTAA
64 AAATTAATACTTTCAACTTTCTCTCAAAAAAAA-CTTTTTCAAAAACTTATTTTCAA
2050949 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAAACCCTTTTTTGAAAATTTATTTTTAAGAAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAAACCCTTTTTTG-AAATTTATTTTTAAGAAA
* ** *
2051014 AATTAATACTTTCAACTTTCTCTC-AAAAATA-TTTTTGGAAAGCTTATTTTCAA
65 AATTAATACTTTCAACTTTCTCTCAAAAAAAACTTTTTCAAAAACTTATTTTCAA
* *
2051067 GGAAAATTGATACTTTTAACTTTTCCTCAAAAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAA
2051100 TATTTTTTTT
Statistics
Matches: 128, Mismatches: 18, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
118 73 0.57
119 1 0.01
120 11 0.09
121 33 0.26
122 10 0.08
ACGTcount: A:0.38, C:0.16, G:0.06, T:0.40
Consensus pattern (119 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAAAAACCCTTTTTTGAAATTTATTTTTAAGAAAA
ATTAATACTTTCAACTTTCTCTCAAAAAAAACTTTTTCAAAAACTTATTTTCAA
Found at i:2051138 original size:4 final size:4
Alignment explanation
Indices: 2051131--2051246 Score: 59
Period size: 4 Copynumber: 28.8 Consensus size: 4
2051121 AAAGAAAAGA
2051131 AAAT AAAT AAAT AAAT -AA- AAAT GAAAAT GAAAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT --AAAT --AAAT AAAT AAAT AAAT
* * * *
2051177 AAAT -AA- AAAT GAAAAT AAA- AAA- AATT AAAC AATT CTAAT ATAAT
1 AAAT AAAT AAAT --AAAT AAAT AAAT AAAT AAAT AAAT -AAAT A-AAT
2051221 -AAT -AAT AATAT AAAT AAAT AAAT AAA
1 AAAT AAAT AA-AT AAAT AAAT AAAT AAA
2051247 CAAAAAAAAA
Statistics
Matches: 91, Mismatches: 8, Indels: 26
0.73 0.06 0.21
Matches are distributed among these distances:
3 19 0.21
4 49 0.54
5 9 0.10
6 14 0.15
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2051174 original size:34 final size:33
Alignment explanation
Indices: 2051131--2051252 Score: 131
Period size: 34 Copynumber: 3.6 Consensus size: 33
2051121 AAAGAAAAGA
2051131 AAATAAATAAATAAATAAAAATGAAAATGAAAAT
1 AAATAAATAAATAAATAAAAATGAAAAT-AAAAT
*
2051165 AAATAAATAAATAAATAAAAATGAAAATAAAAA
1 AAATAAATAAATAAATAAAAATGAAAATAAAAT
* * * * *
2051198 AAATTAAACAATTCTAAT-ATAAT-AATAATAATAT
1 AAA-TAAATAAAT-AAATAAAAATGAA-AATAAAAT
*
2051232 AAATAAATAAATAAACAAAAA
1 AAATAAATAAATAAATAAAAA
2051253 AAAACCTGAG
Statistics
Matches: 72, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
32 2 0.03
33 19 0.26
34 48 0.67
35 3 0.04
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (33 bp):
AAATAAATAAATAAATAAAAATGAAAATAAAAT
Found at i:2052098 original size:12 final size:12
Alignment explanation
Indices: 2052083--2052117 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2052073 AGGAAATAAG
*
2052083 AAAAGAAAAAAT
1 AAAATAAAAAAT
*
2052095 AAAATAAATAAT
1 AAAATAAAAAAT
2052107 AAAATAAAAAA
1 AAAATAAAAAA
2052118 GATAATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:2052124 original size:24 final size:24
Alignment explanation
Indices: 2052076--2052129 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2052066 CGGGTAAAGG
*
2052076 AAATAAGAAAAGAAAAAATAAAAT
1 AAATAAGAAAAGAAAAAAGAAAAT
* * *
2052100 AAATAATAAAATAAAAAAGATAAT
1 AAATAAGAAAAGAAAAAAGAAAAT
2052124 -AATAAG
1 AAATAAG
2052130 GATAATATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (24 bp):
AAATAAGAAAAGAAAAAAGAAAAT
Found at i:2052125 original size:3 final size:3
Alignment explanation
Indices: 2052092--2052301 Score: 114
Period size: 3 Copynumber: 66.7 Consensus size: 3
2052082 GAAAAGAAAA
* * *
2052092 AAT AA- AAT AAAT AAT AA- AAT AA- AAA AGAT AAT AAT AAG GAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
*
2052136 -AT ATT AATT AAT AGAT AAAT AAT AAT AAT AAT AGAT AAAT AAT AAT
1 AAT AAT AA-T AAT A-AT -AAT AAT AAT AAT AAT A-AT -AAT AAT AAT
*
2052182 -AT ATGT AAAT AGAT AAAT AAT AAT AAT AAT AAT ATAT AAAT AGAT AAAT
1 AAT A-AT -AAT A-AT -AAT AAT AAT AAT AAT AAT A-AT -AAT A-AT -AAT
*
2052231 AAT AAT AAT AAT AAT AAT AAAT AA- AAT AA- AA- AAT -AT ATAT ATT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT A-AT AAT
* *
2052274 AAA AAT AGT AAT AAT AAAT AAAT AAT AA
1 AAT AAT AAT AAT AAT -AAT -AAT AAT AA
2052302 ATACATAAAA
Statistics
Matches: 166, Mismatches: 15, Indels: 52
0.71 0.06 0.22
Matches are distributed among these distances:
2 18 0.11
3 99 0.60
4 43 0.26
5 6 0.04
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2052156 original size:44 final size:43
Alignment explanation
Indices: 2052145--2052301 Score: 149
Period size: 40 Copynumber: 3.8 Consensus size: 43
2052135 TATATTAATT
2052145 AATAGATAAATAATAATAATAATAGATAAATAATAATATATGTA
1 AATAGATAAATAATAATAATAATA-ATAAATAATAATATATGTA
2052189 AATAGATAAATAATAATAATAATAAT--AT-ATAA-ATA-GATA
1 AATAGATAAATAATAATAATAATAATAAATAATAATATATG-TA
*
2052228 AATA-AT-AATAATAATAATAATAAATAAAATAA-AA-A-ATATA
1 AATAGATAAATAATAATAATAAT-AAT-AAATAATAATATATGTA
* * *
2052268 TATA-TTAAA-AATAGTAATAATAAATAAATAATAA
1 AATAGATAAATAATAATAATAAT-AATAAATAATAA
2052302 ATACATAAAA
Statistics
Matches: 100, Mismatches: 4, Indels: 22
0.79 0.03 0.17
Matches are distributed among these distances:
37 15 0.15
38 6 0.06
39 15 0.15
40 28 0.28
41 9 0.09
42 1 0.01
43 2 0.02
44 24 0.24
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.31
Consensus pattern (43 bp):
AATAGATAAATAATAATAATAATAATAAATAATAATATATGTA
Found at i:2052179 original size:31 final size:31
Alignment explanation
Indices: 2052097--2052301 Score: 130
Period size: 31 Copynumber: 6.5 Consensus size: 31
2052087 GAAAAAATAA
2052097 AATAAATAATAA-AATAA-AA-AAGAT-AAT
1 AATAAATAATAATAATAATAATAAGATAAAT
*
2052124 AATAAGGATAAT-ATATTAATTAAT-AGATAAAT
1 AATAA--ATAATAATAATAA-TAATAAGATAAAT
2052156 AATAATAATAATAGATAAATAATAATATATG-TAAAT
1 AAT-A-AATAATA-AT-AATAATAATA-A-GATAAAT
*
2052192 AGATAAATAATAATAATAATAAT-ATATAAAT
1 A-ATAAATAATAATAATAATAATAAGATAAAT
2052223 AGATAAATAATAATAATAATAAT-A-ATAAAT
1 A-ATAAATAATAATAATAATAATAAGATAAAT
* *
2052253 AAAATAAAAAAT-ATATATATTAA-AA-ATAGTAAT
1 --AATAAATAATAATA-ATAATAATAAGATA--AAT
2052286 AATAAATAAATAATAA
1 AATAAAT-AATAATAA
2052302 ATACATAAAA
Statistics
Matches: 147, Mismatches: 6, Indels: 45
0.74 0.03 0.23
Matches are distributed among these distances:
27 5 0.03
28 1 0.01
29 9 0.06
30 9 0.06
31 60 0.41
32 16 0.11
33 16 0.11
34 9 0.06
35 11 0.07
36 8 0.05
37 3 0.02
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (31 bp):
AATAAATAATAATAATAATAATAAGATAAAT
Found at i:2052321 original size:31 final size:29
Alignment explanation
Indices: 2052152--2052375 Score: 76
Period size: 31 Copynumber: 7.4 Consensus size: 29
2052142 ATTAATAGAT
*
2052152 AAATAATAAT-AAT-AATAGATAAATAATA
1 AAATAAAAATAAATAAATA-ATAAATAATA
** *
2052180 ATATATGTAAATAGATAAATAAT-AATAATA
1 A-A-ATAAAAATAAATAAATAATAAATAATA
*
2052210 ATAATATATAAATAGATAAATAAT-AATAAT-
1 A-AATA-A-AAATAAATAAATAATAAATAATA
* *
2052240 -AATAATAATAAATAAAATAAAAAATATATA
1 AAATAAAAATAAAT-AAATAATAAATA-ATA
* * *
2052270 TATTAAAAAT-AGT-AATAATAAATAA-A
1 AAATAAAAATAAATAAATAATAAATAATA
*
2052296 TAATAAATACATAAAATACAA-AATAAAGTAAAATA
1 AAATAAA-A-AT-AAATA-AATAATAAA-T--AATA
*
2052331 AAATTAAAATATAAA-AATATAAGAAATACA-A
1 AAA-TAAAA-ATAAATAA-ATAATAAATA-ATA
2052362 AAATACAAAATAAA
1 AAATA-AAAATAAA
2052376 ATGGGCCTAC
Statistics
Matches: 152, Mismatches: 18, Indels: 50
0.69 0.08 0.23
Matches are distributed among these distances:
26 13 0.09
27 9 0.06
28 21 0.14
29 5 0.03
30 26 0.17
31 46 0.30
32 9 0.06
33 3 0.02
34 10 0.07
35 6 0.04
36 4 0.03
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (29 bp):
AAATAAAAATAAATAAATAATAAATAATA
Found at i:2052330 original size:77 final size:73
Alignment explanation
Indices: 2052131--2052343 Score: 191
Period size: 74 Copynumber: 2.8 Consensus size: 73
2052121 AATAATAAGG
* * * ** *
2052131 ATAATATATTAATTAATAGATAAATAATAATAATAATAGATAA-ATAATAATATATGTAAATAGA
1 ATAATA-ATAAATAAATAGATAAATAATAATAATAA-AAATAATA-AATAA-A-ATAAAAATATA
* *
2052195 TA-AATAATAATA
61 TATATTAAAAATA
* *
2052207 ATAATAATATATAAATAGATAAATAATAATAATAATAATAATAAATAAAATAAAAAATATATATA
1 ATAATAATAAATAAATAGATAAATAATAATAATAAAAATAATAAATAAAAT-AAAAATATATATA
2052272 TTAAAAATA
65 TTAAAAATA
* *
2052281 GTAATAATAAATAAATA-ATAAATACATAA-AATACAAAATAAAGTAAAATAAAATTAAAATATA
1 ATAATAATAAATAAATAGATAAATA-ATAATAATA-AAAAT-AA-T-AAATAAAATAAAAATATA
2052344 AAAATATAAG
Statistics
Matches: 115, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
72 2 0.02
73 20 0.17
74 40 0.35
75 29 0.25
76 15 0.13
77 9 0.08
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (73 bp):
ATAATAATAAATAAATAGATAAATAATAATAATAAAAATAATAAATAAAATAAAAATATATATAT
TAAAAATA
Found at i:2052813 original size:21 final size:20
Alignment explanation
Indices: 2052787--2052836 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
2052777 CCTTTCTTAC
*
2052787 ATTTTTTAATTATTTGGTGTT
1 ATTTTTTAATTATTT-GTCTT
*
2052808 ATTTTTCT-ATTATTTTTCTT
1 ATTTTT-TAATTATTTGTCTT
2052828 ATTTTTTAA
1 ATTTTTTAA
2052837 AATTTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 10 0.40
21 13 0.52
22 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (20 bp):
ATTTTTTAATTATTTGTCTT
Found at i:2052875 original size:3 final size:3
Alignment explanation
Indices: 2052867--2052937 Score: 78
Period size: 3 Copynumber: 24.3 Consensus size: 3
2052857 TAGAAATCAT
* *
2052867 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TCA TTA GTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
2052913 TT- TT- TTA TTTA TTA -TA TTA TT- TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA T
2052938 AAGATTTATT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
2 8 0.14
3 45 0.76
4 6 0.10
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2053017 original size:3 final size:3
Alignment explanation
Indices: 2053009--2053046 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2052999 TATTGTTTTC
2053009 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2053047 ATAAAAACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2054146 original size:16 final size:16
Alignment explanation
Indices: 2054123--2054165 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
2054113 AATATTTTAA
2054123 AATT-TTATTTATT-T
1 AATTATTATTTATTAT
2054137 AATTAATTATTTATTAT
1 AATT-ATTATTTATTAT
2054154 AATTATTATTTA
1 AATTATTATTTA
2054166 ATATTATTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.15
16 17 0.65
17 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTATTATTTATTAT
Found at i:2054635 original size:82 final size:82
Alignment explanation
Indices: 2054543--2054707 Score: 276
Period size: 82 Copynumber: 2.0 Consensus size: 82
2054533 TTAAATTGGA
2054543 TGCCTTGTAAAAAATTTCTTGATTTTATGCTTTTATGATTTTATTTTAGACACTTAATTTAATTC
1 TGCCTTGTAAAAAATTTCTTGATTTTATGCTTTTATGATTTTATTTTAGACACTTAATTTAATTC
*
2054608 ATGTAATAAGATTTTTT
66 ATATAATAAGATTTTTT
* ** * *
2054625 TGCCTTGTAAAAAATTTCTTTATTTTATGCTTTTATGATTTTATTTTAGATGCTTAATTTGATTG
1 TGCCTTGTAAAAAATTTCTTGATTTTATGCTTTTATGATTTTATTTTAGACACTTAATTTAATTC
2054690 ATATAATAAGATTTTTT
66 ATATAATAAGATTTTTT
2054707 T
1 T
2054708 AATTTAGCAA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.54
Consensus pattern (82 bp):
TGCCTTGTAAAAAATTTCTTGATTTTATGCTTTTATGATTTTATTTTAGACACTTAATTTAATTC
ATATAATAAGATTTTTT
Found at i:2055059 original size:22 final size:23
Alignment explanation
Indices: 2055020--2055069 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
2055010 AACTTATAAA
2055020 GAAATAAAATTATAATTATATTAT
1 GAAATAAAA-TATAATTATATTAT
* *
2055044 GAAATAAAA-ATTATTATTTTAT
1 GAAATAAAATATAATTATATTAT
2055066 -AAAT
1 GAAAT
2055070 TTTATTATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 11 0.46
24 9 0.38
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
GAAATAAAATATAATTATATTAT
Found at i:2055067 original size:17 final size:17
Alignment explanation
Indices: 2055047--2055090 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2055037 ATATTATGAA
**
2055047 ATAAAAATTATTATTTT
1 ATAAAAATTATTATCAT
**
2055064 ATAAATTTTATTATCAT
1 ATAAAAATTATTATCAT
2055081 ATAAAAATTA
1 ATAAAAATTA
2055091 ATTAACTAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAAAAATTATTATCAT
Found at i:2055281 original size:19 final size:19
Alignment explanation
Indices: 2055246--2055282 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2055236 ATTTGACATA
*
2055246 AAAATATTTACTGATTTTT
1 AAAATATTTACTAATTTTT
*
2055265 AAAATATTTATTAATTTT
1 AAAATATTTACTAATTTT
2055283 ATAGAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (19 bp):
AAAATATTTACTAATTTTT
Found at i:2057420 original size:22 final size:22
Alignment explanation
Indices: 2057395--2057439 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
2057385 TTCAATTAAT
2057395 TCATTTAAGTCTTTCCTATTCA
1 TCATTTAAGTCTTTCCTATTCA
2057417 TCATTTAAGTCTTTCCTATTCA
1 TCATTTAAGTCTTTCCTATTCA
2057439 T
1 T
2057440 TGTTGACTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.04, T:0.51
Consensus pattern (22 bp):
TCATTTAAGTCTTTCCTATTCA
Found at i:2057598 original size:2 final size:2
Alignment explanation
Indices: 2057593--2057634 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2057583 AAATAAATAA
*
2057593 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2057635 TAGAATTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2058839 original size:19 final size:20
Alignment explanation
Indices: 2058817--2058859 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2058807 TTTGACATAA
2058817 AAATAATTTATTG-ATTTT-T
1 AAATAATTTA-TGAATTTTAT
*
2058836 AAATTATTTATGAATTTTAT
1 AAATAATTTATGAATTTTAT
2058856 AAAT
1 AAAT
2058860 GTTAAATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 14 0.67
20 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (20 bp):
AAATAATTTATGAATTTTAT
Found at i:2059486 original size:3 final size:3
Alignment explanation
Indices: 2059478--2059531 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
2059468 TCTTCACTTG
2059478 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2059526 ATA ATA
1 ATA ATA
2059532 TTGCTATTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2059542 original size:3 final size:3
Alignment explanation
Indices: 2059536--2059604 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
2059526 ATAATATTGC
2059536 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2059584 TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
2059605 ATGATAGAGA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2059742 original size:13 final size:13
Alignment explanation
Indices: 2059724--2059749 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2059714 TTTAATTTGT
2059724 CAATTTGTCTATG
1 CAATTTGTCTATG
2059737 CAATTTGTCTATG
1 CAATTTGTCTATG
2059750 TACTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
CAATTTGTCTATG
Found at i:2060234 original size:52 final size:52
Alignment explanation
Indices: 2060145--2060262 Score: 157
Period size: 52 Copynumber: 2.3 Consensus size: 52
2060135 TGGACAAGAA
* * ** * *
2060145 GACTTGCAAAAGAAGAATTCTAGGAGAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAAAATTCTAAAAGAAAGAGAATTCTTAATAGGCAAGTTT
2060197 GACTTGCAAGAGAAAAATTCTAAAAGGAAAG-GAATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAAAATTCTAAAA-GAAAGAGAATTCTTAATAGGCAAGTTT
*
2060249 GACTTACAAGAGAA
1 GACTTGCAAGAGAA
2060263 GAGGAGAGAG
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
52 53 0.91
53 5 0.09
ACGTcount: A:0.43, C:0.09, G:0.23, T:0.25
Consensus pattern (52 bp):
GACTTGCAAGAGAAAAATTCTAAAAGAAAGAGAATTCTTAATAGGCAAGTTT
Found at i:2061181 original size:11 final size:11
Alignment explanation
Indices: 2061165--2061206 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
2061155 AATCTCATAA
2061165 GAGATTTGTTT
1 GAGATTTGTTT
*
2061176 GAGATTTGTTA
1 GAGATTTGTTT
2061187 GAGATTTGTTT
1 GAGATTTGTTT
2061198 GAGATTTGT
1 GAGATTTGT
2061207 CAAATATTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:2061192 original size:22 final size:22
Alignment explanation
Indices: 2061164--2061206 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
2061154 AAATCTCATA
2061164 AGAGATTTGTTTGAGATTTGTT
1 AGAGATTTGTTTGAGATTTGTT
2061186 AGAGATTTGTTTGAGATTTGT
1 AGAGATTTGTTTGAGATTTGT
2061207 CAAATATTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTGAGATTTGTT
Found at i:2061311 original size:52 final size:52
Alignment explanation
Indices: 2061231--2061353 Score: 176
Period size: 52 Copynumber: 2.4 Consensus size: 52
2061221 TGGATAAGAA
* * * * *
2061231 GACTTGCAAAAAAAGAATTCCAAGAG-AAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCAAAAAGAAAAG-GGATTCTTAATAGGCAAGTTT
2061283 GACTTGCAAGAGAAGAATTCAAAAAGAAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCAAAAAGAAAAGGGATTCTTAATAGGCAAGTTT
*
2061335 GACTTACAAGAGAAGAATT
1 GACTTGCAAGAGAAGAATT
2061354 TTAAGATGAG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
52 60 0.94
53 4 0.06
ACGTcount: A:0.45, C:0.10, G:0.22, T:0.24
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCAAAAAGAAAAGGGATTCTTAATAGGCAAGTTT
Found at i:2061371 original size:52 final size:51
Alignment explanation
Indices: 2061243--2061387 Score: 166
Period size: 52 Copynumber: 2.8 Consensus size: 51
2061233 CTTGCAAAAA
* * * *
2061243 AAGAATTCCAAGAGAAAGAGGATTCTTAATAGGTAAGTTTGACTTGCAAGAG
1 AAGAATTCAAAAAG-AAGAGGATTCTTAATAGGCAAGTTTGACTTACAAGAG
*
2061295 AAGAATTCAAAAAGAAAAGGGATTCTTAATAGGCAAGTTTGACTTACAAGAG
1 AAGAATTCAAAAAGAAGA-GGATTCTTAATAGGCAAGTTTGACTTACAAGAG
* * * *
2061347 AAGAATTTTAAGATG-AGAGAGATTCTTAATAAGCAAGTTTG
1 AAGAA-TTCAAAAAGAAGAG-GATTCTTAATAGGCAAGTTTG
2061388 TATGGTTATA
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
51 4 0.05
52 70 0.88
53 6 0.08
ACGTcount: A:0.43, C:0.08, G:0.23, T:0.26
Consensus pattern (51 bp):
AAGAATTCAAAAAGAAGAGGATTCTTAATAGGCAAGTTTGACTTACAAGAG
Found at i:2061987 original size:25 final size:26
Alignment explanation
Indices: 2061919--2062020 Score: 81
Period size: 25 Copynumber: 4.1 Consensus size: 26
2061909 AAGTGGTATC
* *
2061919 AGAGCTAAAGTTTTGAA-ACGT-GAGA
1 AGAGCTAAAGGTTT-AAGATGTGGAGA
* * * *
2061944 AGAGTTGAAGATTCAAGATGTGGA-A
1 AGAGCTAAAGGTTTAAGATGTGGAGA
*
2061969 AGAGCTGAAA-GTTTGAGATGT-GAGA
1 AGAGCT-AAAGGTTTAAGATGTGGAGA
2061994 AGAGCTAAAGGTTTAAGATGTGG-GA
1 AGAGCTAAAGGTTTAAGATGTGGAGA
2062019 AG
1 AG
2062021 TGCATGGTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
24 7 0.12
25 48 0.80
26 5 0.08
ACGTcount: A:0.38, C:0.05, G:0.33, T:0.24
Consensus pattern (26 bp):
AGAGCTAAAGGTTTAAGATGTGGAGA
Found at i:2061994 original size:50 final size:50
Alignment explanation
Indices: 2061919--2062016 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 50
2061909 AAGTGGTATC
* *
2061919 AGAGCTAAAGTTTTGAAACGTGAGAAGAGTTGAAGATTCAAGATGTGGAA
1 AGAGCTAAAGTTTTGAAACGTGAGAAGAGCTAAAGATTCAAGATGTGGAA
* * * *
2061969 AGAGCTGAAAG-TTTGAGATGTGAGAAGAGCTAAAGGTTTAAGATGTGG
1 AGAGCT-AAAGTTTTGAAACGTGAGAAGAGCTAAAGATTCAAGATGTGG
2062017 GAAGTGCATG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 37 0.90
51 4 0.10
ACGTcount: A:0.38, C:0.05, G:0.33, T:0.24
Consensus pattern (50 bp):
AGAGCTAAAGTTTTGAAACGTGAGAAGAGCTAAAGATTCAAGATGTGGAA
Found at i:2062278 original size:11 final size:11
Alignment explanation
Indices: 2062262--2062301 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
2062252 AATCCCATAA
2062262 GAGATTTGTTT
1 GAGATTTGTTT
*
2062273 GAGATTTGTTA
1 GAGATTTGTTT
2062284 GAGATTTGTTT
1 GAGATTTGTTT
*
2062295 GGGATTT
1 GAGATTT
2062302 TTCAGATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:2062467 original size:52 final size:51
Alignment explanation
Indices: 2062329--2062483 Score: 152
Period size: 52 Copynumber: 3.0 Consensus size: 51
2062319 GGACAAGAAG
* * *
2062329 ACTTACAAAAGAAAAATTCCAAGAGAAAGAGGATTCTTAATAGGTAAGTTTG
1 ACTTACAAAAGAAAAATTCTAAGAGAAAG-GGATTCTTAATAGGCAAGTTTA
* * * * *
2062381 ACTTGCAAGAGAAAAATT-TAAAAAAAAAAAGGATTCTTAATAGGCAAGTTTA
1 ACTTACAAAAGAAAAATTCT--AAGAGAAAGGGATTCTTAATAGGCAAGTTTA
* * *
2062433 ACTTACAATAGAAGAATTCTAAGAGGAGAGGGATTCTTAAT-GAGCAAGTTT
1 ACTTACAAAAGAAAAATTCTAAGA-GAAAGGGATTCTTAATAG-GCAAGTTT
2062484 GTATGGTTAT
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
51 4 0.05
52 72 0.87
53 7 0.08
ACGTcount: A:0.46, C:0.09, G:0.19, T:0.26
Consensus pattern (51 bp):
ACTTACAAAAGAAAAATTCTAAGAGAAAGGGATTCTTAATAGGCAAGTTTA
Found at i:2063104 original size:25 final size:25
Alignment explanation
Indices: 2063055--2063110 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
2063045 TTGAAGATTC
* *
2063055 AAGATGTGGAAAGAGCTGGAAGTTT
1 AAGATGTGAAAAGAGCTGAAAGTTT
*
2063080 GAGATGTGAAAAGAGCT-AAAGGTTT
1 AAGATGTGAAAAGAGCTGAAA-GTTT
2063105 AAGATG
1 AAGATG
2063111 CGGGAAGTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.39, C:0.04, G:0.34, T:0.23
Consensus pattern (25 bp):
AAGATGTGAAAAGAGCTGAAAGTTT
Found at i:2063375 original size:11 final size:11
Alignment explanation
Indices: 2063359--2063400 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
2063349 AATCTCATAA
2063359 GAGATTTGTTT
1 GAGATTTGTTT
*
2063370 GAGATTTGTTA
1 GAGATTTGTTT
2063381 GAGATTTGTTT
1 GAGATTTGTTT
*
2063392 AAGATTTGT
1 GAGATTTGT
2063401 CAAATATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:2063386 original size:22 final size:22
Alignment explanation
Indices: 2063358--2063400 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2063348 AAATCTCATA
*
2063358 AGAGATTTGTTTGAGATTTGTT
1 AGAGATTTGTTTAAGATTTGTT
2063380 AGAGATTTGTTTAAGATTTGT
1 AGAGATTTGTTTAAGATTTGT
2063401 CAAATATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTAAGATTTGTT
Found at i:2063565 original size:52 final size:51
Alignment explanation
Indices: 2063425--2063581 Score: 181
Period size: 52 Copynumber: 3.0 Consensus size: 51
2063415 TGGATAAGAA
* * * *
2063425 GACTTGCAAAAAAAGAATTCTAAGAGAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTACAAGAAAAGAATTCTAAGAGAAAG-GGATTTTTAATAGGCAAGTTT
* * * **
2063477 GACTTACAAGAGAAGAATTCTAAAAAAAAAAAGATTTTTAATAGGCAAGTTT
1 GACTTACAAGAAAAGAATTCT-AAGAGAAAGGGATTTTTAATAGGCAAGTTT
*
2063529 GACTTACAAGAAAAGAATTCTAAGAGGAGAGGGATTTTTAAT-GAGCAAGTTT
1 GACTTACAAGAAAAGAATTCTAAGA-GAAAGGGATTTTTAATAG-GCAAGTTT
2063581 G
1 G
2063582 TATGGTTATA
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
51 4 0.05
52 77 0.89
53 6 0.07
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.27
Consensus pattern (51 bp):
GACTTACAAGAAAAGAATTCTAAGAGAAAGGGATTTTTAATAGGCAAGTTT
Found at i:2064196 original size:24 final size:26
Alignment explanation
Indices: 2064151--2064206 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
2064141 TTGAAGATTC
* *
2064151 AAGATGTGGAAAGAGCTGAAA-GTTT
1 AAGATGTGAAAAAAGCTGAAAGGTTT
*
2064176 GAGATGTGAAAAAAGCT-AAAGGTTT
1 AAGATGTGAAAAAAGCTGAAAGGTTT
2064201 AAGATG
1 AAGATG
2064207 CGGGAAGTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 3 0.12
25 23 0.88
ACGTcount: A:0.43, C:0.04, G:0.30, T:0.23
Consensus pattern (26 bp):
AAGATGTGAAAAAAGCTGAAAGGTTT
Found at i:2064471 original size:11 final size:11
Alignment explanation
Indices: 2064455--2064496 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
2064445 AATCTCATAA
2064455 GAGATTTGTTT
1 GAGATTTGTTT
*
2064466 GAGATTTGTTA
1 GAGATTTGTTT
2064477 GAGATTTGTTT
1 GAGATTTGTTT
*
2064488 AAGATTTGT
1 GAGATTTGT
2064497 CAAATATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:2064482 original size:22 final size:22
Alignment explanation
Indices: 2064454--2064496 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
2064444 AAATCTCATA
*
2064454 AGAGATTTGTTTGAGATTTGTT
1 AGAGATTTGTTTAAGATTTGTT
2064476 AGAGATTTGTTTAAGATTTGT
1 AGAGATTTGTTTAAGATTTGT
2064497 CAAATATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (22 bp):
AGAGATTTGTTTAAGATTTGTT
Found at i:2064589 original size:52 final size:52
Alignment explanation
Indices: 2064521--2064677 Score: 201
Period size: 52 Copynumber: 3.0 Consensus size: 52
2064511 TGGATAAGAA
* *
2064521 GACTTGCAAAAAAAGAATTCTAAGAG-AAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAAAAGAATTCTAAGAGAAAAG-GGATTCTTAATAGGCAAGTTT
* * *
2064573 GACTTGCAAGAGAAGAATTCTAAAAGAAAAGGGATTTTTAATAGGCAAGTTT
1 GACTTGCAAGAAAAGAATTCTAAGAGAAAAGGGATTCTTAATAGGCAAGTTT
* * * *
2064625 GACTTACAAGAAAAGAATTCTAAGAGGAGAGGGATTTTTAAT-GAGCAAGTTT
1 GACTTGCAAGAAAAGAATTCTAAGAGAAAAGGGATTCTTAATAG-GCAAGTTT
2064677 G
1 G
2064678 TATGGTTATA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 1 0.01
52 88 0.95
53 4 0.04
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.27
Consensus pattern (52 bp):
GACTTGCAAGAAAAGAATTCTAAGAGAAAAGGGATTCTTAATAGGCAAGTTT
Found at i:2065265 original size:25 final size:25
Alignment explanation
Indices: 2065236--2065293 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 25
2065226 TTCAAGATTC
2065236 AAGATGTGAAAAGAGCTGAAA-GTTT
1 AAGATGTGAAAAGAGCT-AAAGGTTT
*
2065261 GAGATGTGAAAAGAGCTAAAGGTTT
1 AAGATGTGAAAAGAGCTAAAGGTTT
2065286 AAGATGTG
1 AAGATGTG
2065294 GGAAGTGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 3 0.10
25 27 0.90
ACGTcount: A:0.41, C:0.03, G:0.31, T:0.24
Consensus pattern (25 bp):
AAGATGTGAAAAGAGCTAAAGGTTT
Found at i:2065275 original size:50 final size:50
Alignment explanation
Indices: 2065197--2065293 Score: 115
Period size: 50 Copynumber: 1.9 Consensus size: 50
2065187 AAATGATATC
* * *
2065197 AGAGCTGAAGTTTCGAAACGTGAGAAGAGTTCAAGATTCAAGATGTGAAA
1 AGAGCTGAAGTTTCGAAACGTGAAAAGAGCTAAAGATTCAAGATGTGAAA
* * * *
2065247 AGAGCTGAAAGTTT-GAGATGTGAAAAGAGCTAAAGGTTTAAGATGTG
1 AGAGCTG-AAGTTTCGAAACGTGAAAAGAGCTAAAGATTCAAGATGTG
2065294 GGAAGTGGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
50 33 0.85
51 6 0.15
ACGTcount: A:0.39, C:0.07, G:0.30, T:0.24
Consensus pattern (50 bp):
AGAGCTGAAGTTTCGAAACGTGAAAAGAGCTAAAGATTCAAGATGTGAAA
Found at i:2065556 original size:11 final size:11
Alignment explanation
Indices: 2065540--2065571 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
2065530 AATCTCATAA
2065540 GAGATTTGTTT
1 GAGATTTGTTT
2065551 GAGATTTGTTT
1 GAGATTTGTTT
*
2065562 GGGATTTGTT
1 GAGATTTGTT
2065572 AAATATTGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (11 bp):
GAGATTTGTTT
Found at i:2065683 original size:52 final size:52
Alignment explanation
Indices: 2065627--2065751 Score: 180
Period size: 52 Copynumber: 2.4 Consensus size: 52
2065617 AGAGAAAGAT
* * *
2065627 GATTCTTAATAGGTAAGTTTGACTTGCAAGAGAAGAATTCTAAAATAAAAGG
1 GATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCTAAAAGAAAAGG
* * *
2065679 GATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCTAAGAGGAGAGG
1 GATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCTAAAAGAAAAGG
2065731 GATTCTTAAT-GAGCAAGTTTG
1 GATTCTTAATAG-GCAAGTTTG
2065752 TATGGTTATA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 1 0.02
52 65 0.98
ACGTcount: A:0.38, C:0.09, G:0.24, T:0.29
Consensus pattern (52 bp):
GATTCTTAATAGGCAAGTTTGACTTACAAGAGAAGAATTCTAAAAGAAAAGG
Found at i:2066894 original size:18 final size:19
Alignment explanation
Indices: 2066873--2066908 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2066863 TTAGTTTTTA
2066873 ATTATTTATCA-AAAAATT
1 ATTATTTATCATAAAAATT
*
2066891 ATTATTTGTCATAAAAAT
1 ATTATTTATCATAAAAAT
2066909 AATTTACTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (19 bp):
ATTATTTATCATAAAAATT
Found at i:2066941 original size:19 final size:20
Alignment explanation
Indices: 2066905--2066947 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
2066895 TTTGTCATAA
2066905 AAATAATTTACTGATTTT-T
1 AAATAATTTACTGATTTTGT
*
2066924 AAATAATTTA-TTATTTTTGT
1 AAATAATTTACTGA-TTTTGT
2066944 AAAT
1 AAAT
2066948 GTTAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 14 0.67
20 5 0.24
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (20 bp):
AAATAATTTACTGATTTTGT
Found at i:2067974 original size:18 final size:19
Alignment explanation
Indices: 2067941--2067977 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2067931 TAAATAGTAG
2067941 TATTGACAAATTTTTTTTA
1 TATTGACAAATTTTTTTTA
*
2067960 TATTG-CAACTTTTTTTTA
1 TATTGACAAATTTTTTTTA
2067978 AAAAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.27, C:0.08, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTGACAAATTTTTTTTA
Found at i:2071365 original size:20 final size:21
Alignment explanation
Indices: 2071329--2071371 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
2071319 TAAATATATT
2071329 AAATTACATATAAATTT-TAA
1 AAATTACATATAAATTTATAA
*
2071349 AAATTA-ATTTAACATTTATAA
1 AAATTACATATAA-ATTTATAA
2071370 AA
1 AA
2071372 GTGATAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 10 0.50
21 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTACATATAAATTTATAA
Found at i:2073153 original size:36 final size:35
Alignment explanation
Indices: 2073106--2073182 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 35
2073096 ATTGAATGAC
2073106 TTATAATTTTTATAAATTATAAGATAC-ATAAGTATT
1 TTATAATTTTTATAAATTATAAGATACAATAA-T-TT
*
2073142 TTATAATTTTTATAAATTATAATATACAATAATTT
1 TTATAATTTTTATAAATTATAAGATACAATAATTT
2073177 TTATAA
1 TTATAA
2073183 ATTATAACCA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 8 0.21
36 27 0.69
37 4 0.10
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (35 bp):
TTATAATTTTTATAAATTATAAGATACAATAATTT
Found at i:2074335 original size:22 final size:23
Alignment explanation
Indices: 2074287--2074337 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
2074277 TTGAACTAGG
** * *
2074287 CATATTTTTTGAACTTATTCTAT
1 CATATTTTTTGAACTTAACCAAA
2074310 CATATTTTTTGAA-TTAACCAAA
1 CATATTTTTTGAACTTAACCAAA
2074332 CATATT
1 CATATT
2074338 AATACAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (23 bp):
CATATTTTTTGAACTTAACCAAA
Found at i:2074776 original size:18 final size:17
Alignment explanation
Indices: 2074749--2074797 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 17
2074739 CTTTTTTTTC
*
2074749 TTTTTTTATTTAATAAT
1 TTTTTTTATTTAATAAA
2074766 TTTTTTATATTTAATAAA
1 TTTTTT-TATTTAATAAA
*
2074784 TATTTTTATTTAAT
1 TTTTTTTATTTAAT
2074798 TTTTTTGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTTTTATTTAATAAA
Found at i:2075453 original size:18 final size:18
Alignment explanation
Indices: 2075426--2075460 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2075416 GTATTTATAA
*
2075426 TAATATATTTATAAAAAT
1 TAATAAATTTATAAAAAT
*
2075444 TAATAAATTTTTAAAAA
1 TAATAAATTTATAAAAA
2075461 ACTCTATTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATTTATAAAAAT
Found at i:2075461 original size:20 final size:21
Alignment explanation
Indices: 2075423--2075461 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2075413 CTTGTATTTA
*
2075423 TAATAATATATTTATAAAAAT
1 TAATAATATATTTAAAAAAAT
*
2075444 TAATAA-ATTTTTAAAAAA
1 TAATAATATATTTAAAAAA
2075462 CTCTATTGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATAATATATTTAAAAAAAT
Found at i:2076157 original size:19 final size:20
Alignment explanation
Indices: 2076115--2076157 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
2076105 ATTATTTAAC
*
2076115 ATTTATAAAATCAATATATA
1 ATTTATAAAATCAATAAATA
* *
2076135 ATTTA-AAAATCAGTAAATT
1 ATTTATAAAATCAATAAATA
2076154 ATTT
1 ATTT
2076158 TTTGTCAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (20 bp):
ATTTATAAAATCAATAAATA
Found at i:2076337 original size:19 final size:19
Alignment explanation
Indices: 2076285--2076350 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
2076275 TAATAATATA
*
2076285 ATATAATACTAAATTTTAT
1 ATATAATAATAAATTTTAT
* * * * *
2076304 ATTTAGTTATTAATTTTTT
1 ATATAATAATAAATTTTAT
2076323 ATATAATAATAAA-TTTAT
1 ATATAATAATAAATTTTAT
*
2076341 AAATAATAAT
1 ATATAATAAT
2076351 TTTTAATTCA
Statistics
Matches: 35, Mismatches: 12, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
18 13 0.37
19 22 0.63
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
ATATAATAATAAATTTTAT
Found at i:2076345 original size:15 final size:16
Alignment explanation
Indices: 2076320--2076349 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2076310 TTATTAATTT
2076320 TTTATATAATAATAAA
1 TTTATATAATAATAAA
2076336 TTTATA-AATAATAA
1 TTTATATAATAATAA
2076350 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTATATAATAATAAA
Found at i:2076371 original size:22 final size:21
Alignment explanation
Indices: 2076334--2076374 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2076324 TATAATAATA
*
2076334 AATTTATAAATAATAATTTTT
1 AATTCATAAATAATAATTTTT
2076355 AATTCATAATATAATAATTT
1 AATTCATAA-ATAATAATTT
2076375 ATTTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTCATAAATAATAATTTTT
Found at i:2078437 original size:21 final size:20
Alignment explanation
Indices: 2078390--2078438 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
2078380 GTTGACACTA
2078390 ATTTATTTAATTTTAATAATT
1 ATTT-TTTAATTTTAATAATT
*
2078411 ACTTTTTTAA-TTTAATAAAT
1 A-TTTTTTAATTTTAATAATT
*
2078431 ATATTTTA
1 ATTTTTTA
2078439 GTGAAATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 6 0.24
20 10 0.40
21 6 0.24
22 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTTAATTTTAATAATT
Found at i:2078966 original size:20 final size:20
Alignment explanation
Indices: 2078920--2078966 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2078910 TTTTTAAAAT
*
2078920 TTTTAATATTATTCAATCAC
1 TTTTAATATTATTCAATCAA
*
2078940 TTATAATATTATTCAAT-AA
1 TTTTAATATTATTCAATCAA
2078959 TATTTAAT
1 T-TTTAAT
2078967 TTTTATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTAATATTATTCAATCAA
Found at i:2080279 original size:17 final size:17
Alignment explanation
Indices: 2080240--2080272 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2080230 GACACGTAAT
*
2080240 TTTTTTCTCATTTTTTG
1 TTTTTTATCATTTTTTG
2080257 TTTTTTATCATTTTTT
1 TTTTTTATCATTTTTT
2080273 TTGTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTTATCATTTTTTG
Found at i:2081081 original size:10 final size:9
Alignment explanation
Indices: 2081018--2081126 Score: 51
Period size: 9 Copynumber: 11.7 Consensus size: 9
2081008 AAAAAAATAC
2081018 TAAAAAATT
1 TAAAAAATT
*
2081027 TAAAAATTTT
1 TAAAAA-ATT
**
2081037 TTTAAAATT
1 TAAAAAATT
**
2081046 TTTAAAATT
1 TAAAAAATT
* *
2081055 CAAACAATT
1 TAAAAAATT
2081064 CT-AAAAATT
1 -TAAAAAATT
2081073 TAGAAAAATT
1 TA-AAAAATT
2081083 ATAAAAAATTT
1 -TAAAAAA-TT
**
2081094 TTCAAAATT
1 TAAAAAATT
*
2081103 T-TAAAATT
1 TAAAAAATT
*
2081111 TATAAAAAAT
1 TA-AAAAATT
2081121 TAAAAA
1 TAAAAA
2081127 TAAGAAATAG
Statistics
Matches: 77, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
8 8 0.10
9 35 0.45
10 30 0.39
11 4 0.05
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.39
Consensus pattern (9 bp):
TAAAAAATT
Found at i:2081283 original size:86 final size:86
Alignment explanation
Indices: 2081177--2081353 Score: 354
Period size: 86 Copynumber: 2.1 Consensus size: 86
2081167 GAATTTTTTT
2081177 AAAAAAATTAAAAAATTACAATTTATAAAAATTAAAATTTTTTAAAATTTTAAAAATAAAAAGAA
1 AAAAAAATTAAAAAATTACAATTTATAAAAATTAAAATTTTTTAAAATTTTAAAAATAAAAAGAA
2081242 CTTAAAAAACTGAAAATAAGA
66 CTTAAAAAACTGAAAATAAGA
2081263 AAAAAAATTAAAAAATTACAATTTATAAAAATTAAAATTTTTTAAAATTTTAAAAATAAAAAGAA
1 AAAAAAATTAAAAAATTACAATTTATAAAAATTAAAATTTTTTAAAATTTTAAAAATAAAAAGAA
2081328 CTTAAAAAACTGAAAATAAGA
66 CTTAAAAAACTGAAAATAAGA
2081349 AAAAA
1 AAAAA
2081354 TCTAAAAGCT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 91 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.28
Consensus pattern (86 bp):
AAAAAAATTAAAAAATTACAATTTATAAAAATTAAAATTTTTTAAAATTTTAAAAATAAAAAGAA
CTTAAAAAACTGAAAATAAGA
Found at i:2081513 original size:33 final size:33
Alignment explanation
Indices: 2081463--2081527 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
2081453 AAAATCCAAC
*
2081463 AAATTTAAATTTCAAAAAATAT-ATAAAAATTTG
1 AAATTTAAAATTCAAAAAATATGA-AAAAATTTG
2081496 AAATTGTAAAATT-AAAAAATATGAAAAAATTT
1 AAATT-TAAAATTCAAAAAATATGAAAAAATTT
2081528 TATCATTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.34
Consensus pattern (33 bp):
AAATTTAAAATTCAAAAAATATGAAAAAATTTG
Found at i:2083381 original size:114 final size:113
Alignment explanation
Indices: 2083179--2083407 Score: 336
Period size: 114 Copynumber: 2.0 Consensus size: 113
2083169 CATAAGTTCG
* * *
2083179 AAGATGAAAATTTTATTGCAAAACACACTGGTCTTGGTTTGCCATCAATGGCGTGCTGTTTTATA
1 AAGATGAAAATTTCATTGCAAAACACACTGGTCCTGGTTTGCCATCAATGGCATGCTGTTTTATA
2083244 TATAATATTATGTAGCTGAATTTTTTTTCCTTTTCTCTATAT-TTTTTCA
66 TATAATATTATGTAGCTGAA--TTTTTTCCTTTTCTCTATATATTTTTCA
* * * * *
2083293 AAGATGAAAATTTCATTGGAAAACACGCTGGTCCTGGTTTGCTATCAATGGTATGCTGTTTTCTA
1 AAGATGAAAATTTCATTGCAAAACACACTGGTCCTGGTTTGCCATCAATGGCATGCTGTTTTATA
*
2083358 TATAATATTGTGTAGCT-ACATTTTTTCCTTTTCTCTATATATTTTTCA
66 TATAATATTATGTAGCTGA-ATTTTTTCCTTTTCTCTATATATTTTTCA
2083406 AA
1 AA
2083408 CTGAAAGATT
Statistics
Matches: 104, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
112 20 0.19
113 10 0.10
114 74 0.71
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.45
Consensus pattern (113 bp):
AAGATGAAAATTTCATTGCAAAACACACTGGTCCTGGTTTGCCATCAATGGCATGCTGTTTTATA
TATAATATTATGTAGCTGAATTTTTTCCTTTTCTCTATATATTTTTCA
Found at i:2089848 original size:12 final size:12
Alignment explanation
Indices: 2089830--2089859 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2089820 TTTTTTAATG
2089830 ATTTAATAAAAA
1 ATTTAATAAAAA
*
2089842 TTTTAATAAAAA
1 ATTTAATAAAAA
2089854 ATTTAA
1 ATTTAA
2089860 ATCGATACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTTAATAAAAA
Found at i:2092625 original size:16 final size:16
Alignment explanation
Indices: 2092604--2092637 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2092594 TATAATTAAC
2092604 TTTTTGTATTATATAT
1 TTTTTGTATTATATAT
* *
2092620 TTTTTGTTTTATTTAT
1 TTTTTGTATTATATAT
2092636 TT
1 TT
2092638 CTTTAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTTGTATTATATAT
Done.