Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 20 of 410
Found at i:5196447 original size:19 final size:20
Alignment explanation
Indices: 5196406--5196455 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
5196396 TCTTTACATT
*
5196406 TTTTTATAATTTTCTTACAA
1 TTTTTATAATTGTCTTACAA
**
5196426 TTTTTATAATTGT-TTATGA
1 TTTTTATAATTGTCTTACAA
5196445 TTTTTATAATT
1 TTTTTATAATT
5196456 TTTTTTCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (20 bp):
TTTTTATAATTGTCTTACAA
Found at i:5196460 original size:30 final size:29
Alignment explanation
Indices: 5196426--5196523 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 29
5196416 TTTCTTACAA
5196426 TTTTTATAATTGTTTATGATTTTTATAATTT
1 TTTTTATAATT-TTTATGATTTTTATAA-TT
*
5196457 TTTTTCTAATTTTTAAT-ATTTTTAT-ATT
1 TTTTTATAATTTTT-ATGATTTTTATAATT
* *
5196485 TTTATTA-AAATTTAATGATTTTTTATAAATT
1 TTT-TTATAATTTTTATGA-TTTTTAT-AATT
5196516 TTATTTAT
1 TT-TTTAT
5196524 TTTTAATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
27 2 0.04
28 11 0.20
29 10 0.18
30 11 0.20
31 20 0.36
32 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (29 bp):
TTTTTATAATTTTTATGATTTTTATAATT
Found at i:5196525 original size:20 final size:21
Alignment explanation
Indices: 5196477--5196527 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
5196467 TTTTAATATT
5196477 TTTATATTTTTATTAAAATTTA
1 TTTAT-TTTTTATTAAAATTTA
* * *
5196499 ATGATTTTTTA-TAAATTTTA
1 TTTATTTTTTATTAAAATTTA
5196519 TTTATTTTT
1 TTTATTTTT
5196528 AATTTTTATC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
20 15 0.62
21 6 0.25
22 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTATTTTTTATTAAAATTTA
Found at i:5196526 original size:19 final size:19
Alignment explanation
Indices: 5196425--5196528 Score: 61
Period size: 19 Copynumber: 5.4 Consensus size: 19
5196415 TTTTCTTACA
* *
5196425 ATTTTTATAATTGTTTA-TG
1 ATTTTTATAAAT-TTTATTT
* *
5196444 ATTTTTATAATTTTTTTTCT
1 ATTTTTATAAATTTTATT-T
* *
5196464 AATTTTTA-ATATTTT-TAT
1 -ATTTTTATAAATTTTATTT
* * *
5196482 ATTTTTATTAAAATTTAATG
1 ATTTTTA-TAAATTTTATTT
5196502 ATTTTTTATAAATTTTATTT
1 A-TTTTTATAAATTTTATTT
5196522 ATTTTTA
1 ATTTTTA
5196529 ATTTTTATCA
Statistics
Matches: 65, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
17 7 0.11
18 4 0.06
19 25 0.38
20 16 0.25
21 13 0.20
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (19 bp):
ATTTTTATAAATTTTATTT
Found at i:5199997 original size:11 final size:12
Alignment explanation
Indices: 5199974--5200015 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
5199964 ACAAAAAAAA
5199974 TCAAAATAATTT
1 TCAAAATAATTT
5199986 TCAAAA-AATTT
1 TCAAAATAATTT
5199997 T-AAATATAATTT
1 TCAAA-ATAATTT
*
5200009 TTAAAAT
1 TCAAAAT
5200016 TCAGAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 3 0.11
11 7 0.26
12 14 0.52
13 3 0.11
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (12 bp):
TCAAAATAATTT
Found at i:5202371 original size:31 final size:31
Alignment explanation
Indices: 5202333--5202404 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
5202323 AAAAGAATGA
*
5202333 AATTTTAATTAAAACGATAAAGTTCAAATTT
1 AATTTTAATTAAAACGATAAAATTCAAATTT
*
5202364 AATTTTAATTAAAACGATAAAATTTAAATTT
1 AATTTTAATTAAAACGATAAAATTCAAATTT
*
5202395 ACTTTATAAT
1 AATTT-TAAT
5202405 GCAATGATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
31 33 0.89
32 4 0.11
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.42
Consensus pattern (31 bp):
AATTTTAATTAAAACGATAAAATTCAAATTT
Found at i:5203206 original size:29 final size:29
Alignment explanation
Indices: 5203166--5203229 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
5203156 ACACATTAAT
* *
5203166 ATAAGTGACTGAAATGTAACAATTGAAAC
1 ATAAGTAACTGAAATATAACAATTGAAAC
*
5203195 ATAAGTAACTGAAATATAATAATTGAAAC
1 ATAAGTAACTGAAATATAACAATTGAAAC
5203224 ATAAGT
1 ATAAGT
5203230 GACTAGTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.27
Consensus pattern (29 bp):
ATAAGTAACTGAAATATAACAATTGAAAC
Found at i:5203213 original size:15 final size:15
Alignment explanation
Indices: 5203163--5203229 Score: 57
Period size: 14 Copynumber: 4.6 Consensus size: 15
5203153 ACAACACATT
*
5203163 AATATAAGTGACTGA
1 AATATAAGTAACTGA
* * *
5203178 AATGTAA-CAATTGA
1 AATATAAGTAACTGA
*
5203192 AACATAAGTAACTGA
1 AATATAAGTAACTGA
*
5203207 AATATAA-TAATTGA
1 AATATAAGTAACTGA
*
5203221 AACATAAGT
1 AATATAAGT
5203230 GACTAGTTTA
Statistics
Matches: 39, Mismatches: 11, Indels: 4
0.72 0.20 0.07
Matches are distributed among these distances:
14 21 0.54
15 18 0.46
ACGTcount: A:0.52, C:0.07, G:0.13, T:0.27
Consensus pattern (15 bp):
AATATAAGTAACTGA
Found at i:5203227 original size:14 final size:15
Alignment explanation
Indices: 5203186--5203229 Score: 63
Period size: 14 Copynumber: 3.0 Consensus size: 15
5203176 GAAATGTAAC
5203186 AATTGAAACATAAGT
1 AATTGAAACATAAGT
* *
5203201 AACTGAAATATAA-T
1 AATTGAAACATAAGT
5203215 AATTGAAACATAAGT
1 AATTGAAACATAAGT
5203230 GACTAGTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.27
Consensus pattern (15 bp):
AATTGAAACATAAGT
Found at i:5206274 original size:6 final size:6
Alignment explanation
Indices: 5206263--5206291 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5206253 AGGATTGCAA
5206263 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTT
5206292 CATTGAAACC
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:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:5209483 original size:40 final size:40
Alignment explanation
Indices: 5209398--5209535 Score: 159
Period size: 40 Copynumber: 3.5 Consensus size: 40
5209388 CTCGAGAATA
* ** *
5209398 TAAAGTGGATAGGATTCGTTCCTGATTCACTATAATACCT
1 TAAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAACT
* *
5209438 CAAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAATT
1 TAAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAACT
** * *
5209478 TAAAGTAAATAGGATTTATTCTTGATTCACTATGGTAACT
1 TAAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAACT
* * *
5209518 TAAGGCGGATAAGATTTG
1 TAAAGTGGATAGGATTTG
5209536 ACCTGAAAAG
Statistics
Matches: 80, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.36
Consensus pattern (40 bp):
TAAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAACT
Found at i:5209827 original size:76 final size:76
Alignment explanation
Indices: 5209701--5209853 Score: 288
Period size: 76 Copynumber: 2.0 Consensus size: 76
5209691 AAGGGTTATT
5209701 TCTGAATATGAATTGATGGAATATGGAAATGTACGCTTTGAATGTACTGTTGAAAAATCCATCCG
1 TCTGAATATGAATTGATGGAATATGGAAATGTACGCTTTGAATGTACTGTTGAAAAATCCATCCG
5209766 AACTCCAATGA
66 AACTCCAATGA
* *
5209777 TCTGAATATGAATTGATGGAATATGGAAATGTACGCTTTGAGTGTACTGTTGAAAAATCCATCGG
1 TCTGAATATGAATTGATGGAATATGGAAATGTACGCTTTGAATGTACTGTTGAAAAATCCATCCG
5209842 AACTCCAATGA
66 AACTCCAATGA
5209853 T
1 T
5209854 TCAACGGATA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.31
Consensus pattern (76 bp):
TCTGAATATGAATTGATGGAATATGGAAATGTACGCTTTGAATGTACTGTTGAAAAATCCATCCG
AACTCCAATGA
Found at i:5210864 original size:17 final size:17
Alignment explanation
Indices: 5210839--5210934 Score: 58
Period size: 17 Copynumber: 5.6 Consensus size: 17
5210829 ATTTATAGGA
*
5210839 TAAACATTAAATTAAAT
1 TAAATATTAAATTAAAT
5210856 TAAATATTAAGA-TAATTACT
1 TAAATATTAA-ATTAA--A-T
*
5210876 TTAATATTAAATT-AAT
1 TAAATATTAAATTAAAT
* *
5210892 AAAATACT--ATTAAGAT
1 TAAATATTAAATTAA-AT
*
5210908 T-AGTATTAAATTAAAT
1 TAAATATTAAATTAAAT
*
5210924 TTAATATTAAA
1 TAAATATTAAA
5210935 CTATTAAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 20
0.67 0.10 0.22
Matches are distributed among these distances:
14 3 0.05
15 5 0.08
16 11 0.18
17 26 0.43
18 1 0.02
19 3 0.05
20 11 0.18
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (17 bp):
TAAATATTAAATTAAAT
Found at i:5210890 original size:11 final size:11
Alignment explanation
Indices: 5210876--5210951 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
5210866 GATAATTACT
5210876 TTAATATTAAA
1 TTAATATTAAA
5210887 TTAATA--AAA
1 TTAATATTAAA
*
5210896 -TACTATTAAGA
1 TTAATATTAA-A
*
5210907 TTAGTATTAAA
1 TTAATATTAAA
5210918 TTAA-ATTTAATA
1 TTAATA-TTAA-A
5210930 TTAAACTATTAAA
1 TT-AA-TATTAAA
*
5210943 ATAATATTA
1 TTAATATTA
5210952 TTTTTTGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 18
0.70 0.05 0.24
Matches are distributed among these distances:
8 4 0.08
9 3 0.06
10 3 0.06
11 20 0.38
12 13 0.25
13 4 0.08
14 4 0.08
15 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (11 bp):
TTAATATTAAA
Found at i:5210938 original size:37 final size:38
Alignment explanation
Indices: 5210844--5210946 Score: 108
Period size: 37 Copynumber: 2.8 Consensus size: 38
5210834 TAGGATAAAC
*
5210844 ATTAAATTAA-ATTAAA-TATTAAGATAATTACTTTAAT
1 ATTAAATTAATATTAAACTATTAAGATAAGTAC-TTAAT
* *
5210881 ATTAAATTAATA-AAATACTATTAAGATTAGTA-TTAA-
1 ATTAAATTAATATTAA-ACTATTAAGATAAGTACTTAAT
*
5210917 ATTAAATTTAATATTAAACTATTAAAATAA
1 ATTAAA-TTAATATTAAACTATTAAGATAA
5210947 TATTATTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
36 6 0.11
37 33 0.60
38 4 0.07
39 12 0.22
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (38 bp):
ATTAAATTAATATTAAACTATTAAGATAAGTACTTAAT
Found at i:5222256 original size:24 final size:24
Alignment explanation
Indices: 5222203--5222256 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
5222193 TTCTAATTAA
*
5222203 ATTTTATAAATAATTAATATTTAT
1 ATTTTAAAAATAATTAATATTTAT
*
5222227 -TGTTTAAAAATATTTAA-ATTTTAT
1 AT-TTTAAAAATAATTAATA-TTTAT
5222251 ATTTTA
1 ATTTTA
5222257 TATATTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 2 0.08
24 22 0.88
25 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
ATTTTAAAAATAATTAATATTTAT
Found at i:5232346 original size:30 final size:30
Alignment explanation
Indices: 5232310--5232370 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
5232300 TCCTAAACTT
5232310 TATTTTATATTATTATTAATAATTTTTATA
1 TATTTTATATTATTATTAATAATTTTTATA
5232340 TATTTTATATTATTATTAATAATTTTTATA
1 TATTTTATATTATTATTAATAATTTTTATA
5232370 T
1 T
5232371 GAAGAACAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
TATTTTATATTATTATTAATAATTTTTATA
Found at i:5235242 original size:35 final size:35
Alignment explanation
Indices: 5235196--5235265 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
5235186 CTCCGGAGCT
*
5235196 TTGGCAAATATGGAAAGTAATCTTCAAAGATATGC
1 TTGGCAAATATGGAAAGGAATCTTCAAAGATATGC
* *
5235231 TTGGCAAATATGGAAGGGGATCTTCAAAGATATGC
1 TTGGCAAATATGGAAAGGAATCTTCAAAGATATGC
5235266 GATCCTAGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.27
Consensus pattern (35 bp):
TTGGCAAATATGGAAAGGAATCTTCAAAGATATGC
Found at i:5239327 original size:35 final size:35
Alignment explanation
Indices: 5239288--5239359 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
5239278 CATCTCCGGA
*
5239288 GCTTGGCAAATATGGAAAGTAATCTTCAAAGATAT
1 GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
* *
5239323 GCTTGGCAAATATGGAAGGGGATCTTCAAAGATAT
1 GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
5239358 GC
1 GC
5239360 GATCCTAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.26
Consensus pattern (35 bp):
GCTTGGCAAATATGGAAAGGAATCTTCAAAGATAT
Found at i:5242409 original size:3 final size:3
Alignment explanation
Indices: 5242401--5242445 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
5242391 GAATGGCAAG
5242401 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5242446 GGTATTAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5243021 original size:18 final size:18
Alignment explanation
Indices: 5243000--5243034 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5242990 CTGAATAATT
*
5243000 GACTGTTACAGAATAAAC
1 GACTGATACAGAATAAAC
*
5243018 GACTGATACTGAATAAA
1 GACTGATACAGAATAAA
5243035 TAAATATTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (18 bp):
GACTGATACAGAATAAAC
Found at i:5248927 original size:130 final size:130
Alignment explanation
Indices: 5248724--5248969 Score: 492
Period size: 130 Copynumber: 1.9 Consensus size: 130
5248714 GATACATGGG
5248724 CGTGTGTCCCCTGGTGTTGACATTACAATGAAGTCAGTATGCTCCACACGGTCTCACACACAGGT
1 CGTGTGTCCCCTGGTGTTGACATTACAATGAAGTCAGTATGCTCCACACGGTCTCACACACAGGT
5248789 GTGTGACTGGCCGTGTGGTATAAGTCAGTATACCCCCTATTTGGCACATGGTCATGTTATACGGC
66 GTGTGACTGGCCGTGTGGTATAAGTCAGTATACCCCCTATTTGGCACATGGTCATGTTATACGGC
5248854 CGTGTGTCCCCTGGTGTTGACATTACAATGAAGTCAGTATGCTCCACACGGTCTCACACACAGGT
1 CGTGTGTCCCCTGGTGTTGACATTACAATGAAGTCAGTATGCTCCACACGGTCTCACACACAGGT
5248919 GTGTGACTGGCCGTGTGGTATAAGTCAGTATACCCCCTATTTGGCACATGG
66 GTGTGACTGGCCGTGTGGTATAAGTCAGTATACCCCCTATTTGGCACATGG
5248970 CCTAGCACTC
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 116 1.00
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.28
Consensus pattern (130 bp):
CGTGTGTCCCCTGGTGTTGACATTACAATGAAGTCAGTATGCTCCACACGGTCTCACACACAGGT
GTGTGACTGGCCGTGTGGTATAAGTCAGTATACCCCCTATTTGGCACATGGTCATGTTATACGGC
Found at i:5251409 original size:26 final size:26
Alignment explanation
Indices: 5251380--5251431 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
5251370 AACAACTGGG
*
5251380 TTCATTTTGGTACTTGAACTTAGAAA
1 TTCATTTTGATACTTGAACTTAGAAA
*
5251406 TTCATTTTGATCCTTGAACTTAGAAA
1 TTCATTTTGATACTTGAACTTAGAAA
5251432 AATATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (26 bp):
TTCATTTTGATACTTGAACTTAGAAA
Found at i:5252745 original size:19 final size:20
Alignment explanation
Indices: 5252695--5252745 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 20
5252685 TTTAGTAAAA
*
5252695 GGAAAAGTGAGGAACATGGT
1 GGAAAGGTGAGGAACATGGT
* * * *
5252715 GGAATGGAGAGGCA-ATGTT
1 GGAAAGGTGAGGAACATGGT
5252734 GGAAAGGTGAGG
1 GGAAAGGTGAGG
5252746 GTGCAGACAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.35, C:0.04, G:0.45, T:0.16
Consensus pattern (20 bp):
GGAAAGGTGAGGAACATGGT
Found at i:5258615 original size:9 final size:9
Alignment explanation
Indices: 5258603--5258627 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5258593 CCTTCATCGT
5258603 CTTCTTCCA
1 CTTCTTCCA
5258612 CTTCTTCCA
1 CTTCTTCCA
5258621 CTTCTTC
1 CTTCTTC
5258628 GGCGGCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (9 bp):
CTTCTTCCA
Found at i:5267216 original size:2 final size:2
Alignment explanation
Indices: 5267209--5267243 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5267199 CGAGAAAGTT
5267209 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5267244 TGTTTGATAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5267540 original size:12 final size:12
Alignment explanation
Indices: 5267519--5267582 Score: 67
Period size: 12 Copynumber: 5.2 Consensus size: 12
5267509 CAATTTAATC
5267519 TTTTCTTTTATTT
1 TTTTC-TTTATTT
5267532 TTTTCTTTATTT
1 TTTTCTTTATTT
* * *
5267544 TTCAT-TTTAATC
1 TT-TTCTTTATTT
5267556 TTTTCATTTATTT
1 TTTTC-TTTATTT
5267569 TTTTCTTTATTT
1 TTTTCTTTATTT
5267581 TT
1 TT
5267583 CATTCTCTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
11 1 0.02
12 25 0.60
13 16 0.38
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTCTTTATTT
Found at i:5267553 original size:37 final size:37
Alignment explanation
Indices: 5267512--5267586 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
5267502 TGTTGAGCAA
*
5267512 TTTAATCTTTTCTTTTATTTTTTTCTTTATTTTTCAT
1 TTTAATCTTTTCATTTATTTTTTTCTTTATTTTTCAT
5267549 TTTAATCTTTTCATTTATTTTTTTCTTTATTTTTCAT
1 TTTAATCTTTTCATTTATTTTTTTCTTTATTTTTCAT
5267586 T
1 T
5267587 CTCTTCTGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.75
Consensus pattern (37 bp):
TTTAATCTTTTCATTTATTTTTTTCTTTATTTTTCAT
Found at i:5272347 original size:2 final size:2
Alignment explanation
Indices: 5272303--5272327 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5272293 TCTCTCTCTC
5272303 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5272328 TCCATCTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5273199 original size:126 final size:125
Alignment explanation
Indices: 5272975--5273215 Score: 419
Period size: 126 Copynumber: 1.9 Consensus size: 125
5272965 ACTCATTCAT
* *
5272975 ACAACTGTTTTCAACTATCTGATTATGGTTTTAGCTTTGTATTTATCAATTCATAGCCATGCTTT
1 ACAACTGTTTTCAACTATCTGATTATGGTTTTAGCTTCGTATTTATCAAATCATAGCCATGCTTT
*
5273040 CATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAATCATCAAACTCGTTCATAG
66 CATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAACCATCAAACTCGTTCATAG
* *
5273100 ACAACTGTTTTCAACTATCTGATTATGGTTTTGAGCTTCGTATTTATTAAATCATATCCATGCTT
1 ACAACTGTTTTCAACTATCTGATTATGGTTTT-AGCTTCGTATTTATCAAATCATAGCCATGCTT
*
5273165 TCATAGACAACATTGTTAGGAATTAGTATGATGAGAATGAAACCATCAAAC
65 TCATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAACCATCAAAC
5273216 CAGGACCTGG
Statistics
Matches: 109, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
125 32 0.29
126 77 0.71
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (125 bp):
ACAACTGTTTTCAACTATCTGATTATGGTTTTAGCTTCGTATTTATCAAATCATAGCCATGCTTT
CATAGACAACATTGTTAGGAATTAATATGATGAGAATGAAACCATCAAACTCGTTCATAG
Found at i:5274255 original size:43 final size:42
Alignment explanation
Indices: 5274193--5274274 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 42
5274183 AAGACTTCGT
*
5274193 AATAACTCTATAGCGAGCTTTTCATTGACATCAGATAAAAAA
1 AATAACTCTATAGCAAGCTTTTCATTGACATCAGATAAAAAA
* *
5274235 AATAAGCTCTATAGCAAGCTTTTCGTTGACATTAGATAAA
1 AATAA-CTCTATAGCAAGCTTTTCATTGACATCAGATAAA
5274275 CTGATTATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 5 0.14
43 31 0.86
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (42 bp):
AATAACTCTATAGCAAGCTTTTCATTGACATCAGATAAAAAA
Found at i:5280471 original size:12 final size:12
Alignment explanation
Indices: 5280438--5280471 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5280428 AAATATCTAT
* *
5280438 ATCCATCCACCC
1 ATCCATACATCC
5280450 ATCCATACATCC
1 ATCCATACATCC
5280462 ATCCATACAT
1 ATCCATACAT
5280472 ACATGTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (12 bp):
ATCCATACATCC
Found at i:5283130 original size:34 final size:34
Alignment explanation
Indices: 5283058--5283139 Score: 96
Period size: 33 Copynumber: 2.4 Consensus size: 34
5283048 AATCTATACA
5283058 ATTAAATCAAAATTAAAATTTTATATATACATAT
1 ATTAAATCAAAATTAAAATTTTATATATACATAT
* * * * *
5283092 -TTAAATCATATTTTAAATTTTTTATATA-ATTGT
1 ATTAAATCAAAATTAAAATTTTATATATACA-TAT
5283125 ATTAAATCAAAATTA
1 ATTAAATCAAAATTA
5283140 GTATATAGTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
32 1 0.03
33 26 0.68
34 11 0.29
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (34 bp):
ATTAAATCAAAATTAAAATTTTATATATACATAT
Found at i:5284849 original size:28 final size:26
Alignment explanation
Indices: 5284809--5284860 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 26
5284799 CTTTTTTTAA
5284809 AAATGTTATAATTAAATTATAAAATTTT
1 AAATGTTATAATT-AATT-TAAAATTTT
5284837 AAATGGTTA-AATTAATTTAAAATT
1 AAAT-GTTATAATTAATTTAAAATT
5284861 ATACAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 7 0.30
27 4 0.17
28 8 0.35
29 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (26 bp):
AAATGTTATAATTAATTTAAAATTTT
Found at i:5290703 original size:18 final size:18
Alignment explanation
Indices: 5290676--5290710 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5290666 TGTTAATATA
5290676 GGAGTAAATCCCTGATTG
1 GGAGTAAATCCCTGATTG
* *
5290694 GGAGTCAATCCTTGATT
1 GGAGTAAATCCCTGATT
5290711 AGGATTTATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (18 bp):
GGAGTAAATCCCTGATTG
Found at i:5293641 original size:18 final size:18
Alignment explanation
Indices: 5293618--5293670 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
5293608 GATAAATCCT
5293618 AATCAAGGATTTACTCCC
1 AATCAAGGATTTACTCCC
*
5293636 AATCAAGGATTGACTCCC
1 AATCAAGGATTTACTCCC
*
5293654 AATCAGGGATTTACTCC
1 AATCAAGGATTTACTCC
5293671 TATATTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (18 bp):
AATCAAGGATTTACTCCC
Found at i:5294690 original size:22 final size:21
Alignment explanation
Indices: 5294648--5294690 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
5294638 TAATAAAGGA
* * *
5294648 AAAAGTGTTAAAAAGATGATT
1 AAAAGTCTTAAAAACAAGATT
5294669 AAAAGTCTTGAAAAACAAGATT
1 AAAAGTCTT-AAAAACAAGATT
5294691 TAGAAATTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (21 bp):
AAAAGTCTTAAAAACAAGATT
Found at i:5295067 original size:100 final size:100
Alignment explanation
Indices: 5294894--5295094 Score: 393
Period size: 100 Copynumber: 2.0 Consensus size: 100
5294884 TGTCAAAGGT
5294894 ACTAATAATATTATTGCCGATTATCTTAGCAGGCCTTATGGATAGAGGTAAAAAACCTCTAGAAC
1 ACTAATAATATTATTGCCGATTATCTTAGCAGGCCTTATGGATAGAGGTAAAAAACCTCTAGAAC
5294959 AAGTCGGGGAATGGACTACTGTCCATAAAAAACCC
66 AAGTCGGGGAATGGACTACTGTCCATAAAAAACCC
*
5294994 ACTAATAATATTATTGCTGATTATCTTAGCAGGCCTTATGGATAGAGGTAAAAAACCTCTAGAAC
1 ACTAATAATATTATTGCCGATTATCTTAGCAGGCCTTATGGATAGAGGTAAAAAACCTCTAGAAC
5295059 AAGTCGGGGAATGGACTACTGTCCATAAAAAACCC
66 AAGTCGGGGAATGGACTACTGTCCATAAAAAACCC
5295094 A
1 A
5295095 ACAAAGGAAA
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.25
Consensus pattern (100 bp):
ACTAATAATATTATTGCCGATTATCTTAGCAGGCCTTATGGATAGAGGTAAAAAACCTCTAGAAC
AAGTCGGGGAATGGACTACTGTCCATAAAAAACCC
Found at i:5295141 original size:18 final size:18
Alignment explanation
Indices: 5295118--5295170 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
5295108 GATAAATCCT
5295118 AATCAAGGATTTACTCCC
1 AATCAAGGATTTACTCCC
*
5295136 AATCAAGGATTGACTCCC
1 AATCAAGGATTTACTCCC
*
5295154 AATCAGGGATTTACTCC
1 AATCAAGGATTTACTCC
5295171 TATATTAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (18 bp):
AATCAAGGATTTACTCCC
Found at i:5296347 original size:18 final size:18
Alignment explanation
Indices: 5296316--5296366 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
5296306 TTAATATAGG
*
5296316 AGTAAATCCCTGATTGGA
1 AGTAAATCCTTGATTGGA
* *
5296334 AGTCAATCCTTGATTGGG
1 AGTAAATCCTTGATTGGA
5296352 AGTAAATCCTTGATT
1 AGTAAATCCTTGATT
5296367 AGGATTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (18 bp):
AGTAAATCCTTGATTGGA
Found at i:5297688 original size:18 final size:18
Alignment explanation
Indices: 5297665--5297717 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
5297655 GATAAATCCT
5297665 AATCAAGGATTTACTCCC
1 AATCAAGGATTTACTCCC
* *
5297683 AATCAAGGATTGACTCTC
1 AATCAAGGATTTACTCCC
*
5297701 AATCAGGGATTTACTCC
1 AATCAAGGATTTACTCC
5297718 TATATTAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (18 bp):
AATCAAGGATTTACTCCC
Found at i:5304055 original size:21 final size:19
Alignment explanation
Indices: 5304002--5304055 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
5303992 CAAAGCCACA
5304002 AAAAGAAAATAAAAAAGAT
1 AAAAGAAAATAAAAAAGAT
*
5304021 AAAAGAAAGA-AAAAGCACGAT
1 AAAAGAAA-ATAAAA--AAGAT
*
5304042 AAAGGAAAATAAAA
1 AAAAGAAAATAAAA
5304056 TAAAAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 12 0.41
20 2 0.07
21 15 0.52
ACGTcount: A:0.74, C:0.04, G:0.15, T:0.07
Consensus pattern (19 bp):
AAAAGAAAATAAAAAAGAT
Found at i:5306220 original size:1 final size:1
Alignment explanation
Indices: 5306214--5306244 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
5306204 TGCTTTGGCT
5306214 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
5306245 AAAACCAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:5306782 original size:25 final size:25
Alignment explanation
Indices: 5306754--5306803 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5306744 TCTAAGACCA
5306754 AAATTTTGAAATATGAAAAGTACAG
1 AAATTTTGAAATATGAAAAGTACAG
5306779 AAATTTTGAAATATGAAAAGTACAG
1 AAATTTTGAAATATGAAAAGTACAG
5306804 GAACTGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.16, T:0.28
Consensus pattern (25 bp):
AAATTTTGAAATATGAAAAGTACAG
Found at i:5307783 original size:38 final size:39
Alignment explanation
Indices: 5307729--5307821 Score: 102
Period size: 38 Copynumber: 2.4 Consensus size: 39
5307719 ATTATATTTT
*
5307729 TTTCGAGTTTCAAGTTTATGG-GTTAGGGTTTATATC-AGA
1 TTTCGAGTTT-GAGTTTA-GGAGTTAGGGTTTATATCGAGA
* * *
5307768 TTTCGAGTTTGAGTTTAGGATTTATGGTTTATATCGAGT
1 TTTCGAGTTTGAGTTTAGGAGTTAGGGTTTATATCGAGA
*
5307807 TTTAG-GTTTGAGTTT
1 TTTCGAGTTTGAGTTT
5307822 CATATTTTAG
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
37 2 0.04
38 29 0.62
39 16 0.34
ACGTcount: A:0.20, C:0.05, G:0.26, T:0.48
Consensus pattern (39 bp):
TTTCGAGTTTGAGTTTAGGAGTTAGGGTTTATATCGAGA
Found at i:5310764 original size:35 final size:35
Alignment explanation
Indices: 5310720--5310886 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
5310710 TCCTCATTGA
** *
5310720 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* ***
5310755 AATGCCATACCTACATTTTTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
5310795 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
5310830 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
5310865 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
5310887 CTTTTCCATG
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 88 0.75
39 3 0.03
40 26 0.22
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:5310803 original size:75 final size:73
Alignment explanation
Indices: 5310715--5310886 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 73
5310705 GGTTTTCCTC
** * * ***
5310715 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTTTTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
5310779 TCAGTATGG
65 TCAGTATGG
*
5310788 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
5310853 CTCAGTATGG
64 CTCAGTATGG
5310863 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
5310887 CTTTTCCATG
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
70 21 0.24
73 3 0.03
74 7 0.08
75 57 0.65
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:5314088 original size:35 final size:35
Alignment explanation
Indices: 5314038--5314204 Score: 201
Period size: 35 Copynumber: 4.6 Consensus size: 35
5314028 TTCCTCATTG
** *
5314038 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
5314073 AATGCCATACCTACATTTCTTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
5314113 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
5314148 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
5314183 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
5314205 CTTTTGCCAT
Statistics
Matches: 117, Mismatches: 10, Indels: 10
0.85 0.07 0.07
Matches are distributed among these distances:
35 87 0.74
39 3 0.03
40 27 0.23
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:5314129 original size:75 final size:71
Alignment explanation
Indices: 5314036--5314204 Score: 216
Period size: 75 Copynumber: 2.3 Consensus size: 71
5314026 TTTTCCTCAT
** * * **
5314036 TGAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTTCTTAACTCA
1 TGAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAACTCA
5314100 GTATGGA
65 GTATGGA
*
5314107 TTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAAC
1 --TG--AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAAC
5314172 TCAGTATGGA
62 TCAGTATGGA
5314182 TG-ATACCATACCTACATTTCACA
1 TGAATACCATACCTACATTTCACA
5314205 CTTTTGCCAT
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
70 21 0.24
73 4 0.05
74 3 0.03
75 58 0.67
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.31
Consensus pattern (71 bp):
TGAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACTCAG
TATGGA
Found at i:5321567 original size:35 final size:35
Alignment explanation
Indices: 5321523--5321688 Score: 192
Period size: 35 Copynumber: 4.6 Consensus size: 35
5321513 TCCTCATTGA
** *
5321523 AATACCATACCTACATTTTTCAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
* **
5321558 AATGCCATACCTACATTT-TTAACTCAGTATGGATTTGAT
1 AATACCATACCTACATTTCACAACTCAGTAT-G----GAT
*
5321597 AATACCATACCTACATTTCACAGCTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
5321632 AATACCATACCTACATTTCACAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
5321667 GATACCATACCTACATTTCACA
1 AATACCATACCTACATTTCACA
5321689 CTTTGCCATG
Statistics
Matches: 116, Mismatches: 9, Indels: 12
0.85 0.07 0.09
Matches are distributed among these distances:
34 12 0.10
35 75 0.65
38 2 0.02
39 18 0.16
40 9 0.08
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:5321608 original size:74 final size:73
Alignment explanation
Indices: 5321518--5321688 Score: 217
Period size: 74 Copynumber: 2.4 Consensus size: 73
5321508 GGTTTTCCTC
** * * **
5321518 ATTGAAATACCATACCTACATTTTTCAACTCGGTATGGGA-AATGCCATACCTACATTT-TTAAC
1 ATTGAAATACCATACCTACATTTCACAACTCAGTAT-GGATAATACCATACCTACATTTCACAAC
5321581 TCAGTATGG
65 TCAGTATGG
*
5321590 ATTTGATAATACCATACCTACATTTCACAGCTCAGTATGGATAATACCATACCTACATTTCACAA
1 A-TTGA-AATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAA
5321655 CTCAGTATGG
64 CTCAGTATGG
5321665 A-TG--ATACCATACCTACATTTCACA
1 ATTGAAATACCATACCTACATTTCACA
5321689 CTTTGCCATG
Statistics
Matches: 88, Mismatches: 7, Indels: 10
0.84 0.07 0.10
Matches are distributed among these distances:
70 21 0.24
72 1 0.01
73 9 0.10
74 44 0.50
75 13 0.15
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.32
Consensus pattern (73 bp):
ATTGAAATACCATACCTACATTTCACAACTCAGTATGGATAATACCATACCTACATTTCACAACT
CAGTATGG
Found at i:5323322 original size:36 final size:36
Alignment explanation
Indices: 5323271--5323386 Score: 121
Period size: 36 Copynumber: 3.3 Consensus size: 36
5323261 AGATCATTGG
*
5323271 TGTGCCTAGCACTAGTCGAACAAATCGACAAATTAT
1 TGTGCCCAGCACTAGTCGAACAAATCGACAAATTAT
* * * * *
5323307 TGTGCCCAGCGCTAGTCGGA-TAACCAAC-AA-TAGT
1 TGTGCCCAGCACTAGTCGAACAAATCGACAAATTA-T
* *
5323341 TGTGCCTAGCACTAGTCGAACGAATCGACAAATTAT
1 TGTGCCCAGCACTAGTCGAACAAATCGACAAATTAT
*
5323377 TGCGCCCAGC
1 TGTGCCCAGC
5323387 TCTGGTCAAT
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
33 2 0.03
34 20 0.32
35 10 0.16
36 28 0.45
37 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (36 bp):
TGTGCCCAGCACTAGTCGAACAAATCGACAAATTAT
Found at i:5323353 original size:70 final size:70
Alignment explanation
Indices: 5323271--5323481 Score: 259
Period size: 70 Copynumber: 3.0 Consensus size: 70
5323261 AGATCATTGG
5323271 TGTGCCTAGCACTAGTCGAACAAATCGACAAATTATTGTGCCCAGCGCTAGTCGGATAACCAACA
1 TGTGCCTAGCACTAGTCGAACAAATCGACAAATTATTGTGCCCAGCGCTAGTCGGATAACCAACA
5323336 ATAGT
66 ATAGT
* * * * * *
5323341 TGTGCCTAGCACTAGTCGAACGAATCGACAAATTATTGCGCCCAGCTCTGGTC-AATAACCAACG
1 TGTGCCTAGCACTAGTCGAACAAATCGACAAATTATTGTGCCCAGCGCTAGTCGGATAACCAACA
5323405 ATAGT
66 ATAGT
* * * * *
5323410 TGTGCCCAGCACTAGTCAAATAAA-CTGATAGAA-GATT-TGCACCTAGCGCTAGTCGGATAACC
1 TGTGCCTAGCACTAGTCGAACAAATC-GACA-AATTATTGTGC-CC-AGCGCTAGTCGGATAACC
5323472 AACAATAGT
62 AACAATAGT
5323481 T
1 T
5323482 AACCAAAATT
Statistics
Matches: 119, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
68 3 0.03
69 42 0.35
70 59 0.50
71 15 0.13
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (70 bp):
TGTGCCTAGCACTAGTCGAACAAATCGACAAATTATTGTGCCCAGCGCTAGTCGGATAACCAACA
ATAGT
Found at i:5324356 original size:2 final size:2
Alignment explanation
Indices: 5324337--5324381 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
5324327 ATAACTTAAC
* *
5324337 AT AT AC AT AT AC 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 AT AT AT
5324379 AT A
1 AT A
5324382 ATTCCCCCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5338609 original size:61 final size:62
Alignment explanation
Indices: 5338497--5338612 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 62
5338487 AAGCAAAAAA
** * * *
5338497 AAAAAGGATTAGGTACCAAATTAGGAAAAAAAAAGTCATGGTTAGATACCAAATTGGATCCC
1 AAAAAGGATTAAATACCAAATTAAGAAAAAAAAAGACAAGGTTAGATACCAAATTGGATCCC
* * * *
5338559 AAAAAGGATTAAATACCAACTTAAG-AAAAAAATGACAAGTTTAGGTACCAAATT
1 AAAAAGGATTAAATACCAAATTAAGAAAAAAAAAGACAAGGTTAGATACCAAATT
5338613 AGCAAAAAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
61 24 0.53
62 21 0.47
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (62 bp):
AAAAAGGATTAAATACCAAATTAAGAAAAAAAAAGACAAGGTTAGATACCAAATTGGATCCC
Found at i:5338629 original size:31 final size:32
Alignment explanation
Indices: 5338585--5338733 Score: 141
Period size: 31 Copynumber: 4.8 Consensus size: 32
5338575 CAACTTAAGA
* *
5338585 AAAAAATGACAAGTTTAGGTACCAAATTA-GC
1 AAAAAGTGTCAAGTTTAGGTACCAAATTAGGC
* * *
5338616 AAAAAGTGTCAAGTTTAAGTATCAAATTAGGA
1 AAAAAGTGTCAAGTTTAGGTACCAAATTAGGC
* *
5338648 AAAAAGTGTCAAGTTTAGATACCAAATTGGGC
1 AAAAAGTGTCAAGTTTAGGTACCAAATTAGGC
* *
5338680 -CAAA----CAAAGTTTAGGTACCAAATTATG-
1 AAAAAGTGTC-AAGTTTAGGTACCAAATTAGGC
* *
5338707 AAAAAGTGTCAAATTTAGGCACCAAAT
1 AAAAAGTGTCAAGTTTAGGTACCAAAT
5338734 GTTATATTAA
Statistics
Matches: 94, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
27 1 0.01
28 21 0.22
31 43 0.46
32 29 0.31
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (32 bp):
AAAAAGTGTCAAGTTTAGGTACCAAATTAGGC
Found at i:5338830 original size:17 final size:17
Alignment explanation
Indices: 5338808--5338840 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5338798 ATGATATAAT
*
5338808 TAATTTTTTTATTTTTA
1 TAATTTTATTATTTTTA
5338825 TAATTTTATTATTTTT
1 TAATTTTATTATTTTT
5338841 TTGGATTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TAATTTTATTATTTTTA
Found at i:5344797 original size:20 final size:21
Alignment explanation
Indices: 5344751--5344803 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
5344741 TACTAATTAC
5344751 AAATATTTAATAATTATATTT
1 AAATATTTAATAATTATATTT
5344772 AAATATTTAA-AA-TATAGTTT
1 AAATATTTAATAATTATA-TTT
*
5344792 ATATATTCTAAT
1 AAATATT-TAAT
5344804 TAAATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.14
20 11 0.39
21 13 0.46
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
AAATATTTAATAATTATATTT
Found at i:5345071 original size:13 final size:13
Alignment explanation
Indices: 5345031--5345078 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
5345021 AAAACCAAAT
5345031 TTTTCAAAAACAC
1 TTTTCAAAAACAC
* * **
5345044 TTTTCCACAGTAC
1 TTTTCAAAAACAC
5345057 TTTTCAAAAACAC
1 TTTTCAAAAACAC
*
5345070 TTTTTAAAA
1 TTTTCAAAA
5345079 GTATTGTCAA
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.38
Consensus pattern (13 bp):
TTTTCAAAAACAC
Found at i:5345081 original size:26 final size:25
Alignment explanation
Indices: 5345031--5345089 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
5345021 AAAACCAAAT
* *
5345031 TTTTCAAAAACACTTTTCCACAGTA
1 TTTTCAAAAACACTTTTCAAAAGTA
*
5345056 CTTTTCAAAAACACTTTTTAAAAGTA
1 -TTTTCAAAAACACTTTTCAAAAGTA
*
5345082 TTGTCAAA
1 TTTTCAAA
5345090 TTAGCCCTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 7 0.24
26 22 0.76
ACGTcount: A:0.39, C:0.19, G:0.05, T:0.37
Consensus pattern (25 bp):
TTTTCAAAAACACTTTTCAAAAGTA
Found at i:5345180 original size:2 final size:2
Alignment explanation
Indices: 5345173--5345205 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5345163 AAATAATTTG
5345173 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 A
5345206 ACGTGGTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5350934 original size:3 final size:3
Alignment explanation
Indices: 5350926--5350971 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
5350916 GCTAAAATTT
5350926 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5350972 AAGCAGATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5353359 original size:47 final size:47
Alignment explanation
Indices: 5353290--5353383 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
5353280 ACTCTTTAAT
5353290 GAGTTTGAATCATGATTTCTAGTAAAATTTTTAGTTTAATTTGGTAA
1 GAGTTTGAATCATGATTTCTAGTAAAATTTTTAGTTTAATTTGGTAA
5353337 GAGTTTGAATCATGATTTCTAGTAAAATTTTTAGTTTAATTTGGTAA
1 GAGTTTGAATCATGATTTCTAGTAAAATTTTTAGTTTAATTTGGTAA
5353384 ACTAATATAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (47 bp):
GAGTTTGAATCATGATTTCTAGTAAAATTTTTAGTTTAATTTGGTAA
Found at i:5357370 original size:22 final size:19
Alignment explanation
Indices: 5357328--5357371 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
5357318 TTTTTATCAT
*
5357328 ATTATTTATAATTTTTTTA
1 ATTATTTATAATTTTTGTA
5357347 ATTATTTAATAATATTTTAGTA
1 ATTATTT-ATAAT-TTTT-GTA
5357369 ATT
1 ATT
5357372 TTTTCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 4 0.19
22 5 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
ATTATTTATAATTTTTGTA
Found at i:5359387 original size:21 final size:23
Alignment explanation
Indices: 5359345--5359388 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
5359335 ATACATTTAT
* *
5359345 AATAATATTTTTTATTTATTAAA
1 AATAATATTTTTAAATTATTAAA
5359368 AATAATA-TTTTAAATT-TTAAA
1 AATAATATTTTTAAATTATTAAA
5359389 TTAAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATAATATTTTTAAATTATTAAA
Found at i:5364787 original size:43 final size:43
Alignment explanation
Indices: 5364726--5364812 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
5364716 AGTTACATGG
5364726 TGAGCTCATCCTTATTTCTTGATATTTACATGAAGTATATGAC
1 TGAGCTCATCCTTATTTCTTGATATTTACATGAAGTATATGAC
5364769 TGAGCTCATCCTTATTTCTTGATATTTACATGAAGTATATGAC
1 TGAGCTCATCCTTATTTCTTGATATTTACATGAAGTATATGAC
5364812 T
1 T
5364813 AACATGTTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (43 bp):
TGAGCTCATCCTTATTTCTTGATATTTACATGAAGTATATGAC
Found at i:5375099 original size:11 final size:11
Alignment explanation
Indices: 5375069--5375102 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5375059 ATCAAGAATG
*
5375069 AAAGAATAAAT
1 AAAGAAAAAAT
5375080 AAA-AAAAAAT
1 AAAGAAAAAAT
5375090 AAAGAAAAAAT
1 AAAGAAAAAAT
5375101 AA
1 AA
5375103 CTAGTGAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (11 bp):
AAAGAAAAAAT
Found at i:5380928 original size:196 final size:195
Alignment explanation
Indices: 5380538--5380932 Score: 478
Period size: 196 Copynumber: 2.0 Consensus size: 195
5380528 ATTTTTAAAT
*
5380538 TTATTTTAATTAAGTTTTCTATTTATTTAATTCATTATTTTTAAGAGAATTCACTTAATATTTTT
1 TTATTTTAATTAAGTTTTCTATTTATATAATTCATTATTTTTAAGAG-ATT-ACTTAATATTTTT
* * * *
5380603 TATATGTGTTGAGATTACTTTAATAATTTTACTTTGTTTTAAAAAATCATTATTTTGAAGTTTTA
64 TATATGTGTTGAGACTACTTTAATAACTTTACTTTGTTTTAAAAAATCATCATTTTAAAGTTTTA
* * * * *
5380668 TATTATATTATTTTAACATCTTGTATAACATTTCATTTAAATATTTTTATATATATTTGTACATA
129 TATCATATTATTTTAACATCTTATATAACATTTCATTTAAATAGTTTTATATATAGTGGTACATA
5380733 TA
194 TA
* * *
5380735 TTATTTTAATTGAGTTTTCTATTTGTAATACTT-ATTA-TTTTAA-AG-TT-CTTAATATTTTTA
1 TTATTTTAATTAAGTTTTCTATTTAT-ATAATTCATTATTTTTAAGAGATTACTTAATATTTTT-
* * *
5380795 TATATGTGTTGAG-CTATTTTAATAACTTTATTTTGTTTTTATAAAATCATCATTTTAAAGTTCT
64 TATATGTGTTGAGACTACTTTAATAACTTTACTTTG-TTTTAAAAAATCATCATTTTAAAG----
* * * * *
5380859 TTTTATATCATATTATTTTAACATTTTATATAATATTTCGTTTAAATGGTTTTGTATATAGTGGT
124 TTTTATATCATATTATTTTAACATCTTATATAACATTTCATTTAAATAGTTTTATATATAGTGGT
5380924 ACATATA
189 ACATATA
5380931 TT
1 TT
5380933 TGATCTTAGA
Statistics
Matches: 170, Mismatches: 21, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
191 30 0.18
192 34 0.20
193 2 0.01
195 2 0.01
196 70 0.41
197 28 0.16
198 4 0.02
ACGTcount: A:0.31, C:0.06, G:0.07, T:0.55
Consensus pattern (195 bp):
TTATTTTAATTAAGTTTTCTATTTATATAATTCATTATTTTTAAGAGATTACTTAATATTTTTTA
TATGTGTTGAGACTACTTTAATAACTTTACTTTGTTTTAAAAAATCATCATTTTAAAGTTTTATA
TCATATTATTTTAACATCTTATATAACATTTCATTTAAATAGTTTTATATATAGTGGTACATATA
Found at i:5381890 original size:4 final size:4
Alignment explanation
Indices: 5381881--5381914 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
5381871 AGCAAACGTG
* *
5381881 AGAA AGAA AGAA GGAA AGAA AGAA AGAA AAAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
5381915 GGAAATTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:5382728 original size:47 final size:47
Alignment explanation
Indices: 5382664--5382774 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
5382654 GACATTGAGT
*
5382664 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
5382711 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
5382758 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
5382775 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:5389960 original size:47 final size:47
Alignment explanation
Indices: 5389896--5390006 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
5389886 GACATTGAGT
*
5389896 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
5389943 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
5389990 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
5390007 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:5395481 original size:161 final size:161
Alignment explanation
Indices: 5395209--5395534 Score: 634
Period size: 161 Copynumber: 2.0 Consensus size: 161
5395199 TAGGTATTCA
*
5395209 ACAATGTATAATAGGGCAAAATGACCATTTTGCCCCTAGACTTTCACAAAATGACCATTTTACCC
1 ACAATGCATAATAGGGCAAAATGACCATTTTGCCCCTAGACTTTCACAAAATGACCATTTTACCC
5395274 CTAGACCCAAAACTTGATTTTTATCACATTTTCTACTTAACCAAACCTAACTGACCATTTATTAC
66 CTAGACCCAAAACTTGATTTTTATCACATTTTCTACTTAACCAAACCTAACTGACCATTTATTAC
5395339 TCTTATGACAACCCCAAATTTCCAATATTTC
131 TCTTATGACAACCCCAAATTTCCAATATTTC
*
5395370 ACAATGCATAATAGGTCAAAATGACCATTTTGCCCCTAGACTTTCACAAAATGACCATTTTACCC
1 ACAATGCATAATAGGGCAAAATGACCATTTTGCCCCTAGACTTTCACAAAATGACCATTTTACCC
5395435 CTAGACCCAAAACTTGATTTTTATCACATTTTCTACTTAACCAAACCTAACTGACCATTTATTAC
66 CTAGACCCAAAACTTGATTTTTATCACATTTTCTACTTAACCAAACCTAACTGACCATTTATTAC
5395500 TCTTATGACAACCCCAAATTTCCAATATTTC
131 TCTTATGACAACCCCAAATTTCCAATATTTC
5395531 ACAA
1 ACAA
5395535 CATTATTATC
Statistics
Matches: 163, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 163 1.00
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.32
Consensus pattern (161 bp):
ACAATGCATAATAGGGCAAAATGACCATTTTGCCCCTAGACTTTCACAAAATGACCATTTTACCC
CTAGACCCAAAACTTGATTTTTATCACATTTTCTACTTAACCAAACCTAACTGACCATTTATTAC
TCTTATGACAACCCCAAATTTCCAATATTTC
Found at i:5397602 original size:20 final size:20
Alignment explanation
Indices: 5397555--5397598 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5397545 TAGGATTATA
5397555 ATTTTTATAATTCTTTTACG
1 ATTTTTATAATTCTTTTACG
*
5397575 AATTTTATAATTC-TTTAC-
1 ATTTTTATAATTCTTTTACG
5397593 ATTTTT
1 ATTTTT
5397599 TTATCATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 5 0.23
20 12 0.55
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTTTATAATTCTTTTACG
Found at i:5397629 original size:29 final size:28
Alignment explanation
Indices: 5397597--5397697 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 28
5397587 CTTTACATTT
5397597 TTTTATCATTTTCTTAC-AACTTTATAAAA
1 TTTTATCATTTT-TTACGAA-TTTATAAAA
* * * *
5397626 TTTTATCTATTTTTTTCTATATTTCTATATA
1 TTTTATC-ATTTTTTACGA-ATTTATA-AAA
5397657 TTTTAT-ATTTTTTACGAATTTTATAAAA
1 TTTTATCATTTTTTACGAA-TTTATAAAA
*
5397685 TTTTA-CAATTTTT
1 TTTTATCATTTTTT
5397698 GTAATCTTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 13
0.73 0.10 0.16
Matches are distributed among these distances:
28 14 0.24
29 24 0.41
30 11 0.19
31 9 0.16
ACGTcount: A:0.30, C:0.09, G:0.01, T:0.60
Consensus pattern (28 bp):
TTTTATCATTTTTTACGAATTTATAAAA
Found at i:5397767 original size:37 final size:38
Alignment explanation
Indices: 5397717--5397792 Score: 109
Period size: 37 Copynumber: 2.0 Consensus size: 38
5397707 TTCTAATTTT
* *
5397717 TAATAAAAAATAAATATTTGTTATA-TTTTTATTAAAA
1 TAATAAAAAATAAATATTTCTTAGATTTTTTATTAAAA
* *
5397754 TAATAACAGATAAATATTTCTTAGATTTTTTATTAAAA
1 TAATAAAAAATAAATATTTCTTAGATTTTTTATTAAAA
5397792 T
1 T
5397793 TTAATAACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
37 21 0.62
38 13 0.38
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (38 bp):
TAATAAAAAATAAATATTTCTTAGATTTTTTATTAAAA
Found at i:5422488 original size:35 final size:35
Alignment explanation
Indices: 5422397--5422491 Score: 172
Period size: 35 Copynumber: 2.7 Consensus size: 35
5422387 CATGGCAAAG
* *
5422397 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
5422432 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
5422467 TGTGAAATGTAGGTATGGTATTATC
1 TGTGAAATGTAGGTATGGTATTATC
5422492 AAATCCATAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.28, C:0.09, G:0.26, T:0.36
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
Found at i:5422498 original size:40 final size:37
Alignment explanation
Indices: 5422397--5422563 Score: 166
Period size: 35 Copynumber: 4.6 Consensus size: 37
5422387 CATGGCAAAG
5422397 TGTGAAATGTAGGTATGG--TATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
*
5422432 TGTGAAATGTAGGTATGGTAT-T-ATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
5422467 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-TATC--ATCCATACTGAGT
** * * * *
5422507 TAAGAAATGTAGGTCTGGCATTTC--CCATACCGAGT
1 TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
***
5422542 TAAAAAAATGTAGGTATGGTAT
1 T-GTGAAATGTAGGTATGGTAT
5422564 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
35 61 0.54
36 19 0.17
37 2 0.02
39 3 0.03
40 28 0.25
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (37 bp):
TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
Found at i:5422516 original size:75 final size:75
Alignment explanation
Indices: 5422397--5422568 Score: 196
Period size: 75 Copynumber: 2.4 Consensus size: 75
5422387 CATGGCAAAG
** *
5422397 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
5422456 CCATACTGAGC
65 CCATACCGAGC
*
5422467 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTCTGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
5422532 CATACCGAGT
66 CATACCGAGC
***
5422542 TAAAAAAATGTAGGTATGGTATT-TCAA
1 T-GTGAAATGTAGGTATGGTATTATCAA
5422569 TGAGGAAAAC
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 1 0.01
75 45 0.52
76 18 0.21
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:5422542 original size:35 final size:36
Alignment explanation
Indices: 5422496--5422566 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
5422486 ATTATCAAAT
* * *
5422496 CCATACTGAGTT-AAGAAATGTAGGTCTGGCATTTC
1 CCATACCGAGTTAAAAAAATGTAGGTATGGCATTTC
*
5422531 CCATACCGAGTTAAAAAAATGTAGGTATGGTATTTC
1 CCATACCGAGTTAAAAAAATGTAGGTATGGCATTTC
5422567 AATGAGGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
35 11 0.35
36 20 0.65
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (36 bp):
CCATACCGAGTTAAAAAAATGTAGGTATGGCATTTC
Found at i:5428601 original size:24 final size:24
Alignment explanation
Indices: 5428572--5428620 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5428562 ATTATATGAA
5428572 TAAATGTGGTTTTAAATATTCAAT
1 TAAATGTGGTTTTAAATATTCAAT
*
5428596 TAAATGTGGTTTTAAATATTTAAT
1 TAAATGTGGTTTTAAATATTCAAT
5428620 T
1 T
5428621 GTGATTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (24 bp):
TAAATGTGGTTTTAAATATTCAAT
Found at i:5429959 original size:11 final size:11
Alignment explanation
Indices: 5429943--5429967 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5429933 GACGCTCTGA
5429943 TTTTCACTCAT
1 TTTTCACTCAT
5429954 TTTTCACTCAT
1 TTTTCACTCAT
5429965 TTT
1 TTT
5429968 GCTCTCAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTCACTCAT
Found at i:5431616 original size:21 final size:21
Alignment explanation
Indices: 5431592--5431637 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5431582 TATCACTAAT
*
5431592 TTAATCCATTGTAATTCAGAC
1 TTAATCCATAGTAATTCAGAC
* **
5431613 TTAATCTATAGTAATTTTGAC
1 TTAATCCATAGTAATTCAGAC
5431634 TTAA
1 TTAA
5431638 AATATGACGC
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:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (21 bp):
TTAATCCATAGTAATTCAGAC
Found at i:5433160 original size:20 final size:22
Alignment explanation
Indices: 5433123--5433167 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
5433113 AAGAAATTCA
5433123 AAAAAAAATATTAGAAAACTAT
1 AAAAAAAATATTAGAAAACTAT
* *
5433145 AAAAAAAGTA-TA-AAAAGTAT
1 AAAAAAAATATTAGAAAACTAT
5433165 AAA
1 AAA
5433168 TATTATATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 9 0.43
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (22 bp):
AAAAAAAATATTAGAAAACTAT
Found at i:5446330 original size:36 final size:36
Alignment explanation
Indices: 5446290--5446361 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
5446280 GAATAGCATG
* *
5446290 AGATTTGTTTCCTTTCTAAGGCTTAGAATTATCTAA
1 AGATTTGCTTCCTTTATAAGGCTTAGAATTATCTAA
5446326 AGATTTGCTTCCTTTATAAGGCTTAGAATTATCTAA
1 AGATTTGCTTCCTTTATAAGGCTTAGAATTATCTAA
5446362 CTCTCCACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (36 bp):
AGATTTGCTTCCTTTATAAGGCTTAGAATTATCTAA
Found at i:5447441 original size:18 final size:19
Alignment explanation
Indices: 5447410--5447452 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
5447400 TTATTAAAAA
* *
5447410 TAAATTTTATAAA-TATTT
1 TAAATTTAAAAAATTATTT
5447428 TAAATTTAAAAAATTATTT
1 TAAATTTAAAAAATTATTT
*
5447447 AAAATT
1 TAAATT
5447453 ATTTTGAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTTAAAAAATTATTT
Found at i:5458358 original size:2 final size:2
Alignment explanation
Indices: 5458351--5458377 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5458341 AAACAGCTAT
5458351 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5458378 GAAAGTTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5466112 original size:17 final size:18
Alignment explanation
Indices: 5466090--5466126 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
5466080 AGGCCATCTC
5466090 ATAT-ACATGGAATGAAG
1 ATATAACATGGAATGAAG
5466107 ATATACACATGGAATGAAG
1 ATATA-ACATGGAATGAAG
5466126 A
1 A
5466127 CACAATTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
19 14 0.78
ACGTcount: A:0.49, C:0.08, G:0.22, T:0.22
Consensus pattern (18 bp):
ATATAACATGGAATGAAG
Found at i:5468013 original size:25 final size:25
Alignment explanation
Indices: 5467979--5468029 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
5467969 TTCCTTATAA
**
5467979 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
5468004 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
5468029 A
1 A
5468030 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:5468028 original size:12 final size:12
Alignment explanation
Indices: 5467982--5468029 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
5467972 CTTATAAACT
5467982 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
5467994 TTCTATTAGGACT
1 TTAAATTAGGA-A
5468007 TTAAATTAGGAA
1 TTAAATTAGGAA
*
5468019 TTAGATTAGGA
1 TTAAATTAGGA
5468030 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:5472657 original size:25 final size:25
Alignment explanation
Indices: 5472623--5472673 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
5472613 TTCCTTATAA
**
5472623 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
5472648 ACTTTAAATTAGGAATTAGATTAGG
1 ACTTTAAATTAGGAATTAGATTAGG
5472673 A
1 A
5472674 TTTTCCTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.37
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTAGATTAGG
Found at i:5472672 original size:12 final size:12
Alignment explanation
Indices: 5472626--5472673 Score: 51
Period size: 12 Copynumber: 3.9 Consensus size: 12
5472616 CTTATAAACT
5472626 TTAAATTAGGAA
1 TTAAATTAGGAA
** *
5472638 TTCTATTAGGACT
1 TTAAATTAGGA-A
5472651 TTAAATTAGGAA
1 TTAAATTAGGAA
*
5472663 TTAGATTAGGA
1 TTAAATTAGGA
5472674 TTTTCCTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.38
Consensus pattern (12 bp):
TTAAATTAGGAA
Found at i:5475499 original size:12 final size:12
Alignment explanation
Indices: 5475482--5475525 Score: 88
Period size: 12 Copynumber: 3.7 Consensus size: 12
5475472 TGACCAAGAA
5475482 CCATGCTACACT
1 CCATGCTACACT
5475494 CCATGCTACACT
1 CCATGCTACACT
5475506 CCATGCTACACT
1 CCATGCTACACT
5475518 CCATGCTA
1 CCATGCTA
5475526 TGGGTCTCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.25, C:0.41, G:0.09, T:0.25
Consensus pattern (12 bp):
CCATGCTACACT
Found at i:5478752 original size:5 final size:5
Alignment explanation
Indices: 5478742--5478784 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
5478732 AGCTTTAAAA
* *
5478742 TATTT TATTT TATTT TATTA CATTTT TATTTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TA-TTT TA-TTT TATTT TATTT T
5478785 CTCTATCAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 24 0.73
6 9 0.27
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (5 bp):
TATTT
Found at i:5479894 original size:15 final size:16
Alignment explanation
Indices: 5479876--5479905 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5479866 GGAAAATTCC
5479876 AAAAT-GGACTAAATA
1 AAAATGGGACTAAATA
5479891 AAAATGGGACTAAAT
1 AAAATGGGACTAAAT
5479906 TGGAATATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.20
Consensus pattern (16 bp):
AAAATGGGACTAAATA
Found at i:5481866 original size:8 final size:8
Alignment explanation
Indices: 5481855--5481896 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
5481845 TTTGCCTTTT
5481855 TTTTTATA
1 TTTTTATA
*
5481863 TTTTTATT
1 TTTTTATA
5481871 TTTTTA-A
1 TTTTTATA
*
5481878 GTTTTATA
1 TTTTTATA
5481886 TTTTT-TA
1 TTTTTATA
5481893 TTTT
1 TTTT
5481897 ATTTTGCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 11 0.38
8 18 0.62
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (8 bp):
TTTTTATA
Found at i:5481872 original size:16 final size:15
Alignment explanation
Indices: 5481853--5481901 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
5481843 CTTTTGCCTT
5481853 TTTTTTTATATTTTTA
1 TTTTTTTATA-TTTTA
5481869 TTTTTTTA-AGTTTTA
1 TTTTTTTATA-TTTTA
*
5481884 TATTTTT-TATTTTA
1 TTTTTTTATATTTTA
5481898 TTTT
1 TTTT
5481902 GCTTATTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 8 0.28
15 13 0.45
16 8 0.28
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTTTATATTTTA
Found at i:5481924 original size:23 final size:23
Alignment explanation
Indices: 5481888--5481938 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
5481878 GTTTTATATT
*
5481888 TTTTA-TTTTATTTTGCTTATTTA
1 TTTTATTTTTATTTTG-TTATTAA
5481911 TTTTATTTATT-TTTTGTTATTAA
1 TTTTATTT-TTATTTTGTTATTAA
5481934 TTTTA
1 TTTTA
5481939 GAAAAATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 16 0.64
24 7 0.28
25 2 0.08
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.75
Consensus pattern (23 bp):
TTTTATTTTTATTTTGTTATTAA
Found at i:5481963 original size:13 final size:13
Alignment explanation
Indices: 5481945--5481979 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
5481935 TTTAGAAAAA
5481945 TTGAAATGTATAT
1 TTGAAATGTATAT
5481958 TTGAAATGTATAT
1 TTGAAATGTATAT
5481971 TTGAAATGT
1 TTGAAATGT
5481980 TTTATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (13 bp):
TTGAAATGTATAT
Found at i:5482046 original size:21 final size:20
Alignment explanation
Indices: 5482013--5482051 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
5482003 TTTAAATATT
*
5482013 ATTTTTAAATTATTTTTTAA
1 ATTTTGAAATTATTTTTTAA
5482033 ATTTTGAATATTATTTTTT
1 ATTTTGAA-ATTATTTTTT
5482052 TGAAATTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (20 bp):
ATTTTGAAATTATTTTTTAA
Found at i:5482095 original size:36 final size:34
Alignment explanation
Indices: 5481993--5482277 Score: 141
Period size: 36 Copynumber: 7.9 Consensus size: 34
5481983 ATAATATATT
* *
5481993 TTTTTTAAATTTTAAATAT-TATTTTT-AAATTA
1 TTTTATAAATTTTAAAAATATATTTTTGAAATTA
* * * *
5482025 TTTTTTAAATTTTGAATATTATTTTTTTGAAATTA
1 TTTTATAAATTTT-AAAAATATATTTTTGAAATTA
5482060 TGTCTTATAAATTTTAAAAATATATTTTTGAAATTAA
1 T-T-TTATAAATTTTAAAAATATATTTTTGAAATT-A
* * **
5482097 TTTTTCTAAATTTTAAATTTTAAATGTATTTTAAAAAATATA
1 -TTTTATAAATTTT-AA----AAATATATTTT-TGAAAT-TA
**** ***
5482139 TTTT-TAAACAAAATAAAATA-ATTTCAAAAATATA
1 TTTTATAAATTTTA-AAAATATATTTTTGAAAT-TA
* * *
5482173 TATTTAAAAATAATTTTAAATATATATATTTGAAATTA
1 T-TTT--ATA-AATTTTAAAAATATATTTTTGAAATTA
5482211 TTTCTTATAAATTTTAAAAATATATTTTTGAAATTA
1 -TT-TTATAAATTTTAAAAATATATTTTTGAAATTA
* *
5482247 TTTTTTAAAATTTTAAATAT-TATTTTT-AAAT
1 TTTTAT-AAATTTTAAAAATATATTTTTGAAAT
5482278 ATTAAATATA
Statistics
Matches: 196, Mismatches: 33, Indels: 47
0.71 0.12 0.17
Matches are distributed among these distances:
32 13 0.07
33 7 0.04
34 26 0.13
35 28 0.14
36 57 0.29
37 16 0.08
38 10 0.05
39 14 0.07
40 5 0.03
41 14 0.07
42 5 0.03
43 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (34 bp):
TTTTATAAATTTTAAAAATATATTTTTGAAATTA
Found at i:5482187 original size:26 final size:26
Alignment explanation
Indices: 5482153--5482203 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
5482143 TAAACAAAAT
5482153 AAAATAATTTCAAAAATATATATTTA
1 AAAATAATTTCAAAAATATATATTTA
* *
5482179 AAAATAATTTTAAATATATATATTT
1 AAAATAATTTCAAAAATATATATTT
5482204 GAAATTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
AAAATAATTTCAAAAATATATATTTA
Found at i:5482192 original size:12 final size:12
Alignment explanation
Indices: 5482153--5482192 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5482143 TAAACAAAAT
*
5482153 AAAATAATTTCA
1 AAAATAATTTTA
5482165 AAAATATATATTTA
1 AAAATA-AT-TTTA
5482179 AAAATAATTTTA
1 AAAATAATTTTA
5482191 AA
1 AA
5482193 TATATATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 12 0.48
13 4 0.16
14 9 0.36
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATAATTTTA
Found at i:5482273 original size:13 final size:13
Alignment explanation
Indices: 5482257--5482281 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5482247 TTTTTTAAAA
5482257 TTTTAAATATTAT
1 TTTTAAATATTAT
5482270 TTTTAAATATTA
1 TTTTAAATATTA
5482282 AATATATTTT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAATATTAT
Found at i:5482304 original size:22 final size:22
Alignment explanation
Indices: 5482243--5482305 Score: 80
Period size: 20 Copynumber: 3.0 Consensus size: 22
5482233 TATTTTTGAA
5482243 ATTATTTTTTAAAAT-TTTAAAT
1 ATTA-TTTTTAAAATATTTAAAT
5482265 ATTATTTTT-AAATA-TTAAAT
1 ATTATTTTTAAAATATTTAAAT
5482285 A-TATTTTTAATAATATTTAAA
1 ATTATTTTTAA-AATATTTAAA
5482306 CATTTAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.19
20 12 0.32
21 9 0.24
22 9 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTATTTTTAAAATATTTAAAT
Found at i:5482324 original size:29 final size:29
Alignment explanation
Indices: 5482250--5482324 Score: 68
Period size: 31 Copynumber: 2.6 Consensus size: 29
5482240 GAAATTATTT
* *
5482250 TTTAAAA-TTTTA-AATATTATTTTTAAA
1 TTTAAAATTTTTATAATAATATTTTAAAA
5482277 TATTAAATATATTTT-TAATAATA-TTTAAACA
1 T-TTAAA-AT-TTTTATAATAATATTTTAAA-A
5482308 TTTAAAATTTTTATAAT
1 TTTAAAATTTTTATAAT
5482325 TTTTTTATAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
27 1 0.03
28 9 0.23
29 7 0.18
30 10 0.26
31 12 0.31
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (29 bp):
TTTAAAATTTTTATAATAATATTTTAAAA
Found at i:5482388 original size:14 final size:15
Alignment explanation
Indices: 5482369--5482401 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5482359 ATCTTTAAAA
5482369 ATAA-TTAAAAAATC
1 ATAATTTAAAAAATC
*
5482383 ATAATTTAAAAAATT
1 ATAATTTAAAAAATC
5482398 ATAA
1 ATAA
5482402 AAAAATGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAATTTAAAAAATC
Found at i:5482719 original size:33 final size:32
Alignment explanation
Indices: 5482652--5482752 Score: 139
Period size: 34 Copynumber: 3.0 Consensus size: 32
5482642 ATAATATATA
*
5482652 TATTTTTTAAATTTTAAATATATATTTTTGAAAT
1 TATTTTTTAAAATTTAAATAT-TATTTTT-AAAT
5482686 TATTTTTCTAAAATTTAAATATTATTTTTAAAT
1 TATTTTT-TAAAATTTAAATATTATTTTTAAAT
*
5482719 TATTGTTTAAAAATTTAAATATTATTTTTTAAAT
1 TATT-TTTTAAAATTTAAATATTA-TTTTTAAAT
5482753 ATTAAATATA
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
33 23 0.37
34 26 0.42
35 13 0.21
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (32 bp):
TATTTTTTAAAATTTAAATATTATTTTTAAAT
Found at i:5482734 original size:22 final size:22
Alignment explanation
Indices: 5482717--5482783 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
5482707 TTATTTTTAA
5482717 ATTATTGTTTAAAAATTTAAAT
1 ATTATTGTTTAAAAATTTAAAT
* *
5482739 ATTATTTTTTAAATA-TTAAAT
1 ATTATTGTTTAAAAATTTAAAT
* *
5482760 A-TATT-TTTAATAATATAAAAT
1 ATTATTGTTTAAAAAT-TTAAAT
5482781 ATT
1 ATT
5482784 TAAAGATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 6 0.16
20 4 0.11
21 13 0.35
22 14 0.38
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (22 bp):
ATTATTGTTTAAAAATTTAAAT
Found at i:5482759 original size:21 final size:21
Alignment explanation
Indices: 5482717--5482783 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
5482707 TTATTTTTAA
* *
5482717 ATTATTGTTTAAAAATTTAAAT
1 ATTATTTTTTAAATA-TTAAAT
5482739 ATTATTTTTTAAATATTAAAT
1 ATTATTTTTTAAATATTAAAT
* *
5482760 A-TATTTTTAATAATATAAAAT
1 ATTATTTTTTA-AATATTAAAT
5482781 ATT
1 ATT
5482784 TAAAGATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.21
21 17 0.44
22 14 0.36
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (21 bp):
ATTATTTTTTAAATATTAAAT
Found at i:5482896 original size:17 final size:17
Alignment explanation
Indices: 5482876--5482910 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5482866 ATAAAATAAG
*
5482876 AAAAAAGAAAAAACTTA
1 AAAAAAGAAAAAAATTA
5482893 AAAAAAGAAAAAAATTA
1 AAAAAAGAAAAAAATTA
5482910 A
1 A
5482911 TAACAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.80, C:0.03, G:0.06, T:0.11
Consensus pattern (17 bp):
AAAAAAGAAAAAAATTA
Found at i:5482999 original size:13 final size:12
Alignment explanation
Indices: 5482977--5483041 Score: 53
Period size: 13 Copynumber: 5.3 Consensus size: 12
5482967 CAAATTTTTT
*
5482977 AAAATTAATAACA
1 AAAATAAATAA-A
5482990 AAAATAAATAAA
1 AAAATAAATAAA
*
5483002 ATAAATAAACAAA
1 A-AAATAAATAAA
*
5483015 AAAA-ATAAGAAA
1 AAAATA-AATAAA
*
5483027 AAATTAAA-AAA
1 AAAATAAATAAA
5483038 AAAA
1 AAAA
5483042 GACAAAAGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
11 7 0.16
12 15 0.34
13 22 0.50
ACGTcount: A:0.80, C:0.03, G:0.02, T:0.15
Consensus pattern (12 bp):
AAAATAAATAAA
Found at i:5483008 original size:22 final size:22
Alignment explanation
Indices: 5482976--5483041 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
5482966 TCAAATTTTT
*
5482976 TAAAATTAAT-AACAAAAATAAA
1 TAAAATAAATAAACAAAAA-AAA
5482998 TAAAATAAATAAACAAAAAAAA
1 TAAAATAAATAAACAAAAAAAA
* *
5483020 TAAGAAAAAATTAA-AAAAAAAA
1 TAA-AATAAATAAACAAAAAAAA
5483042 GACAAAAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
22 23 0.59
23 16 0.41
ACGTcount: A:0.79, C:0.03, G:0.02, T:0.17
Consensus pattern (22 bp):
TAAAATAAATAAACAAAAAAAA
Found at i:5483029 original size:10 final size:9
Alignment explanation
Indices: 5482983--5483069 Score: 61
Period size: 10 Copynumber: 9.2 Consensus size: 9
5482973 TTTTAAAATT
*
5482983 AATAACAAA
1 AATAAAAAA
*
5482992 AATAAATAA
1 AATAAAAAA
*
5483001 AAT-AAATA
1 AATAAAAAA
*
5483009 AACAAAAAA
1 AATAAAAAA
5483018 AATAAGAAAA
1 AATAA-AAAA
5483028 AATTAAAAAA
1 AA-TAAAAAA
5483038 AA-AAGACAAA
1 AATAA-A-AAA
*
5483048 AGTTAAAAAA
1 A-ATAAAAAA
5483058 AAGTAAAAAA
1 AA-TAAAAAA
5483068 AA
1 AA
5483070 AATCATAAGG
Statistics
Matches: 61, Mismatches: 9, Indels: 15
0.72 0.11 0.18
Matches are distributed among these distances:
8 7 0.11
9 19 0.31
10 29 0.48
11 4 0.07
12 2 0.03
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (9 bp):
AATAAAAAA
Found at i:5483037 original size:20 final size:20
Alignment explanation
Indices: 5483012--5483069 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
5483002 ATAAATAAAC
5483012 AAAAAAAATAAGAAAAAATT
1 AAAAAAAATAAGAAAAAATT
*
5483032 AAAAAAAA-AAGACAAAAGTT
1 AAAAAAAATAAGA-AAAAATT
5483052 AAAAAAAAGTAA-AAAAAA
1 AAAAAAAA-TAAGAAAAAA
5483070 AATCATAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 4 0.12
20 26 0.79
21 1 0.03
22 2 0.06
ACGTcount: A:0.81, C:0.02, G:0.07, T:0.10
Consensus pattern (20 bp):
AAAAAAAATAAGAAAAAATT
Found at i:5483070 original size:137 final size:134
Alignment explanation
Indices: 5482824--5483072 Score: 319
Period size: 137 Copynumber: 1.8 Consensus size: 134
5482814 TTATTATAAA
* *
5482824 ACATTTCAAATTTTTTAAAATTAATAACAAAAAATAAATAAAATAAAATAAGAAAAAAGAAAAAA
1 ACATTTCAAATTTTTTAAAATTAATAACAAAAAATAAATAAAATAAAAAAAAAAAAAAGAAAAAA
* **
5482889 CTTAAAAAAAGAAAAAAATTAATAACAAATTTAAAATTTTAAAAAATATATATTATAAAACATTT
66 CTTAAAAAAAAAAAAAAATTAATAACAAAAGTAAAA---TAAAAAATATATATTATAAAACATTT
5482954 CAAATAT
128 CAAATAT
5482961 ACATTTCAAATTTTTTAAAATTAATAAC-AAAAATAAATAAAATAAATAAACAAAAAAAATAAGA
1 ACATTTCAAATTTTTTAAAATTAATAACAAAAAATAAATAAAAT--A-AAA-AAAAAAAA-AAGA
5483025 AAAAA-TTAAAAAAAAAAGACAAAAGTTAA-AA-AAAAGTAAAA-AAAAAAT
61 AAAAACTTAAAAAAAAAA-A-AAAA-TTAATAACAAAAGTAAAATAAAAAAT
5483073 CATAAGGGCG
Statistics
Matches: 99, Mismatches: 5, Indels: 16
0.82 0.04 0.13
Matches are distributed among these distances:
136 15 0.15
137 35 0.35
138 1 0.01
139 3 0.03
140 17 0.17
141 18 0.18
142 6 0.06
143 4 0.04
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.25
Consensus pattern (134 bp):
ACATTTCAAATTTTTTAAAATTAATAACAAAAAATAAATAAAATAAAAAAAAAAAAAAGAAAAAA
CTTAAAAAAAAAAAAAAATTAATAACAAAAGTAAAATAAAAAATATATATTATAAAACATTTCAA
ATAT
Found at i:5493742 original size:44 final size:45
Alignment explanation
Indices: 5493647--5493761 Score: 160
Period size: 44 Copynumber: 2.6 Consensus size: 45
5493637 ACAGGACAGA
* *
5493647 ACAGAAATGAGCCATGTAAGTCCATATTATAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAT-AATATGGCATTGGAG
*
5493693 ACAGGATTGAGCCATGTAAGTCCATATTAT-ATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTATAATATGGCATTGGAG
* **
5493737 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
5493762 GTCAAAGACA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 34 0.55
46 28 0.45
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTATAATATGGCATTGGAG
Found at i:5495082 original size:87 final size:87
Alignment explanation
Indices: 5494936--5495103 Score: 336
Period size: 87 Copynumber: 1.9 Consensus size: 87
5494926 AAGTGATTTA
5494936 GAGTTGTTTAAAAGGTAAGATAAGTTTAGTAACACCTCAAGCTTGACTCCGGTGATGGTTTCGGG
1 GAGTTGTTTAAAAGGTAAGATAAGTTTAGTAACACCTCAAGCTTGACTCCGGTGATGGTTTCGGG
5495001 CGTGGGGGCGTTACATTTATTG
66 CGTGGGGGCGTTACATTTATTG
5495023 GAGTTGTTTAAAAGGTAAGATAAGTTTAGTAACACCTCAAGCTTGACTCCGGTGATGGTTTCGGG
1 GAGTTGTTTAAAAGGTAAGATAAGTTTAGTAACACCTCAAGCTTGACTCCGGTGATGGTTTCGGG
5495088 CGTGGGGGCGTTACAT
66 CGTGGGGGCGTTACAT
5495104 ACCGTGCTGG
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.31
Consensus pattern (87 bp):
GAGTTGTTTAAAAGGTAAGATAAGTTTAGTAACACCTCAAGCTTGACTCCGGTGATGGTTTCGGG
CGTGGGGGCGTTACATTTATTG
Found at i:5495349 original size:127 final size:127
Alignment explanation
Indices: 5495103--5495383 Score: 339
Period size: 127 Copynumber: 2.2 Consensus size: 127
5495093 GGGCGTTACA
* *
5495103 TACCGTGCTGGGTTTCGATTTCCCGTTTGTTCAAAGTAATCAAATATTCCTTTAGAATTTCACTC
1 TACCGTGCTGGGTTTCGATTTTCCGTTTGTTCAAAGTAATCAAATATTCATTTAGAATTTCACTC
* * * * *
5495168 GTGTTTTCCAAATTCTAAAACAAGGCAATGTTCAAGGTTTAGAAATTCGGGGAATTGTGCCC
66 GTCTTTTACAAATTCTAAAACAAGGCAATGATCAAGGTTTAGAAATTCGAGGAATCGTGCCC
* * ** * *
5495230 TATCGTGCTGGGTTTCGATTTTCGGTTTGTTCCAAA-TAATTGAATGTTCATTTAGTATTTCACT
1 TACCGTGCTGGGTTTCGATTTTCCGTTTGTT-CAAAGTAATCAAATATTCATTTAGAATTTCACT
* * ** * * *
5495294 CGTCTTTTATAAATTTTAAAGTAAGGCAATGATCAATGTTTGGAAGTTCGAGGAATCGTGCCC
65 CGTCTTTTACAAATTCTAAAACAAGGCAATGATCAAGGTTTAGAAATTCGAGGAATCGTGCCC
* * *
5495357 TACCGTGCCGGGTTTCGGTTTTTCGTT
1 TACCGTGCTGGGTTTCGATTTTCCGTT
5495384 GGACTAAATA
Statistics
Matches: 128, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
127 124 0.97
128 4 0.03
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (127 bp):
TACCGTGCTGGGTTTCGATTTTCCGTTTGTTCAAAGTAATCAAATATTCATTTAGAATTTCACTC
GTCTTTTACAAATTCTAAAACAAGGCAATGATCAAGGTTTAGAAATTCGAGGAATCGTGCCC
Found at i:5496079 original size:17 final size:18
Alignment explanation
Indices: 5496054--5496091 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5496044 ATTGTTAAGT
*
5496054 AATA-TTTTTATCTCAAA
1 AATACTTTTTATCCCAAA
5496071 AATACTTTTTATCCCAAA
1 AATACTTTTTATCCCAAA
5496089 AAT
1 AAT
5496092 GCTTCTAAGA
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:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (18 bp):
AATACTTTTTATCCCAAA
Found at i:5496389 original size:7 final size:7
Alignment explanation
Indices: 5496379--5496403 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5496369 ACAAAAAAAG
5496379 TAAAATA
1 TAAAATA
5496386 TAAAATA
1 TAAAATA
5496393 TAAAATA
1 TAAAATA
5496400 TAAA
1 TAAA
5496404 TTTATTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
TAAAATA
Done.