Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 8 of 24
Found at i:1566222 original size:19 final size:19
Alignment explanation
Indices: 1566191--1566237 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
1566181 ATTTTATATA
1566191 AAAAATATATTAAAAT-AAT
1 AAAAATA-ATTAAAATAAAT
*
1566210 AAAAATAAGTTAAATTAAAT
1 AAAAATAA-TTAAAATAAAT
*
1566230 ATAAATAA
1 AAAAATAA
1566238 ATAATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 1 0.04
19 13 0.54
20 10 0.42
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATAATTAAAATAAAT
Found at i:1566409 original size:2 final size:2
Alignment explanation
Indices: 1566402--1566442 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1566392 GTAACCTTTG
1566402 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1566443 ATATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1567665 original size:9 final size:10
Alignment explanation
Indices: 1567648--1567684 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1567638 AAAATATAAA
1567648 AAAATTATTT
1 AAAATTATTT
1567658 AAAA-TA-TT
1 AAAATTATTT
1567666 AAAA-TATTT
1 AAAATTATTT
1567675 AAAATTATTT
1 AAAATTATTT
1567685 TATTTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.32
9 8 0.32
10 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
AAAATTATTT
Found at i:1567696 original size:16 final size:16
Alignment explanation
Indices: 1567670--1567702 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1567660 AATATTAAAA
1567670 TATTTAAAATT-ATTT
1 TATTTAAAATTAATTT
1567685 TATTTAAAAATTAATTT
1 TATTT-AAAATTAATTT
1567702 T
1 T
1567703 TAAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 6 0.38
17 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTTAAAATTAATTT
Found at i:1567870 original size:2 final size:2
Alignment explanation
Indices: 1567863--1567887 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1567853 TTAAACTTCC
1567863 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
1567888 CACATGAGTT
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:1576770 original size:14 final size:14
Alignment explanation
Indices: 1576733--1576761 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1576723 ACTCATGTAT
1576733 AAAT-TATTATTAA
1 AAATATATTATTAA
1576746 AAATATATTATTAA
1 AAATATATTATTAA
1576760 AA
1 AA
1576762 TATTTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATATTATTAA
Found at i:1578540 original size:7 final size:7
Alignment explanation
Indices: 1578528--1578553 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1578518 TTTCTTTGTG
1578528 AAAAAAT
1 AAAAAAT
1578535 AAAAAAT
1 AAAAAAT
1578542 AAAAAAT
1 AAAAAAT
1578549 AAAAA
1 AAAAA
1578554 GTTGCTGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:1590454 original size:2 final size:2
Alignment explanation
Indices: 1590447--1590484 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1590437 TCCCAATCCC
1590447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1590485 GTTTTAAGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1591309 original size:41 final size:41
Alignment explanation
Indices: 1591264--1591347 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
1591254 AAAATAATAT
*
1591264 AAATTTTAAAATACAAAAATAATAAAATTATTTTATTTAAA
1 AAATTTAAAAATACAAAAATAATAAAATTATTTTATTTAAA
* *
1591305 AAATTTAAAAATACGAAGATAATAAAATTATTTTATTTAAA
1 AAATTTAAAAATACAAAAATAATAAAATTATTTTATTTAAA
1591346 AA
1 AA
1591348 TTAACTTATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (41 bp):
AAATTTAAAAATACAAAAATAATAAAATTATTTTATTTAAA
Found at i:1592177 original size:25 final size:26
Alignment explanation
Indices: 1592133--1592182 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
1592123 AATGTCTTAT
1592133 TTTTATATTTTTATTATTAT-TTTAG
1 TTTTATATTTTTATTATTATCTTTAG
*
1592158 TTTTA-ATTTTTTTTATTTATCTTTA
1 TTTTATATTTTTATTA-TTATCTTTA
1592183 AATTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 9 0.41
25 9 0.41
26 4 0.18
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (26 bp):
TTTTATATTTTTATTATTATCTTTAG
Found at i:1595903 original size:17 final size:17
Alignment explanation
Indices: 1595881--1595917 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
1595871 ACAGCTAGCA
1595881 GACCCTTCATACAAATT
1 GACCCTTCATACAAATT
1595898 GACCCTTCATACAAATT
1 GACCCTTCATACAAATT
1595915 GAC
1 GAC
1595918 TTTTGCTGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.35, C:0.30, G:0.08, T:0.27
Consensus pattern (17 bp):
GACCCTTCATACAAATT
Found at i:1606499 original size:30 final size:31
Alignment explanation
Indices: 1606455--1606520 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 31
1606445 TTGTTATTCC
1606455 TATTTTTCAAATATAAATATCAAAATAAAAT
1 TATTTTTCAAATATAAATATCAAAATAAAAT
* *
1606486 TATTTTT-AAATATAAATATTAAAATATAAT
1 TATTTTTCAAATATAAATATCAAAATAAAAT
1606516 TATTT
1 TATTT
1606521 AAGAATTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 26 0.79
31 7 0.21
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (31 bp):
TATTTTTCAAATATAAATATCAAAATAAAAT
Found at i:1606512 original size:14 final size:14
Alignment explanation
Indices: 1606463--1606519 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
1606453 CCTATTTTTC
*
1606463 AAATATAAATATCA
1 AAATATAAATATTA
*
1606477 AAATA-AAATTATTTTT
1 AAATATAAA-TA--TTA
1606493 AAATATAAATATTA
1 AAATATAAATATTA
*
1606507 AAATATAATTATT
1 AAATATAAATATT
1606520 TAAGAATTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 3 0.09
14 21 0.60
16 8 0.23
17 3 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
AAATATAAATATTA
Found at i:1611160 original size:9 final size:9
Alignment explanation
Indices: 1611146--1611209 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
1611136 ACACTCACAA
1611146 ATTATTTAT
1 ATTATTTAT
1611155 ATTATTTGA-
1 ATTATTT-AT
1611164 ATTATTTAT
1 ATTATTTAT
1611173 -TTATTTA-
1 ATTATTTAT
*
1611180 ATATAATTAT
1 AT-TATTTAT
1611190 A-T-TTTAT
1 ATTATTTAT
*
1611197 GTTATTTA-
1 ATTATTTAT
1611205 ATTAT
1 ATTAT
1611210 AAATATAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
7 4 0.09
8 15 0.34
9 23 0.52
10 2 0.05
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
ATTATTTAT
Found at i:1611168 original size:18 final size:17
Alignment explanation
Indices: 1611145--1611192 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1611135 CACACTCACA
1611145 AATTATTTATATTATTT
1 AATTATTTATATTATTT
1611162 GAATTATTTAT-TTATTT
1 -AATTATTTATATTATTT
*
1611179 AATATAATTATATT
1 AAT-TATTTATATT
1611193 TTATGTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 3 0.11
17 12 0.44
18 12 0.44
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
AATTATTTATATTATTT
Found at i:1611251 original size:18 final size:18
Alignment explanation
Indices: 1611228--1611274 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
1611218 AATATAATTT
1611228 TTTAAATATATAAAAA-AA
1 TTTAAA-ATATAAAAATAA
*
1611246 TTTAAAAT-TAAAAATAT
1 TTTAAAATATAAAAATAA
1611263 TTTAAAAATATA
1 TTT-AAAATATA
1611275 TATTAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.24
17 6 0.24
18 11 0.44
19 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTTAAAATATAAAAATAA
Found at i:1611571 original size:21 final size:20
Alignment explanation
Indices: 1611547--1611590 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1611537 CCTTTACATT
*
1611547 TTATGTATATAATTTAAAATA
1 TTATGTATATAATAT-AAATA
*
1611568 TTATGTATTTAATATAAATA
1 TTATGTATATAATATAAATA
1611588 TTA
1 TTA
1611591 ATATATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TTATGTATATAATATAAATA
Found at i:1611599 original size:20 final size:20
Alignment explanation
Indices: 1611563--1611601 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1611553 ATATAATTTA
*
1611563 AAATATTATGTATTTAATAT
1 AAATATTATATATTTAATAT
1611583 AAATATTA-ATATATTAATA
1 AAATATTATATAT-TTAATA
1611602 ATTTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
AAATATTATATATTTAATAT
Found at i:1611614 original size:20 final size:20
Alignment explanation
Indices: 1611591--1611631 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1611581 ATAAATATTA
1611591 ATATATTAATAATT-TATTTT
1 ATATATTAAT-ATTATATTTT
*
1611611 ATATATTTATATTATATTTT
1 ATATATTAATATTATATTTT
1611631 A
1 A
1611632 ATTATTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATATTAATATTATATTTT
Found at i:1611635 original size:11 final size:13
Alignment explanation
Indices: 1611565--1611636 Score: 53
Period size: 13 Copynumber: 5.5 Consensus size: 13
1611555 ATAATTTAAA
*
1611565 ATATTATGTATTT
1 ATATTATATATTT
*
1611578 A-ATATAAATATTAAT
1 ATAT-TATATATT--T
1611593 ATATTA-ATAATTT
1 ATATTATAT-ATTT
*
1611606 ATTTTATATATTT
1 ATATTATATATTT
1611619 ATATTATAT-TTT
1 ATATTATATATTT
1611631 A-ATTAT
1 ATATTAT
1611637 TTCTAACATT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
11 5 0.10
12 6 0.12
13 25 0.51
14 4 0.08
15 7 0.14
16 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (13 bp):
ATATTATATATTT
Found at i:1612288 original size:27 final size:29
Alignment explanation
Indices: 1612257--1612320 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
1612247 ATAAATAATT
1612257 AATATATTAAA-AT-TTATAATAATAA-AA
1 AATATATTAAATATATTATAAT-ATAATAA
*
1612284 AATATTTTAAATATAATTATAATATAATAA
1 AATATATTAAATAT-ATTATAATATAATAA
1612314 AATATAT
1 AATATAT
1612321 AATTATTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 10 0.32
28 2 0.06
29 4 0.13
30 15 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (29 bp):
AATATATTAAATATATTATAATATAATAA
Found at i:1612973 original size:20 final size:21
Alignment explanation
Indices: 1612945--1613001 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
1612935 TAAAAATAAA
1612945 AAATATTTTAT-ATTAATATTT
1 AAATATTTTATAATTAA-ATTT
1612966 AAAT-TTTTATAATTAAATTT
1 AAATATTTTATAATTAAATTT
1612986 AAATAATTTT-TAATTA
1 AAAT-ATTTTATAATTA
1613002 TTAAATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 14 0.42
21 15 0.45
22 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATATTTTATAATTAAATTT
Found at i:1613021 original size:21 final size:22
Alignment explanation
Indices: 1612987--1613027 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1612977 ATTAAATTTA
**
1612987 AATAATTTTTAATT-ATTAAAT
1 AATAATTTAAAATTAATTAAAT
1613008 AATAATTTAAAATTAATTAA
1 AATAATTTAAAATTAATTAA
1613028 CTTAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATAATTTAAAATTAATTAAAT
Found at i:1620952 original size:22 final size:21
Alignment explanation
Indices: 1620925--1620992 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
1620915 TATTTTATGT
1620925 TTATATAAATTTTAATATTATA
1 TTATATAAA-TTTAATATTATA
1620947 TTATATAAAATTTAA-A--ATA
1 TTATAT-AAATTTAATATTATA
*
1620966 TT-TATATATTT-ATATTATA
1 TTATATAAATTTAATATTATA
1620985 TTTATATA
1 -TTATATA
1620993 TTATTTTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
16 1 0.03
17 6 0.15
18 3 0.08
19 8 0.21
20 2 0.05
21 5 0.13
22 11 0.28
23 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATATAAATTTAATATTATA
Found at i:1620965 original size:24 final size:23
Alignment explanation
Indices: 1620909--1620972 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 23
1620899 ATCATTATTT
*
1620909 TTTAAATATTTTATGTTTATATAAA
1 TTTAAATA-TTTAT-ATTATATAAA
*
1620934 TTTTAATA-TTATATTATATAAAA
1 TTTAAATATTTATATTATAT-AAA
1620957 TTTAAAATATTTATAT
1 TTT-AAATATTTATAT
1620973 ATTTATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
22 6 0.18
23 10 0.30
24 4 0.12
25 13 0.39
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTAAATATTTATATTATATAAA
Found at i:1624811 original size:23 final size:23
Alignment explanation
Indices: 1624782--1624834 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1624772 ATAATTTAAA
* *
1624782 TATTTAATTTAATATAAATTGAAT
1 TATTAAATTAAAT-TAAATTGAAT
* *
1624806 TATTAAATTAAATTAAATTTATT
1 TATTAAATTAAATTAAATTGAAT
1624829 TATTAA
1 TATTAA
1624835 CATGTTTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TATTAAATTAAATTAAATTGAAT
Found at i:1630193 original size:2 final size:2
Alignment explanation
Indices: 1630188--1630215 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1630178 GCGCGCATAC
1630188 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
1630216 GAGTATGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1654483 original size:2 final size:2
Alignment explanation
Indices: 1654476--1654794 Score: 242
Period size: 2 Copynumber: 159.5 Consensus size: 2
1654466 AGGACCGAAG
* * *
1654476 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT GT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1654518 AT AT AT AT AT AT AT AT GT AT AT GT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
1654560 AT AT AT AT AT AT GT GT GT AT AT AT AT AT GT AT AA AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
1654602 GT GT GT AT AT AT AT AT GT AT AT GT AT AT AT AT GT 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
* * * * * * * * * * *
1654644 GT AT GT AT GT AT AT AT AT GT GT GT GT GT GT GT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * * *
1654686 AT GT GT GT AT AT GT AT GT AT AT AT AT GT AT AT GT GT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1654728 AT AT GT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1654770 AT AT AT GT AT AA AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1654795 AGGGCTATTT
Statistics
Matches: 261, Mismatches: 56, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 261 1.00
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1654500 original size:18 final size:18
Alignment explanation
Indices: 1654476--1654793 Score: 267
Period size: 18 Copynumber: 17.2 Consensus size: 18
1654466 AGGACCGAAG
*
1654476 ATATATATATATATATAT
1 ATATGTATATATATATAT
* * *
1654494 GTATATATATATATATGT
1 ATATGTATATATATATAT
1654512 ATATGTATATATATATAT
1 ATATGTATATATATATAT
*
1654530 ATATGTATATGTATATAT
1 ATATGTATATATATATAT
* *
1654548 ATATATATATGTATATAT
1 ATATGTATATATATATAT
* * * *
1654566 ATATATGTGTGTATATAT
1 ATATGTATATATATATAT
* *
1654584 ATATGTATAAATATATGT
1 ATATGTATATATATATAT
* * *
1654602 GTGTGTATATATATATGT
1 ATATGTATATATATATAT
1654620 ATATGTATATATATGTATAT
1 ATATGTATATATA--TATAT
*
1654640 ATATGTATGTATGTATATAT
1 ATATGTA--TATATATATAT
* * * * * *
1654660 ATGTGTGTGTGTGTGTAT
1 ATATGTATATATATATAT
* *
1654678 ATATGTATATGTGTGTATAT
1 ATATGTATA--TATATATAT
* *
1654698 GTATGTATATATATGTAT
1 ATATGTATATATATATAT
* * *
1654716 ATGTGTGTATATATATGT
1 ATATGTATATATATATAT
*
1654734 ATATATATATATATATAT
1 ATATGTATATATATATAT
*
1654752 ATATGTATATGTGTATATAT
1 ATATGTATA--TATATATAT
*
1654772 ATATGTATAAATATATAT
1 ATATGTATATATATATAT
1654790 ATAT
1 ATAT
1654794 AAGGGCTATT
Statistics
Matches: 244, Mismatches: 48, Indels: 16
0.79 0.16 0.05
Matches are distributed among these distances:
18 185 0.76
20 54 0.22
22 5 0.02
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.49
Consensus pattern (18 bp):
ATATGTATATATATATAT
Found at i:1654521 original size:30 final size:30
Alignment explanation
Indices: 1654476--1654794 Score: 276
Period size: 30 Copynumber: 10.8 Consensus size: 30
1654466 AGGACCGAAG
*
1654476 ATATATATATATATATATGTATATATATAT
1 ATATGTATATATATATATGTATATATATAT
*
1654506 ATATGTATATGTATATATATATATATATGTATAT
1 ATATGTATA--TATATATATGTATATA--TATAT
* *
1654540 GTATATATATATATATATGTATATATATAT
1 ATATGTATATATATATATGTATATATATAT
* * *
1654570 ATGTGTGTATATATATATGTATAAATATAT
1 ATATGTATATATATATATGTATATATATAT
* * * *
1654600 GTGTGTGTATATATATATGTATATGTATAT
1 ATATGTATATATATATATGTATATATATAT
* *
1654630 ATATGTATATATATGTATG--TATGTATAT
1 ATATGTATATATATATATGTATATATATAT
* * * * * *
1654658 ATATG----TGTGTGTGTGTGTATATATGT
1 ATATGTATATATATATATGTATATATATAT
* * * *
1654684 ATATGTGTGTATATGTATGTATATATATGT
1 ATATGTATATATATATATGTATATATATAT
* *
1654714 ATATGTGTGTATATATATGTATATATATAT
1 ATATGTATATATATATATGTATATATATAT
* * *
1654744 ATATATATATATGTATATG--TGTATATAT
1 ATATGTATATATATATATGTATATATATAT
* *
1654772 ATATGTATAAATATATATATATA
1 ATATGTATATATATATATGTATA
1654795 AGGGCTATTT
Statistics
Matches: 239, Mismatches: 38, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
24 7 0.03
26 12 0.05
28 37 0.15
30 141 0.59
32 30 0.13
34 12 0.05
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (30 bp):
ATATGTATATATATATATGTATATATATAT
Found at i:1655569 original size:68 final size:68
Alignment explanation
Indices: 1655482--1655618 Score: 222
Period size: 69 Copynumber: 2.0 Consensus size: 68
1655472 GGAATAAAAA
* *
1655482 TTAGACTAAAAATAACAATAAAGAG-AAAACAGATTAAAAACAAAGAAATTATAAGTATAAACAC
1 TTAGACTAAAAAGAACAATAAAGAGAAAAACAGATTAAAAACAAAGAAATTATAACTATAAACAC
1655546 AAT
66 AAT
* *
1655549 TTAGACTAAAAAAGAACAATAAAGAGAAAAACATATTAAAAACAAAGAAATTATAACTATATACA
1 TTAGACT-AAAAAGAACAATAAAGAGAAAAACAGATTAAAAACAAAGAAATTATAACTATAAACA
1655614 CAAT
65 CAAT
1655618 T
1 T
1655619 ACCAGGTAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
67 7 0.11
68 17 0.27
69 40 0.62
ACGTcount: A:0.62, C:0.09, G:0.08, T:0.20
Consensus pattern (68 bp):
TTAGACTAAAAAGAACAATAAAGAGAAAAACAGATTAAAAACAAAGAAATTATAACTATAAACAC
AAT
Found at i:1656761 original size:15 final size:15
Alignment explanation
Indices: 1656734--1656770 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1656724 TATCAATATG
1656734 ATTAATAATATATTA
1 ATTAATAATATATTA
1656749 ATTAA-AATGATATTA
1 ATTAATAAT-ATATTA
1656764 ATTAATA
1 ATTAATA
1656771 TTTTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.15
15 16 0.80
16 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
ATTAATAATATATTA
Found at i:1656833 original size:21 final size:19
Alignment explanation
Indices: 1656790--1656834 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
1656780 TAATTTAATA
* *
1656790 AAAATAATATATTAAATAT
1 AAAATAATATATCAAAAAT
1656809 AAAATATATATAATCAAAAAT
1 AAAATA-ATAT-ATCAAAAAT
1656830 AAAAT
1 AAAAT
1656835 TTTAAAGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 4 0.18
21 12 0.55
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAATAATATATCAAAAAT
Found at i:1657052 original size:16 final size:16
Alignment explanation
Indices: 1657031--1657134 Score: 64
Period size: 16 Copynumber: 6.7 Consensus size: 16
1657021 TAGTTTAATC
1657031 AATTTAATTAATTTTA
1 AATTTAATTAATTTTA
*
1657047 AATTTAAAT-ATTTTAA
1 AATTTAATTAATTTT-A
* *
1657063 AATTAAATTAATTTATT
1 AATTTAATTAATTT-TA
1657080 AATTT--TTATATTTT-
1 AATTTAATTA-ATTTTA
1657094 AA-TTAATTAAATTTTA
1 AATTTAATT-AATTTTA
1657110 TAATTTTAA--AA-TTT-
1 -AA-TTTAATTAATTTTA
1657124 AATTTAATTAA
1 AATTTAATTAA
1657135 ATAATTTAAC
Statistics
Matches: 70, Mismatches: 5, Indels: 28
0.68 0.05 0.27
Matches are distributed among these distances:
12 5 0.07
13 4 0.06
14 4 0.06
15 19 0.27
16 23 0.33
17 10 0.14
18 1 0.01
19 4 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTTAATTAATTTTA
Found at i:1657061 original size:15 final size:16
Alignment explanation
Indices: 1657031--1657076 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
1657021 TAGTTTAATC
*
1657031 AATTTAATTAATTTTA
1 AATTTAAATAATTTTA
1657047 AATTTAAAT-ATTTTA
1 AATTTAAATAATTTTA
*
1657062 AAATTAAATTAATTT
1 AATTTAAA-TAATTT
1657077 ATTAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 13 0.50
16 9 0.35
17 4 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATTTAAATAATTTTA
Found at i:1657102 original size:22 final size:23
Alignment explanation
Indices: 1657070--1657118 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
1657060 TAAAATTAAA
* *
1657070 TTAATTTATTAATTTTTAT-ATT
1 TTAATTAATTAAATTTTATAATT
1657092 TTAATTAATTAAATTTTATAATT
1 TTAATTAATTAAATTTTATAATT
1657115 TTAA
1 TTAA
1657119 AATTTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTAATTAATTAAATTTTATAATT
Found at i:1657107 original size:31 final size:30
Alignment explanation
Indices: 1657034--1657136 Score: 88
Period size: 31 Copynumber: 3.3 Consensus size: 30
1657024 TTTAATCAAT
*
1657034 TTAATT-AATTTTA-AATTTAAATATTTTAA
1 TTAATTAAATTTTATAATTT-TATATTTTAA
1657063 --AATTAAATTAATTTATTAATTTTTATATTTTAA
1 TTAATTAAA-T--TTTA-TAA-TTTTATATTTTAA
* *
1657096 TTAATTAAATTTTATAATTTTAAAATTTAA
1 TTAATTAAATTTTATAATTTTATATTTTAA
1657126 TTTAATTAAAT
1 -TTAATTAAAT
1657137 AATTTAACTA
Statistics
Matches: 61, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
27 4 0.07
28 2 0.03
29 1 0.02
30 11 0.18
31 17 0.28
32 4 0.07
33 11 0.18
34 4 0.07
35 7 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (30 bp):
TTAATTAAATTTTATAATTTTATATTTTAA
Found at i:1657116 original size:56 final size:58
Alignment explanation
Indices: 1657033--1657141 Score: 143
Period size: 56 Copynumber: 1.9 Consensus size: 58
1657023 GTTTAATCAA
* *
1657033 TTTAATTAATTTTAAATTTAAATATTTTAAAA-TTAAATTAATTTATTAATTTTTATAT
1 TTTAATTAA-TTTAAATTTAAATATTTTAAAATTTAAATTAATTAAATAATTTTTATAT
* *
1657091 TTTAATTAA-TTAAATTT-TATAATTTTAAAATTTAATTTAATTAAATAATTT
1 TTTAATTAATTTAAATTTAAAT-ATTTTAAAATTTAAATTAATTAAATAATTT
1657142 AACTAACGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
55 2 0.04
56 17 0.38
57 17 0.38
58 9 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (58 bp):
TTTAATTAATTTAAATTTAAATATTTTAAAATTTAAATTAATTAAATAATTTTTATAT
Found at i:1657125 original size:22 final size:21
Alignment explanation
Indices: 1657077--1657128 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
1657067 AAATTAATTT
*
1657077 ATTAATTTTTATATTTTAATTA
1 ATTAAATTTTATATTTTAA-TA
1657099 ATTAAATTTTATAATTTTAA-A
1 ATTAAATTTTAT-ATTTTAATA
*
1657120 ATTTAATTT
1 ATTAAATTT
1657129 AATTAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 9 0.33
22 11 0.41
23 7 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTAAATTTTATATTTTAATA
Found at i:1659372 original size:1 final size:1
Alignment explanation
Indices: 1659368--1659392 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1659358 TCTTTTTTTT
1659368 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
1659393 AGATAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:1662246 original size:17 final size:17
Alignment explanation
Indices: 1662195--1662253 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
1662185 AGGTGTATTG
1662195 AAATTTATAT-AATA-A
1 AAATTTATATAAATATA
1662210 AAA-TTAT-TAAGATATCA
1 AAATTTATATAA-ATAT-A
1662227 AAATTTATATAAATATA
1 AAATTTATATAAATATA
*
1662244 AAATATATAT
1 AAATTTATAT
1662254 GCTGAGGTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 1 0.03
14 5 0.14
15 6 0.16
17 14 0.38
18 8 0.22
19 3 0.08
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATTTATATAAATATA
Found at i:1665290 original size:48 final size:48
Alignment explanation
Indices: 1665212--1665308 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
1665202 TCTTCAAGTT
* *
1665212 GATTGATTTACCTGATTATTTACAACCCGTATTAACTTTCGCTTTGTC
1 GATTGATTTACCTGATTATTCACAAACCGTATTAACTTTCGCTTTGTC
1665260 GATTGATTTACCTGATTATTCACAAACCGTATTAACTTTCGCTTTGTC
1 GATTGATTTACCTGATTATTCACAAACCGTATTAACTTTCGCTTTGTC
1665308 G
1 G
1665309 GCAAATCCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (48 bp):
GATTGATTTACCTGATTATTCACAAACCGTATTAACTTTCGCTTTGTC
Found at i:1675002 original size:482 final size:474
Alignment explanation
Indices: 1674078--1675034 Score: 1708
Period size: 482 Copynumber: 2.0 Consensus size: 474
1674068 AATCCTAATA
*
1674078 TATATTAGGATTATGCCATATGAATCGGGTTGGTTTCTTTTATAAAATTGAGTGCATAAAATATG
1 TATATTAGGATTATGCCATATGAATCGGGTTGGTTTCTTTAATAAAATTGAGTGCATAAAATATG
1674143 ATGGCAGTTTATTAATTATTATTGTGTACAAGTTTTAGGAGCAAAGGTTAAGTATATGATGTGTT
66 ATGGCAGTTTATTAATTATTATTGTGTACAAGTTTTAGGAGCAAAGGTTAAGTATATGATGTGTT
1674208 GTTAACAAGTCTGGTTTCATTGGACTAACTAAATTATTTGTAATGTTTATTATGCCTCTATTTCT
131 GTTAACAAGTCTGGTTTCATTGGACTAACTAAATTATTTGTAATGTTTATTATGCCTCTATTTCT
1674273 GCTTATAGTTGATACTTATCATCCAGAGATGTATGATATTGTTTGTAAGCTTTCAGTGATGCTTG
196 GCTTATAGTTGATACTTATCATCCAGAGATGTATGATATTGTTTGTAAGCTTTCAGTGATGCTTG
* * * *
1674338 AATCTCGTTATTTGTTGCCCCGGCATGTTATTCTTATTAACGATATGATACTAAAAGTTTTTGAT
261 AATCTCGGTATTTGTTGCCACGGCATGTTATTCTAATTAACGATATGATACTAAAAGTTTGTGAT
1674403 GATACTCTGCAGTTGGGTCCTCTAGTTAGGCAGATGATGCCAAGATAGAAGCATCTCCAGTTTAT
326 GATACTCTGCAGTTGGGTCCTCTAGTTAGGCAGATGATGCCAAGATAGAAGCATCTCCAGTTTAT
1674468 TCAATGGCTAGGGGTGCTTCAGGTAAATTACATCCTAACTCTTGTCTCTTGTTTCTTGTTTCTTG
391 TCAATGGCTAGGGGTGCTTCAGGTAAATTACATCCTAACTCTTGTCTCTTGTTTCTTGTTTCTTG
1674533 CCCCACCCTCCTTCCTTGT
456 CCCCACCCTCCTTCCTTGT
1674552 TATATTAGGATTATGCCATATGAATCGGGTTGGTTTCTTTAAT-AAATTGAGTGCATAAAATATG
1 TATATTAGGATTATGCCATATGAATCGGGTTGGTTTCTTTAATAAAATTGAGTGCATAAAATATG
1674616 ATGGCAG-TTATTAATTATTATTGTGTACAAGTTATTAGGAGCAAAGGTTAAGTATATGATGTGT
66 ATGGCAGTTTATTAATTATTATTGTGTACAAGTT-TTAGGAGCAAAGGTTAAGTATATGATGTGT
1674680 TGTTAACAAGTCTGGATTTCATTGGA-TCAACTAAAATTATTTGTAATGTTCCTATTATGCCTCA
130 TGTTAACAAGTCTGG-TTTCATTGGACT-AACT-AAATTATTTGTAATGTT--TATTATGCCTC-
*
1674744 TATTTCTGCTTATTAGTTGATACTTATCATCCAGAGATGTATGATATTGTTTGTAAGCTTTCCGT
189 TATTTCTGCTTA-TAGTTGATACTTATCATCCAGAGATGTATGATATTGTTTGTAAGCTTTCAGT
1674809 GACTGCTTGAATCTCGGTATTTGTTGCCACGGCATGTTATTCTAATT-ACGATATATGATACTAA
253 GA-TGCTTGAATCTCGGTATTTGTTGCCACGGCATGTTATTCTAATTAACG--ATATGATACTAA
1674873 AAG-TTGTGATGATACTCTGGCAGTTGGGTCCTCTAGTTAGGCAGATGATGCCAATGATAGAAGC
315 AAGTTTGTGATGATACTCT-GCAGTTGGGTCCTCTAGTTAGGCAGATGATGCCAA-GATAGAAGC
1674937 ATCTCCAGTTTATTCAATGGCTAGGGGTGCTTCAGGTAAATTACATCCTAACTCTTGTCTCTTGT
378 ATCTCCAGTTTATTCAATGGCTAGGGGTGCTTCAGGTAAATTACATCCTAACTCTTGTCTCTTGT
1675002 TTCTTGTTTCTTGCCCCACCCTCCTTCCTTGT
443 TTCTTGTTTCTTGCCCCACCCTCCTTCCTTGT
1675034 T
1 T
1675035 CTTCTCTCTT
Statistics
Matches: 464, Mismatches: 6, Indels: 18
0.95 0.01 0.04
Matches are distributed among these distances:
472 26 0.06
473 74 0.16
474 56 0.12
475 17 0.04
477 11 0.02
478 12 0.03
479 56 0.12
480 55 0.12
481 50 0.11
482 107 0.23
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (474 bp):
TATATTAGGATTATGCCATATGAATCGGGTTGGTTTCTTTAATAAAATTGAGTGCATAAAATATG
ATGGCAGTTTATTAATTATTATTGTGTACAAGTTTTAGGAGCAAAGGTTAAGTATATGATGTGTT
GTTAACAAGTCTGGTTTCATTGGACTAACTAAATTATTTGTAATGTTTATTATGCCTCTATTTCT
GCTTATAGTTGATACTTATCATCCAGAGATGTATGATATTGTTTGTAAGCTTTCAGTGATGCTTG
AATCTCGGTATTTGTTGCCACGGCATGTTATTCTAATTAACGATATGATACTAAAAGTTTGTGAT
GATACTCTGCAGTTGGGTCCTCTAGTTAGGCAGATGATGCCAAGATAGAAGCATCTCCAGTTTAT
TCAATGGCTAGGGGTGCTTCAGGTAAATTACATCCTAACTCTTGTCTCTTGTTTCTTGTTTCTTG
CCCCACCCTCCTTCCTTGT
Found at i:1681286 original size:2 final size:2
Alignment explanation
Indices: 1681279--1681310 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1681269 TGCAGAGTTG
*
1681279 AT AT AT AT CT 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
1681311 TATTTGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1682660 original size:2 final size:2
Alignment explanation
Indices: 1682653--1682684 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1682643 AGGTTTCCCA
1682653 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1682685 ACATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1682736 original size:2 final size:2
Alignment explanation
Indices: 1682687--1682723 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1682677 TCTCTCTCAC
1682687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1682724 GTGCATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1683315 original size:2 final size:2
Alignment explanation
Indices: 1683308--1683334 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1683298 GAATTTCCCC
1683308 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1683335 ACACATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1684209 original size:20 final size:20
Alignment explanation
Indices: 1684168--1684211 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1684158 AAAATATTTT
*
1684168 TTTAAATTATAAAATAAAAA
1 TTTAAATGATAAAATAAAAA
*
1684188 TTTAAATGATTAAAA-AATAA
1 TTTAAATGA-TAAAATAAAAA
1684208 TTTA
1 TTTA
1684212 CTTGAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
TTTAAATGATAAAATAAAAA
Found at i:1685018 original size:10 final size:11
Alignment explanation
Indices: 1684993--1685037 Score: 58
Period size: 10 Copynumber: 4.1 Consensus size: 11
1684983 AATTTTATTT
1684993 ATTTAAATTATA
1 ATTTAAA-TATA
1685005 ATTTAAAT-TA
1 ATTTAAATATA
1685015 ATTT-AATATA
1 ATTTAAATATA
1685025 ATTTAAATTATA
1 ATTTAAA-TATA
1685037 A
1 A
1685038 AATATTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 3 0.10
10 12 0.40
11 3 0.10
12 12 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTTAAATATA
Found at i:1685026 original size:41 final size:43
Alignment explanation
Indices: 1684916--1685028 Score: 112
Period size: 41 Copynumber: 2.7 Consensus size: 43
1684906 TAAACTCTAT
* * *
1684916 TTTATTATTTAAAATAATATTAAAAT-ATATTTTTATATTAATA
1 TTTATAATTTAAATTAAT-TTAAAATAATTTTTTTATATTAATA
*
1684959 TTTATAA-TTAAATTTAA-ATAAAATAATTTTATTTAT-TTAA-A
1 TTTATAATTTAAA-TTAATTTAAAATAATTTT-TTTATATTAATA
*
1685000 -TTATAATTTAAATTAATTTAATATAATTT
1 TTTATAATTTAAATTAATTTAAAATAATTT
1685029 AAATTATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
40 10 0.17
41 22 0.37
42 13 0.22
43 14 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (43 bp):
TTTATAATTTAAATTAATTTAAAATAATTTTTTTATATTAATA
Found at i:1685096 original size:16 final size:16
Alignment explanation
Indices: 1685075--1685106 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1685065 AATGGCTGCC
*
1685075 TGGCTCATACAGTCTT
1 TGGCTCATAAAGTCTT
1685091 TGGCTCATAAAGTCTT
1 TGGCTCATAAAGTCTT
1685107 GGTATGTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.38
Consensus pattern (16 bp):
TGGCTCATAAAGTCTT
Found at i:1686039 original size:27 final size:28
Alignment explanation
Indices: 1685969--1686042 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 28
1685959 ATATTAAAAT
1685969 TTAAATA-A-ATTAAAAATATTTAATTA
1 TTAAATATATATTAAAAATATTTAATTA
* *
1685995 TT-TATATAATATAAAAAAT-TTTAATTA
1 TTAAATAT-ATATTAAAAATATTTAATTA
1686022 TTAAATATATATTGAAAAATA
1 TTAAATATATATT-AAAAATA
1686043 ATATTTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
25 3 0.08
26 2 0.05
27 15 0.39
28 18 0.47
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (28 bp):
TTAAATATATATTAAAAATATTTAATTA
Found at i:1686039 original size:28 final size:27
Alignment explanation
Indices: 1685969--1686042 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 27
1685959 ATATTAAAAT
1685969 TTAAATA-AATTAAAAATATTTAATTA
1 TTAAATATAATTAAAAATATTTAATTA
*
1685995 TT-TATATAATATAAAAA-ATTTTAATTA
1 TTAAATATAAT-TAAAAATA-TTTAATTA
1686022 TTAAATATATATTGAAAAATA
1 TTAAATATA-ATT-AAAAATA
1686043 ATATTTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
25 3 0.08
26 6 0.15
27 16 0.41
28 6 0.15
29 7 0.18
30 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
TTAAATATAATTAAAAATATTTAATTA
Found at i:1686131 original size:21 final size:20
Alignment explanation
Indices: 1686101--1686155 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
1686091 CATACACAAT
1686101 AAAT-ATAATTATATTATTA
1 AAATAATAATTATATTATTA
*
1686120 AATTTAATAATTA-ATTTATTA
1 AA-ATAATAATTATA-TTATTA
*
1686141 AAATATTAATTATAT
1 AAATAATAATTATAT
1686156 AAAAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 2 0.07
20 11 0.38
21 16 0.55
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAATAATAATTATATTATTA
Found at i:1686163 original size:40 final size:40
Alignment explanation
Indices: 1686101--1686177 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
1686091 CATACACAAT
**
1686101 AAATATAATTATATTATTAAATT-TAATAATTAATTTATTA
1 AAATATAATTATATTAAAAAATTATAA-AATTAATTTATTA
1686141 AAATATTAATTATA-TAAAAAATTATAAAATTAATTTA
1 AAATA-TAATTATATTAAAAAATTATAAAATTAATTTA
1686178 ACTTACACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 22 0.67
41 11 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (40 bp):
AAATATAATTATATTAAAAAATTATAAAATTAATTTATTA
Found at i:1686405 original size:2 final size:2
Alignment explanation
Indices: 1686398--1686424 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1686388 ACCCTAAAGG
1686398 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1686425 GAACAACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1687947 original size:17 final size:18
Alignment explanation
Indices: 1687927--1687976 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 18
1687917 ATTCAAATTT
*
1687927 AAATTTATATTAAATA-A
1 AAATATATATTAAATACA
**
1687944 AAATATATATTCGATACA
1 AAATATATATTAAATACA
1687962 AAATATAT-TTAAATA
1 AAATATATATTAAATA
1687977 TTATATTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (18 bp):
AAATATATATTAAATACA
Found at i:1688832 original size:15 final size:16
Alignment explanation
Indices: 1688804--1688833 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1688794 ACTTTTCATA
1688804 TATTTTAGTTATTAAC
1 TATTTTAGTTATTAAC
1688820 TATTTTA-TTATTAA
1 TATTTTAGTTATTAA
1688834 ATAATAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
TATTTTAGTTATTAAC
Found at i:1689248 original size:20 final size:21
Alignment explanation
Indices: 1689213--1689253 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1689203 AATTATATAT
*
1689213 TATATTATAATTTTATTTAAAA
1 TATATTATAA-TTTATATAAAA
1689235 TATATTATAA-TTATATAAA
1 TATATTATAATTTATATAAA
1689254 TTTTAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATATTATAATTTATATAAAA
Found at i:1689249 original size:11 final size:11
Alignment explanation
Indices: 1689204--1689250 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
1689194 AAAATAATAA
1689204 ATTATATATTAT
1 ATTATA-ATTAT
*
1689216 ATTATAATTTT
1 ATTATAATTAT
*
1689227 ATT-TAAAATAT
1 ATTAT-AATTAT
1689238 ATTATAATTAT
1 ATTATAATTAT
1689249 AT
1 AT
1689251 AAATTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
10 1 0.03
11 21 0.72
12 7 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTATAATTAT
Found at i:1689268 original size:15 final size:15
Alignment explanation
Indices: 1689246--1689280 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1689236 ATATTATAAT
1689246 TATA-TAAATTTTAA
1 TATATTAAATTTTAA
1689260 TATATTAAATTTTAA
1 TATATTAAATTTTAA
*
1689275 AATATT
1 TATATT
1689281 TATATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATTAAATTTTAA
Found at i:1689277 original size:23 final size:26
Alignment explanation
Indices: 1689233--1689296 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 26
1689223 TTTTATTTAA
1689233 AATATATTATAATTATATAAAT-TTT
1 AATATATTATAATTATATAAATATTT
*
1689258 AATATATTA-AATTTTA-AAATATTT
1 AATATATTATAATTATATAAATATTT
1689282 -ATATATT-TATATTAT
1 AATATATTATA-ATTAT
1689297 TTTTTATTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 12 0.35
24 13 0.38
25 9 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
AATATATTATAATTATATAAATATTT
Found at i:1693711 original size:20 final size:20
Alignment explanation
Indices: 1693672--1693752 Score: 73
Period size: 20 Copynumber: 4.2 Consensus size: 20
1693662 TTTAAATTTT
* *
1693672 TAAATCAAT-TTAATTGATA
1 TAAATCAATATAAATTAATA
1693691 TAAATCAATATAAATTAATA
1 TAAATCAATATAAATTAATA
*
1693711 TATATCAA-ATTAAATTAATA
1 TAAATCAATA-TAAATTAATA
* *
1693731 AAAAT-AATA-ATA-TAATA
1 TAAATCAATATAAATTAATA
1693748 TAAAT
1 TAAAT
1693753 ATTATTTTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
17 9 0.17
18 2 0.04
19 12 0.23
20 29 0.56
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (20 bp):
TAAATCAATATAAATTAATA
Found at i:1696126 original size:42 final size:42
Alignment explanation
Indices: 1696067--1696151 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
1696057 ACAAAGATTC
*
1696067 CTGCTATTGTTATAATGCCAATTGCACATTTGTTGGTTTGGA
1 CTGCTATTGTTATAATGCCAATTGCACATTTGTTGGATTGGA
*
1696109 CTGCTGTTGTTATAATGCCAATTGCACATTTGTTGGATTGGA
1 CTGCTATTGTTATAATGCCAATTGCACATTTGTTGGATTGGA
1696151 C
1 C
1696152 ATATCGGCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.41
Consensus pattern (42 bp):
CTGCTATTGTTATAATGCCAATTGCACATTTGTTGGATTGGA
Found at i:1698976 original size:15 final size:15
Alignment explanation
Indices: 1698956--1698989 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1698946 ACACGTATCT
1698956 ATATTATATATATAC
1 ATATTATATATATAC
*
1698971 ATATTATATATATAT
1 ATATTATATATATAC
1698986 ATAT
1 ATAT
1698990 AAAAGAATGG
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:0.03, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTATATATATAC
Found at i:1699702 original size:14 final size:15
Alignment explanation
Indices: 1699674--1699720 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
1699664 AGTTATAAAA
1699674 AAATATTATAAATATT
1 AAATATTA-AAATATT
1699690 AAA-ATTAAAATATT
1 AAATATTAAAATATT
*
1699704 AAATTTATAAAATATT
1 AAATAT-TAAAATATT
1699720 A
1 A
1699721 TCACTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 10 0.36
15 5 0.18
16 13 0.46
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAATATTAAAATATT
Found at i:1713357 original size:20 final size:20
Alignment explanation
Indices: 1713332--1713369 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1713322 TTTTAAATTT
1713332 ATTTTTTACTTTAAAATATA
1 ATTTTTTACTTTAAAATATA
* *
1713352 ATTTTTTATTTTTAAATA
1 ATTTTTTACTTTAAAATA
1713370 AAAAAAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTTTTACTTTAAAATATA
Found at i:1713591 original size:24 final size:24
Alignment explanation
Indices: 1713550--1713596 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1713540 TTTCGCACGT
*
1713550 ATTAAAAATAATAATAATGATAAA
1 ATTAAAAATAATAATAATAATAAA
* * *
1713574 ATTAAATATTATACTAATAATAA
1 ATTAAAAATAATAATAATAATAA
1713597 TAATATATGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
ATTAAAAATAATAATAATAATAAA
Found at i:1713661 original size:12 final size:12
Alignment explanation
Indices: 1713644--1713696 Score: 63
Period size: 12 Copynumber: 4.2 Consensus size: 12
1713634 AAGATAAAAA
1713644 TAAAAATATTAT
1 TAAAAATATTAT
1713656 TAAAAATATTAAT
1 TAAAAATATT-AT
1713669 ATAAAAATA-TAT
1 -TAAAAATATTAT
1713681 TAATAAATTATTAT
1 TAA-AAA-TATTAT
1713695 TA
1 TA
1713697 TTATATGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
11 3 0.08
12 15 0.42
13 5 0.14
14 13 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAAAATATTAT
Found at i:1713672 original size:26 final size:27
Alignment explanation
Indices: 1713643--1713693 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
1713633 TAAGATAAAA
1713643 ATAAAAATATTATTAA-AAA-TATTAAT
1 ATAAAAATA-TATTAATAAATTATTAAT
1713669 ATAAAAATATATTAATAAATTATTA
1 ATAAAAATATATTAATAAATTATTA
1713694 TTATTATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 6 0.26
26 12 0.52
27 5 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
ATAAAAATATATTAATAAATTATTAAT
Found at i:1713695 original size:14 final size:13
Alignment explanation
Indices: 1713647--1713696 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
1713637 ATAAAAATAA
1713647 AAATATTATTAA-
1 AAATATTATTAAT
1713659 AAATATTAATATAA-
1 AAATATT-AT-TAAT
1713673 AAATA-TATTAAT
1 AAATATTATTAAT
1713685 AAATTATTATTA
1 AAA-TATTATTA
1713697 TTATATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
11 3 0.09
12 12 0.36
13 5 0.15
14 13 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAATATTATTAAT
Found at i:1714020 original size:50 final size:49
Alignment explanation
Indices: 1713951--1714048 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 49
1713941 TCTAGTTTTT
* * *
1713951 CACCAGAGGGACATTGAGTTAGTTGTACTAATGCTGCAATTCAACTCTAG
1 CACCAGAGGAACAATGAGTTAGTTGT-CCAATGCTGCAATTCAACTCTAG
*
1714001 CACCAGAGGAACAATGAGTTAGTTGTCCCATGCTGCAATTCAACTCTA
1 CACCAGAGGAACAATGAGTTAGTTGTCCAATGCTGCAATTCAACTCTA
1714049 ATAAAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 20 0.45
50 24 0.55
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (49 bp):
CACCAGAGGAACAATGAGTTAGTTGTCCAATGCTGCAATTCAACTCTAG
Found at i:1715547 original size:9 final size:9
Alignment explanation
Indices: 1715535--1715564 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1715525 CTAGACTCTC
*
1715535 TTCGGCAAA
1 TTCGGTAAA
1715544 TTCGGTAAA
1 TTCGGTAAA
1715553 TTCGGTAAA
1 TTCGGTAAA
1715562 TTC
1 TTC
1715565 TCCTTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (9 bp):
TTCGGTAAA
Found at i:1715988 original size:3 final size:3
Alignment explanation
Indices: 1715980--1716008 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1715970 TTGGAAATTT
1715980 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1716009 CTCCCTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1716588 original size:33 final size:32
Alignment explanation
Indices: 1716512--1716652 Score: 120
Period size: 30 Copynumber: 4.6 Consensus size: 32
1716502 TATCGTCAGG
*
1716512 ATAT-AAATATCTTTAATAATAAATTTATA-CA
1 ATATAAAATAT-TTTAATAATAAATTTATATAA
* *
1716543 ATATATATTATTTATACATAA-AAATTTATATAA
1 ATATAAAATATTT-TA-ATAATAAATTTATATAA
*
1716576 ATATAAAATATTTTAA-AATAAA-ATATATAA
1 ATATAAAATATTTTAATAATAAATTTATATAA
* **
1716606 ATATAATATAAATT-AT--TAAATTTA-ATAA
1 ATATAAAATATTTTAATAATAAATTTATATAA
1716634 ATATAAAATACTTTTAATA
1 ATATAAAATA-TTTTAATA
1716653 TAACCATTAT
Statistics
Matches: 87, Mismatches: 13, Indels: 20
0.73 0.11 0.17
Matches are distributed among these distances:
28 17 0.20
29 5 0.06
30 22 0.25
31 10 0.11
32 17 0.20
33 16 0.18
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (32 bp):
ATATAAAATATTTTAATAATAAATTTATATAA
Found at i:1716594 original size:17 final size:18
Alignment explanation
Indices: 1716560--1716641 Score: 60
Period size: 18 Copynumber: 4.3 Consensus size: 18
1716550 TTATTTATAC
1716560 ATAAAAATTTATATAAAT
1 ATAAAAATTTATATAAAT
*
1716578 ATAAAATATTTTAAAATAAAAT
1 ATAAAA-A-TTT-ATAT-AAAT
* *
1716600 ATATAAATATAATATAAAT
1 ATAAAAAT-TTATATAAAT
*
1716619 -TATTAAATTTA-ATAAAT
1 ATA-AAAATTTATATAAAT
1716636 ATAAAA
1 ATAAAA
1716642 TACTTTTAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
17 8 0.16
18 12 0.24
19 10 0.20
20 7 0.14
21 5 0.10
22 9 0.18
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAAAATTTATATAAAT
Found at i:1716625 original size:19 final size:20
Alignment explanation
Indices: 1716593--1716632 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1716583 ATATTTTAAA
1716593 ATAAAATATATAAATATAAT
1 ATAAAATATATAAATATAAT
* *
1716613 ATAAATTAT-TAAATTTAAT
1 ATAAAATATATAAATATAAT
1716632 A
1 A
1716633 AATATAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAATATATAAATATAAT
Found at i:1718546 original size:25 final size:24
Alignment explanation
Indices: 1718470--1718546 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 24
1718460 ATTGACATTG
1718470 TATAATTTTATATATTTATATATCAAA
1 TATAATTTTATA-ATTTATATA--AAA
* *
1718497 TATAATTTTTTTAATTTACT-CAAAA
1 TATAA-TTTTATAATTTA-TATAAAA
*
1718522 TTTAATATTTATAATTTATATAAAA
1 TATAAT-TTTATAATTTATATAAAA
1718547 AGTATAAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
24 2 0.05
25 21 0.51
27 11 0.27
28 7 0.17
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (24 bp):
TATAATTTTATAATTTATATAAAA
Found at i:1718585 original size:19 final size:19
Alignment explanation
Indices: 1718552--1718612 Score: 52
Period size: 21 Copynumber: 3.1 Consensus size: 19
1718542 TAAAAAGTAT
*
1718552 AAAATATAATGATTAAATTAA
1 AAAATATAA--ATTAAATAAA
*
1718573 AAAATATAAATTATATAAA
1 AAAATATAAATTAAATAAA
*
1718592 AATTAATAAAAATTAAA-AAA
1 AA--AATATAAATTAAATAAA
1718612 A
1 A
1718613 TTAAATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.29
20 4 0.12
21 20 0.59
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATATAAATTAAATAAA
Found at i:1718597 original size:30 final size:28
Alignment explanation
Indices: 1718542--1718597 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
1718532 ATAATTTATA
* **
1718542 TAAAAAGTATAAAATATAATGATTAAAT
1 TAAAAAATATAAAATATAAAAATTAAAT
1718570 TAAAAAATATAAATTATATAAAAATTAA
1 TAAAAAATATAAA--ATATAAAAATTAA
1718598 TAAAAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 12 0.52
30 11 0.48
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (28 bp):
TAAAAAATATAAAATATAAAAATTAAAT
Found at i:1718602 original size:10 final size:10
Alignment explanation
Indices: 1718575--1718616 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
1718565 TAAATTAAAA
*
1718575 AATATAAATT
1 AATAAAAATT
1718585 ATATAAAAATT
1 A-ATAAAAATT
1718596 AATAAAAATT
1 AATAAAAATT
1718606 AA-AAAAATT
1 AATAAAAATT
1718615 AA
1 AA
1718617 ATTAATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 9 0.30
10 12 0.40
11 9 0.30
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATAAAAATT
Found at i:1718613 original size:19 final size:21
Alignment explanation
Indices: 1718575--1718616 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1718565 TAAATTAAAA
*
1718575 AATATAAATTATATAAAAATT
1 AATAAAAATTATATAAAAATT
1718596 AATAAAAATTA-A-AAAAATT
1 AATAAAAATTATATAAAAATT
1718615 AA
1 AA
1718617 ATTAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 1 0.05
21 10 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AATAAAAATTATATAAAAATT
Found at i:1719099 original size:16 final size:17
Alignment explanation
Indices: 1719068--1719100 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1719058 AAATATTTTT
*
1719068 AATTTAATTTATAAAAA
1 AATTTAATTAATAAAAA
1719085 AATTTAA-TAATAAAAA
1 AATTTAATTAATAAAAA
1719101 TTGATCTCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTTAATTAATAAAAA
Found at i:1719704 original size:8 final size:8
Alignment explanation
Indices: 1719693--1719721 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1719683 AAATATATAT
1719693 AATTTTAA
1 AATTTTAA
1719701 AATTTTAA
1 AATTTTAA
1719709 AA-TTTAA
1 AATTTTAA
1719716 AATTTT
1 AATTTT
1719722 TTTATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
AATTTTAA
Found at i:1719851 original size:18 final size:17
Alignment explanation
Indices: 1719828--1719879 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 17
1719818 GGTTAAAGAT
1719828 AATTTAATTATTATTTTA
1 AATTTAATT-TTATTTTA
*
1719846 AATTTATTTTTATATTTA
1 AATTTAATTTTAT-TTTA
1719864 ATATATTAATTTTATT
1 A-AT-TTAATTTTATT
1719880 AAATAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 4 0.14
18 13 0.45
19 3 0.10
20 9 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
AATTTAATTTTATTTTA
Found at i:1721527 original size:2 final size:2
Alignment explanation
Indices: 1721520--1721561 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1721510 ACTGGAGCAA
1721520 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1721562 TTCAAGTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1724490 original size:16 final size:17
Alignment explanation
Indices: 1724469--1724502 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1724459 TTAAAAATAT
1724469 TTATA-TCAATACGTAA
1 TTATATTCAATACGTAA
*
1724485 TTATATTCAATACTTAA
1 TTATATTCAATACGTAA
1724502 T
1 T
1724503 CTCACTAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.44
Consensus pattern (17 bp):
TTATATTCAATACGTAA
Found at i:1727594 original size:6 final size:6
Alignment explanation
Indices: 1727576--1727618 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
1727566 AATCTGGCCC
*
1727576 ATATAA A-ATAA ATATAA ATATAA ATATAA ATATAA ATAAAA AT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA AT
1727619 TAGCATTTCC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
ATATAA
Found at i:1727776 original size:2 final size:2
Alignment explanation
Indices: 1727771--1727801 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1727761 GAGTATCTTT
1727771 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1727802 GTGTGTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1729600 original size:21 final size:22
Alignment explanation
Indices: 1729571--1729612 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1729561 AATAAAAAAT
* *
1729571 TTTATTTAATTTA-AAAATTAA
1 TTTAATTAATTCATAAAATTAA
1729592 TTTAATTAATTCATAAAATTA
1 TTTAATTAATTCATAAAATTA
1729613 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAATTAATTCATAAAATTAA
Found at i:1729672 original size:23 final size:23
Alignment explanation
Indices: 1729610--1729683 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
1729600 ATTCATAAAA
* **
1729610 TTATTTTTAAAAATATTATTTAA
1 TTATTTTTAAAATTATTATTTTT
* * **
1729633 TAAATTTTAATGTTTATTATTTTT
1 TTATTTTTAA-AATTATTATTTTT
* *
1729657 TTATTTTTAAAATTATAATATTT
1 TTATTTTTAAAATTATTATTTTT
1729680 TTAT
1 TTAT
1729684 ATAAAAATAT
Statistics
Matches: 37, Mismatches: 13, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
23 21 0.57
24 16 0.43
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (23 bp):
TTATTTTTAAAATTATTATTTTT
Found at i:1734566 original size:2 final size:2
Alignment explanation
Indices: 1734561--1734605 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
1734551 GCTATATATA
* * *
1734561 TG TG TG TG TG CG CG TG CG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1734603 TG T
1 TG T
1734606 AAAAGGTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.07, G:0.49, T:0.44
Consensus pattern (2 bp):
TG
Found at i:1740615 original size:13 final size:13
Alignment explanation
Indices: 1740597--1740621 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1740587 ATGTTTTATC
1740597 AGAAAAAAAAAAA
1 AGAAAAAAAAAAA
1740610 AGAAAAAAAAAA
1 AGAAAAAAAAAA
1740622 GAAAGTTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAAAAA
Found at i:1740617 original size:11 final size:11
Alignment explanation
Indices: 1740601--1740625 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1740591 TTTATCAGAA
1740601 AAAAAAAAAAG
1 AAAAAAAAAAG
1740612 AAAAAAAAAAG
1 AAAAAAAAAAG
1740623 AAA
1 AAA
1740626 GTTAACCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:1741673 original size:5 final size:5
Alignment explanation
Indices: 1741663--1741690 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1741653 TTAATTAAAA
1741663 AATTT AATTT AATTT AATTT AATTT AAT
1 AATTT AATTT AATTT AATTT AATTT AAT
1741691 ATAAACACCT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:1742857 original size:16 final size:17
Alignment explanation
Indices: 1742838--1742873 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1742828 TATTTTTATA
1742838 TATTTA-ATAAAAATAT
1 TATTTATATAAAAATAT
1742854 TA-TTATATAAAAATAT
1 TATTTATATAAAAATAT
1742870 TATT
1 TATT
1742874 AATTAATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.17
16 14 0.78
17 1 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTTATATAAAAATAT
Found at i:1742874 original size:16 final size:16
Alignment explanation
Indices: 1742844--1742874 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1742834 TATATATTTA
1742844 ATAAAAATATTATTAT
1 ATAAAAATATTATTAT
1742860 ATAAAAATATTATTA
1 ATAAAAATATTATTA
1742875 ATTAATACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAAATATTATTAT
Found at i:1743380 original size:10 final size:10
Alignment explanation
Indices: 1743365--1743394 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1743355 AAATAAAATT
1743365 TTTAATTTTA
1 TTTAATTTTA
1743375 TTTAA-TTTA
1 TTTAATTTTA
1743384 TTTAATTTTA
1 TTTAATTTTA
1743394 T
1 T
1743395 AAAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTAATTTTA
Found at i:1747740 original size:111 final size:112
Alignment explanation
Indices: 1747402--1747741 Score: 312
Period size: 111 Copynumber: 3.0 Consensus size: 112
1747392 CAACAAAAAA
*
1747402 AAGACCCTGAATTTAGCTTACTGAGTGTTATCCCATGACTTGCTGAGCTCCGTACTGTAGCATCA
1 AAGACCCTGAATTTAGCTTACTGAGTGTTATCCCATGACTTGCTAAGCTCCGTACTGTAGCATCA
*
1747467 TAGGCTTGTAACCAAGAGGGCATTAAGGTACTCCAATCATATGACTTTG
66 TAGGCTTGTAACCAAGAGGGCATTAAGGTACTCCAATCATATGAC--TC
* ** * * * * * * * * * ** ** ** *
1747516 GAGA-GTTCAATATTCCGAGTTTAAAT-ACTTTTTTCCCCA-GCCATGACCAAAATCTTTGGTAT
1 AAGACCCTGAAT-TT---AGCTT-ACTGAGTGTTAT-CCCATGACTTG-CTAAGCTCCGTACTGT
* * * * * *
1747578 A-AAACAAAAGATTTTATACCAAGAGGGCATTAAGGTACTCCAATCATATGAC-C
59 AGCATCATAGGCTTGTA-ACCAAGAGGGCATTAAGGTACTCCAATCATATGACTC
1747631 AAGACCCTGAATTTAGCTTACTGAGTGTTATCCCATGACTTGCTAAGCTCCGTACTGTAGCATCA
1 AAGACCCTGAATTTAGCTTACTGAGTGTTATCCCATGACTTGCTAAGCTCCGTACTGTAGCATCA
1747696 TAGGCTTGTAACCAAGAGGGCATTAAGGTACTCCAATCATATGACT
66 TAGGCTTGTAACCAAGAGGGCATTAAGGTACTCCAATCATATGACT
1747742 TTGGAGAGTT
Statistics
Matches: 161, Mismatches: 52, Indels: 28
0.67 0.22 0.12
Matches are distributed among these distances:
111 50 0.31
112 22 0.14
113 4 0.02
114 5 0.03
115 5 0.03
116 4 0.02
117 22 0.14
118 49 0.30
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (112 bp):
AAGACCCTGAATTTAGCTTACTGAGTGTTATCCCATGACTTGCTAAGCTCCGTACTGTAGCATCA
TAGGCTTGTAACCAAGAGGGCATTAAGGTACTCCAATCATATGACTC
Found at i:1755848 original size:3 final size:3
Alignment explanation
Indices: 1755840--1755880 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1755830 TAACGATAAG
1755840 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1755881 GCAGCAGAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1756666 original size:25 final size:25
Alignment explanation
Indices: 1756638--1756695 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
1756628 TATTGATATA
* *
1756638 TATTTATTTTGTAAAAAAAATTAA-T
1 TATTTATTAT-TAAAAAAAATAAATT
*
1756663 TATTTTATTATTAAATAAAATAAATT
1 TA-TTTATTATTAAAAAAAATAAATT
1756689 TATTTAT
1 TATTTAT
1756696 AAATTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TATTTATTATTAAAAAAAATAAATT
Found at i:1757534 original size:37 final size:36
Alignment explanation
Indices: 1757474--1757543 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
1757464 TTAATGTATT
* *
1757474 AATTTTTTAAATTTAATAAAAATAATTTTTAAAGTGA
1 AATTTTTTAAATATAATAAAAAT-ATTGTTAAAGTGA
*
1757511 AATTTTTTAAATGATAAT-TAAATATTGTTAAAG
1 AATTTTTTAAAT-ATAATAAAAATATTGTTAAAG
1757544 GCTAATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 9 0.31
37 16 0.55
38 4 0.14
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (36 bp):
AATTTTTTAAATATAATAAAAATATTGTTAAAGTGA
Found at i:1758507 original size:19 final size:19
Alignment explanation
Indices: 1758470--1758518 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1758460 ATATTGTATG
*
1758470 AATATAATGTTATTTAATA-
1 AATATAAT-ATATTTAATAT
1758489 AATATAATATATTTAAATAT
1 AATATAATATATTT-AATAT
1758509 AA-ATAATATA
1 AATATAATATA
1758519 ATATAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 5 0.19
19 20 0.74
20 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AATATAATATATTTAATAT
Found at i:1759862 original size:2 final size:2
Alignment explanation
Indices: 1759849--1759881 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1759839 CAAATGACCA
*
1759849 AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1759882 AATTGATGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1774174 original size:2 final size:2
Alignment explanation
Indices: 1774167--1774214 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1774157 TTTACAGCTC
1774167 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1774209 AT AT AT
1 AT AT AT
1774215 GCATCATTGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1774437 original size:2 final size:2
Alignment explanation
Indices: 1774430--1774467 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1774420 TCTATGAACC
1774430 TA TA TA 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
1774468 CACTCTGCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1783026 original size:11 final size:11
Alignment explanation
Indices: 1783010--1783040 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
1783000 AAATTAAAAA
1783010 ATAAAATTTTT
1 ATAAAATTTTT
1783021 ATAAAATTTTT
1 ATAAAATTTTT
1783032 ATAAAATTT
1 ATAAAATTT
1783041 AAATTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATAAAATTTTT
Found at i:1785839 original size:19 final size:19
Alignment explanation
Indices: 1785800--1785840 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1785790 ATTTAAATTT
*
1785800 TTTTAAAATTAAATTTTAA
1 TTTTAAAATTAAATTTAAA
1785819 TTTTAAAATTTAAA-TTAAA
1 TTTTAAAA-TTAAATTTAAA
1785838 TTT
1 TTT
1785841 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTAAAATTAAATTTAAA
Found at i:1785841 original size:18 final size:18
Alignment explanation
Indices: 1785801--1785867 Score: 57
Period size: 18 Copynumber: 3.7 Consensus size: 18
1785791 TTTAAATTTT
*
1785801 TTTAAAA-TTAAATTTTAAT
1 TTTAAAATTTAAA--TTAAA
1785820 TTTAAAATTTAAATTAAA
1 TTTAAAATTTAAATTAAA
* * *
1785838 TTT-AATTTTAAAATCAA
1 TTTAAAATTTAAATTAAA
*
1785855 TATAAAATTTAAA
1 TTTAAAATTTAAA
1785868 AAATTAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 13 0.32
18 15 0.38
19 7 0.17
20 5 0.12
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTAAAATTTAAATTAAA
Found at i:1785862 original size:24 final size:24
Alignment explanation
Indices: 1785809--1785866 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
1785799 TTTTTAAAAT
* *
1785809 TAAATTTTAATTTTAAAATTTAAA
1 TAAAATTTAATTTTAAAATTCAAA
*
1785833 TTAAATTTAATTTTAAAA-TCAATA
1 TAAAATTTAATTTTAAAATTCAA-A
1785857 TAAAATTTAA
1 TAAAATTTAA
1785867 AAAATTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 3 0.10
24 26 0.90
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAAATTTAATTTTAAAATTCAAA
Found at i:1785867 original size:30 final size:26
Alignment explanation
Indices: 1785801--1785851 Score: 88
Period size: 24 Copynumber: 2.0 Consensus size: 26
1785791 TTTAAATTTT
1785801 TTTAAAATTAAATTTTAATTTTAAAA
1 TTTAAAATTAAATTTTAATTTTAAAA
1785827 TTT-AAATTAAA-TTTAATTTTAAAA
1 TTTAAAATTAAATTTTAATTTTAAAA
1785851 T
1 T
1785852 CAATATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 14 0.56
25 8 0.32
26 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTAAAATTAAATTTTAATTTTAAAA
Found at i:1785868 original size:18 final size:17
Alignment explanation
Indices: 1785821--1785893 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
1785811 AATTTTAATT
*
1785821 TTAAAATTTAAATTAAA
1 TTAAAATTTAAAATAAA
* * *
1785838 TTTAATTTTAAAATCAA
1 TTAAAATTTAAAATAAA
1785855 TATAAAATTT-AAA-AAA
1 T-TAAAATTTAAAATAAA
*
1785871 TTAAAA-ATAAAATAAA
1 TTAAAATTTAAAATAAA
*
1785887 TAAAAAT
1 TTAAAAT
1785894 CCATCTCGAC
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
14 1 0.02
15 8 0.19
16 11 0.26
17 17 0.40
18 6 0.14
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAAATTTAAAATAAA
Found at i:1785985 original size:3 final size:3
Alignment explanation
Indices: 1785977--1786008 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1785967 TGAAGTTTTA
1785977 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1786009 ATTATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:1786439 original size:18 final size:18
Alignment explanation
Indices: 1786383--1786441 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
1786373 TCTTCATTGT
*
1786383 TAAATTTTTATTTTAAATA
1 TAAATATTTA-TTTAAATA
* * *
1786402 -AAATATTAATTT-ATTT
1 TAAATATTTATTTAAATA
*
1786418 TAAATATTTATTTAAGTA
1 TAAATATTTATTTAAATA
1786436 TAAATA
1 TAAATA
1786442 AAAAATTTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
16 2 0.06
17 14 0.45
18 15 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TAAATATTTATTTAAATA
Found at i:1786491 original size:31 final size:30
Alignment explanation
Indices: 1786426--1786494 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
1786416 TTTAAATATT
* ** *
1786426 TATTTAAGTATAAATAAAAAATTTATAATT
1 TATTTAAATATAAATAAAAAAAATATAATA
1786456 TATTTAAATATAAATTAAAAAAAA-ATAAATA
1 TATTTAAATATAAA-TAAAAAAAATAT-AATA
1786487 TATTTAAA
1 TATTTAAA
1786495 ATTATTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (30 bp):
TATTTAAATATAAATAAAAAAAATATAATA
Found at i:1786667 original size:20 final size:19
Alignment explanation
Indices: 1786642--1786705 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 19
1786632 ACGTAAAAAA
1786642 ATAAATAAATTAAAATTAAT
1 ATAAATAAATTAAAATT-AT
*
1786662 ATAAATATATTAAAATTTAT
1 ATAAATAAATTAAAA-TTAT
* *
1786682 ATAACATAAAATATAATTAT
1 ATAA-ATAAATTAAAATTAT
1786702 ATAA
1 ATAA
1786706 TATTTTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 28 0.74
21 10 0.26
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAATAAATTAAAATTAT
Found at i:1793400 original size:25 final size:28
Alignment explanation
Indices: 1793343--1793404 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 28
1793333 AATTTATTTT
*
1793343 TATTTAAAT-TTAATTATAAAATATTAA
1 TATTTTAATATTAATTATAAAATATTAA
1793370 TA--TTAATATTAA-TATAAAA-A-TAA
1 TATTTTAATATTAATTATAAAATATTAA
1793393 TATTTTAATATT
1 TATTTTAATATT
1793405 TTTAATTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
23 5 0.16
24 1 0.03
25 19 0.61
26 4 0.13
27 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TATTTTAATATTAATTATAAAATATTAA
Found at i:1793522 original size:19 final size:19
Alignment explanation
Indices: 1793498--1793544 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1793488 AATAAAATTT
1793498 AAAATATATTTA-ACTATAA
1 AAAATATATTTATAC-ATAA
* * *
1793517 AAAATAAACTTATACATAT
1 AAAATATATTTATACATAA
1793536 AAAATATAT
1 AAAATATAT
1793545 ACAATATTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 20 0.91
20 2 0.09
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATATATTTATACATAA
Found at i:1794066 original size:24 final size:24
Alignment explanation
Indices: 1794014--1794097 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
1794004 ATTATTAAAA
* * *
1794014 ATAATTTTATAAACTTTTAA-ATG
1 ATAATTATATAAATTTTTAATATT
*
1794037 ATTAATTATATTAATTTTT-ATATTT
1 A-TAATTATATAAATTTTTAATA-TT
1794062 ATAA-TATAATAAATTTTTAATATT
1 ATAATTAT-ATAAATTTTTAATATT
*
1794086 ATATTTATATAA
1 ATAATTATATAA
1794098 TAGAATCATA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
23 5 0.10
24 36 0.73
25 8 0.16
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (24 bp):
ATAATTATATAAATTTTTAATATT
Found at i:1794856 original size:12 final size:11
Alignment explanation
Indices: 1794802--1794859 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 11
1794792 AATATTTTTT
1794802 ATTATAAAT--
1 ATTATAAATAA
1794811 ATTATAAATCAAA
1 ATTATAAAT--AA
1794824 ATTA-AAA-AA
1 ATTATAAATAA
*
1794833 ATTATTAATAA
1 ATTATAAATAA
1794844 ATTATAAATTAA
1 ATTATAAA-TAA
1794856 ATTA
1 ATTA
1794860 GATTGAATTG
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
9 15 0.38
10 2 0.05
11 9 0.22
12 10 0.25
13 4 0.10
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTATAAATAA
Done.