Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008826.1 Hibiscus syriacus cultivar Beakdansim tig00112000_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: 3884024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 18
Found at i:1012686 original size:194 final size:198
Alignment explanation
Indices: 1012353--1012746 Score: 726
Period size: 194 Copynumber: 2.0 Consensus size: 198
1012343 AATGAGTTTA
1012353 TTATTTTAAATTATTAGTTTGTTAGTTTATGGTTTAAGTTAAAACAAAATTTTAGTTAATTATTT
1 TTATTTTAAATTATTAGTTTGTTAGTTTATGGTTTAAGTTAAAAC-AAATTTTAGTTAATTATTT
1012418 AATTAGTTTGTTTGATGGTTATATATTAAAAAAATAATTAATTCTTGTGTTAGTCTAATATTAAT
65 AATTAGTTTGTTTGATGGTTATATATTAAAAAAATAATTAATTCTTGTGTTAGTCTAATATTAAT
*
1012483 TAGTTTTGTAGTTAGTTAAATAGTTAAGTTATATTTTGGTTGTTGAATTTA-TAT-TATATAAAT
130 TAGTTTTGTAGTTAGTTAAATAGTTAAGTTATATTTTGGTTGTTGAATTTATTATATA-AAAAAT
1012546 TAGTT
194 TAGTT
1012551 TTATTTTAAATTATTAGTTTGTTAGTTTATGGTTTAAGTTAAAAC-AATTTTAGTTAATTATTTA
1 TTATTTTAAATTATTAGTTTGTTAGTTTATGGTTTAAGTTAAAACAAATTTTAGTTAATTATTTA
1012615 ATTAGTTTGTTTGATGG-T-TATATTAAAAAAATAATTAATTCTTGTGTTAGTCTAATATTAATT
66 ATTAGTTTGTTTGATGGTTATATATTAAAAAAATAATTAATTCTTGTGTTAGTCTAATATTAATT
1012678 AGTTTTGTAGTTAGTTAAATAGTTAAGTTATATTTTGGTTGTTGAATTTATTATATAAAAAATTA
131 AGTTTTGTAGTTAGTTAAATAGTTAAGTTATATTTTGGTTGTTGAATTTATTATATAAAAAATTA
1012743 GTT
196 GTT
1012746 T
1 T
1012747 ATTAGTAGTT
Statistics
Matches: 193, Mismatches: 1, Indels: 7
0.96 0.00 0.03
Matches are distributed among these distances:
194 95 0.49
195 15 0.08
196 38 0.20
198 45 0.23
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.52
Consensus pattern (198 bp):
TTATTTTAAATTATTAGTTTGTTAGTTTATGGTTTAAGTTAAAACAAATTTTAGTTAATTATTTA
ATTAGTTTGTTTGATGGTTATATATTAAAAAAATAATTAATTCTTGTGTTAGTCTAATATTAATT
AGTTTTGTAGTTAGTTAAATAGTTAAGTTATATTTTGGTTGTTGAATTTATTATATAAAAAATTA
GTT
Found at i:1012698 original size:27 final size:28
Alignment explanation
Indices: 1012646--1012703 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
1012636 ATTAAAAAAA
1012646 TAATTAATTCTTGTGTTAGTCTAATA-T
1 TAATTAATTCTTGTGTTAGTCTAATAGT
*
1012673 TAATTAGTT-TTGTAGTTAGT-TAAATAGT
1 TAATTAATTCTTGT-GTTAGTCT-AATAGT
1012701 TAA
1 TAA
1012704 GTTATATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.19
27 18 0.67
28 4 0.15
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.50
Consensus pattern (28 bp):
TAATTAATTCTTGTGTTAGTCTAATAGT
Found at i:1012794 original size:25 final size:24
Alignment explanation
Indices: 1012752--1012800 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1012742 AGTTTATTAG
*
1012752 TAGTTTAAGTTTTATTATAAAAAA
1 TAGTTTAAGTTTAATTATAAAAAA
* *
1012776 TAGTTTTAGTTTAAGTTATATAAAA
1 TAGTTTAAGTTTAA-TTATAAAAAA
1012801 GAATAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (24 bp):
TAGTTTAAGTTTAATTATAAAAAA
Found at i:1012835 original size:18 final size:18
Alignment explanation
Indices: 1012812--1012866 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1012802 AATAATTATT
1012812 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
1012830 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
1012842 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
1012859 TAAATTAG
1 TAAATTAG
1012867 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:1013165 original size:30 final size:30
Alignment explanation
Indices: 1013097--1013191 Score: 97
Period size: 30 Copynumber: 3.1 Consensus size: 30
1013087 ATTAGTTAAT
* * *
1013097 TAGTTTTTTAGTAGTAAATTATAATTAAA-AA
1 TAGTTTATTAGT-TTAAGTTAT-ATTAAAGAA
1013128 TCA-TTTATTAGTTTAAGTTATATTAAAGAA
1 T-AGTTTATTAGTTTAAGTTATATTAAAGAA
*
1013158 TAGTTTATTAG-TTAACGTTATATTAAAGCA
1 TAGTTTATTAGTTTAA-GTTATATTAAAGAA
1013188 TAGT
1 TAGT
1013192 AAGTTATTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
29 11 0.20
30 35 0.62
31 9 0.16
32 1 0.02
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (30 bp):
TAGTTTATTAGTTTAAGTTATATTAAAGAA
Found at i:1015572 original size:14 final size:15
Alignment explanation
Indices: 1015555--1015638 Score: 57
Period size: 14 Copynumber: 5.3 Consensus size: 15
1015545 ATTAGTATCA
1015555 AATAATTAAAT-ATT
1 AATAATTAAATCATT
1015569 AATAA-TAAATCATTAT
1 AATAATTAAATCA-T-T
1015585 AATAATTAGTAAATCATT
1 AATAA-T--TAAATCATT
* *
1015603 AGT-ATCAAATCATT
1 AATAATTAAATCATT
*
1015617 AAATATTTAAAATCATT
1 -AATAATT-AAATCATT
1015634 AATAA
1 AATAA
1015639 ATTACTATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
13 5 0.09
14 14 0.26
15 3 0.06
16 12 0.22
17 9 0.17
18 3 0.06
19 1 0.02
20 7 0.13
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (15 bp):
AATAATTAAATCATT
Found at i:1015684 original size:12 final size:13
Alignment explanation
Indices: 1015639--1015784 Score: 62
Period size: 12 Copynumber: 11.5 Consensus size: 13
1015629 TCATTAATAA
1015639 ATTACTATAAATC
1 ATTACTATAAATC
*
1015652 A-TAGTATAAATC
1 ATTACTATAAATC
1015664 ATT--TATAAAATC
1 ATTACTAT-AAATC
1015676 ATTAC--TAAAT-
1 ATTACTATAAATC
*
1015686 AATACTATTAAATC
1 ATTACTA-TAAATC
* * *
1015700 ATTATTAT-CATT
1 ATTACTATAAATC
*
1015712 ATTA-TATTAATC
1 ATTACTATAAATC
*
1015724 A-TATCATATATAATG
1 ATTA-C-TATA-AATC
*
1015739 ATTATTATCAAATC
1 ATTACTAT-AAATC
*
1015753 ATTAC--TAAATG
1 ATTACTATAAATC
*
1015764 ATTATTATCAAATC
1 ATTACTAT-AAATC
1015778 ATTACTA
1 ATTACTA
1015785 AATCATCAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 35
0.65 0.11 0.23
Matches are distributed among these distances:
10 4 0.04
11 20 0.20
12 30 0.31
13 9 0.09
14 28 0.29
15 5 0.05
16 2 0.02
ACGTcount: A:0.45, C:0.11, G:0.02, T:0.42
Consensus pattern (13 bp):
ATTACTATAAATC
Found at i:1015685 original size:11 final size:10
Alignment explanation
Indices: 1015573--1015713 Score: 60
Period size: 11 Copynumber: 13.2 Consensus size: 10
1015563 AATATTAATA
1015573 ATAAATCATT
1 ATAAATCATT
*
1015583 AT-AATAATT
1 ATAAATCATT
1015592 AGTAAATCATTAGT
1 A-TAAATCA-T--T
1015606 ATCAAATCA-T
1 AT-AAATCATT
1015616 -TAAAT-ATT
1 ATAAATCATT
1015624 -TAAAATCATT
1 AT-AAATCATT
* *
1015634 AATAAATTACT
1 -ATAAATCATT
1015645 ATAAATCATAGT
1 ATAAATCAT--T
1015657 ATAAATCATTT
1 ATAAATCA-TT
1015668 ATAAAATCATT
1 AT-AAATCATT
*
1015679 ACTAAATAATACT
1 A-TAAATCAT--T
1015692 ATTAAATCATT
1 A-TAAATCATT
*
1015703 AT-TATCATT
1 ATAAATCATT
1015712 AT
1 AT
1015714 TATATTAATC
Statistics
Matches: 103, Mismatches: 10, Indels: 37
0.69 0.07 0.25
Matches are distributed among these distances:
7 1 0.01
8 6 0.06
9 20 0.19
10 15 0.15
11 24 0.23
12 18 0.17
13 11 0.11
14 8 0.08
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (10 bp):
ATAAATCATT
Found at i:1015698 original size:24 final size:22
Alignment explanation
Indices: 1015626--1015704 Score: 65
Period size: 24 Copynumber: 3.5 Consensus size: 22
1015616 TAAATATTTA
1015626 AAATCATTAATAAAT-TACTA-T
1 AAATCATT-ATAAATATACTATT
* *
1015647 AAATCATAGTATAAATCAT-TTATA
1 AAATCAT--TATAAAT-ATACTATT
1015671 AAATCATTACTAAATAATACTATT
1 AAATCATTA-TAAAT-ATACTATT
1015695 AAATCATTAT
1 AAATCATTAT
1015705 TATCATTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
21 7 0.15
22 8 0.17
23 11 0.24
24 20 0.43
ACGTcount: A:0.51, C:0.10, G:0.01, T:0.38
Consensus pattern (22 bp):
AAATCATTATAAATATACTATT
Found at i:1015744 original size:25 final size:25
Alignment explanation
Indices: 1015735--1015787 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1015725 TATCATATAT
1015735 AATGATTATTATCAAATCATTACTA
1 AATGATTATTATCAAATCATTACTA
1015760 AATGATTATTATCAAATCATTACTA
1 AATGATTATTATCAAATCATTACTA
1015785 AAT
1 AAT
1015788 CATCAATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (25 bp):
AATGATTATTATCAAATCATTACTA
Found at i:1016009 original size:49 final size:49
Alignment explanation
Indices: 1015926--1016102 Score: 279
Period size: 49 Copynumber: 3.7 Consensus size: 49
1015916 GGGCCCTCCA
*
1015926 TTCATTATTACTAATCATT-GTATCAAATCATTAAAAATTAATAATAAT
1 TTCATTATTACTAATCATTATTATCAAATCATTAAAAATTAATAATAAT
* * * *
1015974 TTCGTTATTACTAATCATTACTATCAAATCATTAAATATTAATGATAAT
1 TTCATTATTACTAATCATTATTATCAAATCATTAAAAATTAATAATAAT
1016023 TTCATTATTACTAATCATTATTATCAAATCATT-AAAATTAATAATAAT
1 TTCATTATTACTAATCATTATTATCAAATCATTAAAAATTAATAATAAT
*
1016071 TTCATTATTACTAATCATCATTA-CAAATCATT
1 TTCATTATTACTAATCATTATTATCAAATCATT
1016103 TGTTCTAATC
Statistics
Matches: 119, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
47 9 0.08
48 53 0.45
49 57 0.48
ACGTcount: A:0.43, C:0.12, G:0.02, T:0.43
Consensus pattern (49 bp):
TTCATTATTACTAATCATTATTATCAAATCATTAAAAATTAATAATAAT
Found at i:1016042 original size:13 final size:14
Alignment explanation
Indices: 1016024--1016130 Score: 53
Period size: 13 Copynumber: 7.4 Consensus size: 14
1016014 AATGATAATT
*
1016024 TCATTATTA-CTAA
1 TCATTATTATCAAA
1016037 TCATTATTATCAAA
1 TCATTATTATCAAA
*
1016051 TCATTAAAATTAATAATAA
1 TCATT---ATT-ATCA-AA
*
1016070 TTTCATTATTA-CTAA
1 --TCATTATTATCAAA
*
1016085 TCATCATTA-CAAA
1 TCATTATTATCAAA
*
1016098 TCATT-TGT-TCTAA
1 TCATTAT-TATCAAA
*
1016111 TCATTACTATCAAA
1 TCATTATTATCAAA
1016125 TCATTA
1 TCATTA
1016131 AAAATTAATA
Statistics
Matches: 72, Mismatches: 10, Indels: 23
0.69 0.10 0.22
Matches are distributed among these distances:
12 1 0.01
13 34 0.47
14 18 0.25
15 2 0.03
17 4 0.06
18 6 0.08
19 2 0.03
21 5 0.07
ACGTcount: A:0.41, C:0.15, G:0.01, T:0.43
Consensus pattern (14 bp):
TCATTATTATCAAA
Found at i:1016152 original size:74 final size:75
Alignment explanation
Indices: 1016033--1016177 Score: 240
Period size: 74 Copynumber: 1.9 Consensus size: 75
1016023 TTCATTATTA
* *
1016033 CTAATCATTATTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATCATCATTA-CAA
1 CTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATCATCACTATCAA
1016097 ATCATTTGTT
66 ATCATTTGTT
*
1016107 CTAATCATTACTATCAAATCATTAAAAATTAATAATAATTT-ATTATTACTAATCATTACTATCA
1 CTAATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATTATTACTAATCATCACTATCA
1016171 AATCATT
65 AATCATT
1016178 AATATTATAA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
74 40 0.61
75 26 0.39
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.42
Consensus pattern (75 bp):
CTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATCATCACTATCAA
ATCATTTGTT
Found at i:1019785 original size:41 final size:40
Alignment explanation
Indices: 1019683--1019786 Score: 102
Period size: 42 Copynumber: 2.5 Consensus size: 40
1019673 GTTTAAAGAC
* * * *
1019683 ACTAACAAATTAATTAATATTTTTTTATATTTAATAACTTA
1 ACTAACAAAATAACTAAT-TTTTTATATATATAATAACTTA
*
1019724 ACTAATAACTAATAACTAATTTTTTATATATATATATAACTTAA
1 ACTAACAA--AATAACTAATTTTTTATATATATA-ATAACTT-A
*
1019768 ACTAACAAACTAA-TAATTT
1 ACTAACAAAATAACTAATTT
1019787 ATACTAACAA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
41 13 0.25
42 16 0.31
43 15 0.29
44 8 0.15
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (40 bp):
ACTAACAAAATAACTAATTTTTTATATATATAATAACTTA
Found at i:1019792 original size:21 final size:21
Alignment explanation
Indices: 1019759--1019807 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1019749 ATATATATAT
1019759 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1019780 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1019801 ATTAACT
1 A-TAACT
1019808 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1020087 original size:21 final size:23
Alignment explanation
Indices: 1020063--1020112 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
1020053 AAATTTGACT
1020063 ATTGAAGAAAATAA-TATT-AGC
1 ATTGAAGAAAATAACTATTGAGC
* **
1020084 ATTGAATAGTATAACTATTGAGC
1 ATTGAAGAAAATAACTATTGAGC
1020107 ATTGAA
1 ATTGAA
1020113 AGGCTTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.46
22 4 0.17
23 9 0.38
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (23 bp):
ATTGAAGAAAATAACTATTGAGC
Found at i:1020537 original size:100 final size:101
Alignment explanation
Indices: 1020412--1020613 Score: 352
Period size: 100 Copynumber: 2.0 Consensus size: 101
1020402 CCCATGCACC
* *
1020412 GATCTCCCCATGCATGCACCGATCTCCCCCCCATGCACACCATGCAGCTCCCGCTCCATGGTCGC
1 GATCTCCCCATGCATGCACCAATCTCCCCCCCATGCACACCATGCAGCTCCCGCTCCATGGTCAC
1020477 CCCGAGTGAATGACGACCTCCTTGGTCGTTGGGCGT
66 CCCGAGTGAATGACGACCTCCTTGGTCGTTGGGCGT
*
1020513 GATCTCCCC-TGCATGCACCAATCTCCCCCCCATGCACACCATGCAGCTCCCGCTCCTTGGTCAC
1 GATCTCCCCATGCATGCACCAATCTCCCCCCCATGCACACCATGCAGCTCCCGCTCCATGGTCAC
* *
1020577 CCCGAGTGCATGGCGACCTCCTTGGTCGTTGGGCGT
66 CCCGAGTGAATGACGACCTCCTTGGTCGTTGGGCGT
1020613 G
1 G
1020614 CATGGAGACC
Statistics
Matches: 96, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 87 0.91
101 9 0.09
ACGTcount: A:0.15, C:0.41, G:0.23, T:0.21
Consensus pattern (101 bp):
GATCTCCCCATGCATGCACCAATCTCCCCCCCATGCACACCATGCAGCTCCCGCTCCATGGTCAC
CCCGAGTGAATGACGACCTCCTTGGTCGTTGGGCGT
Found at i:1020614 original size:29 final size:29
Alignment explanation
Indices: 1020582--1020661 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
1020572 GTCACCCCGA
*
1020582 GTGCATGGCGACCTCCTTGGTCGTTGGGC
1 GTGCATGGCGACCTCTTTGGTCGTTGGGC
*
1020611 GTGCATGGAGACCTCTTTGGTCGTTGGGC
1 GTGCATGGCGACCTCTTTGGTCGTTGGGC
1020640 GTGCATGGCGACCTCTTTGGTC
1 GTGCATGGCGACCTCTTTGGTC
1020662 ACTGTAGAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.09, C:0.25, G:0.36, T:0.30
Consensus pattern (29 bp):
GTGCATGGCGACCTCTTTGGTCGTTGGGC
Found at i:1021087 original size:30 final size:31
Alignment explanation
Indices: 1021043--1021109 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
1021033 TTGCAATACA
*
1021043 GTCCCTCAATATTTAGTCCATTTAAAATATG
1 GTCCCTCAACATTTAGTCCATTTAAAATATG
** *
1021074 GTCCC-CAACATTTAGTCTGTTTACAATATG
1 GTCCCTCAACATTTAGTCCATTTAAAATATG
1021104 GTCCCT
1 GTCCCT
1021110 GACCGTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 26 0.84
31 5 0.16
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (31 bp):
GTCCCTCAACATTTAGTCCATTTAAAATATG
Found at i:1041817 original size:67 final size:67
Alignment explanation
Indices: 1041699--1041830 Score: 167
Period size: 67 Copynumber: 2.0 Consensus size: 67
1041689 AACATTAAAT
* * * ** *
1041699 ATCTAATTTTAATAAAAATTCTTTAGATATTAAAAACTAATTTTGGGTATAATTTAGACACTTAT
1 ATCTAATTTTAATAAAAATTCTTTAAAAATAAAAAACTAAAATTGGATATAATTTAGACACTTAT
1041764 AC
66 AC
* * *
1041766 ATCTATTTTTAATAAAAATTCTTTAAAAATAAAAAAAC-AAAATTGGATATAATTTATACATTTA
1 ATCTAATTTTAATAAAAATTCTTTAAAAAT-AAAAAACTAAAATTGGATATAATTTAGACACTTA
1041830 T
65 T
1041831 TTTTGTATGA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
67 49 0.89
68 6 0.11
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (67 bp):
ATCTAATTTTAATAAAAATTCTTTAAAAATAAAAAACTAAAATTGGATATAATTTAGACACTTAT
AC
Found at i:1042989 original size:16 final size:16
Alignment explanation
Indices: 1042968--1042999 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1042958 CTTCGATGGG
1042968 TAGCACACATTGTTCT
1 TAGCACACATTGTTCT
1042984 TAGCACACATTGTTCT
1 TAGCACACATTGTTCT
1043000 CTCGAATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (16 bp):
TAGCACACATTGTTCT
Found at i:1044328 original size:21 final size:21
Alignment explanation
Indices: 1044302--1044360 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
1044292 ATTTACCGTG
1044302 ATTGCGGCCGTCGCGGGCGCT
1 ATTGCGGCCGTCGCGGGCGCT
*
1044323 ATTGCGGCCGTCGCGGACGCT
1 ATTGCGGCCGTCGCGGGCGCT
1044344 ATTGCGGCCGTCGCGGG
1 ATTGCGGCCGTCGCGGG
1044361 TAACTCGGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.07, C:0.32, G:0.42, T:0.19
Consensus pattern (21 bp):
ATTGCGGCCGTCGCGGGCGCT
Found at i:1047213 original size:159 final size:159
Alignment explanation
Indices: 1046760--1047214 Score: 600
Period size: 159 Copynumber: 2.9 Consensus size: 159
1046750 ATGTGGTTTA
* * *
1046760 AATTTGGTAAAAAAAAGAGACTTAAAATAAATC-ACAAATTGAAGGAATAAGGAGATTATGAAAA
1 AATTTGGTAAAAAAAAAAGACTTAAAATAAA-CGACGAATTGAAGAAATAAGGAGATTATGAAAA
** * * *
1046824 ATTGAAGGACTAAATTGAAAAATAAAAAA-AATTATCAAAAAGAGAAATTGAAAGTACATATGTA
65 ATTGAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTA
*
1046888 TTCAACTATGGTTTAGGAGCATGTATCTCG
130 TTCTACTATGGTTTAGGAGCATGTATCTCG
* * * * * *
1046918 AATTTGG---CAAAAAACGACTTTAAATAAATGACGAATTAAAGAAATAAGAAGATTATGAAAAA
1 AATTTGGTAAAAAAAAAAGACTTAAAATAAACGACGAATTGAAGAAATAAGGAGATTATGAAAAA
* * *
1046980 TTGTAGGACTAAATTGAAAAATAAAAATTTGTTATCAAAAAGATGAATTGAAAGTAAACATGTAT
66 TTGAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTAT
* *
1047045 TTTAATATGGTTTAGGAGCATGTGA-CTC-
131 TCTACTATGGTTTAGGAGCATGT-ATCTCG
*
1047073 AATTTTGGTAAAAAAAAAAAACTTAAAATAAACGACGAATTGAAGAAATAAGGAGATTATGAAAA
1 AA-TTTGGTAAAAAAAAAAGACTTAAAATAAACGACGAATTGAAGAAATAAGGAGATTATGAAAA
* * * *
1047138 ATTAAATGACTAAATTAAAAAATAAAAAATTGTTATAAAAAAGAGGAATTGAAAGTAAACATGTA
65 ATTGAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTA
*
1047203 TTCTGCTATGGT
130 TTCTACTATGGT
1047215 GTTTGAGCAT
Statistics
Matches: 253, Mismatches: 37, Indels: 13
0.83 0.12 0.04
Matches are distributed among these distances:
155 73 0.29
156 58 0.23
157 1 0.00
158 7 0.03
159 114 0.45
ACGTcount: A:0.51, C:0.06, G:0.16, T:0.27
Consensus pattern (159 bp):
AATTTGGTAAAAAAAAAAGACTTAAAATAAACGACGAATTGAAGAAATAAGGAGATTATGAAAAA
TTGAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTAT
TCTACTATGGTTTAGGAGCATGTATCTCG
Found at i:1047223 original size:159 final size:156
Alignment explanation
Indices: 1046760--1047279 Score: 595
Period size: 159 Copynumber: 3.3 Consensus size: 156
1046750 ATGTGGTTTA
* *
1046760 AATTTGGTAAAAAAAAGAGACTTAAAATAAATC-ACAAATTGAAGGAATAAGGAGATTATGAAAA
1 AATTTGGTAAAAAAAA-A-ACTTAAAATAAA-CGACGAATTGAAGAAATAAGGAGATTATGAAAA
** * * *
1046824 ATTGAAGGACTAAATTGAAAAATAAAAAA-AATTATCAAAAAGAGAAATTGAAAGTACATATGTA
63 ATTGAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTA
*
1046888 TTCAACTATGGTTTAGGAGCATGT-ATCTC
128 TTCTACTATGGTTTAGGAGCATGTGA-CTC
* ** * * * *
1046917 GAATTTGG-CAAAAAACGACTTTAAATAAATGACGAATTAAAGAAATAAGAAGATTATGAAAAAT
1 -AATTTGGTAAAAAAAAAACTTAAAATAAACGACGAATTGAAGAAATAAGGAGATTATGAAAAAT
* * *
1046981 TGTAGGACTAAATTGAAAAATAAAAATTTGTTATCAAAAAGATGAATTGAAAGTAAACATGTATT
65 TGAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTATT
* *
1047046 TTAATATGGTTTAGGAGCATGTGACTC
130 CTACTATGGTTTAGGAGCATGTGACTC
1047073 AATTTTGGTAAAAAAAAAAAACTTAAAATAAACGACGAATTGAAGAAATAAGGAGATTATGAAAA
1 AA-TTTGGT--AAAAAAAAAACTTAAAATAAACGACGAATTGAAGAAATAAGGAGATTATGAAAA
* * * *
1047138 ATTAAATGACTAAATTAAAAAATAAAAAATTGTTATAAAAAAGAGGAATTGAAAGTAAACATGTA
63 ATTGAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTA
* * * ** *
1047203 TTCTGCTATGGTGTT-TGAGCATTTGGTTTA
128 TTCTACTATGGT-TTAGGAGCATGT-GACTC
* * *
1047233 AATTT-GTTAAAAATAAACTTAAAATAAAGGA-GAAATTGAAGAAATAA
1 AATTTGGTAAAAAAAAAACTTAAAATAAACGACG-AATTGAAGAAATAA
1047280 CGAAATCATG
Statistics
Matches: 307, Mismatches: 45, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
155 68 0.22
156 93 0.30
157 7 0.02
158 9 0.03
159 124 0.40
160 6 0.02
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (156 bp):
AATTTGGTAAAAAAAAAACTTAAAATAAACGACGAATTGAAGAAATAAGGAGATTATGAAAAATT
GAAGGACTAAATTGAAAAATAAAAAATTGTTATCAAAAAGAGGAATTGAAAGTAAACATGTATTC
TACTATGGTTTAGGAGCATGTGACTC
Found at i:1050159 original size:23 final size:22
Alignment explanation
Indices: 1050119--1050182 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
1050109 TTACAATTTC
*
1050119 ACTTTTTTTCTTTAATTTATTAA
1 ACTTTTTTACTTT-ATTTATTAA
* *
1050142 TACTTTTTTAATTTATTTTTTAA
1 -ACTTTTTTACTTTATTTATTAA
*
1050165 ATTATTTTTACTTTATTT
1 ACT-TTTTTACTTTATTT
1050183 CATTTTTTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 2 0.06
23 21 0.62
24 11 0.32
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (22 bp):
ACTTTTTTACTTTATTTATTAA
Found at i:1050162 original size:12 final size:12
Alignment explanation
Indices: 1050145--1050182 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1050135 TTATTAATAC
1050145 TTTTTTAATTTA
1 TTTTTTAATTTA
*
1050157 TTTTTTAAATTA
1 TTTTTTAATTTA
*
1050169 -TTTTTACTTTA
1 TTTTTTAATTTA
1050180 TTT
1 TTT
1050183 CATTTTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTTAATTTA
Found at i:1050377 original size:17 final size:18
Alignment explanation
Indices: 1050357--1050405 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1050347 TATTTTCCTC
1050357 TTATTTTTTTCTTTC-AT
1 TTATTTTTTTCTTTCTAT
*
1050374 TTATTATTTTCATTTCTAT
1 TTATTTTTTTC-TTTCTAT
*
1050393 TT-TATTTTTCTTT
1 TTATTTTTTTCTTT
1050406 TTGGTTTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 13 0.48
18 10 0.37
19 4 0.15
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATTTTTTTCTTTCTAT
Found at i:1054275 original size:86 final size:86
Alignment explanation
Indices: 1054055--1055117 Score: 1189
Period size: 86 Copynumber: 12.6 Consensus size: 86
1054045 AAAAGCACCT
* * *
1054055 TCAAC-AAAGACCTTCGAGTTCG-TTTCATTCAGCTCAAAGGCATATCAAATTTACAGCATAACT
1 TCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAACT
*
1054118 CAAGGCAAGAAGGGTTATCTG
66 CAAGGCGAGAAGGGTTATCTG
* * * * * * * * *
1054139 TCAAC-CAAGACCTTCGAGTTTGATTACATTCAACTCAAATGCATATCAAATTCATAACATAACT
1 TCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAACT
*
1054203 CAAGGCGAGAAGGGTTATCTA
66 CAAGGCGAGAAGGGTTATCTG
* * * *
1054224 CCAGCAAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCAAATTTACAGCATAGCT
1 TCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAACT
* * *
1054289 CAAGGGGAGAAGGGCTATTTG
66 CAAGGCGAGAAGGGTTATCTG
* * * * *
1054310 TCAACAAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAGGCATATC-CA-GTACA-CATAACT
1 TCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAACT
*
1054372 CAAGGCGAGAA-GGTTATATG
66 CAAGGCGAGAAGGGTTATCTG
*
1054392 TCAAGC--AAGACCTTCGAGTTCGATTACAC-CTAGCTCAAAGGCACATCAAATTTACAGCATAG
1 TCAA-CAAAAGACCTTCGAGTTCGATTACACTC-AGCTCAAAGGCACATCAAATTTACAGCATAA
* * *
1054454 CTCAATGCGAGAAAGGTTATGTG
64 CTCAAGGCGAGAAGGGTTATCTG
* * * * *
1054477 TCAACAAAAAACCTTCGAGTTCGATTACA-TATAGCTCAAAGGCATATTC--A-GTACAACATAA
1 TCAACAAAAGACCTTCGAGTTCGATTACACT-CAGCTCAAAGGCACA-TCAAATTTACAGCATAA
* *
1054538 CTCAAGGCGATAAGGGTTATCTT
64 CTCAAGGCGAGAAGGGTTATCTG
* * *
1054561 TCAATC--AAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGTACATCAAATTTACAGCATAGC
1 TCAA-CAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAAC
* *
1054624 TCAAGGCGAGAAGGGCTATATG
65 TCAAGGCGAGAAGGGTTATCTG
* * * * * *
1054646 TCAATAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATATC-TA-GTACAACATAACT
1 TCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAACT
*
1054709 CAAGGCAAGAAGGGTTATCTG
66 CAAGGCGAGAAGGGTTATCTG
* * * *
1054730 TCAAC-CAAGACCTTCGAGTTCGATTACACTAAGCTCAAATGCACATCAAATTTACAGCATAGCT
1 TCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAACT
* * *
1054794 CAAGGTGAGAAGGGCTATCTA
66 CAAGGCGAGAAGGGTTATCTG
* * * * * * *
1054815 TCAACAAAAGACCTTTGAGTTCGATTATATTCAGCTCAAAGGCATATC-CA-GTACATCATAACT
1 TCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAACT
1054878 CAAGGCGAGAAGGGTTATCTG
66 CAAGGCGAGAAGGGTTATCTG
** * * * * *
1054899 TCAA-GTAAGACCTTCTAATTCGATTACACTCAGCGCAAAGGCACATCAAATTCACAGCATAGCT
1 TCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAACT
*
1054963 CAAGGCGAGAAGGGCTATCTG
66 CAAGGCGAGAAGGGTTATCTG
* * * * * *
1054984 TCAATAAAAGATCTTCGAGTTCGATTACACTTAGCTCAAAGACACATCAAATTTACAGGATAGCT
1 TCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAACT
* *
1055049 CAAGGTGAGAAGGGCTATCTG
66 CAAGGCGAGAAGGGTTATCTG
* *
1055070 TCAACAAAAGACCTTCGAGTTCGATTTCACTCAGCTCAAAGACACATC
1 TCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC
1055118 TGTCAACAAA
Statistics
Matches: 815, Mismatches: 138, Indels: 50
0.81 0.14 0.05
Matches are distributed among these distances:
80 1 0.00
81 36 0.04
82 14 0.02
83 124 0.15
84 139 0.17
85 170 0.21
86 329 0.40
87 2 0.00
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (86 bp):
TCAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAACT
CAAGGCGAGAAGGGTTATCTG
Found at i:1054625 original size:169 final size:168
Alignment explanation
Indices: 1054055--1055117 Score: 1386
Period size: 169 Copynumber: 6.3 Consensus size: 168
1054045 AAAAGCACCT
* * * *
1054055 TCAACAAAGACCTTCGAGTTCG-TTTCATTCAGCTCAAAGGCATATCAAATTTACAGCATAACTC
1 TCAAC-AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTC
* * * * * *
1054119 AAGGCAAGAAGGGTTATCTGTCAAC-CAAGACCTTCGAGTTTGATTACATTCAACTCAAATGCAT
65 AAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
* * *
1054183 ATCAAATTCATAACATAACTCAAGGCGAGAAGGGTTATCTA
130 ATC-AAGT-ACAACATAACTCAAGGCGAGAAGGGTTATCTG
* * *
1054224 CCAGCAAAAGACCTTCGAGTTCGATTACACTCAACTCAAAGGCACATCAAATTTACAGCATAGCT
1 TCA--ACAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCT
* * *
1054289 CAAGGGGAGAAGGGCTATTTGTCAACAAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAGGCA
64 CAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCA
* *
1054354 TATCCAGTAC-ACATAACTCAAGGCGAGAA-GGTTATATG
129 TATCAAGTACAACATAACTCAAGGCGAGAAGGGTTATCTG
1054392 TCAAGCAAGACCTTCGAGTTCGATTACAC-CTAGCTCAAAGGCACATCAAATTTACAGCATAGCT
1 TCAA-CAAGACCTTCGAGTTCGATTACACTC-AGCTCAAAGGCACATCAAATTTACAGCATAGCT
* * * * *
1054456 CAATGCGAGAAAGGTTATGTGTCAACAAAAAACCTTCGAGTTCGATTACATAT-AGCTCAAAGGC
64 CAAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACAT-TCAGCTCAAAGGC
* *
1054520 ATATTC-AGTACAACATAACTCAAGGCGATAAGGGTTATCTT
128 ATA-TCAAGTACAACATAACTCAAGGCGAGAAGGGTTATCTG
* *
1054561 TCAATCAAGACCTTCGAGTTTGATTACACTCAGCTCAAAGGTACATCAAATTTACAGCATAGCTC
1 TCAA-CAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTC
* *
1054626 AAGGCGAGAAGGGCTATATGTCAATAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
65 AAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
* *
1054691 ATCTAGTACAACATAACTCAAGGCAAGAAGGGTTATCTG
130 ATCAAGTACAACATAACTCAAGGCGAGAAGGGTTATCTG
* *
1054730 TCAACCAAGACCTTCGAGTTCGATTACACTAAGCTCAAATGCACATCAAATTTACAGCATAGCTC
1 TCAA-CAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTC
* * * *
1054795 AAGGTGAGAAGGGCTATCTATCAACAAAAGACCTTTGAGTTCGATTATATTCAGCTCAAAGGCAT
65 AAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCAT
* *
1054860 ATCCAGTACATCATAACTCAAGGCGAGAAGGGTTATCTG
130 ATCAAGTACAACATAACTCAAGGCGAGAAGGGTTATCTG
* * * * *
1054899 TCAAGTAAGACCTTCTAATTCGATTACACTCAGCGCAAAGGCACATCAAATTCACAGCATAGCTC
1 TCAA-CAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTC
* * *
1054964 AAGGCGAGAAGGGCTATCTGTCAATAAAAGATCTTCGAGTTCGATTACACTT-AGCTCAAAGACA
65 AAGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACA-TTCAGCTCAAAGGCA
* * ** * * *
1055028 CATCAAATTTACAGGATAGCTCAAGGTGAGAAGGGCTATCTG
129 TATC-AA-GTACAACATAACTCAAGGCGAGAAGGGTTATCTG
* *
1055070 TCAACAAAAGACCTTCGAGTTCGATTTCACTCAGCTCAAAGACACATC
1 TCAAC--AAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATC
1055118 TGTCAACAAA
Statistics
Matches: 789, Mismatches: 87, Indels: 33
0.87 0.10 0.04
Matches are distributed among these distances:
166 2 0.00
167 118 0.15
168 33 0.04
169 447 0.57
170 21 0.03
171 93 0.12
172 75 0.10
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (168 bp):
TCAACAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCAAATTTACAGCATAGCTCA
AGGCGAGAAGGGCTATCTGTCAACAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCATA
TCAAGTACAACATAACTCAAGGCGAGAAGGGTTATCTG
Found at i:1055123 original size:50 final size:51
Alignment explanation
Indices: 1055065--1055161 Score: 160
Period size: 51 Copynumber: 1.9 Consensus size: 51
1055055 GAGAAGGGCT
*
1055065 ATCTGTCAAC-AAAAGACCTTCGAGTTCGATTTCACTCAGCTCAAAGACAC
1 ATCTGTCAACAAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACAC
* *
1055115 ATCTGTCAACAAAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAG
1 ATCTGTCAACAAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAG
1055162 GCATATCCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
50 10 0.23
51 33 0.77
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.26
Consensus pattern (51 bp):
ATCTGTCAACAAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGACAC
Found at i:1056737 original size:18 final size:18
Alignment explanation
Indices: 1056705--1056739 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1056695 GATTTATTAT
*
1056705 TTTATTTTCTCTTATTTA
1 TTTATTTTATCTTATTTA
*
1056723 TTTATTTTATTTTATTT
1 TTTATTTTATCTTATTT
1056740 TTAAGTTTTT
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:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATTTTATCTTATTTA
Found at i:1056850 original size:4 final size:4
Alignment explanation
Indices: 1056841--1056890 Score: 52
Period size: 4 Copynumber: 13.0 Consensus size: 4
1056831 ATTATTATTA
* *
1056841 TTAT TTAT TTAT TTCT TTGAT TTAT TTA- ATAT TTAT TT-T TTAT TT-T
1 TTAT TTAT TTAT TTAT TT-AT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1056887 TTAT
1 TTAT
1056891 CTAACATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 8 0.21
4 27 0.71
5 3 0.08
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:1056873 original size:24 final size:21
Alignment explanation
Indices: 1056846--1056889 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 21
1056836 TATTATTATT
1056846 TATTTATTTCTTTGATTTATTTAA
1 TATTTATTT-TTT-ATTT-TTTAA
1056870 TATTTATTTTTTATTTTTTA
1 TATTTATTTTTTATTTTTTA
1056890 TCTAACATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 4 0.20
23 3 0.15
24 9 0.45
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TATTTATTTTTTATTTTTTAA
Found at i:1056882 original size:7 final size:8
Alignment explanation
Indices: 1056841--1056890 Score: 52
Period size: 7 Copynumber: 6.5 Consensus size: 8
1056831 ATTATTATTA
1056841 TTATTTAT
1 TTATTTAT
*
1056849 TTATTTCT
1 TTATTTAT
1056857 TTGATTTAT
1 TT-ATTTAT
*
1056866 TTA-ATAT
1 TTATTTAT
1056873 TTATTT-T
1 TTATTTAT
1056880 TTATTT-T
1 TTATTTAT
1056887 TTAT
1 TTAT
1056891 CTAACATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 18 0.50
8 11 0.31
9 7 0.19
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (8 bp):
TTATTTAT
Found at i:1057702 original size:2 final size:2
Alignment explanation
Indices: 1057697--1057728 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1057687 ACTATATAAG
1057697 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
1057729 TTTTCACATT
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:1058579 original size:28 final size:27
Alignment explanation
Indices: 1058548--1058635 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 27
1058538 TTAAAGTATT
*
1058548 TTTTTGTTAAAATAAATACTTAAACTTA
1 TTTTTGTCAAAATAAATACTTAAA-TTA
* *
1058576 TTTTTTTGTCAAAATGAATA-TCTAAAGTA
1 --TTTTTGTCAAAATAAATACT-TAAATTA
*
1058605 TTTTATGTCAAAATAAGTACTTAAATTA
1 TTTT-TGTCAAAATAAATACTTAAATTA
1058633 TTT
1 TTT
1058636 AAAATTTTTC
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
27 4 0.08
28 21 0.43
29 4 0.08
30 20 0.41
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (27 bp):
TTTTTGTCAAAATAAATACTTAAATTA
Found at i:1058580 original size:30 final size:29
Alignment explanation
Indices: 1058498--1058635 Score: 111
Period size: 30 Copynumber: 4.7 Consensus size: 29
1058488 CTTATCTCAT
* *
1058498 AAATAAATACATAAATTATATATTTTTTTC-
1 AAATAAATACTTAAATTAT-T-TTTTTGTCA
** * * * *
1058528 ATTTAAGTATTTAAAGTATTTTTTTGTTA
1 AAATAAATACTTAAATTATTTTTTTGTCA
1058557 AAATAAATACTTAAACTTATTTTTTTGTCA
1 AAATAAATACTTAAA-TTATTTTTTTGTCA
* * *
1058587 AAATGAATA-TCTAAAGTA-TTTTATGTCA
1 AAATAAATACT-TAAATTATTTTTTTGTCA
*
1058615 AAATAAGTACTTAAATTATTT
1 AAATAAATACTTAAATTATTT
1058636 AAAATTTTTC
Statistics
Matches: 83, Mismatches: 20, Indels: 11
0.73 0.18 0.10
Matches are distributed among these distances:
28 28 0.34
29 18 0.22
30 37 0.45
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (29 bp):
AAATAAATACTTAAATTATTTTTTTGTCA
Found at i:1058717 original size:29 final size:29
Alignment explanation
Indices: 1058675--1058788 Score: 120
Period size: 29 Copynumber: 3.9 Consensus size: 29
1058665 TAACGTGACA
* * *
1058675 TTAATTAAAGAATACTTTAAGTATTTATT
1 TTAATCAAAAAATACTTTAAGTACTTATT
*
1058704 TTAATCAAAAAATACTTTAGGTACTTATT
1 TTAATCAAAAAATACTTTAAGTACTTATT
* * *
1058733 TTGATCAGAAAAATAATTTTAGATACTTATT
1 TTAATCA-AAAAATACTTTAAG-TACTTATT
* * *
1058764 TTGACCAAAAAAAACTTTAAGTACT
1 TTAATCAAAAAATACTTTAAGTACT
1058789 AAAATGAAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
29 35 0.49
30 22 0.31
31 14 0.20
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (29 bp):
TTAATCAAAAAATACTTTAAGTACTTATT
Found at i:1059511 original size:23 final size:24
Alignment explanation
Indices: 1059466--1059511 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
1059456 TAGAAATATC
* *
1059466 AAAAATTAGAGAATTAGGGTTTTA
1 AAAAATTAGAGAATTAAGATTTTA
*
1059490 AAAAATT-GGGAATTAAGATTTT
1 AAAAATTAGAGAATTAAGATTTT
1059512 TATGAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.35
Consensus pattern (24 bp):
AAAAATTAGAGAATTAAGATTTTA
Found at i:1060274 original size:17 final size:17
Alignment explanation
Indices: 1060252--1060287 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1060242 TATTTAATAA
1060252 AATAAGGAAAAAACAAT
1 AATAAGGAAAAAACAAT
* *
1060269 AATAAGGGAAAAATAAT
1 AATAAGGAAAAAACAAT
1060286 AA
1 AA
1060288 AAAATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (17 bp):
AATAAGGAAAAAACAAT
Found at i:1060310 original size:23 final size:23
Alignment explanation
Indices: 1060277--1060330 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1060267 ATAATAAGGG
1060277 AAAAATAATAAAAAATATATACAT
1 AAAAAT-ATAAAAAATATATACAT
* *
1060301 AAAAATATAAAATATATATATAT
1 AAAAATATAAAAAATATATACAT
*
1060324 ATAAATA
1 AAAAATA
1060331 AAATATTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 21 0.78
24 6 0.22
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
AAAAATATAAAAAATATATACAT
Found at i:1060334 original size:21 final size:20
Alignment explanation
Indices: 1060288--1060352 Score: 69
Period size: 21 Copynumber: 3.2 Consensus size: 20
1060278 AAAATAATAA
*
1060288 AAAATATATACATAAAAATAT
1 AAAATATATACATAATAA-AT
*
1060309 AAAATATATATATATATAAAT
1 AAAATATATACATA-ATAAAT
* *
1060330 AAAATAT-TAGAAAATAAAT
1 AAAATATATACATAATAAAT
1060349 AAAA
1 AAAA
1060353 AAAGATAGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
19 10 0.26
20 4 0.10
21 22 0.56
22 3 0.08
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAATATATACATAATAAAT
Found at i:1060354 original size:21 final size:22
Alignment explanation
Indices: 1060278--1060354 Score: 65
Period size: 21 Copynumber: 3.7 Consensus size: 22
1060268 TAATAAGGGA
1060278 AAAAT-AATAAAAAATATATAC
1 AAAATAAATAAAAAATATATAC
* * *
1060299 ATAA-AAATATAAAATATATAT
1 AAAATAAATAAAAAATATATAC
* *
1060320 ATATATAAAT--AAAATAT-TAG
1 A-AAATAAATAAAAAATATATAC
1060340 AAAATAAATAAAAAA
1 AAAATAAATAAAAAA
1060355 AGATAGTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
19 7 0.16
20 3 0.07
21 29 0.66
22 1 0.02
23 4 0.09
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (22 bp):
AAAATAAATAAAAAATATATAC
Found at i:1060386 original size:9 final size:9
Alignment explanation
Indices: 1060324--1060389 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
1060314 ATATATATAT
1060324 ATAAATAAA
1 ATAAATAAA
* *
1060333 ATATTAGAAA
1 ATA-AATAAA
1060343 ATAAATAAA
1 ATAAATAAA
* *
1060352 AAAAGATAGTA
1 ATAA-ATA-AA
1060363 ATAAAT-AA
1 ATAAATAAA
1060371 ATAAATAAA
1 ATAAATAAA
*
1060380 ATGAATAAA
1 ATAAATAAA
1060389 A
1 A
1060390 AATATGTAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
8 7 0.16
9 21 0.48
10 12 0.27
11 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (9 bp):
ATAAATAAA
Found at i:1060392 original size:24 final size:24
Alignment explanation
Indices: 1060324--1060393 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
1060314 ATATATATAT
* *
1060324 ATAAATAAAAT-ATTAGAAAATAA
1 ATAAATAAAATGAATAAAAAATAA
*
1060347 ATAAA-AAAA-GATAGTAATAAATAA
1 ATAAATAAAATGA-A-TAAAAAATAA
1060371 ATAAATAAAATGAATAAAAAATA
1 ATAAATAAAATGAATAAAAAATA
1060394 TGTAATAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
22 5 0.13
23 5 0.13
24 21 0.55
25 5 0.13
26 2 0.05
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (24 bp):
ATAAATAAAATGAATAAAAAATAA
Found at i:1060511 original size:40 final size:41
Alignment explanation
Indices: 1060425--1060531 Score: 107
Period size: 41 Copynumber: 2.7 Consensus size: 41
1060415 AAGAAATAAA
* *
1060425 AAAAAAAAAAATAAATA-TATATTAATAATAATAGGGACAG
1 AAAAAAAAAAATAAATATTATATAAATAATAATAGAGACAG
*
1060465 AGAAAAAAAAAATAAATATGTCTATAAATAATAA-A-AGA-ATG
1 A-AAAAAAAAAATAAATAT-TATATAAATAATAATAGAGACA-G
* *
1060506 AAAAAAATAAGTAAATA-TATATAAAT
1 AAAAAAAAAAATAAATATTATATAAAT
1060532 GAAAAATGTT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
38 8 0.14
40 16 0.28
41 20 0.35
42 1 0.02
43 12 0.21
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.23
Consensus pattern (41 bp):
AAAAAAAAAAATAAATATTATATAAATAATAATAGAGACAG
Found at i:1061785 original size:31 final size:31
Alignment explanation
Indices: 1061747--1061819 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
1061737 GCTCACTAAT
**
1061747 TTTGGTCACTTACATTATTGTTTAATTAAGC
1 TTTGGTCACTTACATTATAATTTAATTAAGC
* * *
1061778 TTTGGTCACTTACGTTATAATTTTATTAAGT
1 TTTGGTCACTTACATTATAATTTAATTAAGC
1061809 TTTGGTCACTT
1 TTTGGTCACTT
1061820 GGACGTGGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (31 bp):
TTTGGTCACTTACATTATAATTTAATTAAGC
Found at i:1063644 original size:20 final size:20
Alignment explanation
Indices: 1063616--1063660 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1063606 TTTTCATCAC
*
1063616 AAAAAAGAAAATCGAGAGA-
1 AAAAAAGAAAACCGAGAGAT
*
1063635 AAAAAGAGAAAACCTAGAGAT
1 AAAAA-AGAAAACCGAGAGAT
1063656 AAAAA
1 AAAAA
1063661 CTTACCTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 12 0.55
21 5 0.23
ACGTcount: A:0.69, C:0.07, G:0.18, T:0.07
Consensus pattern (20 bp):
AAAAAAGAAAACCGAGAGAT
Found at i:1064234 original size:26 final size:26
Alignment explanation
Indices: 1064198--1064248 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1064188 GATAATAACG
1064198 TAAACCCTAGAATATGG-ATGGTGGTA
1 TAAACCCTAGAATA-GGAATGGTGGTA
1064224 TAAACCCTAGAATAGGAATGGTGGT
1 TAAACCCTAGAATAGGAATGGTGGT
1064249 GGAGTCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.25
Consensus pattern (26 bp):
TAAACCCTAGAATAGGAATGGTGGTA
Found at i:1067530 original size:32 final size:32
Alignment explanation
Indices: 1067482--1067544 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
1067472 AGAGTCAGTA
*
1067482 TTGCATTCAGATAATGCATAATAGAATTAGTC
1 TTGCATTCAGACAATGCATAATAGAATTAGTC
* * *
1067514 TTGCATTTAGACAATGCATAGTAGATTTAGT
1 TTGCATTCAGACAATGCATAATAGAATTAGT
1067545 AGCACACTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (32 bp):
TTGCATTCAGACAATGCATAATAGAATTAGTC
Found at i:1068474 original size:2 final size:2
Alignment explanation
Indices: 1068467--1068519 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1068457 ATGATTTGTT
1068467 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1068509 TA TA TA TA TA T
1 TA TA TA TA TA T
1068520 GATAGTTATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1076818 original size:67 final size:67
Alignment explanation
Indices: 1076737--1076880 Score: 234
Period size: 67 Copynumber: 2.1 Consensus size: 67
1076727 CTGTTGCAAT
*
1076737 AAAATATACTGAAACAAATCAAATATGATACATCAAGGACAATACACCAACATTATGCTCTGCAA
1 AAAATATACCGAAACAAATCAAATATGATACATCAAGGACAATACACCAACATTATGCTCTGCAA
1076802 CC
66 CC
* * **
1076804 AAAATATACCGAAACAAATCAAATATGATATATCAAGGACCATACACCAGTATTATGCTCTGCAA
1 AAAATATACCGAAACAAATCAAATATGATACATCAAGGACAATACACCAACATTATGCTCTGCAA
1076869 CC
66 CC
*
1076871 AAAATTTACC
1 AAAATATACC
1076881 ATCAAAACTC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 71 1.00
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (67 bp):
AAAATATACCGAAACAAATCAAATATGATACATCAAGGACAATACACCAACATTATGCTCTGCAA
CC
Found at i:1087486 original size:14 final size:15
Alignment explanation
Indices: 1087451--1087483 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1087441 ATCAACAAAT
1087451 ATAATTTTTTTATAA
1 ATAATTTTTTTATAA
1087466 ATAATTTTTATT-TAA
1 ATAATTTTT-TTATAA
1087481 ATA
1 ATA
1087484 TTTAGAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.88
16 2 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATAATTTTTTTATAA
Found at i:1087675 original size:20 final size:20
Alignment explanation
Indices: 1087639--1087676 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1087629 ATTCTATTTC
**
1087639 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1087659 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1087677 ATGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1093648 original size:22 final size:22
Alignment explanation
Indices: 1093620--1093669 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1093610 TTTCAGAATT
*
1093620 GAAGCGTAGGGGAACTGATAGG
1 GAAGCGTAAGGGAACTGATAGG
1093642 GAAGCGTAAGGGAACTGATAGG
1 GAAGCGTAAGGGAACTGATAGG
1093664 GAAGCG
1 GAAGCG
1093670 GTGGCGGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.34, C:0.10, G:0.44, T:0.12
Consensus pattern (22 bp):
GAAGCGTAAGGGAACTGATAGG
Found at i:1099343 original size:24 final size:23
Alignment explanation
Indices: 1099307--1099404 Score: 124
Period size: 24 Copynumber: 4.1 Consensus size: 23
1099297 ATTTTCGATT
1099307 TGGAGTTTTATATGATACTTGACC
1 TGGA-TTTTATATGATACTTGACC
*
1099331 TAGATTTTGATATGATACTTGACC
1 TGGATTTT-ATATGATACTTGACC
*
1099355 TGGATTTTTATATGATACTTGACA
1 TGGA-TTTTATATGATACTTGACC
* *
1099379 TGGATTCTAATATGCTACTTGACC
1 TGGATT-TTATATGATACTTGACC
1099403 TG
1 TG
1099405 AATTATACTT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
23 6 0.09
24 55 0.85
25 4 0.06
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (23 bp):
TGGATTTTATATGATACTTGACC
Found at i:1099392 original size:48 final size:48
Alignment explanation
Indices: 1099307--1099404 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 48
1099297 ATTTTCGATT
* * *
1099307 TGGAGTTTTATATGATACTTGACCTAGATTTTGATATGATACTTGACC
1 TGGAGTTTTATATGATACTTGACATAGATTCTAATATGATACTTGACC
* * *
1099355 TGGATTTTTATATGATACTTGACATGGATTCTAATATGCTACTTGACC
1 TGGAGTTTTATATGATACTTGACATAGATTCTAATATGATACTTGACC
1099403 TG
1 TG
1099405 AATTATACTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (48 bp):
TGGAGTTTTATATGATACTTGACATAGATTCTAATATGATACTTGACC
Found at i:1100040 original size:15 final size:16
Alignment explanation
Indices: 1100020--1100053 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1100010 ACGTCTTTTA
1100020 AAAT-AATTTTAAGAC
1 AAATAAATTTTAAGAC
1100035 AAATAAATTTTAAGAC
1 AAATAAATTTTAAGAC
1100051 AAA
1 AAA
1100054 AATGGTATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
AAATAAATTTTAAGAC
Found at i:1101797 original size:3 final size:3
Alignment explanation
Indices: 1101789--1101829 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
1101779 ACAAAATTTG
1101789 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1101830 ATTAAAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1101813 original size:17 final size:17
Alignment explanation
Indices: 1101791--1101825 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1101781 AAAATTTGTA
1101791 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
1101808 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
1101825 A
1 A
1101826 ATAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:1101814 original size:20 final size:20
Alignment explanation
Indices: 1101789--1101828 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1101779 ACAAAATTTG
1101789 TAATAATAATAATAATAATA
1 TAATAATAATAATAATAATA
1101809 TAATAATAATAATAATAATA
1 TAATAATAATAATAATAATA
1101829 AATTAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TAATAATAATAATAATAATA
Found at i:1102091 original size:40 final size:40
Alignment explanation
Indices: 1101993--1102096 Score: 120
Period size: 43 Copynumber: 2.5 Consensus size: 40
1101983 TGTTGTGGAC
**
1101993 GACACTGCTCATACGTGATGAGGAGTTCGGGTCGTCTAAGGGT
1 GACACTGCTCATACGTGATGAGGAAATCGGGTCG--T-AGGGT
* * *
1102036 GACACTGTTCCTACGTGATGAGGAAATCTGGTCG-AGGGAT
1 GACACTGCTCATACGTGATGAGGAAATCGGGTCGTAGGG-T
1102076 GACACTGCTCATACGTGATGA
1 GACACTGCTCATACGTGATGA
1102097 AGAGTTCTTG
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
39 4 0.08
40 20 0.38
43 29 0.55
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (40 bp):
GACACTGCTCATACGTGATGAGGAAATCGGGTCGTAGGGT
Found at i:1102298 original size:134 final size:133
Alignment explanation
Indices: 1102027--1102393 Score: 398
Period size: 134 Copynumber: 2.7 Consensus size: 133
1102017 GTTCGGGTCG
* * * ** * *
1102027 TCTAAGGGTGACACTGTTCCTACGTGATGAGGAAATCTGGTC-GAGGGATGACACTG-CTCATAC
1 TCTAAGGGTGACACAGCTCCTACATGATGAGGAGGTCTGGTCAG-GGGATGACAC-GATTCCTAC
* * * **
1102090 GTGATGAAGA-GTTCTTGGCCATCTTTAGGAATGGTGATAACTCGGTTCCTACACAATGAGGACG
64 ATGATGAGGACG-AC-TGGCCATCTTTAGG-ATTATGATAACTCGGTTCCTACACAATGAGGACG
*
1102154 ACTGGTTA
126 ACTGATTA
* *
1102162 TCTAAGGGTGACACAGCTCCTACATGATGAGGAGGTCTGGTTAGGGGATGACACGATTCCTATAT
1 TCTAAGGGTGACACAGCTCCTACATGATGAGGAGGTCTGGTCAGGGGATGACACGATTCCTACAT
*** *
1102227 GATGAGGACGACTGGCCATCTTTAGGAGTTATGATAACTCGGTTCCTACGTGATGAGGATGACTG
66 GATGAGGACGACTGGCCATCTTTAGGA-TTATGATAACTCGGTTCCTACACAATGAGGACGACTG
1102292 ATTA
130 ATTA
* * * * * * * *
1102296 TCTATGGTTGACACGGGTCCTATATGGTGAGGAGGTCTGGTCAGGGGATGACACGGTTCCTACGT
1 TCTAAGGGTGACACAGCTCCTACATGATGAGGAGGTCTGGTCAGGGGATGACACGATTCCTACAT
*
1102361 GATGAGGACGGCTGGCCATCTTTAGTGATTATG
66 GATGAGGACGACTGGCCATCTTTAG-GATTATG
1102394 GTTTCAAGGG
Statistics
Matches: 197, Mismatches: 30, Indels: 11
0.83 0.13 0.05
Matches are distributed among these distances:
133 1 0.01
134 133 0.68
135 61 0.31
136 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (133 bp):
TCTAAGGGTGACACAGCTCCTACATGATGAGGAGGTCTGGTCAGGGGATGACACGATTCCTACAT
GATGAGGACGACTGGCCATCTTTAGGATTATGATAACTCGGTTCCTACACAATGAGGACGACTGA
TTA
Found at i:1102434 original size:28 final size:28
Alignment explanation
Indices: 1102394--1102473 Score: 117
Period size: 28 Copynumber: 2.9 Consensus size: 28
1102384 AGTGATTATG
**
1102394 GTTTCAAGGGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
1102422 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
*
1102450 GTTTCAAGAA-AAACAAACTCAAAG
1 GTTTCAA-AAGAAACAGACTCAAAG
1102474 GTTATGTGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
28 46 0.96
29 2 0.04
ACGTcount: A:0.46, C:0.15, G:0.16, T:0.23
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATTT
Found at i:1102656 original size:32 final size:33
Alignment explanation
Indices: 1102609--1102741 Score: 101
Period size: 36 Copynumber: 3.8 Consensus size: 33
1102599 CAAAGATCAG
*
1102609 TGTTTCGAGAGAAACAAACTCAAAGATGT-TTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGTATTT
* * *
1102641 TGTTTCAAGAAAAACATAA-TTAAAGATTTTGTTTGTTT
1 TGTTTCAAGAGAAACA-AACTCAAAGA---TG--TATTT
*
1102679 TGTTTCAAGGGAAACAAACTCAAAGATGGTAAATTT
1 TGTTTCAAGAGAAACAAACTCAAAGAT-GT--ATTT
*
1102715 TGTTTCCAA-AGAAACAGACTCAAAGAT
1 TGTTT-CAAGAGAAACAAACTCAAAGAT
1102742 TTTCTTAAAA
Statistics
Matches: 80, Mismatches: 9, Indels: 20
0.73 0.08 0.18
Matches are distributed among these distances:
32 20 0.25
33 2 0.03
34 1 0.01
35 3 0.04
36 25 0.31
37 6 0.08
38 23 0.29
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (33 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGTATTT
Found at i:1102778 original size:64 final size:63
Alignment explanation
Indices: 1102709--1102846 Score: 186
Period size: 64 Copynumber: 2.2 Consensus size: 63
1102699 CAAAGATGGT
* *
1102709 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTCTTAAAAGAAACTGTCTCAAAAGAGATA
1 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTT-TCAAAAGAAACTGTCTCAAAAGAGACA
* * * ** *
1102773 AAATTTTGTTTCCAAAGAAACATATTCAATGATTTTTCAAAAGAATTTGTCTCAAGAGAGACA
1 AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCAAAAGAAACTGTCTCAAAAGAGACA
*
1102836 AAACTTTGTTT
1 AAATTTTGTTT
1102847 TTCAGAAAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
63 32 0.49
64 33 0.51
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (63 bp):
AAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTCAAAAGAAACTGTCTCAAAAGAGACA
Found at i:1102848 original size:39 final size:37
Alignment explanation
Indices: 1102805--1102892 Score: 90
Period size: 38 Copynumber: 2.4 Consensus size: 37
1102795 TATTCAATGA
*
1102805 TTTTTCAAAAGAATT-TGTCTCAAGAGAGACAAAACTTT
1 TTTTTCAAAAGAATTGTATCT-AAGAGAGACAAAA-TTT
* *
1102843 GTTTTTCAGAA-AATTGTATCTAAGTGAGACAAAATTT
1 -TTTTTCAAAAGAATTGTATCTAAGAGAGACAAAATTT
* *
1102880 TATTTCCAAAGAA
1 TTTTTCAAAAGAA
1102893 ACAAATTCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
36 7 0.17
37 5 0.12
38 16 0.39
39 13 0.32
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (37 bp):
TTTTTCAAAAGAATTGTATCTAAGAGAGACAAAATTT
Found at i:1102949 original size:101 final size:101
Alignment explanation
Indices: 1102767--1102950 Score: 248
Period size: 101 Copynumber: 1.8 Consensus size: 101
1102757 TGTCTCAAAA
* * * * **
1102767 GAGATAAAATTTTGTTTCCAAAGAAACATATTCAATGATTTTTCAAAAGAATTTGTCTCAAGAGA
1 GAGACAAAATTTTATTTCCAAAGAAACAAATTCAAAGATTTTTCAAAAGAAACTGTCTCAAGAGA
*
1102832 GACAAAACTTTGTTTTTCAGAAAATTGTATCTAAGT
66 GACAAAACCTTGTTTTTCAGAAAATTGTATCTAAGT
1102868 GAGACAAAATTTTATTTCCAAAGAAACAAATTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAG
1 GAGACAAAATTTTATTTCCAAAGAAACAAATTCAAAGA--TTT-TTCAAAAGAAACTGTCTCAAG
*
1102933 -G-GATAAAACCTT-TTTTTC
63 AGAGACAAAACCTTGTTTTTC
1102951 TAGAGAAACA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
101 40 0.56
102 9 0.12
103 4 0.06
104 19 0.26
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (101 bp):
GAGACAAAATTTTATTTCCAAAGAAACAAATTCAAAGATTTTTCAAAAGAAACTGTCTCAAGAGA
GACAAAACCTTGTTTTTCAGAAAATTGTATCTAAGT
Found at i:1103119 original size:30 final size:30
Alignment explanation
Indices: 1103076--1103143 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
1103066 GGAAAAAAAT
* * * *
1103076 TGTTTTAATAGAAACGATCTCAAAGGT-GTG
1 TGTTTCAAGAGAAACGAACTCAAAGATAG-G
*
1103106 TGTTTCAAGAGAAACTAACTCAAAGATAGG
1 TGTTTCAAGAGAAACGAACTCAAAGATAGG
1103136 TGTTTCAA
1 TGTTTCAA
1103144 AATAAAGTAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (30 bp):
TGTTTCAAGAGAAACGAACTCAAAGATAGG
Found at i:1103421 original size:30 final size:31
Alignment explanation
Indices: 1103367--1103425 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1103357 ATTTTTTCAT
*
1103367 TTTGTTTCAAATGAAACAGACTCAAAGATCC
1 TTTGTTTCAAAAGAAACAGACTCAAAGATCC
*
1103398 TTTGTTTCAAAAGAAA-TGACTCAAAGAT
1 TTTGTTTCAAAAGAAACAGACTCAAAGAT
1103426 GATGTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.31
Consensus pattern (31 bp):
TTTGTTTCAAAAGAAACAGACTCAAAGATCC
Found at i:1103503 original size:36 final size:35
Alignment explanation
Indices: 1103463--1103571 Score: 112
Period size: 35 Copynumber: 3.1 Consensus size: 35
1103453 ATAATTTGGA
* *
1103463 AAATTGCCTCAAGTGAGACAACATTTATTTTTAGAG
1 AAATTGTCTCAAGCGAGACAA-ATTTATTTTTAGAG
* * * * *
1103499 AAATTGTGTCAAACAAGACAATTTTTTTTTTAGAG
1 AAATTGTCTCAAGCGAGACAAATTTATTTTTAGAG
* *
1103534 AAATTGTCTCAAGCGAGATAAAGTTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGACAAA-TTTATTTTTAGAG
1103569 AAA
1 AAA
1103572 ACGATCTCAA
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
35 35 0.59
36 24 0.41
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (35 bp):
AAATTGTCTCAAGCGAGACAAATTTATTTTTAGAG
Found at i:1103570 original size:35 final size:35
Alignment explanation
Indices: 1103463--1103599 Score: 105
Period size: 36 Copynumber: 3.8 Consensus size: 35
1103453 ATAATTTGGA
* * * *
1103463 AAATTGCCTCAAGTGAGACAACATTTATTTTTAGAG
1 AAATTGTCTCAAGCGAGATAA-ATTTGTTTTTAGAG
* * * * * *
1103499 AAATTGTGTCAAACAAGACAATTTTTTTTTTAGAG
1 AAATTGTCTCAAGCGAGATAAATTTGTTTTTAGAG
1103534 AAATTGTCTCAAGCGAGATAAAGTTTGTTTTT-GAG
1 AAATTGTCTCAAGCGAGATAAA-TTTGTTTTTAGAG
** * *
1103569 AAAACGATCTCAAGTGAGATCAACTTTGTTT
1 AAATTG-TCTCAAGCGAGAT-AAATTTGTTT
1103600 AATGTGAAAC
Statistics
Matches: 81, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
35 36 0.44
36 43 0.53
37 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (35 bp):
AAATTGTCTCAAGCGAGATAAATTTGTTTTTAGAG
Found at i:1103905 original size:36 final size:36
Alignment explanation
Indices: 1103852--1103935 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 36
1103842 ATTCTCAAAA
*
1103852 TTTATGAGAAATGTCTCAAGTGAGA-AAGAATTTATT
1 TTTATGAGAAATGTCTCAAGCGAGACAA-AATTTATT
*
1103888 TTTA-GAGAAATTGTCTCAAGCGAGACAAAGTTTATTT
1 TTTATGAGAAA-TGTCTCAAGCGAGACAAAATTTA-TT
*
1103925 TTTTTGAGAAA
1 TTTATGAGAAA
1103936 ACGATCTCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
35 6 0.15
36 22 0.54
37 7 0.17
38 6 0.15
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (36 bp):
TTTATGAGAAATGTCTCAAGCGAGACAAAATTTATT
Found at i:1104088 original size:71 final size:72
Alignment explanation
Indices: 1103999--1104139 Score: 196
Period size: 71 Copynumber: 2.0 Consensus size: 72
1103989 TATCTCAAAG
* * ** * *
1103999 GAAAAGTGTCTCAAGCGAGACGGAATTTGTTTTTCA-AGAAATTGTCTTAAGTGAGAC-AAAATT
1 GAAAACTGTCTAAAGCGAGACAAAATTTG-TTTTCAGAGAAATTGTCTCAAGCGAGACAAAAATT
1104062 TGTTTTTA
65 TGTTTTTA
*
1104070 GAAAACTGTCTAAAGCGAGACAAAATTTGTTTTGAGAGAAATTGTCTCAAGCGAGACAAAAATTT
1 GAAAACTGTCTAAAGCGAGACAAAATTTGTTTTCAGAGAAATTGTCTCAAGCGAGACAAAAATTT
1104135 GTTTT
66 GTTTT
1104140 AAAATTCTCA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
70 5 0.08
71 44 0.72
72 12 0.20
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.33
Consensus pattern (72 bp):
GAAAACTGTCTAAAGCGAGACAAAATTTGTTTTCAGAGAAATTGTCTCAAGCGAGACAAAAATTT
GTTTTTA
Found at i:1104090 original size:35 final size:36
Alignment explanation
Indices: 1104005--1104139 Score: 175
Period size: 36 Copynumber: 3.8 Consensus size: 36
1103995 AAAGGAAAAG
**
1104005 TGTCTCAAGCGAGACGGAATTTGTTTTTCA-AGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTT-AGAGAAAT
* * *
1104041 TGTCTTAAGTGAGACAAAATTTGTTTTTAGA-AAAC
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* *
1104076 TGTCTAAAGCGAGACAAAATTTGTTTTGAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
1104112 TGTCTCAAGCGAGACAAAAATTTGTTTT
1 TGTCTCAAGCGAGAC-AAAATTTGTTTT
1104140 AAAATTCTCA
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
35 32 0.37
36 42 0.49
37 12 0.14
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:1104500 original size:4 final size:4
Alignment explanation
Indices: 1104493--1104540 Score: 62
Period size: 4 Copynumber: 12.0 Consensus size: 4
1104483 TATGTATATA
* *
1104493 TATG TATG TATG TATG TATG TATA TATG TATG TAAG TAT- TGATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG T-ATG TATG
1104541 CTTTTCTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 1 0.03
4 36 0.95
5 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.23, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:1105724 original size:12 final size:12
Alignment explanation
Indices: 1105707--1105825 Score: 104
Period size: 12 Copynumber: 9.7 Consensus size: 12
1105697 TCTTTGTCAT
1105707 CTTTTTTCTTTG
1 CTTTTTTCTTTG
1105719 C-TTTTTCTTTG
1 CTTTTTTCTTTG
*
1105730 TTTTTTTCTTTG
1 CTTTTTTCTTTG
1105742 -TTGTTTTCTTTG
1 CTT-TTTTCTTTG
* *
1105754 TTTCTTTCTCTTTT
1 CTT-TTT-TCTTTG
1105768 CTTTTTT-TGTTG
1 CTTTTTTCT-TTG
1105780 --TTTTTCTTTG
1 CTTTTTTCTTTG
1105790 CTTTTTTCTTTG
1 CTTTTTTCTTTG
1105802 CTTCTTTTTTCTTTG
1 ---CTTTTTTCTTTG
1105817 CTTATTTTC
1 CTT-TTTTC
1105826 AATTTGTTTT
Statistics
Matches: 90, Mismatches: 5, Indels: 23
0.76 0.04 0.19
Matches are distributed among these distances:
10 8 0.09
11 14 0.16
12 36 0.40
13 13 0.14
14 7 0.08
15 12 0.13
ACGTcount: A:0.01, C:0.15, G:0.08, T:0.76
Consensus pattern (12 bp):
CTTTTTTCTTTG
Found at i:1105793 original size:27 final size:28
Alignment explanation
Indices: 1105754--1105825 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 28
1105744 GTTTTCTTTG
* *
1105754 TTTCTTTCTCTTTTCTTTTTTTG-TT-GTT
1 TTTCTTT-GCTTTT-TTTCTTTGCTTCGTT
*
1105782 TTTCTTTGC-TTTTTTCTTTGCTTCTTT
1 TTTCTTTGCTTTTTTTCTTTGCTTCGTT
*
1105809 TTTCTTTGCTTATTTTC
1 TTTCTTTGCTTTTTTTC
1105826 AATTTGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
25 7 0.19
26 5 0.14
27 12 0.32
28 13 0.35
ACGTcount: A:0.01, C:0.17, G:0.07, T:0.75
Consensus pattern (28 bp):
TTTCTTTGCTTTTTTTCTTTGCTTCGTT
Found at i:1105810 original size:15 final size:15
Alignment explanation
Indices: 1105790--1105824 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1105780 TTTTTCTTTG
1105790 CTTTTTTCTTTGCTT
1 CTTTTTTCTTTGCTT
1105805 CTTTTTTCTTTGCTT
1 CTTTTTTCTTTGCTT
*
1105820 ATTTT
1 CTTTT
1105825 CAATTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.03, C:0.17, G:0.06, T:0.74
Consensus pattern (15 bp):
CTTTTTTCTTTGCTT
Found at i:1107183 original size:16 final size:17
Alignment explanation
Indices: 1107151--1107183 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1107141 AATAAAAGCC
1107151 TTCACATTACAAGACAT
1 TTCACATTACAAGACAT
*
1107168 TTCACTTTAC-AGACAT
1 TTCACATTACAAGACAT
1107184 GCCTTCACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (17 bp):
TTCACATTACAAGACAT
Found at i:1107680 original size:30 final size:33
Alignment explanation
Indices: 1107613--1107680 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 33
1107603 ATGAAAAAAG
1107613 ACACAAACAAATGAGAAGAAAAAATGAGTTAGTAT
1 ACACAAACAAA-GAGAAGAAAAAATGAGTTAG-AT
*
1107648 ACACAAACAAA-AGAA-AAAAAATTAGTTA-AT
1 ACACAAACAAAGAGAAGAAAAAATGAGTTAGAT
1107678 ACA
1 ACA
1107681 TGTCAGACAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 5 0.16
32 12 0.38
33 4 0.12
35 11 0.34
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.16
Consensus pattern (33 bp):
ACACAAACAAAGAGAAGAAAAAATGAGTTAGAT
Found at i:1110136 original size:2 final size:2
Alignment explanation
Indices: 1110129--1110174 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
1110119 CGTTTCGTGT
1110129 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1110169 TA TA TA
1 TA TA TA
1110175 ATAAACAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1110149 original size:15 final size:15
Alignment explanation
Indices: 1110128--1110173 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
1110118 TCGTTTCGTG
1110128 TTATATATATATAT-
1 TTATATATATATATA
1110142 TATATATATATATATA
1 T-TATATATATATATA
1110158 TTATATATATATATA
1 TTATATATATATATA
1110173 T
1 T
1110174 AATAAACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTATATATATATATA
Found at i:1110151 original size:17 final size:17
Alignment explanation
Indices: 1110129--1110174 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
1110119 CGTTTCGTGT
1110129 TATATATATATATTATA
1 TATATATATATATTATA
1110146 TATATATATATATTATA
1 TATATATATATATTATA
1110163 TATATATATATA
1 TATATATATATA
1110175 ATAAACAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATATATATTATA
Found at i:1110837 original size:19 final size:20
Alignment explanation
Indices: 1110800--1110837 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1110790 GTTCGTCGGT
1110800 GGCTTGGGAGTCAACGGCGC
1 GGCTTGGGAGTCAACGGCGC
*
1110820 GGCTTGGG-GTCGACGGCG
1 GGCTTGGGAGTCAACGGCG
1110838 GCACTCACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.11, C:0.24, G:0.50, T:0.16
Consensus pattern (20 bp):
GGCTTGGGAGTCAACGGCGC
Found at i:1116578 original size:2 final size:2
Alignment explanation
Indices: 1116573--1116628 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
1116563 TCCAAAAATA
1116573 AT AT AT AT AT AT AT AT AT A- 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
1116614 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1116629 ACGTAAAACG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1117305 original size:13 final size:14
Alignment explanation
Indices: 1117287--1117315 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1117277 ATTGTTATAA
1117287 AAATATTAA-ATTT
1 AAATATTAATATTT
1117300 AAATATTAATATTT
1 AAATATTAATATTT
1117314 AA
1 AA
1117316 TTTTAGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATATTAATATTT
Found at i:1117524 original size:17 final size:18
Alignment explanation
Indices: 1117499--1117533 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1117489 TTTCAATGGA
1117499 AAATAAAATAATA-TATT
1 AAATAAAATAATAGTATT
*
1117516 AAATTAAATAATAGTATT
1 AAATAAAATAATAGTATT
1117534 TTAAAACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (18 bp):
AAATAAAATAATAGTATT
Found at i:1117972 original size:22 final size:24
Alignment explanation
Indices: 1117933--1117985 Score: 74
Period size: 22 Copynumber: 2.2 Consensus size: 24
1117923 TGTACTAGAG
1117933 ACGATGGACGGAGAGCTTTGCGCAT
1 ACGA-GGACGGAGAGCTTTGCGCAT
1117958 ACGAGGA-GGAG-GCTTTGCGCAT
1 ACGAGGACGGAGAGCTTTGCGCAT
*
1117980 GCGAGG
1 ACGAGG
1117986 GGCAAATTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 16 0.59
23 4 0.15
24 3 0.11
25 4 0.15
ACGTcount: A:0.23, C:0.19, G:0.42, T:0.17
Consensus pattern (24 bp):
ACGAGGACGGAGAGCTTTGCGCAT
Found at i:1118606 original size:14 final size:14
Alignment explanation
Indices: 1118587--1118617 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1118577 CATTCTCAAT
1118587 CAATTTTATCACAC
1 CAATTTTATCACAC
1118601 CAATTTTATCACAC
1 CAATTTTATCACAC
1118615 CAA
1 CAA
1118618 ATTCTCTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (14 bp):
CAATTTTATCACAC
Found at i:1118895 original size:111 final size:108
Alignment explanation
Indices: 1118768--1118985 Score: 355
Period size: 111 Copynumber: 2.0 Consensus size: 108
1118758 TGGAAATCAT
* *
1118768 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAATAA
* * * *
1118833 TATTTAGTTATTTATTTAATGCATGATTATTATATTAATAATTAAA
66 TAGTT-G--ATTCATTTAATGCATGATTATTAGATTAAGAATTAAA
1118879 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAATAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAATAA
1118944 TAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
1118986 TTTTGTAATT
Statistics
Matches: 101, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
108 33 0.33
110 1 0.01
111 67 0.66
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (108 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAATAA
TAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAAA
Found at i:1124599 original size:49 final size:46
Alignment explanation
Indices: 1124499--1124603 Score: 142
Period size: 49 Copynumber: 2.2 Consensus size: 46
1124489 TTATACAAAA
1124499 CGCGGTACCTGCCCCCGTATAAAATTATTCAGGAGTAAAGGTATGT
1 CGCGGTACCTGCCCCCGTATAAAATTATTCAGGAGTAAAGGTATGT
*
1124545 CGCGGTACCTGCCCCGCGCTATATAAAATTATT-AGGAGTAAATGTATAG-
1 CGCGGTACCTGCCCC-CG---TATAAAATTATTCAGGAGTAAAGGTAT-GT
1124594 CGCGGTACCT
1 CGCGGTACCT
1124604 AATCCGCGCT
Statistics
Matches: 53, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
46 15 0.28
47 2 0.04
49 23 0.43
50 13 0.25
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (46 bp):
CGCGGTACCTGCCCCCGTATAAAATTATTCAGGAGTAAAGGTATGT
Found at i:1124611 original size:49 final size:50
Alignment explanation
Indices: 1124516--1124616 Score: 143
Period size: 49 Copynumber: 2.0 Consensus size: 50
1124506 CCTGCCCCCG
**
1124516 TATAAAATTATTCAGGAGTAAAGGTATGTCGCGGTACCTGCCCCGCGCTA
1 TATAAAATTATTCAGGAGTAAAGGTATGTCGCGGTACCTAACCCGCGCTA
* *
1124566 TATAAAATTATT-AGGAGTAAATGTATAG-CGCGGTACCTAATCCGCGCTA
1 TATAAAATTATTCAGGAGTAAAGGTAT-GTCGCGGTACCTAACCCGCGCTA
1124615 TA
1 TA
1124617 CCCCTATGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
49 33 0.72
50 13 0.28
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.28
Consensus pattern (50 bp):
TATAAAATTATTCAGGAGTAAAGGTATGTCGCGGTACCTAACCCGCGCTA
Found at i:1124707 original size:50 final size:51
Alignment explanation
Indices: 1124629--1124755 Score: 157
Period size: 51 Copynumber: 2.5 Consensus size: 51
1124619 CCTATGTGGT
* * * * **
1124629 GTATAGCGCGCTGCAGGGGCCGCACTATA-CCCACGTGTCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATATCCCACGTGACGCCAAATCACC
*
1124679 GTATAGCGCGGTGCAGGGGGCGCGCTATATCCCACGTGACGCCAAATCATC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATATCCCACGTGACGCCAAATCACC
* * *
1124730 GTATAGCCCCGTACAGGGGGCGCGCT
1 GTATAGCGCGGTGCAGGGGGCGCGCT
1124756 TTACTGCTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 26 0.39
51 40 0.61
ACGTcount: A:0.19, C:0.33, G:0.31, T:0.17
Consensus pattern (51 bp):
GTATAGCGCGGTGCAGGGGGCGCGCTATATCCCACGTGACGCCAAATCACC
Found at i:1125024 original size:16 final size:16
Alignment explanation
Indices: 1125005--1125037 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1124995 CGTTTCCAAT
1125005 CGGCTCCATTTTTTCA
1 CGGCTCCATTTTTTCA
1125021 CGGCTCCATTTTTTCA
1 CGGCTCCATTTTTTCA
1125037 C
1 C
1125038 TATCGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.33, G:0.12, T:0.42
Consensus pattern (16 bp):
CGGCTCCATTTTTTCA
Found at i:1143698 original size:2 final size:2
Alignment explanation
Indices: 1143693--1143719 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1143683 TGTGTGTATG
1143693 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1143720 CACAAAGGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1145210 original size:12 final size:13
Alignment explanation
Indices: 1145195--1145289 Score: 80
Period size: 12 Copynumber: 7.6 Consensus size: 13
1145185 TTATACACAC
1145195 ATATATATA-ATA
1 ATATATATATATA
1145207 ATATAT-TATGA-A
1 ATATATATAT-ATA
*
1145219 ATATATAT-TCGTA
1 ATATATATAT-ATA
*
1145232 ATA-ACAATACTATA
1 ATATA-TATA-TATA
1145246 ATATATATATAT-
1 ATATATATATATA
1145258 ATATATATATAT-
1 ATATATATATATA
1145270 ATATATATATAT-
1 ATATATATATATA
1145282 ATATATAT
1 ATATATAT
1145290 GTAGATAGAT
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
11 2 0.03
12 47 0.67
13 11 0.16
14 8 0.11
15 2 0.03
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (13 bp):
ATATATATATATA
Found at i:1145212 original size:14 final size:14
Alignment explanation
Indices: 1145195--1145288 Score: 72
Period size: 14 Copynumber: 6.6 Consensus size: 14
1145185 TTATACACAC
1145195 ATATATATAATAAT
1 ATATATATAATAAT
*
1145209 ATAT-TATGA-AAT
1 ATATATATAATAAT
* *
1145221 ATATATTCGTAATAAC
1 ATATA-T-ATAATAAT
1145237 A-ATACTATAAT-AT
1 ATATA-TATAATAAT
1145250 ATATATAT-ATATAT
1 ATATATATAATA-AT
1145264 ATATATATATATATAT
1 ATATATATA-ATA-AT
1145280 ATATATATA
1 ATATATATA
1145289 TGTAGATAGA
Statistics
Matches: 64, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
12 9 0.14
13 9 0.14
14 22 0.34
15 6 0.09
16 18 0.28
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (14 bp):
ATATATATAATAAT
Found at i:1145253 original size:2 final size:2
Alignment explanation
Indices: 1145242--1145289 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
1145232 ATAACAATAC
1145242 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1145283 TA TA TA T
1 TA TA TA T
1145290 GTAGATAGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1145418 original size:25 final size:25
Alignment explanation
Indices: 1145359--1145442 Score: 64
Period size: 29 Copynumber: 3.2 Consensus size: 25
1145349 AACTAGTAAT
*
1145359 AATAACTAATAAT-TAATCCTTATATA
1 AATAACTAATAATATAAT--ATATATA
* *
1145385 ACT-AGTAATAATATAATATATATA
1 AATAACTAATAATATAATATATATA
*
1145409 AATAACTAATTATAACAATAATATATATA
1 AATAACT-A--ATAA-TATAATATATATA
1145438 AATAA
1 AATAA
1145443 ACCCAAACAA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
24 8 0.17
25 10 0.22
26 7 0.15
28 4 0.09
29 17 0.37
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.36
Consensus pattern (25 bp):
AATAACTAATAATATAATATATATA
Found at i:1145977 original size:130 final size:131
Alignment explanation
Indices: 1145634--1146006 Score: 378
Period size: 130 Copynumber: 2.8 Consensus size: 131
1145624 ATGCTCTGCT
* ** ** *
1145634 ATTTTTTGGGTAATCATATC-TGAAAAATTTTGATTCACTTTTGTGCTCTTCAAAGAAGGTTGAA
1 ATTTTTCGGGTAATCA-ATCTTGAAAAATTTTGATTCACTTTACTGCTCTTCAGGGAAGATTGAA
* * * * *
1145698 TTGAAGTCGATTTGCTTCAGTGCTCTTCAGGAAGACCAAATCTGAAAGAAGGAGGATATGCTCCA
65 TCGAACTTGATTTGCTTC-GTGCTCTTCAGGAAGACCAAATCTGAAAGAAGGAAGATATGCTACA
1145763 CTA
129 CTA
* ** * * ** * * * *
1145766 CTCTTTAGGGGAAATCAAACTCAAAAAAGTTTTGATCCACTTTGCTGTTATTCAGGGAAGATTGA
1 AT-TTTTCGGGTAATCAATCTTGAAAAA-TTTTGATTCACTTTACTGCTCTTCAGGGAAGATTGA
*
1145831 ATCAAACTTGATTTGCTTCGCTGCTCTTCAGGAAGACCAAATCTGAAAGAA-GAAGA-AT-CTAC
64 ATCGAACTTGATTTGCTTCG-TGCTCTTCAGGAAGACCAAATCTGAAAGAAGGAAGATATGCTAC
*
1145893 TCTA
128 ACTA
* * *
1145897 ATTTTTCGGGTAATCAGATCTTGAAAATTTTTGATTCACTTTACTGCTCTTTAGGGAAGATTAAA
1 ATTTTTCGGGTAATCA-ATCTTGAAAAATTTTGATTCACTTTACTGCTCTTCAGGGAAGATTGAA
**
1145962 TCGAACTTGATTTGCTT-GAATGCTCTTCAAAAAGACCAAATCTGA
65 TCGAACTTGATTTGCTTCG--TGCTCTTCAGGAAGACCAAATCTGA
1146007 GAAAAATGAG
Statistics
Matches: 195, Mismatches: 40, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
129 1 0.01
130 81 0.42
131 14 0.07
132 5 0.03
133 21 0.11
134 73 0.37
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (131 bp):
ATTTTTCGGGTAATCAATCTTGAAAAATTTTGATTCACTTTACTGCTCTTCAGGGAAGATTGAAT
CGAACTTGATTTGCTTCGTGCTCTTCAGGAAGACCAAATCTGAAAGAAGGAAGATATGCTACACT
A
Found at i:1151455 original size:45 final size:45
Alignment explanation
Indices: 1151367--1151589 Score: 286
Period size: 45 Copynumber: 4.9 Consensus size: 45
1151357 CTTCATACTT
* ** *
1151367 ATAATGCA-CCATTATGCATTTTCATTTATGGCATTTTTTCATGCCA
1 ATAATGCACCCA-TATGCA-TTTCAATTATGGCATCCTTTCATGCCG
* * *
1151413 ATAGTGCACCCATATGCATTTTAATTATGGCACCCTTTCATGCCG
1 ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGCCG
* * * *
1151458 ATAATACACCCATATGCATTTCAATTATGGTATCTTTTCATGACG
1 ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGCCG
*
1151503 ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGCCT
1 ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGCCG
* * *
1151548 ATAATGCACCCATATGCATTTCATTTAAGGCATTCTTTCATG
1 ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATG
1151590 ACTTTTATAC
Statistics
Matches: 154, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
45 138 0.90
46 13 0.08
47 3 0.02
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (45 bp):
ATAATGCACCCATATGCATTTCAATTATGGCATCCTTTCATGCCG
Found at i:1151613 original size:90 final size:89
Alignment explanation
Indices: 1151366--1151637 Score: 253
Period size: 90 Copynumber: 3.0 Consensus size: 89
1151356 CCTTCATACT
* * * * * * * *
1151366 TATAATGCA-CCATTATGCATTTTCATTTATGGCATTTTTTCATGCCAATAGTGCACCCATATGC
1 TATAATACACCCA-TATGCA-TTTCAATTAAGGCATCTTTTCATGACGATAAT-CACCCATATAC
* *
1151430 ATTTTAATTATGGCACCCTTTCATGCC
63 ATTTCAATTATGGCATCCTTTCATGCC
* * * *
1151457 GATAATACACCCATATGCATTTCAATTATGGTATCTTTTCATGACGATAATGCACCCATATGCAT
1 TATAATACACCCATATGCATTTCAATTAAGGCATCTTTTCATGACGATAAT-CACCCATATACAT
1151522 TTCAATTATGGCATCCTTTCATGCC
65 TTCAATTATGGCATCCTTTCATGCC
* * ** * *
1151547 TATAATGCACCCATATGCATTTCATTTAAGGCAT-TCTTTCATGACTTTTAT-ACGCTATTATAC
1 TATAATACACCCATATGCATTTCAATTAAGGCATCT-TTTCATGACGATAATCAC-CCA-TATAC
* **
1151610 ATTTCATTTATGTTATCCTTTCATGCC
63 ATTTCAATTATGGCATCCTTTCATGCC
1151637 T
1 T
1151638 TTTATACAAT
Statistics
Matches: 154, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
88 2 0.01
89 3 0.02
90 133 0.86
91 13 0.08
92 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.40
Consensus pattern (89 bp):
TATAATACACCCATATGCATTTCAATTAAGGCATCTTTTCATGACGATAATCACCCATATACATT
TCAATTATGGCATCCTTTCATGCC
Found at i:1151613 original size:135 final size:136
Alignment explanation
Indices: 1151367--1151634 Score: 317
Period size: 135 Copynumber: 2.0 Consensus size: 136
1151357 CTTCATACTT
* ** *
1151367 ATAATGCACCATTATGCATTTTCATTTATGGCATTTTTTCATGCCAATAGTGCACCCATATGCAT
1 ATAATGCACCATTATGCATTTTCAATTATGGCATCCTTTCATGCCAATAATGCACCCATATGCAT
* * * * *
1151432 TTTAATTATGGCACCCTTTCATGCCGATAATACACCCATATGCATTTCAATTATGGTATCTTTTC
66 TTCAATTAAGGCACCCTTTCATGACGATAATACACCCATATACATTTCAATTATGGTATCCTTTC
1151497 ATGACG
131 ATGACG
*
1151503 ATAATGCACCCA-TATGCA-TTTCAATTATGGCATCCTTTCATGCCTATAATGCACCCATATGCA
1 ATAATGCA-CCATTATGCATTTTCAATTATGGCATCCTTTCATGCCAATAATGCACCCATATGCA
* ** ** * * * * *
1151566 TTTCATTTAAGGCATTCTTTCATGACTTTTATAC-GCTATTATACATTTCATTTATGTTATCCTT
65 TTTCAATTAAGGCACCCTTTCATGACGATAATACACCCA-TATACATTTCAATTATGGTATCCTT
1151630 TCATG
129 TCATG
1151635 CCTTTTATAC
Statistics
Matches: 110, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
134 2 0.02
135 91 0.83
136 14 0.13
137 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (136 bp):
ATAATGCACCATTATGCATTTTCAATTATGGCATCCTTTCATGCCAATAATGCACCCATATGCAT
TTCAATTAAGGCACCCTTTCATGACGATAATACACCCATATACATTTCAATTATGGTATCCTTTC
ATGACG
Found at i:1151786 original size:81 final size:81
Alignment explanation
Indices: 1151671--1151825 Score: 238
Period size: 81 Copynumber: 1.9 Consensus size: 81
1151661 ATACATCTAG
* * * *
1151671 TCTTTTACTCAAAGGCATTTAACCTTTAATCTAACTGGCATGATTGCCACCTTTTTGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTAATCTAACTGACATAATTGACACCTTTATGTCAAATGC
*
1151736 ACAGCTAGGCCATTAA
66 ACAACTAGGCCATTAA
* * *
1151752 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGATACCTTTATGTCAAATGC
1 TCTTTTACTCAAAGGCATTTAACCTTTAATCTAACTGACATAATTGACACCTTTATGTCAAATGC
1151817 ACAACTAGG
66 ACAACTAGG
1151826 TCTCAAAGGC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGCATTTAACCTTTAATCTAACTGACATAATTGACACCTTTATGTCAAATGC
ACAACTAGGCCATTAA
Found at i:1151872 original size:68 final size:68
Alignment explanation
Indices: 1151759--1152302 Score: 786
Period size: 68 Copynumber: 8.0 Consensus size: 68
1151749 TAATCTTTTA
* * * * * *
1151759 CTCAAAGGTATTTAACCTTTCATCTAACTGACATAATTGATACCTTTATGTCAAATGCACAACTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTA
*
1151824 GGT
66 GGC
*
1151827 CTCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGACACCTTTCTGTCAAATGCACAACTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTA
*
1151892 GTC
66 GGC
* * * * *
1151895 CTCAAAGACACTTAACCTTTCATGTAA-TGGCATAATTGATACATTTCTGTCAAATGCACAACTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTA
1151959 GGC
66 GGC
* * *
1151962 CTCAAAGGCAGC-TATCCTTTCATCTAATTGGCATAATTGACACCTTTCTGTCAAATGCACAATT
1 CTCAAAGGCA-CTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACT
1152026 AGGC
65 AGGC
* * * * *
1152030 CTTAAAGACACTTATCCTTTCATCTAACTAGCATAATTGACACCTTTCTGTCAGATGCACAACTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTA
1152095 GGC
66 GGC
* *
1152098 CTCAAAGGCAATTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATTCACAACTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTA
1152163 GGC
66 GGC
* * * **
1152166 CTCAAATGCACTTAGCATTTCATCTAACTGACATAATTGACATATTTCTGTCAAATGCACAACTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTA
1152231 GGC
66 GGC
* *
1152234 CTCAAAGGCACTTAGCCTTTCATTTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTA
1152299 GGC
66 GGC
1152302 C
1 C
1152303 ATTAATCTTT
Statistics
Matches: 424, Mismatches: 49, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
67 59 0.14
68 365 0.86
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.31
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTA
GGC
Found at i:1152592 original size:56 final size:58
Alignment explanation
Indices: 1152513--1152719 Score: 300
Period size: 57 Copynumber: 3.7 Consensus size: 58
1152503 TTCTTAAACG
* *
1152513 GAAATTTATAAGC-AATTATGAATTTCTTAACTTTTTGCACCA-AAAGTGCCCATA-C
1 GAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACCACAAAGTGCCCATATC
* *
1152568 GAAATTCATAAA-ACAATTACGAATTTCTTAACTTTTTTC-CCACAAAGTGCCCATATC
1 GAAATTCATAAACA-AATTATGAATTTCTTAACTTTTTGCACCACAAAGTGCCCATATC
*
1152625 GAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCA-CACAAAGTGCCCATATG
1 GAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACCACAAAGTGCCCATATC
* *
1152682 GAAATTCATAAACAAATTATGAATTTCCTAACATTTTG
1 GAAATTCATAAACAAATTATGAATTTCTTAACTTTTTG
1152720 TACACTTAGT
Statistics
Matches: 137, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
55 13 0.09
56 35 0.26
57 88 0.64
58 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.34
Consensus pattern (58 bp):
GAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACCACAAAGTGCCCATATC
Found at i:1152649 original size:113 final size:113
Alignment explanation
Indices: 1152513--1152718 Score: 310
Period size: 113 Copynumber: 1.8 Consensus size: 113
1152503 TTCTTAAACG
* *
1152513 GAAATTTATAAGCAATTATGAATTTCTTAACTTTTTGCAC-CAAAAGTGCCCATA-CGAAATTCA
1 GAAATTCATAAACAATTATGAATTTCTTAACTTTTTGCACAC-AAAGTGCCCATATCGAAATTCA
* *
1152576 TAAA-ACAATTACGAATTTCTTAACTTTTTTCCCACAAAGTGCCCATATC
65 TAAACA-AATTACGAATTTCCTAACATTTTTCCCACAAAGTGCCCATATC
*
1152625 GAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATATGGAAATTCA
1 GAAATTCATAAAC-AATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATATCGAAATTCA
*
1152690 TAAACAAATTATGAATTTCCTAACATTTT
65 TAAACAAATTACGAATTTCCTAACATTTT
1152719 GTACACTTAG
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
112 11 0.13
113 39 0.46
114 33 0.39
115 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.34
Consensus pattern (113 bp):
GAAATTCATAAACAATTATGAATTTCTTAACTTTTTGCACACAAAGTGCCCATATCGAAATTCAT
AAACAAATTACGAATTTCCTAACATTTTTCCCACAAAGTGCCCATATC
Found at i:1157441 original size:21 final size:22
Alignment explanation
Indices: 1157412--1157455 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
1157402 GTCTCTGGGA
*
1157412 TTTCATCATATCTTCTTGTATC
1 TTTCATCATATCTTATTGTATC
* *
1157434 TTTC-TCATGTTTTATTGTATC
1 TTTCATCATATCTTATTGTATC
1157455 T
1 T
1157456 CTTGCCGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.16, C:0.18, G:0.07, T:0.59
Consensus pattern (22 bp):
TTTCATCATATCTTATTGTATC
Found at i:1157657 original size:21 final size:21
Alignment explanation
Indices: 1157631--1157670 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1157621 AATGCGGAAG
1157631 ATAAAATGCA-ATGTGAAAAAA
1 ATAAAATGCAGATGT-AAAAAA
1157652 ATAAAATGCAGATGTAAAA
1 ATAAAATGCAGATGTAAAA
1157671 TGCAAGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.05, G:0.15, T:0.20
Consensus pattern (21 bp):
ATAAAATGCAGATGTAAAAAA
Found at i:1160955 original size:24 final size:24
Alignment explanation
Indices: 1160928--1160999 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
1160918 AAACGGAGAT
1160928 ATCAGAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
*
1160952 ATCAGATATCAAAACAGAA-TCTAG
1 ATCAGAAATCAAAACAGAATTC-AG
* *
1160976 ATCAGAAATCAGAATAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
1161000 GTAATGTATC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.05
24 38 0.90
25 2 0.05
ACGTcount: A:0.51, C:0.15, G:0.14, T:0.19
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1161010 original size:48 final size:49
Alignment explanation
Indices: 1160928--1161036 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 49
1160918 AAACGGAGAT
* * *
1160928 ATCAGAAATCAAAACAGAATTCAGATCAGATATCAAAACAGAA-TCTAG
1 ATCAGAAATCAGAACAGAATTCAGATAAGATATCAAAACAGAATTCAAG
* * *
1160976 ATCAGAAATCAGAATAGAATTCAGGTAATG-TATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAGATAA-GATATCAAAACAGAATTCAAG
*
1161025 -TCGGAAATCAGA
1 ATCAGAAATCAGA
1161037 TAAAATATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
48 47 0.90
49 5 0.10
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20
Consensus pattern (49 bp):
ATCAGAAATCAGAACAGAATTCAGATAAGATATCAAAACAGAATTCAAG
Found at i:1161034 original size:24 final size:25
Alignment explanation
Indices: 1160928--1161036 Score: 93
Period size: 24 Copynumber: 4.5 Consensus size: 25
1160918 AAACGGAGAT
*
1160928 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
1160952 ATCAGATATCAAAACAGAA-TCTAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
1160976 ATCAGAAATCAGAATAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
1161000 GTAATG-TATCAGAACAGAATTCAAG
1 ATCA-GAAATCAGAACAGAATTCAAG
*
1161025 -TCGGAAATCAGA
1 ATCAGAAATCAGA
1161037 TAAAATATTT
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
23 3 0.04
24 61 0.88
25 5 0.07
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:1163461 original size:20 final size:18
Alignment explanation
Indices: 1163422--1163463 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
1163412 GGTCAATAGT
*
1163422 GGTCAACGTCGGTCAACG
1 GGTCAACGTCGGTAAACG
1163440 GGTCAACGGTCGGGTAAACG
1 GGTCAAC-GTC-GGTAAACG
1163460 GGTC
1 GGTC
1163464 GGGTTATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 3 0.14
20 11 0.52
ACGTcount: A:0.21, C:0.24, G:0.38, T:0.17
Consensus pattern (18 bp):
GGTCAACGTCGGTAAACG
Found at i:1170327 original size:42 final size:42
Alignment explanation
Indices: 1170268--1170351 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
1170258 ACCAGCGGCA
1170268 GGAGGTAAATTTCTCGGGGTCGTAGGATCAGGATCAACTGTC
1 GGAGGTAAATTTCTCGGGGTCGTAGGATCAGGATCAACTGTC
1170310 GGAGGTAAATTTCTCGGGGTCGTAGGATCAGGATCAACTGTC
1 GGAGGTAAATTTCTCGGGGTCGTAGGATCAGGATCAACTGTC
1170352 TGTAAATCTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (42 bp):
GGAGGTAAATTTCTCGGGGTCGTAGGATCAGGATCAACTGTC
Found at i:1171097 original size:20 final size:20
Alignment explanation
Indices: 1171061--1171098 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1171051 TGTCCCAATA
*
1171061 GTACAATAAAATCATAGTAG
1 GTACAATAAAATAATAGTAG
1171081 GTAC-ATAAAAGTAATAGT
1 GTACAATAAAA-TAATAGT
1171099 TCAGAAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.26
Consensus pattern (20 bp):
GTACAATAAAATAATAGTAG
Found at i:1172321 original size:28 final size:28
Alignment explanation
Indices: 1172263--1172345 Score: 130
Period size: 28 Copynumber: 2.9 Consensus size: 28
1172253 CAATCACCTC
** *
1172263 TTTAAAAATAATTATAAAAATATAATCGT
1 TTTAAAAATAATTACCAAAATATCA-CGT
1172292 TTTAAAAATAATTACCAAAATATCACGT
1 TTTAAAAATAATTACCAAAATATCACGT
1172320 TTTAAAAATAATTACCAAAATATCAC
1 TTTAAAAATAATTACCAAAATATCAC
1172346 CGGGTGGGTC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 29 0.57
29 22 0.43
ACGTcount: A:0.53, C:0.11, G:0.02, T:0.34
Consensus pattern (28 bp):
TTTAAAAATAATTACCAAAATATCACGT
Found at i:1172379 original size:19 final size:19
Alignment explanation
Indices: 1172357--1172398 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1172347 GGGTGGGTCG
*
1172357 GGTCAACCCGGTTCGGACC
1 GGTCAACCCGGTTCAGACC
**
1172376 GGTCAGTCCGGTTCAGACC
1 GGTCAACCCGGTTCAGACC
1172395 GGTC
1 GGTC
1172399 CAGCCCGTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.33, G:0.33, T:0.19
Consensus pattern (19 bp):
GGTCAACCCGGTTCAGACC
Found at i:1176323 original size:20 final size:20
Alignment explanation
Indices: 1176294--1176364 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
1176284 TTGATGCTAT
* *
1176294 AAGAATAATATCGGTACTTG
1 AAGAACAATATCGGTACTGG
*
1176314 AAGAACAATATCGATACTAAGG
1 AAGAACAATATCGGTACT--GG
*
1176336 ATGAACAATATCGGTA-TGG
1 AAGAACAATATCGGTACTGG
1176355 AAGAACAATA
1 AAGAACAATA
1176365 CTTGTACCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 11 0.26
20 16 0.37
21 1 0.02
22 15 0.35
ACGTcount: A:0.46, C:0.11, G:0.20, T:0.23
Consensus pattern (20 bp):
AAGAACAATATCGGTACTGG
Found at i:1176778 original size:37 final size:35
Alignment explanation
Indices: 1176719--1176800 Score: 85
Period size: 37 Copynumber: 2.3 Consensus size: 35
1176709 ATATTTTTAT
* *
1176719 GTCGGGTCGGGTCGAGTTGAGGATATAAACGTTTTGG
1 GTCGGGTCGAGTCGAGTGGAGGATATAAA--TTTTGG
* * *
1176756 GTCGGGTCGAGTC-AGGTGGAGGATGTAGATTTTTG
1 GTCGGGTCGAGTCGA-GTGGAGGATATAAATTTTGG
1176791 GTCGGGTCGA
1 GTCGGGTCGA
1176801 TTGACCAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
35 15 0.38
36 1 0.03
37 23 0.59
ACGTcount: A:0.17, C:0.11, G:0.43, T:0.29
Consensus pattern (35 bp):
GTCGGGTCGAGTCGAGTGGAGGATATAAATTTTGG
Done.