Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168037.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_29, whole genome shotgun sequence
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: 14313602
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 50000 characters in sequence are not A, C, G, or T
File 67 of 74
Found at i:13257532 original size:26 final size:24
Alignment explanation
Indices: 13257394--13257576 Score: 112
Period size: 22 Copynumber: 7.4 Consensus size: 24
13257384 TTTAAATTAA
13257394 TAATATTCATTATT-ATATTATTTAT
1 TAATATT-A-TATTAATATTATTTAT
* *
13257419 TAATA-TATAATAATATTATTTCT
1 TAATATTATATTAATATTATTTAT
13257442 TAATATATTATATTAATATTATATTACT
1 T-A-ATATTATATTAATATTAT-TTA-T
* *
13257470 TATTCATAATTATTATATATTAATTTA-
1 TAAT-ATTA-TATTA-ATATT-ATTTAT
13257497 T--TATT-TATTAATATATGATTTAT
1 TAATATTATATTAATAT-T-ATTTAT
*
13257520 TAATATAATATT-AT-TTATTTAT
1 TAATATTATATTAATATTATTTAT
* * *
13257542 TAATATAATTTTATTATTTATTTAT
1 TAATATTATATTAATA-TTATTTAT
13257567 ATAATATTAT
1 -TAATATTAT
13257577 TTATAAGTAA
Statistics
Matches: 127, Mismatches: 12, Indels: 37
0.72 0.07 0.21
Matches are distributed among these distances:
21 4 0.03
22 31 0.24
23 15 0.12
24 5 0.04
25 22 0.17
26 26 0.20
27 7 0.06
28 7 0.06
29 8 0.06
30 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (24 bp):
TAATATTATATTAATATTATTTAT
Found at i:13257543 original size:76 final size:77
Alignment explanation
Indices: 13257365--13257550 Score: 181
Period size: 78 Copynumber: 2.4 Consensus size: 77
13257355 TTTACTCATA
*
13257365 TATTAGTATAATATT-TTTATTTA--AATTAATAATATTCATTATTATATTATTTATTAATATAT
1 TATTAATATAATATTATTTATTTATTAATTAATAATATTCATTATTATATTATTTATTAATATAT
*
13257427 AATAATATTATT
66 AATAATATGATT
* * * * *
13257439 TCTTAATATATTATATTA-ATATTATATTACTTATTCATAATT-ATTA-TATATTAATTTATT-A
1 TATTAATATA--ATATTATTTATT-TATTAATTAATAAT-ATTCATTATTATATT-ATTTATTAA
*
13257500 TTTATTAAT-ATATGATT
61 TATA-TAATAATATGATT
13257517 TATTAATATAATATTATTTATTTATTAATATAAT
1 TATTAATATAATATTATTTATTTATTAAT-TAAT
13257551 TTTATTATTT
Statistics
Matches: 89, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
74 8 0.09
76 21 0.24
77 9 0.10
78 26 0.29
79 22 0.25
80 3 0.03
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (77 bp):
TATTAATATAATATTATTTATTTATTAATTAATAATATTCATTATTATATTATTTATTAATATAT
AATAATATGATT
Found at i:13257558 original size:76 final size:77
Alignment explanation
Indices: 13257365--13257581 Score: 177
Period size: 76 Copynumber: 2.8 Consensus size: 77
13257355 TTTACTCATA
* ** *
13257365 TATTAGTATAATATT-TTTATTTA--AATTAATAATATTCATTATTATATT-ATTTATTA-ATAT
1 TATTAATATAATATTATTTATTTATTAATTAATTTTATT-ATTA-TATATTAATTTATTATTTAT
*
13257425 ATAATAATATTATT
64 ATAATAATATGATT
* * * *
13257439 TCTTAATATATTATATTA-ATATTATATTACTT-ATTCATAATTATTATATATTAATTTATTATT
1 TATTAATATA--ATATTATTTATT-TATTAATTAATT--TTATTATTATATATTAATTTATTATT
13257502 TAT-TAAT-ATATGATT
61 TATATAATAATATGATT
*
13257517 TATTAATATAATATTATTTATTTATTAATATAATTTTATTATT-TAT-TTATATAATATTATTTA
1 TATTAATATAATATTATTTATTTATTAAT-TAATTTTATTATTATATATTA-AT-TTATTATTTA
13257580 TA
63 TA
13257582 AGTAAAATTA
Statistics
Matches: 113, Mismatches: 14, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
74 11 0.10
75 5 0.04
76 38 0.34
77 7 0.06
78 27 0.24
79 19 0.17
80 6 0.05
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (77 bp):
TATTAATATAATATTATTTATTTATTAATTAATTTTATTATTATATATTAATTTATTATTTATAT
AATAATATGATT
Found at i:13258299 original size:22 final size:22
Alignment explanation
Indices: 13258265--13258329 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
13258255 AATAAAAAGA
*
13258265 AAAAAATAT-AAAAAATAATTT
1 AAAATATATAAAAAAATAATTT
*
13258286 AAAATATATAAAAAAAGAATTT
1 AAAATATATAAAAAAATAATTT
***
13258308 TGTATAT-TAAAAAATATAATTT
1 AAAATATATAAAAAA-ATAATTT
13258330 TGAAATATCC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 15 0.42
22 21 0.58
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (22 bp):
AAAATATATAAAAAAATAATTT
Found at i:13259961 original size:28 final size:28
Alignment explanation
Indices: 13259929--13259986 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
13259919 CCATACATAG
13259929 TTAAAAATTAAAAACATAGCATTTTTTA
1 TTAAAAATTAAAAACATAGCATTTTTTA
13259957 TTAAAAATTAAAAACATAGCATTTTTTA
1 TTAAAAATTAAAAACATAGCATTTTTTA
13259985 TT
1 TT
13259987 TAATCTTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.41
Consensus pattern (28 bp):
TTAAAAATTAAAAACATAGCATTTTTTA
Found at i:13260103 original size:14 final size:15
Alignment explanation
Indices: 13260079--13260109 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
13260069 ATTTATCATT
13260079 TATATAATATAAAAA
1 TATATAATATAAAAA
13260094 TATA-AATATAAAAA
1 TATATAATATAAAAA
13260108 TA
1 TA
13260110 ATACACATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TATATAATATAAAAA
Found at i:13260373 original size:50 final size:50
Alignment explanation
Indices: 13260270--13260473 Score: 268
Period size: 50 Copynumber: 4.1 Consensus size: 50
13260260 CTCTTTAATG
* * * *
13260270 TATCTAATATTAATATTACACTCCTTTTTAATCATGCTCTTGGATTATATC
1 TATCTAATATTAATA-TAAACTTCTTTATAATTATGCTCTTGGATTATATC
*
13260321 TATCTAATATTAATATAAACTTCTTTATAATTATGCTCTTGGATTATGTC
1 TATCTAATATTAATATAAACTTCTTTATAATTATGCTCTTGGATTATATC
* * *
13260371 TATCTAATATTAATATATATAC--CTTTGTAATTATTCTCTTGGATTGTATC
1 TATCTAATATTAATATA-A-ACTTCTTTATAATTATGCTCTTGGATTATATC
* * *
13260421 TATCTAATATTAATATATACTTCTTTATAATTATGTTCTTGGATTGTATC
1 TATCTAATATTAATATAAACTTCTTTATAATTATGCTCTTGGATTATATC
13260471 TAT
1 TAT
13260474 GTTTATATGA
Statistics
Matches: 136, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
48 2 0.01
50 116 0.85
51 16 0.12
52 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (50 bp):
TATCTAATATTAATATAAACTTCTTTATAATTATGCTCTTGGATTATATC
Found at i:13260427 original size:100 final size:100
Alignment explanation
Indices: 13260270--13260465 Score: 304
Period size: 100 Copynumber: 1.9 Consensus size: 100
13260260 CTCTTTAATG
*
13260270 TATCTAATATTAATATTACACTCCTTTTTAATCATGCTCTTGGATTATATCTATCTAATATTAAT
1 TATCTAATATTAATATTACAC-CCTTTGTAATCATGCTCTTGGATTATATCTATCTAATATTAAT
13260335 ATAAACTTCTTTATAATTATGCTCTTGGATTATGTC
65 ATAAACTTCTTTATAATTATGCTCTTGGATTATGTC
* * * *
13260371 TATCTAATATTAATATATATA-CCTTTGTAATTATTCTCTTGGATTGTATCTATCTAATATTAAT
1 TATCTAATATTAATAT-TACACCCTTTGTAATCATGCTCTTGGATTATATCTATCTAATATTAAT
* *
13260435 ATATACTTCTTTATAATTATGTTCTTGGATT
65 ATAAACTTCTTTATAATTATGCTCTTGGATT
13260466 GTATCTATGT
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
100 68 0.78
101 16 0.18
102 3 0.03
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (100 bp):
TATCTAATATTAATATTACACCCTTTGTAATCATGCTCTTGGATTATATCTATCTAATATTAATA
TAAACTTCTTTATAATTATGCTCTTGGATTATGTC
Found at i:13261828 original size:27 final size:27
Alignment explanation
Indices: 13261797--13261857 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
13261787 CTAATAAAAA
* *
13261797 ATTAATTTTAAATATTTTTTAAGA-TCT
1 ATTAATTATAAATA-CTTTTAAGATTCT
*
13261824 ATTAAATATAAATACTTTTAAGATTCT
1 ATTAATTATAAATACTTTTAAGATTCT
13261851 A-TAATTA
1 ATTAATTA
13261858 ATTTTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 13 0.45
27 16 0.55
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (27 bp):
ATTAATTATAAATACTTTTAAGATTCT
Found at i:13262757 original size:14 final size:14
Alignment explanation
Indices: 13262718--13262760 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
13262708 TAGTCATTAA
13262718 TTAATATTAAAAAT
1 TTAATATTAAAAAT
* *
13262732 TT-TTCATAAAAAAT
1 TTAAT-ATTAAAAAT
13262746 TTAATATTAAAAAT
1 TTAATATTAAAAAT
13262760 T
1 T
13262761 GGATGGAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
13 1 0.04
14 21 0.91
15 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (14 bp):
TTAATATTAAAAAT
Found at i:13264490 original size:16 final size:15
Alignment explanation
Indices: 13264462--13264503 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
13264452 TAAGTGTTAA
13264462 AATATTAAAAATTATTT
1 AATATT-AAAATTA-TT
*
13264479 ATTATTAAAATTATT
1 AATATTAAAATTATT
13264494 AATATTAAAA
1 AATATTAAAA
13264504 AAATCATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 11 0.48
16 7 0.30
17 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATTAAAATTATT
Found at i:13264504 original size:16 final size:17
Alignment explanation
Indices: 13264462--13264504 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
13264452 TAAGTGTTAA
13264462 AATATTAAAAATTATTT
1 AATATTAAAAATTATTT
*
13264479 ATTATT-AAAATTA-TT
1 AATATTAAAAATTATTT
13264494 AATATTAAAAA
1 AATATTAAAAA
13264505 AATCATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 11 0.48
17 5 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATTAAAAATTATTT
Found at i:13264646 original size:17 final size:17
Alignment explanation
Indices: 13264626--13264712 Score: 52
Period size: 17 Copynumber: 4.9 Consensus size: 17
13264616 ATTATAATTC
13264626 TTAAAATATTATTTTTA
1 TTAAAATATTATTTTTA
* * *
13264643 TTAATATAATAATATTTA
1 TTAAAAT-ATTATTTTTA
* *
13264661 -AAATAATAATATTTATTA
1 TTAA-AATATTATTT-TTA
**
13264679 TTAAAATATT-TATACTA
1 TTAAAATATTAT-TTTTA
13264696 TTAAAATAGTTATTTTT
1 TTAAAATA-TTATTTTT
13264713 GTATTGAAAG
Statistics
Matches: 49, Mismatches: 14, Indels: 13
0.64 0.18 0.17
Matches are distributed among these distances:
17 23 0.47
18 23 0.47
19 3 0.06
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (17 bp):
TTAAAATATTATTTTTA
Found at i:13264661 original size:15 final size:15
Alignment explanation
Indices: 13264643--13264690 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 15
13264633 ATTATTTTTA
13264643 TTAATATAATAATAT
1 TTAATATAATAATAT
*
13264658 TTAAAATAATAATAT
1 TTAATATAATAATAT
*
13264673 TTATTATTAA-AATAT
1 TTAATA-TAATAATAT
13264688 TTA
1 TTA
13264691 TACTATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 26 0.90
16 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAATATAATAATAT
Found at i:13264691 original size:15 final size:15
Alignment explanation
Indices: 13264668--13264709 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
13264658 TTAAAATAAT
13264668 AATATTTATTATTAA
1 AATATTTATTATTAA
13264683 AATATTTATACTATTAA
1 AATATTTAT--TATTAA
*
13264700 AATAGTTATT
1 AATATTTATT
13264710 TTTGTATTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 10 0.42
17 14 0.58
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (15 bp):
AATATTTATTATTAA
Found at i:13264876 original size:20 final size:20
Alignment explanation
Indices: 13264847--13264903 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
13264837 AATAAATTAT
13264847 TAAAAATATTCATTTTATGA
1 TAAAAATATTCATTTTATGA
* *
13264867 -AAATAATATT-GTTTTATTA
1 TAAA-AATATTCATTTTATGA
*
13264886 TGAAAATATTCATTTTAT
1 TAAAAATATTCATTTTAT
13264904 TATATTATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (20 bp):
TAAAAATATTCATTTTATGA
Found at i:13264888 original size:22 final size:24
Alignment explanation
Indices: 13264861--13264921 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
13264851 AATATTCATT
13264861 TTATGAAAATAATATTGT-TT-TA
1 TTATGAAAATAATATTGTATTATA
* *
13264883 TTATGAAAATATTCATTTTATTATA
1 TTATGAAAATAAT-ATTGTATTATA
*
13264908 TTATTAAAATAATA
1 TTATGAAAATAATA
13264922 AAAATGATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 12 0.38
23 4 0.12
24 3 0.09
25 13 0.41
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (24 bp):
TTATGAAAATAATATTGTATTATA
Found at i:13264904 original size:20 final size:20
Alignment explanation
Indices: 13264842--13264907 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
13264832 ATAAAAATAA
13264842 ATTATTAAAAATATTCATTTT
1 ATTA-TAAAAATATTCATTTT
* *
13264863 ATGA-AAATAATATT-GTTTT
1 ATTATAAA-AATATTCATTTT
*
13264882 ATTATGAAAATATTCATTTT
1 ATTATAAAAATATTCATTTT
13264902 ATTATA
1 ATTATA
13264908 TTATTAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 16 0.44
20 17 0.47
21 3 0.08
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
ATTATAAAAATATTCATTTT
Found at i:13265640 original size:19 final size:19
Alignment explanation
Indices: 13265618--13265662 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
13265608 TTTTTTACAA
*
13265618 ATATTTTCA-TTTCTTATAT
1 ATATTTTAATTTTCTT-TAT
13265637 ATATTTTAATTTTTCTTTAT
1 ATATTTTAA-TTTTCTTTAT
13265657 ATATTT
1 ATATTT
13265663 ATTTTAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 9 0.39
21 6 0.26
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (19 bp):
ATATTTTAATTTTCTTTAT
Found at i:13265665 original size:24 final size:24
Alignment explanation
Indices: 13265632--13265679 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
13265622 TTTCATTTCT
* *
13265632 TATATATATTTTAATTTTTCTTTA
1 TATATATATTTTAATGTTACTTTA
*
13265656 TATATTTATTTTAATGTTACTTTA
1 TATATATATTTTAATGTTACTTTA
13265680 AATACTAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (24 bp):
TATATATATTTTAATGTTACTTTA
Found at i:13265896 original size:3 final size:3
Alignment explanation
Indices: 13265884--13265923 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
13265874 AAAAGTAATA
13265884 ATT ATT -TT 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
13265924 CATCAAAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:13277689 original size:2 final size:2
Alignment explanation
Indices: 13277682--13277717 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
13277672 TGCCCTTATT
13277682 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
13277718 AAAGATGGAT
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):
TA
Found at i:13280475 original size:17 final size:17
Alignment explanation
Indices: 13280453--13280488 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
13280443 TATTTCTACT
*
13280453 AAAACTTGCTTTATTCA
1 AAAACTTGCGTTATTCA
13280470 AAAACTTGCGTTATTCA
1 AAAACTTGCGTTATTCA
13280487 AA
1 AA
13280489 TAGATAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (17 bp):
AAAACTTGCGTTATTCA
Found at i:13288934 original size:15 final size:15
Alignment explanation
Indices: 13288916--13288953 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
13288906 TTATTATTTT
13288916 TATTTA-ATATAGTAG
1 TATTTATATATA-TAG
*
13288931 TATTTATATATATTG
1 TATTTATATATATAG
13288946 TATTTATA
1 TATTTATA
13288954 AAACATCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (15 bp):
TATTTATATATATAG
Found at i:13292761 original size:5 final size:5
Alignment explanation
Indices: 13292751--13292775 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
13292741 ATAAATAGAG
13292751 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
13292776 ACTAAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:13293520 original size:100 final size:101
Alignment explanation
Indices: 13293339--13293531 Score: 307
Period size: 100 Copynumber: 1.9 Consensus size: 101
13293329 ATAAATAGAA
13293339 TATAAATATGCACTAAACTATATTTTTATTTAGTTTTTTATAAAAAAAAATTGACTAATGAATGG
1 TATAAATATGCACTAAACTATATTTTTATTTAGTTTTTTATAAAAAAAAATTGACTAATGAATGG
*
13293404 TTTGGTTCAAGCACGATAAGCATTTTTAGAATAAAT
66 TTTGGTTCAAGCACGATAAACATTTTTAGAATAAAT
* * * * *
13293440 TATAAATATGTACTAAACTATCTTTTTATTTAG-TTTTTATTATAAAAAATTGACTGATGAATGG
1 TATAAATATGCACTAAACTATATTTTTATTTAGTTTTTTATAAAAAAAAATTGACTAATGAATGG
* *
13293504 TTTGGTTCAAGTACGATAAATATTTTTA
66 TTTGGTTCAAGCACGATAAACATTTTTA
13293532 AAGGAGATCA
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
100 53 0.63
101 31 0.37
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (101 bp):
TATAAATATGCACTAAACTATATTTTTATTTAGTTTTTTATAAAAAAAAATTGACTAATGAATGG
TTTGGTTCAAGCACGATAAACATTTTTAGAATAAAT
Found at i:13294360 original size:32 final size:31
Alignment explanation
Indices: 13294318--13294391 Score: 76
Period size: 32 Copynumber: 2.4 Consensus size: 31
13294308 TTAACTCTTG
* * *
13294318 AAAAACAAAATATCAATATCGAAATCCATTA
1 AAAAATAAAATATAAAAATCGAAATCCATTA
* **
13294349 CAAAAATAAAATGTAAAAATTTAAATCCATTA
1 -AAAAATAAAATATAAAAATCGAAATCCATTA
*
13294381 AAAATTAAAAT
1 AAAAATAAAAT
13294392 CCAAAATAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
31 10 0.29
32 25 0.71
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.26
Consensus pattern (31 bp):
AAAAATAAAATATAAAAATCGAAATCCATTA
Found at i:13294384 original size:17 final size:17
Alignment explanation
Indices: 13294362--13294394 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
13294352 AAATAAAATG
*
13294362 TAAAAATTTAAATCCAT
1 TAAAAATTAAAATCCAT
13294379 TAAAAATTAAAATCCA
1 TAAAAATTAAAATCCA
13294395 AAATAAACCA
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:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAAAATTAAAATCCAT
Found at i:13298325 original size:18 final size:19
Alignment explanation
Indices: 13298302--13298341 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
13298292 ACATTAAAAG
*
13298302 AAAAATTCA-AAAAATTTT
1 AAAAATTCATAAAAATTCT
13298320 AAAAATTCATAAAAATTCT
1 AAAAATTCATAAAAATTCT
13298339 AAA
1 AAA
13298342 TTTTTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAATTCATAAAAATTCT
Found at i:13298341 original size:9 final size:9
Alignment explanation
Indices: 13298302--13298341 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
13298292 ACATTAAAAG
*
13298302 AAAAATTCA
1 AAAAATTCT
*
13298311 AAAAATTTT
1 AAAAATTCT
13298320 AAAAATTCAT
1 AAAAATTC-T
13298330 AAAAATTCT
1 AAAAATTCT
13298339 AAA
1 AAA
13298342 TTTTTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAAATTCT
Found at i:13298362 original size:20 final size:21
Alignment explanation
Indices: 13298329--13298367 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
13298319 TAAAAATTCA
13298329 TAAAAATTCTAAAT-TTTTTT
1 TAAAAATTCTAAATATTTTTT
13298349 TAAAAATT-TGAAATATTTT
1 TAAAAATTCT-AAATATTTT
13298368 AAAAAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 12 0.71
21 4 0.24
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (21 bp):
TAAAAATTCTAAATATTTTTT
Found at i:13298425 original size:32 final size:34
Alignment explanation
Indices: 13298379--13298441 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 34
13298369 AAAAATTATA
* *
13298379 AAAAATTTATGAAAC-T-AAAATATTAAAAAAAT
1 AAAAATTAAGGAAACTTAAAAATATTAAAAAAAT
*
13298411 AAAAATTAAGGAAACTTAAAAATTTTAAAAA
1 AAAAATTAAGGAAACTTAAAAATATTAAAAA
13298442 CTCAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 13 0.50
33 1 0.04
34 12 0.46
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (34 bp):
AAAAATTAAGGAAACTTAAAAATATTAAAAAAAT
Found at i:13298490 original size:18 final size:18
Alignment explanation
Indices: 13298467--13298505 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
13298457 AATAATCCAA
*
13298467 AAAATTCAAAAAAAATTG
1 AAAATTCAAAAAAAATAG
* *
13298485 AAAATTTAATAAAAATAG
1 AAAATTCAAAAAAAATAG
13298503 AAA
1 AAA
13298506 TTTCTTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (18 bp):
AAAATTCAAAAAAAATAG
Found at i:13298695 original size:30 final size:28
Alignment explanation
Indices: 13298659--13298738 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 28
13298649 TTAAAATTTT
13298659 AAATTTTATATATTTTTGAATTTTTCAAT-A
1 AAATTTTATAT-TTTTTGAATTTTT--ATGA
* **
13298689 AAATTTTCAAATTTTTTTTATTTTTATGA
1 AAATTTT-ATATTTTTTGAATTTTTATGA
13298718 AAATTTTAT-TTTTTTGAATTT
1 AAATTTTATATTTTTTGAATTT
13298739 AAAAAAAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
27 10 0.24
28 3 0.07
29 8 0.19
30 18 0.43
31 3 0.07
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.61
Consensus pattern (28 bp):
AAATTTTATATTTTTTGAATTTTTATGA
Found at i:13298785 original size:19 final size:19
Alignment explanation
Indices: 13298763--13298833 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
13298753 TTTTTTATAT
13298763 AATTTTTAGATTTTTTCAA
1 AATTTTTAGATTTTTTCAA
13298782 AATTTTTAGATTTTTT--A
1 AATTTTTAGATTTTTTCAA
* * *
13298799 AATTTTAAAATATTTTCAA
1 AATTTTTAGATTTTTTCAA
** *
13298818 AAAATTTGGATTTTTT
1 AATTTTTAGATTTTTT
13298834 ATTTTTAGTT
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
17 14 0.34
19 27 0.66
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (19 bp):
AATTTTTAGATTTTTTCAA
Found at i:13298943 original size:20 final size:21
Alignment explanation
Indices: 13298906--13298945 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
13298896 ATTTTCATTT
13298906 TTTGAATTTTTAAGATTTTTA
1 TTTGAATTTTTAAGATTTTTA
* *
13298927 TTTG-ATTTTTCATATTTTT
1 TTTGAATTTTTAAGATTTTT
13298946 TGAATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.03, G:0.07, T:0.68
Consensus pattern (21 bp):
TTTGAATTTTTAAGATTTTTA
Found at i:13299007 original size:28 final size:25
Alignment explanation
Indices: 13298933--13299009 Score: 64
Period size: 28 Copynumber: 2.8 Consensus size: 25
13298923 TTTATTTGAT
*
13298933 TTTTCATATTTTTTGAATTTTAAAAA
1 TTTTCATA-TTTTTGATTTTTAAAAA
* *
13298959 TTATCATAAATTTTATAATTTTTAAAAAA
1 TTTTCAT--ATTTT-TGATTTTT-AAAAA
13298988 TATTTCATATTATTTGATTTTT
1 T-TTTCATATT-TTTGATTTTT
13299010 TATAATATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
26 6 0.15
27 4 0.10
28 17 0.43
29 8 0.20
30 5 0.12
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (25 bp):
TTTTCATATTTTTGATTTTTAAAAA
Found at i:13299123 original size:24 final size:24
Alignment explanation
Indices: 13299096--13299141 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
13299086 AAATTTAAAA
*
13299096 ATTTAAAATTTTTTGTATTTTTGT
1 ATTTAAAATTTTTTATATTTTTGT
**
13299120 ATTTTTAATTTTTTATATTTTT
1 ATTTAAAATTTTTTATATTTTT
13299142 TTTATGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (24 bp):
ATTTAAAATTTTTTATATTTTTGT
Found at i:13308413 original size:42 final size:42
Alignment explanation
Indices: 13308366--13308450 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
13308356 AGTGAAATCT
13308366 TTTTAAAAGGTTGTAGATGGGAAATGCAATTTTCAAAGGTTA
1 TTTTAAAAGGTTGTAGATGGGAAATGCAATTTTCAAAGGTTA
*
13308408 TTTTAAAATGTTGTAGATGGGAAATGCAATTTTCAAAGGTTA
1 TTTTAAAAGGTTGTAGATGGGAAATGCAATTTTCAAAGGTTA
13308450 T
1 T
13308451 GAATGAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (42 bp):
TTTTAAAAGGTTGTAGATGGGAAATGCAATTTTCAAAGGTTA
Found at i:13308476 original size:30 final size:30
Alignment explanation
Indices: 13308442--13308500 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
13308432 TGCAATTTTC
13308442 AAAGGTTATGAATGAAAATGAAACATTAAT
1 AAAGGTTATGAATGAAAATGAAACATTAAT
* * *
13308472 AAAGGTTGTGGATGAAAATGAAATATTAA
1 AAAGGTTATGAATGAAAATGAAACATTAA
13308501 CAAAAGTCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.51, C:0.02, G:0.20, T:0.27
Consensus pattern (30 bp):
AAAGGTTATGAATGAAAATGAAACATTAAT
Found at i:13308515 original size:30 final size:30
Alignment explanation
Indices: 13308453--13308515 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
13308443 AAGGTTATGA
* * * *
13308453 ATGAAAATGAAACATTAATAAAGGTTGTGG
1 ATGAAAATGAAACATTAACAAAAGTCGCGG
*
13308483 ATGAAAATGAAATATTAACAAAAGTCGCGG
1 ATGAAAATGAAACATTAACAAAAGTCGCGG
13308513 ATG
1 ATG
13308516 CTACATGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.24
Consensus pattern (30 bp):
ATGAAAATGAAACATTAACAAAAGTCGCGG
Found at i:13310449 original size:2 final size:2
Alignment explanation
Indices: 13310442--13310475 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13310432 GTGGGAGGAG
13310442 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
13310476 GGAACTGTGC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13313144 original size:18 final size:18
Alignment explanation
Indices: 13313107--13313140 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13313097 CTATGCTTGA
*
13313107 TTAATTTTGAGTATGATG
1 TTAAGTTTGAGTATGATG
13313125 TTAAGTTTG-GTATGAT
1 TTAAGTTTGAGTATGAT
13313141 TGTTTCTTTA
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:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (18 bp):
TTAAGTTTGAGTATGATG
Found at i:13314398 original size:4 final size:4
Alignment explanation
Indices: 13314391--13314429 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
13314381 TATATATATA
13314391 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
13314430 AAAAGATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:13316839 original size:41 final size:41
Alignment explanation
Indices: 13316772--13316856 Score: 143
Period size: 41 Copynumber: 2.1 Consensus size: 41
13316762 ACAAAATTTA
* *
13316772 CATAGTAAACAAGCCTTGATGCCATTTGTTTTCTACTTTCT
1 CATAATAAACAAGCCTTGATGCCATTTATTTTCTACTTTCT
*
13316813 CATAATAAAGAAGCCTTGATGCCATTTATTTTCTACTTTCT
1 CATAATAAACAAGCCTTGATGCCATTTATTTTCTACTTTCT
13316854 CAT
1 CAT
13316857 TCCTTTCAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.41
Consensus pattern (41 bp):
CATAATAAACAAGCCTTGATGCCATTTATTTTCTACTTTCT
Found at i:13320347 original size:2 final size:2
Alignment explanation
Indices: 13320340--13320366 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13320330 GAGAAACTTG
13320340 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
13320367 TGAAACTTAT
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:13328509 original size:2 final size:2
Alignment explanation
Indices: 13328504--13328536 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
13328494 TTATCCTACA
13328504 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
13328537 GAACGCTTCC
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:13336942 original size:18 final size:17
Alignment explanation
Indices: 13336907--13336941 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13336897 TAGATCTGGA
13336907 TATTTGTTAGATGATTT
1 TATTTGTTAGATGATTT
13336924 TATTATGTTAGAT-ATTT
1 TATT-TGTTAGATGATTT
13336941 T
1 T
13336942 TTCTTACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (17 bp):
TATTTGTTAGATGATTT
Found at i:13339337 original size:18 final size:20
Alignment explanation
Indices: 13339300--13339337 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
13339290 GATATGAATT
13339300 TTTAGAAAAAAAAATCTTGA
1 TTTAGAAAAAAAAATCTTGA
13339320 TTTA-AAAAAAAAAT-TTGA
1 TTTAGAAAAAAAAATCTTGA
13339338 AGTTTTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (20 bp):
TTTAGAAAAAAAAATCTTGA
Found at i:13343987 original size:119 final size:119
Alignment explanation
Indices: 13343776--13344006 Score: 435
Period size: 119 Copynumber: 1.9 Consensus size: 119
13343766 ATTATACTCT
13343776 TGTGATTAAATACATGTATGTGAATTTCATTATGCATATTACACTTGATTATATGCATTCATTAT
1 TGTGATTAAATACATGTATGTGAATTTCATTATGCATATTACACTTGATTATATGCATTCATTAT
* *
13343841 ACTCATGATGTTATTGGTATCATGTATTTTGTCCCATATCTTGAATTTCATGTA
66 AATCATGATGTTATTGGTATCATGTATTTTGTCCCATACCTTGAATTTCATGTA
13343895 TGTGATTAAATACATGTATGTGAATTTCATTATGCATATTACACTTGATTATATGCATTCATTAT
1 TGTGATTAAATACATGTATGTGAATTTCATTATGCATATTACACTTGATTATATGCATTCATTAT
*
13343960 AATCATGATGTTATTGGTATTATGTATTTTGTCCCATACCTTGAATT
66 AATCATGATGTTATTGGTATCATGTATTTTGTCCCATACCTTGAATT
13344007 GATCTGTCTT
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
119 109 1.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.45
Consensus pattern (119 bp):
TGTGATTAAATACATGTATGTGAATTTCATTATGCATATTACACTTGATTATATGCATTCATTAT
AATCATGATGTTATTGGTATCATGTATTTTGTCCCATACCTTGAATTTCATGTA
Found at i:13350107 original size:35 final size:36
Alignment explanation
Indices: 13350014--13350108 Score: 101
Period size: 35 Copynumber: 2.7 Consensus size: 36
13350004 TTGATGAGCC
* *
13350014 ATTATAGTAATTTTGATCGATTATGATAAAAGGAGT
1 ATTATAATAATTTTAATCGATTATGATAAAAGGAGT
*
13350050 ATTATAAT-ATTTTAATCAATTAT-AGTAGAAA-GA-T
1 ATTATAATAATTTTAATCGATTATGA-TA-AAAGGAGT
13350084 ATTATAATAATTTT-ATCCGATTATG
1 ATTATAATAATTTTAAT-CGATTATG
13350109 GGAATGGGGG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
34 12 0.24
35 28 0.56
36 10 0.20
ACGTcount: A:0.41, C:0.04, G:0.13, T:0.42
Consensus pattern (36 bp):
ATTATAATAATTTTAATCGATTATGATAAAAGGAGT
Found at i:13350806 original size:186 final size:188
Alignment explanation
Indices: 13350480--13350853 Score: 477
Period size: 186 Copynumber: 2.0 Consensus size: 188
13350470 ATATCAATAT
** * * **
13350480 TCTATATATTAAAAGTATCCCTAAAAGTTTAGTTTAGGGAGTTGACAGTTGTCTTGGCTTATAGG
1 TCTATATATTAAAAGTATCCCTAAAAG--T-GTTTAGGGAGTTGACAACTATCCTAACTTATAGG
* * *
13350545 TTTTGTGAGCTTTGAGGTATGAGAGACAGGTCTATGTTTAACTATTTGTATTTTTTGGGTGTTGT
63 TTTTGTGAGCTTTGAGGTATGAGAGACAGGTCTATGTTTAACTACTTATATTTTTTGGGTGTGGT
* ** *
13350610 GAGCTTTAGAGTTTATGGTTTCTTAGTTATTGTTTATTGGGTTGTTTTAAATTGTTAATGC
128 GAGCTTTAGAGCTTATGGGATCTTAGTTATTGTTTATTGGGTTGCTTTAAATTGTTAATGC
13350671 TCTATATATTAAAAGTATCCCT-AAAG-GTTTAGGGAGTTGACAACTATCCTAACTTAT-GAGTT
1 TCTATATATTAAAAGTATCCCTAAAAGTGTTTAGGGAGTTGACAACTATCCTAACTTATAG-GTT
* ** * *
13350733 TTGTGGGCTTTGAGGTATGAGA-AGTGGTTCTATGTTTGACTGCTTATATTTTTTGGGTGTGGTG
65 TTGTGAGCTTTGAGGTATGAGAGACAGG-TCTATGTTTAACTACTTATATTTTTTGGGTGTGGTG
* * * *
13350797 GGTTTTAGAGCTTGTGGGATCTTAGTTATTGTTTATTGGTTTGCTTTAAATTGTTAA
129 AGCTTTAGAGCTTATGGGATCTTAGTTATTGTTTATTGGGTTGCTTTAAATTGTTAA
13350854 ATGAAAGCCC
Statistics
Matches: 159, Mismatches: 22, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
185 4 0.03
186 129 0.81
190 4 0.03
191 22 0.14
ACGTcount: A:0.22, C:0.08, G:0.25, T:0.45
Consensus pattern (188 bp):
TCTATATATTAAAAGTATCCCTAAAAGTGTTTAGGGAGTTGACAACTATCCTAACTTATAGGTTT
TGTGAGCTTTGAGGTATGAGAGACAGGTCTATGTTTAACTACTTATATTTTTTGGGTGTGGTGAG
CTTTAGAGCTTATGGGATCTTAGTTATTGTTTATTGGGTTGCTTTAAATTGTTAATGC
Found at i:13352317 original size:12 final size:12
Alignment explanation
Indices: 13352300--13352324 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13352290 TAAATGAAAA
13352300 AATTAAATATTT
1 AATTAAATATTT
13352312 AATTAAATATTT
1 AATTAAATATTT
13352324 A
1 A
13352325 TTATTAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AATTAAATATTT
Found at i:13354066 original size:29 final size:29
Alignment explanation
Indices: 13354032--13354094 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
13354022 AGAAATTTTC
13354032 AAAAATTCAAAAAAATTTAAAAAATATAT
1 AAAAATTCAAAAAAATTTAAAAAATATAT
* *** * *
13354061 CAAAATTTTCAAAAATTTTAAAAATTTAT
1 AAAAATTCAAAAAAATTTAAAAAATATAT
13354090 AAAAA
1 AAAAA
13354095 AAATCCAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (29 bp):
AAAAATTCAAAAAAATTTAAAAAATATAT
Found at i:13354075 original size:10 final size:10
Alignment explanation
Indices: 13354024--13354087 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
13354014 GTATTACAAG
13354024 AAATTTTCAA
1 AAATTTTCAA
13354034 AAA--TTCAAA
1 AAATTTTC-AA
* *
13354043 AAAATTTAAA
1 AAATTTTCAA
*
13354053 AAATATATC-A
1 AAAT-TTTCAA
13354063 AAATTTTCAA
1 AAATTTTCAA
13354073 AAATTTT-AA
1 AAATTTTCAA
13354082 AAATTT
1 AAATTT
13354088 ATAAAAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
8 3 0.07
9 16 0.36
10 21 0.48
11 4 0.09
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (10 bp):
AAATTTTCAA
Found at i:13354092 original size:10 final size:10
Alignment explanation
Indices: 13354032--13354094 Score: 60
Period size: 10 Copynumber: 6.5 Consensus size: 10
13354022 AGAAATTTTC
* *
13354032 AAAAATTCAA
1 AAAAATTTAT
13354042 AAAAATTTA-
1 AAAAATTTAT
*
13354051 AAAAATATAT
1 AAAAATTTAT
*
13354061 CAAAATTT-T
1 AAAAATTTAT
13354070 CAAAAATTT-T
1 -AAAAATTTAT
13354080 AAAAATTTAT
1 AAAAATTTAT
13354090 AAAAA
1 AAAAA
13354095 AAATCCAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 17 0.38
10 28 0.62
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:13354094 original size:19 final size:20
Alignment explanation
Indices: 13354024--13354087 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 20
13354014 GTATTACAAG
*
13354024 AAATTTTCAAAAATTCA-AA
1 AAATTTTCAAAAATTTATAA
* * * *
13354043 AAAATTTAAAAAATATATCA
1 AAATTTTCAAAAATTTATAA
13354063 AAATTTTCAAAAATTT-TAA
1 AAATTTTCAAAAATTTATAA
13354082 AAATTT
1 AAATTT
13354088 ATAAAAAAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 21 0.60
20 14 0.40
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (20 bp):
AAATTTTCAAAAATTTATAA
Found at i:13354596 original size:18 final size:18
Alignment explanation
Indices: 13354570--13354614 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
13354560 AAATATCTAC
13354570 AAAAATTTT-AAAAATCAT
1 AAAAATTTTAAAAAATC-T
*
13354588 AAGAATTTTAAAAAATCT
1 AAAAATTTTAAAAAATCT
13354606 AAAAATTTT
1 AAAAATTTT
13354615 TCCAAAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (18 bp):
AAAAATTTTAAAAAATCT
Found at i:13354615 original size:19 final size:20
Alignment explanation
Indices: 13354564--13354653 Score: 64
Period size: 20 Copynumber: 4.6 Consensus size: 20
13354554 ATCCACAAAT
*
13354564 ATCTACAAAAATTTT-AAAA
1 ATCTACAAAATTTTTAAAAA
*
13354583 ATCATA-AGAA-TTTTAAAAA
1 ATC-TACAAAATTTTTAAAAA
*
13354602 ATCTA-AAAATTTTTCCAAAA
1 ATCTACAAAATTTTT-AAAAA
* *
13354622 ATC-AGAAATATTTTTAAATA
1 ATCTACAAA-ATTTTTAAAAA
*
13354642 ATCAACAAAATT
1 ATCTACAAAATT
13354654 GAAAAAGAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
18 9 0.16
19 18 0.31
20 21 0.36
21 10 0.17
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.33
Consensus pattern (20 bp):
ATCTACAAAATTTTTAAAAA
Found at i:13354975 original size:18 final size:17
Alignment explanation
Indices: 13354954--13355003 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
13354944 AATTTTATAA
*
13354954 AATTTTTCATATCTTTTG
1 AATTTTTCATAT-TTTTC
**
13354972 AATTTTTGTTATTTTTC
1 AATTTTTCATATTTTTC
13354989 AATTTTTCA-ATTTTT
1 AATTTTTCATATTTTT
13355004 TTAATATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 6 0.22
17 11 0.41
18 10 0.37
ACGTcount: A:0.22, C:0.08, G:0.04, T:0.66
Consensus pattern (17 bp):
AATTTTTCATATTTTTC
Found at i:13355027 original size:35 final size:35
Alignment explanation
Indices: 13354939--13355028 Score: 85
Period size: 34 Copynumber: 2.5 Consensus size: 35
13354929 TATTTTTGAC
* *
13354939 TTTTTAATTTTATAAAATTTTTCATATCTTTTGAATT
1 TTTTT-ATTTTA-ACAATTTTTCATATCTTTTGAATA
* * *
13354976 TTTGTTATTTT-TCAATTTTTCA-ATTTTTTTAATA
1 TTT-TTATTTTAACAATTTTTCATATCTTTTGAATA
13355010 TTTTTACTTTTAACAATTT
1 TTTTTA-TTTTAACAATTT
13355029 GTTTTTGAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
33 3 0.07
34 16 0.36
35 15 0.34
37 8 0.18
38 2 0.05
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.64
Consensus pattern (35 bp):
TTTTTATTTTAACAATTTTTCATATCTTTTGAATA
Found at i:13355100 original size:17 final size:17
Alignment explanation
Indices: 13355052--13355092 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
13355042 TTGGATTTCT
** *
13355052 AATTTTATTTTTTTCAA
1 AATTTTATAATTTTGAA
13355069 AATTTTATAATTTTGAA
1 AATTTTATAATTTTGAA
13355086 AATTTTA
1 AATTTTA
13355093 AACTTTTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (17 bp):
AATTTTATAATTTTGAA
Found at i:13355205 original size:16 final size:17
Alignment explanation
Indices: 13355174--13355206 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
13355164 AAACATTTAA
*
13355174 ATTTTCTTAAATATTTT
1 ATTTTCTTAAAAATTTT
13355191 ATTTT-TTAAAAATTTT
1 ATTTTCTTAAAAATTTT
13355207 TTAAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTCTTAAAAATTTT
Found at i:13357036 original size:12 final size:12
Alignment explanation
Indices: 13357019--13357045 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
13357009 ATCTATCTCC
13357019 TCTTAAAATTCT
1 TCTTAAAATTCT
13357031 TCTTAAAATTCT
1 TCTTAAAATTCT
13357043 TCT
1 TCT
13357046 CTTGTAAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.52
Consensus pattern (12 bp):
TCTTAAAATTCT
Found at i:13357138 original size:52 final size:52
Alignment explanation
Indices: 13357027--13357159 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
13357017 CCTCTTAAAA
* * *
13357027 TTCTTCTTAAAATTCTTCTCTTGTAAGTCAAATTTGCTTATTAAAAATCACTT
1 TTCTT-TTAAAATTCTTCTCTTGCAAGTCAAACTTACTTATTAAAAATCACTT
* * * * ***
13357080 TACTTTTATAATTCTTCTCTTGCAAGTCAAACTTATTTATTAAGAATTTTTT
1 TTCTTTTAAAATTCTTCTCTTGCAAGTCAAACTTACTTATTAAAAATCACTT
* * * *
13357132 TTCTTTTAGAATTTTTCTTTTACAAGTC
1 TTCTTTTAAAATTCTTCTCTTGCAAGTC
13357160 TTATTATCTA
Statistics
Matches: 65, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
52 61 0.94
53 4 0.06
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (52 bp):
TTCTTTTAAAATTCTTCTCTTGCAAGTCAAACTTACTTATTAAAAATCACTT
Found at i:13357199 original size:11 final size:12
Alignment explanation
Indices: 13357183--13357215 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
13357173 AGCAATATCT
13357183 AACAAATCTC-A
1 AACAAATCTCTA
13357194 AACAAAT-TCTA
1 AACAAATCTCTA
13357205 AACAAATCTCT
1 AACAAATCTCT
13357216 TATGAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 2 0.10
11 15 0.75
12 3 0.15
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (12 bp):
AACAAATCTCTA
Found at i:13357649 original size:16 final size:15
Alignment explanation
Indices: 13357630--13357680 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
13357620 GACGAATTCA
13357630 ATTTAAATTTGAATT
1 ATTTAAATTTGAATT
*
13357645 GATTTAAATTTAAATT
1 -ATTTAAATTTGAATT
*
13357661 ATTTTAAATTTGAATC
1 A-TTTAAATTTGAATT
13357677 ATTT
1 ATTT
13357681 CGTTCTCGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 4 0.13
16 27 0.87
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (15 bp):
ATTTAAATTTGAATT
Found at i:13361363 original size:3 final size:3
Alignment explanation
Indices: 13361355--13361398 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
13361345 CATAATGTAT
13361355 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA T
13361399 GTTAATTTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:13361406 original size:25 final size:25
Alignment explanation
Indices: 13361353--13361406 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
13361343 ATCATAATGT
*
13361353 ATTTATTATTATTATTATTATTATT
1 ATTTATTATTATTATTATTATTATA
13361378 ATTTATTATTATTATTATTATGT-TA
1 ATTTATTATTATTATTATTAT-TATA
13361403 ATTT
1 ATTT
13361407 TCCAGTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
ATTTATTATTATTATTATTATTATA
Found at i:13361487 original size:2 final size:2
Alignment explanation
Indices: 13361480--13361512 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
13361470 ATACAAGGGT
*
13361480 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13361513 TGCTAGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13364424 original size:31 final size:30
Alignment explanation
Indices: 13364380--13364445 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
13364370 TCAACACCTC
*
13364380 AAAAATATTTAAATTTAACTAATTAAATTA
1 AAAAATACTTAAATTTAACTAATTAAATTA
* * *
13364410 AAAAATTACTTAAATTTAAGTGATTAAGTTA
1 AAAAA-TACTTAAATTTAACTAATTAAATTA
13364441 AAAAA
1 AAAAA
13364446 ATTAATAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAAATACTTAAATTTAACTAATTAAATTA
Found at i:13366282 original size:84 final size:84
Alignment explanation
Indices: 13366073--13366342 Score: 335
Period size: 84 Copynumber: 3.2 Consensus size: 84
13366063 TTTTACGATG
* *
13366073 CATGTATATTGCATTCCA-AACTCCTATCAACAGCTCTCCAACAAATCTATAACATTCAGACTTC
1 CATGTATATTGCATT-CAGAACTGCTATCAACAGCTTTCCAACAAATCTATAACATTCAGACTTC
13366137 CTGATTGAAGCATACGAATATATA
65 CTGATTGAAGCAT--GAA-A-ATA
* * ** * * * * *
13366161 TATGTATATTGTATTCAGAAGAGCTATCAACAACTTTCCGACAAGTCTCTAACATTCAGACTTCT
1 CATGTATATTGCATTCAGAACTGCTATCAACAGCTTTCCAACAAATCTATAACATTCAGACTTCC
*
13366226 TGATTGAAGCATGAGAATA
66 TGATTGAAGCATGAAAATA
* *
13366245 CATGTATATTGCATTCAGAATTGCTATCAACAGCTTTCCAACAAATCTATAACATTTAGACTTCC
1 CATGTATATTGCATTCAGAACTGCTATCAACAGCTTTCCAACAAATCTATAACATTCAGACTTCC
* *
13366310 TGATCGGAGCATGAAAATA
66 TGATTGAAGCATGAAAATA
*
13366329 AATGTATATTGCAT
1 CATGTATATTGCAT
13366343 GTTCTGCACT
Statistics
Matches: 155, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
84 87 0.56
85 1 0.01
86 2 0.01
87 2 0.01
88 63 0.41
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (84 bp):
CATGTATATTGCATTCAGAACTGCTATCAACAGCTTTCCAACAAATCTATAACATTCAGACTTCC
TGATTGAAGCATGAAAATA
Found at i:13373012 original size:21 final size:22
Alignment explanation
Indices: 13372973--13373028 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
13372963 ACCAGAAATT
*
13372973 AATA-AAATATTATTTTTTTTAA
1 AATATAAATA-TATTATTTTTAA
*
13372995 AATATAAA-ATATTATTTTTTA
1 AATATAAATATATTATTTTTAA
13373016 AATATAAATATAT
1 AATATAAATATAT
13373029 AATTATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 18 0.60
22 9 0.30
23 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATAAATATATTATTTTTAA
Found at i:13373015 original size:22 final size:22
Alignment explanation
Indices: 13372974--13373028 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 22
13372964 CCAGAAATTA
13372974 ATAAAATATTATTTTTTTTAAAAT
1 ATAAAATATTA-TTTTTTT-AAAT
13372998 ATAAAATATTA-TTTTTTAAAT
1 ATAAAATATTATTTTTTTAAAT
13373019 ATAAATATAT
1 ATAAA-ATAT
13373029 AATTATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.30
22 10 0.33
24 11 0.37
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAAAATATTATTTTTTTAAAT
Found at i:13373050 original size:18 final size:18
Alignment explanation
Indices: 13373017--13373051 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13373007 TATTTTTTAA
* *
13373017 ATATAAATATATAATTAT
1 ATATAAATAAAAAATTAT
13373035 ATATAAATAAAAAATTA
1 ATATAAATAAAAAATTA
13373052 AAAAAATAAT
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATATAAATAAAAAATTAT
Found at i:13379078 original size:28 final size:27
Alignment explanation
Indices: 13379033--13379086 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 27
13379023 AAAATCTTTT
* *
13379033 ATTTTTTATTTTCATTTTCTAGAAAATA
1 ATTTTTAATTTTCATTTTATA-AAAATA
**
13379061 ATTTTTAATTTTTGTTTTATAAAAAT
1 ATTTTTAATTTTCATTTTATAAAAAT
13379087 TTAATTAGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (27 bp):
ATTTTTAATTTTCATTTTATAAAAATA
Found at i:13380318 original size:18 final size:18
Alignment explanation
Indices: 13380297--13380334 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
13380287 TTTTGTAACA
13380297 TTGTTGAT-TTGTTTATTG
1 TTGTTGATGTTG-TTATTG
*
13380315 TTGTTGTTGTTGTTATTG
1 TTGTTGATGTTGTTATTG
13380333 TT
1 TT
13380335 ACAAAAGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (18 bp):
TTGTTGATGTTGTTATTG
Found at i:13383550 original size:24 final size:24
Alignment explanation
Indices: 13383522--13383569 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
13383512 TTCAAAAATC
13383522 CATTTCCATGAATCATTTTGTATT
1 CATTTCCATGAATCATTTTGTATT
**
13383546 CATTTCTGTGAATCATTTTGTATT
1 CATTTCCATGAATCATTTTGTATT
13383570 TTCAAAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (24 bp):
CATTTCCATGAATCATTTTGTATT
Found at i:13384686 original size:13 final size:13
Alignment explanation
Indices: 13384668--13384702 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
13384658 AAAAAATAGA
13384668 TTTTATTAAAGAT
1 TTTTATTAAAGAT
13384681 TTTTATTAAAGAT
1 TTTTATTAAAGAT
13384694 TTTTATTAA
1 TTTTATTAA
13384703 TTAATAAATA
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:0.06, T:0.57
Consensus pattern (13 bp):
TTTTATTAAAGAT
Found at i:13389938 original size:14 final size:13
Alignment explanation
Indices: 13389918--13389951 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
13389908 TCTTCTTGGG
*
13389918 ATTTTTTTTGTTA
1 ATTTTTTTAGTTA
*
13389931 ATTTTTTTAGTTT
1 ATTTTTTTAGTTA
13389944 ATTTTTTT
1 ATTTTTTT
13389952 CTTCAAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (13 bp):
ATTTTTTTAGTTA
Found at i:13390943 original size:121 final size:123
Alignment explanation
Indices: 13390697--13390932 Score: 397
Period size: 121 Copynumber: 1.9 Consensus size: 123
13390687 CTGCTTTATC
*
13390697 CTCTCATAGGTGAAGTTGTTTTCATCTCTTTATCATGCATTTATGCTCATTTTTATCTATTTTTT
1 CTCTCATAGGTGAAGTTGTTTTCATCTCTTTATCAGGCATTTATGCTCATTTTTATCTATTTTTT
* *
13390762 ATATTATGAGAGCACACTGCTATTGCTTTAAAGTAAATCATTTTCATTCTAATCTGTT
66 ATATTATGAGAGAACACTGCTATTGCTTTAAAGTAAATAATTTTCATTCTAATCTGTT
* *
13390820 CTCTCATTGGTGAAGTT-TTTTCATCTCTTTATCAGGCA-TTATGTTCATTTTTATCTATTTTTT
1 CTCTCATAGGTGAAGTTGTTTTCATCTCTTTATCAGGCATTTATGCTCATTTTTATCTATTTTTT
13390883 ATATTATGA-AGGAACACTGCTATTGCTTTAAAGTAAATAATTTTCATTCT
66 ATATTATGAGA-GAACACTGCTATTGCTTTAAAGTAAATAATTTTCATTCT
13390933 GATGTTTTCT
Statistics
Matches: 107, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
120 1 0.01
121 70 0.65
122 20 0.19
123 16 0.15
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.48
Consensus pattern (123 bp):
CTCTCATAGGTGAAGTTGTTTTCATCTCTTTATCAGGCATTTATGCTCATTTTTATCTATTTTTT
ATATTATGAGAGAACACTGCTATTGCTTTAAAGTAAATAATTTTCATTCTAATCTGTT
Found at i:13393947 original size:116 final size:117
Alignment explanation
Indices: 13393741--13393975 Score: 298
Period size: 116 Copynumber: 2.0 Consensus size: 117
13393731 GTATCACTTA
* * * *
13393741 GATTAAAAATTGTTTTGGTGTAGATAGGGGGGCATTTGTTCATTTCTGATTTTAGTTTGATCCTT
1 GATTAAAAATTGTTTTGGTGTAGATA-GGGGGCATATGTTCATATCTGATATTACTTTGATCCTT
* * * *
13393806 AGCCATTTGTTAGGGAGTGATAGCTAAAGACTTGGGTGACATGTAATGTGGTG
65 AGCCATTTGTTAGGGAATGATAGCTAAAGACTCGGATGACATGTAATATGGTG
* *
13393859 GATTAAAATTTGTTTGTGGTGT-GCAT-GGGGGCATATGTTCATATCTGATATT-CTTTGATGCT
1 GATTAAAAATTGTTT-TGGTGTAG-ATAGGGGGCATATGTTCATATCTGATATTACTTTGATCCT
* *
13393921 TAGCCATTTGTT-GAGGAATGATAGCTATAGACTCGGATGACATGTAGTATGGTG
64 TAGCCATTTGTTAG-GGAATGATAGCTAAAGACTCGGATGACATGTAATATGGTG
13393975 G
1 G
13393976 TTATCCCTTA
Statistics
Matches: 102, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
115 1 0.01
116 55 0.54
117 23 0.23
118 15 0.15
119 8 0.08
ACGTcount: A:0.24, C:0.09, G:0.29, T:0.38
Consensus pattern (117 bp):
GATTAAAAATTGTTTTGGTGTAGATAGGGGGCATATGTTCATATCTGATATTACTTTGATCCTTA
GCCATTTGTTAGGGAATGATAGCTAAAGACTCGGATGACATGTAATATGGTG
Found at i:13397890 original size:3 final size:3
Alignment explanation
Indices: 13397882--13397909 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
13397872 AATAGTTTTT
13397882 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
13397910 CATTTATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:13398441 original size:11 final size:12
Alignment explanation
Indices: 13398414--13398446 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
13398404 TATTTAACCT
*
13398414 TTTTTTGTTTTA
1 TTTTTTATTTTA
13398426 TTTTTTATTTTA
1 TTTTTTATTTTA
13398438 -TTTTTATTT
1 TTTTTTATTT
13398447 AAAAGTTAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (12 bp):
TTTTTTATTTTA
Found at i:13398532 original size:8 final size:8
Alignment explanation
Indices: 13398519--13398577 Score: 57
Period size: 8 Copynumber: 7.0 Consensus size: 8
13398509 TTAACATATA
13398519 AATAATTT
1 AATAATTT
13398527 AATAATTT
1 AATAATTT
13398535 ATATTAATTT
1 A-A-TAATTT
*
13398545 ATTAATTT
1 AATAATTT
*
13398553 TATAAATGTT
1 AAT-AAT-TT
13398563 AATAATTT
1 AATAATTT
13398571 AA-AATTT
1 AATAATTT
13398578 TTATTATATA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
7 5 0.12
8 20 0.47
9 7 0.16
10 11 0.26
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (8 bp):
AATAATTT
Found at i:13398544 original size:10 final size:9
Alignment explanation
Indices: 13398520--13398601 Score: 51
Period size: 8 Copynumber: 9.9 Consensus size: 9
13398510 TAACATATAA
13398520 ATAATTTA-
1 ATAATTTAT
13398528 ATAATTTAT
1 ATAATTTAT
13398537 ATTAATTTAT
1 A-TAATTTAT
13398547 -TAATTT-T
1 ATAATTTAT
13398554 ATAAATGTTA-
1 AT-AAT-TTAT
13398564 ATAATTTA-
1 ATAATTTAT
13398572 A-AATTT-T
1 ATAATTTAT
13398579 -T-ATTATAT
1 ATAATT-TAT
13398587 ATAATTT-T
1 ATAATTTAT
13398595 -TAATTTA
1 ATAATTTA
13398602 ATGTCTTTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 26
0.70 0.00 0.30
Matches are distributed among these distances:
6 3 0.05
7 13 0.21
8 21 0.34
9 9 0.15
10 15 0.25
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (9 bp):
ATAATTTAT
Found at i:13398544 original size:18 final size:18
Alignment explanation
Indices: 13398521--13398571 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
13398511 AACATATAAA
13398521 TAATTTAATAATTTATAT
1 TAATTTAATAATTTATAT
*
13398539 TAATTTATTAATTT-TAT
1 TAATTTAATAATTTATAT
*
13398556 AAATGTTAATAATTTA
1 TAAT-TTAATAATTTA
13398572 AAATTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 6 0.21
18 22 0.79
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
TAATTTAATAATTTATAT
Found at i:13406490 original size:8 final size:8
Alignment explanation
Indices: 13406479--13406515 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
13406469 TTTTTATTTA
13406479 TATATATT
1 TATATATT
*
13406487 TATATAAT
1 TATATATT
13406495 TATATATT
1 TATATATT
*
13406503 TAAATATT
1 TATATATT
13406511 TATAT
1 TATAT
13406516 TTAAAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (8 bp):
TATATATT
Found at i:13406519 original size:14 final size:16
Alignment explanation
Indices: 13406479--13406533 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
13406469 TTTTTATTTA
*
13406479 TATATATTTATATAAT
1 TATATATTTAAATAAT
13406495 TATATATTTAAAT-AT
1 TATATATTTAAATAAT
*
13406510 T-TATATTTAAAAAAT
1 TATATATTTAAATAAT
*
13406525 AATAT-TTTA
1 TATATATTTA
13406534 TATTTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 10 0.29
15 9 0.26
16 15 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATATTTAAATAAT
Found at i:13406579 original size:20 final size:22
Alignment explanation
Indices: 13406505--13406578 Score: 134
Period size: 22 Copynumber: 3.5 Consensus size: 22
13406495 TATATATTTA
13406505 AATA-TTTATA-TTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
13406525 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
13406547 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
13406569 AATATTTTAT
1 AATATTTTAT
13406579 TAATTTCGAG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.08
21 6 0.12
22 42 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:13407288 original size:21 final size:21
Alignment explanation
Indices: 13407259--13407298 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13407249 ACAATTATAA
13407259 AAAATAATTAATTAATTCGTAT
1 AAAATAATTAATT-ATTCGTAT
*
13407281 AAAA-AATTTATTATTCGT
1 AAAATAATTAATTATTCGT
13407299 GATATATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 7 0.41
22 4 0.24
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (21 bp):
AAAATAATTAATTATTCGTAT
Found at i:13407572 original size:16 final size:15
Alignment explanation
Indices: 13407533--13407573 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
13407523 TATTTATTTT
13407533 ATATTTTAAT-AAAA
1 ATATTTTAATAAAAA
*
13407547 A-ATTTAAATAAACAA
1 ATATTTTAATAAA-AA
13407562 ATATTTTAATAA
1 ATATTTTAATAA
13407574 TTTTAGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 7 0.32
14 3 0.14
15 3 0.14
16 9 0.41
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATTTTAATAAAAA
Found at i:13407661 original size:219 final size:221
Alignment explanation
Indices: 13407404--13407827 Score: 676
Period size: 220 Copynumber: 1.9 Consensus size: 221
13407394 ATATTCATCT
* * *
13407404 ATTATCTATTTATATATGTAAAATATATAAAATTTTATATTTGTAGAAAG-TTTAGACCATAAAA
1 ATTATCCATTTATATATGTAAAATATATAAAATTTTATATTTATAGAAAGTTTTAAACCATAAAA
*
13407468 AATAATTTTTATTTATTATTAATTAAAAATAAACTTAAATTTTAAATTAAATTCTTATTTATTTT
66 AATAAATTTTATTTATTATTAATTAAAAATAAACTTAAATTTTAAATTAAATTCTTATTTATTTT
13407533 ATATTTTAATAAAAAATTT-AAATAAACAAATATTTTAATA-ATTTTAGATATTTAAACAAATAA
131 ATATTTTAAT-AAAAATTTCAAATAAACAAATATTTTAA-AGATTTTAGATATTTAAACAAATAA
13407596 TACTTATGTAAACGGATTCGAATTTGAA
194 TACTTATGTAAACGGATTCGAATTTGAA
* * *
13407624 ATTATCCATTTATGTAT-TAAAATATATAAAATTTTATATTTATAGAAAGTTTTAAATCTTAAAA
1 ATTATCCATTTATATATGTAAAATATATAAAATTTTATATTTATAGAAAGTTTTAAACCATAAAA
*
13407688 AATAAATTTTATTTATTATTAATTAAAAATAAACTTAAATTTTAAATTAAATTCTTATTTGTTTT
66 AATAAATTTTATTTATTATTAATTAAAAATAAACTTAAATTTTAAATTAAATTCTTATTTATTTT
* * * *
13407753 ATATTTTGATAAAAATTTCAAATAAATAAATATTTTAAAGATTTTATATATTTAAATAAATAATA
131 ATATTTTAATAAAAATTTCAAATAAACAAATATTTTAAAGATTTTAGATATTTAAACAAATAATA
* *
13407818 TTTATTTAAA
196 CTTATGTAAA
13407828 TAAATTTAAA
Statistics
Matches: 187, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
219 40 0.21
220 147 0.79
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (221 bp):
ATTATCCATTTATATATGTAAAATATATAAAATTTTATATTTATAGAAAGTTTTAAACCATAAAA
AATAAATTTTATTTATTATTAATTAAAAATAAACTTAAATTTTAAATTAAATTCTTATTTATTTT
ATATTTTAATAAAAATTTCAAATAAACAAATATTTTAAAGATTTTAGATATTTAAACAAATAATA
CTTATGTAAACGGATTCGAATTTGAA
Found at i:13407820 original size:15 final size:15
Alignment explanation
Indices: 13407800--13407857 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
13407790 AAGATTTTAT
13407800 ATATTTAAATAAATA
1 ATATTTAAATAAATA
**
13407815 ATATTTATTTAAATA
1 ATATTTAAATAAATA
13407830 A-ATTTAAATTCAAATA
1 ATATTTAAA-T-AAATA
13407846 ATGATATTAAAT
1 AT-AT-TTAAAT
13407858 TTAAATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 5 0.15
15 15 0.44
16 6 0.18
18 3 0.09
19 5 0.15
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
ATATTTAAATAAATA
Found at i:13411493 original size:16 final size:16
Alignment explanation
Indices: 13411460--13411494 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
13411450 TATTTAAACC
* *
13411460 TTTTATATTATATTGT
1 TTTTATATTAAATAGT
13411476 TTTTATATTAAATAGT
1 TTTTATATTAAATAGT
13411492 TTT
1 TTT
13411495 CCTTATTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (16 bp):
TTTTATATTAAATAGT
Found at i:13415033 original size:15 final size:15
Alignment explanation
Indices: 13415013--13415043 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13415003 AGATTTGGCC
13415013 CAAATCTAAATTCAT
1 CAAATCTAAATTCAT
13415028 CAAATCTAAATTCAT
1 CAAATCTAAATTCAT
13415043 C
1 C
13415044 TTTTTAAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (15 bp):
CAAATCTAAATTCAT
Found at i:13421103 original size:27 final size:25
Alignment explanation
Indices: 13421049--13421105 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
13421039 TTTTTTTTGA
*
13421049 ATTTGATTTAATTTTATAAAATAAAT
1 ATTTGATTTAATTATATAAAAT-AAT
13421075 ATTTGAATTTAATTGATATTAAAAT-AT
1 ATTTG-ATTTAATT-ATA-TAAAATAAT
13421102 ATTT
1 ATTT
13421106 TTTATATCCG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.19
27 14 0.52
28 2 0.07
29 6 0.22
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (25 bp):
ATTTGATTTAATTATATAAAATAAT
Found at i:13421225 original size:17 final size:17
Alignment explanation
Indices: 13421182--13421238 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 17
13421172 AATTTAATAA
* *
13421182 TTTTAATTTAATATAAT
1 TTTTAATATAATATTAT
*
13421199 ATTT-ATATAATATTAT
1 TTTTAATATAATATTAT
13421215 TTTTAATATAA-ATTAT
1 TTTTAATATAATATTAT
13421231 ATTTTAAT
1 -TTTTAAT
13421239 TACATAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
16 18 0.53
17 16 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTAATATAATATTAT
Found at i:13422371 original size:37 final size:37
Alignment explanation
Indices: 13422323--13422394 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
13422313 AAATACATTT
13422323 TATTAAGAAATAAATTTAAAATATGTTGAATAAAAAA
1 TATTAAGAAATAAATTTAAAATATGTTGAATAAAAAA
*
13422360 TATTACGAAATAAATTTAAAATATGTTGAATAAAA
1 TATTAAGAAATAAATTTAAAATATGTTGAATAAAA
13422395 GGTGAGGCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.33
Consensus pattern (37 bp):
TATTAAGAAATAAATTTAAAATATGTTGAATAAAAAA
Found at i:13422879 original size:9 final size:9
Alignment explanation
Indices: 13422867--13422896 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
13422857 GATATTTTAT
13422867 TAATTAAAA
1 TAATTAAAA
13422876 TAATTAAAA
1 TAATTAAAA
13422885 TATATTAAAA
1 TA-ATTAAAA
13422895 TA
1 TA
13422897 TAAAAATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:13422893 original size:10 final size:10
Alignment explanation
Indices: 13422869--13422898 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
13422859 TATTTTATTA
13422869 ATTAAAATA-
1 ATTAAAATAT
13422878 ATTAAAATAT
1 ATTAAAATAT
13422888 ATTAAAATAT
1 ATTAAAATAT
13422898 A
1 A
13422899 AAAATTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:13431259 original size:28 final size:30
Alignment explanation
Indices: 13431219--13431277 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
13431209 AAAATTCAAA
* *
13431219 TTTTAGGGTTTTGGTTTGAG-TTTTGAGGG
1 TTTTAGGGTTTTGGTTTAAGATTTAGAGGG
13431248 TTTTAGGG-TTTGGTTTAAGATTTAGAGGG
1 TTTTAGGGTTTTGGTTTAAGATTTAGAGGG
13431277 T
1 T
13431278 CTTAAGGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.49
Consensus pattern (30 bp):
TTTTAGGGTTTTGGTTTAAGATTTAGAGGG
Found at i:13431742 original size:3 final size:3
Alignment explanation
Indices: 13431730--13431758 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
13431720 AAATAAAAAA
13431730 ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
13431759 TTTTAGAGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:13432946 original size:7 final size:7
Alignment explanation
Indices: 13432910--13432959 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
13432900 TTTTTTTTTG
13432910 TTTTAAT
1 TTTTAAT
*
13432917 TATT-A-
1 TTTTAAT
13432922 TTTTAAT
1 TTTTAAT
*
13432929 AATTTTGAT
1 --TTTTAAT
13432938 TTTTAAT
1 TTTTAAT
13432945 TTTTAAT
1 TTTTAAT
13432952 TTTTAAT
1 TTTTAAT
13432959 T
1 T
13432960 AAATCAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
7 24 0.69
9 6 0.17
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (7 bp):
TTTTAAT
Found at i:13432953 original size:14 final size:13
Alignment explanation
Indices: 13432910--13432959 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 13
13432900 TTTTTTTTTG
*
13432910 TTTTAATTATTAT
1 TTTTAATTTTTAT
*
13432923 TTTAATAATTTTGAT
1 TTT--TAATTTTTAT
13432938 TTTTAATTTTTAAT
1 TTTTAATTTTT-AT
13432952 TTTTAATT
1 TTTTAATT
13432960 AAATCAATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 10 0.32
14 10 0.32
15 11 0.35
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TTTTAATTTTTAT
Found at i:13445365 original size:117 final size:117
Alignment explanation
Indices: 13445152--13445389 Score: 343
Period size: 117 Copynumber: 2.0 Consensus size: 117
13445142 TACGTGATTA
* * *
13445152 TTGATTAAAAAGAAGTGATTAGTTGTCTTTTTTTTGCACGAGCATGTGAAACAAAAAAAAATAAA
1 TTGAATAAAAAGAAGTGATTAGTTGTCTTTTTTTTGCAAGAGCATGTGAAAC--AAAAAAAGAAA
* *
13445217 ATGAAAAGACATGTGTCCCTACTTTTATATTTATTATTGTAATTTTATTTGGTT
64 ATGAAAAGACATGTGTCCCTACTTTTATATTTATTATTGCAAGTTTATTTGGTT
* * * *
13445271 TTGAATAAAAAGAAGTGATTAGTTGTCTCTTTTTTTTCAAGTGCATGTGAAAC-ACAAAAGAAGA
1 TTGAATAAAAAGAAGTGATTAGTTGTCT-TTTTTTTGCAAGAGCATGTGAAACAAAAAAAGAAAA
* *
13445335 TGAAACGACATGTGTCCCTAGTTTTATATTTATTATTGCAAGTTTATTTGGTT
65 TGAAAAGACATGTGTCCCTACTTTTATATTTATTATTGCAAGTTTATTTGGTT
13445388 TT
1 TT
13445390 AAAGTAATTT
Statistics
Matches: 107, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
117 59 0.55
119 27 0.25
120 21 0.20
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.40
Consensus pattern (117 bp):
TTGAATAAAAAGAAGTGATTAGTTGTCTTTTTTTTGCAAGAGCATGTGAAACAAAAAAAGAAAAT
GAAAAGACATGTGTCCCTACTTTTATATTTATTATTGCAAGTTTATTTGGTT
Found at i:13446660 original size:21 final size:21
Alignment explanation
Indices: 13446616--13446660 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
13446606 GGAGAGAAAC
* *
13446616 TTGAAGAAAAGAGGCGTCACA
1 TTGAAGAAAAGAGGAGGCACA
* *
13446637 TTGAAGAAAAGAGTAGGCATA
1 TTGAAGAAAAGAGGAGGCACA
13446658 TTG
1 TTG
13446661 TTGAGAAGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.29, T:0.20
Consensus pattern (21 bp):
TTGAAGAAAAGAGGAGGCACA
Found at i:13448404 original size:2 final size:2
Alignment explanation
Indices: 13448397--13448430 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
13448387 TCTTCCTTAA
*
13448397 AT AT AT AT AC 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
13448431 GCAAGTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13449345 original size:15 final size:15
Alignment explanation
Indices: 13449322--13449370 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
13449312 CTTCCTTTAT
13449322 TATTATTTTT-TTAAA
1 TATT-TTTTTATTAAA
*
13449337 TATTTTTTTAATTAAT
1 TATTTTTTT-ATTAAA
*
13449353 TAATTTTTTATTAAA
1 TATTTTTTTATTAAA
13449368 TAT
1 TAT
13449371 ATATAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 5 0.18
15 11 0.39
16 12 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTTTTTATTAAA
Found at i:13449893 original size:23 final size:22
Alignment explanation
Indices: 13449853--13449921 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
13449843 TATATATAAA
13449853 ATATATTT-TATTAGTTATTTAAC
1 ATATATTTATA-TA-TTATTTAAC
* *
13449876 TTTATATTTATATATTATTAAAC
1 -ATATATTTATATATTATTTAAC
13449899 ATATATTTAATATATTAATTTAA
1 ATATATTT-ATATATT-ATTTAA
13449922 TAAATTTATG
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
22 7 0.18
23 15 0.39
24 14 0.37
25 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (22 bp):
ATATATTTATATATTATTTAAC
Found at i:13450104 original size:15 final size:16
Alignment explanation
Indices: 13450070--13450108 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
13450060 TTAAGTTCTA
*
13450070 AATTTTATTTGTATTTT
1 AATTTT-TTTGTAGTTT
13450087 AATTTTTTT-TAGTTT
1 AATTTTTTTGTAGTTT
13450102 AATTTTT
1 AATTTTT
13450109 GTTTGTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 3 0.14
17 6 0.29
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (16 bp):
AATTTTTTTGTAGTTT
Found at i:13450240 original size:26 final size:25
Alignment explanation
Indices: 13450198--13450249 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
13450188 GTATAAAAAA
13450198 TCTTAGATTTATATTAGATTTTAAC
1 TCTTAGATTTATATTAGATTTTAAC
*
13450223 TCTTGGATTCTATATTAGATTTTAAC
1 TCTTAGATT-TATATTAGATTTTAAC
13450249 T
1 T
13450250 TTAATGGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (25 bp):
TCTTAGATTTATATTAGATTTTAAC
Found at i:13450843 original size:45 final size:47
Alignment explanation
Indices: 13450786--13450890 Score: 144
Period size: 47 Copynumber: 2.3 Consensus size: 47
13450776 TGTTTGCATA
* *
13450786 ATTAATATATTTATTTATGTGATT-TA-TT-ATTATATTTGCATGACT
1 ATTAATATATTTATTTATATGATTATATTTAATT-TAATTGCATGACT
* *
13450831 ATTAATATATTTATTTGTATGATTATATTTAATTTAATTGCATGATT
1 ATTAATATATTTATTTATATGATTATATTTAATTTAATTGCATGACT
13450878 ATTAATATATTTA
1 ATTAATATATTTA
13450891 ATTGCTTGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
45 22 0.42
46 2 0.04
47 26 0.49
48 3 0.06
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (47 bp):
ATTAATATATTTATTTATATGATTATATTTAATTTAATTGCATGACT
Found at i:13450847 original size:24 final size:23
Alignment explanation
Indices: 13450767--13450941 Score: 129
Period size: 24 Copynumber: 7.8 Consensus size: 23
13450757 TTTATTTGCC
*
13450767 TAATATATTTGTTTGCAT-A-AT
1 TAATATATTTATTTGCATGATAT
13450788 TAATATATTTATTT--ATG-TGAT
1 TAATATATTTATTTGCATGAT-AT
*
13450809 TTAT-TATTATATTTGCATGACTAT
1 TAATATATT-TATTTGCATGA-TAT
*
13450833 TAATATATTTATTTGTATG--AT
1 TAATATATTTATTTGCATGATAT
* *
13450854 TATATTTAATTTAATTGCATGATTAT
1 TA-ATAT-ATTTATTTGCATGA-TAT
* *
13450880 TAATATATTTAATTGCTTGATGAT
1 TAATATATTTATTTGCATGAT-AT
*
13450904 TAATATATTTATTGGCATG--AT
1 TAATATATTTATTTGCATGATAT
*
13450925 T-ATATATTTAATTGCAT
1 TAATATATTTATTTGCAT
13450942 ATTTTTTTGC
Statistics
Matches: 125, Mismatches: 14, Indels: 31
0.74 0.08 0.18
Matches are distributed among these distances:
19 2 0.02
20 18 0.14
21 30 0.24
22 3 0.02
23 15 0.12
24 45 0.36
25 8 0.06
26 4 0.03
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (23 bp):
TAATATATTTATTTGCATGATAT
Found at i:13450974 original size:23 final size:20
Alignment explanation
Indices: 13450940--13450985 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 20
13450930 ATTTAATTGC
13450940 ATATTTTTTTGCATGATTTAT
1 ATATTTTTTTGCATGA-TTAT
13450961 ATATTATTGTTTGCATGATTAT
1 ATATT-TT-TTTGCATGATTAT
13450983 ATA
1 ATA
13450986 GTTAATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.22
22 9 0.39
23 9 0.39
ACGTcount: A:0.28, C:0.04, G:0.11, T:0.57
Consensus pattern (20 bp):
ATATTTTTTTGCATGATTAT
Found at i:13450991 original size:55 final size:55
Alignment explanation
Indices: 13450899--13451161 Score: 345
Period size: 55 Copynumber: 4.8 Consensus size: 55
13450889 TAATTGCTTG
* * *
13450899 ATGATTAATATA-T-TTATTGGCATGATTATATATTTAATTGCATATTTTTTTGC
1 ATGATTTATATATTATTATTTGCATGATTATATATTTAATTGCATATTTATTTGC
* * * *
13450952 ATGATTTATATATTATTGTTTGCATGATTATATAGTTAATTTCATGTTTATTTGC
1 ATGATTTATATATTATTATTTGCATGATTATATATTTAATTGCATATTTATTTGC
* * *
13451007 ATGATTAATATATTACTATTTGCATGATTATATATTTAATTCCATATTTATTTGC
1 ATGATTTATATATTATTATTTGCATGATTATATATTTAATTGCATATTTATTTGC
* * * *
13451062 ATGGTTTATATATT-TTATTTGCTTGATTATATATTTAATTACATGTTTATTTGC
1 ATGATTTATATATTATTATTTGCATGATTATATATTTAATTGCATATTTATTTGC
*
13451116 ATGA-TTATTAATATTATTATTTGCATGATTATATATTTAATCGCAT
1 ATGATTTA-T-ATATTATTATTTGCATGATTATATATTTAATTGCAT
13451162 GTCTAATTGT
Statistics
Matches: 182, Mismatches: 23, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
53 14 0.08
54 41 0.23
55 100 0.55
56 27 0.15
ACGTcount: A:0.30, C:0.06, G:0.10, T:0.53
Consensus pattern (55 bp):
ATGATTTATATATTATTATTTGCATGATTATATATTTAATTGCATATTTATTTGC
Found at i:13451042 original size:22 final size:23
Alignment explanation
Indices: 13451000--13451042 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
13450990 ATTTCATGTT
13451000 TATTTGCATGATTAATATATTAC
1 TATTTGCATGATTAATATATTAC
13451023 TATTTGCATGATT-ATATATT
1 TATTTGCATGATTAATATATT
13451043 TAATTCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.51
Consensus pattern (23 bp):
TATTTGCATGATTAATATATTAC
Found at i:13451053 original size:110 final size:108
Alignment explanation
Indices: 13450899--13451156 Score: 392
Period size: 110 Copynumber: 2.4 Consensus size: 108
13450889 TAATTGCTTG
* * *
13450899 ATGATTAATATATT-TATTGGCATGATTATATATTTAATTGCATATTTTTTTGCATGATTTATAT
1 ATGATTAATATATTATATTTGCATGATTATATATTTAATTCCATATTTATTTGCATGATTTATAT
* *
13450963 ATTATTGTTTGCATGATTATATAGTTAATTTCATGTTTATTTGC
66 ATT-TTATTTGCATGATTATATAGTTAATTACATGTTTATTTGC
*
13451007 ATGATTAATATATTACTATTTGCATGATTATATATTTAATTCCATATTTATTTGCATGGTTTATA
1 ATGATTAATATATTA-TATTTGCATGATTATATATTTAATTCCATATTTATTTGCATGATTTATA
* *
13451072 TATTTTATTTGCTTGATTATATATTTAATTACATGTTTATTTGC
65 TATTTTATTTGCATGATTATATAGTTAATTACATGTTTATTTGC
*
13451116 ATGATTATTAATATTATTATTTGCATGATTATATATTTAAT
1 ATGATTAAT-ATATTA-TATTTGCATGATTATATATTTAAT
13451157 CGCATGTCTA
Statistics
Matches: 137, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
108 14 0.10
109 44 0.32
110 79 0.58
ACGTcount: A:0.30, C:0.06, G:0.10, T:0.54
Consensus pattern (108 bp):
ATGATTAATATATTATATTTGCATGATTATATATTTAATTCCATATTTATTTGCATGATTTATAT
ATTTTATTTGCATGATTATATAGTTAATTACATGTTTATTTGC
Found at i:13451074 original size:21 final size:20
Alignment explanation
Indices: 13451050--13451111 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
13451040 ATTTAATTCC
13451050 ATATTTATTTGCATGGTTTAT
1 ATATTTATTTGCAT-GTTTAT
* *
13451071 ATATTTTATTTGCTTGATTAT
1 ATA-TTTATTTGCATGTTTAT
* *
13451092 ATATTTAATTACATGTTTAT
1 ATATTTATTTGCATGTTTAT
13451112 TTGCATGATT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 13 0.38
21 11 0.32
22 10 0.29
ACGTcount: A:0.27, C:0.05, G:0.10, T:0.58
Consensus pattern (20 bp):
ATATTTATTTGCATGTTTAT
Found at i:13451080 original size:22 final size:21
Alignment explanation
Indices: 13451053--13451097 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13451043 TAATTCCATA
*
13451053 TTTATTTGCATGGTTTATATAT
1 TTTATTTGC-TGGATTATATAT
*
13451075 TTTATTTGCTTGATTATATAT
1 TTTATTTGCTGGATTATATAT
13451096 TT
1 TT
13451098 AATTACATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.22, C:0.04, G:0.11, T:0.62
Consensus pattern (21 bp):
TTTATTTGCTGGATTATATAT
Done.