Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002890.1 Hibiscus syriacus cultivar Beakdansim tig00005974_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5046466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 21
Found at i:1776307 original size:39 final size:39
Alignment explanation
Indices: 1776225--1776328 Score: 113
Period size: 39 Copynumber: 2.7 Consensus size: 39
1776215 ATGCTCTTCA
* * * *
1776225 GCTTTGTGCTCAAGGTAAGTCCTTATTGTAGGCTTATTG
1 GCTTTGTGCTCAGGGTAAGACCTTACTGCAGGCTTATTG
*
1776264 GCTTTGTGCTCAGGGTAAGACCTTACTGCAGGCTTCTCT-
1 GCTTTGTGCTCAGGGTAAGACCTTACTGCAGGCTTAT-TG
* *
1776303 GCTTTGAGCAT-AGGGTAAGCCCTTAC
1 GCTTTGTGC-TCAGGGTAAGACCTTAC
1776329 CGAGTGTACA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 54 0.96
40 2 0.04
ACGTcount: A:0.18, C:0.21, G:0.26, T:0.35
Consensus pattern (39 bp):
GCTTTGTGCTCAGGGTAAGACCTTACTGCAGGCTTATTG
Found at i:1779806 original size:39 final size:39
Alignment explanation
Indices: 1779763--1779844 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
1779753 ACCACTTTCC
* * *
1779763 GCAGGCTCCTTAGCTTTGTGCTCAGGGTAAGTCCTTACT
1 GCAGGATCCTTAGCTTTGTGCTCAGGGTAAGACATTACT
* * * *
1779802 GCAGGATCTTTGGCTTTGTGTTGAGGGTAAGACATTACT
1 GCAGGATCCTTAGCTTTGTGCTCAGGGTAAGACATTACT
1779841 GCAG
1 GCAG
1779845 ACTCTTCTGT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (39 bp):
GCAGGATCCTTAGCTTTGTGCTCAGGGTAAGACATTACT
Found at i:1787467 original size:47 final size:47
Alignment explanation
Indices: 1787397--1787638 Score: 398
Period size: 47 Copynumber: 5.2 Consensus size: 47
1787387 TATAAAATCT
* * * * *
1787397 CTTACCATTT--ATCCCATAAGCTCGTAAGCTCATTATACCAAAATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
*
1787442 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAACATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1787489 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
*
1787536 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTTTTTTATCAATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1787583 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
*
1787630 CTTGCCATT
1 CTTACCATT
1787639 ATGCATAAGC
Statistics
Matches: 186, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
45 10 0.05
47 176 0.95
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (47 bp):
CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
Found at i:1789682 original size:30 final size:29
Alignment explanation
Indices: 1789623--1789701 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 29
1789613 ATTTGTAATT
* * *
1789623 TTTCCAAAATTATATTTTGGTCCCTAAAC
1 TTTCCAAATTTATAATTTGATCCCTAAAC
*
1789652 TTTCCAAAGTTTATACTTTGATCACC-AAAC
1 TTTCCAAA-TTTATAATTTGATC-CCTAAAC
1789682 TTTACCAAATTTATAATTTG
1 TTT-CCAAATTTATAATTTG
1789702 GTCATTAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
29 8 0.19
30 28 0.65
31 7 0.16
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (29 bp):
TTTCCAAATTTATAATTTGATCCCTAAAC
Found at i:1791517 original size:16 final size:15
Alignment explanation
Indices: 1791498--1791579 Score: 62
Period size: 16 Copynumber: 5.3 Consensus size: 15
1791488 CATCTTTACA
1791498 TTTTTTTCTCTTTTTC
1 TTTTTTT-TCTTTTTC
1791514 TTTTCTTTTCTTTTTC
1 TTTT-TTTTCTTTTTC
*
1791530 AATTTTTTTTCATTTTC
1 --TTTTTTTTCTTTTTC
* *
1791547 ATTTTATTT-TTTAT-
1 -TTTTTTTTCTTTTTC
*
1791561 TGTTTTTTCTTTTT-
1 TTTTTTTTCTTTTTC
1791575 TTTTT
1 TTTTT
1791580 CTGTTTTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
13 6 0.11
14 8 0.15
15 3 0.06
16 20 0.37
17 13 0.24
18 4 0.07
ACGTcount: A:0.07, C:0.11, G:0.01, T:0.80
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:1791539 original size:17 final size:17
Alignment explanation
Indices: 1791496--1791556 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
1791486 TTCATCTTTA
1791496 CATTTT-TTTCTCTTTTT
1 CATTTTATTT-TCTTTTT
*
1791513 C-TTTTCTTTTCTTTTT
1 CATTTTATTTTCTTTTT
*
1791529 CAATTTT-TTTTCATTTT
1 C-ATTTTATTTTCTTTTT
1791546 CATTTTATTTT
1 CATTTTATTTT
1791557 TTATTGTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
16 17 0.44
17 18 0.46
18 4 0.10
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.75
Consensus pattern (17 bp):
CATTTTATTTTCTTTTT
Found at i:1791578 original size:10 final size:10
Alignment explanation
Indices: 1791498--1791588 Score: 58
Period size: 11 Copynumber: 8.7 Consensus size: 10
1791488 CATCTTTACA
*
1791498 TTTTTTTCTC
1 TTTTTTTTTC
1791508 TTTTTCTTTTC
1 TTTTT-TTTTC
1791519 TTTTCTTTTTC
1 TTTT-TTTTTC
*
1791530 AATTTTTTTTC
1 -TTTTTTTTTC
* **
1791541 ATTTTCATT-
1 TTTTTTTTTC
* *
1791550 TTATTTTTTA
1 TTTTTTTTTC
*
1791560 TTGTTTTTTC
1 TTTTTTTTTC
1791570 TTTTTTTTTTC
1 -TTTTTTTTTC
1791581 TGTTTTTT
1 T-TTTTTT
1791589 ATATATTATT
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
9 5 0.08
10 21 0.33
11 34 0.53
12 4 0.06
ACGTcount: A:0.07, C:0.11, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:1794434 original size:47 final size:47
Alignment explanation
Indices: 1794364--1794582 Score: 333
Period size: 47 Copynumber: 4.8 Consensus size: 47
1794354 TATAAAATCT
* * * *
1794364 CTTACCATTT--ATCCCATAAGCTCGTAAGCTCATTTTACCAAAATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1794409 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1794456 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
*
1794503 TTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
* *
1794550 CTTGCCA-TT--ATT-CATAAGCTCATAAGCTTATTT
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTT
1794583 GCATACTTAC
Statistics
Matches: 164, Mismatches: 8, Indels: 6
0.92 0.04 0.03
Matches are distributed among these distances:
43 20 0.12
44 3 0.02
45 10 0.06
46 2 0.01
47 129 0.79
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.40
Consensus pattern (47 bp):
CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
Found at i:1794812 original size:61 final size:61
Alignment explanation
Indices: 1794697--1794812 Score: 135
Period size: 61 Copynumber: 1.9 Consensus size: 61
1794687 CTAAACCTGC
* * * *
1794697 ACTAAGCTTACGCCATAGTGTTAATCCAGATATGACACATAAGGTCGTGCCCACCACCTAT
1 ACTAAGCTTACACCATAGTGCTAATCCAGACATGACACATAAGGTCGTACCCACCACCTAT
* * * * *
1794758 ACTAAGCTTACACTATAGTGCTAATCC-GAACATGATACATTAGGTTGTATCCACC
1 ACTAAGCTTACACCATAGTGCTAATCCAG-ACATGACACATAAGGTCGTACCCACC
1794813 TTACCGCACT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
60 1 0.02
61 44 0.98
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.27
Consensus pattern (61 bp):
ACTAAGCTTACACCATAGTGCTAATCCAGACATGACACATAAGGTCGTACCCACCACCTAT
Found at i:1795766 original size:29 final size:29
Alignment explanation
Indices: 1795700--1795766 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
1795690 CAACAACTCA
* * * *
1795700 TCAATTTTCCAGAATTTATGAATTGATCC
1 TCAATTTTTCAAAACTTATGAAATGATCC
* * *
1795729 CCAACTTTTCAAAACTTATGAAATGGTCC
1 TCAATTTTTCAAAACTTATGAAATGATCC
1795758 TCAATTTTT
1 TCAATTTTT
1795767 GTAAGGCTTG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.40
Consensus pattern (29 bp):
TCAATTTTTCAAAACTTATGAAATGATCC
Found at i:1797137 original size:20 final size:19
Alignment explanation
Indices: 1797085--1797144 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 19
1797075 TTCTAAACCG
1797085 TTTATTTTGATTTTTAAAA
1 TTTATTTTGATTTTTAAAA
** * *
1797104 TTTATAAATCATTTTTAAAGT
1 TTTAT-TTTGATTTTTAAA-A
*
1797125 TTTATTTTGATTTTCAAAA
1 TTTATTTTGATTTTTAAAA
1797144 T
1 T
1797145 CAACTTTGGC
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
19 6 0.20
20 19 0.63
21 5 0.17
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.58
Consensus pattern (19 bp):
TTTATTTTGATTTTTAAAA
Found at i:1797152 original size:19 final size:19
Alignment explanation
Indices: 1797130--1797166 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1797120 AAAGTTTTAT
*
1797130 TTTGATTTTCAAAATCAAC
1 TTTGACTTTCAAAATCAAC
*
1797149 TTTGGCTTTCAAAATCAA
1 TTTGACTTTCAAAATCAA
1797167 ATCATTTTCA
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:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (19 bp):
TTTGACTTTCAAAATCAAC
Found at i:1798134 original size:64 final size:65
Alignment explanation
Indices: 1797929--1798138 Score: 214
Period size: 65 Copynumber: 3.2 Consensus size: 65
1797919 TTTTTCAGAG
* * * **
1797929 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGAATTAAATTG--AACATCGAATGC
1 TGATGCATCGATGCACCAA-CCATGCACCGATGCACTCA-GGATTTTA-TGAAAACATCGAATGC
1797991 ATT
63 ATT
* ** *
1797994 TCATGCATCGATGCACTTACCATGCACCGATGCACTGAGGATTTTATGAAAACATCGAATGCATT
1 TGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATTTTATGAAAACATCGAATGCATT
* ** * * *
1798059 TGATGCATCGATGCACCAACCGTGCATTGATGCACTCTGGCTATTT-TG-AAACATCGAATGCAC
1 TGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGAT-TTTATGAAAACATCGAATGCAT
1798122 T
65 T
1798123 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
1798139 TCTGGCTATT
Statistics
Matches: 122, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
63 2 0.02
64 51 0.42
65 66 0.54
66 3 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (65 bp):
TGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGATTTTATGAAAACATCGAATGCATT
Found at i:1798137 original size:45 final size:45
Alignment explanation
Indices: 1798081--1798186 Score: 203
Period size: 45 Copynumber: 2.4 Consensus size: 45
1798071 GCACCAACCG
*
1798081 TGCATTGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGA
1 TGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGA
1798126 TGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGA
1 TGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGA
1798171 TGCATCGATGCACTCT
1 TGCATCGATGCACTCT
1798187 TAGTGCACCG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (45 bp):
TGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGA
Found at i:1798183 original size:17 final size:19
Alignment explanation
Indices: 1798155--1798203 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1798145 TATTTTGAAA
1798155 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
1798173 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
1798192 CACCGATGCACT
1 CATCGATGCACT
1798204 AAGGGCCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:1798442 original size:11 final size:11
Alignment explanation
Indices: 1798422--1798457 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1798412 ACAAGCAACT
1798422 AGAATCAAGAG
1 AGAATCAAGAG
*
1798433 AGAATGAAGAG
1 AGAATCAAGAG
1798444 AGAATCAA-AG
1 AGAATCAAGAG
1798454 AGAA
1 AGAA
1798458 AGCATCAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.26
11 17 0.74
ACGTcount: A:0.58, C:0.06, G:0.28, T:0.08
Consensus pattern (11 bp):
AGAATCAAGAG
Found at i:1805483 original size:21 final size:21
Alignment explanation
Indices: 1805441--1805484 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1805431 ACTCCGGGAG
* *
1805441 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
1805462 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
1805483 CT
1 CT
1805485 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:1806612 original size:65 final size:64
Alignment explanation
Indices: 1806499--1806697 Score: 183
Period size: 65 Copynumber: 3.1 Consensus size: 64
1806489 AGTGATGCAC
* * * *
1806499 CGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGCATTTCATG
1 CGATGCACC-AGCCATGCACCGATGCACTCAGGATATT---TTGAAACATCGAATGCATTTGATG
1806561 AAT
62 AAT
* * *
1806564 CGATGCACTTA-CCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGC
1 CGATGCAC-CAGCCATGCACCGATGCACTCAGGATATTT-TG-AAACATCGAATGCATTTGATGA
1806627 AT
63 AT
* * * * * *
1806629 CGATGCACCAGGCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGTAT
1 CGATGCACCAGCCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTGATGAAT
1806693 CGATG
1 CGATG
1806698 TACTCTTAGT
Statistics
Matches: 112, Mismatches: 14, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 43 0.38
65 63 0.56
66 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (64 bp):
CGATGCACCAGCCATGCACCGATGCACTCAGGATATTTTGAAACATCGAATGCATTTGATGAAT
Found at i:1808988 original size:20 final size:20
Alignment explanation
Indices: 1808965--1809002 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1808955 TTGGTATCGG
1808965 TACCATATGAACAGTATCTA
1 TACCATATGAACAGTATCTA
1808985 TACCATATGAACAGTATC
1 TACCATATGAACAGTATC
1809003 AATATTGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (20 bp):
TACCATATGAACAGTATCTA
Found at i:1816528 original size:22 final size:23
Alignment explanation
Indices: 1816500--1816543 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1816490 TTTCTGTTTG
1816500 GGTGTTA-TTTGTGTAAA-ATTTA
1 GGTGTTAGTTTG-GTAAATATTTA
1816522 GGTGTTAGTTTGGTAAATATTT
1 GGTGTTAGTTTGGTAAATATTT
1816544 GTAAAATGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (23 bp):
GGTGTTAGTTTGGTAAATATTTA
Found at i:1821570 original size:22 final size:23
Alignment explanation
Indices: 1821542--1821585 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
1821532 TTTCTGTTTG
1821542 GGTGTTA-TTTGTGTAAA-ATTTA
1 GGTGTTAGTTTG-GTAAATATTTA
1821564 GGTGTTAGTTTGGTAAATATTT
1 GGTGTTAGTTTGGTAAATATTT
1821586 GCAGAATGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (23 bp):
GGTGTTAGTTTGGTAAATATTTA
Found at i:1824452 original size:32 final size:31
Alignment explanation
Indices: 1824379--1824455 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
1824369 TTAATGTGAC
* *
1824379 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
** * **
1824410 TCTCGGGTAGGCCCTGTGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-CAT
1824442 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
1824456 CATGGCCCCA
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATCAT
Found at i:1826599 original size:26 final size:26
Alignment explanation
Indices: 1826563--1826644 Score: 128
Period size: 26 Copynumber: 3.2 Consensus size: 26
1826553 ATAAACTGAT
1826563 GCCCCTACATGCTGCCCTGGGCCGTC
1 GCCCCTACATGCTGCCCTGGGCCGTC
* *
1826589 GCCCCTACATGCTGCCCTGTGTCGTC
1 GCCCCTACATGCTGCCCTGGGCCGTC
* *
1826615 GCCCCTACATTCTGCCCTGGGCTGTC
1 GCCCCTACATGCTGCCCTGGGCCGTC
1826641 GCCC
1 GCCC
1826645 ATCTGGCACA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.07, C:0.45, G:0.24, T:0.23
Consensus pattern (26 bp):
GCCCCTACATGCTGCCCTGGGCCGTC
Found at i:1830570 original size:27 final size:29
Alignment explanation
Indices: 1830540--1830601 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 29
1830530 ATAACATAAT
*
1830540 TTAATTTAGTTCCTAAACATGTT-TAT-C
1 TTAATTTAGTTCCTAAACAGGTTGTATGC
**
1830567 TTAACCTAGTTCCTAAACAGGTTGTATGC
1 TTAATTTAGTTCCTAAACAGGTTGTATGC
1830596 TTAATT
1 TTAATT
1830602 AAGGGTCGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 20 0.71
28 3 0.11
29 5 0.18
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (29 bp):
TTAATTTAGTTCCTAAACAGGTTGTATGC
Found at i:1831123 original size:15 final size:16
Alignment explanation
Indices: 1831095--1831132 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1831085 TTATATGGTT
*
1831095 TAAAAATGACAATAAC
1 TAAAAAGGACAATAAC
*
1831111 TAAAAAGGA-AATAAT
1 TAAAAAGGACAATAAC
1831126 TAAAAAG
1 TAAAAAG
1831133 TTAAATTACC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.66, C:0.05, G:0.11, T:0.18
Consensus pattern (16 bp):
TAAAAAGGACAATAAC
Found at i:1832429 original size:21 final size:21
Alignment explanation
Indices: 1832405--1832448 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1832395 GGGGAGAGTT
1832405 TTGAAAA-TATTTGGTCCATAA
1 TTGAAAACT-TTTGGTCCATAA
*
1832426 TTGAAAACTTTTGGTCCTTAA
1 TTGAAAACTTTTGGTCCATAA
1832447 TT
1 TT
1832449 TTTAGAGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (21 bp):
TTGAAAACTTTTGGTCCATAA
Found at i:1834050 original size:3 final size:3
Alignment explanation
Indices: 1834042--1834097 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
1834032 TCCGGGTTTA
* * *
1834042 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAC TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1834090 TAT TAT TA
1 TAT TAT TA
1834098 CTTTTGCAGG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1844057 original size:20 final size:20
Alignment explanation
Indices: 1844034--1844095 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 20
1844024 ATTGTTTTTC
1844034 CTTGAAACATAAGATTTTAT
1 CTTGAAACATAAGATTTTAT
*
1844054 CTTG---C-TCAAGATTGTTTTT
1 CTTGAAACAT-AAGA-T-TTTAT
1844073 CCTTGAAACATAAGATTTTAT
1 -CTTGAAACATAAGATTTTAT
1844094 CT
1 CT
1844096 CACTCAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 16
0.64 0.04 0.32
Matches are distributed among these distances:
16 1 0.03
17 5 0.16
18 1 0.03
19 4 0.12
20 10 0.31
21 4 0.12
22 1 0.03
23 5 0.16
24 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (20 bp):
CTTGAAACATAAGATTTTAT
Found at i:1844423 original size:40 final size:40
Alignment explanation
Indices: 1843882--1844430 Score: 710
Period size: 40 Copynumber: 13.7 Consensus size: 40
1843872 CATTTAATAT
* * *
1843882 AGAATATTTTATCTC-ATTCAAGATTCTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGCTT-AAGATTGTTTTTCCTTGAAAC
*
1843922 AGAAGATTTTATCTCG-TTCAAGATTGTTTTTCTTTGAAAC
1 AGAAGATTTTATCTCGCTT-AAGATTGTTTTTCCTTGAAAC
*
1843962 AGAAGATTTTATCTCG-TTCATGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGCTT-AAGATTGTTTTTCCTTGAAAC
* *
1844002 TGAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGCTTAAGATTGTTTTTCCTTGAAAC
* * *
1844042 ATAAGATTTTATCTTGCTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGCTTAAGATTGTTTTTCCTTGAAAC
* * *
1844082 ATAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGCTTAAGATTGTTTTTCCTTGAAAC
* * *
1844122 ATAAGATTTTATCTCACTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGCTTAAGATTGTTTTTCCTTGAAAC
* *
1844162 AGAAGATTTTATCTTGCTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGCTTAAGATTGTTTTTCCTTGAAAC
* *
1844202 ATAAGATTTTATCTCACTTAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGCTTAAGATTGTTTTTCCTTGAAAC
* *
1844242 AAAAGATTTTATCTCGCTCAAGATTGTTTTTCCTTGAAAC
1 AGAAGATTTTATCTCGCTTAAGATTGTTTTTCCTTGAAAC
* * *
1844282 AGAAGATTTTATCTCACTTGAGATTGTTTTTCCTCGAAAC
1 AGAAGATTTTATCTCGCTTAAGATTGTTTTTCCTTGAAAC
* * *
1844322 AAAAGATTTTATCTCGCTTGAGATTGTTTTTCCTCGAAAC
1 AGAAGATTTTATCTCGCTTAAGATTGTTTTTCCTTGAAAC
* * * *
1844362 AAAAGATTTTATCTCGTTTGAGATTGTTTTT-CTTCAAAAC
1 AGAAGATTTTATCTCGCTTAAGATTGTTTTTCCTT-GAAAC
* * * *
1844402 AAAAGATTTTATCCCGCTTGAGATAGTTT
1 AGAAGATTTTATCTCGCTTAAGATTGTTT
1844431 CCCTCGAAAC
Statistics
Matches: 470, Mismatches: 36, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
39 2 0.00
40 467 0.99
41 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (40 bp):
AGAAGATTTTATCTCGCTTAAGATTGTTTTTCCTTGAAAC
Found at i:1844564 original size:35 final size:36
Alignment explanation
Indices: 1844418--1844597 Score: 166
Period size: 35 Copynumber: 4.9 Consensus size: 36
1844408 TTTTATCCCG
* * *
1844418 CTTGAGATAGTTTCCCTCGAAACAAATTTTTTTTGTCTCT
1 CTTGAGACAGTTTCCCTTGAAACAAA----TTTTGTCTCC
* * *** *
1844458 CTTGAGACAATTTCCCTCGAAACAAAAAAAAT-TCTCT
1 CTTGAGACAGTTTCCCTTGAAAC--AAATTTTGTCTCC
* *
1844495 CTTGAGACAATTTCCCTTTAAACAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCC
1844531 CTTGAGACAGTTTCCCTTGAAA-AAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCC
* *
1844566 CTTGAGATAGTTTCTCTTGAAACACAATTTTG
1 CTTGAGACAGTTTCCCTTGAAACA-AATTTTG
1844598 AGAACGTTTC
Statistics
Matches: 120, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
35 37 0.31
36 25 0.21
37 33 0.28
38 1 0.01
40 21 0.17
42 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.38
Consensus pattern (36 bp):
CTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCC
Found at i:1844607 original size:63 final size:63
Alignment explanation
Indices: 1844532--1844660 Score: 181
Period size: 63 Copynumber: 2.0 Consensus size: 63
1844522 TTTGTCTCCC
* * * *
1844532 TTGAGACAGTTTCCCTTGAAAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACACAA-TT
1 TTGAGACAGTTTCCCTTGAAAAAAATTTGTATACCTTGAGACAGTTTCTCTTGAAACA-AAGTT
*
1844595 TTGAGA-ACGTTTCCCTTGAAAAAAATTTGTATATCTTGAGACAGTTTCTCTTGAAACAAAGTT
1 TTGAGACA-GTTTCCCTTGAAAAAAATTTGTATACCTTGAGACAGTTTCTCTTGAAACAAAGTT
1844658 TTG
1 TTG
1844661 TCTCCCTTAA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
62 3 0.05
63 56 0.95
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (63 bp):
TTGAGACAGTTTCCCTTGAAAAAAATTTGTATACCTTGAGACAGTTTCTCTTGAAACAAAGTT
Found at i:1845507 original size:20 final size:20
Alignment explanation
Indices: 1845445--1845508 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
1845435 TTCTAGAAGA
1845445 GTTCATAATGAGAAGAAC-T
1 GTTCATAATGAGAAGAACAT
** * * *
1845464 CATC-CAATGAGGAAGAAGAA
1 GTTCATAATGA-GAAGAACAT
1845484 GTTCATAATGAGAAGAACAT
1 GTTCATAATGAGAAGAACAT
1845504 GTTCA
1 GTTCA
1845509 ACCTTGGTTT
Statistics
Matches: 32, Mismatches: 10, Indels: 5
0.68 0.21 0.11
Matches are distributed among these distances:
18 5 0.16
19 8 0.25
20 14 0.44
21 5 0.16
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACAT
Found at i:1845592 original size:117 final size:117
Alignment explanation
Indices: 1845229--1845980 Score: 845
Period size: 117 Copynumber: 6.6 Consensus size: 117
1845219 CATTTTCAGA
*
1845229 AGAGTTCATAATGAGAAGAACTCGTCCTAA--AGG-AG-A-AAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCC-AATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * * * *
1845289 T---CC-T--TTCAAGTCCATCACAGAAAGAGATGGATCAACATTTCCAATAG
65 TCAACCTTGGTTTAATTCCATCAAAGAAAGAGGTGGATCAATATTTTCAATGG
*
1845336 AGAGTTCATAATGAGAAGAACTCATCCAACGA-G--GAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
** * * * * * * *
1845398 ---CCTT--TCAAATT-CACCATAGAAGGAGGTGAACCAATA-TTTCTA-GA
66 CAACCTTGGTTTAATTCCATCAAAGAAAGAGGTGGATCAATATTTTCAATGG
*
1845442 AGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACATGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * *
1845507 CAACCTTGGTTTGATTCCATCAAAGAAAGAGGTGGATCAACATTTTCAGTGG
66 CAACCTTGGTTTAATTCCATCAAAGAAAGAGGTGGATCAATATTTTCAATGG
* *
1845559 ATAGTTCATACTGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
1845624 CAGCCTTGGTTTGATTCCATCAAAGAAAGAGGTGGATCAAAATTTTCAGTGG
66 CAACCTTGGTTTAATTCCATCAAAGAAAGAGGTGGATCAATATTTTCAATGG
* * * *
1845676 AGTGTTC---ATGAGAAGAACTCATCCAATGAGAAATAAGAAGTTCATAATGAGAATAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * ** *
1845738 CAACCTTGGTTTCAAGTCCACCGTAGAAGGAGGT-GACTCAATATTTTCAATGG
66 CAACCTTGGTTT-AATTCCATCAAAGAAAGAGGTGGA-TCAATATTTTCAATGG
* * * * *
1845791 AGAGTTCATAATGAGAATAACTCATCCAATGAGGGAGGATAAGTTCATAATTAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * * * *
1845856 AAACATTGATTCAATTCCATCACAGAATGAGGTGGATCAATATTTACAATGG
66 CAACCTTGGTTTAATTCCATCAAAGAAAGAGGTGGATCAATATTTTCAATGG
*
1845908 AGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1845973 CAACCTTG
66 CAACCTTG
1845981 CATCAGTATT
Statistics
Matches: 547, Mismatches: 76, Indels: 34
0.83 0.12 0.05
Matches are distributed among these distances:
106 34 0.06
107 33 0.06
108 46 0.08
109 33 0.06
112 4 0.01
114 68 0.12
115 54 0.10
116 4 0.01
117 214 0.39
118 57 0.10
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.26
Consensus pattern (117 bp):
AGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTGGTTTAATTCCATCAAAGAAAGAGGTGGATCAATATTTTCAATGG
Found at i:1845875 original size:232 final size:232
Alignment explanation
Indices: 1845229--1845980 Score: 798
Period size: 232 Copynumber: 3.3 Consensus size: 232
1845219 CATTTTCAGA
*
1845229 AGAGTTCATAATGAGAAGAACTCGTCCTAA--AGG-AG-A-AAGTTCATAATGAGAAGAACTTGT
1 AGAGTTC--AATGAGAAGAACTCATCC-AATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * * *
1845289 T---CC-T--TTCAAGTCCATCACAGAAAGAGATGGATCAACATTTCCAATAGAGAGTTCATAAT
63 TCAACCTTGGTTTAAGTCCACCAAAGAAAGAGGTGGATCAACATTTTCAATGGAGAGTTCATAAT
* *
1845348 GAGAAGAACTCATCCAACGA-G--GAAGAAGTTCATAATGAGAAGAACTTGTT---C-CT--TTC
128 GAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACATTGATTC
* * * * * * * *
1845404 AAATT-CACCATAGAAGGAGGTGAACCAATATTT-CTA-GA
193 -AATTCCATCAAAGAAAGAGGTGGATCAAAATTTACAATGG
*
1845442 AGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACATGTT
1 AGAGTTC--AATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * * *
1845507 CAACCTTGGTTTGATTCCATCAAAGAAAGAGGTGGATCAACATTTTCAGTGGATAGTTCATACTG
64 CAACCTTGGTTTAAGTCCACCAAAGAAAGAGGTGGATCAACATTTTCAATGGAGAGTTCATAATG
* * * * **
1845572 AGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAGCCTTGGTTTG
129 AGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACATTGATTCA
* *
1845637 ATTCCATCAAAGAAAGAGGTGGATCAAAATTTTCAGTGG
194 ATTCCATCAAAGAAAGAGGTGGATCAAAATTTACAATGG
* * * *
1845676 AGTGTTC-ATGAGAAGAACTCATCCAATGAGAAATAAGAAGTTCATAATGAGAATAACTTGTTCA
1 AGAGTTCAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
** * *
1845740 ACCTTGGTTTCAAGTCCACCGTAGAAGGAGGT-GACTCAATATTTTCAATGGAGAGTTCATAATG
66 ACCTTGGTTT-AAGTCCACCAAAGAAAGAGGTGGA-TCAACATTTTCAATGGAGAGTTCATAATG
* * * * *
1845804 AGAATAACTCATCCAATGAGGGAGGATAAGTTCATAATTAGAAGAACTTGTTAAACATTGATTCA
129 AGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACATTGATTCA
* * *
1845869 ATTCCATCACAGAATGAGGTGGATCAATATTTACAATGG
194 ATTCCATCAAAGAAAGAGGTGGATCAAAATTTACAATGG
*
1845908 AGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTC--AATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1845973 CAACCTTG
64 CAACCTTG
1845981 CATCAGTATT
Statistics
Matches: 450, Mismatches: 61, Indels: 34
0.83 0.11 0.06
Matches are distributed among these distances:
212 2 0.00
213 26 0.06
214 3 0.01
215 2 0.00
216 1 0.00
217 24 0.05
220 2 0.00
221 1 0.00
223 64 0.14
224 1 0.00
226 29 0.06
229 1 0.00
230 1 0.00
231 68 0.15
232 158 0.35
233 1 0.00
234 7 0.02
235 59 0.13
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.26
Consensus pattern (232 bp):
AGAGTTCAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
ACCTTGGTTTAAGTCCACCAAAGAAAGAGGTGGATCAACATTTTCAATGGAGAGTTCATAATGAG
AAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTAAACATTGATTCAAT
TCCATCAAAGAAAGAGGTGGATCAAAATTTACAATGG
Found at i:1845929 original size:349 final size:335
Alignment explanation
Indices: 1845229--1845980 Score: 912
Period size: 349 Copynumber: 2.2 Consensus size: 335
1845219 CATTTTCAGA
*
1845229 AGAGTTCATAATGAGAAGAACTCGTCCTAA-AGG-AG-A-AAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCC-AAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
1845290 --CC-T-TTCAAGTCCATCACAGAAAGAGATGGATCAACATTTCCAATAGAGAGTTCATAATGAG
65 CACCTTGTTCAAGTCCATCAAAGAAAGAGATGGATCAAAATTTCCAATAGAGAGTTC--AATGAG
*
1845351 AAGAACTCATCCAACGAGGAAGAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATTCACCATA
128 AAGAACTCATCCAACGAGGAAGAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCACCATA
*
1845416 GAAGGAGGTGAACCAATATTTCTAGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAA
193 GAAGGAGGTGAACCAATATTTCAAGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAA
* * * **
1845481 GAAGTTCATAATGAGAAGAACATGTTCAACCTTGGTTTGATTCCATCAAAGAAAGAGGTGGATCA
258 GAAGTTCATAATGAGAAGAACATGTTAAACATTGATTCAATTCCATCAAAGAAAGAGGTGGATCA
* *
1845546 ACATTTTCAGTGG
323 ACATTTACAATGG
* *
1845559 ATAGTTCATACTGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCAA-GAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
** * * * * * *
1845624 CAGCCTTGGTTTGATTCCATCAAAGAAAGAGGTGGATCAAAATTTTCAGTGGAGTGTTC-ATGAG
65 CA-CCTT-GTTCAAGTCCATCAAAGAAAGAGATGGATCAAAATTTCCAATAGAGAGTTCAATGAG
* * *
1845688 AAGAACTCATCCAATGAGAAATAAGAAGTTCATAATGAGAATAACTTGTTCAACCTTGGTTTCAA
128 AAGAACTCATCCAACGAG---GAAGAAGTTCATAATGAGAAGAACTTGTT---CC----TTTCAA
* * * *
1845753 GTCCACCGTAGAAGGAGGTG-ACTCAATATTTTCAATGGAGAGTTCATAATGAGAATAACTCATC
183 ATCCACCATAGAAGGAGGTGAAC-CAATA-TTTCAA-GAAGAGTTCATAATGAGAAGAACTCATC
* * * * * *
1845817 CAATGAGGGAGGATAAGTTCATAATTAGAAGAACTTGTTAAACATTGATTCAATTCCATCACAGA
245 CAATGAGGAAGAAGAAGTTCATAATGAGAAGAACATGTTAAACATTGATTCAATTCCATCAAAGA
* *
1845882 ATGAGGTGGATCAATATTTACAATGG
310 AAGAGGTGGATCAACATTTACAATGG
1845908 AGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCC-AAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1845973 CAACCTTG
65 C-ACCTTG
1845981 CATCAGTATT
Statistics
Matches: 357, Mismatches: 39, Indels: 34
0.83 0.09 0.08
Matches are distributed among these distances:
329 2 0.01
330 24 0.07
331 3 0.01
332 2 0.01
333 1 0.00
334 25 0.07
337 24 0.07
338 1 0.00
340 67 0.19
343 2 0.01
346 2 0.01
347 28 0.08
348 6 0.02
349 167 0.47
350 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.26
Consensus pattern (335 bp):
AGAGTTCATAATGAGAAGAACTCATCCAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
ACCTTGTTCAAGTCCATCAAAGAAAGAGATGGATCAAAATTTCCAATAGAGAGTTCAATGAGAAG
AACTCATCCAACGAGGAAGAAGTTCATAATGAGAAGAACTTGTTCCTTTCAAATCCACCATAGAA
GGAGGTGAACCAATATTTCAAGAAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAA
GTTCATAATGAGAAGAACATGTTAAACATTGATTCAATTCCATCAAAGAAAGAGGTGGATCAACA
TTTACAATGG
Found at i:1845973 original size:20 final size:20
Alignment explanation
Indices: 1845910--1845974 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
1845900 TACAATGGAG
1845910 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
1845930 CA-TCCA-AA-GAGGAAGAAGA
1 -AGTTCATAATGA-GAAGAACT
1845949 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
1845969 TGTTCA
1 AGTTCA
1845975 ACCTTGCATC
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:1846051 original size:91 final size:91
Alignment explanation
Indices: 1845891--1846066 Score: 284
Period size: 91 Copynumber: 1.9 Consensus size: 91
1845881 AATGAGGTGG
*
1845891 ATCAATATTTACAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCAT
1 ATCAATATTTACAATGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCAT
*
1845956 AATGAGAAGAACTTGTTCAACCTTGC
66 AATGAGAAGAAATTGTTCAACCTTGC
* *
1845982 ATCAGTATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAATA-A-GAGAGAAGAAGTTC
1 ATCAATATTTACAATGAAGAGTTCATAATGAGAAGAACTCATCCAA-AGAGGA-AGAAGAAGTTC
1846045 ATAATGAGAAGAAATTGTTCAA
64 ATAATGAGAAGAAATTGTTCAA
1846067 TCCAATGCTT
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
90 2 0.03
91 76 0.96
92 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.24
Consensus pattern (91 bp):
ATCAATATTTACAATGAAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTCAT
AATGAGAAGAAATTGTTCAACCTTGC
Found at i:1846227 original size:3 final size:3
Alignment explanation
Indices: 1846219--1846289 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
1846209 TCCGGGTTTA
1846219 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
1846267 TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
1846290 CATTTGCAGG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1848558 original size:46 final size:46
Alignment explanation
Indices: 1848491--1848582 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
1848481 CCCCATGCGT
1848491 AACCGACTCCCGAACCCATTTTAATTGAATCTTTGGAAAACGCAGA
1 AACCGACTCCCGAACCCATTTTAATTGAATCTTTGGAAAACGCAGA
1848537 AACCGACTCCCGAACCCATTTTAATTGAATCTTTGGAAAACGCAGA
1 AACCGACTCCCGAACCCATTTTAATTGAATCTTTGGAAAACGCAGA
1848583 CCAATTTCTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (46 bp):
AACCGACTCCCGAACCCATTTTAATTGAATCTTTGGAAAACGCAGA
Found at i:1857100 original size:19 final size:19
Alignment explanation
Indices: 1857065--1857123 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 19
1857055 TTTCTCAAAT
*
1857065 AATAATAAATAT-TTTTTAA
1 AATAA-AAATATGATTTTAA
1857084 AATAAAAATATGATTTTTAA
1 AATAAAAATATGA-TTTTAA
* **
1857104 AGTGTAAA-ATGATTTTAA
1 AATAAAAATATGATTTTAA
1857122 AA
1 AA
1857124 AAATGACTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
18 13 0.39
19 9 0.27
20 11 0.33
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.41
Consensus pattern (19 bp):
AATAAAAATATGATTTTAA
Found at i:1857102 original size:20 final size:19
Alignment explanation
Indices: 1857065--1857104 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
1857055 TTTCTCAAAT
1857065 AATAATAAATATTTTTTAA
1 AATAATAAATATTTTTTAA
1857084 AATAA-AAATATGATTTTTAA
1 AATAATAAATAT--TTTTTAA
1857104 A
1 A
1857105 GTGTAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 5 0.26
20 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AATAATAAATATTTTTTAA
Found at i:1857654 original size:21 final size:21
Alignment explanation
Indices: 1857630--1857673 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1857620 GGGGAGAGTT
1857630 TTGAAAATATTTGGTCCATAA
1 TTGAAAATATTTGGTCCATAA
* *
1857651 TTGAAAATTTTTGGTCCTTAA
1 TTGAAAATATTTGGTCCATAA
1857672 TT
1 TT
1857674 TTTAGAGGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (21 bp):
TTGAAAATATTTGGTCCATAA
Found at i:1860098 original size:27 final size:28
Alignment explanation
Indices: 1860068--1860131 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
1860058 AACATAATTT
* *
1860068 TTTTAATTTAGTTCATAAACATGTT-TA
1 TTTTAATTCAATTCATAAACATGTTGTA
**
1860095 TTTTAACCCAATTCATAAACATGTTGTA
1 TTTTAATTCAATTCATAAACATGTTGTA
1860123 TGTTTAATT
1 T-TTTAATT
1860132 AAGGGTCAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 21 0.72
28 3 0.10
29 5 0.17
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (28 bp):
TTTTAATTCAATTCATAAACATGTTGTA
Found at i:1862085 original size:21 final size:21
Alignment explanation
Indices: 1862061--1862113 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
1862051 ACGGCTTACC
1862061 GAGTTTGAATTTGGCAAAACG
1 GAGTTTGAATTTGGCAAAACG
1862082 GAGTTTGAATTTGGCAAAACG
1 GAGTTTGAATTTGGCAAAACG
*
1862103 GACTTTGAATT
1 GAGTTTGAATT
1862114 CGAGCTCAGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (21 bp):
GAGTTTGAATTTGGCAAAACG
Found at i:1863335 original size:20 final size:21
Alignment explanation
Indices: 1863310--1863348 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1863300 CACTGAACTT
*
1863310 CCAAAAATTTTAA-AACTAGC
1 CCAAAAATCTTAATAACTAGC
1863330 CCAAAAATCTTAATAACTA
1 CCAAAAATCTTAATAACTA
1863349 TCCATTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.51, C:0.21, G:0.03, T:0.26
Consensus pattern (21 bp):
CCAAAAATCTTAATAACTAGC
Found at i:1867425 original size:16 final size:16
Alignment explanation
Indices: 1867406--1867436 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1867396 AACATTCAAA
1867406 CTGGTCAAAGTCAACT
1 CTGGTCAAAGTCAACT
*
1867422 CTGGTCAATGTCAAC
1 CTGGTCAAAGTCAAC
1867437 GAGTTAACTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (16 bp):
CTGGTCAAAGTCAACT
Found at i:1867625 original size:25 final size:25
Alignment explanation
Indices: 1867588--1867639 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
1867578 CAGCACAAGA
*
1867588 GCCCCATGCGCACTACCAATGCGTG
1 GCCCCACGCGCACTACCAATGCGTG
* *
1867613 GCCCCACGTGCACTGCCAATGCGTG
1 GCCCCACGCGCACTACCAATGCGTG
1867638 GC
1 GC
1867640 GACGTGTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.17, C:0.40, G:0.27, T:0.15
Consensus pattern (25 bp):
GCCCCACGCGCACTACCAATGCGTG
Found at i:1878016 original size:28 final size:26
Alignment explanation
Indices: 1877975--1878117 Score: 112
Period size: 28 Copynumber: 5.3 Consensus size: 26
1877965 AAGATGAGAA
*
1877975 AAGAAAAAAAAGAAATAGAAATAAAAG
1 AAGAAAAAAAAGAAAAAGAAA-AAAAG
*
1878002 AGAGAAAAAATAGAAAAAGAAAAAAAG
1 A-AGAAAAAAAAGAAAAAGAAAAAAAG
* *
1878029 AAAAAAAAGGAAAAACAAAAGAAAAAGAAG
1 AAGAAAAA--AAAGA-AAAAGAAAAA-AAG
* *
1878059 AA-AAAAAAAACAAAAGAAGAAAAAATG
1 AAGAAAAAAAA-GAAA-AAGAAAAAAAG
* * *
1878086 AAGAAAAGAAA-AAAGAGAGAAAAAG
1 AAGAAAAAAAAGAAAAAGAAAAAAAG
1878111 AA-AAAAA
1 AAGAAAAA
1878118 TTGAAAGAAG
Statistics
Matches: 97, Mismatches: 11, Indels: 19
0.76 0.09 0.15
Matches are distributed among these distances:
24 4 0.04
25 10 0.10
26 9 0.09
27 16 0.16
28 38 0.39
29 15 0.15
30 5 0.05
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (26 bp):
AAGAAAAAAAAGAAAAAGAAAAAAAG
Found at i:1878025 original size:25 final size:24
Alignment explanation
Indices: 1877997--1878109 Score: 74
Period size: 27 Copynumber: 4.5 Consensus size: 24
1877987 AAATAGAAAT
1877997 AAAAGAGAGAAAAAATAGAAAAAGA
1 AAAAGA-AGAAAAAATAGAAAAAGA
* *
1878022 AAAA-AAGAAAAAAAAGGAAAAACAA
1 AAAAGAAGAAAAAATA-GAAAAA-GA
* *
1878047 AAGAAAAAGAAGAAAA-A-AAAAA-C
1 AA-AAGAAGAA-AAAATAGAAAAAGA
1878070 AAAAGAAGAAAAAAT-GAAGAAAAGAA
1 AAAAGAAGAAAAAATAG-A-AAAAG-A
1878096 AAAAGAGAGAAAAA
1 AAAAGA-AGAAAAA
1878110 GAAAAAAATT
Statistics
Matches: 71, Mismatches: 5, Indels: 22
0.72 0.05 0.22
Matches are distributed among these distances:
21 4 0.06
22 7 0.10
23 12 0.17
24 11 0.15
25 12 0.17
26 8 0.11
27 13 0.18
28 4 0.06
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (24 bp):
AAAAGAAGAAAAAATAGAAAAAGA
Found at i:1878048 original size:12 final size:10
Alignment explanation
Indices: 1877971--1878117 Score: 84
Period size: 10 Copynumber: 13.9 Consensus size: 10
1877961 TTTGAAGATG
1877971 AGAAAAGAAAA
1 AGAAAA-AAAA
* *
1877982 A-AAAGAAAT
1 AGAAAAAAAA
1877991 AGAAATAAAAGA
1 AGAAA-AAAA-A
1878003 GAGAAAAAATAGA
1 -AGAAAAAA-A-A
*
1878016 AAAAGAAAAAA
1 AGAA-AAAAAA
1878027 AGAAAAAAAA
1 AGAAAAAAAA
*
1878037 GGAAAAACAAA
1 AGAAAAA-AAA
*
1878048 AG-AAAAAGA
1 AGAAAAAAAA
1878057 AGAAAAAAAA
1 AGAAAAAAAA
* *
1878067 A-ACAAAAGA
1 AGAAAAAAAA
*
1878076 AGAAAAAATGA
1 AGAAAAAA-AA
1878087 AGAAAAGAAAAA
1 AG-AAA-AAAAA
* *
1878099 AGAGAGAAAA
1 AGAAAAAAAA
1878109 AGAAAAAAA
1 AGAAAAAAA
1878118 TTGAAAGAAG
Statistics
Matches: 106, Mismatches: 18, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.14
10 45 0.42
11 18 0.17
12 13 0.12
13 15 0.14
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:1878048 original size:21 final size:20
Alignment explanation
Indices: 1877971--1878117 Score: 84
Period size: 21 Copynumber: 7.0 Consensus size: 20
1877961 TTTGAAGATG
* *
1877971 AGAAAAGAAAAAA-AAGAAAT
1 AGAAAA-AAAAAAGAAAAAAA
*
1877991 AGAAATAAAAGAGAGAAAAAATA
1 AGAAA-AAAA-AAAGAAAAAA-A
*
1878014 GAAAAAGAAAAAAAGAAAAAAA
1 -AGAAA-AAAAAAAGAAAAAAA
* *
1878036 AGGAAAAACAAAAGAAAAAGA
1 A-GAAAAAAAAAAGAAAAAAA
* *
1878057 AGAAAAAAAAAA-CAAAAGA
1 AGAAAAAAAAAAGAAAAAAA
**
1878076 AGAAAAAATGAAGAAAAGAAA
1 AGAAAAAAAAAAGAAAA-AAA
*
1878097 A-AAGAGAGAAAAAGAAAAAAA
1 AGAA-A-AAAAAAAGAAAAAAA
1878118 TTGAAAGAAG
Statistics
Matches: 99, Mismatches: 18, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
19 16 0.16
20 23 0.23
21 25 0.25
22 18 0.18
23 9 0.09
24 8 0.08
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (20 bp):
AGAAAAAAAAAAGAAAAAAA
Found at i:1878053 original size:19 final size:16
Alignment explanation
Indices: 1877973--1878117 Score: 92
Period size: 17 Copynumber: 8.3 Consensus size: 16
1877963 TGAAGATGAG
*
1877973 AAAAGAAAAAAAAGAA
1 AAAAAAAAAAAAAGAA
* * *
1877989 ATAGAAATAAAAGAGAGA
1 A-AAAAAAAAAAAAGA-A
* *
1878007 AAAAATAGAAAAAGAA
1 AAAAAAAAAAAAAGAA
1878023 AAAAAGAAAAAAAAGGAAA
1 AAAAA-AAAAAAAA-G-AA
1878042 AACAAAAGAAAAAGAAGAA
1 AA-AAAA-AAAAA-AAGAA
*
1878061 AAAAAAAACAAAAGAA
1 AAAAAAAAAAAAAGAA
*
1878077 GAAAAAATGAAGAAAAGAA
1 -AAAAAA--AAAAAAAGAA
* *
1878096 AAAAGAGAGAAAAAGAA
1 AAAA-AAAAAAAAAGAA
1878113 AAAAA
1 AAAAA
1878118 TTGAAAGAAG
Statistics
Matches: 101, Mismatches: 16, Indels: 24
0.72 0.11 0.17
Matches are distributed among these distances:
16 13 0.13
17 47 0.47
18 11 0.11
19 19 0.19
20 9 0.09
21 2 0.02
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (16 bp):
AAAAAAAAAAAAAGAA
Found at i:1878053 original size:44 final size:44
Alignment explanation
Indices: 1878004--1878117 Score: 117
Period size: 45 Copynumber: 2.5 Consensus size: 44
1877994 AATAAAAGAG
1878004 AGAAAAAATAGAAAAAGAAAAAAAGAA-AAAAAAGGAA-AAACAAA
1 AGAAAAAA-AGAAAAAGAAAAAAAGAAGAAAAAAGGAAGAAA-AAA
* *
1878048 AGAAAAAGAAGAAAAAAAAAACAAAAGAAGAAAAAATGAAGAAAAGAA
1 AGAAAAA-AAG-AAAAAGAAA-AAAAGAAGAAAAAAGGAAGAAAA-AA
* *
1878096 A-AAAGAGAGAAAAAGAAAAAAA
1 AGAAAAAAAGAAAAAGAAAAAAA
1878118 TTGAAAGAAG
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
44 13 0.22
45 17 0.29
46 9 0.15
47 14 0.24
48 6 0.10
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (44 bp):
AGAAAAAAAGAAAAAGAAAAAAAGAAGAAAAAAGGAAGAAAAAA
Found at i:1878083 original size:72 final size:74
Alignment explanation
Indices: 1877973--1878109 Score: 183
Period size: 73 Copynumber: 1.9 Consensus size: 74
1877963 TGAAGATGAG
* * *
1877973 AAAAGAAAAAAAAGAAATAGAAATAAAAGAGAGAAAAAAT--AGAAAAAGAAAAAA-AGAAAAAA
1 AAAAGAAAAAAAAGAAAAAAAAACAAAAGAGAGAAAAAATGAAG-AAAAGAAAAAAGAGAAAAAA
1878035 AAGGAAAAAC
65 AAGGAAAAAC
* *
1878045 AAAAGAAAAAGAAGAAAAAAAAAACAAAAGA-AGAAAAAATGAAGAAAAGAAAAAAGAGAGAAAA
1 AAAAGAAAAAAAAG-AAAAAAAAACAAAAGAGAGAAAAAATGAAGAAAAGAAAAAAGAGAAAAAA
1878109 A
65 A
1878110 GAAAAAAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
72 22 0.39
73 24 0.43
74 10 0.18
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (74 bp):
AAAAGAAAAAAAAGAAAAAAAAACAAAAGAGAGAAAAAATGAAGAAAAGAAAAAAGAGAAAAAAA
AGGAAAAAC
Found at i:1878088 original size:11 final size:10
Alignment explanation
Indices: 1877975--1878092 Score: 73
Period size: 9 Copynumber: 12.7 Consensus size: 10
1877965 AAGATGAGAA
1877975 AAGAAAAAA-
1 AAGAAAAAAG
*
1877984 AAG-AAATAG
1 AAGAAAAAAG
*
1877993 AA-ATAAAAG
1 AAGAAAAAAG
1878002 AGAGAAAAAA-
1 A-AGAAAAAAG
*
1878012 TAG-AAAAAG
1 AAGAAAAAAG
1878021 -A-AAAAAAG
1 AAGAAAAAAG
1878029 AA-AAAAAAG
1 AAGAAAAAAG
*
1878038 --GAAAAACAA
1 AAGAAAAA-AG
1878047 AAG-AAAAAG
1 AAGAAAAAAG
1878056 AAGAAAAAA-
1 AAGAAAAAAG
1878065 AA-AACAAAAG
1 AAGAA-AAAAG
1878075 AAGAAAAAATG
1 AAGAAAAAA-G
1878086 AAGAAAA
1 AAGAAAA
1878093 GAAAAAAGAG
Statistics
Matches: 86, Mismatches: 7, Indels: 30
0.70 0.06 0.24
Matches are distributed among these distances:
8 23 0.27
9 31 0.36
10 16 0.19
11 16 0.19
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.03
Consensus pattern (10 bp):
AAGAAAAAAG
Found at i:1878116 original size:73 final size:72
Alignment explanation
Indices: 1877973--1878116 Score: 177
Period size: 72 Copynumber: 2.0 Consensus size: 72
1877963 TGAAGATGAG
* * *
1877973 AAAAGAAAAAAAAGAAATAGAAATAAAAGAGAGAAAAAATAGAAAAAGAAAAAAAGAAAAAAAAG
1 AAAAGAAAAAAAAGAAAAAAAAACAAAAGAGAGAAAAAATAGAAAAAGAAAAAAAGAAAAAAAAG
*
1878038 GAAAAAC
66 AAAAAAC
* *
1878045 AAAAGAAAAAGAAGAAAAAAAAAACAAAAGA-AGAAAAAAT-GAAGAAA-AGAAAAAAGAGAGAA
1 AAAAGAAAAAAAAG-AAAAAAAAACAAAAGAGAGAAAAAATAGAA-AAAGA-AAAAAAGA-AAAA
1878107 AAAGAAAAAA
62 AAAGAAAAAA
1878117 ATTGAAAGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
71 4 0.06
72 33 0.53
73 25 0.40
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.03
Consensus pattern (72 bp):
AAAAGAAAAAAAAGAAAAAAAAACAAAAGAGAGAAAAAATAGAAAAAGAAAAAAAGAAAAAAAAG
AAAAAAC
Found at i:1878123 original size:16 final size:16
Alignment explanation
Indices: 1877981--1878123 Score: 74
Period size: 18 Copynumber: 8.2 Consensus size: 16
1877971 AGAAAAGAAA
*
1877981 AAAAAGAAATAGAAAT-
1 AAAAAGAAA-AAAAATG
*
1877997 AAAAGAGAGAAAAAATAG
1 AAAA-AGAAAAAAAAT-G
**
1878015 AAAAAGAAAAAAAGAAA
1 AAAAAGAAAAAAA-ATG
*
1878032 AAAAAGGAAAAACAAAAG
1 AAAAA-GAAAAA-AAATG
**
1878050 AAAAAGAAGAAAAAAAAA
1 AAAAAG-A-AAAAAAATG
1878068 ACAAAAGAAGAAAAAATG
1 A-AAAAGAA-AAAAAATG
1878086 AAGAAAAGAAAAAAGAGA-G
1 -A-AAAAGAAAAAA-A-ATG
*
1878105 AAAAAGAAAAAAATTG
1 AAAAAGAAAAAAAATG
1878121 AAA
1 AAA
1878124 GAAGGTTCAA
Statistics
Matches: 102, Mismatches: 11, Indels: 28
0.72 0.08 0.20
Matches are distributed among these distances:
16 14 0.14
17 30 0.29
18 36 0.35
19 21 0.21
20 1 0.01
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.04
Consensus pattern (16 bp):
AAAAAGAAAAAAAATG
Found at i:1881905 original size:106 final size:106
Alignment explanation
Indices: 1881750--1882259 Score: 767
Period size: 106 Copynumber: 4.8 Consensus size: 106
1881740 TTCAACCTTA
* * *
1881750 GATCAACA-TTTCCAGTGGATAGTTCATAATGAAAAGAACTCATCCGATAGAGGGAGAAGAAGTT
1 GATCAACATTTTCGA-TGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTT
*
1881814 CATAATGAGAAGAACTTGTTTAACCCAATACCTCACTCGAGG
65 CATAATGAGAAGAACTTGTTCAACCCAATACCTCACTCGAGG
*
1881856 GATCAACATTTTCGATGGAGAGTTCATAATGAGAAGAGA-TCATCTGATAGAGGGAGAA-AAGTT
1 GATCAACATTTTCGATGGAGAGTTCATAATGAGAAGA-ACTCATCCGATAGAGGGAGAAGAAGTT
**
1881919 CATAATGAGAAGAACTTGTTCAACATAATACCTCACTCGAGG
65 CATAATGAGAAGAACTTGTTCAACCCAATACCTCACTCGAGG
* * *
1881961 GATCAACATTTTCGATGGAGAGTTCATATTGAGAAGAACTCATCCGAAAGAAGGAGAAGAAGTTC
1 GATCAACATTTTCGATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
* *
1882026 ATAATAAGAATAACTTGTTCAACCCAATACCTCACTCGAGG
66 ATAATGAGAAGAACTTGTTCAACCCAATACCTCACTCGAGG
* * *
1882067 GATCATCATTTTCGATGGAGAGTTCATAATGAGAAGAACTCATCTGATAGAGAGAGAAGAAGTTC
1 GATCAACATTTTCGATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
* * *
1882132 ATAATGAGAATAACTCGTTCAACCCAACACCTCACTCGAGG
66 ATAATGAGAAGAACTTGTTCAACCCAATACCTCACTCGAGG
* * * *
1882173 AATCAACTTTTTCGATGGAGAGTTCATAATGAGAAGAACTCATCCAAT-GAGGGAGAATAAGTTC
1 GATCAACATTTTCGATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
*
1882237 ATAATGAAAAGAACTTGTTCAAC
66 ATAATGAGAAGAACTTGTTCAAC
1882260 ATTAGCTTGT
Statistics
Matches: 366, Mismatches: 34, Indels: 9
0.89 0.08 0.02
Matches are distributed among these distances:
104 1 0.00
105 130 0.36
106 229 0.63
107 6 0.02
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (106 bp):
GATCAACATTTTCGATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCCAATACCTCACTCGAGG
Found at i:1882114 original size:211 final size:212
Alignment explanation
Indices: 1881750--1882259 Score: 778
Period size: 211 Copynumber: 2.4 Consensus size: 212
1881740 TTCAACCTTA
* * * *
1881750 GATCAACA-TTTCCAGTGGATAGTTCATAATGAAAAGAACTCATCCGATAGAGGGAGAAGAAGTT
1 GATCAACATTTTCGA-TGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTT
* *
1881814 CATAATGAGAAGAACTTGTTTAACCCAATACCTCACTCGAGGGATCAACATTTTCGATGGAGAGT
65 CATAATAAGAAGAACTTGTTCAACCCAATACCTCACTCGAGGGATCAACATTTTCGATGGAGAGT
* *
1881879 TCATAATGAGAAGAGATCATCTGATAGAGGGAGAA-AAGTTCATAATGAGAAGAACTTGTTCAAC
130 TCATAATGAGAAGAGATCATCTGATAGAGAGAGAAGAAGTTCATAATGAGAAGAACTCGTTCAAC
* *
1881943 ATAATACCTCACTCGAGG
195 ACAACACCTCACTCGAGG
* *
1881961 GATCAACATTTTCGATGGAGAGTTCATATTGAGAAGAACTCATCCGAAAGAAGGAGAAGAAGTTC
1 GATCAACATTTTCGATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTC
* *
1882026 ATAATAAGAATAACTTGTTCAACCCAATACCTCACTCGAGGGATCATCATTTTCGATGGAGAGTT
66 ATAATAAGAAGAACTTGTTCAACCCAATACCTCACTCGAGGGATCAACATTTTCGATGGAGAGTT
*
1882091 CATAATGAGAAGA-ACTCATCTGATAGAGAGAGAAGAAGTTCATAATGAGAATAACTCGTTCAAC
131 CATAATGAGAAGAGA-TCATCTGATAGAGAGAGAAGAAGTTCATAATGAGAAGAACTCGTTCAAC
*
1882155 CCAACACCTCACTCGAGG
195 ACAACACCTCACTCGAGG
* * * *
1882173 AATCAACTTTTTCGATGGAGAGTTCATAATGAGAAGAACTCATCC-AATGAGGGAGAATAAGTTC
1 GATCAACATTTTCGATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTC
1882237 ATAATGAA-AAGAACTTGTTCAAC
66 ATAAT-AAGAAGAACTTGTTCAAC
1882260 ATTAGCTTGT
Statistics
Matches: 272, Mismatches: 23, Indels: 8
0.90 0.08 0.03
Matches are distributed among these distances:
210 1 0.00
211 180 0.66
212 91 0.33
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (212 bp):
GATCAACATTTTCGATGGAGAGTTCATAATGAGAAGAACTCATCCGAAAGAGGGAGAAGAAGTTC
ATAATAAGAAGAACTTGTTCAACCCAATACCTCACTCGAGGGATCAACATTTTCGATGGAGAGTT
CATAATGAGAAGAGATCATCTGATAGAGAGAGAAGAAGTTCATAATGAGAAGAACTCGTTCAACA
CAACACCTCACTCGAGG
Found at i:1882576 original size:15 final size:18
Alignment explanation
Indices: 1882544--1882584 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
1882534 TTTTTTCAGT
1882544 TTATTATATATATATATA
1 TTATTATATATATATATA
*
1882562 TTATT-TAT-TATTATAAA
1 TTATTATATATA-TATATA
1882579 TTATTA
1 TTATTA
1882585 CAAACCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 2 0.10
17 13 0.65
18 5 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATTATATATATATATA
Found at i:1898628 original size:11 final size:11
Alignment explanation
Indices: 1898612--1898636 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1898602 TTATGAAGAA
1898612 GTTGCTGAGTT
1 GTTGCTGAGTT
1898623 GTTGCTGAGTT
1 GTTGCTGAGTT
1898634 GTT
1 GTT
1898637 AATAAAATAA
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:0.08, C:0.08, G:0.36, T:0.48
Consensus pattern (11 bp):
GTTGCTGAGTT
Found at i:1901612 original size:3 final size:3
Alignment explanation
Indices: 1901604--1901632 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1901594 AGAAGTGTTT
1901604 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1901633 TTGGTATTTT
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:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1904371 original size:39 final size:40
Alignment explanation
Indices: 1904328--1904471 Score: 147
Period size: 39 Copynumber: 3.7 Consensus size: 40
1904318 GGCTCGTCTT
1904328 CTTTGTGC-TCAGGGTAAGTCCTTACTGCAGGCTCCT-TG
1 CTTTGTGCATCAGGGTAAGTCCTTACTGCAGGCTCCTATG
* * *
1904366 ACTTTGTGC-TCAGGGTAAGTTCATACTGCAGGCTCCTCTG
1 -CTTTGTGCATCAGGGTAAGTCCTTACTGCAGGCTCCTATG
* * ** *
1904406 CTTTATGCACCA-CATAAGACCTTA-TCGCAGGCTCCTATG
1 CTTTGTGCATCAGGGTAAGTCCTTACT-GCAGGCTCCTATG
*
1904445 CTTTGTGCAT-AGGGTAAGCCCTTACTG
1 CTTTGTGCATCAGGGTAAGTCCTTACTG
1904472 TGTGTATAGG
Statistics
Matches: 85, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
38 2 0.02
39 78 0.92
40 5 0.06
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (40 bp):
CTTTGTGCATCAGGGTAAGTCCTTACTGCAGGCTCCTATG
Found at i:1904774 original size:2 final size:2
Alignment explanation
Indices: 1904769--1904794 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1904759 TATCGTCTTG
1904769 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
1904795 GTATTACCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1909668 original size:16 final size:18
Alignment explanation
Indices: 1909641--1909678 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1909631 ACCGTATTCA
*
1909641 TTTTCAACTTTACAAT-C
1 TTTTCAACTTTAAAATGC
1909658 TTTTC-ACTTTAAAATGC
1 TTTTCAACTTTAAAATGC
1909675 TTTT
1 TTTT
1909679 ATTATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTTCAACTTTAAAATGC
Found at i:1918873 original size:39 final size:39
Alignment explanation
Indices: 1918819--1919000 Score: 186
Period size: 39 Copynumber: 4.7 Consensus size: 39
1918809 CTTTCTGCAA
1918819 GCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACCACAG
1 GCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACCACAG
* ** **
1918858 GCTCCTCAACTTTGTGCTCATAGTAAGTCCTTACTGCAG
1 GCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACCACAG
* * ** * *
1918897 TCTCCTCGGCTTTGTGCTCAATGTAAGTCCTTACTACAA
1 GCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACCACAG
* * * * *
1918936 GCTCCTCTA-CTTTATGCACAGGATAAGACCTTACCACAT
1 GCTCCTC-AGCTTTGTGCTCAGGGTAAGTCCTTACCACAG
* *
1918975 GCTCCTCTGCTTTGTGCACAGGGTAA
1 GCTCCTCAGCTTTGTGCTCAGGGTAA
1919001 ACCCTTACTG
Statistics
Matches: 116, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
39 116 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (39 bp):
GCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACCACAG
Found at i:1919007 original size:78 final size:77
Alignment explanation
Indices: 1918818--1919009 Score: 206
Period size: 78 Copynumber: 2.5 Consensus size: 77
1918808 GCTTTCTGCA
* * * * *
1918818 AGCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACCACAGGCTCCTCAACTTTGTGCTCATAGTA
1 AGCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACTACAAGCTCCTCAACTTTATGCACAGAGTA
* **
1918883 AGTCCTTACTGC
66 AGACCTTACCAC
* ** *
1918895 AGTCTCCTCGGCTTTGTGCTCAATGTAAGTCCTTACTACAAGCTCCTCTACTTTATGCACAG-GA
1 AG-CTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACTACAAGCTCCTCAACTTTATGCACAGAG-
1918959 TAAGACCTTACCAC
64 TAAGACCTTACCAC
* * **
1918973 ATGCTCCTCTGCTTTGTGCACAGGGTAAACCCTTACT
1 A-GCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACT
1919010 GGGTGTACAG
Statistics
Matches: 94, Mismatches: 18, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
77 3 0.03
78 90 0.96
79 1 0.01
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.31
Consensus pattern (77 bp):
AGCTCCTCAGCTTTGTGCTCAGGGTAAGTCCTTACTACAAGCTCCTCAACTTTATGCACAGAGTA
AGACCTTACCAC
Found at i:1927737 original size:16 final size:16
Alignment explanation
Indices: 1927694--1927742 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
1927684 AAATTAAAAT
1927694 AATATAATAG-ATATAA
1 AATATAATAGAAT-TAA
*
1927710 AATA-AACA-AATTAA
1 AATATAATAGAATTAA
1927724 AATATAATAGAATTAA
1 AATATAATAGAATTAA
1927740 AAT
1 AAT
1927743 TCTTATCTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 7 0.25
15 8 0.29
16 13 0.46
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (16 bp):
AATATAATAGAATTAA
Found at i:1931320 original size:3 final size:3
Alignment explanation
Indices: 1931312--1931364 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
1931302 ATCACCAAAT
1931312 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1931360 TTA TT
1 TTA TT
1931365 TCAGATTAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1934032 original size:23 final size:23
Alignment explanation
Indices: 1934006--1934131 Score: 146
Period size: 23 Copynumber: 5.5 Consensus size: 23
1933996 ATTTATTATT
*
1934006 TTATTAATTACGATTCTAGTTTG
1 TTATTAATTAGGATTCTAGTTTG
* *
1934029 TTATTAATTAGGATTCTAATATG
1 TTATTAATTAGGATTCTAGTTTG
* * *
1934052 CTATTATTTAGGATTATAGTTTG
1 TTATTAATTAGGATTCTAGTTTG
* *
1934075 TTATTAATTAGGATTCTAATTTA
1 TTATTAATTAGGATTCTAGTTTG
* *
1934098 CTATTATTTAGGATTCTAGTTT-
1 TTATTAATTAGGATTCTAGTTTG
1934120 TCTATTAATTAG
1 T-TATTAATTAG
1934132 AATTTAAAAT
Statistics
Matches: 84, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
23 84 1.00
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (23 bp):
TTATTAATTAGGATTCTAGTTTG
Found at i:1934072 original size:46 final size:46
Alignment explanation
Indices: 1934007--1934131 Score: 189
Period size: 46 Copynumber: 2.7 Consensus size: 46
1933997 TTTATTATTT
* * *
1934007 TATTAATTACGATTCTAGTTTGTTATTAATTAGGATTCTAATATGC
1 TATTATTTAGGATTCTAGTTTGTTATTAATTAGGATTCTAATATAC
* *
1934053 TATTATTTAGGATTATAGTTTGTTATTAATTAGGATTCTAATTTAC
1 TATTATTTAGGATTCTAGTTTGTTATTAATTAGGATTCTAATATAC
1934099 TATTATTTAGGATTCTAGTTT-TCTATTAATTAG
1 TATTATTTAGGATTCTAGTTTGT-TATTAATTAG
1934132 AATTTAAAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
45 1 0.01
46 71 0.99
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (46 bp):
TATTATTTAGGATTCTAGTTTGTTATTAATTAGGATTCTAATATAC
Found at i:1941292 original size:22 final size:23
Alignment explanation
Indices: 1941248--1941293 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
1941238 AAATTTGAAT
** *
1941248 ACAATGGTAAGTGTATTGTGCAA
1 ACAATGGTAAGTGTAAGGGGCAA
1941271 ACAATGGTAA-TGTAAGGGGCAA
1 ACAATGGTAAGTGTAAGGGGCAA
1941293 A
1 A
1941294 AATTTATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.39, C:0.09, G:0.28, T:0.24
Consensus pattern (23 bp):
ACAATGGTAAGTGTAAGGGGCAA
Found at i:1941994 original size:14 final size:14
Alignment explanation
Indices: 1941975--1942028 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
1941965 TTTGACCCAA
1941975 CCGAGTCAACTCGT
1 CCGAGTCAACTCGT
* *
1941989 CCGAGTTAACACGT
1 CCGAGTCAACTCGT
* *
1942003 CTGAGTCAACTCGA
1 CCGAGTCAACTCGT
*
1942017 CTGAGTCAACTC
1 CCGAGTCAACTC
1942029 ACTGATTTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.22
Consensus pattern (14 bp):
CCGAGTCAACTCGT
Found at i:1944263 original size:31 final size:31
Alignment explanation
Indices: 1944225--1944308 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 31
1944215 TAAGGCGACC
* * *
1944225 CTTGGGTAGGCTTTGAGGCCCCGAGAACTTT
1 CTTGGGTAGGCTCTGAGGCCCCGAAAACTAT
* * * *
1944256 CTTGGGTAGGCCCCGAGTCCCTGAAAACTAT
1 CTTGGGTAGGCTCTGAGGCCCCGAAAACTAT
*
1944287 CTTGGGTAGGCTCTCAGGCCCC
1 CTTGGGTAGGCTCTGAGGCCCC
1944309 AAGATGCTCT
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.17, C:0.29, G:0.30, T:0.25
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGAGGCCCCGAAAACTAT
Found at i:1946684 original size:17 final size:18
Alignment explanation
Indices: 1946645--1946694 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
1946635 CTTTATATAT
*
1946645 ATAATT-TATTTATAATTA
1 ATAATTATATTGA-AATTA
1946663 ATAATTA-ATTGAAATTA
1 ATAATTATATTGAAATTA
*
1946680 TTAATTATATTGAAA
1 ATAATTATATTGAAA
1946695 AAATTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 11 0.39
18 17 0.61
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (18 bp):
ATAATTATATTGAAATTA
Found at i:1946700 original size:18 final size:17
Alignment explanation
Indices: 1946664--1946703 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1946654 TTATAATTAA
**
1946664 TAATTAATTGAAATTAT
1 TAATTAATTGAAAAAAT
1946681 TAATTATATTGAAAAAAT
1 TAATTA-ATTGAAAAAAT
1946699 TAATT
1 TAATT
1946704 TAACGATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
TAATTAATTGAAAAAAT
Found at i:1947569 original size:2 final size:2
Alignment explanation
Indices: 1947562--1947621 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1947552 AGACTCATCC
1947562 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
1947604 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1947622 TCATTTCACT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1968856 original size:57 final size:58
Alignment explanation
Indices: 1968763--1968898 Score: 159
Period size: 57 Copynumber: 2.3 Consensus size: 58
1968753 ACTATTCAAA
* * * * * *
1968763 CATA-ATTTTAAAATTAATGAAATTAAATATGGTATACTTTCCCATTTTCTTTACTGTT
1 CATATATTTTGAAATTAA-AAAATTAAAGACGGTATACTTTCCCATTGTCTTCACTGTT
** *
1968821 CAT-TATTTTTTAATTAAAAAATTAAAGACGGTATACTTTCTCATTGTCTTCACTGTT
1 CATATATTTTGAAATTAAAAAATTAAAGACGGTATACTTTCCCATTGTCTTCACTGTT
1968878 CATAATATTTTGAAATTAAAA
1 CAT-ATATTTTGAAATTAAAA
1968899 TAAGGTATAT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
57 37 0.57
58 14 0.22
59 14 0.22
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (58 bp):
CATATATTTTGAAATTAAAAAATTAAAGACGGTATACTTTCCCATTGTCTTCACTGTT
Found at i:1969796 original size:48 final size:48
Alignment explanation
Indices: 1969728--1969820 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
1969718 GACAAAATAT
* *
1969728 AGTAAGTATATGTATGTTTTATTTTCTAAATTAAGTAATATTATAGTA
1 AGTAAGTAAATGTATATTTTATTTTCTAAATTAAGTAATATTATAGTA
* *
1969776 AGTAAGTAAATGTATATTTTATTTTCTAAATTAATTAATTTTATA
1 AGTAAGTAAATGTATATTTTATTTTCTAAATTAAGTAATATTATA
1969821 TAATTTTGCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (48 bp):
AGTAAGTAAATGTATATTTTATTTTCTAAATTAAGTAATATTATAGTA
Found at i:1970188 original size:24 final size:22
Alignment explanation
Indices: 1970132--1970188 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 22
1970122 CTATTTTAAT
* *
1970132 TTAAGTAATATAAATATTTATA
1 TTAATTAATTTAAATATTTATA
*
1970154 TT--TTAAATTAAATATGTTATGA
1 TTAATTAATTTAAATAT-TTAT-A
1970176 TTAATTAATTTAA
1 TTAATTAATTTAA
1970189 TCATTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
20 10 0.37
21 4 0.15
22 5 0.19
24 8 0.30
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TTAATTAATTTAAATATTTATA
Found at i:1971826 original size:33 final size:33
Alignment explanation
Indices: 1971784--1971852 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1971774 GTTGATGAAT
*
1971784 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
1971817 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
1971850 GAA
1 GAA
1971853 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:1972274 original size:19 final size:20
Alignment explanation
Indices: 1972227--1972277 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1972217 GAAATCCCTT
**
1972227 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
1972247 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
1972266 TGAAGATACATG
1 TGAAAATACATG
1972278 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:1975842 original size:33 final size:33
Alignment explanation
Indices: 1975800--1975868 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
1975790 GTTGATGAAT
*
1975800 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
1975833 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
1975866 GAA
1 GAA
1975869 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:1976290 original size:19 final size:20
Alignment explanation
Indices: 1976243--1976293 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1976233 GAAATCCCTT
**
1976243 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
1976263 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
1976282 TGAAGATACATG
1 TGAAAATACATG
1976294 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:1978730 original size:29 final size:31
Alignment explanation
Indices: 1978697--1978769 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
1978687 AAATTTTAGA
* *
1978697 TAGTGACCAAAATA-AAATTTTTG-AAAGTT
1 TAGTGACCAAAATATAAACTTTAGAAAAGTT
* *
1978726 TAGTGACTAAAGTATAAACTTTAGAAAAGTT
1 TAGTGACCAAAATATAAACTTTAGAAAAGTT
1978757 TAAG-GACCAAAAT
1 T-AGTGACCAAAAT
1978770 GGTAATTTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 12 0.34
30 7 0.20
31 14 0.40
32 2 0.06
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.30
Consensus pattern (31 bp):
TAGTGACCAAAATATAAACTTTAGAAAAGTT
Found at i:1980806 original size:40 final size:40
Alignment explanation
Indices: 1980732--1980811 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
1980722 AGTACAAGTC
*
1980732 AGGTGAGCAAAGCTCGACCTCAGCACTACGGTGCATTATT
1 AGGTGAGCAAAGCTCGACCTCAGCACTACGGTGCAATATT
* **
1980772 AGGTGAGCAAAGCTCGACCTTAGCACTATTGTGCAATATT
1 AGGTGAGCAAAGCTCGACCTCAGCACTACGGTGCAATATT
1980812 TGACTCCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.25
Consensus pattern (40 bp):
AGGTGAGCAAAGCTCGACCTCAGCACTACGGTGCAATATT
Found at i:1985697 original size:41 final size:41
Alignment explanation
Indices: 1985623--1985754 Score: 165
Period size: 41 Copynumber: 3.2 Consensus size: 41
1985613 GATTACACAT
*** * * *
1985623 ATAGTGGCGTTTATTCCTAAAATGTCGCAATAGTGATAATAA
1 ATAGTGGCGTTT-TTAAAAAAATGCCGCAATAGTGTTAATCA
* *
1985665 ATAGTGGCGTTTTTAGACAAATGCCGCAATAGTGTTAATCA
1 ATAGTGGCGTTTTTAAAAAAATGCCGCAATAGTGTTAATCA
* *
1985706 ATAGTGGCGTTTTTAAAAAAATGCCGTAATAGTTTTAATCA
1 ATAGTGGCGTTTTTAAAAAAATGCCGCAATAGTGTTAATCA
1985747 ATAGTGGC
1 ATAGTGGC
1985755 ATTGTTTTAA
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 67 0.85
42 12 0.15
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (41 bp):
ATAGTGGCGTTTTTAAAAAAATGCCGCAATAGTGTTAATCA
Found at i:1985768 original size:83 final size:81
Alignment explanation
Indices: 1985623--1985801 Score: 180
Period size: 82 Copynumber: 2.2 Consensus size: 81
1985613 GATTACACAT
*** * *
1985623 ATAGTGGCGTTTATTCCTAAAATGTCGCAATAGTGATAATAAATAGTGGCGTTTTTAGACAAATG
1 ATAGTGGCGTTT-TTAAAAAAATGCCGCAATAGTGATAATAAATAGTGGCGTTTTTAGACAAACG
* *
1985688 CCGCAATAGTGTTAATCA
65 CCACAATAGTG-CAATCA
* ** * *
1985706 ATAGTGGCGTTTTTAAAAAAATGCCGTAATAGTTTTAATCAATAGTGGCATTGTTTTA-ACAAAC
1 ATAGTGGCGTTTTTAAAAAAATGCCGCAATAGTGATAATAAATAGTGGC-GT-TTTTAGACAAAC
*
1985770 GCCATAATAGTGCAATCA
64 GCCACAATAGTGCAATCA
* *
1985788 ATTGTGGCATTTTT
1 ATAGTGGCGTTTTT
1985802 TTGTATAAAC
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
82 46 0.58
83 28 0.35
84 5 0.06
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.35
Consensus pattern (81 bp):
ATAGTGGCGTTTTTAAAAAAATGCCGCAATAGTGATAATAAATAGTGGCGTTTTTAGACAAACGC
CACAATAGTGCAATCA
Found at i:1985787 original size:41 final size:40
Alignment explanation
Indices: 1985651--1985802 Score: 126
Period size: 41 Copynumber: 3.7 Consensus size: 40
1985641 AAAATGTCGC
* * * * **
1985651 AATAGTGATAATAAATAGTGGC-GTTTTTAGACAAATGCCGC
1 AATAGTG-TAATCAATAGTGGCATTTTTTA-AAAAACGCCAT
* * * *
1985692 AATAGTGTTAATCAATAGTGGCGTTTTTAAAAAAATGCCGT
1 AATAGTG-TAATCAATAGTGGCATTTTTTAAAAAACGCCAT
* *
1985733 AATAGTTTTAATCAATAGTGGCATTGTTTTAACAAACGCCAT
1 AATAG-TGTAATCAATAGTGGCATT-TTTTAAAAAACGCCAT
* *
1985775 AATAGTGCAATCAATTGTGGCATTTTTT
1 AATAGTGTAATCAATAGTGGCATTTTTT
1985803 TGTATAAACG
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
40 4 0.04
41 66 0.71
42 23 0.25
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (40 bp):
AATAGTGTAATCAATAGTGGCATTTTTTAAAAAACGCCAT
Found at i:1987107 original size:43 final size:43
Alignment explanation
Indices: 1987021--1987135 Score: 114
Period size: 43 Copynumber: 2.7 Consensus size: 43
1987011 AAGGTAATTA
* *
1987021 GCGGCGTTTGTATCCAAAAATGCCGCTATAGATATAGCATTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTAAAGATATAGCATTTT
* *
1987064 GCGGCGTTTGTATCCAAACACGGCGCTAAAGAGTCATA-C-TTTT
1 GCGGCGTTTGTATCCAAAAACGCCGCTAAAGA-T-ATAGCATTTT
* *
1987107 GTGGTG-TT-T-TCCAACAAACGCCGCTAAAG
1 GCGGCGTTTGTATCCAA-AAACGCCGCTAAAG
1987136 GTCAGATCTA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
40 5 0.08
41 13 0.21
42 2 0.03
43 36 0.59
44 2 0.03
45 3 0.05
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (43 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTAAAGATATAGCATTTT
Found at i:1987381 original size:42 final size:42
Alignment explanation
Indices: 1987326--1987413 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
1987316 GTTTTTGAGT
*
1987326 AAACGCCGCAATAGAGTTGGAATATAGAAGCGTTTGGTTTAC
1 AAACACCGCAATAGAGTTGGAATATAGAAGCGTTTGGTTTAC
* * * **
1987368 AAACACCGCAATAGAGTTGGCATGTGGTGGCGTTTGGTTTAC
1 AAACACCGCAATAGAGTTGGAATATAGAAGCGTTTGGTTTAC
1987410 AAAC
1 AAAC
1987414 GCAGTGAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (42 bp):
AAACACCGCAATAGAGTTGGAATATAGAAGCGTTTGGTTTAC
Found at i:1996811 original size:43 final size:43
Alignment explanation
Indices: 1996750--1996998 Score: 234
Period size: 43 Copynumber: 5.8 Consensus size: 43
1996740 CATTTTTAGC
* * * * *
1996750 AAAAATGCCGCAAAACATCAACACCTACTGCGGCGTTTGTGAG
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCAG
* * *
1996793 AAAAATGCCGCTAAACATCATA-ACCTATTACGGCGTTTGTCTA-
1 AAAAACGCCGCTAAATATCA-ACACCTATTGCGGCGTTTGTC-AG
* * * *
1996836 AAAAACGCTGCTAAATATCAACAACTATTGCGGTGTTT-TTATG
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCA-G
* * * *
1996879 AAAAATGCCGCTAAATATCAACACCTATTGCGGCATTTTTCTG
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCAG
* * * * *
1996922 ACAAACACCGCTAAATATCAACAACTATTGTGGCGTTTGTCAC
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCAG
* * *
1996965 ACAAACGCCGCTAAATATTAATACCTATTGCGGC
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGC
1996999 ATTTTTTAAC
Statistics
Matches: 168, Mismatches: 32, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
41 1 0.01
42 2 0.01
43 162 0.96
44 3 0.02
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.27
Consensus pattern (43 bp):
AAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTCAG
Found at i:1997004 original size:129 final size:129
Alignment explanation
Indices: 1996737--1997013 Score: 299
Period size: 129 Copynumber: 2.1 Consensus size: 129
1996727 AGACCTTTAC
* * **
1996737 CGGCATTTTTAGCAAAAATGCCGCAAAACATCAACACCTACTGCGGCGTTTGTGAGAAAAATGCC
1 CGGCATTTTTAGCAAAAATGCCGCAAAACATCAACACCTACTGCGGCATTTGTCAGAAAAACACC
* *
1996802 GCTAAACATCATAACCTATTACGGCGTTTGTCTAAAAAACGCTGCTAAATATCAACAACTATTG
66 GCTAAACATCATAAACTATTACGGCGTTTGTCTAAAAAACGCCGCTAAATATCAACAACTATTG
** * * * * * *
1996866 CGGTGTTTTTATG-AAAAATGCCGCTAAATATCAACACCTATTGCGGCATTTTTCTGACAAACAC
1 CGGCATTTTTA-GCAAAAATGCCGCAAAACATCAACACCTACTGCGGCATTTGTCAGAAAAACAC
* ** * * * *
1996930 CGCTAAATATCA-ACAACTATTGTGGCGTTTGTC-ACACAAACGCCGCTAAATATTAATACCTAT
65 CGCTAAACATCATA-AACTATTACGGCGTTTGTCTA-AAAAACGCCGCTAAATATCAACAACTAT
1996993 TG
128 TG
*
1996995 CGGCATTTTTTAACAAAAA
1 CGGCA-TTTTTAGCAAAAA
1997014 ATGTCACAAA
Statistics
Matches: 119, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
128 2 0.02
129 105 0.88
130 12 0.10
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (129 bp):
CGGCATTTTTAGCAAAAATGCCGCAAAACATCAACACCTACTGCGGCATTTGTCAGAAAAACACC
GCTAAACATCATAAACTATTACGGCGTTTGTCTAAAAAACGCCGCTAAATATCAACAACTATTG
Found at i:1999089 original size:30 final size:30
Alignment explanation
Indices: 1999053--1999117 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
1999043 TTTTCGGAAG
1999053 ACTGTAGCAGTTACTGTAGCGTATCGATGC
1 ACTGTAGCAGTTACTGTAGCGTATCGATGC
** *
1999083 ACTGTAGTGGTTACTGTATCGTATCGATGC
1 ACTGTAGCAGTTACTGTAGCGTATCGATGC
1999113 ACTGT
1 ACTGT
1999118 TCACTGTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (30 bp):
ACTGTAGCAGTTACTGTAGCGTATCGATGC
Found at i:2000022 original size:31 final size:30
Alignment explanation
Indices: 1999951--2000023 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
1999941 GTTATAATCC
* *
1999951 TTAGAAAAATTTGGGGACCATTTTGTAACTT
1 TTAG-AAAAGTTGGGGACCAATTTGTAACTT
*
1999982 TT-TAAAAGTTGGCGGACCAATTTGATAA-TT
1 TTAGAAAAGTTGG-GGACCAATTTG-TAACTT
2000012 TTAGAAAAGTTG
1 TTAGAAAAGTTG
2000024 TGAATGGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 8 0.23
30 14 0.40
31 13 0.37
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (30 bp):
TTAGAAAAGTTGGGGACCAATTTGTAACTT
Found at i:2000594 original size:24 final size:24
Alignment explanation
Indices: 2000566--2000612 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2000556 CATGACATCG
2000566 TACATAGATGTTTTATACATCATA
1 TACATAGATGTTTTATACATCATA
2000590 TACATAGATGTTTTATACATCAT
1 TACATAGATGTTTTATACATCAT
2000613 CAAGACGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.43
Consensus pattern (24 bp):
TACATAGATGTTTTATACATCATA
Found at i:2006486 original size:59 final size:57
Alignment explanation
Indices: 2006348--2006486 Score: 165
Period size: 59 Copynumber: 2.4 Consensus size: 57
2006338 GTACATTGTA
* *
2006348 TTTAATTTTTTAATT-AAAAAATAATGAACAGTGAATACGATGTGAAAGTATTCTAT
1 TTTAATTTTTTAATTAAAAAAATAATGAACAGTGAAGACGATGGGAAAGTATTCTAT
* * *
2006404 TTTACTTTCTTTAATTTAAAAAAATAGTGAACAGTGAAGATGATGGGAAAGTATATCGT-T
1 TTTAATTT-TTTAA-TTAAAAAAATAATGAACAGTGAAGACGATGGGAAAGTAT-TC-TAT
*
2006464 TTTAATTTTTAAATTCAAAAAAA
1 TTTAATTTTTTAATT-AAAAAAA
2006487 AATATGTTTG
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
56 7 0.10
57 5 0.07
58 4 0.06
59 43 0.61
60 10 0.14
61 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (57 bp):
TTTAATTTTTTAATTAAAAAAATAATGAACAGTGAAGACGATGGGAAAGTATTCTAT
Found at i:2016529 original size:40 final size:40
Alignment explanation
Indices: 2016474--2016553 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
2016464 TAGCACTTTT
2016474 GTTGGGACACTTGATGCTTATTTTGTTTTATTTTCTTCAA
1 GTTGGGACACTTGATGCTTATTTTGTTTTATTTTCTTCAA
2016514 GTTGGGACACTTGATGCTTATTTTGTTTTATTTTCTTCAA
1 GTTGGGACACTTGATGCTTATTTTGTTTTATTTTCTTCAA
2016554 ATAGTTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.53
Consensus pattern (40 bp):
GTTGGGACACTTGATGCTTATTTTGTTTTATTTTCTTCAA
Found at i:2019409 original size:29 final size:29
Alignment explanation
Indices: 2019375--2019459 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
2019365 AATTTATGGA
* * *
2019375 ATTTACTTGGCGCCAAGACCAATGGCTCC
1 ATTTACTTGGCACCAGGGCCAATGGCTCC
2019404 ATTTACTTGGCACCAGGGCCAATGGCTCC
1 ATTTACTTGGCACCAGGGCCAATGGCTCC
2019433 ATTTACTTGGCACCAGGGCCAATGGCT
1 ATTTACTTGGCACCAGGGCCAATGGCT
2019460 TCTTTGTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (29 bp):
ATTTACTTGGCACCAGGGCCAATGGCTCC
Found at i:2020052 original size:61 final size:61
Alignment explanation
Indices: 2019948--2020072 Score: 187
Period size: 61 Copynumber: 2.0 Consensus size: 61
2019938 TATCGAACAA
* *
2019948 TAAGTCAAGTTGAGCAATAAATTTTTTAACGAGAACGAATCAAGTAAAAGTTTATTGAGCT
1 TAAGTCAAGTTAAGCAATAAATTTTTTAACGAGAACGAATCAAGTAAAAGTTTATTGAACT
* * * * *
2020009 TAAGTCGAGTTAAGCAATAAGTTTTTTAACGAGTACGAGTCAAGTAAAATTTTATTGAACT
1 TAAGTCAAGTTAAGCAATAAATTTTTTAACGAGAACGAATCAAGTAAAAGTTTATTGAACT
2020070 TAA
1 TAA
2020073 CGAGCAACAT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.33
Consensus pattern (61 bp):
TAAGTCAAGTTAAGCAATAAATTTTTTAACGAGAACGAATCAAGTAAAAGTTTATTGAACT
Found at i:2021819 original size:47 final size:47
Alignment explanation
Indices: 2021750--2021844 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
2021740 GTATAAATGC
2021750 TTAATTCGGATTGACTCGAGGTCTTCACGAGTTTAGTCTAACAAAGT
1 TTAATTCGGATTGACTCGAGGTCTTCACGAGTTTAGTCTAACAAAGT
2021797 TTAATTCGGATTGACTCGAGGTCTTCACGAGTTTAGTCTAACAAAGT
1 TTAATTCGGATTGACTCGAGGTCTTCACGAGTTTAGTCTAACAAAGT
2021844 T
1 T
2021845 CAACTTGATT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (47 bp):
TTAATTCGGATTGACTCGAGGTCTTCACGAGTTTAGTCTAACAAAGT
Found at i:2022704 original size:2 final size:2
Alignment explanation
Indices: 2022699--2022732 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2022689 ATTGTTATTA
2022699 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
2022733 GTTATTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2025250 original size:86 final size:86
Alignment explanation
Indices: 2025105--2025278 Score: 348
Period size: 86 Copynumber: 2.0 Consensus size: 86
2025095 CAAGCTTTTC
2025105 ATGCTTGAAATCCTAAGTTCTTTGAATTGGATGGATGAAGGGGATGTTAGGTTTTGATGTTCCAA
1 ATGCTTGAAATCCTAAGTTCTTTGAATTGGATGGATGAAGGGGATGTTAGGTTTTGATGTTCCAA
2025170 AGCTTGATTATGATATAGTTG
66 AGCTTGATTATGATATAGTTG
2025191 ATGCTTGAAATCCTAAGTTCTTTGAATTGGATGGATGAAGGGGATGTTAGGTTTTGATGTTCCAA
1 ATGCTTGAAATCCTAAGTTCTTTGAATTGGATGGATGAAGGGGATGTTAGGTTTTGATGTTCCAA
2025256 AGCTTGATTATGATATAGTTG
66 AGCTTGATTATGATATAGTTG
2025277 AT
1 AT
2025279 ATTGTAGAAT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 88 1.00
ACGTcount: A:0.27, C:0.08, G:0.26, T:0.39
Consensus pattern (86 bp):
ATGCTTGAAATCCTAAGTTCTTTGAATTGGATGGATGAAGGGGATGTTAGGTTTTGATGTTCCAA
AGCTTGATTATGATATAGTTG
Found at i:2032037 original size:55 final size:55
Alignment explanation
Indices: 2031874--2032387 Score: 466
Period size: 54 Copynumber: 9.4 Consensus size: 55
2031864 TCATCCTATG
** ** * * ** *
2031874 TGATGAATAACTATACAAACACTATGTGTGC-ATTTCACAAAATTCATAATGAGT
1 TGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGT
* * * *
2031928 TGATGAATAACCGTACAGGAACTATGTGTGC-ATTTCACGGAATTCATCAAGAGT
1 TGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGT
* * *
2031982 TTATGAATAATCC-TATAGGCACTGTGTGTGCAAATCCACGGAATTCATCATGAGT
1 TGATGAATAA-CCGTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGT
* ** **
2032037 TGATGAATAACCGTACATGCACTATGTGTGC-AGCCCATAGAATTCATCATGAGT
1 TGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGT
* * * * * * ** * *
2032091 TGATGAATAACCGTACAAGTACTATGTATG-TATTTCACATAATTAATCA-CATGT
1 TGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGA-GT
* ** * * *
2032145 TGATGAAGAACCGTACATACACTATGTGTGAAAATCCATGGAATTCATCATCAGT
1 TGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGT
** * * * *
2032200 TGATGAATAACCGTTTAGGCACTATGTGTGGAAATCCATGAAATTCATTATGAGT
1 TGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGT
* * * * * *
2032255 TGATGAATAATCTTACAGGAACTATGTGTGCAAACCCACGAAATTCATTATGAGT
1 TGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGT
* * * *
2032310 TGATGAATAACCGTACAGGCACAATGTGTAC-AACCCACGAAATTCATCATGAGT
1 TGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGT
* *
2032364 TGATGAATTACCGTATAGGCACTA
1 TGATGAATAACCGTACAGGCACTA
2032388 CATGTGCATC
Statistics
Matches: 381, Mismatches: 72, Indels: 14
0.82 0.15 0.03
Matches are distributed among these distances:
53 1 0.00
54 199 0.52
55 179 0.47
56 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (55 bp):
TGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGT
Found at i:2032045 original size:109 final size:109
Alignment explanation
Indices: 2031874--2032387 Score: 475
Period size: 109 Copynumber: 4.7 Consensus size: 109
2031864 TCATCCTATG
** ** * * * *
2031874 TGATGAATAACTATACAAACACTATGTGTGC-ATTTCACAAAATTCATAATGAGTTGATGAATAA
1 TGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAA
*** *
2031938 CCGTACAGGAACTATGTGTGCATTTCACGGAATTCATCAAGAGT
66 CCGTACAGGAACTATGTGTGCAACCCACGGAATTCATCATGAGT
* * * *
2031982 TTATGAATAATCC-TATAGGCACTGTGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATA
1 TGATGAATAA-CCGTACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATA
* * * **
2032046 ACCGTACATGCACTATGTGTGCAGCCCATAGAATTCATCATGAGT
65 ACCGTACAGGAACTATGTGTGCAACCCACGGAATTCATCATGAGT
* * * * * * * * *
2032091 TGATGAATAACCGTACAAGTACTATGTATG-TATTTCAC-ATAATTAATCA-CATGTTGATGAAG
1 TGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGA-AATTCATCATGA-GTTGATGAAT
* * * * *
2032153 AACCGTACA-TACACTATGTGTGAAAATCCATGGAATTCATCATCAGT
64 AACCGTACAGGA-ACTATGTGTG-CAACCCACGGAATTCATCATGAGT
** * * *
2032200 TGATGAATAACCGTTTAGGCACTATGTGTGGAAATCCATGAAATTCATTATGAGTTGATGAATAA
1 TGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAA
* * * *
2032265 TCTTACAGGAACTATGTGTGCAAACCCACGAAATTCATTATGAGT
66 CCGTACAGGAACTATGTGTGC-AACCCACGGAATTCATCATGAGT
* * * *
2032310 TGATGAATAACCGTACAGGCACAATGTGTAC-AACCCACGAAATTCATCATGAGTTGATGAATTA
1 TGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAA
* *
2032374 CCGTATAGGCACTA
66 CCGTACAGGAACTA
2032388 CATGTGCATC
Statistics
Matches: 320, Mismatches: 74, Indels: 23
0.77 0.18 0.06
Matches are distributed among these distances:
107 1 0.00
108 66 0.21
109 169 0.53
110 81 0.25
111 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (109 bp):
TGATGAATAACCGTACAGGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAA
CCGTACAGGAACTATGTGTGCAACCCACGGAATTCATCATGAGT
Found at i:2032063 original size:163 final size:163
Alignment explanation
Indices: 2031874--2032396 Score: 525
Period size: 163 Copynumber: 3.2 Consensus size: 163
2031864 TCATCCTATG
** ** *
2031874 TGATGAATAACTATACAAACACTATGTGTGCATTTCACAAAATTCATAATGAGTTGATGAATAAC
1 TGATGAATAACCGTACAGGCACTATGTGTGCATATCACAAAATTCATAATGAGTTGATGAATAAC
* * *
2031939 CGTACAGGAACTATGTGTGCATTTCACGGAATTCATCAAGAGTTTATGAATAATCC-TATAGGCA
66 CGTACAGGAACTATGTGTGCATTTCACGAAATTCATCAAGAGTTGATGAATAA-CCGTACAGGCA
*
2032003 CTGTGTGTGCAAATCCACGGAATTCATCATGAGT
130 CTATGTGTGCAAATCCACGGAATTCATCATGAGT
* *** * * *
2032037 TGATGAATAACCGTACATGCACTATGTGTGCAGCCCATAGAATTCATCATGAGTTGATGAATAAC
1 TGATGAATAACCGTACAGGCACTATGTGTGCATATCACAAAATTCATAATGAGTTGATGAATAAC
* * * * * * * **
2032102 CGTACAAGTACTATGTATGTATTTCAC-ATAATTAATCACA-TGTTGATGAAGAACCGTACATAC
66 CGTACAGGAACTATGTGTGCATTTCACGA-AATTCATCA-AGAGTTGATGAATAACCGTACAGGC
* * *
2032165 ACTATGTGTGAAAATCCATGGAATTCATCATCAGT
129 ACTATGTGTGCAAATCCACGGAATTCATCATGAGT
** * * *
2032200 TGATGAATAACCGTTTAGGCACTATGTGTGGAAATC-CATGAAATTCATTATGAGTTGATGAATA
1 TGATGAATAACCGTACAGGCACTATGTGTGCATATCACA--AAATTCATAATGAGTTGATGAATA
* * *** * *
2032264 ATCTTACAGGAACTATGTGTGCAAACCCACGAAATTCATTATGAGTTGATGAATAACCGTACAGG
64 ACCGTACAGGAACTATGTGTGC-ATTTCACGAAATTCATCAAGAGTTGATGAATAACCGTACAGG
* * * *
2032329 CACAATGTGTAC-AACCCACGAAATTCATCATGAGT
128 CACTATGTGTGCAAATCCACGGAATTCATCATGAGT
* * **
2032364 TGATGAATTACCGTATAGGCACTACATGTGCAT
1 TGATGAATAACCGTACAGGCACTATGTGTGCAT
2032397 CTTAATAAAT
Statistics
Matches: 287, Mismatches: 65, Indels: 15
0.78 0.18 0.04
Matches are distributed among these distances:
162 3 0.01
163 160 0.56
164 85 0.30
165 38 0.13
166 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (163 bp):
TGATGAATAACCGTACAGGCACTATGTGTGCATATCACAAAATTCATAATGAGTTGATGAATAAC
CGTACAGGAACTATGTGTGCATTTCACGAAATTCATCAAGAGTTGATGAATAACCGTACAGGCAC
TATGTGTGCAAATCCACGGAATTCATCATGAGT
Found at i:2040208 original size:3 final size:3
Alignment explanation
Indices: 2040184--2040247 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
2040174 CTACAAAATC
* * *
2040184 AAT ATT AAT ATT AAT AAAT AAT AAT AAT AAT AAT GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2040230 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
2040248 GGGATGAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:2040693 original size:111 final size:115
Alignment explanation
Indices: 2040485--2040724 Score: 328
Period size: 111 Copynumber: 2.1 Consensus size: 115
2040475 TCATTTATGA
** *
2040485 AATATCAAATCTTGAAAGAGATTTGATCTGTTCCACTTCTTCTGAGTGAATATATCAGATCTAGG
1 AATATCAAATCTTGAAAGAGATGGGATCTGTTCCACTTCCTCTGAGTGAATATATCAGATCTAGG
** *
2040550 AAAGTTGATCCATTGAATCAGGGTAGACTTGTTCCACTGT-CGCTCAA-GG
66 AAAGTTGATCCATTGAATCAAAGCAGACTTGTTCCACT-TACGCTCAATGG
* * *
2040599 AATACCAAATCTTGAAAGAGA-GGGATCTGTTCCACTTCCTCTGAG-GGA-ATATCAGATCTGGG
1 AATATCAAATCTTGAAAGAGATGGGATCTGTTCCACTTCCTCTGAGTGAATATATCAGATCTAGG
* * *
2040661 AAAGTTGATTCATTGAATCAAAGCAGACTTGTTCCACTTACTCTGAATGG
66 AAAGTTGATCCATTGAATCAAAGCAGACTTGTTCCACTTACGCTCAATGG
2040711 AATATCAAATCTTG
1 AATATCAAATCTTG
2040725 GAGATATTGA
Statistics
Matches: 111, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
110 1 0.01
111 52 0.47
112 17 0.15
113 21 0.19
114 20 0.18
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (115 bp):
AATATCAAATCTTGAAAGAGATGGGATCTGTTCCACTTCCTCTGAGTGAATATATCAGATCTAGG
AAAGTTGATCCATTGAATCAAAGCAGACTTGTTCCACTTACGCTCAATGG
Found at i:2040751 original size:66 final size:66
Alignment explanation
Indices: 2040626--2041338 Score: 1261
Period size: 66 Copynumber: 10.8 Consensus size: 66
2040616 GAGAGGGATC
* * * * *
2040626 TGTTCCACTTCCTCTG-AGGGAATATCAGATCTGGGA-AAGTTGATTCATTGAATCAAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2040689 T
66 T
*
2040690 TGTTCCACTTACTCTGAATGGAATATCAAATCTTGGAGATA-TTGATCCATTGAATCGAAGCAGA
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGA-AGTTGATCCATTGAATCGAAGCAGA
2040754 CT
65 CT
*
2040756 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGTAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2040821 T
66 T
2040822 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2040887 T
66 T
2040888 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2040953 T
66 T
* * *
2040954 TGTTCCACTTACTCTAAAGGGAATATCAAATATTGGAGAAGTTGATCCATTGAATCGAAGTAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2041019 T
66 T
* *
2041020 TGTTCCACTTACTCTGAAGGGAATATTAAATCTTGAAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2041085 T
66 T
*
2041086 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGTAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2041151 T
66 T
*
2041152 TGTTCCATTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2041217 T
66 T
2041218 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
2041283 T
66 T
*
2041284 TGTTCCACTTACTGTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAAT
1 TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAAT
2041339 TGGGATCGAT
Statistics
Matches: 621, Mismatches: 24, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
64 15 0.02
65 18 0.03
66 587 0.95
67 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (66 bp):
TGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGTTGATCCATTGAATCGAAGCAGAC
T
Found at i:2042543 original size:22 final size:23
Alignment explanation
Indices: 2042504--2042554 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
2042494 CCTTCTTTTA
* *
2042504 TTTTTCTTTTCTTTTTTCCTTAT
1 TTTTTCTTTTCCTTTTTCATTAT
*
2042527 TTTTTC-TTTCCTTTTTCATTTT
1 TTTTTCTTTTCCTTTTTCATTAT
2042549 TTTTTC
1 TTTTTC
2042555 AGGCGAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (23 bp):
TTTTTCTTTTCCTTTTTCATTAT
Found at i:2042552 original size:23 final size:23
Alignment explanation
Indices: 2042496--2042554 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
2042486 TCTTGAACCC
* *
2042496 TTCTTTTATTTTTCTTTTCTTTT
1 TTCTTTTTTTTTTCTTTTCCTTT
* *
2042519 TTCCTTATTTTTTC-TTTCCTTT
1 TTCTTTTTTTTTTCTTTTCCTTT
*
2042541 TTCATTTTTTTTTC
1 TTCTTTTTTTTTTC
2042555 AGGCGAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (23 bp):
TTCTTTTTTTTTTCTTTTCCTTT
Found at i:2055866 original size:3 final size:3
Alignment explanation
Indices: 2055855--2055894 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
2055845 ATATTATTAT
*
2055855 TAA TAAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2055895 CGGGATGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2063933 original size:54 final size:53
Alignment explanation
Indices: 2063846--2063951 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 53
2063836 AACAGTCTGT
* * *
2063846 ACGGTTATTCATCACATAGGATGAATTCTGTGAAATGCACAATTAGTGCCTAA
1 ACGGTTATTCATCACATAGGATGAAGTCCGTGAAATGCACAATTAGTACCTAA
* *
2063899 ACGGTTATTCATCCATATAGGATGAAGTCCGTGAAATGCACACTTAGTACCTA
1 ACGGTTATTCAT-CACATAGGATGAAGTCCGTGAAATGCACAATTAGTACCTA
2063952 TTTGGTAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 12 0.26
54 35 0.74
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (53 bp):
ACGGTTATTCATCACATAGGATGAAGTCCGTGAAATGCACAATTAGTACCTAA
Found at i:2064506 original size:77 final size:79
Alignment explanation
Indices: 2064397--2064548 Score: 175
Period size: 77 Copynumber: 1.9 Consensus size: 79
2064387 AAATAAAATA
*
2064397 TTATTTAATTAATTCAAATTAAATATACATT-AAAGACTTATAATCTAAATTACAATC-TTTAAT
1 TTATTTAATTAATTCAAATTAAATATACATTAAAAGACTTATAATCAAAATTACAATCTTTTAAT
* *
2064460 GGTTATTTAAAAAC
66 GCTTACTTAAAAAC
* ** * * * * *
2064474 TTATTTAATTATTTTGAATTATATAT-CAATTAAAAGAGTTGTAATCAAAATTGCATTCTTTTAA
1 TTATTTAATTAATTCAAATTAAATATAC-ATTAAAAGACTTATAATCAAAATTACAATCTTTTAA
2064538 TGCTTACTTAA
65 TGCTTACTTAA
2064549 TATATTCGGG
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
76 1 0.02
77 25 0.41
78 21 0.34
79 14 0.23
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (79 bp):
TTATTTAATTAATTCAAATTAAATATACATTAAAAGACTTATAATCAAAATTACAATCTTTTAAT
GCTTACTTAAAAAC
Found at i:2065711 original size:55 final size:55
Alignment explanation
Indices: 2065587--2065898 Score: 342
Period size: 55 Copynumber: 5.7 Consensus size: 55
2065577 TATTTCACGG
* * * * * *
2065587 AATTCATCATGAGTTGATGAATAGCCTTACAGGCACTATGTGTAC-ATTTCATGG
1 AATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCATGA
* ** * * *
2065641 AATTCATCACGAGTTGATGAATAACTATACATGCACTATTTGTGCAAATCCATGG
1 AATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCATGA
* * * *
2065696 AATTCATCATGAGTTGATGAATAACCCTAAAGGCACTATGTATACAAATCCATGA
1 AATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCATGA
* *
2065751 AATTCATTATGAGTTCATGAATAACCGTACAGGCACTATGTGTGCAAATCCACT-A
1 AATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCA-TGA
* * * * *
2065806 AATTCATTATGAGTTGATGAATAACCGTACATGCACAATGTGTGC-AACCCACGA
1 AATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCATGA
* * * * *
2065860 AATTCATTAGGAGTTGATGAATTACCGTATAGACACTAT
1 AATTCATCATGAGTTGATGAATAACCGTACAGGCACTAT
2065899 ATATGCATCT
Statistics
Matches: 220, Mismatches: 35, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
54 77 0.35
55 142 0.65
56 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (55 bp):
AATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAATCCATGA
Found at i:2068178 original size:19 final size:19
Alignment explanation
Indices: 2068153--2068198 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2068143 ACATTTTTAA
*
2068153 GAACAGTAATATACGTTAT
1 GAACAGTAATATACGGTAT
*
2068172 TAACAGTAATATACGGTAT
1 GAACAGTAATATACGGTAT
2068191 GAACAGTA
1 GAACAGTA
2068199 CCGTGAACAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.28
Consensus pattern (19 bp):
GAACAGTAATATACGGTAT
Found at i:2068926 original size:31 final size:31
Alignment explanation
Indices: 2068881--2069038 Score: 228
Period size: 31 Copynumber: 5.1 Consensus size: 31
2068871 ACTCGTATAA
* *
2068881 TAATCTGTCTATATATCCCGAAGAACATAGG
1 TAATATGTCCATATATCCCGAAGAACATAGG
2068912 TAATATGTCCATATATCCCGAAGAACATAGG
1 TAATATGTCCATATATCCCGAAGAACATAGG
*
2068943 TAAAATGTCCATATATCCCGAAGAACATAGG
1 TAATATGTCCATATATCCCGAAGAACATAGG
* * * *
2068974 TAATATATCCATATGTCCCGAAAAACCTAGG
1 TAATATGTCCATATATCCCGAAGAACATAGG
*
2069005 TAA-ACTGTCCATATGTCCCGAAGAACATAGG
1 TAATA-TGTCCATATATCCCGAAGAACATAGG
2069036 TAA
1 TAA
2069039 ACCCTCGACT
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
30 1 0.01
31 114 0.99
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (31 bp):
TAATATGTCCATATATCCCGAAGAACATAGG
Found at i:2088680 original size:58 final size:58
Alignment explanation
Indices: 2088590--2088755 Score: 262
Period size: 58 Copynumber: 2.9 Consensus size: 58
2088580 TGTTCGTTTC
* * * *
2088590 TTCCAAAGATCCATAAATATCTCTCAT-GATCGAGAGGACATGGAAGGTTTGTCATTTT
1 TTCCAAAGATACATCAATAACTCTC-TCGATCGAGAGGACATGGAAGGTTTGTCATTTA
*
2088648 TTCCAAAGATACATCAATAACTCTCTCGATCGAGAGGACATGGAAGGTTTGTCGTTTA
1 TTCCAAAGATACATCAATAACTCTCTCGATCGAGAGGACATGGAAGGTTTGTCATTTA
*
2088706 TTCCAAAAATACATCAATAACTCTCTCGATCGAGAGGACATGGAAGGTTT
1 TTCCAAAGATACATCAATAACTCTCTCGATCGAGAGGACATGGAAGGTTT
2088756 ACATCATTCG
Statistics
Matches: 101, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
57 1 0.01
58 100 0.99
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (58 bp):
TTCCAAAGATACATCAATAACTCTCTCGATCGAGAGGACATGGAAGGTTTGTCATTTA
Found at i:2090929 original size:20 final size:20
Alignment explanation
Indices: 2090904--2090952 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2090894 CATGACAAGT
* *
2090904 AGCTGAATG-TAACTGAATGG
1 AGCTGAATGAGAACT-AAAGG
*
2090924 AGCTGAACGAGAACTAAAGG
1 AGCTGAATGAGAACTAAAGG
2090944 AGCTGAATG
1 AGCTGAATG
2090953 GGAGTTGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 20 0.83
21 4 0.17
ACGTcount: A:0.39, C:0.12, G:0.31, T:0.18
Consensus pattern (20 bp):
AGCTGAATGAGAACTAAAGG
Found at i:2095639 original size:35 final size:35
Alignment explanation
Indices: 2095574--2095641 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
2095564 TCTTAGGTCC
*
2095574 ATAAGGAATTACCAGCTCGATCAGTCTGAACCTAT
1 ATAAGGAATTACCAGCTCGATCAGTATGAACCTAT
* * *
2095609 ATAAGTAATTACCAGTTTGATCAAG-ATGAACCT
1 ATAAGGAATTACCAGCTCGATC-AGTATGAACCT
2095642 GCAGAGACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 26 0.93
36 2 0.07
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (35 bp):
ATAAGGAATTACCAGCTCGATCAGTATGAACCTAT
Done.