Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 63 of 226
Found at i:20403168 original size:24 final size:24
Alignment explanation
Indices: 20403139--20403210 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 24
20403129 AAAAAAAAAA
20403139 ACTTAAACATAGAATTTTATAAAT
1 ACTTAAACATAGAATTTTATAAAT
* *
20403163 AGTT-AACATGAAGTGTTATTTTATAAAT
1 ACTTAAACAT--A--G-AATTTTATAAAT
20403191 ACTTAAACATAGAATTTTAT
1 ACTTAAACATAGAATTTTAT
20403211 TGTTGCCTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
23 5 0.13
24 10 0.26
25 2 0.05
27 2 0.05
28 14 0.37
29 5 0.13
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.40
Consensus pattern (24 bp):
ACTTAAACATAGAATTTTATAAAT
Found at i:20404808 original size:23 final size:23
Alignment explanation
Indices: 20404777--20404829 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
20404767 TGATTTAAAC
* *
20404777 AAATGTTCATA-TTTATATTATTA
1 AAATATTCATATTTTATACTA-TA
20404800 AAATATTCATATTTTATACTATA
1 AAATATTCATATTTTATACTATA
20404823 AAATATT
1 AAATATT
20404830 TTTACTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (23 bp):
AAATATTCATATTTTATACTATA
Found at i:20404875 original size:22 final size:23
Alignment explanation
Indices: 20404850--20404905 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
20404840 TTATAAATTG
*
20404850 TAATATATTTTT-ATTAAAATAT
1 TAATATATTTTTCAATAAAATAT
20404872 TAATATGATTTTTCAATAAAATAT
1 TAATAT-ATTTTTCAATAAAATAT
20404896 TAATAATATT
1 TAAT-ATATT
20404906 AATTCAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 6 0.20
23 6 0.20
24 16 0.53
25 2 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TAATATATTTTTCAATAAAATAT
Found at i:20409616 original size:13 final size:13
Alignment explanation
Indices: 20409592--20409616 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20409582 ATTTTTTTAA
20409592 TGAATAATTTTTT
1 TGAATAATTTTTT
20409605 TGAATAATTTTT
1 TGAATAATTTTT
20409617 ATTTTAATTA
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:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
TGAATAATTTTTT
Found at i:20418543 original size:84 final size:85
Alignment explanation
Indices: 20418421--20418607 Score: 349
Period size: 84 Copynumber: 2.2 Consensus size: 85
20418411 TAGCAACAAA
20418421 AAAATATATAAAATAAAAAATAAAAAAATCCAACAAACTTTAAAAAGAAAAAATCTTCTCCTTCC
1 AAAA-ATATAAAATAAAAAATAAAAAAATCCAACAAACTTTAAAAAGAAAAAATCTTCTCCTTCC
20418486 TTTATTATTATTCTTCTATCC
65 TTTATTATTATTCTTCTATCC
20418507 AAAAATATAAAATAAAAAAT-AAAAAATCCAACAAACTTTAAAAAGAAAAAATCTTCTCCTTCCT
1 AAAAATATAAAATAAAAAATAAAAAAATCCAACAAACTTTAAAAAGAAAAAATCTTCTCCTTCCT
20418571 TTATTATTATTCTTCTATCC
66 TTATTATTATTCTTCTATCC
*
20418591 AAAAATATAAAAGAAAA
1 AAAAATATAAAATAAAA
20418608 TAAATTCCTT
Statistics
Matches: 100, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
84 80 0.80
85 16 0.16
86 4 0.04
ACGTcount: A:0.53, C:0.15, G:0.02, T:0.30
Consensus pattern (85 bp):
AAAAATATAAAATAAAAAATAAAAAAATCCAACAAACTTTAAAAAGAAAAAATCTTCTCCTTCCT
TTATTATTATTCTTCTATCC
Found at i:20421019 original size:16 final size:15
Alignment explanation
Indices: 20420998--20421027 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20420988 AAGTTTTAAA
20420998 AAAACTTTAACAAAAT
1 AAAACTTTAA-AAAAT
20421014 AAAACTTTAAAAAA
1 AAAACTTTAAAAAA
20421028 GTTTAAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAACTTTAAAAAAT
Found at i:20426114 original size:18 final size:18
Alignment explanation
Indices: 20426070--20426105 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
20426060 TTTCTTATAG
* *
20426070 AATTTAGTTTTTTTAATA
1 AATTTAATTCTTTTAATA
20426088 AATTTAATTCTTTTAATA
1 AATTTAATTCTTTTAATA
20426106 TTTTTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (18 bp):
AATTTAATTCTTTTAATA
Found at i:20429193 original size:14 final size:15
Alignment explanation
Indices: 20429176--20429205 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
20429166 TTGATTAAAT
20429176 TAATAAAG-TTAAGA
1 TAATAAAGATTAAGA
20429190 TAATAAAGATTAAGA
1 TAATAAAGATTAAGA
20429205 T
1 T
20429206 GTTTTGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.57, C:0.00, G:0.13, T:0.30
Consensus pattern (15 bp):
TAATAAAGATTAAGA
Found at i:20434122 original size:21 final size:21
Alignment explanation
Indices: 20434077--20434122 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
20434067 AGTTGACAAT
* *
20434077 GAAACAATCGATTGAAAATAA
1 GAAACAATCAATTGAAAAGAA
* *
20434098 GAAACAATCAATTGAACAGAG
1 GAAACAATCAATTGAAAAGAA
20434119 GAAA
1 GAAA
20434123 GAATGAATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.15
Consensus pattern (21 bp):
GAAACAATCAATTGAAAAGAA
Found at i:20441562 original size:25 final size:25
Alignment explanation
Indices: 20441498--20441583 Score: 97
Period size: 25 Copynumber: 3.5 Consensus size: 25
20441488 GCGGGCACAG
*
20441498 CACAGCTTGTACT-AGCTTACCGATT
1 CACAGCTCGTA-TGAGCTTACCGATT
*
20441523 -TCAGCTCGTGA-GAGCTTACCGATT
1 CACAGCTCGT-ATGAGCTTACCGATT
*
20441547 CACAGCTTGTATGAGCTTACCGATT
1 CACAGCTCGTATGAGCTTACCGATT
*
20441572 TACAGCTCGTAT
1 CACAGCTCGTAT
20441584 AAGCATACAT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
24 20 0.39
25 31 0.61
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (25 bp):
CACAGCTCGTATGAGCTTACCGATT
Found at i:20446514 original size:27 final size:27
Alignment explanation
Indices: 20446465--20446519 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
20446455 GTATAGCAAC
* *
20446465 CAAGGTAGTCCACTGGGATAGTAAACA
1 CAAGGTAGTCCACTGGCACAGTAAACA
* *
20446492 CAAGGTAGTCTACTGTCACAGTAAACA
1 CAAGGTAGTCCACTGGCACAGTAAACA
20446519 C
1 C
20446520 GATGATTACG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (27 bp):
CAAGGTAGTCCACTGGCACAGTAAACA
Found at i:20451179 original size:26 final size:26
Alignment explanation
Indices: 20451150--20451223 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
20451140 CTTATGGTAG
20451150 ACACACTCTAGCAAACCCTATGGCAA
1 ACACACTCTAGCAAACCCTATGGCAA
* ** * **
20451176 ACACACTTTAGTGAACCCTATAGTGA
1 ACACACTCTAGCAAACCCTATGGCAA
* *
20451202 ACTCACTCTAACAAACCCTATG
1 ACACACTCTAGCAAACCCTATG
20451224 CCTGGAGAAC
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.36, C:0.31, G:0.11, T:0.22
Consensus pattern (26 bp):
ACACACTCTAGCAAACCCTATGGCAA
Found at i:20453678 original size:21 final size:23
Alignment explanation
Indices: 20453639--20453680 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
20453629 TTCGTAACTC
20453639 AATATTTTAATTCTAATTATTTT
1 AATATTTTAATTCTAATTATTTT
20453662 AATATTTT-ATT-TAATTATT
1 AATATTTTAATTCTAATTATT
20453681 CCTAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (23 bp):
AATATTTTAATTCTAATTATTTT
Found at i:20453688 original size:10 final size:8
Alignment explanation
Indices: 20453668--20453701 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
20453658 TTTTAATATT
20453668 TTATTTAA
1 TTATTTAA
20453676 TTATTCCTAA
1 TTATT--TAA
20453686 TTATTTAA
1 TTATTTAA
20453694 TTATTTAA
1 TTATTTAA
20453702 CCTAAATACG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 16 0.67
10 8 0.33
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.59
Consensus pattern (8 bp):
TTATTTAA
Found at i:20453690 original size:23 final size:23
Alignment explanation
Indices: 20453639--20453695 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
20453629 TTCGTAACTC
*
20453639 AATATTTTAATTCTAATTATTTT
1 AATATTTTAATTCTAATTATTCT
20453662 AATATTTT-ATT-TAATTATTCCT
1 AATATTTTAATTCTAATTATT-CT
20453684 AAT-TATTTAATT
1 AATAT-TTTAATT
20453696 ATTTAACCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
21 9 0.30
22 10 0.33
23 11 0.37
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (23 bp):
AATATTTTAATTCTAATTATTCT
Found at i:20459168 original size:32 final size:30
Alignment explanation
Indices: 20459121--20459194 Score: 114
Period size: 32 Copynumber: 2.4 Consensus size: 30
20459111 ATTTTGCTTC
20459121 AATAAAAAAATATATATGTAGTGTATTTTAAA
1 AATAAAAAAA-ATATATGTAGTGTA-TTTAAA
20459153 AATAATAAAAAATATATGTAGTGTATTTAAA
1 AATAA-AAAAAATATATGTAGTGTATTTAAA
20459184 AA-AAAAAAAAT
1 AATAAAAAAAAT
20459195 TAATCTGATG
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
29 7 0.17
30 2 0.05
31 8 0.20
32 19 0.46
33 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (30 bp):
AATAAAAAAAATATATGTAGTGTATTTAAA
Found at i:20459305 original size:21 final size:22
Alignment explanation
Indices: 20459281--20459334 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
20459271 CACCATTGTT
20459281 TCTAATCTCACCGCTACAGT-A
1 TCTAATCTCACCGCTACAGTAA
*
20459302 TCTAATCTTACCGCTACAGTAA
1 TCTAATCTCACCGCTACAGTAA
20459324 T-TAATCTCACC
1 TCTAATCTCACC
20459335 ACCACCGCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.31, G:0.07, T:0.31
Consensus pattern (22 bp):
TCTAATCTCACCGCTACAGTAA
Found at i:20466879 original size:6 final size:6
Alignment explanation
Indices: 20466868--20466896 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
20466858 TAAAGCAAAT
20466868 ATTTTA ATTTTA ATTTTA ATTTTA ATTTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTT
20466897 TTAAGTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
ATTTTA
Found at i:20467067 original size:17 final size:17
Alignment explanation
Indices: 20467031--20467081 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
20467021 ATTTACTTTG
*
20467031 AAATTTAAT-TAATTTAT
1 AAATTTAATGTTATTT-T
20467048 AAATTTAATGTTATTTT
1 AAATTTAATGTTATTTT
*
20467065 AAAATT-ATGTT-TTTT
1 AAATTTAATGTTATTTT
20467080 AA
1 AA
20467082 TTTCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 6 0.19
16 5 0.16
17 15 0.48
18 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (17 bp):
AAATTTAATGTTATTTT
Found at i:20470069 original size:49 final size:46
Alignment explanation
Indices: 20470016--20470120 Score: 122
Period size: 47 Copynumber: 2.2 Consensus size: 46
20470006 TAGTATAACT
*
20470016 ATGGTCTTGCACAT-AATCACATATCACAAACCAAAGCCATAGCCCAGCC
1 ATGGTCTT--ACATGAAGCACATATCAC--ACCAAAGCCATAGCCCAGCC
* * *
20470065 ATGGTCTTACATGGAAGCACATATCACACCGATGCCATAGCCCAGCT
1 ATGGTCTTACAT-GAAGCACATATCACACCAAAGCCATAGCCCAGCC
20470112 ATGGTCTTA
1 ATGGTCTTA
20470121 TACGGAAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
47 30 0.60
49 20 0.40
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (46 bp):
ATGGTCTTACATGAAGCACATATCACACCAAAGCCATAGCCCAGCC
Found at i:20473546 original size:33 final size:32
Alignment explanation
Indices: 20473509--20473586 Score: 75
Period size: 33 Copynumber: 2.4 Consensus size: 32
20473499 TGACCTTGCC
** * *
20473509 ATGGTCTTACATTTGTAGTGCCATAACCCAGTT
1 ATGGTCTTACATCAG-AATGCCATAACCCAGCT
* * *
20473542 ATGGTTTTATCATCAGAATGTCATAGCCCAGCT
1 ATGGTCTTA-CATCAGAATGCCATAACCCAGCT
20473575 ATGGTCTTACAT
1 ATGGTCTTACAT
20473587 ATATATATAC
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
32 3 0.08
33 29 0.81
34 4 0.11
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (32 bp):
ATGGTCTTACATCAGAATGCCATAACCCAGCT
Found at i:20481168 original size:33 final size:32
Alignment explanation
Indices: 20481052--20481216 Score: 123
Period size: 33 Copynumber: 4.9 Consensus size: 32
20481042 TTGTAGTGCA
* * *
20481052 ATAACCCAGTTATGGTCTTATCATCAGAATGTC
1 ATAACCCAGTTATGGTCTTA-CATTAAAATGCC
*
20481085 ATAACCCAGCTATGGTCTTACATATATATATACTGCC
1 ATAACCCAGTTATGGTCTTACAT-TA-A-A-A-TGCC
*** * * **
20481122 ATGGTCTAATTATGGTCTTACATTCAAGGTGCC
1 ATAACCCAGTTATGGTCTTACATT-AAAATGCC
*
20481155 ATAACCCAGTTATGGTCTTTTCATTAAAATGCC
1 ATAACCCAGTTATGGTC-TTACATTAAAATGCC
* *
20481188 ATAGCCCAGCTATGGTCTTACATTTAAAA
1 ATAACCCAGTTATGGTCTTACA-TTAAAA
20481217 ATTGCCATGG
Statistics
Matches: 101, Mismatches: 23, Indels: 16
0.72 0.16 0.11
Matches are distributed among these distances:
32 7 0.07
33 63 0.62
34 6 0.06
35 1 0.01
36 3 0.03
37 21 0.21
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (32 bp):
ATAACCCAGTTATGGTCTTACATTAAAATGCC
Found at i:20483713 original size:23 final size:23
Alignment explanation
Indices: 20483686--20483784 Score: 171
Period size: 23 Copynumber: 4.3 Consensus size: 23
20483676 AGTGTTATTG
20483686 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
20483709 TTCAGTGGTAACTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
20483732 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
20483755 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
20483778 ATCAGTG
1 ATCAGTG
20483785 TGGCACTTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:20483739 original size:46 final size:46
Alignment explanation
Indices: 20483686--20483784 Score: 189
Period size: 46 Copynumber: 2.2 Consensus size: 46
20483676 AGTGTTATTG
20483686 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAACTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAACTTCGGCTACAT
*
20483732 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAACTTCGGCTACAT
20483778 ATCAGTG
1 ATCAGTG
20483785 TGGCACTTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.32
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAACTTCGGCTACAT
Found at i:20484751 original size:2 final size:2
Alignment explanation
Indices: 20484746--20484777 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20484736 GACATATATA
20484746 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
20484778 ATAATAATGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:20488423 original size:23 final size:23
Alignment explanation
Indices: 20488388--20488443 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
20488378 ATTATTTTAA
*
20488388 TAATATTTAATATTAAATTTAATC
1 TAATA-TTAATATTAAATTAAATC
* * *
20488412 TAATATTGATATTAGATTAAATT
1 TAATATTAATATTAAATTAAATC
20488435 TAATATTAA
1 TAATATTAA
20488444 AGTGATTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (23 bp):
TAATATTAATATTAAATTAAATC
Found at i:20497160 original size:21 final size:21
Alignment explanation
Indices: 20497134--20497180 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
20497124 GTGATGAGAA
*
20497134 TAAAATCTCTTTT-TCCTTATT
1 TAAAATATCTTTTCT-CTTATT
*
20497155 TAAAATATCTTTTCTTTTATT
1 TAAAATATCTTTTCTCTTATT
20497176 TAAAA
1 TAAAA
20497181 AGGAATAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (21 bp):
TAAAATATCTTTTCTCTTATT
Found at i:20511255 original size:13 final size:13
Alignment explanation
Indices: 20511239--20511271 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
20511229 AAGTACCGTG
20511239 GAAAAGTATTTTT
1 GAAAAGTATTTTT
20511252 GAAAAGTATTTTT
1 GAAAAGTATTTTT
20511265 GAAAAGT
1 GAAAAGT
20511272 TTGGTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (13 bp):
GAAAAGTATTTTT
Found at i:20518646 original size:20 final size:20
Alignment explanation
Indices: 20518612--20518653 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
20518602 AACTAATTAA
** *
20518612 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
20518632 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
20518652 AT
1 AT
20518654 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:20518775 original size:21 final size:21
Alignment explanation
Indices: 20518751--20518795 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
20518741 ATGAGATTTC
* *
20518751 ATTTGGAAATCATACCAACAA
1 ATTTGGAAACCACACCAACAA
20518772 ATTTGGAAACCACACCAACAA
1 ATTTGGAAACCACACCAACAA
20518793 ATT
1 ATT
20518796 CTAATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (21 bp):
ATTTGGAAACCACACCAACAA
Found at i:20518816 original size:30 final size:30
Alignment explanation
Indices: 20518771--20518831 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
20518761 CATACCAACA
*
20518771 AATTTGGAAACCACACCAACAAATTCTAAT
1 AATTTAGAAACCACACCAACAAATTCTAAT
*
20518801 AATTTAGAAATCACACCAACAAATTCTAAT
1 AATTTAGAAACCACACCAACAAATTCTAAT
20518831 A
1 A
20518832 TTCTTTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.49, C:0.21, G:0.05, T:0.25
Consensus pattern (30 bp):
AATTTAGAAACCACACCAACAAATTCTAAT
Found at i:20529630 original size:37 final size:39
Alignment explanation
Indices: 20529547--20529639 Score: 93
Period size: 39 Copynumber: 2.4 Consensus size: 39
20529537 TCCAGTATGG
* *
20529547 CACCCAGTGTCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGTCTCATCGGAAAGTCCGAAGCAATAGTTGA
* *
20529586 CATCCAGTGTCTCATCGGCAAAG-CCGAAG-AA-AGTTGG
1 CACCCAGTGTCTCATCGG-AAAGTCCGAAGCAATAGTTGA
* **
20529623 TACCCAGTACCTCATCG
1 CACCCAGTGTCTCATCG
20529640 AATCTATCCA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
37 18 0.40
38 2 0.04
39 22 0.49
40 3 0.07
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (39 bp):
CACCCAGTGTCTCATCGGAAAGTCCGAAGCAATAGTTGA
Found at i:20537301 original size:31 final size:31
Alignment explanation
Indices: 20537266--20537326 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
20537256 TAATAGAATC
*
20537266 ATTAAACTATT-TAAAATTTTTTATTTAAGTT
1 ATTAAACTATTCGAAAA-TTTTTATTTAAGTT
20537297 ATTAAACTATTCGAAAATTTTTATTTAAGT
1 ATTAAACTATTCGAAAATTTTTATTTAAGT
20537327 CATTGGTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (31 bp):
ATTAAACTATTCGAAAATTTTTATTTAAGTT
Found at i:20542521 original size:21 final size:21
Alignment explanation
Indices: 20542497--20542538 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20542487 ATGTTTAACC
20542497 TAATTTTATCTTGTTTTACAT
1 TAATTTTATCTTGTTTTACAT
*
20542518 TAATTTTGTCTTGTTTTACAT
1 TAATTTTATCTTGTTTTACAT
20542539 GATTTCAATC
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:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (21 bp):
TAATTTTATCTTGTTTTACAT
Found at i:20546073 original size:17 final size:17
Alignment explanation
Indices: 20546042--20546084 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
20546032 TATTTCATTG
*
20546042 TTTATTTTTCTTTATTTA
1 TTTA-TTTTCGTTATTTA
*
20546060 TTTCTTTTCGTTATTTA
1 TTTATTTTCGTTATTTA
20546077 TTTATTTT
1 TTTATTTT
20546085 TATCCCTTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTATTTTCGTTATTTA
Found at i:20550921 original size:103 final size:103
Alignment explanation
Indices: 20550738--20550943 Score: 385
Period size: 103 Copynumber: 2.0 Consensus size: 103
20550728 AATATAAGTA
20550738 AAAAAAATCCAGTATAGTAGCAGGTGCGGTTGTGTGGCAACCTCCGAGTCTCTCGCAGCACCGGT
1 AAAAAAATCCAGTATAGTAGCAGGTGCGGTTGTGTGGCAACCTCCGAGTCTCTCGCAGCACCGGT
*
20550803 CCTTAAGACTGGGGATTACCTGTAAGAAAAACAGAGGG
66 CCTTAAGACTAGGGATTACCTGTAAGAAAAACAGAGGG
* *
20550841 AAAAAAATCCAGTATAGTAGCAGGTGCGGTTGTGTGGCCACCTCCGAGTCTCTCGCAGCACTGGT
1 AAAAAAATCCAGTATAGTAGCAGGTGCGGTTGTGTGGCAACCTCCGAGTCTCTCGCAGCACCGGT
20550906 CCTTAAGACTAGGGATTACCTGTAAGAAAAACAGAGGG
66 CCTTAAGACTAGGGATTACCTGTAAGAAAAACAGAGGG
20550944 GGTGAGTTTA
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (103 bp):
AAAAAAATCCAGTATAGTAGCAGGTGCGGTTGTGTGGCAACCTCCGAGTCTCTCGCAGCACCGGT
CCTTAAGACTAGGGATTACCTGTAAGAAAAACAGAGGG
Found at i:20562622 original size:28 final size:28
Alignment explanation
Indices: 20562559--20562709 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
20562549 ATATTAAGTC
*
20562559 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
20562586 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
20562614 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
*
20562642 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
20562670 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
20562699 CGCACACTTAG
1 CGCACACTTAG
20562710 CGCCAATCTC
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 22 0.19
28 77 0.67
29 16 0.14
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:20563174 original size:12 final size:12
Alignment explanation
Indices: 20563157--20563183 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20563147 TGGGCATACT
20563157 TATGTATATATA
1 TATGTATATATA
20563169 TATGTATATATA
1 TATGTATATATA
20563181 TAT
1 TAT
20563184 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:20571921 original size:14 final size:15
Alignment explanation
Indices: 20571902--20571935 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20571892 ATGTAGTAGA
*
20571902 TTTTGT-TGTTTCTG
1 TTTTGTATGGTTCTG
20571916 TTTTGTATGGTTCTG
1 TTTTGTATGGTTCTG
20571931 TTTTG
1 TTTTG
20571936 GATGAACACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.03, C:0.06, G:0.24, T:0.68
Consensus pattern (15 bp):
TTTTGTATGGTTCTG
Found at i:20573172 original size:14 final size:14
Alignment explanation
Indices: 20573149--20573179 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20573139 CAAATTTTTT
*
20573149 TATACCTATATATA
1 TATACATATATATA
20573163 TATACATATATATA
1 TATACATATATATA
20573177 TAT
1 TAT
20573180 TACTTTTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (14 bp):
TATACATATATATA
Found at i:20573635 original size:6 final size:6
Alignment explanation
Indices: 20573624--20573648 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20573614 ACGAAATTAT
20573624 ATTTAA ATTTAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA A
20573649 ATGTTCAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:20573729 original size:98 final size:98
Alignment explanation
Indices: 20573557--20573734 Score: 218
Period size: 98 Copynumber: 1.8 Consensus size: 98
20573547 ATCAATACAA
*** * **
20573557 AAACTAATCAATGATCAAACTTTGAACATGCTTTATTAAATCTTCGCATTTCATTATACGAAATT
1 AAACTAATCAATGATCAAACTTTGAACATGCTTTATTAAATCTAAACATATCATTATACGAAAAG
* *
20573622 ATATTTAAATTTAAATTTAAATTTAAAATGTTC
66 AAATGTAAATTTAAATTTAAATTTAAAATGTTC
* *
20573655 AAACTAATCCATGTTCAAACTTTGAACATGCTTTAATT-AA-CTAAACAATAT-ATTAATACGAA
1 AAACTAATCAATGATCAAACTTTGAACATGCTTT-ATTAAATCTAAAC-ATATCATT-ATACGAA
20573717 AAGAAATGTAAATTTAAA
63 AAGAAATGTAAATTTAAA
20573735 ATGTTATAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
97 6 0.09
98 58 0.87
99 3 0.04
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (98 bp):
AAACTAATCAATGATCAAACTTTGAACATGCTTTATTAAATCTAAACATATCATTATACGAAAAG
AAATGTAAATTTAAATTTAAATTTAAAATGTTC
Found at i:20573880 original size:15 final size:15
Alignment explanation
Indices: 20573860--20573895 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
20573850 CAAATACCAA
20573860 CAATTAATTTTAGGT
1 CAATTAATTTTAGGT
20573875 CAATTAATTTTAGGT
1 CAATTAATTTTAGGT
20573890 CAATTA
1 CAATTA
20573896 TACATATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.44
Consensus pattern (15 bp):
CAATTAATTTTAGGT
Found at i:20577173 original size:89 final size:91
Alignment explanation
Indices: 20577004--20577209 Score: 283
Period size: 89 Copynumber: 2.3 Consensus size: 91
20576994 TTGATTTTAG
* *
20577004 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
* *
20577069 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATATTAATTATTTTAAATTATA
* *
20577096 TAAATTCATATAAGAAAATTTATTATCACGAATTTTATGAAATTATAT-T-ATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
20577159 TGTAATAATT-ATTATTTTAAATTATA
66 TGTAAT-ATTAATTATTTTAAATTATA
* * * *
20577185 AAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
20577210 GTTATAATTA
Statistics
Matches: 103, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
89 54 0.52
90 4 0.04
91 29 0.28
92 16 0.16
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTATA
TGTAATATTAATTATTTTAAATTATA
Found at i:20577302 original size:59 final size:57
Alignment explanation
Indices: 20577214--20577634 Score: 179
Period size: 54 Copynumber: 7.1 Consensus size: 57
20577204 TTATTAGTTA
* *
20577214 TAATTATTTTAAATT-TTATTAA--ATCATATATTTTAATTAAAATATATTTAATAT
1 TAATTATTTAAAATTATTTTTAAGTATCATATATTTTAATTAAAATATATTTAATAT
* * * **
20577268 TAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATA
1 TAATTATTTAAAATTAT-TTTTA-AGTATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATA
20577333 T
57 T
* * * *
20577334 TAATTA-TTAAGAATT-TTATTAA--ATTATATATTTTAATTATAATATATTTAATAG
1 TAATTATTTAA-AATTATTTTTAAGTATCATATATTTTAATTAAAATATATTTAATAT
* * * * * **
20577388 TAATTATTTTAATTTATATTTTACGGTATCATATATTATGATTTGAGTAAATTCATATAAGAATA
1 TAATTATTTAAAATTAT-TTTTA-AGTATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATA
20577453 T
57 T
* * * *
20577454 TAATTA-TTAAGAATT-TTATTAA--ATTATATATTTTAATTATAATATATTTAATAA
1 TAATTATTTAA-AATTATTTTTAAGTATCATATATTTTAATTAAAATATATTTAATAT
* * * * **
20577508 TAATTATTTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATA
1 TAATTATTTAAAATTAT-TTTTA-AGTATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATA
20577573 T
57 T
* * * *
20577574 TAATTA-TTAAGAATT-TTATTAA--ATTATATATTTTAATTATAATATATTTAATAA
1 TAATTATTTAA-AATTATTTTTAAGTATCATATATTTTAATTAAAATATATTTAATAT
20577628 TAATTAT
1 TAATTAT
20577635 GTTTAAATAT
Statistics
Matches: 268, Mismatches: 57, Indels: 83
0.66 0.14 0.20
Matches are distributed among these distances:
54 50 0.19
55 21 0.08
56 15 0.06
57 8 0.03
59 31 0.12
60 24 0.09
61 30 0.11
63 9 0.03
64 15 0.06
65 24 0.09
66 41 0.15
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (57 bp):
TAATTATTTAAAATTATTTTTAAGTATCATATATTTTAATTAAAATATATTTAATAT
Found at i:20577334 original size:66 final size:64
Alignment explanation
Indices: 20577263--20577581 Score: 232
Period size: 66 Copynumber: 5.2 Consensus size: 64
20577253 AAATATATTT
*
20577263 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTTAAAATTAT-TTTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
20577328 G
64 G
* * * * **
20577329 AATATTAATTA-TTAAGAATT-TTATTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTAA-AATTATTTTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* * * *
20577383 AATAGTAATTATTTTAATTTATATTTTACGGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTTAAAATTAT-TTTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
20577448 G
64 G
* * * * **
20577449 AATATTAATTA-TTAAGAATT-TTATTAA--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTAA-AATTATTTTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* * *
20577503 AATAATAATTATTTTAATTTATATTTTACAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTTAAAATTAT-TTTTA-AGTATCATATATTATGATTTGAGTAAATTCATATAA
20577568 G
64 G
20577569 AATATTAATTATT
1 AATATTAATTATT
20577582 AAGAATTTTA
Statistics
Matches: 188, Mismatches: 37, Indels: 56
0.67 0.13 0.20
Matches are distributed among these distances:
54 26 0.14
55 16 0.09
56 10 0.05
57 5 0.03
58 2 0.01
59 20 0.11
60 16 0.09
61 20 0.11
62 2 0.01
63 5 0.03
64 10 0.05
65 16 0.09
66 40 0.21
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (64 bp):
AATATTAATTATTTAAAATTATTTTTAAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:20577349 original size:120 final size:120
Alignment explanation
Indices: 20577225--20577640 Score: 742
Period size: 120 Copynumber: 3.5 Consensus size: 120
20577215 AATTATTTTA
* * * * * *
20577225 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTTAATTTATATTTT
*
20577290 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
20577345 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAGTAATTATTTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTTAATTTATATTTT
*
20577410 ACGGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
20577465 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTTAATTTATATTTT
20577530 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
20577585 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAA
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTAT-TTTAA
20577641 ATATGATTCA
Statistics
Matches: 285, Mismatches: 10, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
120 280 0.98
121 5 0.02
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATTTTAATTTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:20577365 original size:61 final size:61
Alignment explanation
Indices: 20577298--20577605 Score: 253
Period size: 61 Copynumber: 5.1 Consensus size: 61
20577288 TTATAGTATC
20577298 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * **** *
20577359 ATATATTTTAATTAT-AATATATTTA-AT-AGTAATTATT--TTAATTTA-TATTTTACGGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAG-AA-TATTAATT-ATTAAGAATTTTATTAAATT
20577418 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * * * * *
20577479 ATATATTTTAATTAT-AATATATTTA-ATAATAATTATT--TTAATTTA-TATTTTA-CAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAA-TATTAATT-ATTAAGAATTTTATTA-AATT
20577538 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
20577599 ATATATT
1 ATATATT
20577606 TTAATTATAA
Statistics
Matches: 181, Mismatches: 46, Indels: 40
0.68 0.17 0.15
Matches are distributed among these distances:
58 3 0.02
59 66 0.36
60 36 0.20
61 73 0.40
62 3 0.02
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:20577505 original size:15 final size:15
Alignment explanation
Indices: 20577470--20577521 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
20577460 TTAAGAATTT
*
20577470 TATTAAATTAT-ATA
1 TATTTAATTATAATA
20577484 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
20577498 TATTTAATAATAAT-
1 TATTTAATTATAATA
20577512 TATTTTAATT
1 TA-TTTAATT
20577522 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 7 0.22
15 17 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:20577620 original size:16 final size:16
Alignment explanation
Indices: 20577599--20577640 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
20577589 TTATTAAATT
*
20577599 ATATATTTTAATTATA
1 ATATATTTTAATAATA
20577615 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
20577630 AT-TATGTTTAA
1 ATATAT-TTTAA
20577641 ATATGATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:20577625 original size:15 final size:15
Alignment explanation
Indices: 20577590--20577631 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
20577580 TTAAGAATTT
*
20577590 TATTAAATTAT-ATA
1 TATTTAATTATAATA
20577604 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
20577618 TATTTAATAATAAT
1 TATTTAATTATAAT
20577632 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:20577752 original size:157 final size:157
Alignment explanation
Indices: 20577574--20577890 Score: 580
Period size: 157 Copynumber: 2.0 Consensus size: 157
20577564 ATAAGAATAT
*
20577574 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
20577639 AAATATGATTCAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
* *
20577704 TAATAATTTACCAAAATAAATTTCTGC
131 TAATAATTTACCAAAACAAATTTATGC
20577731 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
20577796 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
*
20577861 TAATTATTTACCAAAACAAATTTATGC
131 TAATAATTTACCAAAACAAATTTATGC
20577888 TAA
1 TAA
20577891 GGGTATTCTA
Statistics
Matches: 154, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
TAATAATTTACCAAAACAAATTTATGC
Found at i:20577771 original size:18 final size:17
Alignment explanation
Indices: 20577743--20577777 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
20577733 ATTATTAAGA
*
20577743 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
20577760 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
20577778 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:20577811 original size:75 final size:75
Alignment explanation
Indices: 20577575--20577813 Score: 191
Period size: 75 Copynumber: 3.1 Consensus size: 75
20577565 TAAGAATATT
*
20577575 AATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
*
20577640 AATATGATTC
66 AATATGATTA
* ** * * * * *
20577650 AATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATA-A--CAATAATAATT
1 AATTATTAAGAATT-TTATT-A-AA--TTA-TATATTTTAATTAA-AATATATTTAATAATAATT
**** * *
20577712 -TACCAAAATAAAT-TTCTGCT
59 ATGTTTAAAT--ATGAT-T--A
20577732 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
1 AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
20577797 AATATGATTA
66 AATATGATTA
20577807 AATTATT
1 AATTATT
20577814 TATTATTGAT
Statistics
Matches: 118, Mismatches: 29, Indels: 34
0.65 0.16 0.19
Matches are distributed among these distances:
75 22 0.19
76 16 0.14
77 7 0.06
78 18 0.15
79 18 0.15
80 7 0.06
81 15 0.13
82 15 0.13
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (75 bp):
AATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTA
AATATGATTA
Found at i:20578023 original size:45 final size:44
Alignment explanation
Indices: 20577942--20578032 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
20577932 ACCTCTATTC
*
20577942 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTAAACCTCTATTCCATTA
*** *
20577986 CATTCAACCAAACAGTTGATTTGCTATTAAACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTAAACCTCTATTCCATTA
20578031 CA
1 CA
20578033 GCGAACCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 16 0.39
45 25 0.61
ACGTcount: A:0.36, C:0.27, G:0.04, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTAAACCTCTATTCCATTA
Found at i:20583008 original size:21 final size:21
Alignment explanation
Indices: 20582959--20583008 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
20582949 CATTTTCTTT
*
20582959 AATTTGTCGCTTTGATACTTA
1 AATTTGTTGCTTTGATACTTA
20582980 AATTTGTTGCTTTGATACTTA
1 AATTTGTTGCTTTGATACTTA
20583001 AATTTGTT
1 AATTTGTT
20583009 AAATGATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.52
Consensus pattern (21 bp):
AATTTGTTGCTTTGATACTTA
Found at i:20586650 original size:6 final size:6
Alignment explanation
Indices: 20586639--20586670 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
20586629 TTAATTAATT
20586639 ATTTTA ATTTTA ATTTTA A-TTTA A-TTTA ATTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTT
20586671 ATTTAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTTA
Found at i:20586654 original size:12 final size:12
Alignment explanation
Indices: 20586639--20586670 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
20586629 TTAATTAATT
20586639 ATTTTAATTTTA
1 ATTTTAATTTTA
20586651 ATTTTAA-TTTA
1 ATTTTAATTTTA
20586662 A-TTTAATTT
1 ATTTTAATTT
20586671 ATTTAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 5 0.26
11 7 0.37
12 7 0.37
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATTTTAATTTTA
Found at i:20586827 original size:31 final size:31
Alignment explanation
Indices: 20586792--20586850 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
20586782 GTTACTAACA
*
20586792 TTTTAGATAATTTCTATTTTAGTCACTCACG
1 TTTTAAATAATTTCTATTTTAGTCACTCACG
** *
20586823 TTTTAAATTGTTTCTATTTTGGTCACTC
1 TTTTAAATAATTTCTATTTTAGTCACTC
20586851 TCCATTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.22, C:0.15, G:0.10, T:0.53
Consensus pattern (31 bp):
TTTTAAATAATTTCTATTTTAGTCACTCACG
Found at i:20590086 original size:16 final size:16
Alignment explanation
Indices: 20590037--20590087 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
20590027 CAGGGTGACT
*
20590037 AAATAAAAATAATTTA
1 AAATAAAAATAATCTA
* * *
20590053 AAATATAAGTGA-CTA
1 AAATAAAAATAATCTA
*
20590068 AAATACAAATAATCTA
1 AAATAAAAATAATCTA
20590084 AAAT
1 AAAT
20590088 GTTAGTAGCT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (16 bp):
AAATAAAAATAATCTA
Found at i:20597374 original size:39 final size:39
Alignment explanation
Indices: 20597317--20597512 Score: 284
Period size: 39 Copynumber: 5.0 Consensus size: 39
20597307 CCAAGGCACC
* *
20597317 GTGATTTTCAGGGAAGAGATTCAAGTTCTGCGGGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCGAGGGGCA
* *
20597356 GTGATTTTCATGGCAGAGATTCAAGTTCTGCTAGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCGAGGGGCA
* * *
20597395 GTGATTTTCAGGGCAAAGATTCAAGTTCAGCTAGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCGAGGGGCA
20597434 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCGAGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCGAGGGGCA
* * * * *
20597473 GTGACTTCCTGGGCAGAGATTCAAGTTTTGCTAGGGGCA
1 GTGATTTTCAGGGCAGAGATTCAAGTTCTGCGAGGGGCA
20597512 G
1 G
20597513 GTCCTCATCG
Statistics
Matches: 142, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 142 1.00
ACGTcount: A:0.23, C:0.15, G:0.34, T:0.27
Consensus pattern (39 bp):
GTGATTTTCAGGGCAGAGATTCAAGTTCTGCGAGGGGCA
Found at i:20600619 original size:23 final size:23
Alignment explanation
Indices: 20600570--20600620 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
20600560 TCTCTTCCAC
* *
20600570 AATCCTTCAAGAATTGAAGCAAA
1 AATCCTTCAAGAATAGAAACAAA
*
20600593 AATCCTATCAAGAA-AGAAACAAG
1 AATCCT-TCAAGAATAGAAACAAA
20600616 AATCC
1 AATCC
20600621 AGTCTCTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.51, C:0.20, G:0.12, T:0.18
Consensus pattern (23 bp):
AATCCTTCAAGAATAGAAACAAA
Found at i:20606301 original size:21 final size:21
Alignment explanation
Indices: 20606277--20606316 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20606267 TATGATTTAA
*
20606277 GTCTAAAATGTTGTTATAGGT
1 GTCTAAAATGTTATTATAGGT
**
20606298 GTCTTGAATGTTATTATAG
1 GTCTAAAATGTTATTATAG
20606317 ATATATATCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.45
Consensus pattern (21 bp):
GTCTAAAATGTTATTATAGGT
Found at i:20608440 original size:11 final size:11
Alignment explanation
Indices: 20608424--20608465 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
20608414 TGTAAAGCAA
20608424 AAAAGAATAGT
1 AAAAGAATAGT
**
20608435 AAAAGAATAAA
1 AAAAGAATAGT
20608446 AAAAGAATAGT
1 AAAAGAATAGT
20608457 AAAAGAATA
1 AAAAGAATA
20608466 TCCTATCCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (11 bp):
AAAAGAATAGT
Found at i:20608450 original size:22 final size:22
Alignment explanation
Indices: 20608422--20608465 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
20608412 TGTGTAAAGC
20608422 AAAAAAGAATAGTAAAAGAATA
1 AAAAAAGAATAGTAAAAGAATA
20608444 AAAAAAGAATAGTAAAAGAATA
1 AAAAAAGAATAGTAAAAGAATA
20608466 TCCTATCCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (22 bp):
AAAAAAGAATAGTAAAAGAATA
Found at i:20609495 original size:15 final size:14
Alignment explanation
Indices: 20609474--20609509 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
20609464 ATAATCCTTA
*
20609474 ATAATTATCTTAAT
1 ATAATTATCCTAAT
20609488 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
20609503 ATAATTA
1 ATAATTA
20609510 AAATAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:20614827 original size:34 final size:33
Alignment explanation
Indices: 20614784--20614870 Score: 90
Period size: 32 Copynumber: 2.7 Consensus size: 33
20614774 TCCAATACTC
*
20614784 AAATCAATTCAGCAATATATATGTATAC-ATATAA
1 AAATCAATTCAG-AATATATATATAT-CTATATAA
* * **
20614818 AAATCAATTC-GAAAATGTATATATCTATATTT
1 AAATCAATTCAGAATATATATATATCTATATAA
20614850 AAATCAATTCAGAA-ATATATA
1 AAATCAATTCAGAATATATATA
20614871 AAACATATAC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
31 1 0.02
32 30 0.67
33 4 0.09
34 10 0.22
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.34
Consensus pattern (33 bp):
AAATCAATTCAGAATATATATATATCTATATAA
Found at i:20616911 original size:29 final size:27
Alignment explanation
Indices: 20616852--20616914 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 27
20616842 ACACATTGGG
*
20616852 TTTTTAAGAATTAAAGCAACCACAGGG
1 TTTTTAAGAATTAAAGCAACCACAGGA
* * *
20616879 TTTTTAAGTAAATTAAAGCAGCGATAGGA
1 TTTTTAAG--AATTAAAGCAACCACAGGA
20616908 TTTTTAA
1 TTTTTAA
20616915 AAATGTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 8 0.27
29 22 0.73
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (27 bp):
TTTTTAAGAATTAAAGCAACCACAGGA
Found at i:20618856 original size:48 final size:50
Alignment explanation
Indices: 20618775--20618891 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 50
20618765 AAACATGTTC
* * * *
20618775 AACAGAAAAAAGAAGAGAAAAGGAAATTGGGAA-GAAGAAACATCACTAGGA
1 AACAGAAAAAA-AAAAGAAAAGGAAATAGGGAAGGAA-AAACATCACCAAGA
20618826 AACAGAAAAAAAAAAG-AAA-GAAATAGGGAAGGAAAAACATCACCAAGA
1 AACAGAAAAAAAAAAGAAAAGGAAATAGGGAAGGAAAAACATCACCAAGA
*
20618874 AAAAGAAAGACAAAAAAG
1 AACAGAAA-A-AAAAAAG
20618892 GAAATAGTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
48 29 0.50
49 7 0.12
50 11 0.19
51 11 0.19
ACGTcount: A:0.65, C:0.09, G:0.21, T:0.05
Consensus pattern (50 bp):
AACAGAAAAAAAAAAGAAAAGGAAATAGGGAAGGAAAAACATCACCAAGA
Found at i:20631159 original size:47 final size:47
Alignment explanation
Indices: 20631108--20631200 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
20631098 AAAATTGGAG
*
20631108 AAAAAAAATTAGTGGTTAAAATTTACATGTTTAAATTATTAATGAGA
1 AAAAAAAATTAGTGGTTAAAATTTAAATGTTTAAATTATTAATGAGA
*
20631155 AAAAATAATTAGTGGTTAAAATTTAAATGTTTAAATTATTAATGAG
1 AAAAAAAATTAGTGGTTAAAATTTAAATGTTTAAATTATTAATGAG
20631201 TCTATTTTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.48, C:0.01, G:0.13, T:0.38
Consensus pattern (47 bp):
AAAAAAAATTAGTGGTTAAAATTTAAATGTTTAAATTATTAATGAGA
Found at i:20634165 original size:68 final size:68
Alignment explanation
Indices: 20634056--20634231 Score: 307
Period size: 68 Copynumber: 2.6 Consensus size: 68
20634046 GTGTTATAAT
20634056 GTTCATGTTTTGGTTTATGTTAAGTTCATGTTTTGGTTTATGTGTTATAATGTTCATGTTTCTGT
1 GTTCATGTTTTGGTTTATGTTAAGTTCATGTTTTGGTTTATGTGTTATAATGTTCATGTTTCTGT
20634121 TAA
66 TAA
* *
20634124 GTTCATGTTTTGGTTTCTGTTAAGTTCATGTTTAGGTTTATGTGTTATAATGTTCATGTTTCTGT
1 GTTCATGTTTTGGTTTATGTTAAGTTCATGTTTTGGTTTATGTGTTATAATGTTCATGTTTCTGT
20634189 TAA
66 TAA
**
20634192 GTTCATGTTTTGGTTTATGTTTTGGTTCATGTTTTGGTTT
1 GTTCATGTTTTGGTTTATG-TTAAGTTCATGTTTTGGTTT
20634232 CTGTTAAGTT
Statistics
Matches: 101, Mismatches: 6, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
68 84 0.83
69 17 0.17
ACGTcount: A:0.15, C:0.06, G:0.22, T:0.57
Consensus pattern (68 bp):
GTTCATGTTTTGGTTTATGTTAAGTTCATGTTTTGGTTTATGTGTTATAATGTTCATGTTTCTGT
TAA
Found at i:20634177 original size:45 final size:46
Alignment explanation
Indices: 20634128--20634248 Score: 156
Period size: 45 Copynumber: 2.6 Consensus size: 46
20634118 TGTTAAGTTC
20634128 ATGTTTTGGTTTCTGTTAAGTTCATGTTTAGGTTTATGTGTT-ATA
1 ATGTTTTGGTTTCTGTTAAGTTCATGTTTAGGTTTATGTGTTGATA
* * * * *
20634173 ATGTTCAT-GTTTCTGTTAAGTTCATGTTTTGGTTTATGTTTTGGTTC
1 ATGTT-TTGGTTTCTGTTAAGTTCATGTTTAGGTTTATGTGTT-GATA
*
20634220 ATGTTTTGGTTTCTGTTAAGTTGATGTTT
1 ATGTTTTGGTTTCTGTTAAGTTCATGTTT
20634249 TCTGTTTCTG
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
45 37 0.57
46 2 0.03
47 26 0.40
ACGTcount: A:0.15, C:0.06, G:0.22, T:0.57
Consensus pattern (46 bp):
ATGTTTTGGTTTCTGTTAAGTTCATGTTTAGGTTTATGTGTTGATA
Found at i:20634213 original size:12 final size:12
Alignment explanation
Indices: 20634196--20634236 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
20634186 TGTTAAGTTC
20634196 ATGTTTTGGTTT
1 ATGTTTTGGTTT
*
20634208 ATGTTTTGGTTC
1 ATGTTTTGGTTT
20634220 ATGTTTTGGTTT
1 ATGTTTTGGTTT
*
20634232 CTGTT
1 ATGTT
20634237 AAGTTGATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.07, C:0.05, G:0.24, T:0.63
Consensus pattern (12 bp):
ATGTTTTGGTTT
Found at i:20634255 original size:24 final size:23
Alignment explanation
Indices: 20634056--20634260 Score: 179
Period size: 23 Copynumber: 8.9 Consensus size: 23
20634046 GTGTTATAAT
*
20634056 GTTCATGTTTTGGTTTATGTTAA
1 GTTCATGTTTTGGTTTCTGTTAA
* *
20634079 GTTCATGTTTTGGTTTATGTGTTA
1 GTTCATGTTTTGGTTTCTGT-TAA
* *
20634103 --TAATGTTCAT-GTTTCTGTTAA
1 GTTCATGTT-TTGGTTTCTGTTAA
20634124 GTTCATGTTTTGGTTTCTGTTAA
1 GTTCATGTTTTGGTTTCTGTTAA
* * *
20634147 GTTCATGTTTAGGTTTATGTGTTA
1 GTTCATGTTTTGGTTTCTGT-TAA
* *
20634171 --TAATGTTCAT-GTTTCTGTTAA
1 GTTCATGTT-TTGGTTTCTGTTAA
* **
20634192 GTTCATGTTTTGGTTTATGTTTTG
1 GTTCATGTTTTGGTTTCTG-TTAA
20634216 GTTCATGTTTTGGTTTCTGTTAA
1 GTTCATGTTTTGGTTTCTGTTAA
* *
20634239 GTTGATGTTTTCTGTTTCTGTT
1 GTTCATGTTTT-GGTTTCTGTT
20634261 TATGGATTAT
Statistics
Matches: 145, Mismatches: 25, Indels: 23
0.75 0.13 0.12
Matches are distributed among these distances:
21 4 0.03
22 28 0.19
23 80 0.55
24 33 0.23
ACGTcount: A:0.15, C:0.07, G:0.21, T:0.57
Consensus pattern (23 bp):
GTTCATGTTTTGGTTTCTGTTAA
Found at i:20635212 original size:116 final size:115
Alignment explanation
Indices: 20635087--20635337 Score: 468
Period size: 116 Copynumber: 2.2 Consensus size: 115
20635077 TAAAGTTTGG
*
20635087 ATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAATAAAAATAATTAAA
1 ATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAAGAAAAATAATTAAA
20635152 TGCATAAAACTAATCAAATTATATATTTACAAATTAATTAAATTAAATTA
66 TGCATAAAACTAATCAAATTATATATTTACAAATTAATTAAATTAAATTA
20635202 TATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAAGAAAAATAATTAA
1 -ATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAAGAAAAATAATTAA
*
20635267 ATGCATAAAACTAATTAAATTATATATTTACAAATTAATTAAATTAAATTA
65 ATGCATAAAACTAATCAAATTATATATTTACAAATTAATTAAATTAAATTA
20635318 A-ATTTTTTATTTTTAATATT
1 ATATTTTTTATTTTTAATATT
20635338 TTTTATTTTT
Statistics
Matches: 133, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
114 19 0.14
115 1 0.01
116 113 0.85
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (115 bp):
ATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAAGAAAAATAATTAAA
TGCATAAAACTAATCAAATTATATATTTACAAATTAATTAAATTAAATTA
Found at i:20635340 original size:16 final size:16
Alignment explanation
Indices: 20635315--20635353 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
20635305 TTAAATTAAA
20635315 TTAA-ATTTTTTATTT
1 TTAATATTTTTTATTT
20635330 TTAATATTTTTTATTT
1 TTAATATTTTTTATTT
20635346 TTAATATT
1 TTAATATT
20635354 CCAATTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTAATATTTTTTATTT
Found at i:20635341 original size:130 final size:132
Alignment explanation
Indices: 20635203--20635498 Score: 533
Period size: 130 Copynumber: 2.3 Consensus size: 132
20635193 ATTAAATTAT
20635203 ATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAAGAAAAATAATTAAA
1 ATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAAGAAAAATAATTAAA
*
20635268 TGCATAAAACTAATTAAATTATATATTTACAAATTAATTAAATTAAATT-AAA-TTTTTTATTTT
66 TGCATAAAACTAATTAAATTATATATTAACAAATTAATTAAATTAAATTAAAATTTTTTTATTTT
20635331 TA
131 TA
* * *
20635333 ATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATTTTTTAAAATAAAAATAATTAAA
1 ATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAAGAAAAATAATTAAA
*
20635398 TGCATAAAACTAATTAAATTATGTATTAACAAATTAATTAAATTAAATTAAAATTTTTTTATTTT
66 TGCATAAAACTAATTAAATTATATATTAACAAATTAATTAAATTAAATTAAAATTTTTTTATTTT
20635463 TA
131 TA
20635465 ATATTTTTTATTTTTAATATTCCAATTTATTAAA
1 ATATTTTTTATTTTTAATATTCCAATTTATTAAA
20635499 ATAAAAATAA
Statistics
Matches: 159, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
130 109 0.69
131 3 0.02
132 47 0.30
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.48
Consensus pattern (132 bp):
ATATTTTTTATTTTTAATATTCCAATTTATTAAATAATGCATCTGTTAAAAGAAAAATAATTAAA
TGCATAAAACTAATTAAATTATATATTAACAAATTAATTAAATTAAATTAAAATTTTTTTATTTT
TA
Found at i:20635471 original size:16 final size:16
Alignment explanation
Indices: 20635452--20635485 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
20635442 AAATTAAAAT
20635452 TTTTTTATTTTTAATA
1 TTTTTTATTTTTAATA
20635468 TTTTTTATTTTTAATA
1 TTTTTTATTTTTAATA
20635484 TT
1 TT
20635486 CCAATTTATT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTATTTTTAATA
Found at i:20637775 original size:49 final size:49
Alignment explanation
Indices: 20637718--20637821 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
20637708 TCATGTGTTA
* * * *
20637718 TAATTTTATACAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
20637767 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
20637816 TAATTT
1 TAATTT
20637822 ATTTTTTTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:20639333 original size:120 final size:120
Alignment explanation
Indices: 20639206--20640289 Score: 1811
Period size: 120 Copynumber: 9.0 Consensus size: 120
20639196 AAGTAGATTA
** * *
20639206 TAAATTATATTTTATAGTACCATATATTAAGATTTTAGTAAATTCATATAATAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
20639271 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
* *
20639326 TAGATTATATTTTATAGTATTATATATTATGATTATAGTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* * *
20639391 AAGAATTTTATTAAATTATATACTTTTAATAAATTATACTTAATAATAATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
20639446 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* * *
20639511 AAGAATTTTATTAAATTATATCTTTTTATTAAATTATATTTAAAAATAATTAATT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
20639566 TAAATTATATTTTATAGTATTATATATATTATGATTTTAGTAAATTC---TAAGAATATTTAATA
1 TAAATTATATTTTATAGTA-T-TATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATA
* * *
20639628 TTAAGAATTTTATTAAATTATATATTTTTACTAATTTATATTTTTAATAATTATTATTT
64 TTAAGAATTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATAATTATTT
* *
20639687 TAAATTATATTTTATAGTGTTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* * *
20639752 AAGAATTTTATTAAATTATATATTTTTATTAACTTATATTTAAAAATAATTAATT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
20639807 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTC---TAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
*
20639869 AAGAATTTTATTAAATTATATATTTTTACTAAATTATATTTTTAATAATAATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATA--TTTAATAATAATTATTT
*
20639926 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
*
20639991 AAGAATTTTATTAAATTATATATTTTTATTAAATTTTATTTAATAATAATTATTT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
*
20640046 TAAATTATATTTTATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
20640111 AAGAATTTTATTAAATTATATGTTTTTATTAAATTATATTTAATAATAATTATGT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
* *
20640166 TAAATTATATTTTATAGTATTATATATTATGATTTAAGAAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
*
20640231 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
20640286 TAAA
1 TAAA
20640290 ATATGATTAA
Statistics
Matches: 907, Mismatches: 45, Indels: 24
0.93 0.05 0.02
Matches are distributed among these distances:
117 53 0.06
119 137 0.15
120 553 0.61
121 33 0.04
122 131 0.14
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (120 bp):
TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTT
Found at i:20639669 original size:16 final size:17
Alignment explanation
Indices: 20639643--20639687 Score: 67
Period size: 16 Copynumber: 2.8 Consensus size: 17
20639633 AATTTTATTA
*
20639643 AATTATATATTTTTACT
1 AATTATATATTTTTAAT
20639660 AATT-TATATTTTTAAT
1 AATTATATATTTTTAAT
20639676 AATTAT-TATTTT
1 AATTATATATTTT
20639688 AAATTATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 21 0.81
17 5 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTATATATTTTTAAT
Found at i:20639860 original size:239 final size:238
Alignment explanation
Indices: 20639206--20640282 Score: 1807
Period size: 239 Copynumber: 4.5 Consensus size: 238
20639196 AAGTAGATTA
** * *
20639206 TAAATTATATTTTATAGTACCATATATTAAGATTTTAGTAAATTCATATAATAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
20639271 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAGATTATAT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
*
20639336 TTTATAGTATTATATATTATGATTATAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTA
131 TTTATAGTATTATATATTATGATTTTAGTAAATTC--ATAAGAATATTTAATATTAAGAATTTTA
* * *
20639401 TTAAATTATATACTTTTAATAAATTATACTTAATAATAATTATTT
194 TTAAATTATATATTTTTACTAAATTATATTTAATAATAATTATTT
20639446 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
20639511 AAGAATTTTATTAAATTATATCTTTTTATTAAATTATATTTAAAAATAATTAATTTAAATTATAT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
20639576 TTTATAGTATTATATATATTATGATTTTAGTAAATTC-TAAGAATATTTAATATTAAGAATTTTA
131 TTTATAGTA-T-TATATATTATGATTTTAGTAAATTCATAAGAATATTTAATATTAAGAATTTTA
* *
20639640 TTAAATTATATATTTTTACTAATTTATATTTTTAATAATTATTATTT
194 TTAAATTATATATTTTTACTAAATTATA--TTTAATAATAATTATTT
* *
20639687 TAAATTATATTTTATAGTGTTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
20639752 AAGAATTTTATTAAATTATATATTTTTATTAACTTATATTTAAAAATAATTAATTTAAATTATAT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
20639817 TTTATAGTATTATATATTATGATTTTAGTAAATTC-TAAGAATATTTAATATTAAGAATTTTATT
131 TTTATAGTATTATATATTATGATTTTAGTAAATTCATAAGAATATTTAATATTAAGAATTTTATT
20639881 AAATTATATATTTTTACTAAATTATATTTTTAATAATAATTATTT
196 AAATTATATATTTTTACTAAATTATA--TTTAATAATAATTATTT
*
20639926 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATTTAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
* *
20639991 AAGAATTTTATTAAATTATATATTTTTATTAAATTTTATTTAATAATAATTATTTTAAATTATAT
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
*
20640056 TTTATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTA
131 TTTATAGTATTATATATTATGATTTTAGTAAATTC--ATAAGAATATTTAATATTAAGAATTTTA
* * *
20640121 TTAAATTATATGTTTTTATTAAATTATATTTAATAATAATTATGT
194 TTAAATTATATATTTTTACTAAATTATATTTAATAATAATTATTT
* *
20640166 TAAATTATATTTTATAGTATTATATATTATGATTTAAGAAAATTCATATAAGAATATTTAATATT
1 TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
20640231 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTA
66 AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTA
20640283 TGTTAAAATA
Statistics
Matches: 797, Mismatches: 33, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
239 308 0.39
240 261 0.33
241 151 0.19
242 77 0.10
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (238 bp):
TAAATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATT
AAGAATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAATTTAAATTATAT
TTTATAGTATTATATATTATGATTTTAGTAAATTCATAAGAATATTTAATATTAAGAATTTTATT
AAATTATATATTTTTACTAAATTATATTTAATAATAATTATTT
Found at i:20639895 original size:18 final size:17
Alignment explanation
Indices: 20639874--20639911 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
20639864 ATATTAAGAA
*
20639874 TTTTATTAAATTATATAT
1 TTTTACTAAATTATAT-T
20639892 TTTTACTAAATTATATT
1 TTTTACTAAATTATATT
20639909 TTT
1 TTT
20639912 AATAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTACTAAATTATATT
Found at i:20649283 original size:2 final size:2
Alignment explanation
Indices: 20649276--20649303 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20649266 TTAATAAAAT
20649276 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
20649304 AGGTTTCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:20675751 original size:22 final size:23
Alignment explanation
Indices: 20675709--20675754 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
20675699 TAAAGCGAAT
*
20675709 AAATATTTATGTTTTTAATTTTA
1 AAATATTTATGTATTTAATTTTA
*
20675732 AAAT-TTTATGTAATTTATTTTTA
1 AAATATTTATGT-ATTTAATTTTA
20675755 TTTTCTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
AAATATTTATGTATTTAATTTTA
Found at i:20678599 original size:7 final size:7
Alignment explanation
Indices: 20678587--20678612 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20678577 TAGTCGATTC
20678587 GTATTTA
1 GTATTTA
20678594 GTATTTA
1 GTATTTA
20678601 GTATTTA
1 GTATTTA
20678608 GTATT
1 GTATT
20678613 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:20679261 original size:18 final size:18
Alignment explanation
Indices: 20679238--20679281 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20679228 ATGCCAAGTG
* *
20679238 TGTATCCTATCCCTTTTA
1 TGTATCCTAACCCTTATA
20679256 TGTATCCTAACCCTTATA
1 TGTATCCTAACCCTTATA
*
20679274 TGTTTCCT
1 TGTATCCT
20679282 TTTTCTAGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.18, C:0.27, G:0.07, T:0.48
Consensus pattern (18 bp):
TGTATCCTAACCCTTATA
Found at i:20679547 original size:21 final size:21
Alignment explanation
Indices: 20679523--20679569 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
20679513 CAACACTGAT
* *
20679523 AACCA-AATCCCTTACCGGAGG
1 AACCAGAATCCC-CACCGGAGC
20679544 AACCAGAATCCCCACCGGAGC
1 AACCAGAATCCCCACCGGAGC
20679565 AACCA
1 AACCA
20679570 CAACCCCCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.36, C:0.38, G:0.17, T:0.09
Consensus pattern (21 bp):
AACCAGAATCCCCACCGGAGC
Found at i:20679577 original size:21 final size:21
Alignment explanation
Indices: 20679536--20679577 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
20679526 CAAATCCCTT
* * *
20679536 ACCGGAGGAACCAGAATCCCC
1 ACCGGAGCAACCACAACCCCC
20679557 ACCGGAGCAACCACAACCCCC
1 ACCGGAGCAACCACAACCCCC
20679578 GTCGAAAGCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.45, G:0.19, T:0.02
Consensus pattern (21 bp):
ACCGGAGCAACCACAACCCCC
Found at i:20680935 original size:15 final size:15
Alignment explanation
Indices: 20680893--20680940 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
20680883 CAAACCAACC
* *
20680893 AGAACAGGGCAAAGC
1 AGAACAGAGCAAAGT
* * *
20680908 AGAACATAACAAAAT
1 AGAACAGAGCAAAGT
20680923 AGAACAGAGCAAAGT
1 AGAACAGAGCAAAGT
20680938 AGA
1 AGA
20680941 GCATGTATGT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.56, C:0.15, G:0.23, T:0.06
Consensus pattern (15 bp):
AGAACAGAGCAAAGT
Found at i:20683233 original size:58 final size:58
Alignment explanation
Indices: 20683143--20683278 Score: 236
Period size: 58 Copynumber: 2.3 Consensus size: 58
20683133 AATAATAGCC
*
20683143 TCTTTCATCTATGGTCTTACACCGTATACCTTATACCTTTTACCATGTTGTCATGACA
1 TCTTTCATCCATGGTCTTACACCGTATACCTTATACCTTTTACCATGTTGTCATGACA
* * *
20683201 TCTTTCATCCATGGTATTACACTGTATACCTTATACCTTTTACCATGTTGTCATGGCA
1 TCTTTCATCCATGGTCTTACACCGTATACCTTATACCTTTTACCATGTTGTCATGACA
20683259 TCTTTCATCCATGGTCTTAC
1 TCTTTCATCCATGGTCTTAC
20683279 GCAACGTACC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 73 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (58 bp):
TCTTTCATCCATGGTCTTACACCGTATACCTTATACCTTTTACCATGTTGTCATGACA
Found at i:20684605 original size:85 final size:85
Alignment explanation
Indices: 20684488--20684649 Score: 225
Period size: 85 Copynumber: 1.9 Consensus size: 85
20684478 CCTGTACTTG
* * ** * *
20684488 CATAAAATGTCTAATGTGGTACTTGTACTTTGAAAATGTTTATTATGGTATATGAACTATTAATA
1 CATAAAATGTCCAATGTGGTACATGTACTTTGAAAATGTCCAATATGGTATACGAACTATTAATA
20684553 TATGTTTTATTATGCTCTTT
66 TATGTTTTATTATGCTCTTT
* * * *
20684573 CATAAAATGTCCAATGTGGTACATGTAGTTTGAAAATGTCCAATGTGGTATCCGAACTATTTATA
1 CATAAAATGTCCAATGTGGTACATGTACTTTGAAAATGTCCAATATGGTATACGAACTATTAATA
*
20684638 TGTGTTTTATTA
66 TATGTTTTATTA
20684650 CGGTACTTGT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 66 1.00
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (85 bp):
CATAAAATGTCCAATGTGGTACATGTACTTTGAAAATGTCCAATATGGTATACGAACTATTAATA
TATGTTTTATTATGCTCTTT
Found at i:20687774 original size:14 final size:16
Alignment explanation
Indices: 20687755--20687786 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
20687745 TTAACTTCTC
20687755 ATTTAATT-TTT-AAA
1 ATTTAATTGTTTCAAA
20687769 ATTTAATTGTTTCAAA
1 ATTTAATTGTTTCAAA
20687785 AT
1 AT
20687787 AGATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
ATTTAATTGTTTCAAA
Found at i:20688399 original size:3 final size:3
Alignment explanation
Indices: 20688356--20688382 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20688346 TTTGGAATTG
20688356 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
20688383 AAGAAACCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:20696118 original size:16 final size:16
Alignment explanation
Indices: 20696097--20696133 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
20696087 TAATTAACAT
20696097 AGATAAAAA-TAATTAA
1 AGATAAAAATTAATT-A
20696113 AGATAAAAATTAATTA
1 AGATAAAAATTAATTA
20696129 AGATA
1 AGATA
20696134 TAAGATCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (16 bp):
AGATAAAAATTAATTA
Found at i:20700149 original size:13 final size:13
Alignment explanation
Indices: 20700131--20700155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20700121 TAAGAAAAAA
20700131 AAATATCAAATTC
1 AAATATCAAATTC
20700144 AAATATCAAATT
1 AAATATCAAATT
20700156 AGATGAAAAA
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:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATCAAATTC
Found at i:20704504 original size:51 final size:51
Alignment explanation
Indices: 20704387--20704690 Score: 417
Period size: 51 Copynumber: 6.1 Consensus size: 51
20704377 CTTGCGTATG
* * *
20704387 ATCACTTATCACTTGTCCCTGATAAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * *
20704437 ATCACTTGCCATTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
20704488 ATCACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
20704539 ATCACTTGCCACTTGTCACTGATCAGATAAGTGTAGCTGAAG------C-T
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* * *
20704583 ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
20704634 ATCACTTGTCATTTGTCACTGATCAGATAAGTGTAGCTAAAGTTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
20704685 ATCACT
1 ATCACT
20704691 GATCAGAAGT
Statistics
Matches: 225, Mismatches: 21, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
44 41 0.18
45 1 0.00
50 33 0.15
51 150 0.67
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:20704611 original size:95 final size:94
Alignment explanation
Indices: 20704387--20704690 Score: 437
Period size: 95 Copynumber: 3.1 Consensus size: 94
20704377 CTTGCGTATG
* *
20704387 ATCACTTATCACTTGTCCCTGATAAGATAAGTGTAGCTAAGCTACCACTTATCACTTGCCATTTG
1 ATCACTTATCACTTGTCACTGATAAGATAAGTGTAGCTAAGCTATCACTTATCACTTGCCATTTG
*
20704452 TCATTGATCAGATAAGTGTAGCTAAAGCT
66 TCACTGATCAGATAAGTGTAGCTAAAGCT
*
20704481 ACCACTTATCACTTGTCACTTGTCACTGATTAGATAAGTGTAGCTAAAGCTATCACTTATCACTT
1 ATCACTTATCACTTGTCAC-TG--A-T-A--AGATAAGTGTAGCT-AAGCTATCACTTATCACTT
* *
20704546 GCCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCT
58 GCCATTTGTCACTGATCAGATAAGTGTAGCTAAAGCT
* *
20704583 ATCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTATCACTTGTCATTT
1 ATCACTTATCACTTGTCACTGATAAGATAAGTGTAGCT-AAGCTATCACTTATCACTTGCCATTT
*
20704648 GTCACTGATCAGATAAGTGTAGCTAAAGTT
65 GTCACTGATCAGATAAGTGTAGCTAAAGCT
*
20704678 ACCACTTATCACT
1 ATCACTTATCACT
20704691 GATCAGAAGT
Statistics
Matches: 188, Mismatches: 14, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
94 17 0.09
95 80 0.43
97 1 0.01
98 2 0.01
99 2 0.01
101 16 0.09
102 70 0.37
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (94 bp):
ATCACTTATCACTTGTCACTGATAAGATAAGTGTAGCTAAGCTATCACTTATCACTTGCCATTTG
TCACTGATCAGATAAGTGTAGCTAAAGCT
Found at i:20704630 original size:37 final size:39
Alignment explanation
Indices: 20704548--20704639 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 39
20704538 TATCACTTGC
20704548 CACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTATCACTTAT
1 CACTTGTCACTGATCAGATAAGTGTAGCTGAAG-----ACTTAT
20704592 CACTTGTCACTGATCAGATAAGTGTAGCTGAAG-C-TAT
1 CACTTGTCACTGATCAGATAAGTGTAGCTGAAGACTTAT
*
20704629 CACTTATCACT
1 CACTTGTCACT
20704640 TGTCATTTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
37 13 0.28
38 1 0.02
44 33 0.70
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (39 bp):
CACTTGTCACTGATCAGATAAGTGTAGCTGAAGACTTAT
Found at i:20710864 original size:114 final size:114
Alignment explanation
Indices: 20710429--20710855 Score: 739
Period size: 114 Copynumber: 3.7 Consensus size: 114
20710419 TGTTTCTGAA
* * *
20710429 AAAGCGTCGCAAAAATACTTCAGCCCAACGATGCCGTTTTCTGAGCTGAGAAGGATTTAGTGGCG
1 AAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTGAGAAGGATTTAGTAGCG
*
20710494 TTTTTATGCAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGGG
66 TTTTTATGTAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGGG
* * *
20710543 AAAGCGCCGCAAAAATACTTCAGTCTAACGACGCCGTTTTTTGAGCTGAGAAGGATTTAGTAGCG
1 AAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTGAGAAGGATTTAGTAGCG
*
20710608 TTTTTATGTAAGCACCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGGG
66 TTTTTATGTAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGGG
*
20710657 AAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTTTGAGCTGAGAAGGATTTAGT-GTC
1 AAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTGAGAAGGATTTAGTAG-C
*
20710721 GTTTTTATGTAAGCGCCGCTAGTGGTCAGGTCTTTAGCGGCGTTTTTGGG
65 GTTTTTATGTAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGGG
*
20710771 AAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTGAGAATGATTTAGTAGCG
1 AAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTGAGAAGGATTTAGTAGCG
20710836 TTTTTATGTAAGCGCCGCTA
66 TTTTTATGTAAGCGCCGCTA
20710856 ATACTCAGGG
Statistics
Matches: 297, Mismatches: 14, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
113 1 0.00
114 295 0.99
115 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (114 bp):
AAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTCTGAGCTGAGAAGGATTTAGTAGCG
TTTTTATGTAAGCGCCGCTACTGGTCAGGTCTTTAGCGGCGTTTTTGGG
Found at i:20711131 original size:14 final size:15
Alignment explanation
Indices: 20711098--20711131 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
20711088 TAAGTTTTAT
20711098 AGATTATGGAATTAG
1 AGATTATGGAATTAG
20711113 AGATTATGG-ATTAG
1 AGATTATGGAATTAG
*
20711127 GGATT
1 AGATT
20711132 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (15 bp):
AGATTATGGAATTAG
Found at i:20711173 original size:14 final size:14
Alignment explanation
Indices: 20711154--20711208 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
20711144 TTAATGTGAT
* *
20711154 TTAAGGTTTATGGG
1 TTAAGGGTTAGGGG
20711168 TTAAGGGTTAGGGG
1 TTAAGGGTTAGGGG
* **
20711182 TTAGGGGTTAGATG
1 TTAAGGGTTAGGGG
*
20711196 TTAAGAGTTAGGG
1 TTAAGGGTTAGGG
20711209 ATTTAGGGAT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.35
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:20711417 original size:83 final size:82
Alignment explanation
Indices: 20711244--20711459 Score: 283
Period size: 83 Copynumber: 2.6 Consensus size: 82
20711234 TCAGTGTTAG
* * * *
20711244 GTTAGAGTTTAGGGTTTAGATTAATTAGTATATTTTAA-TTATATATTAAATAAGGTTTAGGGGT
1 GTTAGGGTTTAGGGTTTAGATTAATTAGTATTTTTTAATTTATATATTAAAAAAAGTTTAGGGGT
* *
20711308 TAGGGGTTAGGGATCGG
66 TAGGGGTTAGAGATCGA
* *
20711325 GTTATGGTTTAGGGTTTAGATTAATTAGAATTTTTTTAATTTATATATTAAAAAAAGTTTAGGGG
1 GTTAGGGTTTAGGGTTTAGATTAATTAGTA-TTTTTTAATTTATATATTAAAAAAAGTTTAGGGG
*
20711390 TTAGGGATTTAGAG-TCGA
65 TTAGGG-GTTAGAGATCGA
* * *
20711408 GTTAGGGTTTAAGATTTGGATTAATTAGTACTTTTTTAATTTATATATTAAA
1 GTTAGGGTTTAGGGTTTAGATTAATTAGTA-TTTTTTAATTTATATATTAAA
20711460 TAAGTTCTTT
Statistics
Matches: 117, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
81 27 0.23
82 7 0.06
83 78 0.67
84 5 0.04
ACGTcount: A:0.31, C:0.01, G:0.23, T:0.44
Consensus pattern (82 bp):
GTTAGGGTTTAGGGTTTAGATTAATTAGTATTTTTTAATTTATATATTAAAAAAAGTTTAGGGGT
TAGGGGTTAGAGATCGA
Found at i:20711564 original size:21 final size:21
Alignment explanation
Indices: 20711511--20711564 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
20711501 TAAAGATTAT
20711511 TAATTTAAAA-TTGATATGCAA
1 TAATTTAAAATTTGATAT-CAA
*
20711532 T-ATATAATAATTTGAATAT-AA
1 TAATTTAA-AATTTG-ATATCAA
20711553 TAATTTAAAATT
1 TAATTTAAAATT
20711565 GTAAAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
20 5 0.19
21 10 0.37
22 8 0.30
23 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.43
Consensus pattern (21 bp):
TAATTTAAAATTTGATATCAA
Found at i:20711584 original size:12 final size:12
Alignment explanation
Indices: 20711567--20711592 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
20711557 TTAAAATTGT
20711567 AAAAATTGTAAA
1 AAAAATTGTAAA
20711579 AAAAATTGTAAA
1 AAAAATTGTAAA
20711591 AA
1 AA
20711593 TTACAAAAAA
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:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (12 bp):
AAAAATTGTAAA
Found at i:20711600 original size:21 final size:21
Alignment explanation
Indices: 20711559--20711602 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
20711549 ATAATAATTT
**
20711559 AAAATTGTAAAAATTGTAAAA
1 AAAATTGTAAAAATTACAAAA
20711580 AAAATTGTAAAAATTACAAAA
1 AAAATTGTAAAAATTACAAAA
20711601 AA
1 AA
20711603 TAAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (21 bp):
AAAATTGTAAAAATTACAAAA
Found at i:20711618 original size:18 final size:18
Alignment explanation
Indices: 20711597--20711638 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
20711587 TAAAAATTAC
*
20711597 AAAAAATAAAATTA-AAAT
1 AAAAAATAAAA-AAGAAAT
20711615 AAAAAATAAAAAAGAAAT
1 AAAAAATAAAAAAGAAAT
20711633 AAAAAA
1 AAAAAA
20711639 ACTAAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.14
Consensus pattern (18 bp):
AAAAAATAAAAAAGAAAT
Found at i:20711702 original size:46 final size:45
Alignment explanation
Indices: 20711635--20711728 Score: 118
Period size: 46 Copynumber: 2.1 Consensus size: 45
20711625 AAAGAAATAA
** * *
20711635 AAAAACTAAATTTTTATTTTTACCTAA-TTTTTATAAATATTACTT
1 AAAAACTAAATTGATAATTTTACCTAATTTTTTA-AAATATTACCT
*
20711680 AAAAACTAAAATTGATAATTTTATCTAATTTTTTAAAATATTACCT
1 AAAAACT-AAATTGATAATTTTACCTAATTTTTTAAAATATTACCT
20711726 AAA
1 AAA
20711729 TTAACAAAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
45 7 0.17
46 29 0.69
47 6 0.14
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.46
Consensus pattern (45 bp):
AAAAACTAAATTGATAATTTTACCTAATTTTTTAAAATATTACCT
Found at i:20713862 original size:7 final size:7
Alignment explanation
Indices: 20713850--20713908 Score: 91
Period size: 7 Copynumber: 8.3 Consensus size: 7
20713840 TGTTTCTTTA
20713850 TTTTCTG
1 TTTTCTG
20713857 TTTTCTG
1 TTTTCTG
20713864 TTTTCTG
1 TTTTCTG
*
20713871 TTTTCTA
1 TTTTCTG
20713878 TTTTCTG
1 TTTTCTG
20713885 TTTTCTG
1 TTTTCTG
*
20713892 TTTTGCTA
1 TTTT-CTG
20713900 TTTTCTG
1 TTTTCTG
20713907 TT
1 TT
20713909 GAATGAAGTG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
7 41 0.87
8 6 0.13
ACGTcount: A:0.03, C:0.14, G:0.12, T:0.71
Consensus pattern (7 bp):
TTTTCTG
Found at i:20714496 original size:13 final size:13
Alignment explanation
Indices: 20714478--20714622 Score: 89
Period size: 13 Copynumber: 11.0 Consensus size: 13
20714468 ATTTACTCTT
*
20714478 AATATATTACTTG
1 AATATATTACTTA
20714491 AATATATTACTTA
1 AATATATTACTTA
20714504 AATATATTACTTA
1 AATATATTACTTA
*
20714517 CTAA-A-ATTTCGTTA
1 --AATATATTAC-TTA
*
20714531 AATTTATTACTTA
1 AATATATTACTTA
* *
20714544 AATATGTTACTCA
1 AATATATTACTTA
* * *
20714557 GATACATCACTTA
1 AATATATTACTTA
* **
20714570 CTAAAAT-TTGGTTA
1 --AATATATTACTTA
* *
20714584 AATTTTTTACTTA
1 AATATATTACTTA
*
20714597 AATATGTTACTTA
1 AATATATTACTTA
*
20714610 AATACATTACTTA
1 AATATATTACTTA
20714623 CTAAAATTTA
Statistics
Matches: 98, Mismatches: 26, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
12 5 0.05
13 77 0.79
14 12 0.12
15 4 0.04
ACGTcount: A:0.39, C:0.11, G:0.05, T:0.45
Consensus pattern (13 bp):
AATATATTACTTA
Found at i:20714554 original size:53 final size:53
Alignment explanation
Indices: 20714460--20714631 Score: 229
Period size: 53 Copynumber: 3.2 Consensus size: 53
20714450 AACATATTTT
* * * * *
20714460 TTACTAAAATTTAC-TCTTAATATATTACTTGAATATATTACTTAAATATATTAC
1 TTACTAAAATTT-CGT-TAAATTTATTACTTAAATATGTTACTTAAATACATTAC
* * *
20714514 TTACTAAAATTTCGTTAAATTTATTACTTAAATATGTTACTCAGATACATCAC
1 TTACTAAAATTTCGTTAAATTTATTACTTAAATATGTTACTTAAATACATTAC
* *
20714567 TTACTAAAATTTGGTTAAATTTTTTACTTAAATATGTTACTTAAATACATTAC
1 TTACTAAAATTTCGTTAAATTTATTACTTAAATATGTTACTTAAATACATTAC
20714620 TTACTAAAATTT
1 TTACTAAAATTT
20714632 AAGTATATAT
Statistics
Matches: 104, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
53 91 0.88
54 13 0.12
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (53 bp):
TTACTAAAATTTCGTTAAATTTATTACTTAAATATGTTACTTAAATACATTAC
Found at i:20714777 original size:9 final size:9
Alignment explanation
Indices: 20714763--20715082 Score: 202
Period size: 9 Copynumber: 35.8 Consensus size: 9
20714753 TATGTACAAG
20714763 AACTTACAT
1 AACTTACAT
*
20714772 AACTTA-TT
1 AACTTACAT
*
20714780 AATATTTACAT
1 -A-ACTTACAT
20714791 AAACTTACAT
1 -AACTTACAT
*
20714801 AACTATCACAAA
1 AACT-T-AC-AT
*
20714813 AACTTATATGT
1 AACTTACA--T
20714824 AAACTTACAT
1 A-ACTTACAT
20714834 AA--TACAT
1 AACTTACAT
* *
20714841 AATTTACAC
1 AACTTACAT
20714850 AACTTACAT
1 AACTTACAT
*
20714859 AACCTACAT
1 AACTTACAT
20714868 AACTTACAT
1 AACTTACAT
20714877 AA--TACA-
1 AACTTACAT
20714883 AAGCTTACAT
1 AA-CTTACAT
* *
20714893 AACTGAAAT
1 AACTTACAT
* *
20714902 AGCTTACAC
1 AACTTACAT
20714911 AACTTACAT
1 AACTTACAT
20714920 AACTTACAT
1 AACTTACAT
*
20714929 AACTTACAC
1 AACTTACAT
20714938 AACTTACAT
1 AACTTACAT
*
20714947 AATACATA-AT
1 -A-ACTTACAT
20714957 AACTTAC--
1 AACTTACAT
20714964 AACTTACAT
1 AACTTACAT
*
20714973 AACATACAT
1 AACTTACAT
* **
20714982 TACTTTGAT
1 AACTTACAT
20714991 AACTTACAT
1 AACTTACAT
*
20715000 AAGTTACAT
1 AACTTACAT
*
20715009 AA--TACAC
1 AACTTACAT
20715016 AACTTACAT
1 AACTTACAT
** *
20715025 AGTTTACTT
1 AACTTACAT
20715034 AA--TACAT
1 AACTTACAT
20715041 AACTTACAT
1 AACTTACAT
20715050 AACTT--AT
1 AACTTACAT
*
20715057 ACACGTACAT
1 A-ACTTACAT
20715067 AACTTACAT
1 AACTTACAT
*
20715076 AATTTAC
1 AACTTAC
20715083 TTAATACATA
Statistics
Matches: 240, Mismatches: 44, Indels: 54
0.71 0.13 0.16
Matches are distributed among these distances:
6 2 0.01
7 33 0.14
8 8 0.03
9 152 0.63
10 23 0.10
11 11 0.05
12 11 0.05
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:20714868 original size:34 final size:33
Alignment explanation
Indices: 20714829--20714952 Score: 85
Period size: 34 Copynumber: 3.6 Consensus size: 33
20714819 TATGTAAACT
20714829 TACATAA-TACATAATTTACACAA-CTTACATAACC
1 TACATAACTACATAA--TACA-AAGCTTACATAACC
20714863 TACATAACTTACATAATACAAAGCTTACATAA-C
1 TACATAAC-TACATAATACAAAGCTTACATAACC
* * * *
20714896 TGAAATAGCTTACACAACTTACATAA-CTTACATAACT
1 T-ACATAAC-TACATAA--TACA-AAGCTTACATAACC
*
20714933 TACACAACTTACATAATACA
1 TACATAAC-TACATAATACA
20714953 TAATAACTTA
Statistics
Matches: 74, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
33 4 0.05
34 36 0.49
36 31 0.42
37 3 0.04
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (33 bp):
TACATAACTACATAATACAAAGCTTACATAACC
Found at i:20714981 original size:53 final size:51
Alignment explanation
Indices: 20714906--20715025 Score: 152
Period size: 53 Copynumber: 2.3 Consensus size: 51
20714896 TGAAATAGCT
*
20714906 TACACAACTTACATAACTTACATAACTTACACAACTTACATAA-TACATAA
1 TACACAACTTACATAACATACATAACTTACACAACTTACATAAGTACATAA
* ** *
20714956 TAACTTACAACTTACATAACATACATTACTTTGATAACTTACATAAGTTACATAA
1 T-AC--ACAACTTACATAACATACATAACTTACACAACTTACATAAG-TACATAA
20715011 TACACAACTTACATA
1 TACACAACTTACATA
20715026 GTTTACTTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
50 1 0.02
51 2 0.03
52 12 0.20
53 35 0.58
54 2 0.03
55 8 0.13
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.31
Consensus pattern (51 bp):
TACACAACTTACATAACATACATAACTTACACAACTTACATAAGTACATAA
Found at i:20715031 original size:25 final size:25
Alignment explanation
Indices: 20714933--20715090 Score: 106
Period size: 25 Copynumber: 6.2 Consensus size: 25
20714923 TTACATAACT
20714933 TACACAACTTACATAA--TACATAA
1 TACACAACTTACATAATTTACATAA
** *
20714956 TAACTTACAACTTACATAACATACATTACT
1 T-AC--ACAACTTACATAATTTACA-TA-A
** * *
20714986 TTGATAACTTACATAAGTTACATAA
1 TACACAACTTACATAATTTACATAA
* *
20715011 TACACAACTTACATAGTTTACTTAA
1 TACACAACTTACATAATTTACATAA
* **
20715036 TACATAACTTACATAACTTATACA-CG
1 TACACAACTTACATAA-TT-TACATAA
* *
20715062 TACATAACTTACATAATTTACTTAA
1 TACACAACTTACATAATTTACATAA
20715087 TACA
1 TACA
20715091 TAAATATATA
Statistics
Matches: 104, Mismatches: 21, Indels: 18
0.73 0.15 0.13
Matches are distributed among these distances:
23 1 0.01
24 5 0.05
25 39 0.38
26 33 0.32
27 19 0.18
28 4 0.04
29 2 0.02
30 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.34
Consensus pattern (25 bp):
TACACAACTTACATAATTTACATAA
Found at i:20715082 original size:51 final size:50
Alignment explanation
Indices: 20714829--20715093 Score: 162
Period size: 52 Copynumber: 5.1 Consensus size: 50
20714819 TATGTAAACT
* * * * *
20714829 TACATAA--TACATAATTTACACAACTTACATAACCTACATAACTTACATAA
1 TACATAACTTACATAACTTACACAA--TACACAACTTACATAATTTACTTAA
* * * * * *
20714879 TACA-AAGCTTACATAACTGAAATAGCTTACACAACTTACATAACTTACATAA
1 TACATAA-CTTACATAACTTACACA--ATACACAACTTACATAATTTACTTAA
* * ** *
20714931 CTTACACAACTTACATAA--TACATAATAACTTACAACTTACATAACATACATTACT
1 --TACATAACTTACATAACTTACACAAT-AC--ACAACTTACATAATTTAC-TTA-A
** * * *
20714986 TTGATAACTTACATAAGTTACATAATACACAACTTACATAGTTTACTTAA
1 TACATAACTTACATAACTTACACAATACACAACTTACATAATTTACTTAA
* * *
20715036 TACATAACTTACATAACTTATACACGTACATAACTTACATAATTTACTTAA
1 TACATAACTTACATAACTTACACA-ATACACAACTTACATAATTTACTTAA
20715087 TACATAA
1 TACATAA
20715094 ATATATATCA
Statistics
Matches: 171, Mismatches: 28, Indels: 31
0.74 0.12 0.13
Matches are distributed among these distances:
49 2 0.01
50 24 0.14
51 35 0.20
52 53 0.31
53 30 0.18
54 17 0.10
55 10 0.06
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (50 bp):
TACATAACTTACATAACTTACACAATACACAACTTACATAATTTACTTAA
Found at i:20720604 original size:66 final size:66
Alignment explanation
Indices: 20720526--20720654 Score: 213
Period size: 66 Copynumber: 2.0 Consensus size: 66
20720516 CACAGCTGAG
* *
20720526 GTTCAAAGGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGTAGCGAGAGAAGCAAA
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGAGAAGCAAA
20720591 A
66 A
* * *
20720592 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCTGATGCGGCATCGAGAGAAGCA
1 GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGAGAAGCA
20720655 GAGCAGAGCA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.43, C:0.18, G:0.24, T:0.16
Consensus pattern (66 bp):
GTTCAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGAGAAGCAAA
A
Found at i:20720680 original size:66 final size:66
Alignment explanation
Indices: 20720529--20720693 Score: 174
Period size: 66 Copynumber: 2.5 Consensus size: 66
20720519 AGCTGAGGTT
* * * *
20720529 CAAAGGAAATATGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGTAGCGAGAGAAGCAAAAGT
1 CAAAAGAAATACGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGAGAAGCAAAAGA
*
20720594 T
66 G
* * * * *
20720595 CAAAAGAAATATGAAGAACTCCAGCTACAACTTAAAGCTGATGCGGCATCGAGAGAAGCAGAGCA
1 CAAAAGAAATACGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGAGAAGCA-A-AA
20720660 GAG
64 GAG
* *
20720663 C-AAA-AAGTACGACGAACTCCAGC-AGCAACTT
1 CAAAAGAAATACGAAGAACTCCAGCTA-CAACTT
20720694 CAGAGTATGA
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
65 1 0.01
66 77 0.91
67 4 0.05
68 3 0.04
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.13
Consensus pattern (66 bp):
CAAAAGAAATACGAAGAACTCCAGCTACAACTTAAAGCAGAGGCGGCAGCGAGAGAAGCAAAAGA
G
Found at i:20721030 original size:42 final size:42
Alignment explanation
Indices: 20720977--20721200 Score: 234
Period size: 42 Copynumber: 5.3 Consensus size: 42
20720967 TTGAACAAAA
* * * *
20720977 GTTCTTTAGCGGCGCATATTCACAAACGCCGCTAAAGAACAT
1 GTTCTTTAGCGGCGCTTAGTAAAAAACGCCGCTAAAGAACAT
* * * * *
20721019 GTTCTTTAGCGGCGCTTAATAAAAAATGCCACCAAAGATCAT
1 GTTCTTTAGCGGCGCTTAGTAAAAAACGCCGCTAAAGAACAT
* *
20721061 GTTCTTTAGCGGCACTTAGAAAAAAACGCCGCTAAAGAACAT
1 GTTCTTTAGCGGCGCTTAGTAAAAAACGCCGCTAAAGAACAT
* ** ** *** *
20721103 GTTCTTTAGTGGCTTTTTTTTCTAATCGCCGCTAAAGAACAT
1 GTTCTTTAGCGGCGCTTAGTAAAAAACGCCGCTAAAGAACAT
* *
20721145 GATCTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGAACAT
1 GTTCTTTAGCGGCGCTTAGTAAAAAACGCCGCTAAAGAACAT
20721187 -TATCTTTAGCGGCG
1 GT-TCTTTAGCGGCG
20721201 TTTTTGTTTG
Statistics
Matches: 144, Mismatches: 37, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
42 144 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (42 bp):
GTTCTTTAGCGGCGCTTAGTAAAAAACGCCGCTAAAGAACAT
Found at i:20724395 original size:18 final size:18
Alignment explanation
Indices: 20724327--20724398 Score: 72
Period size: 18 Copynumber: 4.0 Consensus size: 18
20724317 TGCTGGGAAA
20724327 GGAGGAGGAAATGGTGGT
1 GGAGGAGGAAATGGTGGT
* **
20724345 GGAGGTGGAGGTGGTGGT
1 GGAGGAGGAAATGGTGGT
* * ***
20724363 GGTGGTGGTGGTGGTGGT
1 GGAGGAGGAAATGGTGGT
20724381 GGAGGAGGAAATGGTGGT
1 GGAGGAGGAAATGGTGGT
20724399 AGTTGCAGTC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.17, C:0.00, G:0.61, T:0.22
Consensus pattern (18 bp):
GGAGGAGGAAATGGTGGT
Done.