Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold127
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: 4281254
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
File 18 of 26
Found at i:2876130 original size:19 final size:19
Alignment explanation
Indices: 2876086--2876131 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2876076 TATATTTTAT
*
2876086 TTTTATTATATTTTAATAA
1 TTTTATTTTATTTTAATAA
* * *
2876105 ATATATTTTATTTTATTAA
1 TTTTATTTTATTTTAATAA
2876124 TTTTATTT
1 TTTTATTT
2876132 ATAAAATTTA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTATTTTATTTTAATAA
Found at i:2876160 original size:24 final size:23
Alignment explanation
Indices: 2876124--2876168 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2876114 ATTTTATTAA
*
2876124 TTTTATTTATAAAATTTAATAAAT
1 TTTTATTTAT-AAATATAATAAAT
*
2876148 TTTTATTTTTAAATATAATAA
1 TTTTATTTATAAATATAATAA
2876169 TTTATCCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTATTTATAAATATAATAAAT
Found at i:2876561 original size:17 final size:18
Alignment explanation
Indices: 2876539--2876586 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
2876529 TAAAATTAAT
2876539 TAATATATTATTAATA-A
1 TAATATATTATTAATATA
*
2876556 TAATATTTTATTAA-ATA
1 TAATATATTATTAATATA
*
2876573 TAATA-ATTAATAAT
1 TAATATATTATTAAT
2876587 TTTATTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATATATTATTAATATA
Found at i:2876787 original size:42 final size:44
Alignment explanation
Indices: 2876734--2876815 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
2876724 GATATCACTC
*
2876734 AAATTTAATAATT-TATTT-ATTTATATCATATTTATATATTTT
1 AAATTTAATAATTATATTTAAATTATATCATATTTATATATTTT
* * *
2876776 AAATTTTATAATTATATTTAAATTATTTTATATTTATATA
1 AAATTTAATAATTATATTTAAATTATATCATATTTATATA
2876816 AATTATGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 12 0.35
43 5 0.15
44 17 0.50
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (44 bp):
AAATTTAATAATTATATTTAAATTATATCATATTTATATATTTT
Found at i:2876819 original size:20 final size:22
Alignment explanation
Indices: 2876778--2876821 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
2876768 TATATTTTAA
*
2876778 ATTTTATAATTATATTTAAATT
1 ATTTTATAATTATATATAAATT
2876800 ATTTTAT-ATT-TATATAAATT
1 ATTTTATAATTATATATAAATT
2876820 AT
1 AT
2876822 GATTCGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 3 0.14
22 7 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATTTTATAATTATATATAAATT
Found at i:2877013 original size:17 final size:18
Alignment explanation
Indices: 2876983--2877016 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2876973 TTTATAATTT
*
2876983 AAAAAACCTAAATACTTA
1 AAAAAAACTAAATACTTA
2877001 AAAAAAACT-AATACTT
1 AAAAAAACTAAATACTT
2877017 TTAATCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAAAAACTAAATACTTA
Found at i:2884975 original size:19 final size:19
Alignment explanation
Indices: 2884951--2884988 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2884941 TATAAAAAAT
2884951 TATTTTTAT-ATTAATATTA
1 TATTTTTATAATTAA-ATTA
2884970 TATTTTTATAATTAAATTA
1 TATTTTTATAATTAAATTA
2884989 AAATAACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTTATAATTAAATTA
Found at i:2885715 original size:27 final size:28
Alignment explanation
Indices: 2885657--2885717 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
2885647 ATGAATGGGT
* * *
2885657 GATTTTTTTTTAAAAAAAATTTGTTATA
1 GATTTTTTTTAAAAAAAAATTTGTAAAA
2885685 -ATTTTTTTTAAAAAAAAATTT-TAAAA
1 GATTTTTTTTAAAAAAAAATTTGTAAAA
2885711 GATTTTT
1 GATTTTT
2885718 CAAAATGGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (28 bp):
GATTTTTTTTAAAAAAAAATTTGTAAAA
Found at i:2885716 original size:26 final size:26
Alignment explanation
Indices: 2885661--2885717 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
2885651 ATGGGTGATT
* * *
2885661 TTTTTTTAAAAAAAATTTGTTATAAT
1 TTTTTTTAAAAAAAAATTGTTAAAAA
2885687 TTTTTTTAAAAAAAAATT-TTAAAAGA
1 TTTTTTTAAAAAAAAATTGTTAAAA-A
2885713 TTTTT
1 TTTTT
2885718 CAAAATGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTTTTTAAAAAAAAATTGTTAAAAA
Found at i:2887706 original size:2 final size:2
Alignment explanation
Indices: 2887694--2887725 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
2887684 ATATCCATAC
2887694 AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
2887726 AATAACTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2888019 original size:2 final size:2
Alignment explanation
Indices: 2888012--2888040 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2888002 TTATAATTGA
2888012 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2888041 CACACACACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2892098 original size:20 final size:20
Alignment explanation
Indices: 2892056--2892105 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
2892046 TGAGAAAATG
* ** *
2892056 TTTTCAATTTTAATTTTTTA
1 TTTTCATTTTTAATAATTCA
2892076 TTTTCATTTTTAATAATTCA
1 TTTTCATTTTTAATAATTCA
2892096 TTTTCATTTT
1 TTTTCATTTT
2892106 CTATTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTCATTTTTAATAATTCA
Found at i:2895092 original size:27 final size:27
Alignment explanation
Indices: 2895062--2895113 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2895052 ATCTTATTAA
*
2895062 TAATAAAAATATTTAA-AATAATAAAAT
1 TAAT-AAAATATTAAACAATAATAAAAT
*
2895089 TAATAATATATTAAACAATAATAAA
1 TAATAAAATATTAAACAATAATAAA
2895114 TATATAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
TAATAAAATATTAAACAATAATAAAAT
Found at i:2895096 original size:15 final size:15
Alignment explanation
Indices: 2895056--2895096 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
2895046 TAATAGATCT
2895056 TATTAATAATAAAAA
1 TATTAATAATAAAAA
2895071 TATTTAA-AATAATAAA
1 TA-TTAATAATAA-AAA
2895087 -ATTAATAATA
1 TATTAATAATA
2895097 TATTAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.17
15 12 0.52
16 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TATTAATAATAAAAA
Found at i:2895431 original size:21 final size:22
Alignment explanation
Indices: 2895394--2895434 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2895384 AATTTAACAA
*
2895394 AAAAAACTAAATTTTAATTATT
1 AAAAAACTAAATATTAATTATT
2895416 AAAAAACT-AATATTAATTA
1 AAAAAACTAAATATTAATTA
2895435 GGAGTGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAAACTAAATATTAATTATT
Found at i:2897124 original size:20 final size:20
Alignment explanation
Indices: 2897101--2897140 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2897091 GATGAATAGA
2897101 TTTAA-ATAAAAATAAATAAT
1 TTTAATATAAAAA-AAATAAT
*
2897121 TTTAATATCAAAAAAATAAT
1 TTTAATATAAAAAAAATAAT
2897141 AAATATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (20 bp):
TTTAATATAAAAAAAATAAT
Found at i:2897180 original size:21 final size:19
Alignment explanation
Indices: 2897156--2897210 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
2897146 TAATAAATAA
2897156 TTAATAAAATTTAAAATTAAT
1 TTAATAAAATTTAAAATT--T
2897177 TTAATAAAA--TAAAATTT
1 TTAATAAAATTTAAAATTT
*
2897194 TAAATATAAATTTAAAA
1 TTAATA-AAATTTAAAA
2897211 AATAATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 6 0.20
18 3 0.10
19 7 0.23
20 5 0.17
21 9 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAATAAAATTTAAAATTT
Found at i:2897205 original size:28 final size:26
Alignment explanation
Indices: 2897158--2897226 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 26
2897148 ATAAATAATT
*
2897158 AATAAAATTTAAA-ATTAATTTAATAA
1 AATAAAATTTAAATATAAATTTAA-AA
2897184 AATAAAATTTTAAATATAAATTTAAAA
1 AATAAAA-TTTAAATATAAATTTAAAA
2897211 AATAATAAATTTAAAT
1 AAT-A-AAATTTAAAT
2897227 CTTATTATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
26 7 0.18
27 11 0.29
28 17 0.45
29 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AATAAAATTTAAATATAAATTTAAAA
Found at i:2897215 original size:13 final size:13
Alignment explanation
Indices: 2897168--2897215 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
2897158 AATAAAATTT
*
2897168 AAAATTAATTTAA
1 AAAATAAATTTAA
*
2897181 TAAAATAAAATTTTA
1 -AAAAT-AAATTTAA
*
2897196 AATATAAATTTAA
1 AAAATAAATTTAA
2897209 AAAATAA
1 AAAATAA
2897216 TAAATTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 13 0.46
14 9 0.32
15 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAATAAATTTAA
Found at i:2897221 original size:16 final size:15
Alignment explanation
Indices: 2897174--2897225 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
2897164 ATTTAAAATT
2897174 AATTTAATAAAATA-A
1 AATTTAA-AAAATATA
*
2897189 AATTT--TAAATATA
1 AATTTAAAAAATATA
2897202 AATTTAAAAAATAATA
1 AATTTAAAAAAT-ATA
2897218 AATTTAAA
1 AATTTAAA
2897226 TCTTATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 5 0.16
13 6 0.19
15 9 0.29
16 11 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTTAAAAAATATA
Found at i:2897302 original size:21 final size:20
Alignment explanation
Indices: 2897265--2897303 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2897255 AGATATAAAA
*
2897265 TTAATTTTTATCGATTTTAT
1 TTAATTTTTATAGATTTTAT
*
2897285 TTAATTTTTTATATATTTT
1 TTAA-TTTTTATAGATTTT
2897304 TAAATTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (20 bp):
TTAATTTTTATAGATTTTAT
Found at i:2900518 original size:23 final size:25
Alignment explanation
Indices: 2900485--2900536 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
2900475 TGTGTAATTA
2900485 TTTAATATTTAATAAATTTAA-AAT
1 TTTAATATTTAATAAATTTAATAAT
**
2900509 TTTAAT-TTTAATATTTTTAATAAT
1 TTTAATATTTAATAAATTTAATAAT
2900533 TTTA
1 TTTA
2900537 TAATTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTTAATATTTAATAAATTTAATAAT
Found at i:2900528 original size:32 final size:30
Alignment explanation
Indices: 2900485--2900543 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
2900475 TGTGTAATTA
2900485 TTTAATATTTAATAAATTTAAAATTTTAAT
1 TTTAATATTTAATAAATTTAAAATTTTAAT
* *
2900515 TTTAATATTTTTAATAATTTTATAATTTT
1 TTTAATA--TTTAATAAATTTAAAATTTT
2900544 TTAAATTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 7 0.28
32 18 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTAATATTTAATAAATTTAAAATTTTAAT
Found at i:2901525 original size:2 final size:2
Alignment explanation
Indices: 2901520--2901553 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2901510 TTTTTAGCAC
2901520 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2901554 TAACTATACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2903428 original size:21 final size:20
Alignment explanation
Indices: 2903404--2903444 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2903394 AAAAAATATA
*
2903404 TTTTATATTTATCTTTTAACT
1 TTTTATATTTAT-ATTTAACT
*
2903425 TTTTATCTTTATATTTAACT
1 TTTTATATTTATATTTAACT
2903445 CAAAATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTATATTTATATTTAACT
Found at i:2903634 original size:21 final size:20
Alignment explanation
Indices: 2903610--2903660 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2903600 TAATAAAATA
2903610 TATATTATATATACATGCAAG
1 TATATTATAT-TACATGCAAG
* *
2903631 TATACTTTTATTACATGCATG
1 TATA-TTATATTACATGCAAG
2903652 TATA-TATAT
1 TATATTATAT
2903661 CTCTCTCTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 4 0.15
21 17 0.65
22 5 0.19
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (20 bp):
TATATTATATTACATGCAAG
Found at i:2903849 original size:14 final size:14
Alignment explanation
Indices: 2903825--2903860 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
2903815 TTTTATTTTT
2903825 AAATATAATTATAAA
1 AAAT-TAATTATAAA
2903840 AAATTAATTATAAA
1 AAATTAATTATAAA
2903854 AAATTAA
1 AAATTAA
2903861 ATAAATGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATTAATTATAAA
Found at i:2905503 original size:26 final size:26
Alignment explanation
Indices: 2905426--2905505 Score: 65
Period size: 27 Copynumber: 3.0 Consensus size: 26
2905416 ACGAGTTGAA
* *
2905426 AATAAAATTAAATAATTTTATATTTAAT
1 AATAAAATTAAATAA-ATTAT-TTAAAT
* *
2905454 AA-ATATATTAAAATTTAATT-TTTAAAT
1 AATA-AAATT-AAA-TAAATTATTTAAAT
2905481 AATAAAATTAAATAAATTATTTAAA
1 AATAAAATTAAATAAATTATTTAAA
2905506 ATTAAATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
25 5 0.12
26 9 0.22
27 12 0.29
28 8 0.20
29 5 0.12
30 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATAAAATTAAATAAATTATTTAAAT
Found at i:2907837 original size:29 final size:29
Alignment explanation
Indices: 2907804--2907862 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2907794 TATTTGAAGG
* *
2907804 TGCCAAACATTAAAGAGATATCAAATCAC
1 TGCCAAACATCAAAGAAATATCAAATCAC
2907833 TGCCAAACATCAAAGAAATATCAAATCAC
1 TGCCAAACATCAAAGAAATATCAAATCAC
2907862 T
1 T
2907863 TAAGCTTGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.49, C:0.22, G:0.08, T:0.20
Consensus pattern (29 bp):
TGCCAAACATCAAAGAAATATCAAATCAC
Found at i:2909880 original size:18 final size:19
Alignment explanation
Indices: 2909843--2909892 Score: 75
Period size: 18 Copynumber: 2.7 Consensus size: 19
2909833 AACTTTAAGA
2909843 AAACCATGTTATGAACAGG
1 AAACCATGTTATGAACAGG
* *
2909862 AAATCATGTT-TGAATAGG
1 AAACCATGTTATGAACAGG
2909880 AAACCATGTTATG
1 AAACCATGTTATG
2909893 TCTTGTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 16 0.59
19 11 0.41
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (19 bp):
AAACCATGTTATGAACAGG
Found at i:2910025 original size:22 final size:22
Alignment explanation
Indices: 2909993--2910075 Score: 85
Period size: 22 Copynumber: 3.6 Consensus size: 22
2909983 TTGATATTTT
*
2909993 TATTAATTGTGTTAGGTAAATA
1 TATTAAATGTGTTAGGTAAATA
* *
2910015 TTTTAAATGTGTTAAGTAAGTAATA
1 TATTAAATGTGTTAGGT-A--AATA
*
2910040 TATTAAATGTGTTAGGTAAACA
1 TATTAAATGTGTTAGGTAAATA
**
2910062 TATTAGGTGTGTTA
1 TATTAAATGTGTTA
2910076 CGTGAACATA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
22 29 0.58
23 1 0.02
24 1 0.02
25 19 0.38
ACGTcount: A:0.36, C:0.01, G:0.19, T:0.43
Consensus pattern (22 bp):
TATTAAATGTGTTAGGTAAATA
Found at i:2910039 original size:25 final size:25
Alignment explanation
Indices: 2910011--2910058 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2910001 GTGTTAGGTA
*
2910011 AATATTTTAAATGTGTTAAGTAAGT
1 AATATATTAAATGTGTTAAGTAAGT
*
2910036 AATATATTAAATGTGTTAGGTAA
1 AATATATTAAATGTGTTAAGTAA
2910059 ACATATTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (25 bp):
AATATATTAAATGTGTTAAGTAAGT
Found at i:2912883 original size:34 final size:34
Alignment explanation
Indices: 2912779--2912883 Score: 129
Period size: 34 Copynumber: 3.0 Consensus size: 34
2912769 CTTTATTAAG
* * * *
2912779 TATGTTAGGTAAACATTTTAGGTGTATTAGGTGG
1 TATGTTAGGTAAATATATTAGGTGTGTTAGGTGA
*
2912813 TATGTTAGGTGAGTAATATATTAAGTGTGTTAGGTGA
1 TATGTTAGGT-A--AATATATTAGGTGTGTTAGGTGA
*
2912850 TGTGTTAGGTAAATATATTAGGTGTGTTAGGTGA
1 TATGTTAGGTAAATATATTAGGTGTGTTAGGTGA
2912884 ACATATTTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
34 32 0.52
35 1 0.02
36 1 0.02
37 27 0.44
ACGTcount: A:0.28, C:0.01, G:0.30, T:0.41
Consensus pattern (34 bp):
TATGTTAGGTAAATATATTAGGTGTGTTAGGTGA
Found at i:2914343 original size:27 final size:28
Alignment explanation
Indices: 2914313--2914462 Score: 89
Period size: 29 Copynumber: 5.2 Consensus size: 28
2914303 TATAATTATA
2914313 TTTAAATT-AT-TTTATATTTATATAAAT
1 TTTAAATTAATATTTATA-TTATATAAAT
2914340 TTTATTATATTAATAATTTATATTATATAAAT
1 TTTA--A-ATTAAT-ATTTATATTATATAAAT
* * *
2914372 TTTAAAATAAATATTCATATCATATAATAT
1 TTT-AAATTAATATTTATATTATATAA-AT
* *** *
2914402 TATCTTTTAA-ATTAATATTAT-TAAAT
1 TTTAAATTAATATTTATATTATATAAAT
2914428 TTATATAATT-ATATTTAATATTAT-TAAA-
1 TT-TA-AATTAATATTT-ATATTATATAAAT
2914456 TTTAAAT
1 TTTAAAT
2914463 AATCTTAAAT
Statistics
Matches: 96, Mismatches: 15, Indels: 25
0.71 0.11 0.18
Matches are distributed among these distances:
26 6 0.06
27 11 0.11
28 16 0.17
29 28 0.29
30 12 0.12
31 3 0.03
32 13 0.14
33 7 0.07
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTAAATTAATATTTATATTATATAAAT
Found at i:2914349 original size:14 final size:14
Alignment explanation
Indices: 2914330--2914375 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 14
2914320 TATTTTATAT
2914330 TTATATAAATTTTA
1 TTATATAAATTTTA
2914344 TTATATTAATAATTTATA
1 TTATA-T-A-AATTT-TA
2914362 TTATATAAATTTTA
1 TTATATAAATTTTA
2914376 AAATAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.25
15 6 0.21
16 2 0.07
17 6 0.21
18 7 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATATAAATTTTA
Found at i:2914363 original size:18 final size:18
Alignment explanation
Indices: 2914302--2914367 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 18
2914292 TCTTATTATG
*
2914302 TTATAATTATATT--TAAA
1 TTAT-ATTATATTAATAAT
*
2914319 TTATTTTATATTTATATAAAT
1 TTATATTATA-TTA-AT-AAT
2914340 TT-TATTATATTAATAAT
1 TTATATTATATTAATAAT
2914357 TTATATTATAT
1 TTATATTATAT
2914368 AAATTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
16 5 0.12
17 11 0.28
18 10 0.25
19 3 0.08
20 7 0.17
21 4 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTATATTATATTAATAAT
Found at i:2914427 original size:14 final size:14
Alignment explanation
Indices: 2914408--2914457 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
2914398 ATATTATCTT
2914408 TTAAATTAATATTA
1 TTAAATTAATATTA
* *
2914422 TTAAATTTATATAA
1 TTAAATTAATATTA
*
2914436 TTATATTTAATATTA
1 TTA-AATTAATATTA
2914451 TTAAATT
1 TTAAATT
2914458 TAAATAATCT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTAAATTAATATTA
Found at i:2914871 original size:16 final size:16
Alignment explanation
Indices: 2914850--2914892 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 16
2914840 TATATTTATA
2914850 TATATAATTAATTTGT
1 TATATAATTAATTTGT
*
2914866 TATATAAAATTAATTTTT
1 TATAT--AATTAATTTGT
*
2914884 TAAATAATT
1 TATATAATT
2914893 TATTATTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
TATATAATTAATTTGT
Found at i:2914890 original size:18 final size:18
Alignment explanation
Indices: 2914855--2914890 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2914845 TTATATATAT
*
2914855 AATTAATTTGTTATATAA
1 AATTAATTTGTTAAATAA
*
2914873 AATTAATTTTTTAAATAA
1 AATTAATTTGTTAAATAA
2914891 TTTATTATTA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTAATTTGTTAAATAA
Found at i:2915173 original size:15 final size:15
Alignment explanation
Indices: 2915134--2915173 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2915124 AAGTCAACGT
*
2915134 AAACTCAATTAAAAA
1 AAACTCAAATAAAAA
* *
2915149 AAAATAAAATAAAAA
1 AAACTCAAATAAAAA
2915164 AAACTCAAAT
1 AAACTCAAAT
2915174 CTTTACTTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.17
Consensus pattern (15 bp):
AAACTCAAATAAAAA
Found at i:2916370 original size:16 final size:16
Alignment explanation
Indices: 2916363--2916417 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
2916353 TCGGGTTCTC
2916363 TCGGGTTCGAGTTTTT
1 TCGGGTTCGAGTTTTT
*
2916379 TCAGGTTCGAGTTTTT
1 TCGGGTTCGAGTTTTT
*
2916395 TCGGGTTCGAGCTTTT
1 TCGGGTTCGAGTTTTT
*
2916411 TCAGGTT
1 TCGGGTT
2916418 TAGACTGTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.09, C:0.15, G:0.29, T:0.47
Consensus pattern (16 bp):
TCGGGTTCGAGTTTTT
Found at i:2916387 original size:32 final size:32
Alignment explanation
Indices: 2916351--2916417 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
2916341 TCAGTCTCAA
* *
2916351 GTTCGGGTTCTCTCGGGTTCGAGTTTTTTCAG
1 GTTCGAGTTCTCTCGGGTTCGAGCTTTTTCAG
* *
2916383 GTTCGAGTTTTTTCGGGTTCGAGCTTTTTCAG
1 GTTCGAGTTCTCTCGGGTTCGAGCTTTTTCAG
2916415 GTT
1 GTT
2916418 TAGACTGTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.07, C:0.16, G:0.30, T:0.46
Consensus pattern (32 bp):
GTTCGAGTTCTCTCGGGTTCGAGCTTTTTCAG
Found at i:2916751 original size:17 final size:16
Alignment explanation
Indices: 2916729--2916760 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2916719 TTGAAAAAAT
2916729 TTGAATTTGAATTTAAA
1 TTGAATTTG-ATTTAAA
2916746 TTGAATTTGATTTAA
1 TTGAATTTGATTTAA
2916761 TTAAAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (16 bp):
TTGAATTTGATTTAAA
Found at i:2917832 original size:24 final size:25
Alignment explanation
Indices: 2917803--2917856 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
2917793 ACATATGACA
*
2917803 TAAAATTA-AAAACTTCAAATACAAC
1 TAAAATTATAAAAC-GCAAATACAAC
*
2917828 -AAAATTATATAACGCAAATACAAC
1 TAAAATTATAAAACGCAAATACAAC
2917852 TAAAA
1 TAAAA
2917857 ATAATTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.61, C:0.15, G:0.02, T:0.22
Consensus pattern (25 bp):
TAAAATTATAAAACGCAAATACAAC
Found at i:2918001 original size:18 final size:18
Alignment explanation
Indices: 2917980--2918014 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2917970 AAATATTTAA
2917980 AAATTAATTTTATATAAT
1 AAATTAATTTTATATAAT
2917998 AAATTAATTTTATATAA
1 AAATTAATTTTATATAA
2918015 ATATAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATTAATTTTATATAAT
Found at i:2918529 original size:16 final size:16
Alignment explanation
Indices: 2918447--2918532 Score: 57
Period size: 16 Copynumber: 4.9 Consensus size: 16
2918437 AAAATTATAT
*
2918447 ATATATTAAATAAAAA
1 ATATATTAAATATAAA
2918463 ATA-ATTTAAATATAGTATAA
1 ATATA-TT-AA-ATA-TA-AA
* *
2918483 ATATATGGATATATTAAA
1 ATATAT-TAAATA-TAAA
*
2918501 ATTTATATAAATATAAA
1 ATATAT-TAAATATAAA
2918518 ATATATTAAATATAA
1 ATATATTAAATATAA
2918533 TTATAAATTT
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
15 1 0.02
16 14 0.26
17 11 0.20
18 14 0.26
19 6 0.11
20 7 0.13
21 1 0.02
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
ATATATTAAATATAAA
Found at i:2918537 original size:28 final size:27
Alignment explanation
Indices: 2918443--2918540 Score: 83
Period size: 28 Copynumber: 3.5 Consensus size: 27
2918433 TCATAAAATT
*
2918443 ATATATATATTAAATAAAAAATA-ATTTAA
1 ATATAT-TA-TAAATATAAAATATA-TTAA
* **
2918472 ATATAGTATAAATATATGGATATATTAA
1 ATATATTATAAATATA-AAATATATTAA
*
2918500 A-ATTTATATAAATATAAAATATATTAA
1 ATATAT-TATAAATATAAAATATATTAA
2918527 ATATAATTATAAAT
1 ATAT-ATTATAAAT
2918541 TTTAATATAA
Statistics
Matches: 55, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
27 19 0.35
28 29 0.53
29 7 0.13
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (27 bp):
ATATATTATAAATATAAAATATATTAA
Found at i:2922565 original size:20 final size:20
Alignment explanation
Indices: 2922537--2922596 Score: 79
Period size: 19 Copynumber: 3.0 Consensus size: 20
2922527 TTAAATTGAT
*
2922537 TTAATTAAAAATTTTAAATA
1 TTAAATAAAAATTTTAAATA
2922557 TTAAATAAATAA-TTT-AATA
1 TTAAATAAA-AATTTTAAATA
*
2922576 TTAAATAAATATTTTAAATA
1 TTAAATAAAAATTTTAAATA
2922596 T
1 T
2922597 AGTAGAGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.03
19 16 0.46
20 16 0.46
21 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAATAAAAATTTTAAATA
Found at i:2923564 original size:18 final size:18
Alignment explanation
Indices: 2923541--2923576 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2923531 AAATAAAAAT
*
2923541 ATATTATTTTAATTTAAA
1 ATATTATTTTAAATTAAA
2923559 ATATTATTTTAAATTAAA
1 ATATTATTTTAAATTAAA
2923577 TTGCTTCTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTATTTTAAATTAAA
Found at i:2925310 original size:2 final size:2
Alignment explanation
Indices: 2925303--2925347 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2925293 TCCTTTTCTT
2925303 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2925345 TA T
1 TA T
2925348 CATGAGGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2927022 original size:16 final size:16
Alignment explanation
Indices: 2927003--2927034 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2926993 TTAGGGATTT
2927003 AGATTGAGTAGATTGA
1 AGATTGAGTAGATTGA
*
2927019 AGATTGAGTATATTGA
1 AGATTGAGTAGATTGA
2927035 GTGTGCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.28, T:0.34
Consensus pattern (16 bp):
AGATTGAGTAGATTGA
Found at i:2931843 original size:2 final size:2
Alignment explanation
Indices: 2931838--2931867 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2931828 ACACAGACAC
*
2931838 AT AT AT AC 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
2931868 CCAGCTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2933639 original size:3 final size:3
Alignment explanation
Indices: 2933631--2933674 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2933621 GTGTTGACAC
*
2933631 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2933675 TACTAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2934054 original size:17 final size:19
Alignment explanation
Indices: 2934017--2934054 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2934007 TAATTTAGTT
2934017 AAATTATTATTTATTAATAA
1 AAATTATTATTTATT-ATAA
2934037 AAATTATT-TTTATT-TAA
1 AAATTATTATTTATTATAA
2934054 A
1 A
2934055 TTTAATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AAATTATTATTTATTATAA
Found at i:2936882 original size:15 final size:15
Alignment explanation
Indices: 2936851--2936885 Score: 61
Period size: 16 Copynumber: 2.3 Consensus size: 15
2936841 TAAAAAACAA
2936851 TTTATAAATTAATTT
1 TTTATAAATTAATTT
2936866 TTTATTAAATTAATTT
1 TTTA-TAAATTAATTT
2936882 TTTA
1 TTTA
2936886 ACTATTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTATAAATTAATTT
Found at i:2937239 original size:16 final size:16
Alignment explanation
Indices: 2937218--2937264 Score: 69
Period size: 15 Copynumber: 3.0 Consensus size: 16
2937208 TATTTCAAAA
2937218 AAAATTAAAATTATTT
1 AAAATTAAAATTATTT
2937234 AAAATTAAAA-TATTT
1 AAAATTAAAATTATTT
* *
2937249 AAATTTAAAATAATTT
1 AAAATTAAAATTATTT
2937265 TAACTCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 14 0.50
16 14 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATTAAAATTATTT
Found at i:2937604 original size:21 final size:21
Alignment explanation
Indices: 2937580--2937620 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2937570 AGTTGATTGT
* *
2937580 AATGATAATTAAAAAAATATG
1 AATGAGAAGTAAAAAAATATG
*
2937601 AATGAGAGGTAAAAAAATAT
1 AATGAGAAGTAAAAAAATAT
2937621 TTAAAATAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.61, C:0.00, G:0.15, T:0.24
Consensus pattern (21 bp):
AATGAGAAGTAAAAAAATATG
Found at i:2937667 original size:16 final size:16
Alignment explanation
Indices: 2937643--2937692 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
2937633 ATAATATAAT
2937643 TATATTAAAATTTATA
1 TATATTAAAATTTATA
* *
2937659 TATAATAAATTATTA-A
1 TATATTAAAAT-TTATA
*
2937675 TATTTTAAAATTTATA
1 TATATTAAAATTTATA
2937691 TA
1 TA
2937693 AGTATTTAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 3 0.11
16 21 0.78
17 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATTAAAATTTATA
Found at i:2937854 original size:2 final size:2
Alignment explanation
Indices: 2937847--2937882 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2937837 TCCATTTTCA
2937847 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2937883 TTCTGCTCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2939129 original size:2 final size:2
Alignment explanation
Indices: 2939124--2939160 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2939114 AAAAAAACAA
2939124 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2939161 ATGGGTGCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2941159 original size:3 final size:3
Alignment explanation
Indices: 2941143--2941216 Score: 98
Period size: 3 Copynumber: 24.3 Consensus size: 3
2941133 GTTTTTATCC
*
2941143 TAT TAT TAA T-T TAT TATT TAT TAT TAT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT
2941189 TAT TAT TAT TAT TAT TAT ATAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT T
2941217 TATGTTTTTT
Statistics
Matches: 64, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
2 3 0.05
3 52 0.81
4 9 0.14
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2941470 original size:25 final size:25
Alignment explanation
Indices: 2941405--2941470 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
2941395 ATAATAAAAA
*
2941405 TAAAATGATTATTAAATATATGATAT
1 TAAAATG-TTATTAAATATATAATAT
2941431 TAAAATGTGTA-TAAATA-ATAAATAGT
1 TAAAATGT-TATTAAATATAT-AATA-T
2941457 TAAAA-GTTATTAAA
1 TAAAATGTTATTAAA
2941471 ATTATATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
24 4 0.11
25 16 0.46
26 15 0.43
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (25 bp):
TAAAATGTTATTAAATATATAATAT
Found at i:2941508 original size:40 final size:42
Alignment explanation
Indices: 2941446--2941523 Score: 124
Period size: 40 Copynumber: 1.9 Consensus size: 42
2941436 TGTGTATAAA
* *
2941446 TAATAAATAGTTAAAAGTTATTAAAATTATATTTATGTTAAT
1 TAATAAATAATTAAAAGTTATTAAAACTATATTTATGTTAAT
2941488 TAAT-AATAATTAAAA-TTATTAAAACTATATTTATGT
1 TAATAAATAATTAAAAGTTATTAAAACTATATTTATGT
2941524 CACAAAAGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
40 20 0.59
41 10 0.29
42 4 0.12
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (42 bp):
TAATAAATAATTAAAAGTTATTAAAACTATATTTATGTTAAT
Found at i:2943443 original size:47 final size:48
Alignment explanation
Indices: 2943360--2943456 Score: 151
Period size: 47 Copynumber: 2.0 Consensus size: 48
2943350 TAAGTTGAGA
* *
2943360 TAACTTGGTTGTGCCTTCCAAACCTAGATCTTGGGATATTTAGTCAAC
1 TAACTTGGTTATGCCTTCCAAACCTAGATCTTGGGATATCTAGTCAAC
* *
2943408 TAACTTGGTTATGCCTT-CGAACCTAGATCTTGGGATCTCTAGTCAAC
1 TAACTTGGTTATGCCTTCCAAACCTAGATCTTGGGATATCTAGTCAAC
2943455 TA
1 TA
2943457 GGTTGGGTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
47 29 0.64
48 16 0.36
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (48 bp):
TAACTTGGTTATGCCTTCCAAACCTAGATCTTGGGATATCTAGTCAAC
Found at i:2947386 original size:17 final size:16
Alignment explanation
Indices: 2947358--2947399 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
2947348 ATAAGAAACT
2947358 AAACAAAGAAAGAAGA
1 AAACAAAGAAAGAAGA
* *
2947374 AAAGAAAGCAAAGAGGA
1 AAACAAAG-AAAGAAGA
2947391 AAACAAAGA
1 AAACAAAGA
2947400 TGATTTTGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.71, C:0.07, G:0.21, T:0.00
Consensus pattern (16 bp):
AAACAAAGAAAGAAGA
Found at i:2948148 original size:273 final size:272
Alignment explanation
Indices: 2947637--2948180 Score: 869
Period size: 273 Copynumber: 2.0 Consensus size: 272
2947627 GCAATAAAAA
2947637 AATAAGGCCCAATACCTTTAAGGCCAAGCTTAAGTCCAACTCAATTCGATGGTAAAGTATGCATA
1 AATAAGGCCCAATACCTTTAAGGCCAAGCTTAAGTCCAACTCAATTCGATGGTAAAGTATGCATA
* * * *
2947702 TGTGCGTGGTCCAATCTCTTGTGAACTTCAACCTCAGCTAAAAGTTTGGGTGCCCATTAGGGTCT
66 TGTGCATGGTCCAATCTCTTGTGAACTTCAACCTAAGCTAAAAATTTAGGTGCCCATTAGGGTCT
* *
2947767 AACCCTACCTTGGAAATTAGGATTTATAAGCCACATAGCCTTATAATTTAGTCACTAATATGGGA
131 AACCCTACCTTGGAAATTAGGATTTATAAGCCACATAGCCTCATAATTTAGTCACTAATATGAGA
2947832 TTCTTTATCACCCAATATTTTGAAAAAAACATTCTTCTTCTTTAAGTGGACATCTTAAGAATAAC
196 TTCTTTATCACCCAATATTTTGAAAAAAACATTCTTCTTCTTTAAGTGGACATCTTAAGAATAAC
*
2947897 TTTTCATTCATC
261 TTCTCATTCATC
* * *
2947909 AATAAGGTCCAATACCTTTAAGGCCAAG-TTCAAGTCCAACTCAATTCGGTGGTGAAGTATGCAT
1 AATAAGGCCCAATACCTTTAAGGCCAAGCTT-AAGTCCAACTCAATTCGATGGTAAAGTATGCAT
*
2947973 ATGTGCATGGTCCAA-CTTTTTGTGAACTTCAACCTTAAGCTAAAAATTTAGGTGCCCATTAGGG
65 ATGTGCATGGTCCAATC-TCTTGTGAACTTCAACC-TAAGCTAAAAATTTAGGTGCCCATTAGGG
*
2948037 TCTAACCCTACCTTGGAAATTAGGATTTATAAGCCACATAGCCTCATACTTTAGTCACTAATATG
128 TCTAACCCTACCTTGGAAATTAGGATTTATAAGCCACATAGCCTCATAATTTAGTCACTAATATG
* * * * * *
2948102 AGATTCTTTATCACCCAATACTTTT-AACAAAGCGTTCTTTTTCTTTAAGTGGACATCTTGATAA
193 AGATTCTTTATCACCCAATA-TTTTGAAAAAAACATTCTTCTTCTTTAAGTGGACATCTTAAGAA
2948166 TAACTTCTCATTCAT
257 TAACTTCTCATTCAT
2948181 TATGGATATC
Statistics
Matches: 250, Mismatches: 18, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
271 3 0.01
272 88 0.35
273 155 0.62
274 4 0.02
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (272 bp):
AATAAGGCCCAATACCTTTAAGGCCAAGCTTAAGTCCAACTCAATTCGATGGTAAAGTATGCATA
TGTGCATGGTCCAATCTCTTGTGAACTTCAACCTAAGCTAAAAATTTAGGTGCCCATTAGGGTCT
AACCCTACCTTGGAAATTAGGATTTATAAGCCACATAGCCTCATAATTTAGTCACTAATATGAGA
TTCTTTATCACCCAATATTTTGAAAAAAACATTCTTCTTCTTTAAGTGGACATCTTAAGAATAAC
TTCTCATTCATC
Found at i:2949641 original size:16 final size:16
Alignment explanation
Indices: 2949620--2949661 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2949610 ATTAATTCTA
2949620 AAAATAATCTAAA-AT
1 AAAATAATCTAAATAT
*
2949635 CAAAATAATTTAAATAT
1 -AAAATAATCTAAATAT
*
2949652 AATATAATCT
1 AAAATAATCT
2949662 TTTAAATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATAATCTAAATAT
Found at i:2949994 original size:16 final size:17
Alignment explanation
Indices: 2949973--2950007 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2949963 ATAATATATT
2949973 AAATAATT-TTATAATA
1 AAATAATTATTATAATA
*
2949989 AAATAATTATTTTAATA
1 AAATAATTATTATAATA
2950006 AA
1 AA
2950008 TCAAACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAATTATTATAATA
Found at i:2950228 original size:4 final size:4
Alignment explanation
Indices: 2950219--2950247 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2950209 AATTTTAAGG
2950219 TTTA TTTA TTTA -TTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
2950248 GGAAAAGGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:2950237 original size:15 final size:15
Alignment explanation
Indices: 2950219--2950247 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2950209 AATTTTAAGG
2950219 TTTATTTATTTATTA
1 TTTATTTATTTATTA
2950234 TTTATTTATTTATT
1 TTTATTTATTTATT
2950248 GGAAAAGGGA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTATTTATTA
Found at i:2950982 original size:44 final size:44
Alignment explanation
Indices: 2950926--2951044 Score: 150
Period size: 44 Copynumber: 2.7 Consensus size: 44
2950916 TAATCACTAA
* *
2950926 TAATTTTAAATTATTATATTTAGTATAATATTATAGATAATCGG
1 TAATCTTAAATTATTATATTTAGTATAATATTATAGATAATCAG
* * *
2950970 TAATCTTAAATTATTGTATTTAGTA-ATATATTATAGATTATTAG
1 TAATCTTAAATTATTATATTTAGTATA-ATATTATAGATAATCAG
* * *
2951014 TGATCTTAAATTATTATATTTGGTATTATAT
1 TAATCTTAAATTATTATATTTAGTATAATAT
2951045 AAAATGATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
43 1 0.02
44 63 0.98
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (44 bp):
TAATCTTAAATTATTATATTTAGTATAATATTATAGATAATCAG
Found at i:2952921 original size:2 final size:2
Alignment explanation
Indices: 2952914--2952949 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2952904 AAGTTTGTCA
2952914 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2952950 GTGATGGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2953012 original size:22 final size:23
Alignment explanation
Indices: 2952972--2953014 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2952962 ATTTCACCTG
* *
2952972 TAATTCATTTTATTGTAATATTA
1 TAATTCATTTAATTATAATATTA
2952995 TAATT-ATTTAATTATAATAT
1 TAATTCATTTAATTATAATAT
2953015 AAAGAACTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
TAATTCATTTAATTATAATATTA
Found at i:2954515 original size:16 final size:17
Alignment explanation
Indices: 2954491--2954523 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2954481 ATTTTTAAAA
*
2954491 TTTATAAAT-ATTATAT
1 TTTAAAAATAATTATAT
2954507 TTTAAAAATAATTATAT
1 TTTAAAAATAATTATAT
2954524 AAATCGATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAAAATAATTATAT
Found at i:2954707 original size:2 final size:2
Alignment explanation
Indices: 2954700--2954734 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2954690 TCAACTTATC
2954700 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2954735 AAAACCACGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2956400 original size:19 final size:19
Alignment explanation
Indices: 2956365--2956406 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2956355 ACTCAAATTC
*
2956365 AAATTTAAATTTAAATTTA
1 AAATTTAAATTTAAATTAA
*
2956384 AAATTTTAATATT-AATTAA
1 AAATTTAAAT-TTAAATTAA
2956403 AAAT
1 AAAT
2956407 AATAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAATTTAAATTTAAATTAA
Found at i:2956746 original size:25 final size:25
Alignment explanation
Indices: 2956700--2956768 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 25
2956690 GTCCTATTCA
2956700 TTTTTATATT-AAT-AA-AA-T-AT
1 TTTTTATATTAAATAAATAATTAAT
* *
2956720 TTTTT-TATTATATTTAATAATTAAT
1 TTTTTATATTA-AATAAATAATTAAT
2956745 TTTTTATATTAAATAAATAATTAA
1 TTTTTATATTAAATAAATAATTAA
2956769 ATAATTTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 4 0.10
20 5 0.13
21 2 0.05
22 2 0.05
23 2 0.05
24 1 0.03
25 18 0.46
26 5 0.13
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTTATATTAAATAAATAATTAAT
Found at i:2956747 original size:24 final size:24
Alignment explanation
Indices: 2956703--2956766 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
2956693 CTATTCATTT
*
2956703 TTATATTAATAAAATATTTTTTTA
1 TTATATTAATAAAATAATTTTTTA
*
2956727 TTATATTTAAT-AATTAATTTTTTA
1 TTATA-TTAATAAAATAATTTTTTA
*
2956751 -TAT-TAAAT-AAATAATT
1 TTATATTAATAAAATAATT
2956767 AAATAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
21 11 0.31
23 3 0.09
24 16 0.46
25 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATATTAATAAAATAATTTTTTA
Found at i:2956753 original size:21 final size:22
Alignment explanation
Indices: 2956722--2956766 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2956712 TAAAATATTT
* *
2956722 TTTTATTATATTTAATAATTAA
1 TTTTATTATATTAAATAAATAA
2956744 TTTT-TTATATTAAATAAATAA
1 TTTTATTATATTAAATAAATAA
2956765 TT
1 TT
2956767 AAATAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTTATTATATTAAATAAATAA
Found at i:2957432 original size:16 final size:15
Alignment explanation
Indices: 2957396--2957439 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2957386 TAAATTAATC
*
2957396 AATTTATATTTTTTA
1 AATTTATATTTATTA
*
2957411 ATTTTATATATTATTA
1 AATTTATAT-TTATTA
*
2957427 AATTTATGTTTAT
1 AATTTATATTTAT
2957440 AATAATCGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (15 bp):
AATTTATATTTATTA
Found at i:2959191 original size:45 final size:46
Alignment explanation
Indices: 2959130--2959217 Score: 126
Period size: 45 Copynumber: 1.9 Consensus size: 46
2959120 TCCTTTATAT
2959130 CTGACATGTAAAATTT-ACACTTAATAGCCAACTCAAATACCAAAAA
1 CTGACATGTAAAATTTAACACTTAATAG-CAACTCAAATACCAAAAA
* * *
2959176 CTGACAT-TTAAATTTAACATTTAATAGCAACTCAAGTACCAA
1 CTGACATGTAAAATTTAACACTTAATAGCAACTCAAATACCAA
2959218 TTAAATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
45 21 0.55
46 17 0.45
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.27
Consensus pattern (46 bp):
CTGACATGTAAAATTTAACACTTAATAGCAACTCAAATACCAAAAA
Found at i:2963483 original size:14 final size:13
Alignment explanation
Indices: 2963462--2963493 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
2963452 AGTGTTTATT
2963462 TTTATTTTTTTAA
1 TTTATTTTTTTAA
2963475 TTTACTTTTTTTAA
1 TTTA-TTTTTTTAA
2963489 TTTAT
1 TTTAT
2963494 GGTGTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTATTTTTTTAA
Found at i:2964340 original size:3 final size:3
Alignment explanation
Indices: 2964334--2964374 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2964324 CATCATCATC
2964334 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2964375 ATTTTACTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2964670 original size:3 final size:3
Alignment explanation
Indices: 2964662--2964686 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2964652 TATTTTTTAT
2964662 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
2964687 GTGATAGCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2966456 original size:21 final size:22
Alignment explanation
Indices: 2966421--2966462 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
2966411 AAATTTATTT
* *
2966421 AATTAAATTTTTAAA-AAATAA
1 AATTAAATATATAAATAAATAA
2966442 AATTAAATATATAAATAAATA
1 AATTAAATATATAAATAAATA
2966463 TTATATGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTAAATATATAAATAAATAA
Found at i:2974589 original size:20 final size:20
Alignment explanation
Indices: 2974538--2974595 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
2974528 ATAATGATGC
*
2974538 TATTTCAATGTCAAATTAAT
1 TATTTCATTGTCAAATTAAT
*
2974558 T-TTT--TT-TCAAATTATT
1 TATTTCATTGTCAAATTAAT
2974574 TATTTCATTGTCAAATTAAT
1 TATTTCATTGTCAAATTAAT
2974594 TA
1 TA
2974596 AGAGATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 10 0.32
17 4 0.13
19 5 0.16
20 12 0.39
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.53
Consensus pattern (20 bp):
TATTTCATTGTCAAATTAAT
Found at i:2974893 original size:12 final size:13
Alignment explanation
Indices: 2974867--2974897 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
2974857 ATTCAATTCG
2974867 ATTTATTTATATT
1 ATTTATTTATATT
2974880 ATTTATTT-TATT
1 ATTTATTTATATT
2974892 ATTTAT
1 ATTTAT
2974898 AATTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.56
13 8 0.44
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTATTTATATT
Found at i:2975140 original size:25 final size:24
Alignment explanation
Indices: 2975108--2975161 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 24
2975098 TTTTTTCAAA
*
2975108 TATTT-AAATTTAAATTTATTTAATT
1 TATTTAAAAATTAAATTTA-TTAA-T
2975133 TATTTAAAAATTAAATTTATTAAT
1 TATTTAAAAATTAAATTTATTAAT
2975157 TATTT
1 TATTT
2975162 GCATATTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 6 0.22
25 9 0.33
26 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTTAAAAATTAAATTTATTAAT
Found at i:2978487 original size:31 final size:28
Alignment explanation
Indices: 2978432--2978516 Score: 89
Period size: 31 Copynumber: 2.8 Consensus size: 28
2978422 AATTTTTAAG
2978432 TTAAAAAAATAAAAAAATTTAAATATAA
1 TTAAAAAAATAAAAAAATTTAAATATAA
*
2978460 TTAAAAAATATAAGAAAATTTTTAAATATAAA
1 TTAAAAAA-ATAA-AAAA-ATTTAAATAT-AA
* *
2978492 GGTAAAAAAATATAAAAAATATAAA
1 -TTAAAAAAATA-AAAAAATTTAAA
2978517 AATTCAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
28 8 0.17
29 4 0.09
30 4 0.09
31 14 0.30
32 9 0.19
33 8 0.17
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (28 bp):
TTAAAAAAATAAAAAAATTTAAATATAA
Found at i:2978639 original size:17 final size:17
Alignment explanation
Indices: 2978595--2978641 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
2978585 TTTTAAACAA
*
2978595 ATATAAATAAAAAAATT
1 ATATAATTAAAAAAATT
*
2978612 -TAAAAACTTAAAAAAATT
1 AT-ATAA-TTAAAAAAATT
2978630 ATATAATTAAAA
1 ATATAATTAAAA
2978642 TTTGTAAGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
16 1 0.04
17 9 0.38
18 13 0.54
19 1 0.04
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
ATATAATTAAAAAAATT
Found at i:2978728 original size:16 final size:16
Alignment explanation
Indices: 2978671--2978728 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
2978661 TAAATCTTAA
2978671 AAAAAAAGGAGAGAAAAG
1 AAAAAAAGGAGAG--AAG
* *
2978689 AAAAAAAGGAAAGGAG
1 AAAAAAAGGAGAGAAG
* *
2978705 GAATAAAGGAGAGAAG
1 AAAAAAAGGAGAGAAG
*
2978721 AAAGAAAG
1 AAAAAAAG
2978729 AAGGGAAAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 20 0.62
18 12 0.38
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (16 bp):
AAAAAAAGGAGAGAAG
Found at i:2979140 original size:35 final size:34
Alignment explanation
Indices: 2979101--2979177 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 34
2979091 TTTTTTTATT
2979101 TTTATTTTTTATAGA-TTTTAATTTTATAATTTCTA
1 TTTATTTTTT-TA-ATTTTTAATTTTATAATTTCTA
* * *
2979136 TTTATATTTTTTAATTTTTGATTTTTTTATTTCTA
1 TTTAT-TTTTTTAATTTTTAATTTTATAATTTCTA
*
2979171 TATATTT
1 TTTATTT
2979178 AAAATTTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
34 3 0.08
35 28 0.78
36 5 0.14
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (34 bp):
TTTATTTTTTTAATTTTTAATTTTATAATTTCTA
Found at i:2979225 original size:17 final size:17
Alignment explanation
Indices: 2979203--2979252 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
2979193 TTTTAATAAT
*
2979203 TGTTTTTAATTTTTAGG
1 TGTTTTTAATTTTTAGA
2979220 TGTTTTTAATTTTATAGA
1 TGTTTTTAATTTT-TAGA
2979238 T-TTTTTATATTTTTA
1 TGTTTTTA-ATTTTTA
2979253 TAATTTTCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 21 0.70
18 9 0.30
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.68
Consensus pattern (17 bp):
TGTTTTTAATTTTTAGA
Found at i:2979243 original size:18 final size:17
Alignment explanation
Indices: 2979192--2979259 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 17
2979182 TTTTAATATT
2979192 ATTTTAATAATTGTTTTTA
1 ATTTT-ATAATT-TTTTTA
* *
2979211 ATTTT-TAGGTGTTTTTA
1 ATTTTATA-ATTTTTTTA
2979228 ATTTTATAGATTTTTTATA
1 ATTTTATA-ATTTTTT-TA
*
2979247 TTTTTATAATTTT
1 ATTTTATAATTTT
2979260 CTGAAATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
17 13 0.32
18 14 0.34
19 14 0.34
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.66
Consensus pattern (17 bp):
ATTTTATAATTTTTTTA
Found at i:2979259 original size:17 final size:17
Alignment explanation
Indices: 2979098--2979259 Score: 58
Period size: 19 Copynumber: 9.3 Consensus size: 17
2979088 GATTTTTTTT
2979098 ATTTTTAT-TTTTTATA
1 ATTTTTATATTTTTATA
2979114 GA-TTTTA-A-TTTTATA
1 -ATTTTTATATTTTTATA
2979129 ATTTCTATTTATATTTTT-TA
1 A--T-T-TTTATATTTTTATA
2979149 ATTTTTGAT-TTTTT-T-
1 ATTTTT-ATATTTTTATA
* * *
2979164 ATTTCTATATATTTAAA
1 ATTTTTATATTTTTATA
*
2979181 ATTTTAATATTATTTTAATA
1 ATTTT--TA-TATTTTTATA
*
2979201 ATTGTTTTTAATTTTTAGGT-
1 ATT-TTTAT-ATTTTTA--TA
*
2979221 GTTTTTA-A-TTTTATA
1 ATTTTTATATTTTTATA
2979236 GATTTTTTATATTTTTATA
1 -A-TTTTTATATTTTTATA
2979255 ATTTT
1 ATTTT
2979260 CTGAAATTTT
Statistics
Matches: 109, Mismatches: 12, Indels: 48
0.64 0.07 0.28
Matches are distributed among these distances:
14 4 0.04
15 16 0.15
16 19 0.17
17 19 0.17
18 5 0.05
19 23 0.21
20 16 0.15
21 7 0.06
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (17 bp):
ATTTTTATATTTTTATA
Found at i:2979527 original size:16 final size:16
Alignment explanation
Indices: 2979506--2979537 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2979496 CTGTCTAACC
2979506 AGATAGAATAGTCCAG
1 AGATAGAATAGTCCAG
2979522 AGATAGAATAGTCCAG
1 AGATAGAATAGTCCAG
2979538 CCGGCTCTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.25, T:0.19
Consensus pattern (16 bp):
AGATAGAATAGTCCAG
Found at i:2979866 original size:45 final size:47
Alignment explanation
Indices: 2979808--2979897 Score: 123
Period size: 45 Copynumber: 1.9 Consensus size: 47
2979798 ATTAATAACA
*
2979808 ATTTTTTAAATTTTATAA-ATCAAATATAATTTATA-TTTAATTTTTAT
1 ATTTTTT-AATTTTATAATA-AAAATATAATTTATATTTTAATTTTTAT
*
2979855 ATTTTTT-ATTTTATAATAAAAATATATTTTATATTTTAATTTT
1 ATTTTTTAATTTTATAATAAAAATATAATTTATATTTTAATTTT
2979898 ATTTGTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 22 0.56
46 10 0.26
47 7 0.18
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (47 bp):
ATTTTTTAATTTTATAATAAAAATATAATTTATATTTTAATTTTTAT
Found at i:2980019 original size:35 final size:36
Alignment explanation
Indices: 2979964--2980041 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 36
2979954 AGTCCCATAT
* *
2979964 TTTTATAATATTTTATTTTTATTAAATTATTTT-TAA
1 TTTT-TAATATTTTAATTTTATTAAATTATTTTAAAA
* **
2980000 TTTTTAATTTTTTAATTTTATTATTTTATTTTAAAA
1 TTTTTAATATTTTAATTTTATTAAATTATTTTAAAA
2980036 TTTTTA
1 TTTTTA
2980042 TATAAATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
35 24 0.67
36 12 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (36 bp):
TTTTTAATATTTTAATTTTATTAAATTATTTTAAAA
Found at i:2980026 original size:15 final size:15
Alignment explanation
Indices: 2979976--2980026 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
2979966 TTATAATATT
**
2979976 TTATTTTT-ATTAAA
1 TTATTTTTAATTTTA
2979990 TTATTTTTAATTTT-
1 TTATTTTTAATTTTA
*
2980004 TAATTTTTTAATTTTA
1 TTA-TTTTTAATTTTA
2980020 TTATTTT
1 TTATTTT
2980027 ATTTTAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 10 0.33
15 18 0.60
16 2 0.07
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTATTTTTAATTTTA
Found at i:2980622 original size:32 final size:33
Alignment explanation
Indices: 2980586--2980650 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
2980576 ATGATACAAA
*
2980586 AATATATTTAAAATTT-TAT-AATATAAATTATT
1 AATATATTT-AAATTTATATAAATATAAAATATT
2980618 AATATATTTAAATTTATATAAATATAAAATATT
1 AATATATTTAAATTTATATAAATATAAAATATT
2980651 TTAACATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 6 0.20
32 12 0.40
33 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
AATATATTTAAATTTATATAAATATAAAATATT
Found at i:2980631 original size:17 final size:16
Alignment explanation
Indices: 2980586--2980632 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
2980576 ATGATACAAA
2980586 AATATATTTAAAATTTT
1 AATATATTT-AAATTTT
*
2980603 -ATA-ATATAAATTATT
1 AATATATTTAAATT-TT
2980618 AATATATTTAAATTT
1 AATATATTTAAATTT
2980633 ATATAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
14 5 0.20
15 5 0.20
16 7 0.28
17 8 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATATATTTAAATTTT
Found at i:2980689 original size:11 final size:10
Alignment explanation
Indices: 2980656--2980704 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 10
2980646 ATATTTTAAC
2980656 ATAATTATAT
1 ATAATTATAT
*
2980666 ATAATAAATAT
1 ATAAT-TATAT
2980677 ATAATTATGAT
1 ATAATTAT-AT
*
2980688 ATAAATATAT
1 ATAATTATAT
2980698 A-AATTAT
1 ATAATTAT
2980705 TAATTTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 5 0.15
10 10 0.30
11 18 0.55
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (10 bp):
ATAATTATAT
Found at i:2980693 original size:19 final size:21
Alignment explanation
Indices: 2980669--2980718 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
2980659 ATTATATATA
*
2980669 ATAAATATAT-AATTA-TGAT
1 ATAAATATATAAATTATTAAT
2980688 ATAAATATATAAATTATTAAT
1 ATAAATATATAAATTATTAAT
*
2980709 TTAAATATAT
1 ATAAATATAT
2980719 TAAAGTAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 10 0.37
20 5 0.19
21 12 0.44
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATAAATATATAAATTATTAAT
Found at i:2981598 original size:25 final size:25
Alignment explanation
Indices: 2981553--2981632 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
2981543 TTTCATATTT
*
2981553 AAAATATTTATATATATATAAATTA
1 AAAATATTTAAATATATATAAATTA
* *
2981578 AAAATATTTAAA-ATTTAATAAATTCG
1 AAAATATTTAAATATAT-ATAAATT-A
* * *
2981604 AACATATATAAA-ATAT-TAAAATA
1 AAAATATTTAAATATATATAAATTA
2981627 AAAATA
1 AAAATA
2981633 ATATATTTAT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
23 5 0.11
24 8 0.18
25 18 0.41
26 13 0.30
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (25 bp):
AAAATATTTAAATATATATAAATTA
Found at i:2982582 original size:13 final size:13
Alignment explanation
Indices: 2982566--2982592 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2982556 ATATTACTTT
2982566 TAAAATAATTAAA
1 TAAAATAATTAAA
2982579 TAAAATAATTAAA
1 TAAAATAATTAAA
2982592 T
1 T
2982593 TAAGCCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAAATAATTAAA
Found at i:2984392 original size:31 final size:29
Alignment explanation
Indices: 2984334--2984400 Score: 91
Period size: 31 Copynumber: 2.3 Consensus size: 29
2984324 TAACTAAATA
* *
2984334 TTAAAA-TTAAAAATATTATTAATATATT
1 TTAAAATTTAAAAATAATATAAATATATT
2984362 TTAAAATTTAAAAATTAATATAAAATATATT
1 TTAAAATTTAAAAA-TAATAT-AAATATATT
2984393 TTAAAATT
1 TTAAAATT
2984401 CCAACTATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 6 0.18
29 7 0.21
30 5 0.15
31 16 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TTAAAATTTAAAAATAATATAAATATATT
Found at i:2994191 original size:25 final size:24
Alignment explanation
Indices: 2994099--2994189 Score: 80
Period size: 24 Copynumber: 3.7 Consensus size: 24
2994089 TGAAACTAGT
*
2994099 AAAATAAATAAATAAAATAAAA-TA
1 AAAATAAAT-AATAAAAGAAAATTA
*
2994123 AAAATACAATATTAAAAGAAAATT-
1 AAAATA-AATAATAAAAGAAAATTA
*
2994147 AAAATTAATAATCACAAA-AAAATTA
1 AAAATAAATAAT-A-AAAGAAAATTA
2994172 AAAATTAAATAATGAAAA
1 AAAA-TAAATAAT-AAAA
2994190 AATCTTGATT
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
23 5 0.09
24 28 0.51
25 14 0.25
26 8 0.15
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.23
Consensus pattern (24 bp):
AAAATAAATAATAAAAGAAAATTA
Found at i:2997361 original size:3 final size:3
Alignment explanation
Indices: 2997353--2997390 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2997343 CAAAAGAAAC
2997353 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2997391 ATAACACGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2997768 original size:28 final size:30
Alignment explanation
Indices: 2997725--2997785 Score: 90
Period size: 28 Copynumber: 2.1 Consensus size: 30
2997715 TTTATCCGGA
*
2997725 TTTAATTTTGATCTTAATTTTAATATTAGT
1 TTTAATTTTGATCTTAATTTTAATATTAAT
*
2997755 TTTAATTTT-A-CTTAATTTTAATTTTAAT
1 TTTAATTTTGATCTTAATTTTAATATTAAT
2997783 TTT
1 TTT
2997786 TAAAAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 19 0.66
29 1 0.03
30 9 0.31
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (30 bp):
TTTAATTTTGATCTTAATTTTAATATTAAT
Found at i:2997769 original size:22 final size:22
Alignment explanation
Indices: 2997744--2997785 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2997734 GATCTTAATT
*
2997744 TTAATATTAGTTTTAATTTTAC
1 TTAATATTAATTTTAATTTTAC
*
2997766 TTAATTTTAATTTTAATTTT
1 TTAATATTAATTTTAATTTT
2997786 TAAAAATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TTAATATTAATTTTAATTTTAC
Found at i:2997788 original size:7 final size:6
Alignment explanation
Indices: 2997725--2997785 Score: 63
Period size: 6 Copynumber: 10.5 Consensus size: 6
2997715 TTTATCCGGA
* * * * *
2997725 TTTAAT TTTGAT CTTAAT TTTAAT ATTAGT TTTAAT TTT-A- CTTAAT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
2997771 TTTAAT TTTAAT TTT
1 TTTAAT TTTAAT TTT
2997786 TAAAAATTCA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
6 39 0.91
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (6 bp):
TTTAAT
Found at i:2998171 original size:6 final size:6
Alignment explanation
Indices: 2998154--2998235 Score: 73
Period size: 6 Copynumber: 13.7 Consensus size: 6
2998144 TAAACTTGTT
* * *
2998154 AATTTT AATTTA AATTTAAA AAATTA AATTAATT AATTTA AATTTA AATTTA
1 AATTTA AATTTA AATTT--A AATTTA AATT--TA AATTTA AATTTA AATTTA
2998206 AA-TT- AATTTA AATTT- AATTT- AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATT
2998236 GATAAAAAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
4 2 0.03
5 14 0.22
6 38 0.59
8 10 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:2998182 original size:5 final size:5
Alignment explanation
Indices: 2998174--2998235 Score: 54
Period size: 5 Copynumber: 12.0 Consensus size: 5
2998164 TAAATTTAAA
* *
2998174 AAATT AAATT -AATT AATTT AAATTT AAATTT AAATT AATTT AAATTT
1 AAATT AAATT AAATT AAATT AAA-TT AAA-TT AAATT AAATT AAA-TT
* *
2998221 AATTT AATTT AAATT
1 AAATT AAATT AAATT
2998236 GATAAAAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
4 4 0.08
5 29 0.60
6 15 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (5 bp):
AAATT
Found at i:2998194 original size:22 final size:24
Alignment explanation
Indices: 2998152--2998249 Score: 71
Period size: 22 Copynumber: 4.2 Consensus size: 24
2998142 ATTAAACTTG
* *
2998152 TTAATTTTAATTTAAATTTAAAAAA
1 TTAAATTTAAATT-AATTTAAAAAA
*
2998177 TTAAA-TT-AATTAATTT--AAAT
1 TTAAATTTAAATTAATTTAAAAAA
*
2998197 TTAAATTTAAATTAATTTAAATTTAA
1 TTAAATTTAAATTAATTTAAA--AAA
* * *
2998223 TTTAATTTAAATTGA-TAAAAAAA
1 TTAAATTTAAATTAATTTAAAAAA
2998246 TTAA
1 TTAA
2998250 TAATCTAAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
20 8 0.14
21 2 0.04
22 14 0.25
23 8 0.14
24 3 0.05
25 8 0.14
26 14 0.25
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (24 bp):
TTAAATTTAAATTAATTTAAAAAA
Found at i:2998235 original size:11 final size:11
Alignment explanation
Indices: 2998152--2998232 Score: 77
Period size: 11 Copynumber: 7.9 Consensus size: 11
2998142 ATTAAACTTG
*
2998152 TTAATTTTAAT
1 TTAAATTTAAT
2998163 TTAAATTTAA-
1 TTAAATTTAAT
* *
2998173 --AAAATTAAA
1 TTAAATTTAAT
2998182 TT-AA-TTAAT
1 TTAAATTTAAT
2998191 TTAAATTTAAAT
1 TTAAATTT-AAT
2998203 TTAAA-TTAAT
1 TTAAATTTAAT
2998213 TTAAATTTAAT
1 TTAAATTTAAT
2998224 TT-AATTTAA
1 TTAAATTTAA
2998233 ATTGATAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
8 7 0.12
9 6 0.10
10 19 0.32
11 20 0.33
12 8 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:2998300 original size:16 final size:17
Alignment explanation
Indices: 2998273--2998308 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2998263 ATCGATATGG
*
2998273 ATTCGAAAATAATTTAA
1 ATTCGAAAATAATTCAA
2998290 ATTCG-AAATAATTCAA
1 ATTCGAAAATAATTCAA
2998306 ATT
1 ATT
2998309 TAAAATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (17 bp):
ATTCGAAAATAATTCAA
Found at i:2998314 original size:16 final size:16
Alignment explanation
Indices: 2998273--2998339 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
2998263 ATCGATATGG
*
2998273 ATTCGAAAATAATTTAA
1 ATTC-AAAATAATTCAA
*
2998290 ATTCGAAATAATTCAA
1 ATTCAAAATAATTCAA
* * **
2998306 ATTTAAAATTATTTGA
1 ATTCAAAATAATTCAA
* *
2998322 ACTCAAAATAATCCAA
1 ATTCAAAATAATTCAA
2998338 AT
1 AT
2998340 AATTAACTCG
Statistics
Matches: 36, Mismatches: 14, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
16 32 0.89
17 4 0.11
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.34
Consensus pattern (16 bp):
ATTCAAAATAATTCAA
Found at i:2998314 original size:32 final size:32
Alignment explanation
Indices: 2998278--2998339 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2998268 TATGGATTCG
* * *
2998278 AAAATAATTTAAATTCGAAATAATTCAAATTT
1 AAAATAATTTAAACTCAAAATAATCCAAATTT
* *
2998310 AAAATTATTTGAACTCAAAATAATCCAAAT
1 AAAATAATTTAAACTCAAAATAATCCAAAT
2998340 AATTAACTCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (32 bp):
AAAATAATTTAAACTCAAAATAATCCAAATTT
Found at i:3002169 original size:92 final size:91
Alignment explanation
Indices: 3002012--3002194 Score: 330
Period size: 92 Copynumber: 2.0 Consensus size: 91
3002002 CAAGCACGAT
3002012 GCATCTTGAGTAATATGATTATTTAGATAAATTACTTATAGGAACTTGATTTTAACCAAACAAAA
1 GCATCTTGAGTAATATGATTATTTAGATAAATTACTTATAGGAACTTGATTTTAACCAAAC-AAA
*
3002077 AAATGAGACAATGTAACGAAATACTAA
65 AAATGAGACAATGTAACAAAATACTAA
*
3002104 GCATCTTGCGTAATATGATTATTTAGATAAATTACTTATAGGAACTTGATTTTAACCAAACAAAA
1 GCATCTTGAGTAATATGATTATTTAGATAAATTACTTATAGGAACTTGATTTTAACCAAACAAAA
*
3002169 AATGAGACAATGTAGCAAAATACTAA
66 AATGAGACAATGTAACAAAATACTAA
3002195 CGATTAACAA
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
91 28 0.32
92 60 0.68
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (91 bp):
GCATCTTGAGTAATATGATTATTTAGATAAATTACTTATAGGAACTTGATTTTAACCAAACAAAA
AATGAGACAATGTAACAAAATACTAA
Found at i:3003918 original size:23 final size:21
Alignment explanation
Indices: 3003863--3003918 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
3003853 AATTATTTAT
3003863 ATTTTAAAATTTAATAAAATAA
1 ATTTTAAAA-TTAATAAAATAA
* *
3003885 AATTAATAAATTAATAAAAATTAA
1 ATTTTA-AAATTAAT-AAAA-TAA
3003909 ATTTTAAAAT
1 ATTTTAAAAT
3003919 ATATATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
22 9 0.33
23 11 0.41
24 7 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATTTTAAAATTAATAAAATAA
Done.