Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 38 of 235
Found at i:12539623 original size:156 final size:156
Alignment explanation
Indices: 12539339--12539649 Score: 622
Period size: 156 Copynumber: 2.0 Consensus size: 156
12539329 TAAATATCTT
12539339 TCTTTTAGCTCAAGAAGCTAACGTGAGTCCAAGTGATAAAGGCAAATGACATGTTTTGTAGATTG
1 TCTTTTAGCTCAAGAAGCTAACGTGAGTCCAAGTGATAAAGGCAAATGACATGTTTTGTAGATTG
12539404 TGCTAGAATTTCTGGTGTGCTCCTTTTTACTTCCATGTGTTGTAAATCTCTTTGTTATATGATTC
66 TGCTAGAATTTCTGGTGTGCTCCTTTTTACTTCCATGTGTTGTAAATCTCTTTGTTATATGATTC
12539469 GTGTAAGGTAAGTAATCTTTCTCTGA
131 GTGTAAGGTAAGTAATCTTTCTCTGA
12539495 TCTTTTAGCTCAAGAAGCTAACGTGAGTCCAAGTGATAAAGGCAAATGACATGTTTTGTAGATTG
1 TCTTTTAGCTCAAGAAGCTAACGTGAGTCCAAGTGATAAAGGCAAATGACATGTTTTGTAGATTG
12539560 TGCTAGAATTTCTGGTGTGCTCCTTTTTACTTCCATGTGTTGTAAATCTCTTTGTTATATGATTC
66 TGCTAGAATTTCTGGTGTGCTCCTTTTTACTTCCATGTGTTGTAAATCTCTTTGTTATATGATTC
12539625 GTGTAAGGTAAGTAATCTTTCTCTG
131 GTGTAAGGTAAGTAATCTTTCTCTG
12539650 TAATGGATGA
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 155 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (156 bp):
TCTTTTAGCTCAAGAAGCTAACGTGAGTCCAAGTGATAAAGGCAAATGACATGTTTTGTAGATTG
TGCTAGAATTTCTGGTGTGCTCCTTTTTACTTCCATGTGTTGTAAATCTCTTTGTTATATGATTC
GTGTAAGGTAAGTAATCTTTCTCTGA
Found at i:12558820 original size:39 final size:39
Alignment explanation
Indices: 12558776--12558860 Score: 152
Period size: 39 Copynumber: 2.2 Consensus size: 39
12558766 AGTATATGTT
12558776 AGTAGATAATGACAACCCAAGCCATAGAATTAGAAATTG
1 AGTAGATAATGACAACCCAAGCCATAGAATTAGAAATTG
*
12558815 AGTAGATAATGACAACCCAAGCCATGGAATTAGAAATTG
1 AGTAGATAATGACAACCCAAGCCATAGAATTAGAAATTG
*
12558854 ATTAGAT
1 AGTAGAT
12558861 TATTTAAGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.45, C:0.14, G:0.19, T:0.22
Consensus pattern (39 bp):
AGTAGATAATGACAACCCAAGCCATAGAATTAGAAATTG
Found at i:12561822 original size:21 final size:21
Alignment explanation
Indices: 12561796--12561837 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12561786 AATGAATAAA
12561796 TCTTTAAGTTAACATTTGACT
1 TCTTTAAGTTAACATTTGACT
*
12561817 TCTTTAAGTTAATATTTGACT
1 TCTTTAAGTTAACATTTGACT
12561838 CGAAATTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.50
Consensus pattern (21 bp):
TCTTTAAGTTAACATTTGACT
Found at i:12573009 original size:36 final size:36
Alignment explanation
Indices: 12572962--12573035 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
12572952 ACATGTCCCT
12572962 ATATGTTTGAACAAAATGGTGTGGTAGAAAGAAAAC
1 ATATGTTTGAACAAAATGGTGTGGTAGAAAGAAAAC
12572998 ATATGTTTGAACAAAATGGTGTGGTAGAAAGAAAAC
1 ATATGTTTGAACAAAATGGTGTGGTAGAAAGAAAAC
12573034 AT
1 AT
12573036 CATCATATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (36 bp):
ATATGTTTGAACAAAATGGTGTGGTAGAAAGAAAAC
Found at i:12575376 original size:40 final size:40
Alignment explanation
Indices: 12575316--12575542 Score: 373
Period size: 40 Copynumber: 5.7 Consensus size: 40
12575306 CAATTGAGGA
*
12575316 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
*
12575356 CTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
12575396 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
*
12575436 TTATTTCCGGGTTAAGCCCCGAAGGCATTCGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
* *
12575476 CTATTTCCGGGTTAAGTCCCGAAGGCATTTGTGCTGGTTG
1 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
** * *
12575516 TTACATCCGGGCTAAATCCCGAAGGCA
1 TTATTTCCGGGTTAAGTCCCGAAGGCA
12575543 ATTGGGTTGG
Statistics
Matches: 175, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 175 1.00
ACGTcount: A:0.17, C:0.22, G:0.29, T:0.32
Consensus pattern (40 bp):
TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
Found at i:12576597 original size:122 final size:121
Alignment explanation
Indices: 12576380--12576623 Score: 461
Period size: 122 Copynumber: 2.0 Consensus size: 121
12576370 TGAATTTCCG
12576380 TACTTATTTGGTAATATTCCTTACCCCCTCCGGTGACGGATATGGGTTAGGGGTGTTACATTTTA
1 TACTTATTTGGTAATATTCCTTACCCCCTCCGGTGACGGATATGGGTTAGGGGTGTTACATTTTA
* *
12576445 TTGGTATCAGAGCTAGGGTTTAGTCGATTCTAGGACTACCGTAAAACATTTGGGGT
66 TTGGTATCAGAGCCACGGTTTAGTCGATTCTAGGACTACCGTAAAACATTTGGGGT
12576501 NTACTTATTTGGTAATATTCCTTACCCCCTCCGGTGACGGATATGGGTTAGGGGTGTTACATTTT
1 -TACTTATTTGGTAATATTCCTTACCCCCTCCGGTGACGGATATGGGTTAGGGGTGTTACATTTT
12576566 ATTGGTATCAGAGCCACGGTTTAGTCGATTCTAGGACTACCGTAAAACATTTGGGGT
65 ATTGGTATCAGAGCCACGGTTTAGTCGATTCTAGGACTACCGTAAAACATTTGGGGT
12576623 T
1 T
12576624 TAGCTATACA
Statistics
Matches: 120, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
121 1 0.01
122 119 0.99
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.35
Consensus pattern (121 bp):
TACTTATTTGGTAATATTCCTTACCCCCTCCGGTGACGGATATGGGTTAGGGGTGTTACATTTTA
TTGGTATCAGAGCCACGGTTTAGTCGATTCTAGGACTACCGTAAAACATTTGGGGT
Found at i:12583124 original size:40 final size:40
Alignment explanation
Indices: 12583064--12583210 Score: 213
Period size: 40 Copynumber: 3.7 Consensus size: 40
12583054 CAATTGAGGA
12583064 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
*
12583104 TTATTTCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
* * * * *
12583144 CTATTTCCAGGTTAAGTCCTGAAGGCATTTGTGCTGGTTG
1 TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
* * *
12583184 TTACATCCGGGCTAAATCCCGAAGGCA
1 TTATATCCGGGTTAAGTCCCGAAGGCA
12583211 ATTGGGTTGG
Statistics
Matches: 95, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 95 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (40 bp):
TTATATCCGGGTTAAGTCCCGAAGGCATTCGTGCTGGTTG
Found at i:12587089 original size:9 final size:9
Alignment explanation
Indices: 12587075--12587100 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12587065 AACATGTATC
12587075 AATTATAAT
1 AATTATAAT
12587084 AATTATAAT
1 AATTATAAT
12587093 AATTATAA
1 AATTATAA
12587101 AAGATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
AATTATAAT
Found at i:12597410 original size:13 final size:13
Alignment explanation
Indices: 12597392--12597418 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12597382 GCTTGGCAGG
12597392 GACACGCCCGTGT
1 GACACGCCCGTGT
12597405 GACACGCCCGTGT
1 GACACGCCCGTGT
12597418 G
1 G
12597419 CTATTACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:12599173 original size:3 final size:3
Alignment explanation
Indices: 12599152--12599195 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
12599142 TTTATTTATG
* * * *
12599152 TTA TTG TTA TTA TTT TTA TTA TTA TTA TGA TTA TTA TTA GTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12599196 TTCCTCCATT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:12600894 original size:3 final size:3
Alignment explanation
Indices: 12600886--12600915 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12600876 TTGAGTCTAT
12600886 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12600916 ATTTCAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12602739 original size:27 final size:27
Alignment explanation
Indices: 12602695--12602770 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 27
12602685 TATTGAAATG
* *
12602695 CCCTCGACTTGTAAAATTACCAAAGTA
1 CCCTCGATTTATAAAATTACCAAAGTA
* * ***
12602722 CCCTCGATTTATAGAATTATCATTTTA
1 CCCTCGATTTATAAAATTACCAAAGTA
*
12602749 CCCTCGATTTACAAAATTACCA
1 CCCTCGATTTATAAAATTACCA
12602771 TTTGCCCTCA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.34, C:0.25, G:0.08, T:0.33
Consensus pattern (27 bp):
CCCTCGATTTATAAAATTACCAAAGTA
Found at i:12602772 original size:27 final size:27
Alignment explanation
Indices: 12602720--12602809 Score: 112
Period size: 27 Copynumber: 3.4 Consensus size: 27
12602710 ATTACCAAAG
* *
12602720 TACCCTCGATTTATAGAATTATCATTT
1 TACCCTCGATTTACAAAATTATCATTT
*
12602747 TACCCTCGATTTACAAAATTACCA-TT
1 TACCCTCGATTTACAAAATTATCATTT
* * *
12602773 TGCCCTC-AGTTACAAAATTATCGTTT
1 TACCCTCGATTTACAAAATTATCATTT
12602799 TACCCTCGATT
1 TACCCTCGATT
12602810 GTGAAATTAC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
25 13 0.25
26 16 0.31
27 23 0.44
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTATCATTT
Found at i:12602844 original size:27 final size:27
Alignment explanation
Indices: 12602813--12602967 Score: 125
Period size: 27 Copynumber: 5.7 Consensus size: 27
12602803 CTCGATTGTG
*
12602813 AAATTACTGAAATACCCCT-GTAGGATA
1 AAATTACCGAAATACCCCTAGTAGG-TA
* * **
12602840 GAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCGAAATACCCCTAGTAGGTA
**
12602867 AAATTACCGAAATACCCCTAGTTTGTA
1 AAATTACCGAAATACCCCTAGTAGGTA
* * *** *
12602894 AAATTACCGAAATACCACTGGTTTATG
1 AAATTACCGAAATACCCCTAGTAGGTA
* **
12602921 AAATTACCGAAATA-CCCTCAATTTGTA
1 AAATTACCGAAATACCCCT-AGTAGGTA
*
12602948 AAATTACCAAAATACCCCTA
1 AAATTACCGAAATACCCCTA
12602968 ATTTACAAAA
Statistics
Matches: 108, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
26 3 0.03
27 98 0.91
28 7 0.06
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (27 bp):
AAATTACCGAAATACCCCTAGTAGGTA
Found at i:12602879 original size:54 final size:53
Alignment explanation
Indices: 12602813--12602991 Score: 196
Period size: 54 Copynumber: 3.3 Consensus size: 53
12602803 CTCGATTGTG
* ** * *
12602813 AAATTACTGAAATACCCCTGTAGGATAGAATTACCAAAATACCCCTAGTTTGTA
1 AAATTACCGAAATACCCCTGTTTG-TAAAATTACCAAAATACCCCTAGTTTATA
* * * *
12602867 AAATTACCGAAATACCCCTAGTTTGTAAAATTACCGAAATACCACTGGTTTATG
1 AAATTACCGAAATACCCCT-GTTTGTAAAATTACCAAAATACCCCTAGTTTATA
** * *
12602921 AAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTAATTTACA
1 AAATTACCGAAATACCC-CTGTTTGTAAAATTACCAAAATACCCCTAGTTTATA
**
12602975 AAATTACAAAAATACCC
1 AAATTACCGAAATACCC
12602992 ATGACTTTCT
Statistics
Matches: 104, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
54 100 0.96
55 4 0.04
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (53 bp):
AAATTACCGAAATACCCCTGTTTGTAAAATTACCAAAATACCCCTAGTTTATA
Found at i:12602907 original size:81 final size:81
Alignment explanation
Indices: 12602808--12602991 Score: 203
Period size: 81 Copynumber: 2.3 Consensus size: 81
12602798 TTACCCTCGA
* * *
12602808 TTGTGAAATTACTGAAATACCCCTGTAGGATA-G-AATTACCAAAATACCC-CTAGTTTGTAAAA
1 TTGTAAAATTACAGAAATACCCCTG--GGATATGAAATTACCAAAATACCCTC-AATTTGTAAAA
* *
12602870 TTACCGAAATACCCCTAGT
63 TTACCAAAATACCCCTAAT
* * ** *
12602889 TTGTAAAATTACCGAAATACCACTGGTTTATGAAATTACCGAAATACCCTCAATTTGTAAAATTA
1 TTGTAAAATTACAGAAATACCCCTGGGATATGAAATTACCAAAATACCCTCAATTTGTAAAATTA
12602954 CCAAAATACCCCTAAT
66 CCAAAATACCCCTAAT
** *
12602970 TTACAAAATTACAAAAATACCC
1 TTGTAAAATTACAGAAATACCC
12602992 ATGACTTTCT
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
79 3 0.03
80 1 0.01
81 81 0.94
82 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (81 bp):
TTGTAAAATTACAGAAATACCCCTGGGATATGAAATTACCAAAATACCCTCAATTTGTAAAATTA
CCAAAATACCCCTAAT
Found at i:12602970 original size:27 final size:27
Alignment explanation
Indices: 12602841--12602991 Score: 178
Period size: 27 Copynumber: 5.6 Consensus size: 27
12602831 TGTAGGATAG
12602841 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
*
12602868 AATTACCGAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * * * *
12602895 AATTACCGAAATACCACTGGTTTATGA
1 AATTACCAAAATACCCCTAGTTTGTAA
* *
12602922 AATTACCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
* **
12602949 AATTACCAAAATACCCCTAATTTACAA
1 AATTACCAAAATACCCCTAGTTTGTAA
*
12602976 AATTACAAAAATACCC
1 AATTACCAAAATACCC
12602992 ATGACTTTCT
Statistics
Matches: 108, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
26 3 0.03
27 101 0.94
28 4 0.04
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:12603042 original size:27 final size:27
Alignment explanation
Indices: 12603003--12603054 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
12602993 TGACTTTCTA
12603003 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
12603030 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
12603055 GTAGGATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:12603150 original size:27 final size:27
Alignment explanation
Indices: 12603086--12603150 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
12603076 ACCCCTAATA
* *
12603086 GGTAAAAAGACCGTAAAGCCTCTGTAG
1 GGTAAAATGACCGTAAACCCTCTGTAG
* *
12603113 GGTAAAGTGACCGTAATACCCT-TGTAT
1 GGTAAAATGACCGTAA-ACCCTCTGTAG
12603140 GGTAAAATGAC
1 GGTAAAATGAC
12603151 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 28 0.88
28 4 0.12
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.23
Consensus pattern (27 bp):
GGTAAAATGACCGTAAACCCTCTGTAG
Found at i:12604709 original size:42 final size:42
Alignment explanation
Indices: 12604650--12604743 Score: 179
Period size: 42 Copynumber: 2.2 Consensus size: 42
12604640 TAGTCTCCCC
*
12604650 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
12604692 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
12604734 AAATGGGCTT
1 AAATGGGCTT
12604744 AAGGGCCATA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:12604792 original size:32 final size:30
Alignment explanation
Indices: 12604756--12604817 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
12604746 GGGCCATACC
*
12604756 ATTTACAGTAAAGGCTTCGACCCAGTGATATG
1 ATTTA-AGGAAAGGCTTCGACCCAGT-ATATG
* *
12604788 ATTTATGGAAAGGCTTCGGCCCAGTATATG
1 ATTTAAGGAAAGGCTTCGACCCAGTATATG
12604818 TCAAGACTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 5 0.19
31 17 0.63
32 5 0.19
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (30 bp):
ATTTAAGGAAAGGCTTCGACCCAGTATATG
Found at i:12606467 original size:25 final size:25
Alignment explanation
Indices: 12606439--12606486 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
12606429 TCCGATGGTT
* * *
12606439 GTCTTCGAGTGTTTTCTGTCTTCGA
1 GTCTTCAAGTGATTTCTGCCTTCGA
*
12606464 GTCTTTAAGTGATTTCTGCCTTC
1 GTCTTCAAGTGATTTCTGCCTTC
12606487 TACTCTCTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.48
Consensus pattern (25 bp):
GTCTTCAAGTGATTTCTGCCTTCGA
Found at i:12606526 original size:16 final size:16
Alignment explanation
Indices: 12606505--12606538 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
12606495 ATGTCCTCCT
12606505 TGATCCTCTTCTAGGA
1 TGATCCTCTTCTAGGA
12606521 TGATCCTCTTCTAGGA
1 TGATCCTCTTCTAGGA
12606537 TG
1 TG
12606539 TTTATATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.38
Consensus pattern (16 bp):
TGATCCTCTTCTAGGA
Found at i:12608392 original size:18 final size:18
Alignment explanation
Indices: 12608371--12608430 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
12608361 CAAAATAGAC
* *
12608371 ATAACAAGAAGAATAAAA
1 ATAAAAAGAAAAATAAAA
*
12608389 ATAAAAATAAAAATAAAA
1 ATAAAAAGAAAAATAAAA
* *
12608407 ATAAGAAGAAAAGATAGAA
1 ATAAAAAGAAAA-ATAAAA
12608426 ATAAA
1 ATAAA
12608431 CATTAACATA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
18 25 0.74
19 9 0.26
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.13
Consensus pattern (18 bp):
ATAAAAAGAAAAATAAAA
Found at i:12608400 original size:5 final size:6
Alignment explanation
Indices: 12608382--12608459 Score: 66
Period size: 6 Copynumber: 12.8 Consensus size: 6
12608372 TAACAAGAAG
* * *
12608382 AATAAA AATAAA AATAAA AATAAA AATAAG AAGAAA AGATAGA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA A-ATAAA AATAAA
* * * * * *
12608431 CATTAA CATAAA CATAAA CATAGA AATAA
1 AATAAA AATAAA AATAAA AATAAA AATAA
12608460 TCAGACTCAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
6 55 0.93
7 4 0.07
ACGTcount: A:0.72, C:0.05, G:0.06, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:12610423 original size:31 final size:31
Alignment explanation
Indices: 12610379--12610441 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
12610369 TTTAACGGTT
* *
12610379 ACTGGGCATAAGCCTTTTCATAAATCATATC
1 ACTGGGCAGAAGCCTTATCATAAATCATATC
*
12610410 ACTGGGCCGAAGCCTTATCATAAATCATATC
1 ACTGGGCAGAAGCCTTATCATAAATCATATC
12610441 A
1 A
12610442 ACAGGGGCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (31 bp):
ACTGGGCAGAAGCCTTATCATAAATCATATC
Found at i:12611441 original size:27 final size:27
Alignment explanation
Indices: 12611411--12611720 Score: 184
Period size: 27 Copynumber: 11.4 Consensus size: 27
12611401 GTAAATCTAC
* * *
12611411 AAACCAAAGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTAT
** *
12611438 AAACCAATAGTATTTCTA-TAATTTTTAG
1 AAACCAAGGGTATTT-TAGTAA-TTTTAT
* *
12611466 AAAGTCAAGGGTATTTCT-GTAATTTTGT
1 AAA-CCAAGGGTATTT-TAGTAATTTTAT
* * *
12611494 AAATC-AGCGGTATTTTGGTAATTTTAC
1 AAACCAAG-GGTATTTTAGTAATTTTAT
*** * *
12611521 AAATTGAGGGTATTTCT-GTAATTTCAC
1 AAACCAAGGGTATTT-TAGTAATTTTAT
* * *
12611548 AAACCAATGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTTAGTAATTTTAT
* * * *
12611575 AAACTAGGGGTATTTTTGTAATTTTAC
1 AAACCAAGGGTATTTTAGTAATTTTAT
* *
12611602 AAACC-AGAGGTATTTTAGCAATTTTAC
1 AAACCAAG-GGTATTTTAGTAATTTTAT
* *
12611629 AGACC-AGGGTATTTTGGTAATTTTACT
1 AAACCAAGGGTATTTTAGTAATTTTA-T
* * * * *
12611656 -GATCGAGGGTATTTTGGTAATTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTAT
*
12611682 AAACCAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTAT
* *
12611709 AAATCGAGGGTA
1 AAACCAAGGGTA
12611721 AAACAGTAAT
Statistics
Matches: 231, Mismatches: 39, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
26 25 0.11
27 174 0.75
28 18 0.08
29 14 0.06
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.40
Consensus pattern (27 bp):
AAACCAAGGGTATTTTAGTAATTTTAT
Found at i:12611596 original size:81 final size:80
Alignment explanation
Indices: 12611502--12611705 Score: 218
Period size: 80 Copynumber: 2.5 Consensus size: 80
12611492 GTAAATCAGC
** * *
12611502 GGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTCT-GTAATTTCACAAACCAATGGTATTTTG
1 GGTATTTTGGTAATTTTACAAACCAGA-GGTATTT-TAGCAATTTCACAAACC-AGGGTATTTTG
12611565 GTAATTTTACAAACTAGG
63 GTAATTTTACAAACTAGG
* * *
12611583 GGTATTTTTGTAATTTTACAAACCAGAGGTATTTTAGCAATTTTACAGACCAGGGTATTTTGGTA
1 GGTATTTTGGTAATTTTACAAACCAGAGGTATTTTAGCAATTTCACAAACCAGGGTATTTTGGTA
** *
12611648 ATTTTACTGA-TCGAG
66 ATTTTACAAACTAG-G
** *
12611663 GGTATTTTGGTAATTTTGTAAACCA-AGGGTATTTTAGTAATTT
1 GGTATTTTGGTAATTTTACAAACCAGA-GGTATTTTAGCAATTT
12611706 TGTAAATCGA
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
79 3 0.03
80 60 0.57
81 40 0.38
82 2 0.02
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (80 bp):
GGTATTTTGGTAATTTTACAAACCAGAGGTATTTTAGCAATTTCACAAACCAGGGTATTTTGGTA
ATTTTACAAACTAGG
Found at i:12611676 original size:80 final size:82
Alignment explanation
Indices: 12611471--12611706 Score: 245
Period size: 81 Copynumber: 2.9 Consensus size: 82
12611461 TTTAGAAAGT
** * **
12611471 CAAGGGTATTTCT-GTAATTTTGTAAATC-AGCGGTATTTTGGTAATTTTACAAA-TTGAGGGTA
1 CAAGGGTATTT-TGGTAATTTTACAAA-CGAGGGGTATTTTGGTAATTTTACAAACCAGAGGGTA
*
12611533 TTTCT-GTAATTTCACAAAC
64 TTT-TAGTAATTTTACAAAC
* * *
12611552 CAATGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTTGTAATTTTACAAACCAGA-GGTATT
1 CAAGGGTATTTTGGTAATTTTACAAACGAGGGGTATTTTGGTAATTTTACAAACCAGAGGGTATT
* *
12611616 TTAGCAATTTTACAGAC
66 TTAGTAATTTTACAAAC
* * **
12611633 C-AGGGTATTTTGGTAATTTTACTGATCGA-GGGTATTTTGGTAATTTTGTAAACCA-AGGGTAT
1 CAAGGGTATTTTGGTAATTTTAC-AAACGAGGGGTATTTTGGTAATTTTACAAACCAGAGGGTAT
12611695 TTTAGTAATTTT
65 TTTAGTAATTTT
12611707 GTAAATCGAG
Statistics
Matches: 131, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
79 1 0.01
80 62 0.47
81 66 0.50
82 2 0.02
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (82 bp):
CAAGGGTATTTTGGTAATTTTACAAACGAGGGGTATTTTGGTAATTTTACAAACCAGAGGGTATT
TTAGTAATTTTACAAAC
Found at i:12611715 original size:54 final size:53
Alignment explanation
Indices: 12611391--12611720 Score: 220
Period size: 54 Copynumber: 6.1 Consensus size: 53
12611381 CATCCTACCG
* * * * * * * *
12611391 GGGTGTTTTGGTAAATCTACAAACCAAAGGTATTTCAGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTT-TGTAATTTTATAAATCGA
** * * * *
12611445 TAGTATTTCT-ATAATTTTTAGAAAGTCAAGGGTATTTCTGTAATTTTGTAAATC-A
1 GGGTATTT-TGGTAA-TTTTACAAA-CCAAGGGTATTT-TGTAATTTTATAAATCGA
*** * * * *
12611500 GCGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCTGTAATTTCACAAACCAA
1 G-GGTATTTTGGTAATTTTACAAACCAAGGGTATTT-TGTAATTTTATAAATCGA
* * * * *
12611555 TGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTTGTAATTTTACAAA-CCA
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTA-TTTTGTAATTTTATAAATCGA
* * * *
12611608 GAGGTATTTTAGCAATTTTACAGACC-AGGGTATTTTGGTAATTTTACT-GATCGA
1 G-GGTATTTTGGTAATTTTACAAACCAAGGGTATTTT-GTAATTTTA-TAAATCGA
** *
12611662 GGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTT-GTAATTTTATAAATCGA
12611716 GGGTA
1 GGGTA
12611721 AAACAGTAAT
Statistics
Matches: 219, Mismatches: 44, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
52 4 0.02
53 37 0.17
54 123 0.56
55 21 0.10
56 34 0.16
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (53 bp):
GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGTAATTTTATAAATCGA
Found at i:12611728 original size:27 final size:27
Alignment explanation
Indices: 12611697--12611800 Score: 145
Period size: 27 Copynumber: 3.9 Consensus size: 27
12611687 AAGGGTATTT
*
12611697 TAGTAATTTTGTAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* * *
12611724 CAGTAATTCTGTAAATCAATGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
*
12611751 TAGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCGAGGGTAAAA
* *
12611778 TGGTAATTGTGTAAATCGAGGGT
1 TAGTAATTCTGTAAATCGAGGGT
12611801 NCGAAGTAGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (27 bp):
TAGTAATTCTGTAAATCGAGGGTAAAA
Found at i:12611793 original size:54 final size:54
Alignment explanation
Indices: 12611670--12611800 Score: 154
Period size: 54 Copynumber: 2.4 Consensus size: 54
12611660 GAGGGTATTT
* * *** * *
12611670 TGGTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAA
1 TGGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAA
** *
12611724 CAGTAATTCTGTAAATCAATGGTAAAATAGTAATTCTATAAATCGAGGGTAAAA
1 TGGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAA
* *
12611778 TGGTAATTGTGTAAATCGAGGGT
1 TGGTAATTCTGTAAATCAAGGGT
12611801 NCGAAGTAGC
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (54 bp):
TGGTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAA
Found at i:12613096 original size:21 final size:20
Alignment explanation
Indices: 12613051--12613096 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
12613041 AATGAAATAA
*
12613051 AAAATAAGAATTAAAGAAAG
1 AAAATAAGAAATAAAGAAAG
*
12613071 AAAATAAAGAAATAAAGAATG
1 AAAAT-AAGAAATAAAGAAAG
12613092 AAAAT
1 AAAAT
12613097 GAAACAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (20 bp):
AAAATAAGAAATAAAGAAAG
Found at i:12620563 original size:38 final size:38
Alignment explanation
Indices: 12620521--12620594 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
12620511 CAAAGTAAGC
12620521 TATAAAGCTTAGTAAGTTCGCTAGCATTTAAATCAAGT
1 TATAAAGCTTAGTAAGTTCGCTAGCATTTAAATCAAGT
*
12620559 TATAAAGTTTAGTAAGTTCGCTAGCATTTAAATCAA
1 TATAAAGCTTAGTAAGTTCGCTAGCATTTAAATCAA
12620595 CTCATCATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (38 bp):
TATAAAGCTTAGTAAGTTCGCTAGCATTTAAATCAAGT
Found at i:12631899 original size:29 final size:29
Alignment explanation
Indices: 12631828--12631943 Score: 121
Period size: 29 Copynumber: 4.1 Consensus size: 29
12631818 ACCCCTACAT
*
12631828 ACATGCATATGGCCCACTT-GGCCC--ATC
1 ACATTCATATGGCCCA-TTAGGCCCAAATC
* * * *
12631855 TCATTCATATGTCCCATCAGGCCCAATTC
1 ACATTCATATGGCCCATTAGGCCCAAATC
*
12631884 ATATTCATATGGCCCATTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
* * *
12631913 ACCTTTATATGGCCCGTTAGGCCCAAATC
1 ACATTCATATGGCCCATTAGGCCCAAATC
12631942 AC
1 AC
12631944 CATATATTCA
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
26 1 0.01
27 18 0.25
29 53 0.74
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.27
Consensus pattern (29 bp):
ACATTCATATGGCCCATTAGGCCCAAATC
Found at i:12632207 original size:16 final size:16
Alignment explanation
Indices: 12632167--12632213 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
12632157 CAAACTTTCA
*
12632167 GCTTTTCGACATTTTG
1 GCTTTTCGGCATTTTG
*
12632183 ACTTTTCGGCATTTTG
1 GCTTTTCGGCATTTTG
12632199 GCTTTTCGGC-TTTTG
1 GCTTTTCGGCATTTTG
12632214 CCGATCTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 5 0.18
16 23 0.82
ACGTcount: A:0.09, C:0.19, G:0.21, T:0.51
Consensus pattern (16 bp):
GCTTTTCGGCATTTTG
Found at i:12633946 original size:14 final size:14
Alignment explanation
Indices: 12633927--12633959 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
12633917 TGCTCGATCG
12633927 GGCCCATTAACTCT
1 GGCCCATTAACTCT
12633941 GGCCCATTAACTCT
1 GGCCCATTAACTCT
12633955 GGCCC
1 GGCCC
12633960 TAGCGCTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.39, G:0.18, T:0.24
Consensus pattern (14 bp):
GGCCCATTAACTCT
Found at i:12636362 original size:29 final size:29
Alignment explanation
Indices: 12636310--12636397 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
12636300 TGGCCCATCT
* ** *
12636310 CATTCATATGGCCCATCAACCCCAATTCA
1 CATTCATATGGCCCATTAGGCCCAAATCA
* *
12636339 TATTCATATGGCCCATTAGGCCCAAATCG
1 CATTCATATGGCCCATTAGGCCCAAATCA
* * *
12636368 CCTTTATATGGCCCGTTAGGCCCAAATCA
1 CATTCATATGGCCCATTAGGCCCAAATCA
12636397 C
1 C
12636398 CATATATTCA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.26
Consensus pattern (29 bp):
CATTCATATGGCCCATTAGGCCCAAATCA
Found at i:12640326 original size:29 final size:27
Alignment explanation
Indices: 12640262--12640337 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 27
12640252 TACATACATG
*
12640262 CATATGGCCCA-CTTGGCCCATCTCATT
1 CATATGGCCCATC-AGGCCCATCTCATT
*
12640289 CATATGGCCCATCAGGCCCATTTCATATT
1 CATATGGCCCATCAGGCCCATCTC--ATT
*
12640318 CATATGGCCCATTAGGCCCA
1 CATATGGCCCATCAGGCCCA
12640338 AATCACCTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 20 0.47
28 1 0.02
29 22 0.51
ACGTcount: A:0.22, C:0.34, G:0.16, T:0.28
Consensus pattern (27 bp):
CATATGGCCCATCAGGCCCATCTCATT
Found at i:12640351 original size:29 final size:29
Alignment explanation
Indices: 12640290--12640379 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
12640280 CATCTCATTC
* ** ** *
12640290 ATATGGCCCATCAGGCCCATTTCATATTC
1 ATATGGCCCATTAGGCCCAAATCACCTTT
12640319 ATATGGCCCATTAGGCCCAAATCACCTTT
1 ATATGGCCCATTAGGCCCAAATCACCTTT
* *
12640348 ATATGGACCGTTAGGCCCAAATCACC-TT
1 ATATGGCCCATTAGGCCCAAATCACCTTT
12640376 ATAT
1 ATAT
12640380 TCATGCTTAC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 6 0.11
29 47 0.89
ACGTcount: A:0.28, C:0.29, G:0.14, T:0.29
Consensus pattern (29 bp):
ATATGGCCCATTAGGCCCAAATCACCTTT
Found at i:12640632 original size:16 final size:16
Alignment explanation
Indices: 12640590--12640633 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
12640580 CGTAGCCAAA
*
12640590 ATTTTGCCTTTTCAGC
1 ATTTTGACTTTTCAGC
*
12640606 ATTTCGACTTTTCAGC
1 ATTTTGACTTTTCAGC
*
12640622 ATTTTGGCTTTT
1 ATTTTGACTTTT
12640634 TGGCTTTTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.14, C:0.20, G:0.14, T:0.52
Consensus pattern (16 bp):
ATTTTGACTTTTCAGC
Found at i:12641185 original size:156 final size:156
Alignment explanation
Indices: 12640901--12641212 Score: 624
Period size: 156 Copynumber: 2.0 Consensus size: 156
12640891 GACTCATATC
12640901 TAACACAAGCCCCCTTACCTTAACTATGACCATTCGGCCAACTAAGATTAAGAGTACTTACCAAC
1 TAACACAAGCCCCCTTACCTTAACTATGACCATTCGGCCAACTAAGATTAAGAGTACTTACCAAC
12640966 GTCTCTCACCTGAAGAGCAAATCGGCAGGGATCTAAAAACTGAAATTCGATACCTATTCCTACCC
66 GTCTCTCACCTGAAGAGCAAATCGGCAGGGATCTAAAAACTGAAATTCGATACCTATTCCTACCC
12641031 AAAAATCGATTAGAAGAAGTGAGGAA
131 AAAAATCGATTAGAAGAAGTGAGGAA
12641057 TAACACAAGCCCCCTTACCTTAACTATGACCATTCGGCCAACTAAGATTAAGAGTACTTACCAAC
1 TAACACAAGCCCCCTTACCTTAACTATGACCATTCGGCCAACTAAGATTAAGAGTACTTACCAAC
12641122 GTCTCTCACCTGAAGAGCAAATCGGCAGGGATCTAAAAACTGAAATTCGATACCTATTCCTACCC
66 GTCTCTCACCTGAAGAGCAAATCGGCAGGGATCTAAAAACTGAAATTCGATACCTATTCCTACCC
12641187 AAAAATCGATTAGAAGAAGTGAGGAA
131 AAAAATCGATTAGAAGAAGTGAGGAA
12641213 CAATAATCGA
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 156 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (156 bp):
TAACACAAGCCCCCTTACCTTAACTATGACCATTCGGCCAACTAAGATTAAGAGTACTTACCAAC
GTCTCTCACCTGAAGAGCAAATCGGCAGGGATCTAAAAACTGAAATTCGATACCTATTCCTACCC
AAAAATCGATTAGAAGAAGTGAGGAA
Found at i:12644093 original size:18 final size:18
Alignment explanation
Indices: 12644046--12644099 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 18
12644036 GAAATTTGAG
* *
12644046 AATAAAAAACAAATAA-A
1 AATAAGAAATAAATAAGA
12644063 AATAAGAAATAAATAAGA
1 AATAAGAAATAAATAAGA
*
12644081 AAT-AGAAATTAAAGAAGA
1 AATAAGAAA-TAAATAAGA
12644099 A
1 A
12644100 TAAAGTGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 19 0.59
18 13 0.41
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.15
Consensus pattern (18 bp):
AATAAGAAATAAATAAGA
Found at i:12644253 original size:30 final size:31
Alignment explanation
Indices: 12644219--12644292 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
12644209 TAAACCCTCG
* * *
12644219 AAGAAAT-AGTCCTTGGAAAATTGAAGGGTA
1 AAGAAATGAATCCCTGGAAAATTGAAAGGTA
12644249 AAG-AATGAATCCCTGGAAAATTGAAAGGTA
1 AAGAAATGAATCCCTGGAAAATTGAAAGGTA
12644279 AAG-AATGAATCCCT
1 AAGAAATGAATCCCT
12644293 CCATCTCTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 3 0.08
30 37 0.93
ACGTcount: A:0.45, C:0.11, G:0.23, T:0.22
Consensus pattern (31 bp):
AAGAAATGAATCCCTGGAAAATTGAAAGGTA
Found at i:12645025 original size:16 final size:17
Alignment explanation
Indices: 12644992--12645025 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12644982 ATATTTGTCC
*
12644992 TCAAATCTTGTCTTTGA
1 TCAAATCTTGTATTTGA
12645009 TCAAATCTTG-ATTTGA
1 TCAAATCTTGTATTTGA
12645025 T
1 T
12645026 TTGCTTGGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (17 bp):
TCAAATCTTGTATTTGA
Found at i:12648744 original size:20 final size:21
Alignment explanation
Indices: 12648703--12648749 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
12648693 AAAATAATAA
*
12648703 AATAATA-AGAGCTAATAAAT
1 AATAATATTGAGCTAATAAAT
* *
12648723 AA-AATATTGAGCTTATATAT
1 AATAATATTGAGCTAATAAAT
12648743 AATAATA
1 AATAATA
12648750 ATTAATCCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 4 0.18
20 14 0.64
21 4 0.18
ACGTcount: A:0.55, C:0.04, G:0.09, T:0.32
Consensus pattern (21 bp):
AATAATATTGAGCTAATAAAT
Found at i:12650295 original size:17 final size:17
Alignment explanation
Indices: 12650270--12650308 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
12650260 AGTATTAGGA
*
12650270 TTGAGTATGCTTGAATT
1 TTGAATATGCTTGAATT
12650287 TTGAATATGCTTGAATT
1 TTGAATATGCTTGAATT
12650304 TTGAA
1 TTGAA
12650309 GTTTTATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.46
Consensus pattern (17 bp):
TTGAATATGCTTGAATT
Found at i:12650944 original size:25 final size:25
Alignment explanation
Indices: 12650916--12651023 Score: 114
Period size: 25 Copynumber: 4.3 Consensus size: 25
12650906 CACAGCTCTT
12650916 ATGAGCTTCCCGATATTCAACTCGC
1 ATGAGCTTCCCGATATTCAACTCGC
* *
12650941 ATGAGCTTCCCGTTATACAACTCGC
1 ATGAGCTTCCCGATATTCAACTCGC
* **
12650966 ATGAGCTTCCCGTTATAT-AGGTCGC
1 ATGAGCTTCCCGATAT-TCAACTCGC
*
12650991 ATGAGCTTCCC-ATTATTCAAATCAG-
1 ATGAGCTTCCCGA-TATTCAACTC-GC
12651016 ATGAGCTT
1 ATGAGCTT
12651024 TCCGTCTCCA
Statistics
Matches: 71, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.01
25 69 0.97
26 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.31
Consensus pattern (25 bp):
ATGAGCTTCCCGATATTCAACTCGC
Found at i:12659167 original size:25 final size:25
Alignment explanation
Indices: 12659139--12659242 Score: 84
Period size: 25 Copynumber: 4.2 Consensus size: 25
12659129 CCTGATACTT
12659139 AACTCGCATGAGCTTCCCGTTATAC
1 AACTCGCATGAGCTTCCCGTTATAC
* * * **
12659164 AACTCGCATGAGTTTCTCATTATTT
1 AACTCGCATGAGCTTCCCGTTATAC
* * **
12659189 AGCTCGTATGAGCTTCCCGTTATTT
1 AACTCGCATGAGCTTCCCGTTATAC
* * * *
12659214 AGCTTGGAGGAGCTTCCCGTT-TAC
1 AACTCGCATGAGCTTCCCGTTATAC
12659238 AACTC
1 AACTC
12659243 ATATGAGAAT
Statistics
Matches: 62, Mismatches: 17, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
24 4 0.06
25 58 0.94
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (25 bp):
AACTCGCATGAGCTTCCCGTTATAC
Found at i:12660051 original size:20 final size:20
Alignment explanation
Indices: 12660019--12660056 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12660009 TGTTTCACAT
12660019 TCATATAACTAATATTTATA
1 TCATATAACTAATATTTATA
*
12660039 TCAT-TAACATAATTTTTA
1 TCATATAAC-TAATATTTA
12660057 ACTTAATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
TCATATAACTAATATTTATA
Found at i:12660567 original size:18 final size:18
Alignment explanation
Indices: 12660544--12660584 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12660534 TACTTTTCTC
12660544 TTTCTA-TCACAATTCCAA
1 TTTCTATTCACAATT-CAA
*
12660562 TTTCTATTCATAATTCAA
1 TTTCTATTCACAATTCAA
12660580 TTTCT
1 TTTCT
12660585 TTTTTTTTNN
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.29, C:0.22, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTCTATTCACAATTCAA
Found at i:12663201 original size:27 final size:27
Alignment explanation
Indices: 12663171--12663257 Score: 83
Period size: 26 Copynumber: 3.3 Consensus size: 27
12663161 AATTATCTGA
12663171 TCTGGTGGCTCAGCCACATATATATGT
1 TCTGGTGGCTCAGCCACATATATATGT
* *
12663198 TCTGGTGG-T-ATGCCACGAT-TATCTGA
1 TCTGGTGGCTCA-GCCAC-ATATATATGT
* *
12663224 TCTGGTGGCTCTGCCACA-ATATTTGT
1 TCTGGTGGCTCAGCCACATATATATGT
12663250 ATCTGGTG
1 -TCTGGTG
12663258 ACTTCGTCAC
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
25 1 0.02
26 25 0.51
27 23 0.47
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCAGCCACATATATATGT
Found at i:12663226 original size:53 final size:54
Alignment explanation
Indices: 12663145--12663257 Score: 167
Period size: 53 Copynumber: 2.1 Consensus size: 54
12663135 AGGAAGCGTC
*
12663145 CTGGTGGCTATGCTACAATTATCTGATCTGGTGGCTCAGCCACATATATATGT-T
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCAGCCACA-ATATATGTAT
* * *
12663199 CTGGTGG-TATGCCACGATTATCTGATCTGGTGGCTCTGCCACAATATTTGTAT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCAGCCACAATATATGTAT
12663252 CTGGTG
1 CTGGTG
12663258 ACTTCGTCAC
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
52 7 0.13
53 40 0.74
54 7 0.13
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.35
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCAGCCACAATATATGTAT
Found at i:12663274 original size:53 final size:52
Alignment explanation
Indices: 12663145--12663275 Score: 140
Period size: 53 Copynumber: 2.4 Consensus size: 52
12663135 AGGAAGCGTC
*
12663145 CTGGTGGCTATGCTACAATTATCTGATCTGGTGGCTCAGCCACATATATATGTT
1 CTGGT-GCTATGCCACAA-TATCTGATCTGGTGGCTCAGCCACATATATATGTT
* * * *
12663199 CTGGTGGTATGCCACGATTATCTGATCTGGTGGCTCTGCCACA-ATATTTGTAT
1 CTGGTGCTATGCCAC-AATATCTGATCTGGTGGCTCAGCCACATATATATGT-T
*
12663252 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTG-CTAT-GCCACAATATCTG
12663276 CCAGCCTCGC
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
52 7 0.11
53 47 0.72
54 11 0.17
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (52 bp):
CTGGTGCTATGCCACAATATCTGATCTGGTGGCTCAGCCACATATATATGTT
Found at i:12663995 original size:12 final size:12
Alignment explanation
Indices: 12663980--12664010 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
12663970 TTCTCTTTTA
12663980 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
12663992 TTTTTCTTTCTC
1 TTTTTCTTTCCC
12664004 TTTTTCT
1 TTTTTCT
12664011 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:12669869 original size:20 final size:20
Alignment explanation
Indices: 12669837--12669874 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12669827 TGTTTCACAT
12669837 TCATATAACTAATATTTATA
1 TCATATAACTAATATTTATA
*
12669857 TCAT-TAACATAATTTTTA
1 TCATATAAC-TAATATTTA
12669875 ACTTAATAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
TCATATAACTAATATTTATA
Found at i:12670384 original size:18 final size:18
Alignment explanation
Indices: 12670361--12670401 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12670351 TACTTTTCTC
12670361 TTTCTA-TCACAATTCTAA
1 TTTCTATTCACAATTC-AA
*
12670379 TTTCTATTCATAATTCAA
1 TTTCTATTCACAATTCAA
12670397 TTTCT
1 TTTCT
12670402 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTCTATTCACAATTCAA
Found at i:12670588 original size:38 final size:39
Alignment explanation
Indices: 12670504--12670638 Score: 116
Period size: 39 Copynumber: 3.4 Consensus size: 39
12670494 ACCAATATGG
*
12670504 CACCCAGTGCCTCATCGGATAGTTCGAAGTAATAGTTGA
1 CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
* * *
12670543 CACCCAGTGTCTCATCGGCCTAG-CCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-ATAGTCCGAAGTAATAGTTGA
* * * *
12670581 TACCCAGTACCTCATCGAATCTA-TCCGAAGAAATTTAG-TGA
1 CACCCAGTGCCTCATCGGA--TAGTCCGAAGTAA--TAGTTGA
*
12670622 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
12670639 ACTCGGGGTC
Statistics
Matches: 75, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
38 19 0.25
39 35 0.47
40 3 0.04
41 16 0.21
42 2 0.03
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAGTCCGAAGTAATAGTTGA
Found at i:12671551 original size:6 final size:6
Alignment explanation
Indices: 12671530--12671572 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
12671520 AAATCCTTAG
* * *
12671530 TTTTCT CTTTTAT TTTTCT TTTCCT TTTTCT TTCTCT TTTTCT
1 TTTTCT -TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
12671573 CCCCTGCTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTCT
Found at i:12674976 original size:33 final size:32
Alignment explanation
Indices: 12674923--12675014 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 32
12674913 TAAGACAATG
12674923 CATTAACTATTTTTTTTTTCTTTCTTACACAC
1 CATTAACTATTTTTTTTTTCTTTCTTACACAC
* *
12674955 CATTAACTATTTTTTTCTTTCTTTCTTACGCAG
1 CATTAACTATTTTTTT-TTTCTTTCTTACACAC
12674988 CATTAACTATTTTTTTTTTCTTTCTTA
1 CATTAACTATTTTTTTTTTCTTTCTTA
12675015 TGTAGCCCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 27 0.47
33 30 0.53
ACGTcount: A:0.20, C:0.20, G:0.02, T:0.59
Consensus pattern (32 bp):
CATTAACTATTTTTTTTTTCTTTCTTACACAC
Found at i:12676048 original size:10 final size:12
Alignment explanation
Indices: 12676020--12676045 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12676010 TTTTATACTC
12676020 TTCTGTATATAT
1 TTCTGTATATAT
12676032 TTCTGTATATAT
1 TTCTGTATATAT
12676044 TT
1 TT
12676046 GTACGATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (12 bp):
TTCTGTATATAT
Found at i:12676065 original size:17 final size:18
Alignment explanation
Indices: 12676043--12676078 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
12676033 TCTGTATATA
12676043 TTTGTACGATAAAT-TTT
1 TTTGTACGATAAATATTT
12676060 TTTGTACGATAAATATTT
1 TTTGTACGATAAATATTT
12676078 T
1 T
12676079 AATAATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.31, C:0.06, G:0.11, T:0.53
Consensus pattern (18 bp):
TTTGTACGATAAATATTT
Found at i:12679948 original size:395 final size:394
Alignment explanation
Indices: 12679261--12679996 Score: 1028
Period size: 394 Copynumber: 1.9 Consensus size: 394
12679251 TAGTGCGAAT
* * *
12679261 ACTCCTCTTAATGTGAACATACCCTTTAGGCCACCAAAACCTTACCCGAACACAACAACCATGTA
1 ACTCCTCTTAATGTGAACATACCCTTTAAGCCACCAAAACCCTACCCGAACACAACAACCATATA
* ** * * * *
12679326 CCAAATTCAGAAAGAATGATTGAATGATTTATCATCATGTACATCCCCTTATGCATTCCACAATG
66 CCAAATTCAAAAAGAATGATAAAATGATGTATCATCATGTACATCCCCTCATACATTCCACAATA
* *
12679391 ATGGCTTATTGGTAGTAGATTTACCATGTCAGCACTACCTACCATATATACTTTTAGCACGATGA
131 ATGGCTTATTGGTAGTAGATTTACCATATCAGCACTACCTACCATATATACTTTTAGCACAATGA
* * * * * * * *
12679456 AAAAGGGATCAATCGTTAAATACTCATAGTAATCCTATAGTCCTGAACATTTTCCTTTTCCTTTG
196 AAAAGAGATCAACCCTTAAAGACTCATAGTAACCCTATAGTCATCAACATTTTCCTTCTCCTTTG
* * * * *
12679521 GGTTCTCAACCTTCTTACTTTGCATACCTCCTTTGGCTCTTCACCTTGTTAGGGTGAATCGGCCT
261 AGTTCTCAACCTTCGTACTTTGCATACCTCC-TTGACCCTTCACCTTGCTAGGGTGAATCGGCCT
*
12679586 TTCTCAACACCATCACATCCTTGTGAACAAGCCACCCTCTCCTCAAAGCACCCGCTTTTCTAGTA
325 TCCTCAACACCATCACATCCTTGTGAACAAGCCACCCTCTCCTCAAAGCACCCGCTTTTCTAGTA
12679651 TGAAC
390 TGAAC
* * * * * *
12679656 ACTCCTCTTGATGTGAACATGCCCTTTAAGCTACC-AAACCCTACCTGAACATAACAACCCTATA
1 ACTCCTCTTAATGTGAACATACCCTTTAAGCCACCAAAACCCTACCCGAACACAACAACCATATA
*
12679720 CCACAATTCAAAAAGAATGATAAAATGA-GTCTCATCATGTACATCCCC-CATACATTCCACAAT
66 CCA-AATTCAAAAAGAATGATAAAATGATGTATCATCATGTACATCCCCTCATACATTCCACAAT
*
12679783 AATGGCTTATTGGTAGTAGGTTTACCATATCAGCACTACCTACCATATATACCTTTTAGCACAAT
130 AATGGCTTATTGGTAGTAGATTTACCATATCAGCACTACCTACCATATATA-CTTTTAGCACAAT
*
12679848 GAAAAATAGATCAACCCTTAAAAGACTCATAGTAACCCTATAGTCATCAACATTTTCCTTCTCCT
194 GAAAAAGAGATCAACCCTT-AAAGACTCATAGTAACCCTATAGTCATCAACATTTTCCTTCTCCT
* * * *** * *
12679913 TTTAGTTTTTAGTTTTCGTACTTTGCATGCCTCCTTGACCCTTCACCTTGCTAGGGTGAATTGGC
258 TTGAGTTCTCAACCTTCGTACTTTGCATACCTCCTTGACCCTTCACCTTGCTAGGGTGAATCGGC
12679978 CTTCCTCAACACCATCACA
323 CTTCCTCAACACCATCACA
12679997 ACCTCTTTCT
Statistics
Matches: 295, Mismatches: 43, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
393 61 0.21
394 117 0.40
395 117 0.40
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (394 bp):
ACTCCTCTTAATGTGAACATACCCTTTAAGCCACCAAAACCCTACCCGAACACAACAACCATATA
CCAAATTCAAAAAGAATGATAAAATGATGTATCATCATGTACATCCCCTCATACATTCCACAATA
ATGGCTTATTGGTAGTAGATTTACCATATCAGCACTACCTACCATATATACTTTTAGCACAATGA
AAAAGAGATCAACCCTTAAAGACTCATAGTAACCCTATAGTCATCAACATTTTCCTTCTCCTTTG
AGTTCTCAACCTTCGTACTTTGCATACCTCCTTGACCCTTCACCTTGCTAGGGTGAATCGGCCTT
CCTCAACACCATCACATCCTTGTGAACAAGCCACCCTCTCCTCAAAGCACCCGCTTTTCTAGTAT
GAAC
Found at i:12682278 original size:30 final size:30
Alignment explanation
Indices: 12682234--12682305 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
12682224 GTTTTGGAAT
*
12682234 CTTTAC-AATTTAATCCCTATAATTTCAAA
1 CTTTACTATTTTAATCCCTATAATTTCAAA
12682263 CTTTACTATTTTAATCCCTATAATTTCAAA
1 CTTTACTATTTTAATCCCTATAATTTCAAA
12682293 CTTTACTATTTTA
1 CTTTACTATTTTA
12682306 CGCTCAACCT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
29 6 0.15
30 35 0.85
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.47
Consensus pattern (30 bp):
CTTTACTATTTTAATCCCTATAATTTCAAA
Found at i:12688142 original size:23 final size:22
Alignment explanation
Indices: 12688098--12688142 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
12688088 TAATAATAAA
* **
12688098 TTAATATTTTAAATAATTTTAT
1 TTAATATTTAAAATAAAATTAT
12688120 TTAATTATTTAAAATAAAATTAT
1 TTAA-TATTTAAAATAAAATTAT
12688143 GCTAATTTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAATATTTAAAATAAAATTAT
Found at i:12698505 original size:19 final size:20
Alignment explanation
Indices: 12698481--12698520 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12698471 CACACCAAAC
*
12698481 AAGTAACTCA-TTTCCAGAA
1 AAGTAAATCATTTTCCAGAA
12698500 AAGTAAATCATTTTCCAGAA
1 AAGTAAATCATTTTCCAGAA
12698520 A
1 A
12698521 TCATTTTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.28
Consensus pattern (20 bp):
AAGTAAATCATTTTCCAGAA
Found at i:12698523 original size:14 final size:14
Alignment explanation
Indices: 12698504--12698541 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
12698494 CCAGAAAAGT
12698504 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
12698518 AAATCATTTTCTAG
1 AAATCATTTTCCAG
*
12698532 AAAACATTTT
1 AAATCATTTT
12698542 ACTGGAAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.05, T:0.39
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:12698551 original size:15 final size:14
Alignment explanation
Indices: 12698508--12698552 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
12698498 AAAAGTAAAT
* *
12698508 CATTTTCCAGAAAT
1 CATTTTCTAGAAAA
12698522 CATTTTCTAGAAAA
1 CATTTTCTAGAAAA
*
12698536 CATTTTACTGGAAAA
1 CATTTT-CTAGAAAA
12698551 CA
1 CA
12698553 AACGGAGCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 18 0.67
15 9 0.33
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (14 bp):
CATTTTCTAGAAAA
Found at i:12699882 original size:21 final size:21
Alignment explanation
Indices: 12699858--12699924 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
12699848 TGAGGGTCTC
12699858 ACACACCCATGTGTCAACTAG
1 ACACACCCATGTGTCAACTAG
** * *
12699879 ACACGA-CTGTGTGTTC--CGAA
1 ACAC-ACCCATGTG-TCAACTAG
12699899 ACACACACCATGTGTCAACTAG
1 ACACAC-CCATGTGTCAACTAG
12699921 ACAC
1 ACAC
12699925 GACTGTGTGT
Statistics
Matches: 32, Mismatches: 8, Indels: 11
0.63 0.16 0.22
Matches are distributed among these distances:
19 1 0.03
20 8 0.25
21 14 0.44
22 9 0.28
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.19
Consensus pattern (21 bp):
ACACACCCATGTGTCAACTAG
Found at i:12699910 original size:42 final size:42
Alignment explanation
Indices: 12699857--12699949 Score: 177
Period size: 42 Copynumber: 2.2 Consensus size: 42
12699847 GTGAGGGTCT
12699857 CACACACCCATGTGTCAACTAGACACGACTGTGTGTTCCGAAA
1 CACACA-CCATGTGTCAACTAGACACGACTGTGTGTTCCGAAA
12699900 CACACACCATGTGTCAACTAGACACGACTGTGTGTTCCGAAA
1 CACACACCATGTGTCAACTAGACACGACTGTGTGTTCCGAAA
12699942 CACACACC
1 CACACACC
12699950 CGTGTGAGAT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 44 0.88
43 6 0.12
ACGTcount: A:0.31, C:0.32, G:0.17, T:0.19
Consensus pattern (42 bp):
CACACACCATGTGTCAACTAGACACGACTGTGTGTTCCGAAA
Found at i:12699933 original size:21 final size:21
Alignment explanation
Indices: 12699867--12699934 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
12699857 CACACACCCA
12699867 TGTGTCAACTAGACACGACTG
1 TGTGTCAACTAGACACGACTG
* **
12699888 TGTGTTCCGAA--ACACAC-ACCA
1 TGTG-T-C-AACTAGACACGACTG
12699909 TGTGTCAACTAGACACGACTG
1 TGTGTCAACTAGACACGACTG
12699930 TGTGT
1 TGTGT
12699935 TCCGAAACAC
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 6 0.17
21 17 0.49
22 6 0.17
23 1 0.03
24 2 0.06
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (21 bp):
TGTGTCAACTAGACACGACTG
Found at i:12709822 original size:75 final size:75
Alignment explanation
Indices: 12709699--12709851 Score: 252
Period size: 75 Copynumber: 2.0 Consensus size: 75
12709689 GTCGCATGTT
** * *
12709699 GTGTGCTAAGCTGTGTAACTCACTGACTTAAAACACCTAGAAATTTCAAATGAGACACGGCCATG
1 GTGTGCTAAGCCATGTAACTCACTGACTTAAAACACCTAGAAATTTCAAATGACACAAGGCCATG
12709764 TAGCCAAGCC
66 TAGCCAAGCC
* *
12709774 GTGTGCTAAGCCATGTAACTCACTGACTTAAAACACTTAGAAATTTCAAATGACACAAGGCTATG
1 GTGTGCTAAGCCATGTAACTCACTGACTTAAAACACCTAGAAATTTCAAATGACACAAGGCCATG
12709839 TAGCCAAGCC
66 TAGCCAAGCC
12709849 GTG
1 GTG
12709852 CGTGTCACAT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (75 bp):
GTGTGCTAAGCCATGTAACTCACTGACTTAAAACACCTAGAAATTTCAAATGACACAAGGCCATG
TAGCCAAGCC
Found at i:12710743 original size:21 final size:21
Alignment explanation
Indices: 12710717--12710759 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
12710707 AATCATGAAA
*
12710717 CATTCCATTTCCTTTACTTAC
1 CATTCCATTTCATTTACTTAC
12710738 CATTCCATTTCATTTACTTAC
1 CATTCCATTTCATTTACTTAC
12710759 C
1 C
12710760 CATTGAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.33, G:0.00, T:0.47
Consensus pattern (21 bp):
CATTCCATTTCATTTACTTAC
Found at i:12716240 original size:68 final size:68
Alignment explanation
Indices: 12716161--12716291 Score: 253
Period size: 68 Copynumber: 1.9 Consensus size: 68
12716151 CGGAGTTCCG
*
12716161 TGAATTTATTCGTAACAATATAAACATGAGTTTAATAATTCTAAGTTAAGAAATTTAATTAATTG
1 TGAATTTATTCGTAACAATATAAACATGAGTTTAATAATTCTAAGTTAAGAAATGTAATTAATTG
12716226 CCA
66 CCA
12716229 TGAATTTATTCGTAACAATATAAACATGAGTTTAATAATTCTAAGTTAAGAAATGTAATTAAT
1 TGAATTTATTCGTAACAATATAAACATGAGTTTAATAATTCTAAGTTAAGAAATGTAATTAAT
12716292 CTAACAAATT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.38
Consensus pattern (68 bp):
TGAATTTATTCGTAACAATATAAACATGAGTTTAATAATTCTAAGTTAAGAAATGTAATTAATTG
CCA
Found at i:12719929 original size:13 final size:12
Alignment explanation
Indices: 12719891--12719929 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
12719881 CCCAAACGTC
*
12719891 AAAATTTTCAAA
1 AAAAATTTCAAA
12719903 AAAAATTTCAAA
1 AAAAATTTCAAA
*
12719915 AAAAATTTCACA
1 AAAAATTTCAAA
12719927 AAA
1 AAA
12719930 TCATTTCGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.64, C:0.10, G:0.00, T:0.26
Consensus pattern (12 bp):
AAAAATTTCAAA
Found at i:12720185 original size:11 final size:11
Alignment explanation
Indices: 12720169--12720205 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
12720159 GATGGAATTA
12720169 AGTGAAATTTT
1 AGTGAAATTTT
*
12720180 AGTGAAATTTC
1 AGTGAAATTTT
12720191 AGTGAAATTTCT
1 AGTGAAATTT-T
12720203 AGT
1 AGT
12720206 TGTCCAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 20 0.87
12 3 0.13
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.41
Consensus pattern (11 bp):
AGTGAAATTTT
Found at i:12721594 original size:43 final size:43
Alignment explanation
Indices: 12721478--12721619 Score: 135
Period size: 43 Copynumber: 3.3 Consensus size: 43
12721468 TTTTACTTTT
* * * * * *
12721478 CATGACCTTTAGCGGCGTTTTTAAGAAAAGCACCACTAAAGAA
1 CATGACTTTTAGCGGCATGTTTAGGAAAAGCGCCGCTAAAGAA
* * * *
12721521 AATCACTTTTAGCGGCATTTTTAGGAAAAGCGTCGCTAAAGAA
1 CATGACTTTTAGCGGCATGTTTAGGAAAAGCGCCGCTAAAGAA
*
12721564 CATGACTTTTAGC-G-ATGTTTATGGAGAAAGCGCCGCTAAAGAT
1 CATGACTTTTAGCGGCATGTTTA-GGA-AAAGCGCCGCTAAAGAA
**
12721607 CATGTTTTTTAGC
1 CATGACTTTTAGC
12721620 TGCGCTTTTC
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
41 6 0.07
42 4 0.05
43 72 0.88
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (43 bp):
CATGACTTTTAGCGGCATGTTTAGGAAAAGCGCCGCTAAAGAA
Found at i:12724171 original size:22 final size:22
Alignment explanation
Indices: 12724146--12724190 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
12724136 ATATTTAATC
12724146 CTTTAAAATTTATAAAATTTTA
1 CTTTAAAATTTATAAAATTTTA
12724168 CTTTAAAATTTATAAAATTTTA
1 CTTTAAAATTTATAAAATTTTA
12724190 C
1 C
12724191 ATTATTACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (22 bp):
CTTTAAAATTTATAAAATTTTA
Found at i:12725762 original size:15 final size:15
Alignment explanation
Indices: 12725744--12725803 Score: 84
Period size: 15 Copynumber: 4.0 Consensus size: 15
12725734 TGTCTGATGT
12725744 TGATGTGTCTAATAG
1 TGATGTGTCTAATAG
**
12725759 TGATGTGTCTGTTAG
1 TGATGTGTCTAATAG
*
12725774 TGATGTATCTAATAG
1 TGATGTGTCTAATAG
*
12725789 TTATGTGTCTAATAG
1 TGATGTGTCTAATAG
12725804 GATTAAGGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.43
Consensus pattern (15 bp):
TGATGTGTCTAATAG
Found at i:12725768 original size:30 final size:30
Alignment explanation
Indices: 12725734--12725803 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
12725724 GAAGAAGAAA
*
12725734 TGTCTGAT-GTTGATGTGTCTAATAGTGATG
1 TGTCTGATAG-TGATGTATCTAATAGTGATG
* *
12725764 TGTCTGTTAGTGATGTATCTAATAGTTATG
1 TGTCTGATAGTGATGTATCTAATAGTGATG
*
12725794 TGTCTAATAG
1 TGTCTGATAG
12725804 GATTAAGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.23, C:0.07, G:0.26, T:0.44
Consensus pattern (30 bp):
TGTCTGATAGTGATGTATCTAATAGTGATG
Found at i:12727814 original size:45 final size:45
Alignment explanation
Indices: 12727772--12727870 Score: 153
Period size: 45 Copynumber: 2.2 Consensus size: 45
12727762 AGCAGTAATA
* * *
12727772 GTAACAGTATTCAACACACAAAGTGTTGAATCTGTAACAGTAACG
1 GTAACAGTATTCAACACACAAAATGTCGAATCGGTAACAGTAACG
* *
12727817 GTAACAATATTCGACACACAAAATGTCGAATCGGTAACAGTAACG
1 GTAACAGTATTCAACACACAAAATGTCGAATCGGTAACAGTAACG
12727862 GTAACAGTA
1 GTAACAGTA
12727871 ACAGTAGTCG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (45 bp):
GTAACAGTATTCAACACACAAAATGTCGAATCGGTAACAGTAACG
Found at i:12727865 original size:12 final size:12
Alignment explanation
Indices: 12727848--12727872 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12727838 AATGTCGAAT
12727848 CGGTAACAGTAA
1 CGGTAACAGTAA
12727860 CGGTAACAGTAA
1 CGGTAACAGTAA
12727872 C
1 C
12727873 AGTAGTCGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTAACAGTAA
Found at i:12728158 original size:40 final size:40
Alignment explanation
Indices: 12728082--12728162 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
12728072 CTTCATTAGA
* * *
12728082 AATTTTACAGTTCAATGCAATATACATAACATTATTCAGT
1 AATTTCACAGTTCAATGCAATATACAAAACAATATTCAGT
* ** *
12728122 AATTTCACAGTTCAATTCGGTATTCAAAACAATATTCAGT
1 AATTTCACAGTTCAATGCAATATACAAAACAATATTCAGT
12728162 A
1 A
12728163 TCCCATAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (40 bp):
AATTTCACAGTTCAATGCAATATACAAAACAATATTCAGT
Found at i:12728959 original size:13 final size:13
Alignment explanation
Indices: 12728941--12728981 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
12728931 TTTCTTTTAT
12728941 ATATAATAATAT-
1 ATATAATAATATA
12728953 A-AT-ATAATATA
1 ATATAATAATATA
*
12728964 ATATAAGAATATA
1 ATATAATAATATA
12728977 ATATA
1 ATATA
12728982 CTTAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 7 0.28
11 3 0.12
12 3 0.12
13 12 0.48
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (13 bp):
ATATAATAATATA
Found at i:12728964 original size:18 final size:18
Alignment explanation
Indices: 12728941--12728981 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12728931 TTTCTTTTAT
*
12728941 ATATAATAATATAATATA
1 ATATAATAATAGAATATA
12728959 ATATAAT-ATAAGAATATA
1 ATATAATAAT-AGAATATA
12728977 ATATA
1 ATATA
12728982 CTTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
ATATAATAATAGAATATA
Found at i:12735139 original size:45 final size:45
Alignment explanation
Indices: 12735044--12735141 Score: 126
Period size: 45 Copynumber: 2.2 Consensus size: 45
12735034 GTAGCAGTAG
* *
12735044 CAGTAACAGTAACAATATTCAACACACAAAGTGCTGAATCTATAA
1 CAGTAACAGTAACAATATTCAACACACAAAGTGCTGAAACGATAA
* * *
12735089 CAGTAACGGTAACAATATTCGACACACAAAGTG-TCGAAACGGTAA
1 CAGTAACAGTAACAATATTCAACACACAAAGTGCT-GAAACGATAA
*
12735134 TAGTAACA
1 CAGTAACA
12735142 ATAGTCGGCA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
44 1 0.02
45 44 0.98
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.20
Consensus pattern (45 bp):
CAGTAACAGTAACAATATTCAACACACAAAGTGCTGAAACGATAA
Found at i:12736213 original size:8 final size:8
Alignment explanation
Indices: 12736200--12736246 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
12736190 TTTCTTTTAT
12736200 ATATAATA
1 ATATAATA
12736208 ATATAAT-
1 ATATAATA
12736215 ATA-ATATA
1 ATATA-ATA
12736223 ATA-ATATA
1 ATATA-ATA
12736231 ATATAATA
1 ATATAATA
12736239 ATATAATA
1 ATATAATA
12736247 TACTTAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
6 1 0.03
7 5 0.14
8 29 0.81
9 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATAATA
Found at i:12736215 original size:5 final size:5
Alignment explanation
Indices: 12736205--12736248 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
12736195 TTTATATATA
12736205 ATAAT ATAAT ATAAT AT-A- ATAAT ATAAT AT-A- ATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
12736249 CTTAATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 4 0.11
4 4 0.11
5 27 0.77
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:12736218 original size:13 final size:13
Alignment explanation
Indices: 12736200--12736248 Score: 82
Period size: 13 Copynumber: 3.8 Consensus size: 13
12736190 TTTCTTTTAT
12736200 ATATAATA-ATATA
1 ATATAATATA-ATA
12736213 ATATAATATAATA
1 ATATAATATAATA
12736226 ATATAATATAATA
1 ATATAATATAATA
12736239 ATATAATATA
1 ATATAATATA
12736249 CTTAATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
13 34 0.97
14 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATAATATAATA
Found at i:12736223 original size:18 final size:18
Alignment explanation
Indices: 12736200--12736248 Score: 82
Period size: 18 Copynumber: 2.7 Consensus size: 18
12736190 TTTCTTTTAT
12736200 ATATAATAATATAATATA
1 ATATAATAATATAATATA
12736218 ATATAATAATATAATATA
1 ATATAATAATATAATATA
12736236 ATA-ATATAATATA
1 ATATA-ATAATATA
12736249 CTTAATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
17 1 0.03
18 29 0.97
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAATAATATAATATA
Found at i:12736287 original size:21 final size:22
Alignment explanation
Indices: 12736197--12736287 Score: 73
Period size: 23 Copynumber: 4.0 Consensus size: 22
12736187 TTGTTTCTTT
* *
12736197 TATATATAATAATATAATATAA
1 TATATATATTAATATAATAAAA
*
12736219 TATA-ATAATATAATATAATAATA
1 TATATAT-AT-TAATATAATAAAA
12736242 TA-ATATACTTAATTATTAA-ACAAA
1 TATATATA-TTAA-TA-TAATA-AAA
12736266 TATATATATTAAT-TAATAAAA
1 TATATATATTAATATAATAAAA
12736287 T
1 T
12736288 CTTTGATATT
Statistics
Matches: 56, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
21 9 0.16
22 11 0.20
23 20 0.36
24 11 0.20
25 5 0.09
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TATATATATTAATATAATAAAA
Found at i:12738880 original size:43 final size:43
Alignment explanation
Indices: 12738820--12738910 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
12738810 CTAAATCATG
12738820 CTCA-TAACAACCCACATTTTCCATCAAATCACATTTCTACTA
1 CTCATTAACAACCCACATTTTCCATCAAATCACATTTCTACTA
*
12738862 CTCATTAACAGCCCACATTTTCCATCAAATCACATTTCTACTA
1 CTCATTAACAACCCACATTTTCCATCAAATCACATTTCTACTA
12738905 CTCATT
1 CTCATT
12738911 CTTACAACTT
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 4 0.09
43 43 0.91
ACGTcount: A:0.33, C:0.33, G:0.01, T:0.33
Consensus pattern (43 bp):
CTCATTAACAACCCACATTTTCCATCAAATCACATTTCTACTA
Found at i:12741283 original size:22 final size:22
Alignment explanation
Indices: 12741258--12741315 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 22
12741248 GCTTGAAAGG
12741258 GCTTACTGTTTAGCTCAATAGA
1 GCTTACTGTTTAGCTCAATAGA
*
12741280 GCTTACCAT-TTTCATCTCAATAGA
1 GCTTA-C-TGTTT-AGCTCAATAGA
12741304 GCTTACTGTTTA
1 GCTTACTGTTTA
12741316 TCAGCTTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
22 7 0.23
23 8 0.26
24 16 0.52
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (22 bp):
GCTTACTGTTTAGCTCAATAGA
Found at i:12744269 original size:13 final size:14
Alignment explanation
Indices: 12744251--12744281 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
12744241 TTATCTTTAG
12744251 TTTAAA-TTTGATT
1 TTTAAATTTTGATT
12744264 TTTAAATTTTGATT
1 TTTAAATTTTGATT
12744278 TTTA
1 TTTA
12744282 GTTGATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (14 bp):
TTTAAATTTTGATT
Found at i:12747709 original size:21 final size:21
Alignment explanation
Indices: 12747683--12747735 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
12747673 CAAGTGGTTG
*
12747683 CCCCAACTCAGCAATAGACTA
1 CCCCAACTCAGCAAGAGACTA
* *
12747704 CCCCAAATCAGTAAGAGACTA
1 CCCCAACTCAGCAAGAGACTA
*
12747725 CCCTAACTCAG
1 CCCCAACTCAG
12747736 GAGGAGGTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.36, G:0.11, T:0.15
Consensus pattern (21 bp):
CCCCAACTCAGCAAGAGACTA
Found at i:12756801 original size:13 final size:13
Alignment explanation
Indices: 12756783--12756809 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12756773 AAAGTAATCG
12756783 CACACGGGCGTGT
1 CACACGGGCGTGT
12756796 CACACGGGCGTGT
1 CACACGGGCGTGT
12756809 C
1 C
12756810 CCTGCCGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:12761810 original size:29 final size:29
Alignment explanation
Indices: 12761777--12761962 Score: 185
Period size: 29 Copynumber: 6.4 Consensus size: 29
12761767 ATCATTGAAC
*
12761777 ATGAAAAGGGATAGCTTCGGCTATCGATT
1 ATGAAAAGGGATAGCTTTGGCTATCGATT
* * * *
12761806 ATGAAAAAGGATAGCTTCGACTATCGAAT
1 ATGAAAAGGGATAGCTTTGGCTATCGATT
12761835 ATGAAAAGGGATAGCTTTGGCTATCGATT
1 ATGAAAAGGGATAGCTTTGGCTATCGATT
* * * * * * * *
12761864 ATGACACGGGATCG-TGATGACCATTGAAT
1 ATGAAAAGGGATAGCT-TTGGCTATCGATT
*
12761893 ATGAAAAGGGATAGTTTTGGCTATCGATT
1 ATGAAAAGGGATAGCTTTGGCTATCGATT
* * * *
12761922 ATGAAAATGGATAGTTTTGTCTATCAATT
1 ATGAAAAGGGATAGCTTTGGCTATCGATT
*
12761951 ATGAAAGGGGAT
1 ATGAAAAGGGAT
12761963 GGTGACGACC
Statistics
Matches: 127, Mismatches: 28, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
28 1 0.01
29 125 0.98
30 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.30
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTTGGCTATCGATT
Found at i:12761934 original size:87 final size:87
Alignment explanation
Indices: 12761805--12761987 Score: 224
Period size: 87 Copynumber: 2.1 Consensus size: 87
12761795 GGCTATCGAT
* * *
12761805 TATGAAAAAGGATAGCTTCGACTATCGAATATGAAAAGGGATAGCTTTGGCTATCGATTATGACA
1 TATGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATAGCTTTGGCTATCAATTATGAAA
* *
12761870 CGGGATCGTGATGACCATTGAA-
66 CGGGATCGTGACGACCA-TCAAC
* * * * * * *
12761892 TATGAAAAGGGATAGTTTTGGCTATCGATTATGAAAATGGATAGTTTTGTCTATCAATTATGAAA
1 TATGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATAGCTTTGGCTATCAATTATGAAA
* *
12761957 GGGGATGGTGACGACCATCAAC
66 CGGGATCGTGACGACCATCAAC
12761979 TATGAAAAG
1 TATGAAAAG
12761988 TGATGGTGAC
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
86 3 0.04
87 78 0.96
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.28
Consensus pattern (87 bp):
TATGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATAGCTTTGGCTATCAATTATGAAA
CGGGATCGTGACGACCATCAAC
Found at i:12761954 original size:58 final size:57
Alignment explanation
Indices: 12761777--12761962 Score: 210
Period size: 58 Copynumber: 3.2 Consensus size: 57
12761767 ATCATTGAAC
* * *
12761777 ATGAAAAGGGATAGCTTCGGCTATCGATTATGAAAAAGGATAGCTTCGACTATCGAAT
1 ATGAAAAGGGATAGCTTTGGCTATCGATTATGAAAAAGGATAGTTTTGACTATC-AAT
* ** * ** * *
12761835 ATGAAAAGGGATAGCTTTGGCTATCGATTATGACACGGGATCGTGATGACCATTGAAT
1 ATGAAAAGGGATAGCTTTGGCTATCGATTATGAAAAAGGATAGTTTTGACTA-TCAAT
* * *
12761893 ATGAAAAGGGATAGTTTTGGCTATCGATTATGAAAATGGATAGTTTTGTCTATCAATT
1 ATGAAAAGGGATAGCTTTGGCTATCGATTATGAAAAAGGATAGTTTTGACTATCAA-T
*
12761951 ATGAAAGGGGAT
1 ATGAAAAGGGAT
12761963 GGTGACGACC
Statistics
Matches: 104, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
57 3 0.03
58 100 0.96
59 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.30
Consensus pattern (57 bp):
ATGAAAAGGGATAGCTTTGGCTATCGATTATGAAAAAGGATAGTTTTGACTATCAAT
Found at i:12761976 original size:29 final size:29
Alignment explanation
Indices: 12761944--12762049 Score: 106
Period size: 29 Copynumber: 3.6 Consensus size: 29
12761934 AGTTTTGTCT
*
12761944 ATCAATTATGAAAGGGGATGGTGACGACC
1 ATCAATTATGAAAAGGGATGGTGACGACC
* * *
12761973 ATCAACTATGAAAAGTGATGGTGACGGCC
1 ATCAATTATGAAAAGGGATGGTGACGACC
** ** *
12762002 ATTGATTAATGAAAAGGGATGGTTTCAACC
1 ATCAATT-ATGAAAAGGGATGGTGACGACC
12762032 ATCGAA-TATGAAAAGGGA
1 ATC-AATTATGAAAAGGGA
12762050 CGATTACGAC
Statistics
Matches: 61, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
29 40 0.66
30 20 0.33
31 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (29 bp):
ATCAATTATGAAAAGGGATGGTGACGACC
Found at i:12762009 original size:87 final size:87
Alignment explanation
Indices: 12761828--12762026 Score: 211
Period size: 87 Copynumber: 2.3 Consensus size: 87
12761818 AGCTTCGACT
* * * * * *
12761828 ATCGAATATGAAAAGGGATAGCTTTGGCTATCGATTATGACACGGGATCGTGATGACCATTGAAT
1 ATCGATTATGAAAAGGGATAGTTTTGGCTATCAATTATGAAACGGGATCGTGACGACCATTCAAT
*** *
12761893 ATGAAAAGGGATAGTTTTGGCT
66 ATGAAAAGGGATAGTGACGGCC
* * * *
12761915 ATCGATTATGAAAATGGATAGTTTTGTCTATCAATTATGAAAGGGGATGGTGACGACCA-TCAAC
1 ATCGATTATGAAAAGGGATAGTTTTGGCTATCAATTATGAAACGGGATCGTGACGACCATTCAA-
* *
12761979 TATGAAAAGTGATGGTGACGGCC
65 TATGAAAAGGGATAGTGACGGCC
* *
12762002 ATTGATTAATGAAAAGGGATGGTTT
1 ATCGATT-ATGAAAAGGGATAGTTT
12762027 CAACCATCGA
Statistics
Matches: 91, Mismatches: 19, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
86 3 0.03
87 73 0.80
88 15 0.16
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (87 bp):
ATCGATTATGAAAAGGGATAGTTTTGGCTATCAATTATGAAACGGGATCGTGACGACCATTCAAT
ATGAAAAGGGATAGTGACGGCC
Found at i:12762063 original size:59 final size:59
Alignment explanation
Indices: 12761951--12762064 Score: 131
Period size: 59 Copynumber: 1.9 Consensus size: 59
12761941 TCTATCAATT
* * * * * *
12761951 ATGAAAGGGGATGGTGACGACCATCAACTATGAAAAGTGATGGTGACGGCCATTGATTA
1 ATGAAAAGGGATGGTGACAACCATCAACTATGAAAAGGGACGATGACGACCATTGATTA
** *
12762010 ATGAAAAGGGATGGTTTCAACCATCGAA-TATGAAAAGGGACGATTACGACCATTG
1 ATGAAAAGGGATGGTGACAACCATC-AACTATGAAAAGGGACGATGACGACCATTG
12762065 TTTAGCACAC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
59 43 0.96
60 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (59 bp):
ATGAAAAGGGATGGTGACAACCATCAACTATGAAAAGGGACGATGACGACCATTGATTA
Found at i:12766481 original size:12 final size:11
Alignment explanation
Indices: 12766459--12766492 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
12766449 TTTATGGACC
*
12766459 TCTTCTTTTTT
1 TCTTTTTTTTT
12766470 TCTTTTTTTTT
1 TCTTTTTTTTT
12766481 TCTTTTTTTTT
1 TCTTTTTTTTT
12766492 T
1 T
12766493 GGGGGGGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:12773934 original size:41 final size:41
Alignment explanation
Indices: 12773886--12773966 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
12773876 ATATTTTATT
12773886 TTATCTTTTAGTAGTCTATTAGAAT-AAGAGAATTATTTTCC
1 TTATCTTTTAGTAGTCTATTAGAATAAAGA-AATTATTTTCC
*
12773927 TTATCTTTTAGTAGTTTATTAGAATAAAGAAATTATTTTC
1 TTATCTTTTAGTAGTCTATTAGAATAAAGAAATTATTTTC
12773967 TCAATTAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 34 0.89
42 4 0.11
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.48
Consensus pattern (41 bp):
TTATCTTTTAGTAGTCTATTAGAATAAAGAAATTATTTTCC
Found at i:12781163 original size:18 final size:18
Alignment explanation
Indices: 12781117--12781166 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
12781107 GCCCATTAAG
*
12781117 CCCCCAAAAAAAACCTAA
1 CCCCCAAAAAAAAACTAA
**
12781135 CCCCCCCAAAAAAACTAA
1 CCCCCAAAAAAAAACTAA
12781153 -CCCCAAAAAAAAAC
1 CCCCCAAAAAAAAAC
12781167 CAAGAAACCC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.56, C:0.40, G:0.00, T:0.04
Consensus pattern (18 bp):
CCCCCAAAAAAAAACTAA
Found at i:12781553 original size:17 final size:18
Alignment explanation
Indices: 12781531--12781579 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
12781521 CGGCCACCGT
12781531 GGGCGGTGGCCGGCGA-C
1 GGGCGGTGGCCGGCGATC
* *
12781548 GGGCGGCGGCCGACGATC
1 GGGCGGTGGCCGGCGATC
* *
12781566 GGCCGGTGACCGGC
1 GGGCGGTGGCCGGC
12781580 CCCCCTTGGC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.08, C:0.33, G:0.53, T:0.06
Consensus pattern (18 bp):
GGGCGGTGGCCGGCGATC
Found at i:12788442 original size:44 final size:42
Alignment explanation
Indices: 12788345--12788470 Score: 144
Period size: 44 Copynumber: 2.9 Consensus size: 42
12788335 TTTATTTGAA
* *
12788345 AAAACGCCGCTAAATGTCATGACTTTTAGCGACGCTTTTCCC
1 AAAACGCCGCTAAAGGTCATGACTTTTAGCGGCGCTTTTCCC
* * **
12788387 ACAAACACCGCTAAAAGGTCATGACTTTTAGCGGCACTTTTCTTG
1 A-AAACGCCGCT-AAAGGTCATGACTTTTAGCGGCGCTTTTC-CC
** *
12788432 AAAACGCCGCTAAAGACCATGACCTTTAGCGGCGCTTTT
1 AAAACGCCGCTAAAGGTCATGACTTTTAGCGGCGCTTTT
12788471 TCTAAACTAT
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 1 0.01
43 33 0.47
44 35 0.50
45 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (42 bp):
AAAACGCCGCTAAAGGTCATGACTTTTAGCGGCGCTTTTCCC
Found at i:12793792 original size:52 final size:52
Alignment explanation
Indices: 12793723--12793827 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
12793713 ATTTTTAACA
*
12793723 TATTTTTGTGGCGTTTTGTCTAAAAATGCCACTATTGCTTAACTTTT-ATTTT
1 TATTTTTGTGGCGTTTTGTCTAAAAACGCCACTATTGCTTAA-TTTTAATTTT
12793775 TATTTTTGTGGCGTTTTGTCTAAAAACGCCACTATTGCTTAATTTTAATTTT
1 TATTTTTGTGGCGTTTTGTCTAAAAACGCCACTATTGCTTAATTTTAATTTT
12793827 T
1 T
12793828 TTATTTTTAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 4 0.08
52 47 0.92
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.51
Consensus pattern (52 bp):
TATTTTTGTGGCGTTTTGTCTAAAAACGCCACTATTGCTTAATTTTAATTTT
Found at i:12794478 original size:15 final size:15
Alignment explanation
Indices: 12794455--12794505 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
12794445 ATACCCATGG
*
12794455 CCATTAAACCTTAAA
1 CCATAAAACCTTAAA
*
12794470 CCATAAAACCCTAAA
1 CCATAAAACCTTAAA
* *
12794485 TCAT-ATACCTTAAA
1 CCATAAAACCTTAAA
*
12794499 CCTTAAA
1 CCATAAA
12794506 TATTAAATAT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.25
Consensus pattern (15 bp):
CCATAAAACCTTAAA
Found at i:12794815 original size:41 final size:41
Alignment explanation
Indices: 12794757--12794904 Score: 199
Period size: 41 Copynumber: 3.6 Consensus size: 41
12794747 AGGGGTTATA
* *
12794757 TGACTTTTAGCAGCGTTTTATCAAAAGCACCGCTAATGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCACCGCTAATGCTC
* *
12794798 CGACTTTTAGCGGCGTTTTACCAAAAGCACAGCTAATGCTC
1 TGACTTTTAGCGGCGTTTTACCAAAAGCACCGCTAATGCTC
* * *
12794839 TGACTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTT
1 TGACTTTTAGCGGCGTTTTACCAAAAGCACCGCTAATGCTC
* * *
12794880 TG-TTTTTAGCGACGTTTTAACAAAA
1 TGACTTTTAGCGGCGTTTTACCAAAA
12794905 AATGCCGCTA
Statistics
Matches: 95, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 20 0.21
41 75 0.79
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (41 bp):
TGACTTTTAGCGGCGTTTTACCAAAAGCACCGCTAATGCTC
Found at i:12802254 original size:35 final size:34
Alignment explanation
Indices: 12802182--12802278 Score: 135
Period size: 35 Copynumber: 2.8 Consensus size: 34
12802172 CAACCCTTTC
12802182 TTTTTTACCCAAATCAGTT--CCCTCCCCAAATCA
1 TTTTTT-CCCAAATCAGTTCCCCCTCCCCAAATCA
*
12802215 TTTTTTCCCAAATCAGTTCCCCCTTCCCCAAATCG
1 TTTTTTCCCAAATCAGTTCCCCC-TCCCCAAATCA
*
12802250 TTTTTCCCCAAATCAGTTCCCCCCTCCCC
1 TTTTTTCCCAAATCAGTT-CCCCCTCCCC
12802279 CTCCCCCTCC
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.21
33 6 0.10
34 3 0.05
35 32 0.55
36 5 0.09
ACGTcount: A:0.21, C:0.42, G:0.04, T:0.33
Consensus pattern (34 bp):
TTTTTTCCCAAATCAGTTCCCCCTCCCCAAATCA
Found at i:12807155 original size:43 final size:43
Alignment explanation
Indices: 12807108--12807230 Score: 117
Period size: 43 Copynumber: 2.9 Consensus size: 43
12807098 TATCATATAT
*
12807108 CGATGCCACTGTCCCACACAGGGTCTTACACG-AAGTCG-ATTAA
1 CGATGCCACTGTCCCACACAGGGTCTTACACGTAA-TCGCAAT-A
* * *
12807151 CGATGTCGA-TGTCCCACACATGGTCTTACATGTAATCGCAATA
1 CGATG-CCACTGTCCCACACAGGGTCTTACACGTAATCGCAATA
* * * * *
12807194 CAATGCCACTATACTACACAGGGTCTTACATGTAATC
1 CGATGCCACTGTCCCACACAGGGTCTTACACGTAATC
12807231 ACATGTCGAT
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
42 2 0.03
43 58 0.88
44 6 0.09
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
CGATGCCACTGTCCCACACAGGGTCTTACACGTAATCGCAATA
Found at i:12814226 original size:230 final size:230
Alignment explanation
Indices: 12813823--12814283 Score: 886
Period size: 230 Copynumber: 2.0 Consensus size: 230
12813813 CTATATCCCC
*
12813823 CTCCTTGAGGTTTTGGAGGATTTCCATCCACTTCTCCTCCGAGATATCCTTTCTCCTTTGTATAG
1 CTCCTTGAGGTTTTGGAGGATTTCCATCCACTTCTCCTCCGAGATATCCTCTCTCCTTTGTATAG
*
12813888 CTGCCTCCTCTCTTAGTGGGGAATAACCTTCGAAAAAGACCCAATAAGAAACCTTGTCTACCTTC
66 CTGCCTCCTCTCTTAGCGGGGAATAACCTTCGAAAAAGACCCAATAAGAAACCTTGTCTACCTTC
12813953 CAAAAGTGTCCATGAAACCATACCATCAATAATTGAGCACATCCAATAAACCGTCCCTCGCCTGT
131 CAAAAGTGTCCATGAAACCATACCATCAATAATTGAGCACATCCAATAAACCGTCCCTCGCCTGT
*
12814018 CTTCCGACATGAGCTCAAAGACCTGAAGGTCTCAA
196 CTTCCGACATGAGCTCAAAGACCTGAACGTCTCAA
12814053 CTCCTTGAGGTTTTGGAGGATTTCCATCCACTTCTCCTCCGAGATATCCTCTCTCCTTTGTATAG
1 CTCCTTGAGGTTTTGGAGGATTTCCATCCACTTCTCCTCCGAGATATCCTCTCTCCTTTGTATAG
12814118 CTGCCTCCTCTCTTAGCGGGGAATAACCTTCGAAAAAGACCCAATAAGAAACCTTGTCTACCTTC
66 CTGCCTCCTCTCTTAGCGGGGAATAACCTTCGAAAAAGACCCAATAAGAAACCTTGTCTACCTTC
*
12814183 TAAAAGTGTCCATGAAACCATACCATCAATAATTGAGCACATCCAATAAACCGTCCCTCGCCTGT
131 CAAAAGTGTCCATGAAACCATACCATCAATAATTGAGCACATCCAATAAACCGTCCCTCGCCTGT
12814248 CTTCCGACATGAGCTCAAAGACCTGAACGTCTCAA
196 CTTCCGACATGAGCTCAAAGACCTGAACGTCTCAA
12814283 C
1 C
12814284 CACTATCGCT
Statistics
Matches: 227, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
230 227 1.00
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (230 bp):
CTCCTTGAGGTTTTGGAGGATTTCCATCCACTTCTCCTCCGAGATATCCTCTCTCCTTTGTATAG
CTGCCTCCTCTCTTAGCGGGGAATAACCTTCGAAAAAGACCCAATAAGAAACCTTGTCTACCTTC
CAAAAGTGTCCATGAAACCATACCATCAATAATTGAGCACATCCAATAAACCGTCCCTCGCCTGT
CTTCCGACATGAGCTCAAAGACCTGAACGTCTCAA
Found at i:12829500 original size:35 final size:34
Alignment explanation
Indices: 12829450--12829515 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
12829440 TAATTGTGTT
*
12829450 ATTAATTTCTTATTTTAAATTTTAAATTTAAATTC
1 ATTAATTTCTTATTTT-AATTTTAAAGTTAAATTC
*
12829485 ATTAATTT-TTAATTTTAGTTTTAAAGTTAAA
1 ATTAATTTCTT-ATTTTAATTTTAAAGTTAAA
12829516 ATTTTCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 15 0.54
35 13 0.46
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (34 bp):
ATTAATTTCTTATTTTAATTTTAAAGTTAAATTC
Found at i:12829507 original size:28 final size:26
Alignment explanation
Indices: 12829437--12829509 Score: 67
Period size: 28 Copynumber: 2.7 Consensus size: 26
12829427 TAGTTTTAGA
* *
12829437 TTTTAATTGT-GTTATTAATTTCTTAT
1 TTTTAATTTTAGTT-TTAAATTCTTAT
* **
12829463 TTTAAATTTTAAATTTAAATTCATTAAT
1 TTTTAATTTTAGTTTTAAATTC-TT-AT
12829491 TTTTAATTTTAGTTTTAAA
1 TTTTAATTTTAGTTTTAAA
12829510 GTTAAAATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 15 0.42
27 3 0.08
28 18 0.50
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (26 bp):
TTTTAATTTTAGTTTTAAATTCTTAT
Found at i:12829518 original size:35 final size:35
Alignment explanation
Indices: 12829450--12829518 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
12829440 TAATTGTGTT
*
12829450 ATTAATTTCTTATTTTAAATTTTAAATTTAAATTC
1 ATTAATTTCTTATTTTAAATTTTAAATTAAAATTC
*
12829485 ATTAATTT-TTAATTTT-AGTTTTAAAGTTAAAATT
1 ATTAATTTCTT-ATTTTAAATTTTAAA-TTAAAATT
12829519 TTCATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 10 0.33
35 20 0.67
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (35 bp):
ATTAATTTCTTATTTTAAATTTTAAATTAAAATTC
Found at i:12829718 original size:43 final size:43
Alignment explanation
Indices: 12829671--12829811 Score: 151
Period size: 43 Copynumber: 3.3 Consensus size: 43
12829661 TTTAATGGCA
* *
12829671 TTTGTGGGAAAAGTGCCGCTAAAGGTCATGTTCTATAGAGACG
1 TTTGTGGGAAAAGTGCCGCTAAAGGCCATGTTCTTTAGAGACG
* ** * *
12829714 TTTGTGGGAAAAATGTTGCTAAAGGCCATGTTCTTTAGCGATG
1 TTTGTGGGAAAAGTGCCGCTAAAGGCCATGTTCTTTAGAGACG
* * *
12829757 -TTGTGGGAAAAGCGCCGCCAAAAGCCATGTTCTTTAGCA-ACG
1 TTTGTGGGAAAAGTGCCGCTAAAGGCCATGTTCTTTAG-AGACG
* *
12829799 TTAGTGAGAAAAG
1 TTTGTGGGAAAAG
12829812 CGTTAGTGGG
Statistics
Matches: 79, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
42 33 0.42
43 46 0.58
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (43 bp):
TTTGTGGGAAAAGTGCCGCTAAAGGCCATGTTCTTTAGAGACG
Found at i:12829817 original size:15 final size:15
Alignment explanation
Indices: 12829797--12829829 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12829787 TCTTTAGCAA
12829797 CGTTAGTGAGAAAAG
1 CGTTAGTGAGAAAAG
*
12829812 CGTTAGTGGGAAAAG
1 CGTTAGTGAGAAAAG
12829827 CGT
1 CGT
12829830 CGCTAAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.09, G:0.36, T:0.21
Consensus pattern (15 bp):
CGTTAGTGAGAAAAG
Found at i:12831646 original size:19 final size:19
Alignment explanation
Indices: 12831609--12831668 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
12831599 TATTTGCGCA
*
12831609 TTTTTTA-TCATTGTCATTT
1 TTTTTTATTC-TTGTTATTT
12831628 TTTTTTATTCTTGTTATTT
1 TTTTTTATTCTTGTTATTT
* *
12831647 TATTAT-TTCTT-TTATTAT
1 TTTTTTATTCTTGTTATT-T
12831665 TTTT
1 TTTT
12831669 GATATTTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 5 0.14
18 9 0.26
19 19 0.54
20 2 0.06
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (19 bp):
TTTTTTATTCTTGTTATTT
Found at i:12831647 original size:17 final size:17
Alignment explanation
Indices: 12831627--12831668 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
12831617 CATTGTCATT
12831627 TTTTTTTA-TTCTTGTTA
1 TTTTTTTATTTCTT-TTA
*
12831644 TTTTATTATTTCTTTTA
1 TTTTTTTATTTCTTTTA
12831661 TTATTTTT
1 TT-TTTTT
12831669 GATATTTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTTTTATTTCTTTTA
Done.