Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 63 of 378
Found at i:16230710 original size:54 final size:54
Alignment explanation
Indices: 16230651--16230801 Score: 151
Period size: 54 Copynumber: 2.8 Consensus size: 54
16230641 TACCCCACAA
** * * *
16230651 GGGTATTTCAGTAATTTTACCCTAC-AGGGGTATTTTAGTAATTTTTCAAACCAT
1 GGGTATTTCAGTAATTTTA-CAAACAAAGGGTATTTTAGTAATTTTACAAACCAG
* ** *
16230705 TGGTATTTTGGTAATTTTATAAACAAAGGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATTTTACAAACCAG
** * * * *
16230759 GGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTGGTAATT
1 GGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATT
16230802 CTGTAAATTG
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
53 2 0.02
54 81 0.98
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (54 bp):
GGGTATTTCAGTAATTTTACAAACAAAGGGTATTTTAGTAATTTTACAAACCAG
Found at i:16230767 original size:81 final size:81
Alignment explanation
Indices: 16230649--16230801 Score: 211
Period size: 81 Copynumber: 1.9 Consensus size: 81
16230639 TTTACCCCAC
** **
16230649 AAGGGTATTTCAGTAATTTTACCCTACAGGGGTATTTTAGTAATTTT-TCAAACCATTGGTATTT
1 AAGGGTATTTCAGTAATTTTACCAAACAGGGGTATTTTAGTAATTTTAT-AAACCAAGGGTATTT
16230713 TGGTAATTTTATAAACA
65 TGGTAATTTTATAAACA
* * *
16230730 AAGGGTATTTTAGTAATTTTA-CAAACCAGGGGTATTTTGGTGATTTTATAAACCAAGGGTATTT
1 AAGGGTATTTCAGTAATTTTACCAAA-CAGGGGTATTTTAGTAATTTTATAAACCAAGGGTATTT
16230794 TGGTAATT
65 TGGTAATT
16230802 CTGTAAATTG
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
80 2 0.03
81 60 0.95
82 1 0.02
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (81 bp):
AAGGGTATTTCAGTAATTTTACCAAACAGGGGTATTTTAGTAATTTTATAAACCAAGGGTATTTT
GGTAATTTTATAAACA
Found at i:16230808 original size:27 final size:27
Alignment explanation
Indices: 16230678--16230801 Score: 160
Period size: 27 Copynumber: 4.6 Consensus size: 27
16230668 TACCCTACAG
* *
16230678 GGGTATTTTAGTAATTTT-TCAAACCAT
1 GGGTATTTTGGTAATTTTAT-AAACCAA
* *
16230705 TGGTATTTTGGTAATTTTATAAACAAA
1 GGGTATTTTGGTAATTTTATAAACCAA
* * *
16230732 GGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAA
*
16230759 GGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
16230786 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
16230802 CTGTAAATTG
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
27 81 0.99
28 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAACCAA
Found at i:16230815 original size:27 final size:26
Alignment explanation
Indices: 16230785--16230855 Score: 70
Period size: 27 Copynumber: 2.7 Consensus size: 26
16230775 TTATAAACCA
* *
16230785 AGGGTATTTTGGTAATTCTGTAAATTG
1 AGGGTAATTTGGTAATTCTGTAAA-TC
***
16230812 AGGGTAAAACGGTAATTCTGTAAATC
1 AGGGTAATTTGGTAATTCTGTAAATC
*
16230838 AGGAGTACTTTGGTAATT
1 AGG-GTAATTTGGTAATT
16230856 TTACAAGTCG
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 4 0.12
27 30 0.88
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.37
Consensus pattern (26 bp):
AGGGTAATTTGGTAATTCTGTAAATC
Found at i:16230817 original size:54 final size:54
Alignment explanation
Indices: 16230678--16230801 Score: 194
Period size: 54 Copynumber: 2.3 Consensus size: 54
16230668 TACCCTACAG
* **
16230678 GGGTATTTTAGTAATTTTTCAAACCATTGGTATTTTGGTAATTTTATAAACAAA
1 GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACAAA
* *
16230732 GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACAAA
*
16230786 GGGTATTTTGGTAATT
1 GGGTATTTTAGTAATT
16230802 CTGTAAATTG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (54 bp):
GGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACAAA
Found at i:16233695 original size:3 final size:3
Alignment explanation
Indices: 16233680--16233718 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
16233670 CAATACACTA
* * *
16233680 AAG AAG AAT AAG AAG AAA AAG AAA AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
16233719 TCCTTAACTG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:16235346 original size:17 final size:19
Alignment explanation
Indices: 16235313--16235347 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
16235303 GAATAGACTA
16235313 GAAAATAGTGTAAATTGAT
1 GAAAATAGTGTAAATTGAT
16235332 GAAAATA-TG-AAATTGA
1 GAAAATAGTGTAAATTGA
16235348 CTTTGAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.29
Consensus pattern (19 bp):
GAAAATAGTGTAAATTGAT
Found at i:16235962 original size:31 final size:31
Alignment explanation
Indices: 16235924--16235986 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
16235914 AAGTGATATA
16235924 TGAGAAAGATTTATATTTGAATGCTTATTAT
1 TGAGAAAGATTTATATTTGAATGCTTATTAT
16235955 TGAGAAAGATTTATATTTGAATGCTTATTAT
1 TGAGAAAGATTTATATTTGAATGCTTATTAT
16235986 T
1 T
16235987 ATAGTTGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (31 bp):
TGAGAAAGATTTATATTTGAATGCTTATTAT
Found at i:16236795 original size:22 final size:22
Alignment explanation
Indices: 16236765--16236813 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
16236755 AGTTGCGTTG
*
16236765 TGACAAGGAA-CCCTCAACGTCA
1 TGACGAGGAACCCCT-AACGTCA
*
16236787 TGACGAGGAACCCCTGACGTCA
1 TGACGAGGAACCCCTAACGTCA
16236809 TGACG
1 TGACG
16236814 TCGACTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.14
Consensus pattern (22 bp):
TGACGAGGAACCCCTAACGTCA
Found at i:16245152 original size:23 final size:22
Alignment explanation
Indices: 16245126--16245179 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
16245116 GGCATCGAAG
16245126 AATTCCCAGTTCACGCAAAAATC
1 AATT-CCAGTTCACGCAAAAATC
*
16245149 AATTGCAGTTCACGCAAAAATC
1 AATTCCAGTTCACGCAAAAATC
*
16245171 AATTGCAGT
1 AATTCCAGT
16245180 AAGGAGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.24
Consensus pattern (22 bp):
AATTCCAGTTCACGCAAAAATC
Found at i:16245157 original size:22 final size:22
Alignment explanation
Indices: 16245132--16245179 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
16245122 GAAGAATTCC
16245132 CAGTTCACGCAAAAATCAATTG
1 CAGTTCACGCAAAAATCAATTG
16245154 CAGTTCACGCAAAAATCAATTG
1 CAGTTCACGCAAAAATCAATTG
16245176 CAGT
1 CAGT
16245180 AAGGAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (22 bp):
CAGTTCACGCAAAAATCAATTG
Found at i:16245883 original size:33 final size:33
Alignment explanation
Indices: 16245841--16245909 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
16245831 GATGAAAAAC
*
16245841 AATGATATTTTAAATATTTTACATATTTGAAAT
1 AATGATATTTGAAATATTTTACATATTTGAAAT
* *
16245874 AATGGTATTTGAAATATTTTACATATTTTAAAT
1 AATGATATTTGAAATATTTTACATATTTGAAAT
16245907 AAT
1 AAT
16245910 AATAATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (33 bp):
AATGATATTTGAAATATTTTACATATTTGAAAT
Found at i:16247550 original size:24 final size:24
Alignment explanation
Indices: 16247522--16247572 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
16247512 TGATATACAT
*
16247522 ATTATTTT-TATTTATATATTATCC
1 ATTATTTTATATCTAT-TATTATCC
*
16247546 ATTATTTTATATCTATTATTATTC
1 ATTATTTTATATCTATTATTATCC
16247570 ATT
1 ATT
16247573 TTTAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTATTTTATATCTATTATTATCC
Found at i:16247566 original size:17 final size:17
Alignment explanation
Indices: 16247520--16247718 Score: 76
Period size: 17 Copynumber: 11.4 Consensus size: 17
16247510 AATGATATAC
*
16247520 ATATTATTTTTATTTAT
1 ATATTATTATTATTTAT
*
16247537 ATATTATCCATTATTTTAT
1 ATATTAT-TATTA-TTTAT
*
16247556 ATCTATTATTATTCATTTTT
1 A--TATTATTATT-ATTTAT
* * *
16247576 AAATTA-TATGTAATTAA
1 ATATTATTAT-TATTTAT
16247593 ATATTATTA-TATTATAT
1 ATATTATTATTATT-TAT
*
16247610 CGTATTA-TATTATTCTAT
1 -ATATTATTATTATT-TAT
*
16247628 ATAGTATATATTA-TTA-
1 ATATTAT-TATTATTTAT
*
16247644 ATATT-TTATTAATTA-
1 ATATTATTATTATTTAT
* *
16247659 ACTATTTTCTAATGTATGTAT
1 A-TATTAT-T-AT-TATTTAT
*
16247680 GTATTATTATTATTT-T
1 ATATTATTATTATTTAT
*
16247696 -TATTAATATTA-TTAT
1 ATATTATTATTATTTAT
16247711 ATTATTAT
1 A-TATTAT
16247719 ATGCTTCCTA
Statistics
Matches: 137, Mismatches: 23, Indels: 44
0.67 0.11 0.22
Matches are distributed among these distances:
14 7 0.05
15 16 0.12
16 12 0.09
17 38 0.28
18 26 0.19
19 14 0.10
20 17 0.12
21 7 0.05
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (17 bp):
ATATTATTATTATTTAT
Found at i:16247606 original size:8 final size:8
Alignment explanation
Indices: 16247593--16247720 Score: 54
Period size: 8 Copynumber: 15.5 Consensus size: 8
16247583 ATGTAATTAA
16247593 ATATTATT
1 ATATTATT
16247601 ATATTA-T
1 ATATTATT
**
16247608 ATCGTATT
1 ATATTATT
16247616 ATATTATT
1 ATATTATT
*
16247624 CTATATAGTAT
1 ATAT-TA-T-T
16247635 ATATTATT
1 ATATTATT
16247643 AATATT-TT
1 -ATATTATT
*
16247651 AT-TAATT
1 ATATTATT
16247658 AACTATT-TT
1 -A-TATTATT
*
16247667 CTAATGTATGT
1 AT-AT-TAT-T
*
16247678 AT-GTATT
1 ATATTATT
16247685 ATTATTATT
1 A-TATTATT
16247694 -T-TTATT
1 ATATTATT
16247700 AATATTATT
1 -ATATTATT
16247709 ATATTATT
1 ATATTATT
16247717 ATAT
1 ATAT
16247721 GCTTCCTATA
Statistics
Matches: 90, Mismatches: 12, Indels: 36
0.65 0.09 0.26
Matches are distributed among these distances:
6 6 0.07
7 13 0.14
8 39 0.43
9 21 0.23
10 5 0.06
11 6 0.07
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.58
Consensus pattern (8 bp):
ATATTATT
Found at i:16247620 original size:20 final size:19
Alignment explanation
Indices: 16247605--16247642 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
16247595 ATTATTATAT
*
16247605 TATATCGTATTATATTATTC
1 TATATAGTA-TATATTATTC
16247625 TATATAGTATATATTATT
1 TATATAGTATATATTATT
16247643 AATATTTTAT
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:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (19 bp):
TATATAGTATATATTATTC
Found at i:16247636 original size:52 final size:53
Alignment explanation
Indices: 16247546--16247658 Score: 117
Period size: 52 Copynumber: 2.2 Consensus size: 53
16247536 TATATTATCC
* * * *
16247546 ATTATTTTATATCTATTATTATTCATTTTTAAATTATATGTAATTAA-ATATT
1 ATTATATTATATCTATTATTATTCATTTATAAAGTATATATAATTAATATATT
* * *
16247598 ATTATATTATATCGTATTA-TATT-ATTCTATATAGTATATATTATTAATATTTT
1 ATTATATTATATC-TATTATTATTCATT-TATAAAGTATATATAATTAATATATT
16247651 ATTA-ATTA
1 ATTATATTA
16247659 ACTATTTTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
51 3 0.06
52 35 0.69
53 13 0.25
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.57
Consensus pattern (53 bp):
ATTATATTATATCTATTATTATTCATTTATAAAGTATATATAATTAATATATT
Found at i:16247689 original size:3 final size:3
Alignment explanation
Indices: 16247681--16247718 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
16247671 TGTATGTATG
* *
16247681 TAT TAT TAT TAT TTT TAT TAA TAT TAT TA- TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16247719 ATGCTTCCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:16248976 original size:13 final size:13
Alignment explanation
Indices: 16248960--16248984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16248950 CAATATATTT
16248960 ATTAATTATAAAC
1 ATTAATTATAAAC
16248973 ATTAATTATAAA
1 ATTAATTATAAA
16248985 TAAAAAAACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTAATTATAAAC
Found at i:16249166 original size:20 final size:21
Alignment explanation
Indices: 16249141--16249183 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
16249131 AGCTTAAAAC
16249141 AATATGAA-A-TAAAAAATACA
1 AATATGAATAGTAAAAAAT-CA
16249161 AATATGAATAGTAAAAAATCA
1 AATATGAATAGTAAAAAATCA
16249182 AA
1 AA
16249184 CTTAAGACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.38
21 5 0.24
22 8 0.38
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (21 bp):
AATATGAATAGTAAAAAATCA
Found at i:16250092 original size:18 final size:19
Alignment explanation
Indices: 16250069--16250107 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
16250059 AATATGTTAT
*
16250069 ATTATGTTATTTATAA-AC
1 ATTATGTAATTTATAATAC
16250087 ATTATGTAATTTATAATAC
1 ATTATGTAATTTATAATAC
16250106 AT
1 AT
16250108 AAAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (19 bp):
ATTATGTAATTTATAATAC
Found at i:16254561 original size:26 final size:26
Alignment explanation
Indices: 16254532--16254639 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
16254522 TGATACAAAT
16254532 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
16254558 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
16254584 TGATAATGGGTTAGGTAATTGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
16254610 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
16254636 TGAT
1 TGAT
16254640 TGGAATTTCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:16256159 original size:26 final size:26
Alignment explanation
Indices: 16256130--16256182 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
16256120 TTTACAGTTT
16256130 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
16256156 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
16256182 T
1 T
16256183 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:16263299 original size:38 final size:38
Alignment explanation
Indices: 16263248--16263596 Score: 509
Period size: 38 Copynumber: 9.1 Consensus size: 38
16263238 ATATTCGATG
*
16263248 TATATCCGGGTTAAATCCCGCAGGCTTCTTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* *
16263286 TATATCCGAGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
** *
16263324 TATATCCAAGTTAAATCCCGTAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* * *
16263362 TATATCCGGGTTAAATCCCACAGGCTTCGGGCTGGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* *
16263400 TATATCCGGGTTAAATCCTGCAGGCTTCATGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
16263438 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* * *
16263476 TATATCCGGGCTTAAAGACCCGCTGGCTTCGTGCTGGTAA
1 TATATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAT
* *
16263516 AATATCCGGGTTAAATCCCGCAAGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* * *
16263554 TATATCCGGGATAAATCCCGCAGGCCTAGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
16263592 TATAT
1 TATAT
16263597 TCAGGCCTTC
Statistics
Matches: 277, Mismatches: 32, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
38 238 0.86
39 10 0.04
40 29 0.10
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
Found at i:16263647 original size:43 final size:43
Alignment explanation
Indices: 16263594--16263705 Score: 188
Period size: 43 Copynumber: 2.6 Consensus size: 43
16263584 GCTGGTATTA
* * *
16263594 TATTCAGGCCTTCATGCCTAGCAGGCTTCGTGCCGATGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCATGCCGATGATGTG
*
16263637 TATTCGGGCCTTCGTGCCTAGCAGGCTTCATGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTCATGCCGATGATGTG
16263680 TATTCGGGCCTTCGTGCCTAGCAGGC
1 TATTCGGGCCTTCGTGCCTAGCAGGC
16263706 GTAATGCTGG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.13, C:0.27, G:0.30, T:0.29
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTCATGCCGATGATGTG
Found at i:16263718 original size:43 final size:43
Alignment explanation
Indices: 16263594--16263718 Score: 178
Period size: 43 Copynumber: 2.9 Consensus size: 43
16263584 GCTGGTATTA
* * ** *
16263594 TATTCAGGCCTTCATGCCTAGCAGGCTTCGTGCCGATGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTAATGCCGGTGATGTG
*
16263637 TATTCGGGCCTTCGTGCCTAGCAGGCTTCATGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTAATGCCGGTGATGTG
* *
16263680 TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCTGGTGA
1 TATTCGGGCCTTCGTGCCTAGCAGGCTTAATGCCGGTGA
16263719 AATGATATGT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.14, C:0.25, G:0.31, T:0.30
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCTTAATGCCGGTGATGTG
Found at i:16273215 original size:119 final size:119
Alignment explanation
Indices: 16273057--16273394 Score: 480
Period size: 119 Copynumber: 2.8 Consensus size: 119
16273047 TAGGCCGCAG
*
16273057 TATAGCAGATCTAGCTTTCAGATGTTTATACTGAAGCAGATCCAAGATAATTTGGTATTCTTGTG
1 TATAGCAGATCTAGCTTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTG
* ** *
16273122 TTTACAAGAAACAAATCGAGGATATAGTAGATTTGACTCTTAGATGTTCTCAAA
66 TTTACAAGAAACAAATCGAGGACATAACAGATTTGACTCTCAGATGTTCTCAAA
* *
16273176 TATAGTAGATCTAGCTTTCAGATGTTTATACTGGAGCAGATCCAAGATGATTTGGTATTCTTGTG
1 TATAGCAGATCTAGCTTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTG
*
16273241 TTTACAAGAAACAAATCGAGGACATAACAGATTTGGCTCTCAGATGTTCTCAAA
66 TTTACAAGAAACAAATCGAGGACATAACAGATTTGACTCTCAGATGTTCTCAAA
* * * * * *
16273295 TATAGCAGATCCCA-CCTTCAGATGTTTATGCTGAAGCAGATCCAAGATGGTTTAGTATCCTTGT
1 TATAGCAGAT-CTAGCTTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGT
** * * * *
16273359 ACTTACAAGGAACAAATCGAAGACATAGCTGATTTG
65 GTTTACAAGAAACAAATCGAGGACATAACAGATTTG
16273395 GCTTCCACGT
Statistics
Matches: 196, Mismatches: 22, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
119 194 0.99
120 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (119 bp):
TATAGCAGATCTAGCTTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTG
TTTACAAGAAACAAATCGAGGACATAACAGATTTGACTCTCAGATGTTCTCAAA
Found at i:16283840 original size:25 final size:25
Alignment explanation
Indices: 16283812--16283930 Score: 132
Period size: 25 Copynumber: 4.8 Consensus size: 25
16283802 CGGATACTCC
*
16283812 ATAGCTTGTAAGAGCATACCGATTT
1 ATAGCTCGTAAGAGCATACCGATTT
* *
16283837 ATAGCTCGTGAGAGCATACCAATTT
1 ATAGCTCGTAAGAGCATACCGATTT
* * *
16283862 ATAGCTTGTGAGAGCATACCGATCT
1 ATAGCTCGTAAGAGCATACCGATTT
* * *
16283887 ACAGCTCG-AGTGAGCATACCGATTC
1 ATAGCTCGTA-AGAGCATACCGATTT
*
16283912 ATAGCTCGTATGAGCATAC
1 ATAGCTCGTAAGAGCATAC
16283931 ATGTACATGA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
25 78 0.99
26 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (25 bp):
ATAGCTCGTAAGAGCATACCGATTT
Found at i:16283893 original size:50 final size:49
Alignment explanation
Indices: 16283811--16283930 Score: 150
Period size: 50 Copynumber: 2.4 Consensus size: 49
16283801 GCGGATACTC
* * *
16283811 CATAGCTTGTAAGAGCATACCGATTTATAGCTCGTGAGAGCATACCAATT
1 CATAGCTTGT-AGAGCATACCGATCTACAGCTCGAGAGAGCATACCAATT
* * *
16283861 TATAGCTTGTGAGAGCATACCGATCTACAGCTCGAGTGAGCATACCGATT
1 CATAGCTTGT-AGAGCATACCGATCTACAGCTCGAGAGAGCATACCAATT
*
16283911 CATAGCTCGTATGAGCATAC
1 CATAGCTTGTA-GAGCATAC
16283931 ATGTACATGA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
49 1 0.02
50 59 0.98
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (49 bp):
CATAGCTTGTAGAGCATACCGATCTACAGCTCGAGAGAGCATACCAATT
Found at i:16286764 original size:43 final size:43
Alignment explanation
Indices: 16286645--16286800 Score: 151
Period size: 42 Copynumber: 3.7 Consensus size: 43
16286635 AGCTCGTACA
* *
16286645 ATGCCAACGTCCCAG-CGTGGTCTTACATGT-AATCAAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCAAATA-CG
* *
16286687 ATTCC-ACTGTCCCAGACAGGGTCTTACACG-AAATCAAATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAAATCAAATACG
* * *
16286729 ATGCCAACATCCCAGACTTGGTCATACACGTAAATCATAAGT-CG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCA-AA-TACG
* * *
16286773 ATGCCAATGTCCCAAACGTGGTCTTACA
1 ATGCCAACGTCCCAGACATGGTCTTACA
16286801 TGATAGCACA
Statistics
Matches: 93, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
41 2 0.02
42 35 0.38
43 28 0.30
44 27 0.29
45 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAATCAAATACG
Found at i:16286796 original size:86 final size:84
Alignment explanation
Indices: 16286645--16286800 Score: 190
Period size: 86 Copynumber: 1.8 Consensus size: 84
16286635 AGCTCGTACA
* * * * * *
16286645 ATGCCAACGTCCCAGCGTGGTCTTACATGTAATCAAATATCGATTCCACTGTCCCAGACAGGGTC
1 ATGCCAACATCCCAGCGTGGTCATACACGTAATCAAATATCGATGCCAATGTCCCAAACAGGGTC
16286710 TTACACGAAATCAAATACG
66 TTACACGAAATCAAATACG
* *
16286729 ATGCCAACATCCCAGACTTGGTCATACACGTAAATCATAA-GTCGATGCCAATGTCCCAAAC-GT
1 ATGCCAACATCCCAG-CGTGGTCATACACGT-AATCA-AATATCGATGCCAATGTCCCAAACAG-
16286792 GGTCTTACA
62 GGTCTTACA
16286801 TGATAGCACA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
84 14 0.23
85 13 0.22
86 31 0.52
87 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (84 bp):
ATGCCAACATCCCAGCGTGGTCATACACGTAATCAAATATCGATGCCAATGTCCCAAACAGGGTC
TTACACGAAATCAAATACG
Found at i:16293947 original size:40 final size:40
Alignment explanation
Indices: 16293881--16294024 Score: 130
Period size: 40 Copynumber: 3.6 Consensus size: 40
16293871 AAATTGAATG
* * *
16293881 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACT
* * ***
16293920 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACT
* * ** *
16293960 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-ATGCTAGAAACT
* *
16294000 CTATCCGGGCCAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCA
16294025 TTTGTGCACG
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 16 0.18
40 71 0.82
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTATGCTAGAAACT
Found at i:16294025 original size:40 final size:39
Alignment explanation
Indices: 16293919--16294047 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 39
16293909 TGCTGGAAAT
* * *
16293919 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
16293959 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* * *
16293999 TCTATCCGGGCCAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
16294039 TATATCCGG
1 TATATCCGG
16294048 TTATATTCCG
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
39 4 0.05
40 71 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:16301883 original size:40 final size:40
Alignment explanation
Indices: 16301817--16301983 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
16301807 AAATTGAATG
* * *
16301817 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
16301856 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
16301896 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
16301936 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
16301976 ATATCCGG
1 ATATCCGG
16301984 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:16311611 original size:13 final size:13
Alignment explanation
Indices: 16311593--16311623 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
16311583 AAATAACCAA
*
16311593 AATTATCAAAATT
1 AATTATAAAAATT
16311606 AATTATAAAAATT
1 AATTATAAAAATT
16311619 AATTA
1 AATTA
16311624 AAATTCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (13 bp):
AATTATAAAAATT
Found at i:16321574 original size:40 final size:39
Alignment explanation
Indices: 16321463--16321613 Score: 151
Period size: 40 Copynumber: 3.8 Consensus size: 39
16321453 TATAACATGT
* ** *
16321463 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACCACTA
*
16321503 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACCACTA
* *** *
16321543 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATATAACCACTA
* *
16321583 GCATAATTGTCTTCGGG-CTTAGCCCGGATAT
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATAT
16321614 CATTCAATTT
Statistics
Matches: 95, Mismatches: 15, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 15 0.16
40 80 0.84
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATATAACCACTA
Found at i:16321597 original size:80 final size:79
Alignment explanation
Indices: 16321463--16321613 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
16321453 TATAACATGT
*
16321463 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGG-CTTAGCC
16321528 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
16321543 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGCTTAGC
16321606 CCGGATAT
64 CCGGATAT
16321614 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:16329509 original size:40 final size:40
Alignment explanation
Indices: 16329464--16329593 Score: 142
Period size: 40 Copynumber: 3.2 Consensus size: 40
16329454 CGGAATATAA
16329464 CCGGATATAAGCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAAGCATGTGCACAAATGCCTTCGGGTCTTAGC
* * *
16329504 CCGGATAGAATG-ACT-CGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA-GCA-TGTGCACAAATGCCTTCGGGTCTTAGC
* * *
16329544 CCGGATAT-AGC-CGCTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAAGCATG-T-GCACAAATGCCTTCGGGTCTTAGC
16329584 CCGGATATAA
1 CCGGATATAA
16329594 TTTCCAGCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 69 0.93
41 3 0.04
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.24
Consensus pattern (40 bp):
CCGGATATAAGCATGTGCACAAATGCCTTCGGGTCTTAGC
Found at i:16329608 original size:40 final size:40
Alignment explanation
Indices: 16329480--16329631 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
16329470 ATAAGCATGT
* * *
16329480 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCAC-CA
** * *
16329520 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCCGCTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCACCA
* **
16329560 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCACCA
* * *
16329600 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
16329632 CATTCAATTT
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
39 2 0.02
40 89 0.96
41 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCACCA
Found at i:16329614 original size:80 final size:80
Alignment explanation
Indices: 16329480--16329631 Score: 200
Period size: 80 Copynumber: 1.9 Consensus size: 80
16329470 ATAAGCATGT
* *
16329480 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
16329545 CGGATATAGCCGCTA
66 CGGATATAGCCGCTA
* * ** * *
16329560 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGGCTTAG
16329623 CCCGGATAT
64 CCCGGATAT
16329632 CATTCAATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
79 3 0.05
80 59 0.95
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATATAGCCGCTA
Found at i:16332435 original size:41 final size:40
Alignment explanation
Indices: 16332390--16332470 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
16332380 ATTAATTAAG
*
16332390 TTAGAATTTAAACAGAAAATTAAACCAAAATACAAAACTAA
1 TTAGAATTTAAACAGAAAAGTAAACCAAAATAC-AAACTAA
* * *
16332431 TTAGAATTTATATAGAAAAGTAAACCAAAATGCAAACTAA
1 TTAGAATTTAAACAGAAAAGTAAACCAAAATACAAACTAA
16332471 CAAATTCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 7 0.19
41 29 0.81
ACGTcount: A:0.58, C:0.11, G:0.07, T:0.23
Consensus pattern (40 bp):
TTAGAATTTAAACAGAAAAGTAAACCAAAATACAAACTAA
Found at i:16333391 original size:21 final size:20
Alignment explanation
Indices: 16333367--16333408 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
16333357 TGAAATGCAA
16333367 TCAAACCAACATGAATTAAAT
1 TCAAACCAACATG-ATTAAAT
* *
16333388 TCAAGCTAACATGATTAAAT
1 TCAAACCAACATGATTAAAT
16333408 T
1 T
16333409 AACCATTCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.29
Consensus pattern (20 bp):
TCAAACCAACATGATTAAAT
Found at i:16339210 original size:17 final size:17
Alignment explanation
Indices: 16339156--16339210 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
16339146 TCAATGTAAT
* *
16339156 TGGCCCACATGCCCGTG
1 TGGCCCACACGCTCGTG
* *
16339173 TGGCCTACCCG-T-GTG
1 TGGCCCACACGCTCGTG
16339188 -GGCCCACACGCTCGTG
1 TGGCCCACACGCTCGTG
16339204 TGGCCCA
1 TGGCCCA
16339211 GACACCCAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
14 8 0.28
15 4 0.14
16 3 0.10
17 14 0.48
ACGTcount: A:0.11, C:0.40, G:0.31, T:0.18
Consensus pattern (17 bp):
TGGCCCACACGCTCGTG
Found at i:16343470 original size:43 final size:43
Alignment explanation
Indices: 16343406--16343529 Score: 169
Period size: 43 Copynumber: 2.9 Consensus size: 43
16343396 AACTCGTACA
* * * *
16343406 ATGCC-ATATCTCAGATATGGTCTTACATGTTATCACATATCG
1 ATGCCAATATCCCAGACATGGTCTTACATGTAATCACATAACG
* * * *
16343448 ATGCCAATGTCCTAGACATGGTCTTACATGAAATCATATAACG
1 ATGCCAATATCCCAGACATGGTCTTACATGTAATCACATAACG
16343491 ATGCCAATATCCCAGACATGGTCTTACATGTAATCACAT
1 ATGCCAATATCCCAGACATGGTCTTACATGTAATCACAT
16343530 CTCGGTAATC
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 5 0.07
43 64 0.93
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (43 bp):
ATGCCAATATCCCAGACATGGTCTTACATGTAATCACATAACG
Found at i:16348281 original size:43 final size:43
Alignment explanation
Indices: 16348234--16348346 Score: 174
Period size: 43 Copynumber: 2.6 Consensus size: 43
16348224 CGTATTAAAT
* * *
16348234 GTGGTCTTACTCGTAATCACATATTGATGCCAATG-TCCTAGAC
1 GTGGTCTTACACGTAATCACATATCGATGCCAACGCTCC-AGAC
16348277 GTGGTCTTACACGTAATCACATATCGATGCCAACGCTCCAGAC
1 GTGGTCTTACACGTAATCACATATCGATGCCAACGCTCCAGAC
*
16348320 GTGGCCTTACACGTAATCACATATCGA
1 GTGGTCTTACACGTAATCACATATCGA
16348347 AAATCCTATT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
43 62 0.95
44 3 0.05
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (43 bp):
GTGGTCTTACACGTAATCACATATCGATGCCAACGCTCCAGAC
Found at i:16349490 original size:14 final size:15
Alignment explanation
Indices: 16349473--16349501 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
16349463 ACACGAAAAT
16349473 TTCACACA-TATAAA
1 TTCACACATTATAAA
16349487 TTCACACATTATAAA
1 TTCACACATTATAAA
16349502 CACAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (15 bp):
TTCACACATTATAAA
Found at i:16354744 original size:43 final size:43
Alignment explanation
Indices: 16354673--16354754 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
16354663 ATCAAATATC
* * *
16354673 GATGCCAATGTCCCTTACATGGTCTTACATGAAATCATATAAT
1 GATGCCAATGTCCCTGACATGGTATTACACGAAATCATATAAT
* *
16354716 GATGCCAATGT-CCTAGACGTGGTATTACACGTAATCATA
1 GATGCCAATGTCCCT-GACATGGTATTACACGAAATCATA
16354755 ATACTATGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 3 0.09
43 30 0.91
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (43 bp):
GATGCCAATGTCCCTGACATGGTATTACACGAAATCATATAAT
Found at i:16366216 original size:18 final size:18
Alignment explanation
Indices: 16366193--16366237 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
16366183 AGTTGGGCCA
16366193 AGTAGGCCCAATGAGCCT
1 AGTAGGCCCAATGAGCCT
*
16366211 AGTAGGCCCAATGGGCCT
1 AGTAGGCCCAATGAGCCT
*
16366229 -GTGGGCCCA
1 AGTAGGCCCA
16366238 TATAGAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.22, C:0.29, G:0.33, T:0.16
Consensus pattern (18 bp):
AGTAGGCCCAATGAGCCT
Found at i:16371812 original size:131 final size:129
Alignment explanation
Indices: 16371666--16372009 Score: 303
Period size: 131 Copynumber: 2.6 Consensus size: 129
16371656 TGCTCAAAGT
* * *
16371666 AATCGAAGGTCCCTTTAGAATTTCACTGATGTCTTCTAAAAATCCTTTAAAACAAAGGCAATACT
1 AATCGAAGATTCCTTTAGAATTTCACTCATGT-TTCTAAAAA-CCTTTAAAACAAAGGCAATACT
* * * * * * * **
16371731 CGGTGTTTGACAATTCGGGAATCATGCTCTATCGTGCTGGGTTGTGATTTCTT-GTTTATTCAAA
64 CGATATTTGACAATTCGAGAACCATGCCCTATCATGCTGGGTTGCGATTT-TTCACTTATTCAAA
16371795 AC
128 AC
* ** * * * * **
16371797 AATCGAATATTCCTTTAGGTTTTCACTCATGTTTATTAAAAACCTTTCAGAACGAAGGCGATGTT
1 AATCGAAGATTCCTTTAGAATTTCACTCATGTTT-CTAAAAACCTTT-AAAACAAAGGCAATACT
* * * * * * *
16371862 TGATATTTGGCGATTTGAGAACCGTGCCCTATCATGCTGGGTTGCGCTTTTTCACTTGTTCAAAA
64 CGATATTTGACAATTCGAGAACCATGCCCTATCATGCTGGGTTGCGATTTTTCACTTATTCAAAA
16371927 C
129 C
* * * *
16371928 AATCGAAGATTCCTTTGGAATTTCACTCACGTTTTCTAAAAACTCTTTAAAACAAAGGAAATCCT
1 AATCGAAGATTCCTTTAGAATTTCACTCATG-TTTCTAAAAAC-CTTTAAAACAAAGGCAATACT
* * *
16371993 TGATTTTTGGCAATTCG
64 CGATATTTGACAATTCG
16372010 GGGAGTAGTG
Statistics
Matches: 165, Mismatches: 43, Indels: 10
0.76 0.20 0.05
Matches are distributed among these distances:
130 9 0.05
131 149 0.90
132 7 0.04
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (129 bp):
AATCGAAGATTCCTTTAGAATTTCACTCATGTTTCTAAAAACCTTTAAAACAAAGGCAATACTCG
ATATTTGACAATTCGAGAACCATGCCCTATCATGCTGGGTTGCGATTTTTCACTTATTCAAAAC
Found at i:16375834 original size:31 final size:31
Alignment explanation
Indices: 16375796--16375862 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
16375786 TCACGTGAAT
16375796 AAATTAATATGTCATCAATGAAAACTACAAC
1 AAATTAATATGTCATCAATGAAAACTACAAC
*
16375827 AAATTAATATGTCATCAGTGAAAACTACAAC
1 AAATTAATATGTCATCAATGAAAACTACAAC
16375858 AAATT
1 AAATT
16375863 CATTAAGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.27
Consensus pattern (31 bp):
AAATTAATATGTCATCAATGAAAACTACAAC
Found at i:16389832 original size:26 final size:26
Alignment explanation
Indices: 16389796--16389852 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
16389786 GCGAGGCTGC
*
16389796 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* * *
16389822 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
16389848 CAGAT
1 CAGAT
16389853 TTATACATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:16398916 original size:40 final size:38
Alignment explanation
Indices: 16398849--16398940 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 38
16398839 ATCTGTATCA
* *
16398849 CACACTTAGTGCCTTCTATAACTGAAGC-TATGCCAACTCG
1 CACACTTAGTG-CTTCTATAACCGAAGCATATG-AAACT-G
* *
16398889 CACACTTAGTGCTATTTATAGCCGAAGCTATATGAAACTG
1 CACACTTAGTGCT-TCTATAACCGAAGC-ATATGAAACTG
16398929 CACACTTAGTGC
1 CACACTTAGTGC
16398941 CAATCATAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
39 2 0.04
40 35 0.78
41 4 0.09
42 4 0.09
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (38 bp):
CACACTTAGTGCTTCTATAACCGAAGCATATGAAACTG
Found at i:16399286 original size:9 final size:9
Alignment explanation
Indices: 16399264--16399297 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
16399254 GTCCTTATTT
16399264 CACAAAAT-
1 CACAAAATA
16399272 CACAAAATA
1 CACAAAATA
16399281 CACAAAATA
1 CACAAAATA
16399290 CACAAAAT
1 CACAAAAT
16399298 TTCTTTGCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.65, C:0.24, G:0.00, T:0.12
Consensus pattern (9 bp):
CACAAAATA
Found at i:16399295 original size:18 final size:17
Alignment explanation
Indices: 16399264--16399297 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
16399254 GTCCTTATTT
16399264 CACAAAATCACAAAATA
1 CACAAAATCACAAAATA
16399281 CACAAAATACACAAAAT
1 CACAAAAT-CACAAAAT
16399298 TTCTTTGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.65, C:0.24, G:0.00, T:0.12
Consensus pattern (17 bp):
CACAAAATCACAAAATA
Found at i:16405223 original size:113 final size:113
Alignment explanation
Indices: 16405059--16405284 Score: 443
Period size: 113 Copynumber: 2.0 Consensus size: 113
16405049 ATGGGACGTA
16405059 GGTTTGGTATTATATAGCATGCATGACATGTTTCTTAAATGATGAAATATGGATTTTAATTATTA
1 GGTTTGGTATTATATAGCATGCATGACATGTTTCTTAAATGATGAAATATGGATTTTAATTATTA
16405124 ATTGATGAAATATAGTTTTTATTAAAACTAAGTTAAAGATCATTTTTC
66 ATTGATGAAATATAGTTTTTATTAAAACTAAGTTAAAGATCATTTTTC
*
16405172 GGTTTGGTATTATATAGCATGCATGACATGTTTTTTAAATGATGAAATATGGATTTTAATTATTA
1 GGTTTGGTATTATATAGCATGCATGACATGTTTCTTAAATGATGAAATATGGATTTTAATTATTA
16405237 ATTGATGAAATATAGTTTTTATTAAAACTAAGTTAAAGATCATTTTTC
66 ATTGATGAAATATAGTTTTTATTAAAACTAAGTTAAAGATCATTTTTC
16405285 CGTTGCTAGA
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 112 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (113 bp):
GGTTTGGTATTATATAGCATGCATGACATGTTTCTTAAATGATGAAATATGGATTTTAATTATTA
ATTGATGAAATATAGTTTTTATTAAAACTAAGTTAAAGATCATTTTTC
Found at i:16407043 original size:46 final size:46
Alignment explanation
Indices: 16406983--16407386 Score: 551
Period size: 46 Copynumber: 9.0 Consensus size: 46
16406973 TTTGACATGA
* * * * * * *
16406983 TGCCATAGTGTCTTTCAACTATGGTCTTACTCAATTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAATTTATATCAGGT
*** **
16407029 TGCCATGGTATCTTTCAACCATGGTCTTGTTC-ATTTCATATCACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAATTT-ATATCAGGT
16407075 TGCCATGGTATCTTTCAACCATGGTCTTACAC-ATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAATTT-ATATCAGGT
*
16407121 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAATTTATATCAGGT
*
16407167 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAATTTATATCAGGT
* *
16407213 TGCCATGGTATCTTTCAACCATGGTCTTGCACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAATTTATATCAGGT
*
16407259 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAATTTATATCAGGT
16407305 TGCCATGGTATCTTTCAACCATGGTCTTACAC--------TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAATTTATATCAGGT
16407343 TGCCATGGTATCTTTCAACCATGGTCTTACAC-ATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACAATTT-ATATCAG
16407387 AGAGCACACT
Statistics
Matches: 331, Mismatches: 17, Indels: 20
0.90 0.05 0.05
Matches are distributed among these distances:
38 38 0.11
45 4 0.01
46 286 0.86
47 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACAATTTATATCAGGT
Found at i:16407350 original size:38 final size:38
Alignment explanation
Indices: 16407299--16407374 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
16407289 ACATTTTATA
16407299 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
16407337 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
16407375 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:16407554 original size:59 final size:54
Alignment explanation
Indices: 16407423--16407555 Score: 144
Period size: 54 Copynumber: 2.4 Consensus size: 54
16407413 TTGCAGCGGG
* * *
16407423 ATTACCAGTCCAGGCTAAATCCCCTGCAATATAAACTCATAGAGTATTGTCGGG
1 ATTACCAGTCCAGGCTAAATCCCCTGCAAGACAAACTCATAGAGTATTGTCGGA
* *
16407477 ATTACCAGTCTAGGCTAAATCCCCTGCAACGACAATTACTC-TAATGAG-ATTGGATCTGA
1 ATTACCAGTCCAGGCTAAATCCCCTGCAA-GACAA--ACTCAT-A-GAGTATT-G-TCGGA
16407536 ATTACCAGTCCAGGCTAAAT
1 ATTACCAGTCCAGGCTAAAT
16407556 TCAGACCCTA
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
54 28 0.42
55 3 0.05
56 1 0.02
57 8 0.12
58 4 0.06
59 22 0.33
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.26
Consensus pattern (54 bp):
ATTACCAGTCCAGGCTAAATCCCCTGCAAGACAAACTCATAGAGTATTGTCGGA
Found at i:16409533 original size:11 final size:11
Alignment explanation
Indices: 16409517--16409568 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
16409507 TATACTAAAT
16409517 AAATAATAATA
1 AAATAATAATA
*
16409528 AAATAAT-ATT
1 AAATAATAATA
* *
16409538 AAATATCTCATA
1 AAATA-ATAATA
*
16409550 AAATATTAATA
1 AAATAATAATA
16409561 AAATAATA
1 AAATAATA
16409569 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:16412465 original size:46 final size:45
Alignment explanation
Indices: 16412405--16412761 Score: 476
Period size: 46 Copynumber: 8.0 Consensus size: 45
16412395 TTTGACATGA
* * * * * *
16412405 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
*** **
16412451 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
*
16412497 TGCCATGGTATCTTTCAATCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
*
16412543 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
*
16412588 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
*
16412634 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
16412680 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
16412718 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAG
16412762 AGAGCACACT
Statistics
Matches: 284, Mismatches: 17, Indels: 20
0.88 0.05 0.06
Matches are distributed among these distances:
38 34 0.12
40 3 0.01
43 1 0.00
44 3 0.01
45 45 0.16
46 198 0.70
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
Found at i:16412629 original size:137 final size:135
Alignment explanation
Indices: 16412405--16412760 Score: 515
Period size: 137 Copynumber: 2.6 Consensus size: 135
16412395 TTTGACATGA
* * * * *
16412405 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTT-T-TCAGGTTGCCATGGTATCTTTCAAC
*** *
16412470 CATGGTCTTGTTCATTTCATATCACATTGCCATGGTATCTTTCAATCATGGTCTTACACATTTCA
63 CATGGTCTTACACATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCA
16412535 TATCAGGT
128 TATCAGGT
16412543 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTATATCAGGTTGCCATGGTATCTTTCAACC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTT-T-TCAGGTTGCCATGGTATCTTTCAACC
* ** *
16412608 ATGGTCTTACACATTTTATATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTAT
64 ATGGTCTTACACATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
16412673 ATCAGGT
129 ATCAGGT
16412680 TGCCATGGTATCTTTCAACCATGGTCTTACAC-----TCAGGTTGCCATGGTATCTTTCAACCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTTCAGGTTGCCATGGTATCTTTCAACCAT
16412740 GGTCTTACACATTTCATATCA
66 GGTCTTACACATTTCATATCA
16412761 GAGAGCACAC
Statistics
Matches: 202, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
130 48 0.24
137 125 0.62
138 29 0.14
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (135 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTTCAGGTTGCCATGGTATCTTTCAACCAT
GGTCTTACACATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
CAGGT
Found at i:16412725 original size:38 final size:38
Alignment explanation
Indices: 16412674--16412749 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
16412664 ACATTTTATA
16412674 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
16412712 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
16412750 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:16416009 original size:30 final size:30
Alignment explanation
Indices: 16415975--16416076 Score: 129
Period size: 30 Copynumber: 3.5 Consensus size: 30
16415965 ATAGTGAATC
*
16415975 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
16416005 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * * *
16416033 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAACT
16416063 CGCACACTTAGTGC
1 CGCACACTTAGTGC
16416077 CAATCTTGTC
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
27 2 0.03
28 22 0.35
30 38 0.60
31 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:16423781 original size:30 final size:30
Alignment explanation
Indices: 16423726--16423856 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
16423716 ATAGTGAATC
*
16423726 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
16423755 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
16423785 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * * *
16423813 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAACT
16423843 CGCACACTTAGTGC
1 CGCACACTTAGTGC
16423857 CAATCTTGTC
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 19 0.21
30 48 0.52
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:16423836 original size:58 final size:58
Alignment explanation
Indices: 16423725--16423856 Score: 176
Period size: 58 Copynumber: 2.3 Consensus size: 58
16423715 TATAGTGAAT
* * * * *
16423725 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC
1 CCGCACACTTAGTGCTATATA-TATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
* *
16423784 TCGCACACTTAGTGCTATATA-ATCAAACTCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATACAATTTTAAAC
16423842 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
16423857 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 2 0.03
58 42 0.66
59 20 0.31
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (58 bp):
CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
Found at i:16433381 original size:27 final size:29
Alignment explanation
Indices: 16433351--16433464 Score: 99
Period size: 30 Copynumber: 4.0 Consensus size: 29
16433341 ATGCAAGAGC
*
16433351 ATATA-GTGAATC-CGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
* **
16433378 ATATATTTTCAGCTCGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
* ** *
16433407 ATATAATTTTCAGCTCGCACACTTAGTGTT
1 ATAT-ATGTGAAGCTCGCACACTTAGTGCT
* * *
16433437 ATATA-ATCAAACTCGCACACTTAGTGCT
1 ATATATGTGAAGCTCGCACACTTAGTGCT
16433465 GTACAATTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
27 5 0.07
28 21 0.28
29 20 0.27
30 28 0.38
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (29 bp):
ATATATGTGAAGCTCGCACACTTAGTGCT
Found at i:16433418 original size:30 final size:30
Alignment explanation
Indices: 16433363--16433493 Score: 162
Period size: 30 Copynumber: 4.5 Consensus size: 30
16433353 ATAGTGAATC
*
16433363 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
16433392 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
16433422 CGCACACTTAGTGTTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * * *
16433450 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAACT
16433480 CGCACACTTAGTGC
1 CGCACACTTAGTGC
16433494 CAATCTTGTC
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
27 2 0.02
28 21 0.23
29 19 0.21
30 47 0.52
31 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:16433473 original size:58 final size:59
Alignment explanation
Indices: 16433362--16433493 Score: 169
Period size: 58 Copynumber: 2.3 Consensus size: 59
16433352 TATAGTGAAT
** * * * *
16433362 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC
1 CCGCACACTTAGTGCTATATATAATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
* *
16433421 TCGCACACTTAGTG-T-TATATAATCAAACTCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATATATAATC-AACTCGCACACTTAGTGCTATACAATTTTAAAC
16433479 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
16433494 CAATCTTGTC
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
57 7 0.11
58 42 0.68
59 13 0.21
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (59 bp):
CCGCACACTTAGTGCTATATATAATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
Found at i:16435417 original size:11 final size:11
Alignment explanation
Indices: 16435401--16435452 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
16435391 TATACTAAAT
16435401 AAATAATAATA
1 AAATAATAATA
*
16435412 AAATAAT-ATT
1 AAATAATAATA
* *
16435422 AAATATCTCATA
1 AAATA-ATAATA
*
16435434 AAATATTAATA
1 AAATAATAATA
16435445 AAATAATA
1 AAATAATA
16435453 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:16438346 original size:46 final size:46
Alignment explanation
Indices: 16438294--16438697 Score: 671
Period size: 46 Copynumber: 9.0 Consensus size: 46
16438284 TTTGACATGA
*** * **
16438294 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
*
16438340 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
16438386 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
16438432 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
16438478 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
16438524 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
*
16438570 TGCCATGGTATCTTTCAACCACGGTCTTACACATTTTATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
16438616 TGCCATGGTATCTTTCAACCATGGTCTTACAC--------TCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
*
16438654 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAG
16438698 AGAGCACACT
Statistics
Matches: 342, Mismatches: 8, Indels: 16
0.93 0.02 0.04
Matches are distributed among these distances:
38 38 0.11
46 304 0.89
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATATCAGGT
Found at i:16438661 original size:38 final size:38
Alignment explanation
Indices: 16438610--16438685 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
16438600 ACATTTTATA
16438610 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
16438648 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
16438686 ATTTCATATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (38 bp):
TCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:16445242 original size:28 final size:28
Alignment explanation
Indices: 16445181--16445278 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
16445171 TCACAAATTG
** * *
16445181 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
*
16445210 GCACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
16445238 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
16445266 GCACTAAGTGTGC
1 GCACTAAGTGTGC
16445279 GGGCTTATTG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.02
28 43 0.72
29 16 0.27
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:16448307 original size:11 final size:11
Alignment explanation
Indices: 16448291--16448342 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
16448281 TATACTAAAT
16448291 AAATAATAATA
1 AAATAATAATA
*
16448302 AAATAAT-ATT
1 AAATAATAATA
* *
16448312 AAATATCTCATA
1 AAATA-ATAATA
*
16448324 AAATATTAATA
1 AAATAATAATA
16448335 AAATAATA
1 AAATAATA
16448343 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:16449322 original size:43 final size:43
Alignment explanation
Indices: 16449258--16449380 Score: 153
Period size: 43 Copynumber: 2.9 Consensus size: 43
16449248 ATTGAGATGT
* *
16449258 GATTACATGTAAGACCTTGTGTGGGACAGTGGCATTG-TATTAC
1 GATTACATGTAAGACCTTGTGTGGGACAGTGGCATCGTTAAT-C
* *
16449301 GATTACATGTAAGACCATGTGTGGGACA-TCCGCATCGTTAATC
1 GATTACATGTAAGACCTTGTGTGGGACAGT-GGCATCGTTAATC
*
16449344 GACTT-CGTGTAAGACCTTGTGTGGGACAGTGGCATCG
1 GA-TTACATGTAAGACCTTGTGTGGGACAGTGGCATCG
16449381 ATACGTGTTA
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
42 1 0.01
43 62 0.90
44 6 0.09
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (43 bp):
GATTACATGTAAGACCTTGTGTGGGACAGTGGCATCGTTAATC
Found at i:16450450 original size:46 final size:45
Alignment explanation
Indices: 16450400--16450575 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 45
16450390 TGGTTGAGCA
*
16450400 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAA-G
*** * *
16450446 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTACGCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-TACGAAG
* * *
16450493 TCCTAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAA-G
* *
16450539 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
16450576 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
44 5 0.05
45 1 0.01
46 67 0.62
47 30 0.28
48 1 0.01
49 4 0.04
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAAG
Found at i:16474399 original size:20 final size:20
Alignment explanation
Indices: 16474352--16474401 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
16474342 TGAAAATTAA
* *
16474352 TTTCCAAAAATATCATATTT
1 TTTCCAAAAATATCAGATAT
16474372 TTTCCCAAAAATCAT-AGATAT
1 TTT-CCAAAAAT-ATCAGATAT
16474393 TTTCCAAAA
1 TTTCCAAAA
16474402 TTAATTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 9 0.35
21 15 0.58
22 2 0.08
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (20 bp):
TTTCCAAAAATATCAGATAT
Found at i:16484092 original size:24 final size:24
Alignment explanation
Indices: 16484060--16484106 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
16484050 TTCAACAGGC
16484060 GCAGTCCCTTGCGCGGGAGCCGGT
1 GCAGTCCCTTGCGCGGGAGCCGGT
16484084 GCAGTCCCTTGCGCGGGAGCCGG
1 GCAGTCCCTTGCGCGGGAGCCGG
16484107 CGCATTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.09, C:0.34, G:0.43, T:0.15
Consensus pattern (24 bp):
GCAGTCCCTTGCGCGGGAGCCGGT
Found at i:16485631 original size:16 final size:17
Alignment explanation
Indices: 16485581--16485631 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
16485571 ATAGAAATAT
*
16485581 AATCTTTAAGGATATGC
1 AATCTTGAAGGATATGC
*
16485598 AATCTTAGATATGATATGC
1 AATCTT-GA-AGGATATGC
16485617 AATCTTGAA-GATATG
1 AATCTTGAAGGATATG
16485632 ATCTTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 6 0.20
17 7 0.23
18 3 0.10
19 14 0.47
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (17 bp):
AATCTTGAAGGATATGC
Found at i:16485650 original size:22 final size:21
Alignment explanation
Indices: 16485591--16485633 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
16485581 AATCTTTAAG
16485591 GATATGCAATCTT--AGATAT
1 GATATGCAATCTTGAAGATAT
16485610 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTTGAAGATAT
16485631 GAT
1 GAT
16485634 CTTGTAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (21 bp):
GATATGCAATCTTGAAGATAT
Found at i:16485862 original size:14 final size:14
Alignment explanation
Indices: 16485843--16485873 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
16485833 CTGTTGTTTG
16485843 TTCTTATTTTATTC
1 TTCTTATTTTATTC
16485857 TTCTTATTTTATTC
1 TTCTTATTTTATTC
16485871 TTC
1 TTC
16485874 GTCTATCTTA
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:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (14 bp):
TTCTTATTTTATTC
Found at i:16491291 original size:10 final size:10
Alignment explanation
Indices: 16491276--16491312 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
16491266 TTCTATTTCA
16491276 AAAAAAAAGG
1 AAAAAAAAGG
16491286 -AAAAAAA-G
1 AAAAAAAAGG
16491294 AAAATAAAAGG
1 AAAA-AAAAGG
16491305 AAAAAAAA
1 AAAAAAAA
16491313 AATAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
8 1 0.04
9 10 0.42
10 8 0.33
11 5 0.21
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGG
Found at i:16491302 original size:19 final size:18
Alignment explanation
Indices: 16491275--16491332 Score: 82
Period size: 17 Copynumber: 3.2 Consensus size: 18
16491265 CTTCTATTTC
*
16491275 AAAAAAAAAGGAAAAAAAG
1 AAAATAAAAGG-AAAAAAG
16491294 AAAATAAAAGGAAAAAA-
1 AAAATAAAAGGAAAAAAG
*
16491311 AAAATAAAAAGAAAAAAG
1 AAAATAAAAGGAAAAAAG
16491329 AAAA
1 AAAA
16491333 AAATGGAGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 16 0.44
18 10 0.28
19 10 0.28
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (18 bp):
AAAATAAAAGGAAAAAAG
Found at i:16492334 original size:44 final size:44
Alignment explanation
Indices: 16492192--16493030 Score: 748
Period size: 44 Copynumber: 19.1 Consensus size: 44
16492182 CAGAGAAACG
16492192 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
* * * * * * **
16492236 AGATCTGACA-CTCCTATGCTTACAGCGAAGCAGATCGAAGATTTC
1 AGATTTGGCATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGC
*
16492281 AGCA--TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGC
16492324 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
* * * * * **
16492368 AGATCTGACA-CTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTC
1 AGATTTGGCATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGC
*
16492413 AGCA--TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGC
16492456 AGATTTGGCATCCCTGTG-TTATAGGGAACAGATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
* * * * * **
16492499 AGATCTGACA-CTCCTGTGCTTACAGCGAAGCAGATCGAAGATTTC
1 AGATTTGGCATC-CCTGTGTTTATAGGGAA-CAGATCGAAGATAGC
* * *
16492544 -GGTATGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGC
* *
16492587 ATATTTGGCATCACTGTGTTTATAGGGAACAGATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
* ** * * * * **
16492631 AGATCTAACATTCCTGTGCTTACAGTGAAGCAGATCGAAGATTTC
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGC
*
16492676 AGCA--TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGC
* *
16492719 AGATTTGGCATCCCTGTATTTATAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
* * * * * * **
16492763 AGATCTGACATTCCTGTGATTACAGCGAAGCAGATCGAAGATTTC
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGC
*
16492808 AGCA--TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGC
* *
16492851 AGATTTGGCATCACTGTGTTTATAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
* * * * * ** ***
16492895 AGATCTGACATTCCTATGCTTATAGCAAAGCAGATCGAAGATTTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGC
* *
16492940 AGCA--TGGCATCCCTGTGTTTATAGGGAACA-AGTTGAAGATAAC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGC
* * *
16492983 AGATTTGGCATCCCTGTGTTTACAGGGAACAAATCGAAGATAAC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
16493027 AGAT
1 AGAT
16493031 CTAGCATCTC
Statistics
Matches: 636, Mismatches: 118, Indels: 82
0.76 0.14 0.10
Matches are distributed among these distances:
42 12 0.02
43 107 0.17
44 419 0.66
45 93 0.15
46 5 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (44 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
Found at i:16492429 original size:132 final size:132
Alignment explanation
Indices: 16492192--16493032 Score: 1468
Period size: 132 Copynumber: 6.4 Consensus size: 132
16492182 CAGAGAAACG
*
16492192 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTATGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
16492257 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
16492322 GC
131 GC
16492324 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
16492389 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
16492454 GC
131 GC
16492456 AGATTTGGCATCCCTGTG-TTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
* *
16492520 ACAGCGAAGCAGATCGAAGATTTCGGTATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
16492585 GC
131 GC
* * * *
16492587 ATATTTGGCATCACTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTAACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
*
16492652 ACAGTGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
16492717 GC
131 GC
* * * *
16492719 AGATTTGGCATCCCTGTATTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
16492784 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
16492849 GC
131 GC
* * * *
16492851 AGATTTGGCATCACTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTATGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
* * *
16492916 ATAGCAAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
*
16492981 AC
131 GC
* * *
16492983 AGATTTGGCATCCCTGTGTTTACAGGGAACAAATCGAAGATAACAGATCT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCT
16493033 AGCATCTCCA
Statistics
Matches: 680, Mismatches: 28, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
131 127 0.19
132 553 0.81
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (132 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGCAGATCTGACACTCCTGTGCTT
ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
GC
Found at i:16493636 original size:19 final size:19
Alignment explanation
Indices: 16493612--16493690 Score: 117
Period size: 19 Copynumber: 4.2 Consensus size: 19
16493602 AATCTTTAAG
*
16493612 GATATGAAATCTTAGATAT
1 GATATGCAATCTTAGATAT
16493631 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
16493650 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
16493667 GATATGCAATCTTAAAGATAT
1 GATATGCAATCTT--AGATAT
16493688 GAT
1 GAT
16493691 CTTGTAATCT
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
17 17 0.31
19 29 0.53
21 9 0.16
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:16493642 original size:36 final size:35
Alignment explanation
Indices: 16493602--16493689 Score: 117
Period size: 36 Copynumber: 2.4 Consensus size: 35
16493592 ATGGAAATAT
16493602 AATCTTTAAGGATATGA-AATCTTAGATATGATATGC
1 AATC-TTAA-GATATGACAATCTTAGATATGATATGC
16493638 AATCTT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTAAGATATG--ACAATCTTAGATATGATATGC
16493674 AATCTTAAAGATATGA
1 AATCTT-AAGATATGA
16493690 TCTTGTAATC
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
33 6 0.13
34 1 0.02
35 3 0.06
36 30 0.64
38 7 0.15
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (35 bp):
AATCTTAAGATATGACAATCTTAGATATGATATGC
Found at i:16493919 original size:14 final size:14
Alignment explanation
Indices: 16493900--16493930 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
16493890 CTGTGGTTTG
16493900 TTCTTATTTTATTC
1 TTCTTATTTTATTC
16493914 TTCTTATTTTATTC
1 TTCTTATTTTATTC
16493928 TTC
1 TTC
16493931 GTCTATCTTA
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:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (14 bp):
TTCTTATTTTATTC
Found at i:16496833 original size:19 final size:18
Alignment explanation
Indices: 16496809--16496849 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
16496799 ATTATGGTTC
16496809 AAAATAAGCTAAAATATA
1 AAAATAAGCTAAAATATA
* *
16496827 TAAAATATGCTGAAATATA
1 -AAAATAAGCTAAAATATA
16496846 AAAA
1 AAAA
16496850 CGTAAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.24
Consensus pattern (18 bp):
AAAATAAGCTAAAATATA
Found at i:16500727 original size:43 final size:42
Alignment explanation
Indices: 16500671--16500800 Score: 136
Period size: 43 Copynumber: 3.0 Consensus size: 42
16500661 TGCTCGTACA
* ** *
16500671 ATGCCATATCCCAGTTATGGTCTTACATGTTATCACATATCG
1 ATGCCATGTCCCAGACATGGTCTTACATGTAATCACATATCG
** * *
16500713 ATGCCACTGTCCCAGACATGGTCTTACACATAATCTCA-ATGCA
1 ATGCCA-TGTCCCAGACATGGTCTTACATGTAATCACATAT-CG
* *
16500756 ATGCCAATGTCCCAAACATGGTCTTACATGTAATCACATCTCG
1 ATGCC-ATGTCCCAGACATGGTCTTACATGTAATCACATATCG
16500799 AT
1 AT
16500801 ATCCTAATGT
Statistics
Matches: 70, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
42 8 0.11
43 60 0.86
44 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (42 bp):
ATGCCATGTCCCAGACATGGTCTTACATGTAATCACATATCG
Found at i:16505786 original size:43 final size:42
Alignment explanation
Indices: 16505720--16505925 Score: 134
Period size: 42 Copynumber: 4.8 Consensus size: 42
16505710 AACAAGTACA
* * * *
16505720 ATGCCGACGTCCCAGA-TGTGGTCTTACATGTAATTCA-ATATCG
1 ATGCCGATGTCCCAGACAG-GGTCTTACACG-AAATCAGATA-CG
**
16505763 ATGCCTCTGTCCCAGACAGGGTCTTACACGAAATCAGATACG
1 ATGCCGATGTCCCAGACAGGGTCTTACACGAAATCAGATACG
* * *
16505805 ATGCCGATGTCCCAGACATGGTCTTATACATAAATCTCA-AT-CG
1 ATGCCGATGTCCCAGACAGGGTCTTACAC-GAAA--TCAGATACG
* ** * *
16505848 AGGCCTG-TGTCTTAGACACGGTCTTACAGGAAATCAGATACG
1 ATGCC-GATGTCCCAGACAGGGTCTTACACGAAATCAGATACG
* * * * *
16505890 ATTCCAATGTCTCAGACATGGTCTTATACGTAAATC
1 ATGCCGATGTCCCAGACAGGGTCTTACACG-AAATC
16505926 TCAATTGAGG
Statistics
Matches: 128, Mismatches: 25, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
40 3 0.02
41 2 0.02
42 59 0.46
43 57 0.45
44 4 0.03
45 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (42 bp):
ATGCCGATGTCCCAGACAGGGTCTTACACGAAATCAGATACG
Found at i:16505865 original size:85 final size:84
Alignment explanation
Indices: 16505776--16505959 Score: 278
Period size: 85 Copynumber: 2.2 Consensus size: 84
16505766 CCTCTGTCCC
* *
16505776 AGACAGGGTCTTACACGAAATCAGATACGATGCCGATGTCCCAGACATGGTCTTATACATAAATC
1 AGACACGGTCTTACACGAAATCAGATACGATGCCAATGTCCCAGACATGGTCTTATACATAAATC
* *
16505841 TCAATCGAGGCCTGTGTCTT
66 TCAATCGAGGCCTAT-TCCT
* * * *
16505861 AGACACGGTCTTACAGGAAATCAGATACGATTCCAATGTCTCAGACATGGTCTTATACGTAAATC
1 AGACACGGTCTTACACGAAATCAGATACGATGCCAATGTCCCAGACATGGTCTTATACATAAATC
*
16505926 TCAATTGAGGCCTATTCCT
66 TCAATCGAGGCCTATTCCT
16505945 AGACACGGTCTTACA
1 AGACACGGTCTTACA
16505960 TGATATCTCA
Statistics
Matches: 90, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
84 18 0.20
85 72 0.80
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (84 bp):
AGACACGGTCTTACACGAAATCAGATACGATGCCAATGTCCCAGACATGGTCTTATACATAAATC
TCAATCGAGGCCTATTCCT
Found at i:16513170 original size:41 final size:41
Alignment explanation
Indices: 16513109--16513229 Score: 147
Period size: 41 Copynumber: 2.9 Consensus size: 41
16513099 ATGCTATCTC
16513109 ATATCGATGCCACTGTCCCAGACAGGGTCTTACACGAATCAA
1 ATATCGATGCCA-TGTCCCAGACAGGGTCTTACACGAATCAA
* * *
16513151 ATA-CGATGCCGATGTCCCAGACATGGTCTTAAACGTAATCAC
1 ATATCGATGCC-ATGTCCCAGACAGGGTCTTACACG-AATCAA
*
16513193 ATATCGATGCCAATGTCCCAGA-TGTGGTCTTACACGA
1 ATATCGATGCC-ATGTCCCAGACAG-GGTCTTACACGA
16513230 GAACACATAT
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
41 28 0.41
42 13 0.19
43 27 0.40
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (41 bp):
ATATCGATGCCATGTCCCAGACAGGGTCTTACACGAATCAA
Found at i:16513237 original size:43 final size:42
Alignment explanation
Indices: 16513072--16513240 Score: 189
Period size: 43 Copynumber: 4.0 Consensus size: 42
16513062 ATATCATACA
* * * *
16513072 ATGCCAACGTCCCAGACGTGGTCTTACATGCTATCTCATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG-AATCACATATCG
* *
16513115 ATGCCACTGTCCCAGACAG-GGTCTTACACGAATCAAATA-CG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGAATCACATATCG
* * *
16513156 ATGCCGATGTCCCAGACATGGTCTTAAACGTAATCACATATCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG-AATCACATATCG
* *
16513199 ATGCCAATGTCCCAGATGTGGTCTTACACGAGAACACATATC
1 ATGCCAATGTCCCAGACGTGGTCTTACACGA-ATCACATATC
16513241 AGAAACCCTA
Statistics
Matches: 105, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
41 27 0.26
42 15 0.14
43 62 0.59
44 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGAATCACATATCG
Found at i:16517724 original size:20 final size:20
Alignment explanation
Indices: 16517701--16517738 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
16517691 CACATCCAAA
*
16517701 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
16517721 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
16517739 GCGAATAAAC
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:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:16526050 original size:29 final size:29
Alignment explanation
Indices: 16526024--16526096 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
16526014 TTTTCAGCTT
* *
16526024 GCACACATAGTGTCATATTTTTCCAGCAC
1 GCACACTTAGTGCCATATTTTTCCAGCAC
*
16526053 GCACACTTAGTGCCATATATTTCCAGCAC
1 GCACACTTAGTGCCATATTTTTCCAGCAC
16526082 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
16526097 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (29 bp):
GCACACTTAGTGCCATATTTTTCCAGCAC
Found at i:16527449 original size:24 final size:24
Alignment explanation
Indices: 16527413--16527464 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
16527403 TCCACACACA
* *
16527413 CTTTTTTTTTTTCTTTTCTAT-TT
1 CTTTTTTATTTTCATTTCTATATT
*
16527436 CTTTTATTATTTTCATTTCTTTATT
1 CTTTT-TTATTTTCATTTCTATATT
16527461 CTTT
1 CTTT
16527465 CTACATAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.21
24 13 0.54
25 6 0.25
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (24 bp):
CTTTTTTATTTTCATTTCTATATT
Found at i:16534125 original size:29 final size:29
Alignment explanation
Indices: 16534099--16534171 Score: 119
Period size: 29 Copynumber: 2.5 Consensus size: 29
16534089 TTTTCAGCTT
* *
16534099 GCACACATAGTGTCATATTTTTCCAGCAC
1 GCACACTTAGTGCCATATTTTTCCAGCAC
*
16534128 GCACACTTAGTGCCATATATTTCCAGCAC
1 GCACACTTAGTGCCATATTTTTCCAGCAC
16534157 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
16534172 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (29 bp):
GCACACTTAGTGCCATATTTTTCCAGCAC
Found at i:16539871 original size:2 final size:2
Alignment explanation
Indices: 16539864--16539893 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16539854 TTACACATAC
16539864 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
16539894 TTGTATATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16550094 original size:18 final size:17
Alignment explanation
Indices: 16550055--16550097 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
16550045 ATTATTAAGA
*
16550055 ATAAATAAAAGAACAAG
1 ATAAATAAAAAAACAAG
* *
16550072 TTAAATAAAAAAATATAG
1 ATAAATAAAAAAACA-AG
16550090 ATAAATAA
1 ATAAATAA
16550098 TAACAATAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.21
Consensus pattern (17 bp):
ATAAATAAAAAAACAAG
Found at i:16552896 original size:15 final size:15
Alignment explanation
Indices: 16552878--16552906 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
16552868 GTTTGATAAA
16552878 CTAAAAAATTAAGTC
1 CTAAAAAATTAAGTC
16552893 CTAAAAAATTAAGT
1 CTAAAAAATTAAGT
16552907 ATTGAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.07, T:0.28
Consensus pattern (15 bp):
CTAAAAAATTAAGTC
Found at i:16554804 original size:111 final size:109
Alignment explanation
Indices: 16554658--16554866 Score: 287
Period size: 111 Copynumber: 1.9 Consensus size: 109
16554648 CTTACATTAT
*
16554658 TCTCAAGTTTCCCTCTCTCTCTCTCTCTTTCTCTTTTTTCTCACTTTCTTATTTCCTTTTGTCAT
1 TCTCAAGTTTCCCTCTCTCTCTCTCCCTTTCTCTTTTTTCTCACTTTCTTATTTCCTTTTG-CAT
16554723 CCCT-TTTTTGCTAATT-CCCAAGCAAATTTCTTTTTAAATTTCGTTC
65 CCCTCTTTTT-CTAATTCCCCAAGC-AATTT-TTTTTAAATTTCGTTC
* * * * * * *
16554769 TCTCATGTTTCCCTCTCTCTGTCTCCCTTTTTCTTTTTTCTCACTTTTTTGTTTCCTTTTGCCTT
1 TCTCAAGTTTCCCTCTCTCTCTCTCCCTTTCTCTTTTTTCTCACTTTCTTATTTCCTTTTGCATC
*
16554834 CCTCTTTTTCTATTTCCCCAAGCAATTTTTTTT
66 CCTCTTTTTCTAATTCCCCAAGCAATTTTTTTT
16554867 CATTTTTGTT
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
109 5 0.06
110 15 0.17
111 67 0.77
ACGTcount: A:0.11, C:0.29, G:0.05, T:0.56
Consensus pattern (109 bp):
TCTCAAGTTTCCCTCTCTCTCTCTCCCTTTCTCTTTTTTCTCACTTTCTTATTTCCTTTTGCATC
CCTCTTTTTCTAATTCCCCAAGCAATTTTTTTTAAATTTCGTTC
Found at i:16564034 original size:46 final size:44
Alignment explanation
Indices: 16563915--16564175 Score: 195
Period size: 46 Copynumber: 5.7 Consensus size: 44
16563905 GTTGTGTGCT
* * * ** * *
16563915 AGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATGAGAACC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTATAAGATGTG--TC
* *
16563961 AGTATAAGACATATCTGGGACATGCATCGGCTATAAGATGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTATAAGATGTGTC
* * *
16564005 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ATTGAGACAAGAG-C
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-T-A-AGATGTGTC
* * ** *
16564052 TAATGTAAGACATGTCCGGGACATGCATCGGCCT-CGAGATGTAAGCC
1 -AGTGTAAGACATGTCTGGGACATGCATCGG-CTATAAGATGT--GTC
* *
16564099 AGTGTAAGACATGCCTGGGACATGCATCGGCTAAAAGATGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTATAAGATGTGTC
* *
16564143 AGCGTGAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
16564176 ACTGGTATAT
Statistics
Matches: 171, Mismatches: 30, Indels: 28
0.75 0.13 0.12
Matches are distributed among these distances:
44 21 0.12
45 29 0.17
46 92 0.54
47 17 0.10
48 12 0.07
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTATAAGATGTGTC
Found at i:16564165 original size:138 final size:138
Alignment explanation
Indices: 16563912--16564176 Score: 390
Period size: 138 Copynumber: 1.9 Consensus size: 138
16563902 TTAGTTGTGT
* * * *
16563912 GCTAGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATGAGAACCAGTATAAGACATATCT
1 GCTAATGTAAGACATGTCCAGGACATGCATCGGCCACATGATGAGAACCAGTATAAGACATACCT
* *
16563977 GGGACATGCATCGGCTATAAGATGTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTG
66 GGGACATGCATCGGCTAAAAGATGTGTCAGCGTAAGACCATGTCTGGGACATGGCATCGGCATTG
16564042 AGACAAGA
131 AGACAAGA
* * * * *
16564050 GCTAATGTAAGACATGTCCGGGACATGCATCGGCCTCGA-GATGTA-AGCCAGTGTAAGACATGC
1 GCTAATGTAAGACATGTCCAGGACATGCATCGGCCAC-ATGATG-AGAACCAGTATAAGACATAC
*
16564113 CTGGGACATGCATCGGCTAAAAGATGTGTCAGCGTGAGACCATGTCTGGGACATGGCATCGGCA
64 CTGGGACATGCATCGGCTAAAAGATGTGTCAGCGTAAGACCATGTCTGGGACATGGCATCGGCA
16564177 CTGGTATATG
Statistics
Matches: 113, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
138 111 0.98
139 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (138 bp):
GCTAATGTAAGACATGTCCAGGACATGCATCGGCCACATGATGAGAACCAGTATAAGACATACCT
GGGACATGCATCGGCTAAAAGATGTGTCAGCGTAAGACCATGTCTGGGACATGGCATCGGCATTG
AGACAAGA
Found at i:16572054 original size:23 final size:23
Alignment explanation
Indices: 16572039--16572087 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
16572029 TCATTGGAGT
16572039 TTAACGTTTCAGCTCAATAGAGC
1 TTAACGTTTCAGCTCAATAGAGC
* *
16572062 TTACCGTTTTAGCTCAATAGAGC
1 TTAACGTTTCAGCTCAATAGAGC
16572085 TTA
1 TTA
16572088 TTGTTCATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (23 bp):
TTAACGTTTCAGCTCAATAGAGC
Found at i:16572121 original size:26 final size:25
Alignment explanation
Indices: 16572047--16572121 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 25
16572037 GTTTAACGTT
* * *
16572047 TCAGCTCAATAGAGCTTACCG-T-T
1 TCAGCTCAAGAGAGCTTACTGATCA
* * * *
16572070 TTAGCTCAATAGAGCTTATTGTTCA
1 TCAGCTCAAGAGAGCTTACTGATCA
16572095 TCAGCTCAAGAGAAGCTTACTGATCA
1 TCAGCTCAAGAG-AGCTTACTGATCA
16572121 T
1 T
16572122 GGCTCGAAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 18 0.44
24 1 0.02
25 10 0.24
26 12 0.29
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.32
Consensus pattern (25 bp):
TCAGCTCAAGAGAGCTTACTGATCA
Found at i:16579473 original size:13 final size:13
Alignment explanation
Indices: 16579455--16579488 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
16579445 GTGTTTTGGT
16579455 GCCACACGGCCTG
1 GCCACACGGCCTG
16579468 GCCACACGGCCTG
1 GCCACACGGCCTG
16579481 GCCACACG
1 GCCACACG
16579489 ACCGTGTGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.29, T:0.06
Consensus pattern (13 bp):
GCCACACGGCCTG
Found at i:16581476 original size:21 final size:20
Alignment explanation
Indices: 16581436--16581477 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
16581426 GAAGATTTTG
16581436 TTTTTTTTTTTATTTCTAGT
1 TTTTTTTTTTTATTTCTAGT
16581456 TTTTTATTTATTTATTT-TAGT
1 TTTTT-TTT-TTTATTTCTAGT
16581477 T
1 T
16581478 GTGGGAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 8 0.40
22 7 0.35
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTTTTTTTATTTCTAGT
Found at i:16582792 original size:20 final size:18
Alignment explanation
Indices: 16582756--16582792 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
16582746 ACGACCTTCT
16582756 GTGTTTGTGTGATTGTTC
1 GTGTTTGTGTGATTGTTC
16582774 GTGTTTGGTGTGCATTGTT
1 GTGTTT-GTGTG-ATTGTT
16582793 GCATTTGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.05, C:0.05, G:0.35, T:0.54
Consensus pattern (18 bp):
GTGTTTGTGTGATTGTTC
Found at i:16584043 original size:91 final size:89
Alignment explanation
Indices: 16583896--16584163 Score: 274
Period size: 91 Copynumber: 3.0 Consensus size: 89
16583886 ACACACCAGA
* ** * * *
16583896 TGCACATAGTGCAAACCCATAGGCTAAATATT-TTTCCTCGATAACACGCCATATTGCTCATAAG
1 TGCACATAGTGCAAACCCGTAGGCTAAATATTCTCCCCT-GATAACATGCTAGATTGCTCATAAG
16583960 AGCTTCCACACCGATATCA-TGCTAAAC
65 AGCTTCC-CACCGATATCACT-C-AAAC
* * *
16583987 -GCACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCTGATAACATGTTAGATTGCTCATAAA
1 TGCACATAGTGCAAA-CCCGTAGGCTAAATATTCTCCCCTGATAACATGCTAGATTGCTCATAAG
* *
16584051 AGCTTTCTCACCGATATCACTCCAAC
65 AGC-TTCCCACCGATATCACTCAAAC
* ** * *
16584077 TGCATATAACGCAAAACCCGTAGGCTAAATATTCTTCCCC-AATAACATGGTAGATTGCTCATAA
1 TGCACATAGTGC-AAACCCGTAGGCTAAATATTC-TCCCCTGATAACATGCTAGATTGCTCATAA
*
16584141 GAGCTTTCCCACCGATAACACTC
64 GAGC-TTCCCACCGATATCACTC
16584164 TAGAATCTTT
Statistics
Matches: 150, Mismatches: 20, Indels: 14
0.82 0.11 0.08
Matches are distributed among these distances:
90 17 0.11
91 117 0.78
92 16 0.11
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.26
Consensus pattern (89 bp):
TGCACATAGTGCAAACCCGTAGGCTAAATATTCTCCCCTGATAACATGCTAGATTGCTCATAAGA
GCTTCCCACCGATATCACTCAAAC
Found at i:16586016 original size:23 final size:23
Alignment explanation
Indices: 16585986--16586034 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
16585976 TGATTACGGC
*
16585986 TTAATTAAATTAACT-AATCATGT
1 TTAATTAAATTAA-TAAAACATGT
*
16586009 TTAATTAATTTAATAAAACATGT
1 TTAATTAAATTAATAAAACATGT
16586032 TTA
1 TTA
16586035 TCGATTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (23 bp):
TTAATTAAATTAATAAAACATGT
Found at i:16587922 original size:17 final size:19
Alignment explanation
Indices: 16587891--16587930 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
16587881 CTCAACTAAT
*
16587891 TAGGCCGTGT-GGGCCACA
1 TAGGCCGTGTAGGCCCACA
16587909 TAGG-CGTGTAGGCCCACA
1 TAGGCCGTGTAGGCCCACA
16587927 TAGG
1 TAGG
16587931 TGAACCGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.20, C:0.25, G:0.38, T:0.17
Consensus pattern (19 bp):
TAGGCCGTGTAGGCCCACA
Found at i:16591962 original size:31 final size:32
Alignment explanation
Indices: 16591924--16591991 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
16591914 AAAAATATGA
16591924 GCCCACATACCC-G-TGTGG-CTTGCCTGTGTGG
1 GCCCACATACCCAGAT-TGGCCTTGCCTGTGT-G
*
16591955 GCCCACATGCCCAGATTGGCCTTGCCTGTGTG
1 GCCCACATACCCAGATTGGCCTTGCCTGTGTG
16591987 GCCCA
1 GCCCA
16591992 TACGGCCTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
31 11 0.33
32 10 0.30
33 12 0.36
ACGTcount: A:0.12, C:0.35, G:0.29, T:0.24
Consensus pattern (32 bp):
GCCCACATACCCAGATTGGCCTTGCCTGTGTG
Found at i:16592001 original size:18 final size:18
Alignment explanation
Indices: 16591978--16592017 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
16591968 GATTGGCCTT
*
16591978 GCCTGTGTGGCCCATACG
1 GCCTGTATGGCCCATACG
16591996 GCCTGTATGGCCCATACG
1 GCCTGTATGGCCCATACG
16592014 GCCT
1 GCCT
16592018 TGCCTAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.35, G:0.30, T:0.23
Consensus pattern (18 bp):
GCCTGTATGGCCCATACG
Found at i:16601365 original size:16 final size:16
Alignment explanation
Indices: 16601344--16601378 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
16601334 CTCACGTTCT
* *
16601344 TTTCTTTTTCTTTTTC
1 TTTCTTTCTCTTTTAC
16601360 TTTCTTTCTCTTTTAC
1 TTTCTTTCTCTTTTAC
16601376 TTT
1 TTT
16601379 TGTTTTTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTCTCTTTTAC
Found at i:16602503 original size:21 final size:21
Alignment explanation
Indices: 16602478--16602520 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
16602468 AGTTACGTTT
*
16602478 ATGATGAGGAGGAACTTCTGG
1 ATGATGAGAAGGAACTTCTGG
*
16602499 ATGATGAGAAGGAAGTTCTGG
1 ATGATGAGAAGGAACTTCTGG
16602520 A
1 A
16602521 AGACTATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.37, T:0.23
Consensus pattern (21 bp):
ATGATGAGAAGGAACTTCTGG
Found at i:16604868 original size:12 final size:12
Alignment explanation
Indices: 16604851--16604880 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16604841 TACAGGTTTG
16604851 ACACGACCTAGC
1 ACACGACCTAGC
*
16604863 ACACGACCTGGC
1 ACACGACCTAGC
16604875 ACACGA
1 ACACGA
16604881 GCGTGTGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.33, C:0.40, G:0.20, T:0.07
Consensus pattern (12 bp):
ACACGACCTAGC
Found at i:16608691 original size:28 final size:28
Alignment explanation
Indices: 16608651--16608711 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
16608641 TAAGTGTAAT
* *
16608651 ATTAAACAAATTGTTTTAATAAAAATCC
1 ATTAAACAAATTGGTTCAATAAAAATCC
16608679 ATTAAACAAATTGGTTCAATAAAAATCC
1 ATTAAACAAATTGGTTCAATAAAAATCC
16608707 ATTAA
1 ATTAA
16608712 TTACATCAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.33
Consensus pattern (28 bp):
ATTAAACAAATTGGTTCAATAAAAATCC
Found at i:16609840 original size:14 final size:13
Alignment explanation
Indices: 16609801--16609842 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
16609791 ATTATTATTT
16609801 AATTAAATAATTG
1 AATTAAATAATTG
16609814 AAGTTCAAA-AATTG
1 AA-TT-AAATAATTG
16609828 AATTAAATTAATTG
1 AATTAAA-TAATTG
16609842 A
1 A
16609843 TCATTGTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.12
13 4 0.16
14 15 0.60
15 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (13 bp):
AATTAAATAATTG
Found at i:16625652 original size:55 final size:54
Alignment explanation
Indices: 16625576--16625680 Score: 165
Period size: 55 Copynumber: 1.9 Consensus size: 54
16625566 TAATACGAGC
*
16625576 GTGCGACACACCATGCCCACCACCCATGGTCGAAACTGTAAAAATAACACGGGT
1 GTGCGACACACCATGCCCACCACCCATGGTCAAAACTGTAAAAATAACACGGGT
* * *
16625630 GTGCGACACACCCATGCCCACCACCCGTGGTCAAAACTTTCAAAATAACAC
1 GTGCGACACA-CCATGCCCACCACCCATGGTCAAAACTGTAAAAATAACAC
16625681 AGGCGTGCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 10 0.22
55 36 0.78
ACGTcount: A:0.33, C:0.34, G:0.17, T:0.15
Consensus pattern (54 bp):
GTGCGACACACCATGCCCACCACCCATGGTCAAAACTGTAAAAATAACACGGGT
Found at i:16629033 original size:40 final size:40
Alignment explanation
Indices: 16628946--16629117 Score: 256
Period size: 40 Copynumber: 4.3 Consensus size: 40
16628936 TCTTCAGGAT
* * * * *
16628946 TTAG-CCGAATATAACCACACGCCCAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
* * *
16628985 TTAACCCGGACATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
16629025 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
*
16629065 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGGC
1 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
16629105 TTAGCCCGGATAT
1 TTAGCCCGGATAT
16629118 CATTCAAATG
Statistics
Matches: 120, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 3 0.03
40 117 0.98
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.22
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTC
Done.