Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_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: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 43
Found at i:3052179 original size:20 final size:19
Alignment explanation
Indices: 3052138--3052182 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3052128 TTAATAGAAT
*
3052138 TAATAATAATTAATAATGA
1 TAATAATAAATAATAATGA
* *
3052157 TAATAATAAAATAATTATTA
1 TAATAAT-AAATAATAATGA
3052177 TAATAA
1 TAATAA
3052183 CATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TAATAATAAATAATAATGA
Found at i:3053671 original size:27 final size:27
Alignment explanation
Indices: 3053633--3053688 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
3053623 ATAGACAGTA
3053633 TTTCCACTAAAAATCTGGGAATGTTTC
1 TTTCCACTAAAAATCTGGGAATGTTTC
3053660 TTTCCACTAAAAATCTGGGAATGTTTC
1 TTTCCACTAAAAATCTGGGAATGTTTC
3053687 TT
1 TT
3053689 GCTTTCTGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (27 bp):
TTTCCACTAAAAATCTGGGAATGTTTC
Found at i:3057136 original size:21 final size:21
Alignment explanation
Indices: 3057088--3057155 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
3057078 ACCGTTATGG
*
3057088 TGCTGATGTGGCAGTTCACAG
1 TGCTGATGTGGCAGTTCACAA
3057109 T-CTGATGCT-GCAGTTCACAA
1 TGCTGATG-TGGCAGTTCACAA
*
3057129 TGCTGATGTGGTAGTTCACAA
1 TGCTGATGTGGCAGTTCACAA
3057150 TGCTGA
1 TGCTGA
3057156 CATAACAGTC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 18 0.43
21 24 0.57
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (21 bp):
TGCTGATGTGGCAGTTCACAA
Found at i:3060304 original size:82 final size:81
Alignment explanation
Indices: 3060153--3060311 Score: 194
Period size: 82 Copynumber: 2.0 Consensus size: 81
3060143 GCATTTCTTT
* ** *
3060153 AACAAACGCCGCGATAGAATAATTTAGCGGCATTTTTAGCATAAACGCTGCAATAAGGTTCATTT
1 AACAAACGCCGCGATAGAATAATTTAGCGGCATTTTTAGCATAAACACCACAATAAGGTTCATTA
*
3060218 ATAGTGGCGTTTTTCC
66 ATAGTGGAGTTTTTCC
* * * * * *
3060234 AACAAACGTCGCGATAAAGAGTATTTTAGCGGTATTTTTAG-ATAAACACCATAATAGGGTTCAT
1 AACAAACGCCGCGAT--AGAATAATTTAGCGGCATTTTTAGCATAAACACCACAATAAGGTTCAT
3060298 TAATAGTGGAGTTT
64 TAATAGTGGAGTTT
3060312 GTTATAAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
81 14 0.22
82 30 0.46
83 21 0.32
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (81 bp):
AACAAACGCCGCGATAGAATAATTTAGCGGCATTTTTAGCATAAACACCACAATAAGGTTCATTA
ATAGTGGAGTTTTTCC
Found at i:3064616 original size:13 final size:13
Alignment explanation
Indices: 3064616--3064691 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
3064606 CCGTTGACCC
3064616 GACCCGACCCGTT
1 GACCCGACCCGTT
*
3064629 TACCCGACCCGTT
1 GACCCGACCCGTT
3064642 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
3064660 GACCCGACCCGTT
1 GACCCGACCCGTT
*
3064673 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
3064688 GACC
1 GACC
3064692 GTTGACCGGA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 29 0.55
15 12 0.23
18 12 0.23
ACGTcount: A:0.16, C:0.45, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3064617 original size:18 final size:18
Alignment explanation
Indices: 3064594--3064670 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
3064584 ACCGGTCACA
3064594 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
3064612 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
3064629 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
3064643 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
3064661 ACCCGACCCG
1 ACCCGACCCG
3064671 TTGACCGTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.23
18 40 0.77
ACGTcount: A:0.17, C:0.51, G:0.21, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:3064637 original size:31 final size:31
Alignment explanation
Indices: 3064598--3064676 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
3064588 GTCACAACCC
3064598 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
3064629 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
3064660 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
3064677 GTTGACCCGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.16, C:0.48, G:0.22, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:3064663 original size:8 final size:8
Alignment explanation
Indices: 3064652--3064698 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
3064642 GACCCGACCC
3064652 GACCCGTT
1 GACCCGTT
3064660 GACCC---
1 GACCCGTT
3064665 GACCCGTT
1 GACCCGTT
3064673 GA-CCGTT
1 GACCCGTT
3064680 GACCCGTT
1 GACCCGTT
3064688 GA-CCGTT
1 GACCCGTT
3064695 GACC
1 GACC
3064699 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:3064680 original size:7 final size:7
Alignment explanation
Indices: 3064668--3064699 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
3064658 TTGACCCGAC
3064668 CCGTTGA
1 CCGTTGA
3064675 CCGTTGA
1 CCGTTGA
3064682 CCCGTTGA
1 -CCGTTGA
3064690 CCGTTGA
1 CCGTTGA
3064697 CCG
1 CCG
3064700 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:3064685 original size:15 final size:15
Alignment explanation
Indices: 3064652--3064698 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
3064642 GACCCGACCC
*
3064652 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
3064665 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
3064680 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
3064695 GACC
1 GACC
3064699 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:3067279 original size:24 final size:24
Alignment explanation
Indices: 3067185--3067284 Score: 94
Period size: 24 Copynumber: 4.2 Consensus size: 24
3067175 ATATTTTATC
* *
3067185 TGATTTCTGATTTGAATTCTGTTT
1 TGATATCTGATCTGAATTCTGTTT
* * *
3067209 TGACATCTGATCTGAAATCTGTTC
1 TGATATCTGATCTGAATTCTGTTT
* * * *
3067233 TGAT-TCCTAACCTGGATTCTGTTA
1 TGATAT-CTGATCTGAATTCTGTTT
*
3067257 TGATATCTGATCTGAATTATGTTT
1 TGATATCTGATCTGAATTCTGTTT
3067281 TGAT
1 TGAT
3067285 TTTTGATATC
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 1 0.02
24 56 0.97
25 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (24 bp):
TGATATCTGATCTGAATTCTGTTT
Found at i:3069441 original size:13 final size:13
Alignment explanation
Indices: 3069441--3069516 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 13
3069431 CCGTTGACCC
3069441 GACCCGACCCGTT
1 GACCCGACCCGTT
*
3069454 TACCCGACCCGTT
1 GACCCGACCCGTT
3069467 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
3069485 GACCCGACCCGTT
1 GACCCGACCCGTT
*
3069498 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
3069513 GACC
1 GACC
3069517 GTTGACCGGA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
13 29 0.55
15 12 0.23
18 12 0.23
ACGTcount: A:0.16, C:0.45, G:0.22, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3069442 original size:18 final size:18
Alignment explanation
Indices: 3069419--3069495 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
3069409 ACCGGTCACA
3069419 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
3069437 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
3069454 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
3069468 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
3069486 ACCCGACCCG
1 ACCCGACCCG
3069496 TTGACCGTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.23
18 40 0.77
ACGTcount: A:0.17, C:0.51, G:0.21, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:3069462 original size:31 final size:31
Alignment explanation
Indices: 3069423--3069501 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
3069413 GTCACAACCC
3069423 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
3069454 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
3069485 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
3069502 GTTGACCCGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.16, C:0.48, G:0.22, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:3069488 original size:8 final size:8
Alignment explanation
Indices: 3069477--3069523 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
3069467 GACCCGACCC
3069477 GACCCGTT
1 GACCCGTT
3069485 GACCC---
1 GACCCGTT
3069490 GACCCGTT
1 GACCCGTT
3069498 GA-CCGTT
1 GACCCGTT
3069505 GACCCGTT
1 GACCCGTT
3069513 GA-CCGTT
1 GACCCGTT
3069520 GACC
1 GACC
3069524 GGAGTTGACC
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.15
7 14 0.41
8 15 0.44
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:3069505 original size:7 final size:7
Alignment explanation
Indices: 3069493--3069524 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
3069483 TTGACCCGAC
3069493 CCGTTGA
1 CCGTTGA
3069500 CCGTTGA
1 CCGTTGA
3069507 CCCGTTGA
1 -CCGTTGA
3069515 CCGTTGA
1 CCGTTGA
3069522 CCG
1 CCG
3069525 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:3069510 original size:15 final size:15
Alignment explanation
Indices: 3069477--3069523 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
3069467 GACCCGACCC
*
3069477 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
3069490 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
3069505 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
3069520 GACC
1 GACC
3069524 GGAGTTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:3072107 original size:24 final size:24
Alignment explanation
Indices: 3072018--3072112 Score: 93
Period size: 24 Copynumber: 4.0 Consensus size: 24
3072008 TTATCCGATT
* *
3072018 TCTGATTTGAATTCTGTTTTGACA
1 TCTGATCTGAATTCTGTTTTGATA
* *
3072042 TCTGATCTGAAATCTGTTCTGAT-
1 TCTGATCTGAATTCTGTTTTGATA
* * * *
3072065 TCCTAACCTGGATTCTGTTATGATA
1 T-CTGATCTGAATTCTGTTTTGATA
*
3072090 TCTGATCTGAATTATGTTTTGAT
1 TCTGATCTGAATTCTGTTTTGAT
3072113 TTTTGATATC
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
23 1 0.02
24 53 0.96
25 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (24 bp):
TCTGATCTGAATTCTGTTTTGATA
Found at i:3073059 original size:43 final size:42
Alignment explanation
Indices: 3073004--3073166 Score: 218
Period size: 43 Copynumber: 3.8 Consensus size: 42
3072994 GCATTTGTAT
*
3073004 CAAAAAGCGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTC
1 CAAAAA-CGCCGCTATAGATCTCACCTTTTGCGGCGTTTGTTC
* * *
3073047 CAAAAAATGCCGCTATAGATCTGACCTATTGCGGCGTTTGTTC
1 C-AAAAACGCCGCTATAGATCTCACCTTTTGCGGCGTTTGTTC
* *
3073090 CAAAAACGCCGCTATAGATGTCATCCTTTTGCAGCGTTTGTTC
1 CAAAAACGCCGCTATAGATCTCA-CCTTTTGCGGCGTTTGTTC
* * *
3073133 TAAAAACGCCGCTATATATCTCAACTTTTGCGGC
1 CAAAAACGCCGCTATAGATCTCACCTTTTGCGGC
3073167 ATTTTTTGTT
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
42 28 0.26
43 73 0.69
44 5 0.05
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (42 bp):
CAAAAACGCCGCTATAGATCTCACCTTTTGCGGCGTTTGTTC
Found at i:3073164 original size:85 final size:86
Alignment explanation
Indices: 3073004--3073166 Score: 222
Period size: 85 Copynumber: 1.9 Consensus size: 86
3072994 GCATTTGTAT
* * *
3073004 CAAAAAGCGCCGCTATAGATCTGACCTTTTGCGGCGTTTGTTCCAAAAAATGCCGCTATAGATCT
1 CAAAAAGCGCCGCTATAGATCTCACCTTTTGCAGCGTTTGTTCCAAAAAACGCCGCTATAGATCT
* *
3073069 GACCTATTGCGGCGTTTGTTC
66 CAACTATTGCGGCGTTTGTTC
* * *
3073090 CAAAAA-CGCCGCTATAGATGTCATCCTTTTGCAGCGTTTGTT-CTAAAAACGCCGCTATATATC
1 CAAAAAGCGCCGCTATAGATCTCA-CCTTTTGCAGCGTTTGTTCCAAAAAACGCCGCTATAGATC
*
3073153 TCAACTTTTGCGGC
65 TCAACTATTGCGGC
3073167 ATTTTTTGTT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
85 44 0.66
86 23 0.34
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (86 bp):
CAAAAAGCGCCGCTATAGATCTCACCTTTTGCAGCGTTTGTTCCAAAAAACGCCGCTATAGATCT
CAACTATTGCGGCGTTTGTTC
Found at i:3080932 original size:3 final size:3
Alignment explanation
Indices: 3080912--3080962 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
3080902 ACAAAATGTA
*
3080912 AAT AAT ATT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3080958 AAT AA
1 AAT AA
3080963 AAACTAGACA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3080946 original size:23 final size:23
Alignment explanation
Indices: 3080912--3080962 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
3080902 ACAAAATGTA
*
3080912 AATAATATTAATAAAATAATAAT
1 AATAATAATAATAAAATAATAAT
*
3080935 AATAATAATAATAATATAATAAT
1 AATAATAATAATAAAATAATAAT
3080958 AATAA
1 AATAA
3080963 AAACTAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AATAATAATAATAAAATAATAAT
Found at i:3081125 original size:2 final size:2
Alignment explanation
Indices: 3081118--3081149 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3081108 GTATACTACC
3081118 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
3081150 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3081674 original size:2 final size:2
Alignment explanation
Indices: 3081667--3081718 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3081657 TTGTCGTATC
3081667 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
3081709 AT AT AT AT AT
1 AT AT AT AT AT
3081719 TTGTTTATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3083561 original size:31 final size:31
Alignment explanation
Indices: 3083540--3083628 Score: 117
Period size: 31 Copynumber: 2.9 Consensus size: 31
3083530 ATCATTGAGT
3083540 TTTAAATAAAATACTAATTTAACTCTTAAAA
1 TTTAAATAAAATACTAATTTAACTCTTAAAA
* * * *
3083571 TTTAGATAAAATATTAATTTAACTTTTAAAT
1 TTTAAATAAAATACTAATTTAACTCTTAAAA
*
3083602 TTTAGATAAAATA-TCAATTTAACTCTT
1 TTTAAATAAAATACT-AATTTAACTCTT
3083629 GAACTCGATC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
30 1 0.02
31 51 0.98
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (31 bp):
TTTAAATAAAATACTAATTTAACTCTTAAAA
Found at i:3085782 original size:16 final size:16
Alignment explanation
Indices: 3085748--3085876 Score: 96
Period size: 16 Copynumber: 8.1 Consensus size: 16
3085738 AATTTAGAGA
* **
3085748 AACCGAAATTAACAAG
1 AACCAAAATTAACCCG
3085764 AACCAAAATTAACCCG
1 AACCAAAATTAACCCG
* *
3085780 AACCAAAAGTAACCTG
1 AACCAAAATTAACCCG
** **
3085796 AACTGAAAGCAACCCG
1 AACCAAAATTAACCCG
** *
3085812 AACTGAAACTAACCCG
1 AACCAAAATTAACCCG
* **
3085828 AACCGAAAGAAACCCG
1 AACCAAAATTAACCCG
* *
3085844 AACCAAATTTAACCTG
1 AACCAAAATTAACCCG
*
3085860 AACCAAATTTAACCCG
1 AACCAAAATTAACCCG
3085876 A
1 A
3085877 TCCGAAAACA
Statistics
Matches: 93, Mismatches: 20, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 93 1.00
ACGTcount: A:0.48, C:0.28, G:0.12, T:0.12
Consensus pattern (16 bp):
AACCAAAATTAACCCG
Found at i:3085873 original size:48 final size:48
Alignment explanation
Indices: 3085821--3085914 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
3085811 GAACTGAAAC
* *
3085821 TAACCCGAACCGAAAGA-AACCCGAACCAAATTTAACCTGAACCAAATT
1 TAACCCGAACCGAAA-ACAACCCAAACCAAATTTAACCCGAACCAAATT
* * * *
3085869 TAACCCGATCCGAAAACAACCTAAACCGAATTTAACCCGATCCAAA
1 TAACCCGAACCGAAAACAACCCAAACCAAATTTAACCCGAACCAAA
3085915 AGCAACCTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 1 0.03
48 38 0.97
ACGTcount: A:0.45, C:0.31, G:0.10, T:0.15
Consensus pattern (48 bp):
TAACCCGAACCGAAAACAACCCAAACCAAATTTAACCCGAACCAAATT
Found at i:3085874 original size:32 final size:31
Alignment explanation
Indices: 3085763--3085955 Score: 111
Period size: 32 Copynumber: 6.0 Consensus size: 31
3085753 AAATTAACAA
*
3085763 GAACCAAAATTAACCCGAACCAAAAGTAACCT
1 GAACCAAATTTAACCCGAACC-AAAGTAACCT
* ** * * *
3085795 GAACTGAAA-GCAACCCGAACTGAAACTAACCC
1 GAAC-CAAATTTAACCCGAAC-CAAAGTAACCT
** *
3085827 GAACCGAAA-GAAACCCGAACCAAATTTAACCT
1 GAACC-AAATTTAACCCGAACCAAA-GTAACCT
* **
3085859 GAACCAAATTTAACCCGATCCGAAAACAACCT
1 GAACCAAATTTAACCCGAACC-AAAGTAACCT
* * * *
3085891 AAACCGAATTTAACCCGATCCAAAAGCAACCT
1 GAACCAAATTTAACCCGAACC-AAAGTAACCT
* * * *
3085923 GAACCGAATTTAACTCAAACCGAAAGCAACCT
1 GAACCAAATTTAACCCGAACC-AAAGTAACCT
3085955 G
1 G
3085956 CACATGTTGA
Statistics
Matches: 130, Mismatches: 25, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
31 6 0.05
32 118 0.91
33 6 0.05
ACGTcount: A:0.45, C:0.30, G:0.12, T:0.13
Consensus pattern (31 bp):
GAACCAAATTTAACCCGAACCAAAGTAACCT
Found at i:3086667 original size:16 final size:16
Alignment explanation
Indices: 3086643--3086696 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
3086633 TGAAAATCAA
*
3086643 CCGATCCGATATTAAC
1 CCGACCCGATATTAAC
*
3086659 CCGACCCGAAATCTAA-
1 CCGACCCGATAT-TAAC
*
3086675 CCGATCCG-TATTAAC
1 CCGACCCGATATTAAC
3086690 CCGACCC
1 CCGACCC
3086697 AAAAATCAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 3 0.10
15 8 0.26
16 17 0.55
17 3 0.10
ACGTcount: A:0.30, C:0.39, G:0.13, T:0.19
Consensus pattern (16 bp):
CCGACCCGATATTAAC
Found at i:3086751 original size:32 final size:31
Alignment explanation
Indices: 3086635--3086776 Score: 135
Period size: 32 Copynumber: 4.5 Consensus size: 31
3086625 ACCTAAACTG
*
3086635 AAAATCAACCGATCCGATATTAACCCGACCC
1 AAAATCAACCGATCCGATATTAACCCGACCA
*
3086666 GAAATCTAACCGATCCG-TATTAACCCGACCCA
1 AAAATC-AACCGATCCGATATTAACCCGA-CCA
* * * *
3086698 AAAATCAACCGATCTGGTATTGACCCGATTCA
1 AAAATCAACCGATCCGATATTAACCCGA-CCA
* * *
3086730 AAAATTAACCGATCCGATATTGATCCGAACCA
1 AAAATCAACCGATCCGATATTAACCCG-ACCA
*
3086762 GAAAA-CAACTGATCC
1 -AAAATCAACCGATCC
3086777 AATAATCACC
Statistics
Matches: 92, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
31 25 0.27
32 62 0.67
33 5 0.05
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.20
Consensus pattern (31 bp):
AAAATCAACCGATCCGATATTAACCCGACCA
Found at i:3087460 original size:23 final size:23
Alignment explanation
Indices: 3087434--3087480 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3087424 GATCCCTCGA
3087434 CAAAGAAAAACCCAAATAA-GAAC
1 CAAAGAAAAACCCAAA-AACGAAC
**
3087457 CAAAGACCAACCCAAAAACGAAC
1 CAAAGAAAAACCCAAAAACGAAC
3087480 C
1 C
3087481 GGCAAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.60, C:0.30, G:0.09, T:0.02
Consensus pattern (23 bp):
CAAAGAAAAACCCAAAAACGAAC
Found at i:3090106 original size:31 final size:31
Alignment explanation
Indices: 3090069--3090133 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
3090059 TGACCTCATC
* * * *
3090069 TTAATTAAATAAAAATGGAAGTGAGTATATA
1 TTAATTAAATAAAAACGAAAGTGACTATAGA
*
3090100 TTAATTAAATTAAAACGAAAGTGACTATAGA
1 TTAATTAAATAAAAACGAAAGTGACTATAGA
3090131 TTA
1 TTA
3090134 TTTTTTTAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (31 bp):
TTAATTAAATAAAAACGAAAGTGACTATAGA
Found at i:3091989 original size:18 final size:18
Alignment explanation
Indices: 3091966--3092057 Score: 70
Period size: 18 Copynumber: 5.3 Consensus size: 18
3091956 ACCGATCATA
3091966 ACCCGACCCGAACCGTTG
1 ACCCGACCCGAACCGTTG
* * *
3091984 ACCCGACCCGACCCATTT
1 ACCCGACCCGAACCGTTG
3092002 ACCCGA--C---CCGTTG
1 ACCCGACCCGAACCGTTG
*
3092015 ACCCCACCC-AACCCGTTG
1 ACCCGACCCGAA-CCGTTG
*
3092033 ACCCGACCCGTTGACCGTTG
1 ACCCGACCCG--AACCGTTG
3092053 ACCCG
1 ACCCG
3092058 TTGACCCGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
13 9 0.16
15 1 0.02
16 1 0.02
18 35 0.60
20 11 0.19
21 1 0.02
ACGTcount: A:0.20, C:0.48, G:0.18, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGAACCGTTG
Found at i:3092013 original size:31 final size:31
Alignment explanation
Indices: 3091970--3092048 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
3091960 ATCATAACCC
* * *
3091970 GACCCGAACCGTTGACCCGACCCGACCCATT
1 GACCCGACCCGTTGACCCCACCCAACCCATT
* *
3092001 TACCCGACCCGTTGACCCCACCCAACCCGTT
1 GACCCGACCCGTTGACCCCACCCAACCCATT
3092032 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
3092049 GTTGACCCGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.20, C:0.48, G:0.18, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCCACCCAACCCATT
Found at i:3092036 original size:8 final size:8
Alignment explanation
Indices: 3092025--3092077 Score: 71
Period size: 8 Copynumber: 7.2 Consensus size: 8
3092015 ACCCCACCCA
3092025 ACCCGTTG
1 ACCCGTTG
3092033 ACCC---G
1 ACCCGTTG
3092038 ACCCGTTG
1 ACCCGTTG
3092046 A-CCGTTG
1 ACCCGTTG
3092053 ACCCGTTG
1 ACCCGTTG
3092061 ACCCGTTG
1 ACCCGTTG
3092069 A-CCGTTG
1 ACCCGTTG
3092076 AC
1 AC
3092078 TGGAGTTGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.12
7 14 0.35
8 21 0.52
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.23
Consensus pattern (8 bp):
ACCCGTTG
Found at i:3092052 original size:7 final size:7
Alignment explanation
Indices: 3092040--3092077 Score: 58
Period size: 7 Copynumber: 5.1 Consensus size: 7
3092030 TTGACCCGAC
3092040 CCGTTGA
1 CCGTTGA
3092047 CCGTTGA
1 CCGTTGA
3092054 CCCGTTGA
1 -CCGTTGA
3092062 CCCGTTGA
1 -CCGTTGA
3092070 CCGTTGA
1 CCGTTGA
3092077 C
1 C
3092078 TGGAGTTGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 15 0.50
8 15 0.50
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:3092057 original size:15 final size:15
Alignment explanation
Indices: 3092025--3092077 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
3092015 ACCCCACCCA
*
3092025 ACCCGTTGACC--CG
1 ACCCGTTGACCGTTG
3092038 ACCCGTTGACCGTTG
1 ACCCGTTGACCGTTG
3092053 ACCCGTTGACCCGTTG
1 ACCCGTTGA-CCGTTG
3092069 A-CCGTTGAC
1 ACCCGTTGAC
3092078 TGGAGTTGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
13 11 0.31
14 1 0.03
15 17 0.47
16 7 0.19
ACGTcount: A:0.15, C:0.38, G:0.25, T:0.23
Consensus pattern (15 bp):
ACCCGTTGACCGTTG
Found at i:3094549 original size:48 final size:48
Alignment explanation
Indices: 3094497--3094628 Score: 137
Period size: 48 Copynumber: 2.8 Consensus size: 48
3094487 AATATTTTAC
*
3094497 CTGATTTTCGATTTGATTTCTGATCTGATACTTGACATGGATTCTGAT
1 CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
* * *
3094545 CTGA-TATCTGACATGGA-TTCTGATCTGATACTTGACTTGGATTCTGAT
1 CTGATTTTC-GA-ATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
** *
3094593 CTG-TTACTT-GACCTGATTTCTGATATGATACTTGAC
1 CTGATT--TTCGAATTGATTTCTGATCTGATACTTGAC
3094629 CTGATTTATG
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
47 5 0.07
48 60 0.87
49 3 0.04
50 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (48 bp):
CTGATTTTCGAATTGATTTCTGATCTGATACTTGACATGGATTCTGAT
Found at i:3094635 original size:24 final size:24
Alignment explanation
Indices: 3094514--3094628 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
3094504 TCGATTTGAT
3094514 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
3094538 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
3094562 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
3094586 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
3094609 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
3094629 CTGATTTATG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:3094651 original size:24 final size:24
Alignment explanation
Indices: 3094565--3094638 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
3094555 ACATGGATTC
* * *
3094565 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
3094589 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
3094613 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
3094637 TG
1 TG
3094639 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:3096822 original size:13 final size:13
Alignment explanation
Indices: 3096822--3096901 Score: 76
Period size: 13 Copynumber: 6.2 Consensus size: 13
3096812 CCGTTGACCC
*
3096822 GACCCGACCCATT
1 GACCCGACCCGTT
*
3096835 TACCCGACCCGTT
1 GACCCGACCCGTT
*
3096848 GACCCCACCC---
1 GACCCGACCCGTT
*
3096858 CACCCGACCCGTT
1 GACCCGACCCGTT
3096871 GACCCGACCCGTT
1 GACCCGACCCGTT
*
3096884 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
3096899 GAC
1 GAC
3096902 TGTTGACCGG
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
10 8 0.15
13 35 0.65
15 11 0.20
ACGTcount: A:0.17, C:0.47, G:0.19, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3096823 original size:18 final size:18
Alignment explanation
Indices: 3096800--3096881 Score: 80
Period size: 18 Copynumber: 4.6 Consensus size: 18
3096790 ACCGATCATA
3096800 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
* *
3096818 ACCCGACCCGACCCATTT
1 ACCCGACCCGACCCGTTG
*
3096836 ACCCGACCCGTTGACCC---C
1 ACCCGACCC---GACCCGTTG
*
3096854 ACCCCACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
3096872 ACCCGACCCG
1 ACCCGACCCG
3096882 TTGACCGTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
15 5 0.10
18 42 0.81
21 5 0.10
ACGTcount: A:0.18, C:0.54, G:0.17, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:3096863 original size:36 final size:36
Alignment explanation
Indices: 3096818--3096887 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
3096808 CGACCCGTTG
* *
3096818 ACCCGACCCGACCCATTTACCCGACCCGTTGACCCC
1 ACCCCACCCGACCCATTGACCCGACCCGTTGACCCC
*
3096854 ACCCCACCCGACCCGTTGACCCGACCCGTTGACC
1 ACCCCACCCGACCCATTGACCCGACCCGTTGACC
3096888 GTTGACCCGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.19, C:0.53, G:0.16, T:0.13
Consensus pattern (36 bp):
ACCCCACCCGACCCATTGACCCGACCCGTTGACCCC
Found at i:3096876 original size:8 final size:8
Alignment explanation
Indices: 3096863--3096901 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
3096853 CACCCCACCC
3096863 GACCCGTT
1 GACCCGTT
3096871 GACCC---
1 GACCCGTT
3096876 GACCCGTT
1 GACCCGTT
3096884 GA-CCGTT
1 GACCCGTT
3096891 GACCCGTT
1 GACCCGTT
3096899 GAC
1 GAC
3096902 TGTTGACCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
5 5 0.19
7 7 0.26
8 15 0.56
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (8 bp):
GACCCGTT
Found at i:3096896 original size:15 final size:15
Alignment explanation
Indices: 3096863--3096909 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
3096853 CACCCCACCC
*
3096863 GACCCGTTGACC--C
1 GACCCGTTGACCGTT
3096876 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
*
3096891 GACCCGTTGACTGTT
1 GACCCGTTGACCGTT
3096906 GACC
1 GACC
3096910 GGAGTTGACC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.40
15 18 0.60
ACGTcount: A:0.15, C:0.36, G:0.26, T:0.23
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:3099463 original size:24 final size:24
Alignment explanation
Indices: 3099342--3099456 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
3099332 TCGATTTGAT
3099342 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
3099366 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
3099390 TTCTGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
3099414 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
3099437 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
3099457 CTGATTTATG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:3099479 original size:24 final size:24
Alignment explanation
Indices: 3099393--3099466 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 24
3099383 ACATGGATTC
* * *
3099393 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
3099417 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
3099441 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
3099465 TG
1 TG
3099467 TTTTGATTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:3101655 original size:13 final size:13
Alignment explanation
Indices: 3101655--3101730 Score: 62
Period size: 13 Copynumber: 5.3 Consensus size: 13
3101645 CCGTTGACCC
*
3101655 GACCCGACCCATT
1 GACCCGACCCGTT
*
3101668 TACCCGACCCGTT
1 GACCCGACCCGTT
3101681 GACCCCACCCGACCCGTT
1 G-----ACCCGACCCGTT
3101699 GACCCGACCCGTT
1 GACCCGACCCGTT
*
3101712 GACCGTTGACCCGTT
1 GACC--CGACCCGTT
3101727 GACC
1 GACC
3101731 GGAGTTGACC
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
13 27 0.52
15 12 0.23
18 13 0.25
ACGTcount: A:0.17, C:0.46, G:0.20, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:3101656 original size:18 final size:18
Alignment explanation
Indices: 3101633--3101709 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
3101623 ACCGATCATA
3101633 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
3101651 ACCCGACCCGACCCATT-
1 ACCCGACCCGACCCGTTG
*
3101668 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
3101682 ACCCCACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
3101700 ACCCGACCCG
1 ACCCGACCCG
3101710 TTGACCGTTG
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
13 11 0.22
18 38 0.78
ACGTcount: A:0.18, C:0.52, G:0.18, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:3101676 original size:31 final size:31
Alignment explanation
Indices: 3101637--3101715 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
3101627 ATCATAACCC
*
3101637 GACCCGACCCGTTGACCCGACCCGACCCATT
1 GACCCGACCCGTTGACCCCACCCGACCCATT
* *
3101668 TACCCGACCCGTTGACCCCACCCGACCCGTT
1 GACCCGACCCGTTGACCCCACCCGACCCATT
3101699 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
3101716 GTTGACCCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.18, C:0.49, G:0.19, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCCACCCGACCCATT
Found at i:3101702 original size:8 final size:8
Alignment explanation
Indices: 3101691--3101730 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
3101681 GACCCCACCC
3101691 GACCCGTT
1 GACCCGTT
3101699 GACCC---
1 GACCCGTT
3101704 GACCCGTT
1 GACCCGTT
3101712 GA-CCGTT
1 GACCCGTT
3101719 GACCCGTT
1 GACCCGTT
3101727 GACC
1 GACC
3101731 GGAGTTGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.18
7 7 0.25
8 16 0.57
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.20
Consensus pattern (8 bp):
GACCCGTT
Found at i:3104219 original size:12 final size:12
Alignment explanation
Indices: 3104182--3104244 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
3104172 ATCTGATACT
3104182 TGACATGGATTC
1 TGACATGGATTC
3104194 TGATC-T-GATATC
1 TGA-CATGGAT-TC
3104206 TGACATGGATTC
1 TGACATGGATTC
* *
3104218 TGATAT-GATAC
1 TGACATGGATTC
*
3104229 TTGACTTGGATTC
1 -TGACATGGATTC
3104242 TGA
1 TGA
3104245 TCTGTTACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
11 8 0.20
12 24 0.60
13 8 0.20
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.38
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:3104219 original size:48 final size:48
Alignment explanation
Indices: 3104163--3104281 Score: 170
Period size: 48 Copynumber: 2.5 Consensus size: 48
3104153 ATTTTCGATT
*
3104163 TGATTTCTGATCTGATACTTGACATGGATTCTGATCTGATA-TCTGACA
1 TGATTTCTGATATGATACTTGACATGGATTCTGATCTGATACT-TGACA
* * *
3104211 TGGA-TTCTGATATGATACTTGACTTGGATTCTGATCTGTTACTTGACC
1 T-GATTTCTGATATGATACTTGACATGGATTCTGATCTGATACTTGACA
3104259 TGATTTCTGATATGATACTTGAC
1 TGATTTCTGATATGATACTTGAC
3104282 CTGATTTATG
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
47 2 0.03
48 59 0.92
49 3 0.05
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (48 bp):
TGATTTCTGATATGATACTTGACATGGATTCTGATCTGATACTTGACA
Found at i:3104288 original size:24 final size:24
Alignment explanation
Indices: 3104167--3104281 Score: 153
Period size: 24 Copynumber: 4.8 Consensus size: 24
3104157 TCGATTTGAT
3104167 TTCTGATCTGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
3104191 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
* *
3104215 TTCTGATATGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
3104239 TTCTGATCTGTTACTTGACCT-GA
1 TTCTGATCTGATACTTGACATGGA
*
3104262 TTTCTGATATGATACTTGAC
1 -TTCTGATCTGATACTTGAC
3104282 CTGATTTATG
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
23 3 0.04
24 77 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:3104304 original size:24 final size:24
Alignment explanation
Indices: 3104218--3104291 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
3104208 ACATGGATTC
* *
3104218 TGATATGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
3104242 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
3104266 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
3104290 TG
1 TG
3104292 TTTTGATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:3106057 original size:18 final size:18
Alignment explanation
Indices: 3106034--3106070 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3106024 TCAGTACTGA
*
3106034 TGCTATTAGTATCGATAC
1 TGCTATGAGTATCGATAC
*
3106052 TGCTATGGGTATCGATAC
1 TGCTATGAGTATCGATAC
3106070 T
1 T
3106071 AAGAGGAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (18 bp):
TGCTATGAGTATCGATAC
Found at i:3108071 original size:30 final size:30
Alignment explanation
Indices: 3108036--3108108 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
3108026 CCCGAAGGAC
*
3108036 CTATCCAGAGGTTATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
3108066 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
3108096 CTATCCATAGGTC
1 CTATCCAGAGGTC
3108109 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:3108210 original size:32 final size:31
Alignment explanation
Indices: 3108094--3108217 Score: 89
Period size: 31 Copynumber: 4.1 Consensus size: 31
3108084 GATCCTCGGT
* * * * *
3108094 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
3108125 AACTGTCTATATGTTCCTTAG---A-AGGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
* *
3108152 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGT-A
*
3108184 AACTGTCCATATGTTCCGTAGAACATAAGTA
1 AACTGTCCATATGTTCCGTAGAACATAGGTA
3108215 AAC
1 AAC
3108218 CCTCGACTCT
Statistics
Matches: 70, Mismatches: 14, Indels: 18
0.69 0.14 0.18
Matches are distributed among these distances:
26 3 0.04
27 17 0.24
30 1 0.01
31 23 0.33
32 22 0.31
33 4 0.06
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTA
Found at i:3109700 original size:21 final size:21
Alignment explanation
Indices: 3109676--3109720 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3109666 TTTTGTTCGT
* *
3109676 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
3109697 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
3109718 TTG
1 TTG
3109721 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:3116163 original size:22 final size:22
Alignment explanation
Indices: 3116138--3116202 Score: 94
Period size: 22 Copynumber: 3.0 Consensus size: 22
3116128 CGATATTGAA
*
3116138 AGGAGTATCAATATCATAGTAT
1 AGGAGTATCAATACCATAGTAT
*
3116160 AGGAGTATCAGTACCATAGTAT
1 AGGAGTATCAATACCATAGTAT
* *
3116182 AGAAGTATCGATACCATAGTA
1 AGGAGTATCAATACCATAGTA
3116203 GGGGTACTAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (22 bp):
AGGAGTATCAATACCATAGTAT
Found at i:3119318 original size:92 final size:92
Alignment explanation
Indices: 3119161--3119344 Score: 350
Period size: 92 Copynumber: 2.0 Consensus size: 92
3119151 CTTTGCTGGT
*
3119161 GCCCCCTTGAGCCTGCCAGACCCTCGATCCTCACCTATTTTAGGCTTAAACAGATTGAGTTCAAT
1 GCCCCCTTGAGCCTGCCAGACCCTCGATCCTCACCCATTTTAGGCTTAAACAGATTGAGTTCAAT
3119226 TCGAGAGGATTCATTTCCCCATGTTCA
66 TCGAGAGGATTCATTTCCCCATGTTCA
*
3119253 GCCCCCTTGAGCCTGCCAGACCCTCGATCCTCACCCATTTTAGGCTTAAACATATTGAGTTCAAT
1 GCCCCCTTGAGCCTGCCAGACCCTCGATCCTCACCCATTTTAGGCTTAAACAGATTGAGTTCAAT
3119318 TCGAGAGGATTCATTTCCCCATGTTCA
66 TCGAGAGGATTCATTTCCCCATGTTCA
3119345 TGCGAGAAAA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (92 bp):
GCCCCCTTGAGCCTGCCAGACCCTCGATCCTCACCCATTTTAGGCTTAAACAGATTGAGTTCAAT
TCGAGAGGATTCATTTCCCCATGTTCA
Found at i:3120332 original size:16 final size:17
Alignment explanation
Indices: 3120313--3120354 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
3120303 TTTAGATACA
3120313 ATAAATATATAT-AAAT
1 ATAAATATATATAAAAT
* *
3120329 ATAAATTTATTTAAAAT
1 ATAAATATATATAAAAT
3120346 ATAAA-ATAT
1 ATAAATATAT
3120355 CTTATTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAAATATATATAAAAT
Found at i:3120840 original size:30 final size:29
Alignment explanation
Indices: 3120792--3120849 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
3120782 ACACGTATAA
3120792 AAAGACTAAAACAAAATACGGGTAAAATTT
1 AAAGACTAAAACAAAATACGGG-AAAATTT
* *
3120822 AAAGAC-AAAATCATAATACGTGAAAATT
1 AAAGACTAAAA-CAAAATACGGGAAAATT
3120850 AATTGCAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.21
Consensus pattern (29 bp):
AAAGACTAAAACAAAATACGGGAAAATTT
Found at i:3121933 original size:3 final size:3
Alignment explanation
Indices: 3121925--3121953 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3121915 TTTAATTATT
3121925 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3121954 CAAATTGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3125968 original size:16 final size:17
Alignment explanation
Indices: 3125942--3125976 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3125932 ACTCATTAAT
3125942 AATATTTTTATAAATAA
1 AATATTTTTATAAATAA
*
3125959 AATA-TTTTATTAATAA
1 AATATTTTTATAAATAA
3125975 AA
1 AA
3125977 AATATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATTTTTATAAATAA
Found at i:3125980 original size:18 final size:18
Alignment explanation
Indices: 3125957--3125991 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3125947 TTTTATAAAT
* *
3125957 AAAATATTTTATTAATAA
1 AAAATATATTATCAATAA
3125975 AAAATATATTATCAATA
1 AAAATATATTATCAATA
3125992 TTTTTAACAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATATATTATCAATAA
Found at i:3126412 original size:30 final size:33
Alignment explanation
Indices: 3126351--3126416 Score: 93
Period size: 30 Copynumber: 2.1 Consensus size: 33
3126341 ATTAAAAATA
*
3126351 TTATACTAACTAAAGTGATATTTTACTATTTGTT
1 TTATACTAACTAAAGTGATA-TTTACAATTTGTT
3126385 TTATACTAA-TAAAGTGATA-TT-CAATTTGTT
1 TTATACTAACTAAAGTGATATTTACAATTTGTT
3126415 TT
1 TT
3126417 TTTAATTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 10 0.32
31 2 0.06
33 10 0.32
34 9 0.29
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (33 bp):
TTATACTAACTAAAGTGATATTTACAATTTGTT
Found at i:3126420 original size:33 final size:34
Alignment explanation
Indices: 3126351--3126416 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 34
3126341 ATTAAAAATA
* *
3126351 TTATACTAACTAAAGTGATATTTTACTATTTGTT
1 TTATACTAACTAAAGTGATATTTCAATATTTGTT
3126385 TTATACTAA-TAAAGTGATA-TTC-A-ATTTGTT
1 TTATACTAACTAAAGTGATATTTCAATATTTGTT
3126415 TT
1 TT
3126417 TTTAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 9 0.30
32 2 0.07
33 10 0.33
34 9 0.30
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (34 bp):
TTATACTAACTAAAGTGATATTTCAATATTTGTT
Found at i:3128103 original size:14 final size:13
Alignment explanation
Indices: 3128075--3128100 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3128065 CAAGTCATTA
3128075 AAAAATTTATTTT
1 AAAAATTTATTTT
3128088 AAAAATTTATTTT
1 AAAAATTTATTTT
3128101 TAATACTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AAAAATTTATTTT
Found at i:3131488 original size:26 final size:27
Alignment explanation
Indices: 3131430--3131493 Score: 85
Period size: 26 Copynumber: 2.3 Consensus size: 27
3131420 TTTTCATGTC
3131430 TTTTTTTTCTCTTTTTTTTCGAACAACA
1 TTTTTTTT-TCTTTTTTTTCGAACAACA
**
3131458 TTTTTTTTTC-TTTTTTTCGAACTGCTA
1 TTTTTTTTTCTTTTTTTTCGAACAAC-A
3131485 TTTTTTTTT
1 TTTTTTTTT
3131494 TTGCATTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 13 0.39
27 12 0.36
28 8 0.24
ACGTcount: A:0.12, C:0.14, G:0.05, T:0.69
Consensus pattern (27 bp):
TTTTTTTTTCTTTTTTTTCGAACAACA
Found at i:3133051 original size:13 final size:13
Alignment explanation
Indices: 3133033--3133057 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3133023 CTTGATCGAA
3133033 TAAAAATAAAAAG
1 TAAAAATAAAAAG
3133046 TAAAAATAAAAA
1 TAAAAATAAAAA
3133058 TTTAACAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAG
Found at i:3143305 original size:24 final size:25
Alignment explanation
Indices: 3143263--3143309 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3143253 TAAACTTAAC
* *
3143263 AATAATTAAAATAATTAAAACAATA
1 AATAATAAAAATAAGTAAAACAATA
3143288 AATAATAAAAAT-AGTAAAACAA
1 AATAATAAAAATAAGTAAAACAA
3143310 CCAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.23
Consensus pattern (25 bp):
AATAATAAAAATAAGTAAAACAATA
Found at i:3144911 original size:52 final size:52
Alignment explanation
Indices: 3144825--3144948 Score: 185
Period size: 52 Copynumber: 2.4 Consensus size: 52
3144815 TTCTAAGATG
* *
3144825 AGTTCTTCTTATTATGAACTCTATACTAAAAATGTTGATCCAAGGCCGAACA
1 AGTTCTTCTCATTATGAACTCTACACTAAAAATGTTGATCCAAGGCCGAACA
* *** *
3144877 AGTTCTTCTCATTATGAACTCTCCACTGTGAATGTTGATCCAAGGTCGAACA
1 AGTTCTTCTCATTATGAACTCTACACTAAAAATGTTGATCCAAGGCCGAACA
3144929 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
3144949 TCTTCTCCCT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.35
Consensus pattern (52 bp):
AGTTCTTCTCATTATGAACTCTACACTAAAAATGTTGATCCAAGGCCGAACA
Found at i:3145032 original size:91 final size:91
Alignment explanation
Indices: 3144877--3145172 Score: 511
Period size: 91 Copynumber: 3.3 Consensus size: 91
3144867 AGGCCGAACA
* * *
3144877 AGTTCTTCTCATTATGAACTCTCCACTGTGAATGTTGATCCAAGGTCGAACAAGTTCTTCTCATT
1 AGTTCTTCTCATTATGAACTCTCCACTGAGAATGTTAAGCCAAGGTCGAACAAGTTCTTCTCATT
* *
3144942 ATGAACTTCTTCTCCCTCTTTGGACG
66 ATGAACTTCTTCTCCCTCGTTGGATG
3144968 AGTTCTTCTCATTATGAACTCTCCACTGAGAATGTTAAGCCAAGGTCGAACAAGTTCTTCTCATT
1 AGTTCTTCTCATTATGAACTCTCCACTGAGAATGTTAAGCCAAGGTCGAACAAGTTCTTCTCATT
*
3145033 ATGAACTTCTTCTCTCTCGTTGGATG
66 ATGAACTTCTTCTCCCTCGTTGGATG
* *
3145059 AGTTCTTCTCATTATGAACTCTCCACTGAGAATGTTAAGCCAAGGTTGAGCAAGTTCTTCTCATT
1 AGTTCTTCTCATTATGAACTCTCCACTGAGAATGTTAAGCCAAGGTCGAACAAGTTCTTCTCATT
3145124 ATGAACTTCTTCTCCCTCGTTGGATG
66 ATGAACTTCTTCTCCCTCGTTGGATG
*
3145150 AGTTCTTCTCATGATGAACTCTC
1 AGTTCTTCTCATTATGAACTCTC
3145173 TATTTGAAAT
Statistics
Matches: 195, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 195 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (91 bp):
AGTTCTTCTCATTATGAACTCTCCACTGAGAATGTTAAGCCAAGGTCGAACAAGTTCTTCTCATT
ATGAACTTCTTCTCCCTCGTTGGATG
Found at i:3150279 original size:24 final size:23
Alignment explanation
Indices: 3150252--3150318 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 23
3150242 GTAATAATAC
*
3150252 TAATAATAATAAT-TTAAA-AAA
1 TAATAATAATAATAATAAACAAA
3150273 TAATAATAAT-ATAATAAACAAA
1 TAATAATAATAATAATAAACAAA
* *
3150295 TAA-AATAAGAATAAAAAACTAAA
1 TAATAATAATAATAATAAAC-AAA
3150318 T
1 T
3150319 GAAAAAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
20 2 0.05
21 19 0.49
22 14 0.36
23 4 0.10
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (23 bp):
TAATAATAATAATAATAAACAAA
Found at i:3150290 original size:21 final size:19
Alignment explanation
Indices: 3150253--3150302 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
3150243 TAATAATACT
3150253 AATAATAATAATTTAAA-A
1 AATAATAATAATTTAAACA
3150271 AATAATAATAATATAATAAACA
1 AATAATAATAAT-T--TAAACA
3150293 AATAA-AATAA
1 AATAATAATAA
3150303 GAATAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 12 0.43
19 1 0.04
21 9 0.32
22 6 0.21
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
AATAATAATAATTTAAACA
Found at i:3150801 original size:123 final size:120
Alignment explanation
Indices: 3150672--3151116 Score: 556
Period size: 123 Copynumber: 3.7 Consensus size: 120
3150662 GAATCAAATT
* *
3150672 AAGGTTGAACAAGTTCTTCTCATTATGAACTTGTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* * * * * *
3150737 GAACTTTCTTTAGAAATGTTGATGCTGATCTATATTCTACTATGATAGAGTCATGCAA
66 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATA-TCCA-TGTGATAGAGTCA-ACAA
**
3150795 AAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* *
3150860 GAACTTTCTCTGGAAAAG-TGTATGCTGATCTATCTCCATTTGTGGTAGAGTCACACAA
66 GAACTTTCTCTGGAAAAGTTG-ATGCTGATCTATATCCA--TGTGATAGAGTCA-ACAA
3150918 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
* *
3150983 GAACTTTCTCTGGAAAAGTTGAT-C----C---ATCGA-GTGAT-GAATTCGAACAA
66 GAACTTTCTCTGGAAAAGTTGATGCTGATCTATATCCATGTGATAG-AGTC-AACAA
*
3151030 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
*
3151095 TGAACTCTTC-C-GGAAATGTTGA
65 TGAACT-TTCTCTGGAAAAGTTGA
3151117 CCATTGAGTG
Statistics
Matches: 293, Mismatches: 22, Indels: 25
0.86 0.06 0.07
Matches are distributed among these distances:
111 1 0.00
112 61 0.21
113 31 0.11
114 3 0.01
115 3 0.01
118 1 0.00
122 6 0.02
123 185 0.63
124 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.39
Consensus pattern (120 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAT
GAACTTTCTCTGGAAAAGTTGATGCTGATCTATATCCATGTGATAGAGTCAACAA
Found at i:3151045 original size:112 final size:111
Alignment explanation
Indices: 3150914--3151134 Score: 365
Period size: 112 Copynumber: 2.0 Consensus size: 111
3150904 GTAGAGTCAC
3150914 ACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
1 ACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
3150978 ATTATGAACT-TTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGA
66 ATTATGAACTCTTC-C-GGAAAAGTTGA-CCATCGAGTGATGAATTCGA
*
3151026 ACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 ACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
* * *
3151091 ATTATGAACTCTTCCGGAAATGTTGACCATTGAGTGATGGATTC
66 ATTATGAACTCTTCCGGAAAAGTTGACCATCGAGTGATGAATTC
3151135 AAATCTTTAC
Statistics
Matches: 103, Mismatches: 4, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
111 16 0.16
112 54 0.52
113 30 0.29
114 3 0.03
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (111 bp):
ACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTC
ATTATGAACTCTTCCGGAAAAGTTGACCATCGAGTGATGAATTCGA
Found at i:3151442 original size:22 final size:22
Alignment explanation
Indices: 3151417--3151513 Score: 131
Period size: 22 Copynumber: 4.4 Consensus size: 22
3151407 AAATATTTCT
3151417 TCTTTGAAAAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCTATCA
* *
3151439 TCTTTTAAGAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCTATCA
* *
3151461 TCTTTGGAGAGAGAATCTATCA
1 TCTTTGAAAAGAGAATCTATCA
*
3151483 TCTTTGAAAAAAAGAATCTATCA
1 TCTTTG-AAAAGAGAATCTATCA
*
3151506 TATTTGAA
1 TCTTTGAA
3151514 GAATGTAGAT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
22 48 0.73
23 18 0.27
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.34
Consensus pattern (22 bp):
TCTTTGAAAAGAGAATCTATCA
Found at i:3152162 original size:18 final size:19
Alignment explanation
Indices: 3152139--3152182 Score: 72
Period size: 18 Copynumber: 2.3 Consensus size: 19
3152129 TATATAAAAG
3152139 AATAAATTGAATTTC-AAA
1 AATAAATTGAATTTCGAAA
3152157 AATAAATTGAATTTCGAAA
1 AATAAATTGAATTTCGAAA
3152176 AGATAAA
1 A-ATAAA
3152183 CTTGGAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 15 0.62
19 4 0.17
20 5 0.21
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (19 bp):
AATAAATTGAATTTCGAAA
Found at i:3152551 original size:10 final size:10
Alignment explanation
Indices: 3152538--3152574 Score: 65
Period size: 10 Copynumber: 3.6 Consensus size: 10
3152528 CTATTTTCTT
3152538 TTTTTTTTCA
1 TTTTTTTTCA
3152548 TTTTTTTTTCA
1 -TTTTTTTTCA
3152559 TTTTTTTTCA
1 TTTTTTTTCA
3152569 TTTTTT
1 TTTTTT
3152575 CTTCTTCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTTCA
Found at i:3152551 original size:11 final size:11
Alignment explanation
Indices: 3152531--3152574 Score: 72
Period size: 11 Copynumber: 4.1 Consensus size: 11
3152521 TCCTTTTCTA
*
3152531 TTTTCTTTTTT
1 TTTTCATTTTT
3152542 TTTTCATTTTT
1 TTTTCATTTTT
3152553 TTTTCA-TTTT
1 TTTTCATTTTT
3152563 TTTTCATTTTT
1 TTTTCATTTTT
3152574 T
1 T
3152575 CTTCTTCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 10 0.32
11 21 0.68
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCATTTTT
Found at i:3163392 original size:18 final size:16
Alignment explanation
Indices: 3163369--3163447 Score: 54
Period size: 18 Copynumber: 4.6 Consensus size: 16
3163359 AACGCAAAGA
3163369 AAAAAAGAAATGATATAG
1 AAAAAAGAAAT-A-ATAG
*
3163387 AAAAAAGGAAAACAATAG
1 AAAAAA-G-AAATAATAG
*
3163405 --AAAAGAAATAAAAG
1 AAAAAAGAAATAATAG
*
3163419 AAATAAAGAAATAAAAGAG
1 AAA-AAAGAAAT--AATAG
3163438 AAAAAAGAAA
1 AAAAAAGAAA
3163448 AAAGAAATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
14 7 0.14
15 1 0.02
16 5 0.10
17 8 0.16
18 17 0.34
19 9 0.18
20 3 0.06
ACGTcount: A:0.75, C:0.01, G:0.15, T:0.09
Consensus pattern (16 bp):
AAAAAAGAAATAATAG
Found at i:3163419 original size:9 final size:9
Alignment explanation
Indices: 3163405--3163479 Score: 88
Period size: 9 Copynumber: 8.7 Consensus size: 9
3163395 AAAACAATAG
3163405 AAAAGAAAT
1 AAAAGAAAT
3163414 AAAAGAAAT
1 AAAAGAAAT
3163423 -AAAGAAAT
1 AAAAGAAAT
3163431 AAAAGAGAA-
1 AAAAGA-AAT
3163440 AAAAG-AA-
1 AAAAGAAAT
3163447 AAAAGAAAT
1 AAAAGAAAT
3163456 AAAAGGAAA-
1 AAAA-GAAAT
*
3163465 AAAAGAAAA
1 AAAAGAAAT
3163474 AAAAGA
1 AAAAGA
3163480 GAGAATGAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
7 7 0.12
8 14 0.23
9 33 0.55
10 6 0.10
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (9 bp):
AAAAGAAAT
Found at i:3163426 original size:17 final size:16
Alignment explanation
Indices: 3163405--3163476 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 16
3163395 AAAACAATAG
3163405 AAAAGAAATAAAAGAAA
1 AAAAGAAAT-AAAGAAA
*
3163422 TAAAGAAATAAAAGAGAA
1 AAAAGAAAT-AAAGA-AA
3163440 AAAAGAAA-AAAGAAA
1 AAAAGAAATAAAGAAA
*
3163455 TAAAAGGAAAAAAAGAAA
1 -AAAA-GAAATAAAGAAA
3163473 AAAA
1 AAAA
3163477 AGAGAGAATG
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.04
16 9 0.18
17 22 0.45
18 16 0.33
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.06
Consensus pattern (16 bp):
AAAAGAAATAAAGAAA
Found at i:3163441 original size:43 final size:41
Alignment explanation
Indices: 3163364--3163500 Score: 127
Period size: 43 Copynumber: 3.2 Consensus size: 41
3163354 TTGATAACGC
* *
3163364 AAAGAAA-AAAAGAAATGATATAG-AAAAAAG-GAAAACAATAGA
1 AAAGAAATAAAAGAAAT-A-A-AGAAAAAAAGAGAAAA-AAGAAA
3163406 AAAGAAATAAAAGAAATAAAGAAATAAAAGAGAAAAAAGAAA
1 AAAGAAATAAAAGAAATAAAGAAA-AAAAGAGAAAAAAGAAA
* *
3163448 AAAGAAATAAAAGGAAAAAAAGAAAAAAAAGAGAGAATGAAAGAAG
1 AAAGAAATAAAA-GAAATAAAG-AAAAAAAGAGA-AA--AAAGAAA
3163494 AAAGAAA
1 AAAGAAA
3163501 AACAAATCCA
Statistics
Matches: 82, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
40 2 0.02
41 3 0.04
42 29 0.35
43 30 0.37
44 5 0.06
46 13 0.16
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.07
Consensus pattern (41 bp):
AAAGAAATAAAAGAAATAAAGAAAAAAAGAGAAAAAAGAAA
Found at i:3163460 original size:51 final size:51
Alignment explanation
Indices: 3163364--3163476 Score: 131
Period size: 51 Copynumber: 2.2 Consensus size: 51
3163354 TTGATAACGC
* * * * *
3163364 AAAGAAAAAAAGAAATGATATAGAAAAAAGGAAAACAATAGAAAA-GAAATA
1 AAAGAAAAAAAGAAATAAAAGAGAAAAAAGGAAAAAAAAAGAAAAGGAAA-A
* *
3163415 AAAGAAATAAAGAAATAAAAGAGAAAAAA-GAAAAAAGAAATAAAAGGAAAA
1 AAAGAAAAAAAGAAATAAAAGAGAAAAAAGGAAAAAA-AAAGAAAAGGAAAA
3163466 AAAGAAAAAAA
1 AAAGAAAAAAA
3163477 AGAGAGAATG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
50 6 0.12
51 42 0.81
52 4 0.08
ACGTcount: A:0.77, C:0.01, G:0.15, T:0.07
Consensus pattern (51 bp):
AAAGAAAAAAAGAAATAAAAGAGAAAAAAGGAAAAAAAAAGAAAAGGAAAA
Found at i:3163489 original size:25 final size:23
Alignment explanation
Indices: 3163386--3163502 Score: 81
Period size: 25 Copynumber: 4.7 Consensus size: 23
3163376 AAATGATATA
* *
3163386 GAAAAAAGGAAAACAATAGAAAAG
1 GAAAAAA-GAAAAAAAAAGAAAAG
* *
3163410 AAATAAAAGAAATAAAGAAATAAAAG
1 GAA-AAAAGAAA-AAA-AAAGAAAAG
*
3163436 AGAAAAAAGAAAAAAGAAATAAAAG
1 -GAAAAAAGAAAAAA-AAAGAAAAG
* *
3163461 GAAAAAAAGAAAAAAAAGAGAGAAT
1 G-AAAAAAGAAAAAAAA-AGAAAAG
* *
3163486 GAAAGAAGAAAGAAAAA
1 GAAAAAAGAAAAAAAAA
3163503 CAAATCCAAC
Statistics
Matches: 77, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.01
24 22 0.29
25 37 0.48
26 15 0.19
27 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (23 bp):
GAAAAAAGAAAAAAAAAGAAAAG
Found at i:3163495 original size:42 final size:42
Alignment explanation
Indices: 3163387--3163500 Score: 131
Period size: 43 Copynumber: 2.6 Consensus size: 42
3163377 AATGATATAG
* * *
3163387 AAAAAAG-GAAAACAATAGAAAAGAAATAAAAGAAATAAAGAA
1 AAAAAAGAGAAAA-AAGAAAAAAGAAATAAAAGAAAAAAAGAA
*
3163429 ATAAAAGAGAAAAAAGAAAAAAGAAATAAAAGGAAAAAAAGAA
1 AAAAAAGAGAAAAAAGAAAAAAGAAATAAAA-GAAAAAAAGAA
*
3163472 AAAAAAGAGAGAATGAAAGAAGAAAGAAA
1 AAAAAAGAGA-AA--AAAGAAAAAAGAAA
3163501 AACAAATCCA
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
42 22 0.36
43 24 0.39
44 2 0.03
46 13 0.21
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (42 bp):
AAAAAAGAGAAAAAAGAAAAAAGAAATAAAAGAAAAAAAGAA
Found at i:3164994 original size:39 final size:39
Alignment explanation
Indices: 3164939--3165244 Score: 334
Period size: 39 Copynumber: 7.9 Consensus size: 39
3164929 TTTAAAGAAT
* *
3164939 ATTTTATCTCGTTTGAGATAGTTTCCCTCGAAACAAAAG
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAG
* * *
3164978 ATTTTGTCTCACTTGAGATAGTTTTCCTCGAAACAGAAG
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAG
* * * *
3165017 ATTTTATCTCGCTTGAGATAGATTCCATCGAAACAGAAG
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAG
* * *
3165056 ATTTTGTCTCGCTTAAGATAGTTTCCCTTGAAACAGAAG
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAG
* * *
3165095 ATTTTATCTCGCTTGAGATAGATTCCCTCGAAACAGAAG
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAG
* * * *
3165134 ATTTTGTCTCTCTTGAGATAGTTTACCTTGAAA-TAAA-
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAG
* * *
3165171 ATTTTGTCTCCCTTGAGACAGTTTTTCCT-GAAAC-AAAG
1 ATTTTGTCTCGCTTGAGATAG-TTTCCCTCGAAACAAAAG
* * * *
3165209 -TATTGTCTCTCTAGAGACAGTTTCCCTCGAAACAAA
1 ATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAA
3165245 TCTTACTTGA
Statistics
Matches: 229, Mismatches: 33, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
36 6 0.03
37 48 0.21
38 10 0.04
39 165 0.72
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (39 bp):
ATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAAAAG
Found at i:3165026 original size:78 final size:78
Alignment explanation
Indices: 3164934--3165242 Score: 376
Period size: 78 Copynumber: 4.0 Consensus size: 78
3164924 ATGTTTTTAA
* * * *
3164934 AGAATATTTTATCTCGTTTGAGATAGTTTCCCTCGAAACAAAAGATTTTGTCTCACTTGAGATAG
1 AGAAGATTTTATCTCGCTTGAGATAGATTCCCTCGAAACAAAAGATTTTGTCTCTCTTGAGATAG
*
3164999 TTTTCCTCGAAAC
66 TTTCCCTCGAAAC
* * * *
3165012 AGAAGATTTTATCTCGCTTGAGATAGATTCCATCGAAACAGAAGATTTTGTCTCGCTTAAGATAG
1 AGAAGATTTTATCTCGCTTGAGATAGATTCCCTCGAAACAAAAGATTTTGTCTCTCTTGAGATAG
*
3165077 TTTCCCTTGAAAC
66 TTTCCCTCGAAAC
*
3165090 AGAAGATTTTATCTCGCTTGAGATAGATTCCCTCGAAACAGAAGATTTTGTCTCTCTTGAGATAG
1 AGAAGATTTTATCTCGCTTGAGATAGATTCCCTCGAAACAAAAGATTTTGTCTCTCTTGAGATAG
* * *
3165155 TTTACCTTGAAAT
66 TTTCCCTCGAAAC
* * * * * * * *
3165168 A-AA-ATTTTGTCTCCCTTGAGACAGTTTTTCCT-GAAAC-AAAG-TATTGTCTCTCTAGAGACA
1 AGAAGATTTTATCTCGCTTGAGATAG-ATTCCCTCGAAACAAAAGATTTTGTCTCTCTTGAGATA
3165228 GTTTCCCTCGAAAC
65 GTTTCCCTCGAAAC
3165242 A
1 A
3165243 AATCTTACTT
Statistics
Matches: 204, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
74 28 0.14
75 3 0.01
76 23 0.11
77 7 0.03
78 143 0.70
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (78 bp):
AGAAGATTTTATCTCGCTTGAGATAGATTCCCTCGAAACAAAAGATTTTGTCTCTCTTGAGATAG
TTTCCCTCGAAAC
Found at i:3165689 original size:91 final size:90
Alignment explanation
Indices: 3165534--3166117 Score: 656
Period size: 91 Copynumber: 6.4 Consensus size: 90
3165524 GATAAACCAG
* * *
3165534 TCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCA-CGGGGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATA
* * *
3165599 ATGAGAAGAACTTGTTCAATCTTGCA
65 ATGAGAAGAACTTGTCCAACCTTACA
** *
3165625 TCAACATTTCCAACAAGGAGTTCATAATGAGAAGAACTCATCTAATGAGGAAGAAGAAGTTCATA
1 TCAACATTTCC-ACGGGGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATA
3165690 ATGAGAAGAACTTGTCCAACCTTACA
65 ATGAGAAGAACTTGTCCAACCTTACA
* * * * * ** * *
3165716 TCAACATTTCCTGCGAGGAGTTCATAATAAAAAGAACTCATCCGATGAGGGGGAATAATTTCATA
1 TCAACATTTCC-ACGGGGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATA
* * *
3165781 CTGAGAAGAACTTGTTCAACCTTGGC-
65 ATGAGAAGAACTTGTCCAACCTT-ACA
* * * *
3165807 TCAAAAGTTCCA-GTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAGGAATAAGTTCAT
1 TCAACATTTCCACG-GG-GAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCAT
3165871 AATGAGAAGAACTTGTCCAACCTTACA
64 AATGAGAAGAACTTGTCCAACCTTACA
* * * * *
3165898 TCAACATTTCCGGCGGGGAATTTATAATGAGAAGAACTCATCCGAA-GAGGGAGAAGAAGTTTAT
1 TCAACATTTCC-ACGGGGAGTTCATAATGAGAAGAACTCATCC-AATGAGGAAGAAGAAGTTCAT
** *
3165962 AATGAGAAGAACTTGTTTAACCTTGGC-
64 AATGAGAAGAACTTGTCCAACCTT-ACA
* * * *
3165989 TCAACAGTTCCA-GTGGAGAGTTCATAATGAGAAGAACTCGTCCAATGAGGAGGAAGAAGTTTAT
1 TCAACATTTCCACG-GG-GAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCAT
* *
3166053 TATGAGAAGAACATGTCCAACCTTACA
64 AATGAGAAGAACTTGTCCAACCTTACA
* *
3166080 TCAACATTTCCGGCGGGGAGTTCATAATAAGAAGAACT
1 TCAACATTTCC-ACGGGGAGTTCATAATGAGAAGAACT
3166118 TGTTCAACCT
Statistics
Matches: 416, Mismatches: 62, Indels: 30
0.82 0.12 0.06
Matches are distributed among these distances:
89 2 0.00
90 7 0.02
91 396 0.95
92 9 0.02
93 2 0.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (90 bp):
TCAACATTTCCACGGGGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTCCAACCTTACA
Found at i:3165841 original size:182 final size:182
Alignment explanation
Indices: 3165534--3166117 Score: 852
Period size: 182 Copynumber: 3.2 Consensus size: 182
3165524 GATAAACCAG
* * * *
3165534 TCAACATTTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCC-AACGAGGGAGAAGAAGTTCAT
1 TCAACATTTCCGGCGGGGAGTTCATAATAAGAAGAACTCATCCGAA-GAGGGAGAAGAATTTCAT
* * ***
3165598 AATGAGAAGAACTTGTTCAATCTT-GCATCAACATTTCCA-ACAAGGAGTTCATAATGAGAAGAA
65 AATGAGAAGAACTTGTTCAACCTTGGC-TCAACAGTTCCAGTGGA-GAGTTCATAATGAGAAGAA
* *
3165661 CTCATCTAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTCCAACCTTACA
128 CTCATCCAATGAGGAGGAAGAAGTTCATAATGAGAAGAACTTGTCCAACCTTACA
* * * * * *
3165716 TCAACATTTCCTGCGAGGAGTTCATAATAAAAAGAACTCATCCGATGAGGGGGAATAATTTCATA
1 TCAACATTTCCGGCGGGGAGTTCATAATAAGAAGAACTCATCCGAAGAGGGAGAAGAATTTCATA
* *
3165781 CTGAGAAGAACTTGTTCAACCTTGGCTCAAAAGTTCCAGTGGAGAGTTCATAATGAGAAGAACTC
66 ATGAGAAGAACTTGTTCAACCTTGGCTCAACAGTTCCAGTGGAGAGTTCATAATGAGAAGAACTC
*
3165846 ATCCAATGAGGAGGAATAAGTTCATAATGAGAAGAACTTGTCCAACCTTACA
131 ATCCAATGAGGAGGAAGAAGTTCATAATGAGAAGAACTTGTCCAACCTTACA
* * *
3165898 TCAACATTTCCGGCGGGGAATTTATAATGAGAAGAACTCATCCGAAGAGGGAGAAGAAGTTT-AT
1 TCAACATTTCCGGCGGGGAGTTCATAATAAGAAGAACTCATCCGAAGAGGGAGAAGAA-TTTCAT
*
3165962 AATGAGAAGAACTTGTTTAACCTTGGCTCAACAGTTCCAGTGGAGAGTTCATAATGAGAAGAACT
65 AATGAGAAGAACTTGTTCAACCTTGGCTCAACAGTTCCAGTGGAGAGTTCATAATGAGAAGAACT
* * * *
3166027 CGTCCAATGAGGAGGAAGAAGTTTATTATGAGAAGAACATGTCCAACCTTACA
130 CATCCAATGAGGAGGAAGAAGTTCATAATGAGAAGAACTTGTCCAACCTTACA
3166080 TCAACATTTCCGGCGGGGAGTTCATAATAAGAAGAACT
1 TCAACATTTCCGGCGGGGAGTTCATAATAAGAAGAACT
3166118 TGTTCAACCT
Statistics
Matches: 359, Mismatches: 39, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
182 352 0.98
183 7 0.02
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (182 bp):
TCAACATTTCCGGCGGGGAGTTCATAATAAGAAGAACTCATCCGAAGAGGGAGAAGAATTTCATA
ATGAGAAGAACTTGTTCAACCTTGGCTCAACAGTTCCAGTGGAGAGTTCATAATGAGAAGAACTC
ATCCAATGAGGAGGAAGAAGTTCATAATGAGAAGAACTTGTCCAACCTTACA
Found at i:3166061 original size:273 final size:273
Alignment explanation
Indices: 3165541--3166117 Score: 729
Period size: 273 Copynumber: 2.1 Consensus size: 273
3165531 CAGTCAACAT
3165541 TTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAA
1 TTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAA
* * * * *
3165606 GAACTTGTTCAATCTTGCATCAACATTTCCAACAAGGAGTTCATAATGAGAAGAACTCATCTAAT
66 GAACTTGTCCAACCTTACATCAACATTTCCAACAAGGAATTCATAATGAGAAGAACTCATCGAAT
*
3165671 GAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTCCAACCTTACATCAACATTTCCTGCGAGGAG
131 GAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTCCAACCTTACATCAACAGTTCCTGCGAGGAG
* * * * *
3165736 TTCATAATAAAAAGAACTCATCCGATGAGGGGGAATAATTTCATACTGAGAAGAACTTGTTCAAC
196 TTCATAATAAAAAGAACTCATCCAATGAGGAGGAAGAATTTCATACTGAGAAGAACATGTCCAAC
*
3165801 CTTGGC-TCAAAAG
261 CTT-ACATCAAAAG
* * *
3165814 TTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGA-GGAGGAATAAGTTCATAATGAGA
1 TTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGA-GAAGAAGTTCATAATGAGA
** ** *
3165878 AGAACTTGTCCAACCTTACATCAACATTTCCGGCGGGGAATTTATAATGAGAAGAACTCATCCGA
65 AGAACTTGTCCAACCTTACATCAACATTTCCAACAAGGAATTCATAATGAGAAGAACTCAT-CGA
* * ** *
3165943 A-GAGGGAGAAGAAGTTTATAATGAGAAGAACTTGTTTAACCTTGGC-TCAACAGTTCCAGTG-G
129 ATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTCCAACCTT-ACATCAACAGTTCC--TGCG
* * *
3166005 A-GAGTTCATAATGAGAAGAACTCGTCCAATGAGGAGGAAGAAGTTT-ATTA-TGAGAAGAACAT
191 AGGAGTTCATAATAAAAAGAACTCATCCAATGAGGAGGAAGAA-TTTCA-TACTGAGAAGAACAT
* *
3166067 GTCCAACCTTACATCAACAT
254 GTCCAACCTTACATCAAAAG
* * *
3166087 TTCCGGCGGGGAGTTCATAATAAGAAGAACT
1 TTCCAGTGGGGAGTTCATAATGAGAAGAACT
3166118 TGTTCAACCT
Statistics
Matches: 262, Mismatches: 34, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
272 4 0.02
273 245 0.94
274 11 0.04
275 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (273 bp):
TTCCAGTGGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATGAGAA
GAACTTGTCCAACCTTACATCAACATTTCCAACAAGGAATTCATAATGAGAAGAACTCATCGAAT
GAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTCCAACCTTACATCAACAGTTCCTGCGAGGAG
TTCATAATAAAAAGAACTCATCCAATGAGGAGGAAGAATTTCATACTGAGAAGAACATGTCCAAC
CTTACATCAAAAG
Found at i:3166133 original size:143 final size:143
Alignment explanation
Indices: 3165955--3166220 Score: 392
Period size: 143 Copynumber: 1.9 Consensus size: 143
3165945 AGGGAGAAGA
* * *
3165955 AGTTTATAATGAGAAGAACTTGTTTAACCTTGGCTCAACAGTTCCAGTGGAGAGTTCATAATGAG
1 AGTTCATAATAAGAAGAACTTGTTCAACCTTGGCTCAACAGTTCCAGTGGAGAGTTCATAATGAG
* * *
3166020 AAGAACTCGTCCAATGA-GGAGGAAGAAGTTTATTATGAGAAGAACA-TGTCCAACCTTACATCA
66 AAGAACTCATCCAATGAGGGA-GAAGAAGTTCATAATGAGAAGAA-ATTGTCCAACCTTACATCA
3166083 ACATTTCCGGCGGGG
129 ACATTTCCGGCGGGG
* ** *
3166098 AGTTCATAATAAGAAGAACTTGTTCAACCTTGGCTCAACATTTGTAGTGGAGAGTTCATATTGAG
1 AGTTCATAATAAGAAGAACTTGTTCAACCTTGGCTCAACAGTTCCAGTGGAGAGTTCATAATGAG
* *
3166163 AAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAAATTGTTCAACCTTA
66 AAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGAGAAGAAATTGTCCAACCTTA
3166221 GATGTATTCC
Statistics
Matches: 109, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
142 1 0.01
143 105 0.96
144 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (143 bp):
AGTTCATAATAAGAAGAACTTGTTCAACCTTGGCTCAACAGTTCCAGTGGAGAGTTCATAATGAG
AAGAACTCATCCAATGAGGGAGAAGAAGTTCATAATGAGAAGAAATTGTCCAACCTTACATCAAC
ATTTCCGGCGGGG
Found at i:3167379 original size:14 final size:14
Alignment explanation
Indices: 3167360--3167396 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
3167350 AGGCTCGTGT
3167360 GAGATCCGGTGTCC
1 GAGATCCGGTGTCC
3167374 GAGATCCGGTGTCC
1 GAGATCCGGTGTCC
3167388 GAGATCCGG
1 GAGATCCGG
3167397 AGTGAGAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.16, C:0.27, G:0.38, T:0.19
Consensus pattern (14 bp):
GAGATCCGGTGTCC
Found at i:3167823 original size:29 final size:29
Alignment explanation
Indices: 3167762--3167817 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
3167752 TTATTTCAAG
*
3167762 TTAACTACTAACTTTTATTTTATTGCATA
1 TTAACAACTAACTTTTATTTTATTGCATA
3167791 TTAACAACTAACTTTTATTTTATTGCA
1 TTAACAACTAACTTTTATTTTATTGCA
3167818 CTTTAATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.50
Consensus pattern (29 bp):
TTAACAACTAACTTTTATTTTATTGCATA
Found at i:3168124 original size:24 final size:25
Alignment explanation
Indices: 3168092--3168147 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
3168082 TATTAATATT
*
3168092 CTAAATTTTA-TTTTATTGA-TCATA
1 CTAACTTTTATTTTTATT-ATTCATA
*
3168116 CTAACTTTTATTTTTATTATTCTTA
1 CTAACTTTTATTTTTATTATTCATA
3168141 CTAACTT
1 CTAACTT
3168148 ACTAACATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.29, C:0.12, G:0.02, T:0.57
Consensus pattern (25 bp):
CTAACTTTTATTTTTATTATTCATA
Found at i:3168369 original size:8 final size:8
Alignment explanation
Indices: 3168356--3168410 Score: 65
Period size: 8 Copynumber: 6.5 Consensus size: 8
3168346 TTTATTGTTT
3168356 TTTTTTTA
1 TTTTTTTA
3168364 TTTTTTTA
1 TTTTTTTA
3168372 CTGTTTTTTA
1 -T-TTTTTTA
* *
3168382 TTATTATA
1 TTTTTTTA
3168390 CTTTTTTTA
1 -TTTTTTTA
3168399 TTTTTTTA
1 TTTTTTTA
3168407 TTTT
1 TTTT
3168411 AAATAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 25 0.62
9 8 0.20
10 7 0.17
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTTTTA
Found at i:3168371 original size:35 final size:35
Alignment explanation
Indices: 3168332--3168406 Score: 80
Period size: 35 Copynumber: 2.1 Consensus size: 35
3168322 TTTATTTTTA
* **
3168332 TTTTA-AGTTCATTATTTATTGTTTTTTTTTTATTT
1 TTTTACAGTTCATTA-TTATTATACTTTTTTTATTT
* **
3168367 TTTTACTGTTTTTTATTATTATACTTTTTTTATTT
1 TTTTACAGTTCATTATTATTATACTTTTTTTATTT
3168402 TTTTA
1 TTTTA
3168407 TTTTAAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
35 27 0.82
36 6 0.18
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (35 bp):
TTTTACAGTTCATTATTATTATACTTTTTTTATTT
Found at i:3168378 original size:18 final size:17
Alignment explanation
Indices: 3168356--3168410 Score: 76
Period size: 18 Copynumber: 3.2 Consensus size: 17
3168346 TTTATTGTTT
3168356 TTTTTTTATTTTTTTAC
1 TTTTTTTATTTTTTTAC
* *
3168373 TGTTTTTTATTATTATAC
1 T-TTTTTTATTTTTTTAC
3168391 TTTTTTTATTTTTTTA-
1 TTTTTTTATTTTTTTAC
3168407 TTTT
1 TTTT
3168411 AAATAAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 4 0.12
17 14 0.42
18 15 0.45
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTTTTATTTTTTTAC
Found at i:3188492 original size:53 final size:54
Alignment explanation
Indices: 3188347--3188530 Score: 271
Period size: 53 Copynumber: 3.4 Consensus size: 54
3188337 TATATGTTGC
* * * *
3188347 AATTACCGTATTGGCACTATGTGTGCAACCCCACGAAATTCATAATGAGTTTATG
1 AATTACCGTATTGGCACTATGTGTGCAA-CCTAAGTAATTCATAATGAGTTTGTG
* *
3188402 AATTTCCGTATTGGCACTATGTGTGCAACCTAAGTAATTAATAATGAGTTTGTG
1 AATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTG
* *
3188456 AATTACCGTATT-ACACTATGTGTGCAACCTAAGTAATTCATAATGAGATTGTG
1 AATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTG
*
3188509 AATTACCGTATCGGCACTATGT
1 AATTACCGTATTGGCACTATGT
3188531 ATGTAAAACA
Statistics
Matches: 116, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
53 49 0.42
54 40 0.34
55 27 0.23
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (54 bp):
AATTACCGTATTGGCACTATGTGTGCAACCTAAGTAATTCATAATGAGTTTGTG
Found at i:3189164 original size:2 final size:2
Alignment explanation
Indices: 3189157--3189181 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3189147 GTTTAATATG
3189157 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
3189182 AAATTGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:3194890 original size:26 final size:26
Alignment explanation
Indices: 3194849--3194902 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
3194839 ACTAACTGCA
* * *
3194849 TATGGTGGGCATGACCTTATGTGTAT
1 TATGGTGGACACGACCTTAAGTGTAT
3194875 TATGGTGGACACGACCTTAAGTGTAT
1 TATGGTGGACACGACCTTAAGTGTAT
3194901 TA
1 TA
3194903 GCACATCGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.35
Consensus pattern (26 bp):
TATGGTGGACACGACCTTAAGTGTAT
Found at i:3198862 original size:20 final size:22
Alignment explanation
Indices: 3198821--3198871 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
3198811 GTGAACTCGA
3198821 TATCGATAC--TACCCTACGAG
1 TATCGATACTTTACCCTACGAG
3198841 TATCGATACTTTA-CCTAC-AG
1 TATCGATACTTTACCCTACGAG
*
3198861 TATTGATACTT
1 TATCGATACTT
3198872 CTAACCTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 21 0.75
21 5 0.18
22 2 0.07
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (22 bp):
TATCGATACTTTACCCTACGAG
Found at i:3200383 original size:10 final size:10
Alignment explanation
Indices: 3200368--3200451 Score: 87
Period size: 10 Copynumber: 8.1 Consensus size: 10
3200358 CATTTAAATA
3200368 ATAAACGAAC
1 ATAAACGAAC
3200378 ATAAACGAAC
1 ATAAACGAAC
** *
3200388 ACGAATGAAC
1 ATAAACGAAC
*
3200398 ATAAAAGAAC
1 ATAAACGAAC
**
3200408 ACGAACGAAC
1 ATAAACGAAC
3200418 ATAAACGAACAC
1 ATAAACG-A-AC
3200430 AATAAACGAAC
1 -ATAAACGAAC
3200441 ATAAACGAAC
1 ATAAACGAAC
3200451 A
1 A
3200452 ACACAAACAC
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
10 47 0.78
11 3 0.05
12 3 0.05
13 7 0.12
ACGTcount: A:0.60, C:0.20, G:0.12, T:0.08
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:3201566 original size:14 final size:16
Alignment explanation
Indices: 3201547--3201578 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
3201537 GCCCTCTGTT
3201547 CGAACATA-AA-TGAA
1 CGAACATATAATTGAA
3201561 CGAACATATAATTGAA
1 CGAACATATAATTGAA
3201577 CG
1 CG
3201579 TTCACGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (16 bp):
CGAACATATAATTGAA
Found at i:3203090 original size:25 final size:25
Alignment explanation
Indices: 3203056--3203105 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3203046 CTAGAGGCAT
3203056 GGGCACGACCTGGGGCAAGACGCAA
1 GGGCACGACCTGGGGCAAGACGCAA
* *
3203081 GGGCATGACCTGGGGCACGACGCAA
1 GGGCACGACCTGGGGCAAGACGCAA
3203106 TCCAAAGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.26, C:0.28, G:0.40, T:0.06
Consensus pattern (25 bp):
GGGCACGACCTGGGGCAAGACGCAA
Found at i:3205945 original size:27 final size:27
Alignment explanation
Indices: 3205914--3206002 Score: 74
Period size: 27 Copynumber: 3.2 Consensus size: 27
3205904 AATCAAGTTT
3205914 CATCATGAAGAAACTTATAACCAGTCG
1 CATCATGAAGAAACTTATAACCAGTCG
** * **
3205941 CATCA-GCCAACG-AACAAATAAATCAAGTTT
1 CATCATG--AA-GAAACTTAT-AA-CCAGTCG
3205971 CATCATGAAGAAACTTATAACCAGTCG
1 CATCATGAAGAAACTTATAACCAGTCG
3205998 CATCA
1 CATCA
3206003 GCTTGATCGG
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
26 1 0.02
27 14 0.31
28 10 0.22
29 10 0.22
30 9 0.20
31 1 0.02
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.21
Consensus pattern (27 bp):
CATCATGAAGAAACTTATAACCAGTCG
Found at i:3205956 original size:57 final size:57
Alignment explanation
Indices: 3205889--3206004 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
3205879 ATTTACCATT
*
3205889 GCCAATGAACAAATAAATCAAGTTTCATCATGAAGAAACTTATAACCAGTCGCATCA
1 GCCAACGAACAAATAAATCAAGTTTCATCATGAAGAAACTTATAACCAGTCGCATCA
3205946 GCCAACGAACAAATAAATCAAGTTTCATCATGAAGAAACTTATAACCAGTCGCATCA
1 GCCAACGAACAAATAAATCAAGTTTCATCATGAAGAAACTTATAACCAGTCGCATCA
3206003 GC
1 GC
3206005 TTGATCGGAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.43, C:0.22, G:0.13, T:0.22
Consensus pattern (57 bp):
GCCAACGAACAAATAAATCAAGTTTCATCATGAAGAAACTTATAACCAGTCGCATCA
Found at i:3209719 original size:35 final size:35
Alignment explanation
Indices: 3209646--3209719 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
3209636 CGTCAAGTCC
* * **
3209646 AGTATGGCCCTGAGCACACAGCCGAGGAGCCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
3209681 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
3209716 AGTA
1 AGTA
3209720 TTCTTCCTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.30, C:0.30, G:0.30, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:3209810 original size:24 final size:24
Alignment explanation
Indices: 3209800--3209914 Score: 169
Period size: 24 Copynumber: 4.8 Consensus size: 24
3209790 CATAATTCAC
* * *
3209800 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
*
3209824 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
3209848 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
3209872 GTCATA-TATCAGATCATAATCCAT
1 GTCA-AGTATCAGATCAGAATCCAT
3209896 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCAGATCAGAA
3209915 ATCAAATCAA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 81 0.98
25 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:3209931 original size:48 final size:49
Alignment explanation
Indices: 3209776--3209931 Score: 165
Period size: 48 Copynumber: 3.2 Consensus size: 49
3209766 AAACGGATAT
* * * * *
3209776 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCA-AAATCCAG
1 ATCAAAAATCAGATCATAATCCAAGTCAAGTATCAGATCAGAAATCCAA
* ** * *
3209824 GTCAAGTATCAGATCAGAATCCAAGTCAAGTATCAGATCAG-AATCCAT
1 ATCAAAAATCAGATCATAATCCAAGTCAAGTATCAGATCAGAAATCCAA
* * * *
3209872 GTCATATATCAGATCATAATCCATGTCAAGTATCAGATCAGAAAT-CAA
1 ATCAAAAATCAGATCATAATCCAAGTCAAGTATCAGATCAGAAATCCAA
3209920 ATCAAAAATCAG
1 ATCAAAAATCAG
3209932 GTAAAATATT
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
48 86 0.97
49 3 0.03
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (49 bp):
ATCAAAAATCAGATCATAATCCAAGTCAAGTATCAGATCAGAAATCCAA
Found at i:3209931 original size:72 final size:72
Alignment explanation
Indices: 3209776--3209931 Score: 190
Period size: 72 Copynumber: 2.2 Consensus size: 72
3209766 AAACGGATAT
* * * *
3209776 ATCAAAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCCAGGTCAAGTATCAGATCAG
1 ATCAAAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCAG
3209841 AATCCAA
66 AATCCAA
* ** * * *
3209848 GTCAAGTATCAGATCAGAATCCATGTCATA-TATCAGATCATAATCCATGTCAAGTATCAGATCA
1 ATCAAAAATCAGATCAGAATCCACGTCA-AGTATCAGATCAAAATCCAGGTCAAGTATCAGATCA
3209912 GAAAT-CAA
65 G-AATCCAA
3209920 ATCAAAAATCAG
1 ATCAAAAATCAG
3209932 GTAAAATATT
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
72 65 0.94
73 4 0.06
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.24
Consensus pattern (72 bp):
ATCAAAAATCAGATCAGAATCCACGTCAAGTATCAGATCAAAATCCAGGTCAAGTATCAGATCAG
AATCCAA
Found at i:3219944 original size:18 final size:18
Alignment explanation
Indices: 3219921--3219959 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3219911 AGTGTCGCCG
3219921 TTTTTATTT-ATTTATTTA
1 TTTTTATTTAATTT-TTTA
3219939 TTTTTATTTAATTTTTTA
1 TTTTTATTTAATTTTTTA
3219957 TTT
1 TTT
3219960 GAATCTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTATTTAATTTTTTA
Found at i:3220459 original size:446 final size:446
Alignment explanation
Indices: 3219927--3220825 Score: 1717
Period size: 446 Copynumber: 2.0 Consensus size: 446
3219917 GCCGTTTTTA
*
3219927 TTTATTTATTTATTTTTATTTAATTTTTTATTTGAATCTAAATTAACATCATTGCTCGTTTCTAT
1 TTTATTTATTTATTTATATTTAATTTTTTATTTGAATCTAAATTAACATCATTGCTCGTTTCTAT
*
3219992 ATATCTTGATTTCTTATTCTTCTTTTCCGCATATTTTTGAAGTATTTGATTTTATCTGTTTTTGT
66 ATATCTTGATTTCTTATTCTTCTTTTCCGCATATTTTTGAAGTATTTGATTTTATATGTTTTTGT
3220057 GACACGATTGTTCATTTGTTTTTATATATAATTTCTCTATCTTTTTGGTAGTTTAATGTTTCATT
131 GACACGATTGTTCATTTGTTTTTATATATAATTTCTCTATCTTTTTGGTAGTTTAATGTTTCATT
3220122 TGCATTCATCACGACACACCTATTAATCAAAAAATACCGACAGTCTTTCATAGTTGAATCCTTTT
196 TGCATTCATCACGACACACCTATTAATCAAAAAATACCGACAGTCTTTCATAGTTGAATCCTTTT
*
3220187 ACGATAATTTTTTTGTGCAGTCAAAATTTTTCGTGGAATAATCTATAAGATTGATTCTATAAATC
261 ACGATAATTTTTTTGTGCAGTCAAAACTTTTCGTGGAATAATCTATAAGATTGATTCTATAAATC
3220252 TCTACCTCTACATTAAAATTGTATCTAATTTTAAATATGGACATGGAGATCATTAATAATTGTTA
326 TCTACCTCTACATTAAAATTGTATCTAATTTTAAATATGGACATGGAGATCATTAATAATTGTTA
3220317 CATGTGTCTGTGTATCTTTTTATAAGATGGAGCATGTATTTGAAAAGAAGATTAAT
391 CATGTGTCTGTGTATCTTTTTATAAGATGGAGCATGTATTTGAAAAGAAGATTAAT
*
3220373 TTTATTTATTTATTTATATTTAATTTTTTATTTGAATCTAAATTAACATCCTTGCTCGTTTCTAT
1 TTTATTTATTTATTTATATTTAATTTTTTATTTGAATCTAAATTAACATCATTGCTCGTTTCTAT
3220438 ATATCTTGATTTCTTATTCTTCTTTTCCGCATATTTTTGAAGTATTTGATTTTATATGTTTTTGT
66 ATATCTTGATTTCTTATTCTTCTTTTCCGCATATTTTTGAAGTATTTGATTTTATATGTTTTTGT
* *
3220503 GACACGATTGTTCGTTTGTTTTTATATATAATTTCTCTATCTTTTTGGTAGTTTGATGTTTCATT
131 GACACGATTGTTCATTTGTTTTTATATATAATTTCTCTATCTTTTTGGTAGTTTAATGTTTCATT
* *
3220568 TGCATTCATCACGACACACCTATTAATCAAGAAATGCCGACAGTCTTTCATAGTTGAATCCTTTT
196 TGCATTCATCACGACACACCTATTAATCAAAAAATACCGACAGTCTTTCATAGTTGAATCCTTTT
3220633 ACGATAATTTTTTTGTGCAGTCAAAACTTTTCGTGGAATAATCTATAAGATTGATTCTATAAATC
261 ACGATAATTTTTTTGTGCAGTCAAAACTTTTCGTGGAATAATCTATAAGATTGATTCTATAAATC
*
3220698 TCTACCTCTACATTAATATTGTATCTAATTTTAAATATGGACATGGAGATCATTAATAATTGTTA
326 TCTACCTCTACATTAAAATTGTATCTAATTTTAAATATGGACATGGAGATCATTAATAATTGTTA
3220763 CATGTGTCTGTGTATCTTTTTATAAGATGGAGCATGTATTTGAAAAGAAGATTAAT
391 CATGTGTCTGTGTATCTTTTTATAAGATGGAGCATGTATTTGAAAAGAAGATTAAT
3220819 TTTATTT
1 TTTATTT
3220826 TCAGAACGGA
Statistics
Matches: 444, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
446 444 1.00
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (446 bp):
TTTATTTATTTATTTATATTTAATTTTTTATTTGAATCTAAATTAACATCATTGCTCGTTTCTAT
ATATCTTGATTTCTTATTCTTCTTTTCCGCATATTTTTGAAGTATTTGATTTTATATGTTTTTGT
GACACGATTGTTCATTTGTTTTTATATATAATTTCTCTATCTTTTTGGTAGTTTAATGTTTCATT
TGCATTCATCACGACACACCTATTAATCAAAAAATACCGACAGTCTTTCATAGTTGAATCCTTTT
ACGATAATTTTTTTGTGCAGTCAAAACTTTTCGTGGAATAATCTATAAGATTGATTCTATAAATC
TCTACCTCTACATTAAAATTGTATCTAATTTTAAATATGGACATGGAGATCATTAATAATTGTTA
CATGTGTCTGTGTATCTTTTTATAAGATGGAGCATGTATTTGAAAAGAAGATTAAT
Found at i:3220883 original size:19 final size:20
Alignment explanation
Indices: 3220859--3220899 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
3220849 GTTATATCTT
3220859 AATTTT-TTTTATTTAA-TAA
1 AATTTTATTTT-TTTAATTAA
3220878 AATTTTATTTTTTTAATTAA
1 AATTTTATTTTTTTAATTAA
3220898 AA
1 AA
3220900 ATATAGAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
AATTTTATTTTTTTAATTAA
Found at i:3225355 original size:246 final size:245
Alignment explanation
Indices: 3224905--3225396 Score: 959
Period size: 246 Copynumber: 2.0 Consensus size: 245
3224895 AACGATAGTG
3224905 AAGTTAATGTTTTTTGGTTTTGGTTGGATTTCAAAATGAGTAAGATGGATTGAGTGTTATCATTC
1 AAGTTAATGTTTTTTGGTTTTGGTTGGATTTCAAAATGAGTAAGATGGATTGAGTGTTATCATTC
3224970 TGATTTATATCTATAAAAAATTTTGTAATATTTTAATCCTAAATTGCACTTTAGCCTAGATAATA
66 TGATTTATATCTATAAAAAATTTTGTAATATTTTAATCCTAAATTGCACTTTAGCCTAGATAATA
3225035 GAGATGTGGGTTGCTTTAAATGTTTAGTAGTAGGTCATGGTTTCAACACCAATAGCCACAAAATT
131 GAGATGTGGGTTGCTTTAAATGTTTA-TAGTAGGTCATGGTTTCAACACCAATAGCCACAAAATT
3225100 CCATTTTTTTTCATTTTTATGTCCAAATGATGATGGATAAAATCATGCTCA
195 CCATTTTTTTTCATTTTTATGTCCAAATGATGATGGATAAAATCATGCTCA
3225151 AAGTTAATGTTTTTTGGTTTTGGTTGGATTTCAAAATGAGTAAGATGGATTGAGTGTTATCATTC
1 AAGTTAATGTTTTTTGGTTTTGGTTGGATTTCAAAATGAGTAAGATGGATTGAGTGTTATCATTC
3225216 TGATTTATATCTATAAAAAATTTTGTAATATTTTAATCCTAAATTGCACTTTAGCCTAGATAATA
66 TGATTTATATCTATAAAAAATTTTGTAATATTTTAATCCTAAATTGCACTTTAGCCTAGATAATA
3225281 GAGATGTGGGTTGCTTTAAATGTTT-TAGTAGGTCATGGTTTCAACACCAATAGCCACACAAATT
131 GAGATGTGGGTTGCTTTAAATGTTTATAGTAGGTCATGGTTTCAACACCAATAGCCACA-AAATT
3225345 CCATTTTTTTTCATTTTTATGTCCAAATGATGATGGATAAAATCATGCTCA
195 CCATTTTTTTTCATTTTTATGTCCAAATGATGATGGATAAAATCATGCTCA
3225396 A
1 A
3225397 GGCCCTAAAC
Statistics
Matches: 245, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
244 33 0.13
245 57 0.23
246 155 0.63
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (245 bp):
AAGTTAATGTTTTTTGGTTTTGGTTGGATTTCAAAATGAGTAAGATGGATTGAGTGTTATCATTC
TGATTTATATCTATAAAAAATTTTGTAATATTTTAATCCTAAATTGCACTTTAGCCTAGATAATA
GAGATGTGGGTTGCTTTAAATGTTTATAGTAGGTCATGGTTTCAACACCAATAGCCACAAAATTC
CATTTTTTTTCATTTTTATGTCCAAATGATGATGGATAAAATCATGCTCA
Found at i:3230904 original size:21 final size:21
Alignment explanation
Indices: 3230880--3230919 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3230870 GAGGGATTAT
3230880 AGTGGTCCTTC-GGGACATATC
1 AGTGGTCCTTCAGGG-CATATC
3230901 AGTGGTCCTTCAGGGCATA
1 AGTGGTCCTTCAGGGCATA
3230920 GTGGTCCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.20, C:0.23, G:0.30, T:0.28
Consensus pattern (21 bp):
AGTGGTCCTTCAGGGCATATC
Found at i:3230924 original size:18 final size:19
Alignment explanation
Indices: 3230878--3230928 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
3230868 TCGAGGGATT
3230878 ATAGTGGTCCTTCGGGACA
1 ATAGTGGTCCTTCGGGACA
3230897 TATCAGTGGTCCTTCAGGG-C-
1 -AT-AGTGGTCCTTC-GGGACA
3230917 ATAGTGGTCCTT
1 ATAGTGGTCCTT
3230929 TGGAACAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.34
19 2 0.07
20 2 0.07
21 12 0.41
22 3 0.10
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (19 bp):
ATAGTGGTCCTTCGGGACA
Done.