Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold134
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: 811437
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
File 2 of 5
Found at i:205212 original size:3 final size:3
Alignment explanation
Indices: 205204--205229 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
205194 CTGATATAAC
205204 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
205230 AAATAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:205308 original size:15 final size:15
Alignment explanation
Indices: 205288--205324 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
205278 CTTAGCAAAA
* *
205288 TTATTTTCTTTATTT
1 TTATTTTCCTAATTT
205303 TTATTTTCCTAATTT
1 TTATTTTCCTAATTT
205318 TTATTTT
1 TTATTTT
205325 TATTTTATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTTCCTAATTT
Found at i:206135 original size:18 final size:16
Alignment explanation
Indices: 206114--206188 Score: 57
Period size: 19 Copynumber: 4.4 Consensus size: 16
206104 AGACATTAAA
206114 ATAAGATATAAATTTTAT
1 ATAA-ATATAAA-TTTAT
206132 ATAAATA-AAA-TTAT
1 ATAAATATAAATTTAT
206146 -TAATATATTAAAATTTAT
1 ATAA-ATA-T-AAATTTAT
206164 ATAAATATAATATTAATAT
1 ATAAATATAA-ATT--TAT
206183 ATAAAT
1 ATAAAT
206189 TATTAAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
13 3 0.06
14 7 0.15
16 5 0.10
17 10 0.21
18 11 0.23
19 12 0.25
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (16 bp):
ATAAATATAAATTTAT
Found at i:206168 original size:32 final size:31
Alignment explanation
Indices: 206122--206184 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 31
206112 AAATAAGATA
*
206122 TAAATTTTATATAAATAAAATTATTAATATAT
1 TAAAATTTATATAAATAAAA-TATTAATATAT
*
206154 TAAAATTTATATAAATATAATATTAATATAT
1 TAAAATTTATATAAATAAAATATTAATATAT
206185 AAATTATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 11 0.38
32 18 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (31 bp):
TAAAATTTATATAAATAAAATATTAATATAT
Found at i:206194 original size:15 final size:15
Alignment explanation
Indices: 206119--206217 Score: 66
Period size: 15 Copynumber: 6.6 Consensus size: 15
206109 TTAAAATAAG
206119 ATATAAATT-TTATAT
1 ATATAAATTATTA-AT
*
206134 AAATAAAATTATTAAT
1 ATAT-AAATTATTAAT
206150 ATATTAAAATTTATATAA-
1 ATA-T-AAA-TTAT-TAAT
206168 ATAT-AA-TATTAAT
1 ATATAAATTATTAAT
*
206181 ATATAAATTATTAAA
1 ATATAAATTATTAAT
* *
206196 AAATAAATTAATAA-
1 ATATAAATTATTAAT
206210 ATA-AAATT
1 ATATAAATT
206218 CTTTGATATC
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
12 3 0.04
13 12 0.17
14 4 0.06
15 23 0.33
16 9 0.13
17 9 0.13
18 7 0.10
19 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATAAATTATTAAT
Found at i:206523 original size:2 final size:2
Alignment explanation
Indices: 206516--206576 Score: 56
Period size: 2 Copynumber: 32.0 Consensus size: 2
206506 TTTTAAAATA
* * * * *
206516 AT AT AT AT TT AT AT AA AT AT -T AT -T AT AT TT GT AA 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
206556 AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
206577 TTTAATTATT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:206538 original size:38 final size:40
Alignment explanation
Indices: 206495--206592 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 40
206485 TTATATTTTC
*
206495 TATTATAATTATTTTAAAATA-ATATATATTTATATA-AA
1 TATTATAATTATTTTAAAATATATATATATATATATATAA
* *
206533 TATTATTA-TATTTGTAAATATATATATATATATATATATTA
1 TATTATAATTATTT-TAAA-ATATATATATATATATATATAA
*
206574 TATTTTAATTA-TTTAAAAT
1 TATTATAATTATTTTAAAAT
206593 GTAAGAATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
37 5 0.10
38 11 0.22
39 5 0.10
40 18 0.36
41 9 0.18
42 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (40 bp):
TATTATAATTATTTTAAAATATATATATATATATATATAA
Found at i:213793 original size:21 final size:21
Alignment explanation
Indices: 213759--213813 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
213749 ATTTTTTATT
213759 ATATAAAATT-AATTTAAATTTA
1 ATAT-AAATTAAATTT-AATTTA
*
213781 AT-TAATTTAAATTTAATTTA
1 ATATAAATTAAATTTAATTTA
213801 ATATAAATTAAAT
1 ATATAAATTAAAT
213814 ATGTGAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 12 0.41
21 15 0.52
22 2 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATAAATTAAATTTAATTTA
Found at i:213809 original size:26 final size:26
Alignment explanation
Indices: 213762--213811 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
213752 TTTTATTATA
*
213762 TAAAATTAATTTAAATTTAATTAATT
1 TAAAATTAATTTAAATTAAATTAATT
*
213788 TAAATTTAATTT-AATATAAATTAA
1 TAAAATTAATTTAAAT-TAAATTAA
213812 ATATGTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TAAAATTAATTTAAATTAAATTAATT
Found at i:213811 original size:15 final size:15
Alignment explanation
Indices: 213765--213809 Score: 72
Period size: 15 Copynumber: 2.9 Consensus size: 15
213755 TATTATATAA
213765 AATTAATTTAAATTT
1 AATTAATTTAAATTT
213780 AATTAATTTAAATTT
1 AATTAATTTAAATTT
*
213795 AATTTAATATAAATT
1 AA-TTAATTTAAATT
213810 AAATATGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
15 17 0.61
16 11 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTAATTTAAATTT
Found at i:214093 original size:20 final size:21
Alignment explanation
Indices: 214070--214112 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
214060 TAACTGAATT
*
214070 TAAAATATT-ATATGTTTATA
1 TAAAATATTAATATGTTAATA
*
214090 T-AAATTTTAATATGTTAATA
1 TAAAATATTAATATGTTAATA
214110 TAA
1 TAA
214113 TTTTTGTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
19 6 0.32
20 12 0.63
21 1 0.05
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
TAAAATATTAATATGTTAATA
Found at i:214117 original size:20 final size:20
Alignment explanation
Indices: 214079--214116 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
214069 TTAAAATATT
*
214079 ATATGTTTATATAAATTTTA
1 ATATGTTAATATAAATTTTA
214099 ATATGTTAATAT-AATTTT
1 ATATGTTAATATAAATTTT
214117 TGTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
ATATGTTAATATAAATTTTA
Found at i:221068 original size:18 final size:18
Alignment explanation
Indices: 221042--221083 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 18
221032 ATATATAATA
221042 TTAATATATATATATATATG
1 TTAATATAT-TATATAT-TG
221062 TTAATATATTATATATTG
1 TTAATATATTATATATTG
221080 TTAA
1 TTAA
221084 CGTGATTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 6 0.27
19 7 0.32
20 9 0.41
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (18 bp):
TTAATATATTATATATTG
Found at i:225712 original size:29 final size:29
Alignment explanation
Indices: 225676--225733 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
225666 GAGTGTTAAC
225676 GTGATTAGAGAGATAGCTGTCAATAACAA
1 GTGATTAGAGAGATAGCTGTCAATAACAA
225705 GTGATTAGAGAGATAGCTGTCAATAACAA
1 GTGATTAGAGAGATAGCTGTCAATAACAA
225734 AATTATAGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.24, T:0.24
Consensus pattern (29 bp):
GTGATTAGAGAGATAGCTGTCAATAACAA
Found at i:233127 original size:2 final size:2
Alignment explanation
Indices: 233120--233152 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
233110 TCTGTTTTTC
233120 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
233153 AGAGATCATA
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:236490 original size:9 final size:11
Alignment explanation
Indices: 236465--236529 Score: 71
Period size: 11 Copynumber: 5.9 Consensus size: 11
236455 AAAATTTATT
236465 ATATAATATAA
1 ATATAATATAA
236476 ATATAATA-AA
1 ATATAATATAA
236486 A-ATAATTATAA
1 ATATAA-TATAA
* *
236497 ATACATTATAA
1 ATATAATATAA
*
236508 AAATTAATATAA
1 ATA-TAATATAA
236520 ATATAATATA
1 ATATAATATA
236530 TTATGTAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
9 4 0.09
10 5 0.11
11 25 0.57
12 10 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
ATATAATATAA
Found at i:236529 original size:23 final size:22
Alignment explanation
Indices: 236467--236529 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
236457 AATTTATTAT
236467 ATAATATAAATAT-A-ATAAAA
1 ATAATATAAATATAATATAAAA
* *
236487 ATAATTATAAATACATTATAAAA
1 ATAA-TATAAATATAATATAAAA
236510 ATTAATATAAATATAATATA
1 A-TAATATAAATATAATATA
236530 TTATGTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 4 0.11
21 8 0.23
23 20 0.57
24 3 0.09
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
ATAATATAAATATAATATAAAA
Found at i:243870 original size:2 final size:2
Alignment explanation
Indices: 243863--243915 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
243853 AACACGTCAA
* *
243863 AT AT AT AT AT AT AT AT AT AT AT -T GT AT AT AA AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
243903 AT AT -T TT AT AT AT
1 AT AT AT AT AT AT AT
243916 TTTTTTAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:249978 original size:14 final size:15
Alignment explanation
Indices: 249947--249979 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
249937 CATTTCATTG
*
249947 AAAATAAATATTTTA
1 AAAATAAATATTTGA
249962 AAAATAAAT-TTTGA
1 AAAATAAATATTTGA
249976 AAAA
1 AAAA
249980 AAAGATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (15 bp):
AAAATAAATATTTGA
Found at i:250894 original size:2 final size:2
Alignment explanation
Indices: 250884--250977 Score: 63
Period size: 2 Copynumber: 48.0 Consensus size: 2
250874 ATATTTTAAC
* *
250884 AT AT TT AT AT A- AT -T AT AT -T GT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
250922 -T TT TT AGT AT CAT ACC AT AT TT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT -AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
*
250964 AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT
250978 TATGTGTTAA
Statistics
Matches: 74, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
1 5 0.07
2 64 0.86
3 5 0.07
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:250908 original size:31 final size:30
Alignment explanation
Indices: 250846--250908 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
250836 ATTTATAAAA
*
250846 ATTTTAATATATTAATAATTCATATTATAT
1 ATTTTAACATATTAATAATTCATATTATAT
*
250876 ATTTTAACATATTTATATAATT-ATATTGTAT
1 ATTTTAACATA-TTA-ATAATTCATATTATAT
250907 AT
1 AT
250909 ATATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 10 0.34
31 13 0.45
32 6 0.21
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (30 bp):
ATTTTAACATATTAATAATTCATATTATAT
Found at i:251577 original size:33 final size:33
Alignment explanation
Indices: 251519--251610 Score: 82
Period size: 32 Copynumber: 2.8 Consensus size: 33
251509 AACTTAAAAA
* *
251519 ATATACAATATCA-AAAAATAT-TATAATAACGAT
1 ATATA-AATAT-ATAAAAATTTATATAATAACAAT
**
251552 ATATAAATATATAAAAATTTATATAATATTAAT
1 ATATAAATATATAAAAATTTATATAATAACAAT
* * *
251585 -TATTAATATTTTAAAATTTATATAAT
1 ATATAAATATATAAAAATTTATATAAT
251611 TATATAATAT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
31 1 0.02
32 35 0.70
33 14 0.28
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (33 bp):
ATATAAATATATAAAAATTTATATAATAACAAT
Found at i:251641 original size:27 final size:28
Alignment explanation
Indices: 251572--251641 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 28
251562 ATAAAAATTT
251572 ATATAA-TATTAAT-TATTAATATTTTAA
1 ATATAATTA-TAATATATTAATATTTTAA
*
251599 A-AT-TTATATAAT-TATATAATATTTTAA
1 ATATAAT-TATAATATAT-TAATATTTTAA
251626 ATATAATTATAATATA
1 ATATAATTATAATATA
251642 AAAATAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
26 9 0.26
27 15 0.43
28 8 0.23
29 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
ATATAATTATAATATATTAATATTTTAA
Found at i:251860 original size:16 final size:15
Alignment explanation
Indices: 251837--251921 Score: 74
Period size: 13 Copynumber: 6.0 Consensus size: 15
251827 TTATATAATT
251837 TTTAATTAAATAAAA
1 TTTAATTAAATAAAA
251852 TTATAATT-AATAAAA
1 TT-TAATTAAATAAAA
* *
251867 TTTATTTAAA-AATA
1 TTTAATTAAATAAAA
251881 TTTAA-TAAAT-AAA
1 TTTAATTAAATAAAA
**
251894 TTTAA--AGTTAAAA
1 TTTAATTAAATAAAA
*
251907 TTTAATTATATAAAA
1 TTTAATTAAATAAAA
251922 AATTTATATA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
12 2 0.04
13 19 0.34
14 11 0.20
15 19 0.34
16 5 0.09
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (15 bp):
TTTAATTAAATAAAA
Found at i:251933 original size:28 final size:27
Alignment explanation
Indices: 251846--251935 Score: 78
Period size: 30 Copynumber: 3.3 Consensus size: 27
251836 TTTTAATTAA
251846 ATAAAATTATAATTAAT--AAAATTTAT
1 ATAAAATT-TAATTAATAAAAAATTTAT
* * * *
251872 TTAAAA-ATATTTAATAAATAAATTTAA
1 ATAAAATTTAATTAATAAA-AAATTTAT
251899 AGTTAAAATTTAATTATATAAAAAATTTAT
1 A--TAAAATTTAATTA-ATAAAAAATTTAT
251929 ATAAAAT
1 ATAAAAT
251936 ATAAGATAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
24 7 0.14
26 6 0.12
27 7 0.14
28 6 0.12
29 5 0.10
30 13 0.27
31 5 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (27 bp):
ATAAAATTTAATTAATAAAAAATTTAT
Found at i:251955 original size:17 final size:17
Alignment explanation
Indices: 251930--251991 Score: 54
Period size: 17 Copynumber: 3.6 Consensus size: 17
251920 AAAATTTATA
*
251930 TAAAATATAAGATAAAT
1 TAAAATATAACATAAAT
*
251947 TAAACTATAACATAAA-
1 TAAAATATAACATAAAT
* * *
251963 TATAATATTAAAAAATAAT
1 TAAAATA-TAACATA-AAT
251982 TAAAATATAA
1 TAAAATATAA
251992 TATGACAGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
16 5 0.14
17 19 0.54
18 5 0.14
19 6 0.17
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.31
Consensus pattern (17 bp):
TAAAATATAACATAAAT
Found at i:251980 original size:24 final size:25
Alignment explanation
Indices: 251953--252014 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
251943 AAATTAAACT
*
251953 ATAACATAAATATAATATTA-AAAA
1 ATAACATAAATATAATATGACAAAA
* *
251977 ATAA-TTAAAATATAATATGACAGAA
1 ATAACAT-AAATATAATATGACAAAA
252002 AT-ACATAAATATA
1 ATAACATAAATATA
252015 TAAATATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
23 1 0.03
24 24 0.77
25 6 0.19
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (25 bp):
ATAACATAAATATAATATGACAAAA
Found at i:252054 original size:14 final size:14
Alignment explanation
Indices: 252009--252060 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
251999 GAAATACATA
252009 AATATATAAATATTT
1 AATATATAAATA-TT
*
252024 ATATAAAATAAATTATT
1 A-AT-ATATAAA-TATT
252041 AATATATAAATATT
1 AATATATAAATATT
*
252055 TATATA
1 AATATA
252061 AAAAATATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 9 0.29
15 7 0.23
16 4 0.13
17 9 0.29
18 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATATAAATATT
Found at i:252066 original size:15 final size:15
Alignment explanation
Indices: 252016--252068 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
252006 ATAAATATAT
252016 AAATATTTATATAAAA
1 AAATATTTATAT-AAA
* *
252032 TAAATTATTAATAT-AT
1 -AAA-TATTTATATAAA
252048 AAATATTTATATAAA
1 AAATATTTATATAAA
252063 AAATAT
1 AAATAT
252069 CACGAATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 8 0.27
15 10 0.33
16 1 0.03
17 3 0.10
18 8 0.27
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATTTATATAAA
Found at i:252896 original size:8 final size:8
Alignment explanation
Indices: 252883--252944 Score: 79
Period size: 8 Copynumber: 7.2 Consensus size: 8
252873 AAGTACATAA
252883 TTTTTTTC
1 TTTTTTTC
252891 TTTTTTTC
1 TTTTTTTC
252899 TTTTTTTC
1 TTTTTTTC
*
252907 TTTTCTTTT
1 TTTT-TTTC
252916 TTTCTCCTTTC
1 TTT-T--TTTC
252927 TTTTTTTC
1 TTTTTTTC
252935 TTTTTTTC
1 TTTTTTTC
252943 TT
1 TT
252945 GACAGAAATA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
8 34 0.69
9 6 0.12
10 2 0.04
11 7 0.14
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTTC
Found at i:252904 original size:15 final size:15
Alignment explanation
Indices: 252883--252940 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
252873 AAGTACATAA
252883 TTTTTTTCTTTTTTTC
1 TTTTTTTC-TTTTTTC
252899 TTTTTTTC--TTTTC
1 TTTTTTTCTTTTTTC
**
252912 TTTTTTTCTCCTTTC
1 TTTTTTTCTTTTTTC
252927 TTTTTTTCTTTTTT
1 TTTTTTTCTTTTTT
252941 TCTTGACAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
13 13 0.35
15 16 0.43
16 8 0.22
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTCTTTTTTC
Found at i:252910 original size:13 final size:13
Alignment explanation
Indices: 252894--252938 Score: 72
Period size: 13 Copynumber: 3.3 Consensus size: 13
252884 TTTTTTCTTT
252894 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
252907 TTTTCTTTTTTTC
1 TTTTCTTTTTTTC
252920 TCCTTTCTTTTTTTC
1 T--TTTCTTTTTTTC
252935 TTTT
1 TTTT
252939 TTTCTTGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 17 0.57
15 13 0.43
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:252917 original size:23 final size:23
Alignment explanation
Indices: 252898--252943 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
252888 TTCTTTTTTT
*
252898 CTTTTTTTCTTTTCTTTTTTTCTC
1 CTTTCTTT-TTTTCTTTTTTTCTC
252922 CTTTCTTTTTTTCTTTTTTTCT
1 CTTTCTTTTTTTCTTTTTTTCT
252944 TGACAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (23 bp):
CTTTCTTTTTTTCTTTTTTTCTC
Found at i:253004 original size:12 final size:12
Alignment explanation
Indices: 252987--253015 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
252977 TAAAACGAAT
252987 TATTAATATAAA
1 TATTAATATAAA
252999 TATTAATATAAA
1 TATTAATATAAA
253011 T-TTAA
1 TATTAA
253016 AATACTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TATTAATATAAA
Found at i:253869 original size:33 final size:33
Alignment explanation
Indices: 253831--253895 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
253821 CGAATTATTC
* *
253831 ATATATTAAAAAATTATATAAAAATATAATATTTT
1 ATATA-TAAAAAATAACATAAAAATA-AATATTTT
*
253866 ATATATAAAAAATAACATAAATATAAATAT
1 ATATATAAAAAATAACATAAAAATAAATAT
253896 AAATATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 5 0.19
34 17 0.63
35 5 0.19
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (33 bp):
ATATATAAAAAATAACATAAAAATAAATATTTT
Found at i:254597 original size:19 final size:19
Alignment explanation
Indices: 254551--254598 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
254541 AACTCCTTTA
*
254551 AATATAATATTTAAAAATAT
1 AATATAAAATTTAAAAAT-T
254571 AATA-AAAATTT-AAAATT
1 AATATAAAATTTAAAAATT
254588 AATTATAAAAT
1 AA-TATAAAAT
254599 AATAATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 3 0.12
18 7 0.28
19 11 0.44
20 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATAAAATTTAAAAATT
Found at i:254949 original size:6 final size:6
Alignment explanation
Indices: 254925--254967 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
254915 ATACATTATT
254925 TTAAAA -TAAAA TTAAAAAA TTAAAA TTAAAA TTAAAA TTAAAA
1 TTAAAA TTAAAA TT--AAAA TTAAAA TTAAAA TTAAAA TTAAAA
254968 AATAAAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 5 0.15
6 23 0.68
8 6 0.18
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
TTAAAA
Found at i:254960 original size:26 final size:25
Alignment explanation
Indices: 254925--254975 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
254915 ATACATTATT
*
254925 TTAAAATAAAATTAAAAAATTAAAA
1 TTAAAATAAAATTAAAAAATAAAAA
254950 TTAAAATTAAAATTAAAAAATAAAAA
1 TTAAAA-TAAAATTAAAAAATAAAAA
254976 AGATTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (25 bp):
TTAAAATAAAATTAAAAAATAAAAA
Found at i:255078 original size:17 final size:16
Alignment explanation
Indices: 255058--255111 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
255048 ATATATAATT
255058 TTAAAATAAATTAAAAC
1 TTAAAA-AAATTAAAAC
255075 TTAAAAAAATTAAAA-
1 TTAAAAAAATTAAAAC
* * *
255090 ATACAAAACTTAAAA-
1 TTAAAAAAATTAAAAC
255105 TTAAAAA
1 TTAAAAA
255112 CCTAAGTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
15 17 0.53
16 9 0.28
17 6 0.19
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
TTAAAAAAATTAAAAC
Found at i:255285 original size:13 final size:13
Alignment explanation
Indices: 255267--255320 Score: 69
Period size: 13 Copynumber: 4.2 Consensus size: 13
255257 ATCAATTTTT
255267 TTTAAAATAATAA
1 TTTAAAATAATAA
255280 TTTAAAATAA-AA
1 TTTAAAATAATAA
255292 TATTAAAAT--TAA
1 T-TTAAAATAATAA
255304 TTATAAAATAATAA
1 TT-TAAAATAATAA
255318 TTT
1 TTT
255321 TTTAATTAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
11 1 0.03
12 12 0.33
13 18 0.50
14 5 0.14
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTTAAAATAATAA
Found at i:255290 original size:18 final size:19
Alignment explanation
Indices: 255269--255320 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
255259 CAATTTTTTT
255269 TAAAATAATAATTTAA-AA
1 TAAAATAATAATTTAATAA
* * *
255287 TAAAATATTAAAATTAATTA
1 TAAAATAAT-AATTTAATAA
255307 TAAAATAATAATTT
1 TAAAATAATAATTT
255321 TTTAATTAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 8 0.30
19 10 0.37
20 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATAATAATTTAATAA
Found at i:255361 original size:26 final size:25
Alignment explanation
Indices: 255282--255361 Score: 69
Period size: 22 Copynumber: 3.2 Consensus size: 25
255272 AATAATAATT
*
255282 TAAAATA-AAATATTAAAATTAATTA
1 TAAAATATAAATATT-AAATTAGTTA
* * *
255307 TAAAATAATAATTTTTTAATTAG-T-
1 TAAAAT-ATAAATATTAAATTAGTTA
255331 T-AAATATAAATATTAAATTGAGTTA
1 TAAAATATAAATATTAAATT-AGTTA
255356 TAAAAT
1 TAAAAT
255362 TTTACGTCAA
Statistics
Matches: 42, Mismatches: 7, Indels: 11
0.70 0.12 0.18
Matches are distributed among these distances:
22 11 0.26
23 6 0.14
24 2 0.05
25 8 0.19
26 10 0.24
27 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (25 bp):
TAAAATATAAATATTAAATTAGTTA
Found at i:255422 original size:6 final size:6
Alignment explanation
Indices: 255395--255436 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
255385 ATATATTATT
* *
255395 TTAAAA -TAAAA TTAAAA GTTAAAA TTAAAA TAAAAA ATAAAA
1 TTAAAA TTAAAA TTAAAA -TTAAAA TTAAAA TTAAAA TTAAAA
255437 AATTATTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
5 5 0.16
6 20 0.65
7 6 0.19
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (6 bp):
TTAAAA
Found at i:255882 original size:16 final size:17
Alignment explanation
Indices: 255853--255893 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
255843 ATTTTTAAAT
255853 AAATTTTA-TTAATT-A
1 AAATTTTATTTAATTAA
255868 AAATTTTATTTAATTAA
1 AAATTTTATTTAATTAA
255885 AAATTTTAT
1 AAATTTTAT
255894 AAATATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 8 0.33
16 6 0.25
17 10 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AAATTTTATTTAATTAA
Found at i:255904 original size:17 final size:18
Alignment explanation
Indices: 255853--255906 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 18
255843 ATTTTTAAAT
255853 AAATTTTATT--A-ATTA
1 AAATTTTATTAAATATTA
* *
255868 AAATTTTATTTAAT-TAA
1 AAATTTTATTAAATATTA
255885 AAATTTTA-TAAATATTA
1 AAATTTTATTAAATATTA
255902 AAATT
1 AAATT
255907 CCAAGGGAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 10 0.31
16 4 0.12
17 18 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTTTATTAAATATTA
Found at i:256269 original size:14 final size:14
Alignment explanation
Indices: 256242--256284 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 14
256232 GAATATATAA
*
256242 TTTTT-TTTCGTTT
1 TTTTTCTTTCTTTT
256255 TTTTTC--TCTTTT
1 TTTTTCTTTCTTTT
256267 TTTTTCTTTCTTTT
1 TTTTTCTTTCTTTT
256281 TTTT
1 TTTT
256285 CAAAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 11 0.42
13 5 0.19
14 10 0.38
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (14 bp):
TTTTTCTTTCTTTT
Found at i:256627 original size:14 final size:14
Alignment explanation
Indices: 256608--256647 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
256598 TTATTTTCTC
256608 TTTTTTCTTTCCTT
1 TTTTTTCTTTCCTT
*
256622 TTTTTTTTTTCCTT
1 TTTTTTCTTTCCTT
*
256636 TTCTTTCTTTCC
1 TTTTTTCTTTCC
256648 CAGCTAAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTCTTTCCTT
Found at i:259187 original size:13 final size:13
Alignment explanation
Indices: 259169--259193 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
259159 TTATATTTAC
259169 TTATATTTAATAT
1 TTATATTTAATAT
259182 TTATATTTAATA
1 TTATATTTAATA
259194 CATATTTAAA
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):
TTATATTTAATAT
Found at i:261750 original size:2 final size:2
Alignment explanation
Indices: 261743--261772 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
261733 GAAGTCTGAG
261743 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
261773 GAGTTTCGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:262206 original size:16 final size:16
Alignment explanation
Indices: 262185--262218 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
262175 TTATTATCAT
262185 TTATATTACTCGAATG
1 TTATATTACTCGAATG
262201 TTATATTACTCGAATG
1 TTATATTACTCGAATG
262217 TT
1 TT
262219 CAGTCGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (16 bp):
TTATATTACTCGAATG
Found at i:262303 original size:8 final size:8
Alignment explanation
Indices: 262290--262314 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
262280 TATATATTAA
262290 AAAAATTT
1 AAAAATTT
262298 AAAAATTT
1 AAAAATTT
262306 AAAAATTT
1 AAAAATTT
262314 A
1 A
262315 TATTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAAAATTT
Found at i:264996 original size:8 final size:8
Alignment explanation
Indices: 264983--265014 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
264973 CTTGAATTAC
264983 AATAATAA
1 AATAATAA
264991 AATAATAA
1 AATAATAA
264999 AATAATAA
1 AATAATAA
265007 AATAATAA
1 AATAATAA
265015 TATATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AATAATAA
Found at i:264997 original size:3 final size:3
Alignment explanation
Indices: 264983--265023 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
264973 CTTGAATTAC
264983 AAT AAT AA- AAT AAT AA- AAT AAT AA- AAT AAT AAT ATAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT A
265024 TATTTAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 6 0.18
3 25 0.74
4 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:265058 original size:14 final size:14
Alignment explanation
Indices: 265014--265058 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
265004 TAAAATAATA
265014 ATATATAATATATTT
1 ATATATAATA-ATTT
* *
265029 AAATATAATTATTT
1 ATATATAATAATTT
*
265043 ATATTTAATAATTT
1 ATATATAATAATTT
265057 AT
1 AT
265059 CTTTATATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATATATAATAATTT
Found at i:272037 original size:13 final size:14
Alignment explanation
Indices: 272019--272057 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
272009 ATTAAGTACA
272019 TATTTATTTTTG-T
1 TATTTATTTTTGAT
272032 TATTTATTTTTGAT
1 TATTTATTTTTGAT
*
272046 TTTTTATATTTT
1 TATTTAT-TTTT
272058 ATTTTACATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.52
14 7 0.30
15 4 0.17
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (14 bp):
TATTTATTTTTGAT
Found at i:272051 original size:14 final size:14
Alignment explanation
Indices: 272021--272062 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
272011 TAAGTACATA
*
272021 TTTATTTTTG-TTA
1 TTTATTTTTGATTT
272034 TTTATTTTTGATTT
1 TTTATTTTTGATTT
272048 TTTATATTTT-ATTT
1 TTTAT-TTTTGATTT
272062 T
1 T
272063 ACATCATTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 10 0.38
14 12 0.46
15 4 0.15
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.79
Consensus pattern (14 bp):
TTTATTTTTGATTT
Found at i:273981 original size:49 final size:49
Alignment explanation
Indices: 273927--274024 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
273917 CCAAGAGAAG
273927 CTGGTAGAGAAGCTATAAGAGACTGGCTCAAATTAAGGACTCGAAGCTT
1 CTGGTAGAGAAGCTATAAGAGACTGGCTCAAATTAAGGACTCGAAGCTT
273976 CTGGTAGAGAAGCTATAAGAGACTGGCTCAAATTAAGGACTCGAAGCTT
1 CTGGTAGAGAAGCTATAAGAGACTGGCTCAAATTAAGGACTCGAAGCTT
274025 TCTAAGTACT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (49 bp):
CTGGTAGAGAAGCTATAAGAGACTGGCTCAAATTAAGGACTCGAAGCTT
Found at i:281500 original size:19 final size:20
Alignment explanation
Indices: 281459--281500 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
281449 ATGTATCGTA
* *
281459 TTATATTTGTTATATTATTT
1 TTATATTTGTTATATCATAT
281479 TTATATTT-TTATATCATAT
1 TTATATTTGTTATATCATAT
281498 TTA
1 TTA
281501 AAATTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
TTATATTTGTTATATCATAT
Found at i:281936 original size:27 final size:27
Alignment explanation
Indices: 281858--281936 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
281848 CAAAAACCAC
*
281858 CCTTTGTGTTTGTCAAAAATGGTAGTT
1 CCTTTGTGTTTGTCAAAAATGGTGGTT
* *
281885 ACTTTGTATTTGTCAAAAATGGTGGTT
1 CCTTTGTGTTTGTCAAAAATGGTGGTT
* * *
281912 CCTTTTTGTTTGTAAAAAATTGTGG
1 CCTTTGTGTTTGTCAAAAATGGTGG
281937 CTTGTTGTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.46
Consensus pattern (27 bp):
CCTTTGTGTTTGTCAAAAATGGTGGTT
Found at i:281953 original size:24 final size:24
Alignment explanation
Indices: 281917--281962 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
281907 TGGTTCCTTT
*
281917 TTGTTTGTAAAAAATT-GTGGCTTG
1 TTGTTTAT-AAAAATTGGTGGCTTG
*
281941 TTGTTTATCAAAATTGGTGGCT
1 TTGTTTATAAAAATTGGTGGCT
281963 AATTTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.46
Consensus pattern (24 bp):
TTGTTTATAAAAATTGGTGGCTTG
Found at i:281970 original size:23 final size:23
Alignment explanation
Indices: 281927--281971 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
281917 TTGTTTGTAA
**
281927 AAAATTGTGGCTTGTTGTTTATC
1 AAAATTGTGGCTAATTGTTTATC
281950 AAAATTGGTGGCTAATT-TTTAT
1 AAAATT-GTGGCTAATTGTTTAT
281972 TGCAAAATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (23 bp):
AAAATTGTGGCTAATTGTTTATC
Found at i:286386 original size:27 final size:27
Alignment explanation
Indices: 286355--286428 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
286345 AAAAACTACC
286355 CTTTGTGTTTGTCAAAAATTATGGTTA
1 CTTTGTGTTTGTCAAAAATTATGGTTA
* * * *
286382 CTTTGTATTTGTTAAAAATGATGGTTT
1 CTTTGTGTTTGTCAAAAATTATGGTTA
* * *
286409 TTTTTTGTTTATCAAAAATT
1 CTTTGTGTTTGTCAAAAATT
286429 GTGGCTTGTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.27, C:0.05, G:0.15, T:0.53
Consensus pattern (27 bp):
CTTTGTGTTTGTCAAAAATTATGGTTA
Found at i:286442 original size:24 final size:24
Alignment explanation
Indices: 286413--286458 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
286403 TGGTTTTTTT
286413 TTGTTTATCAAAAATT-GTGGCTTG
1 TTGTTTATC-AAAATTGGTGGCTTG
*
286437 TTGTTTGTCAAAATTGGTGGCT
1 TTGTTTATCAAAATTGGTGGCT
286459 AATTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.46
Consensus pattern (24 bp):
TTGTTTATCAAAATTGGTGGCTTG
Found at i:288264 original size:18 final size:18
Alignment explanation
Indices: 288243--288277 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
288233 TTAAATTAAA
288243 TATATATTTATCTATATC
1 TATATATTTATCTATATC
*
288261 TATATCTTTATCTATAT
1 TATATATTTATCTATAT
288278 TTTCATATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATATTTATCTATATC
Found at i:291616 original size:18 final size:16
Alignment explanation
Indices: 291595--291639 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 16
291585 AATATAAATA
291595 TAAATATAAACAAATTAT
1 TAAATATAAA-AAATT-T
*
291613 TAAATATATTAAAATTT
1 TAAATATA-AAAAATTT
291630 TAAATATAAA
1 TAAATATAAA
291640 TATGATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 1 0.04
17 9 0.38
18 13 0.54
19 1 0.04
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATATAAAAAATTT
Found at i:291676 original size:19 final size:19
Alignment explanation
Indices: 291652--291694 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
291642 TGATATATTA
291652 TATATTATGT-TGTATTTAT
1 TATATTATGTATGTATTT-T
*
291671 TATATTATTTATGTATTTT
1 TATATTATGTATGTATTTT
291690 TATAT
1 TATAT
291695 CATATTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (19 bp):
TATATTATGTATGTATTTT
Found at i:292319 original size:2 final size:2
Alignment explanation
Indices: 292307--292340 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
292297 TTTACTACTG
*
292307 TA TA CA 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
292341 AATAAACGAT
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):
TA
Found at i:292771 original size:64 final size:64
Alignment explanation
Indices: 292697--292819 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 64
292687 AAAATTAACC
* *
292697 ATTCAACTTAAAATTAATGAATAATAGGTAAATAAAA-TTTAACTTGAATAAAATCACAAGTAAA
1 ATTCAACTTAAAATAAATGAATAATAGGTAAA-AAAAGTTCAACTTGAATAAAATCACAAGTAAA
* * * *
292761 ATTCAGCTTAAAATAAATGGATAATAGTTAAAAAAAGTTCAACTTGAATAAGATCACAA
1 ATTCAACTTAAAATAAATGAATAATAGGTAAAAAAAGTTCAACTTGAATAAAATCACAA
292820 CTAGAGGTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 4 0.08
64 48 0.92
ACGTcount: A:0.53, C:0.09, G:0.10, T:0.28
Consensus pattern (64 bp):
ATTCAACTTAAAATAAATGAATAATAGGTAAAAAAAGTTCAACTTGAATAAAATCACAAGTAAA
Found at i:292970 original size:14 final size:14
Alignment explanation
Indices: 292953--292995 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
292943 TTTAAAAAAT
292953 TATTTTTATATTAA
1 TATTTTTATATTAA
*
292967 TATTTTATATATT-T
1 TATTTT-TATATTAA
292981 TATTTTTATTATTAA
1 TATTTTTA-TATTAA
292996 AAAATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 2 0.08
14 16 0.67
15 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTTATATTAA
Found at i:293582 original size:24 final size:23
Alignment explanation
Indices: 293537--293583 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
293527 ATTTGAAGTT
293537 GATATTGAATATTAATAGATATTG
1 GATATTGAATATTAATA-ATATTG
293561 GATATTGATATATTTAAT-ATATT
1 GATATTGA-ATA-TTAATAATATT
293584 TTAAAGATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 13 0.62
25 3 0.14
26 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (23 bp):
GATATTGAATATTAATAATATTG
Found at i:296589 original size:22 final size:22
Alignment explanation
Indices: 296534--296589 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
296524 TTTTATTTAA
*
296534 ATTTAAT--TATAAAAATACTT
1 ATTTAATAATATAAAAATAATT
* *
296554 ATTTATTAACATAAAAATAA-T
1 ATTTAATAATATAAAAATAATT
296575 ATATTAATAATATAA
1 AT-TTAATAATATAA
296590 TAAACAAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 6 0.21
21 3 0.11
22 19 0.68
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTTAATAATATAAAAATAATT
Found at i:297935 original size:91 final size:91
Alignment explanation
Indices: 297780--297962 Score: 348
Period size: 91 Copynumber: 2.0 Consensus size: 91
297770 ATGTTTTAAG
*
297780 GTTTTCATAACCAAAAATTTTATGAAAGATTAATAAAATTGTATCCAATGTAATAAAATATTATA
1 GTTTTCATAACCAAAAATTTTATGAAAGATTAATAAAATTATATCCAATGTAATAAAATATTATA
*
297845 TTGAAACTTTGTTGTGCTTATTGTAT
66 TCGAAACTTTGTTGTGCTTATTGTAT
297871 GTTTTCATAACCAAAAATTTTATGAAAGATTAATAAAATTATATCCAATGTAATAAAATATTATA
1 GTTTTCATAACCAAAAATTTTATGAAAGATTAATAAAATTATATCCAATGTAATAAAATATTATA
297936 TCGAAACTTTGTTGTGCTTATTGTAT
66 TCGAAACTTTGTTGTGCTTATTGTAT
297962 G
1 G
297963 CTTACCATTA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 90 1.00
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (91 bp):
GTTTTCATAACCAAAAATTTTATGAAAGATTAATAAAATTATATCCAATGTAATAAAATATTATA
TCGAAACTTTGTTGTGCTTATTGTAT
Found at i:299928 original size:13 final size:13
Alignment explanation
Indices: 299912--299983 Score: 108
Period size: 13 Copynumber: 5.5 Consensus size: 13
299902 GGGATATAAA
299912 AGAGGGATGCTTG
1 AGAGGGATGCTTG
* *
299925 AGAGAGATGCTTA
1 AGAGGGATGCTTG
299938 AGAGGGATGCTTG
1 AGAGGGATGCTTG
* *
299951 AGAGAGATGCTTA
1 AGAGGGATGCTTG
299964 AGAGGGATGCTTG
1 AGAGGGATGCTTG
299977 AGAGGGA
1 AGAGGGA
299984 GGAGGGAGCC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 51 1.00
ACGTcount: A:0.31, C:0.07, G:0.42, T:0.21
Consensus pattern (13 bp):
AGAGGGATGCTTG
Found at i:299940 original size:26 final size:26
Alignment explanation
Indices: 299911--299980 Score: 140
Period size: 26 Copynumber: 2.7 Consensus size: 26
299901 AGGGATATAA
299911 AAGAGGGATGCTTGAGAGAGATGCTT
1 AAGAGGGATGCTTGAGAGAGATGCTT
299937 AAGAGGGATGCTTGAGAGAGATGCTT
1 AAGAGGGATGCTTGAGAGAGATGCTT
299963 AAGAGGGATGCTTGAGAG
1 AAGAGGGATGCTTGAGAG
299981 GGAGGAGGGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.31, C:0.07, G:0.40, T:0.21
Consensus pattern (26 bp):
AAGAGGGATGCTTGAGAGAGATGCTT
Found at i:300106 original size:27 final size:27
Alignment explanation
Indices: 300039--300140 Score: 111
Period size: 27 Copynumber: 3.9 Consensus size: 27
300029 TAAAAATTAG
* *
300039 CCACCAATTTTGACAAACAATAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
**
300063 CCATAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * *
300090 CCACCATTTTTGACAAATACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
300117 CCACCATTTTTGACAAACATAAAG
1 CCACCATTTTTGACAAACAAAAAG
300141 AGTGATTTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
24 19 0.30
25 1 0.02
27 44 0.69
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.24
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:304461 original size:11 final size:13
Alignment explanation
Indices: 304431--304461 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
304421 AGGGATACAA
304431 GAGAGAGATGCTT
1 GAGAGAGATGCTT
304444 GAGAGAGATGCTT
1 GAGAGAGATGCTT
*
304457 AAGAG
1 GAGAG
304462 GGAGGAGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.39, T:0.19
Consensus pattern (13 bp):
GAGAGAGATGCTT
Found at i:304546 original size:24 final size:24
Alignment explanation
Indices: 304518--304616 Score: 67
Period size: 27 Copynumber: 3.9 Consensus size: 24
304508 AATAAAAATT
304518 AGCCACCAATTTTGACAAACAATA
1 AGCCACCAATTTTGACAAACAATA
* *
304542 AGCCA-TAATTTTTGACAAACAAAA
1 AGCCACCAA-TTTTGACAAACAATA
* *
304566 AGGAACAACCATTTTTGACAAATACAAAGTA
1 A-G--CCACCAATTTTGAC-AA-AC-AA-TA
*
304597 A-CCACCATTTTTGACAAACA
1 AGCCACCAATTTTGACAAACA
304617 TAAAGAGTGG
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
23 2 0.03
24 21 0.36
25 3 0.05
26 2 0.03
27 22 0.37
28 3 0.05
29 2 0.03
30 2 0.03
31 2 0.03
ACGTcount: A:0.46, C:0.21, G:0.09, T:0.23
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAATA
Found at i:304587 original size:27 final size:27
Alignment explanation
Indices: 304549--304621 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
304539 ATAAGCCATA
304549 ATTTTTGACAAACAAAAAGGAACAACC
1 ATTTTTGACAAACAAAAAGGAACAACC
* * * *
304576 ATTTTTGACAAATACAAAGTAACCACC
1 ATTTTTGACAAACAAAAAGGAACAACC
*
304603 ATTTTTGACAAACATAAAG
1 ATTTTTGACAAACAAAAAG
304622 AGTGGTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.25
Consensus pattern (27 bp):
ATTTTTGACAAACAAAAAGGAACAACC
Found at i:309921 original size:13 final size:12
Alignment explanation
Indices: 309905--309952 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
309895 TCCAATTTAG
309905 ATATTTGAATTTT
1 ATATTT-AATTTT
* *
309918 ATATTGATTTTT
1 ATATTTAATTTT
*
309930 ATATTTAATTAT
1 ATATTTAATTTT
309942 -TATTTAATTTT
1 ATATTTAATTTT
309953 TTTTAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
11 10 0.34
12 14 0.48
13 5 0.17
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (12 bp):
ATATTTAATTTT
Found at i:310931 original size:33 final size:33
Alignment explanation
Indices: 310894--310957 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
310884 TTGAAAATTA
310894 ATAAAAACCAGTGTATATATCTTTTATATTTTT
1 ATAAAAACCAGTGTATATATCTTTTATATTTTT
310927 ATAAAAACCAGTGTATATATCTTTTATATTT
1 ATAAAAACCAGTGTATATATCTTTTATATTT
310958 AATTTATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (33 bp):
ATAAAAACCAGTGTATATATCTTTTATATTTTT
Found at i:310969 original size:2 final size:2
Alignment explanation
Indices: 310962--310988 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
310952 ATATTTAATT
310962 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
310989 CTTTAGATGG
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:316520 original size:25 final size:24
Alignment explanation
Indices: 316492--316542 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
316482 ATGAGTTTAA
316492 ATCTTAACATTTACAATTTTTTTTT
1 ATCTTAACA-TTACAATTTTTTTTT
* * *
316517 ATCTTTAGATTATAATTTTTTTTT
1 ATCTTAACATTACAATTTTTTTTT
316541 AT
1 AT
316543 AAAAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.63
Consensus pattern (24 bp):
ATCTTAACATTACAATTTTTTTTT
Found at i:319856 original size:17 final size:17
Alignment explanation
Indices: 319812--319859 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
319802 CAATTGTGGC
*
319812 AAAGGAAGAAAGAAAGGAA
1 AAAGGAA-AAA-AAAAGAA
*
319831 ATAGAGAAAAAAAAAGAA
1 AAAG-GAAAAAAAAAGAA
319849 AAAGGAAAAAA
1 AAAGGAAAAAA
319860 GAGAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 7 0.28
18 9 0.36
19 6 0.24
20 3 0.12
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (17 bp):
AAAGGAAAAAAAAAGAA
Found at i:320558 original size:26 final size:26
Alignment explanation
Indices: 320528--320582 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
320518 TATAATGTAC
*
320528 ATATTATGAATTATA-TCTGTATATTT
1 ATATTAT-AATTATATTATGTATATTT
* *
320554 ATATTATATTTATATTATTTATATTT
1 ATATTATAATTATATTATGTATATTT
320580 ATA
1 ATA
320583 GTTTACTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (26 bp):
ATATTATAATTATATTATGTATATTT
Found at i:320563 original size:11 final size:11
Alignment explanation
Indices: 320547--320571 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
320537 ATTATATCTG
320547 TATATTTATAT
1 TATATTTATAT
320558 TATATTTATAT
1 TATATTTATAT
320569 TAT
1 TAT
320572 TTATATTTAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:320569 original size:17 final size:17
Alignment explanation
Indices: 320537--320587 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 17
320527 CATATTATGA
320537 ATTATATCTGTATATTTAT
1 ATTATAT-T-TATATTTAT
320556 ATTATATTTATA-TTAT
1 ATTATATTTATATTTAT
320572 -TTATATTTATAGTTTA
1 ATTATATTTATA-TTTA
320588 CTGTAAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 11 0.37
16 4 0.13
17 7 0.23
18 1 0.03
19 7 0.23
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (17 bp):
ATTATATTTATATTTAT
Found at i:321650 original size:11 final size:11
Alignment explanation
Indices: 321634--321674 Score: 75
Period size: 11 Copynumber: 3.8 Consensus size: 11
321624 ATTAAATTTA
321634 TATATTTATGT
1 TATATTTATGT
321645 TATATTTATGT
1 TATATTTATGT
321656 TATATTTATGT
1 TATATTTATGT
321667 TAT-TTTAT
1 TATATTTAT
321675 ATGTAGAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 5 0.17
11 25 0.83
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (11 bp):
TATATTTATGT
Found at i:328122 original size:33 final size:33
Alignment explanation
Indices: 328080--328142 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
328070 TAAAAGAAAA
328080 TTTCATTCAATTCAAAGGTTATTCCACGGATAT
1 TTTCATTCAATTCAAAGGTTATTCCACGGATAT
*
328113 TTTCATTCAATTCAAAGGTTATTCTACGGA
1 TTTCATTCAATTCAAAGGTTATTCCACGGA
328143 AATAGTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (33 bp):
TTTCATTCAATTCAAAGGTTATTCCACGGATAT
Found at i:328435 original size:11 final size:12
Alignment explanation
Indices: 328413--328442 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
328403 TTGTTCCCTT
328413 ATTTTGTTTTTA
1 ATTTTGTTTTTA
328425 ATTTT-TTTTTA
1 ATTTTGTTTTTA
328436 ATTTTGT
1 ATTTTGT
328443 AGTGTAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (12 bp):
ATTTTGTTTTTA
Found at i:328685 original size:34 final size:34
Alignment explanation
Indices: 328615--328833 Score: 298
Period size: 34 Copynumber: 6.5 Consensus size: 34
328605 TGGAGGAATA
* * *
328615 CATTGTTGATTAAAT-GGTGATTTAGTAGTTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* * * *
328648 CATTGTTGATTAAATGGGTGATTTGGTGGTTTGC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
*
328682 CATTGTTGACTAAAT-GGAGATTTGGTAGCTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
*
328715 CATTGTTGATTAAATGGGAAATTTGGTAGCTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* *
328749 CATTGTTGATTAAATGGGTGATTTGGTGGCTTAC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
* * *
328783 CATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
328817 CATTGTTGATTAAATGG
1 CATTGTTGATTAAATGG
328834 TGGTTTTTAC
Statistics
Matches: 165, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 43 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
CATTGTTGATTAAATGGGAGATTTGGTAGCTTAC
Found at i:328799 original size:68 final size:67
Alignment explanation
Indices: 328615--328835 Score: 325
Period size: 67 Copynumber: 3.3 Consensus size: 67
328605 TGGAGGAATA
* * * * *
328615 CATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTT
1 CATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
328680 GC
66 GC
* * *
328682 CATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTT
1 CATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
*
328747 AC
66 GC
* * *
328749 CATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGT
1 CATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCT
328814 TGC
65 TGC
328817 CATTGTTGATTAAATGGTG
1 CATTGTTGATTAAATGGTG
328836 GTTTTTACCA
Statistics
Matches: 137, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 76 0.55
68 61 0.45
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
CATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
GC
Found at i:329194 original size:19 final size:19
Alignment explanation
Indices: 329138--329194 Score: 87
Period size: 19 Copynumber: 3.0 Consensus size: 19
329128 TGGTTGTCGA
**
329138 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
329157 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
329176 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
329195 ATTACTGTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:333335 original size:34 final size:34
Alignment explanation
Indices: 333266--333483 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
333256 AAGTGGGAGA
* * *
333266 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
333299 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
333333 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
333366 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
333400 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
333434 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
333468 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
333484 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:333449 original size:68 final size:67
Alignment explanation
Indices: 333266--333485 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
333256 AAGTGGGAGA
* * * * *
333266 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
333331 CC
66 CC
* * * *
333333 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
333398 CC
66 CC
* * *
333400 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
333465 GCC
65 GCC
333468 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
333486 GTTTTTACCA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:335987 original size:27 final size:27
Alignment explanation
Indices: 335932--335987 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
335922 TAATACGACA
* *
335932 ATGATAAAAAAATAATTAAAATATTAT
1 ATGATAAAAAAATAATTAAAACATGAT
*
335959 ATGATAAAAAAATAACTT-GAACATGAT
1 ATGATAAAAAAATAA-TTAAAACATGAT
335986 AT
1 AT
335988 AAATGCGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (27 bp):
ATGATAAAAAAATAATTAAAACATGAT
Found at i:336349 original size:17 final size:17
Alignment explanation
Indices: 336323--336369 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
336313 TGGCAAAGGA
* *
336323 AGAAAGAAAGGAAATAG
1 AGAAAAAAAGGAAAAAG
336340 AGAAAAAAA-GAAAAAG
1 AGAAAAAAAGGAAAAAG
336356 -GAAAAAAA-GAAAAA
1 AGAAAAAAAGGAAAAA
336370 TATTCGTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 14 0.50
16 6 0.21
17 8 0.29
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (17 bp):
AGAAAAAAAGGAAAAAG
Found at i:336361 original size:15 final size:15
Alignment explanation
Indices: 336341--336369 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
336331 AGGAAATAGA
336341 GAAAAAAAGAAAAAG
1 GAAAAAAAGAAAAAG
336356 GAAAAAAAGAAAAA
1 GAAAAAAAGAAAAA
336370 TATTCGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
GAAAAAAAGAAAAAG
Found at i:336614 original size:11 final size:12
Alignment explanation
Indices: 336581--336619 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
336571 GTGCTCCTAT
336581 TATTATTTTTTA
1 TATTATTTTTTA
*
336593 TATTATATTTTA
1 TATTATTTTTTA
336605 -ATTATTTTTTTA
1 TATTA-TTTTTTA
336617 TAT
1 TAT
336620 CATGTTTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 4 0.17
12 17 0.74
13 2 0.09
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTATTTTTTA
Found at i:339695 original size:17 final size:17
Alignment explanation
Indices: 339669--339717 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 17
339659 TATTAATTTG
*
339669 ATTTATTGATTTGATTA
1 ATTTAATGATTTGATTA
*
339686 ATTTAATGATATGATT-
1 ATTTAATGATTTGATTA
*
339702 -TTTAAT-ATTTAATTA
1 ATTTAATGATTTGATTA
339717 A
1 A
339718 AAATTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
14 6 0.23
15 6 0.23
17 14 0.54
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (17 bp):
ATTTAATGATTTGATTA
Found at i:340541 original size:16 final size:16
Alignment explanation
Indices: 340520--340551 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
340510 ATCATTTTTA
*
340520 GGTTCGGGTCATTTCG
1 GGTTCGGATCATTTCG
340536 GGTTCGGATCATTTCG
1 GGTTCGGATCATTTCG
340552 AATTCAGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.19, G:0.34, T:0.38
Consensus pattern (16 bp):
GGTTCGGATCATTTCG
Found at i:340613 original size:53 final size:54
Alignment explanation
Indices: 340533--340647 Score: 153
Period size: 53 Copynumber: 2.1 Consensus size: 54
340523 TCGGGTCATT
340533 TCGGGTTCGGATCATTTCGAATTCAGGTCAATCGGGTTTAACACTTAAGTT-AA
1 TCGGGTTCGGATCATTTCGAATTCAGGTCAATCGGGTTTAACACTTAAGTTAAA
* * * * **
340586 TCGGGTTCGGGTCA-TTCTGGATTCAGGTCAATTGGGTTTAACATTTGGGTTAAA
1 TCGGGTTCGGATCATTTC-GAATTCAGGTCAATCGGGTTTAACACTTAAGTTAAA
340640 TCGGGTTC
1 TCGGGTTC
340648 AAATTATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
52 3 0.06
53 41 0.76
54 10 0.19
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.36
Consensus pattern (54 bp):
TCGGGTTCGGATCATTTCGAATTCAGGTCAATCGGGTTTAACACTTAAGTTAAA
Found at i:341363 original size:16 final size:16
Alignment explanation
Indices: 341344--341446 Score: 125
Period size: 16 Copynumber: 6.4 Consensus size: 16
341334 TAAATTCTGG
* *
341344 TCATTTCGGGTTCGGG
1 TCATTTCGGGTTCAGA
* *
341360 TCATTTTGGGTTCGGA
1 TCATTTCGGGTTCAGA
*
341376 TCATTTCGAGTTCAGA
1 TCATTTCGGGTTCAGA
*
341392 TCATTTCGTGTTCAGA
1 TCATTTCGGGTTCAGA
* *
341408 TCATTTCAGGTTCAAA
1 TCATTTCGGGTTCAGA
341424 TCATTTTCGGGTTCAGA
1 TCA-TTTCGGGTTCAGA
341441 TCATTT
1 TCATTT
341447 TCATGTTCGG
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
16 61 0.81
17 14 0.19
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.42
Consensus pattern (16 bp):
TCATTTCGGGTTCAGA
Found at i:345418 original size:27 final size:27
Alignment explanation
Indices: 345385--345457 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
345375 AGCCACCATT
345385 TGTTTGTCAAAAATGGTGGTTAT-TTTG
1 TGTTTGTCAAAAATGGTGGTT-TCTTTG
* *
345412 TGTTTGTCAAAAATGGTGATTTCTTTT
1 TGTTTGTCAAAAATGGTGGTTTCTTTG
*
345439 TATTTGTCAAAAATGGTGG
1 TGTTTGTCAAAAATGGTGG
345458 CATGTTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 1 0.02
27 40 0.98
ACGTcount: A:0.25, C:0.05, G:0.23, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTTCTTTG
Found at i:350012 original size:27 final size:27
Alignment explanation
Indices: 349951--350015 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
349941 ACCCTTTGTT
* *
349951 TGTCAAAAATGGTGGTTATTTTGTGTT
1 TGTCAAAAATGGTGGTTATTTTGTATA
*
349978 TGTCAAAAATGGTGGTT-TCTTTTTATA
1 TGTCAAAAATGGTGGTTAT-TTTGTATA
*
350005 TGTTAAAAATG
1 TGTCAAAAATG
350016 ATGGCATGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.28, C:0.05, G:0.22, T:0.46
Consensus pattern (27 bp):
TGTCAAAAATGGTGGTTATTTTGTATA
Found at i:350746 original size:19 final size:19
Alignment explanation
Indices: 350718--350762 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
350708 CTCTATTTTC
350718 TAAA-AAAAGGTCAAAATT
1 TAAAGAAAAGGTCAAAATT
350736 TAAAGAAAAGGTCAAAATT
1 TAAAGAAAAGGTCAAAATT
350755 TAAAGAAA
1 TAAAGAAA
350763 TTAAGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.20
Consensus pattern (19 bp):
TAAAGAAAAGGTCAAAATT
Found at i:351710 original size:10 final size:11
Alignment explanation
Indices: 351685--351709 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
351675 GGTTTACAAC
351685 AAAATTAAAAA
1 AAAATTAAAAA
351696 AAAATTAAAAA
1 AAAATTAAAAA
351707 AAA
1 AAA
351710 TATTTTTTAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAAATTAAAAA
Found at i:353852 original size:19 final size:18
Alignment explanation
Indices: 353830--353877 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
353820 TATATTATAA
*
353830 ATATTGTGTTGTATTTATT
1 ATATTATGTTGTATTT-TT
*
353849 ATATTATTTCTGTATTTTT
1 ATATTATGT-TGTATTTTT
353868 ATATTATGTT
1 ATATTATGTT
353878 TAAAATTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 17 0.68
20 7 0.28
ACGTcount: A:0.23, C:0.02, G:0.10, T:0.65
Consensus pattern (18 bp):
ATATTATGTTGTATTTTT
Found at i:353997 original size:64 final size:64
Alignment explanation
Indices: 353890--354017 Score: 193
Period size: 64 Copynumber: 2.0 Consensus size: 64
353880 AAATTAACTA
** * *
353890 TTCAACTTAAAATTAATGAATAATAGGTAAAGAAAATTTAACTTGAATAAGGTCACAAGTAGAG
1 TTCAACTTAAAACAAATGAATAATAGGTAAAGAAAATTCAACTTGAATAAGATCACAAGTAGAG
* * *
353954 TTCAACTTAAAACAAATGGATAATAGTTAAAGAAAGTTCAACTTGAATAAGATCACAAGTAGAG
1 TTCAACTTAAAACAAATGAATAATAGGTAAAGAAAATTCAACTTGAATAAGATCACAAGTAGAG
354018 GTGTTTATTG
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.27
Consensus pattern (64 bp):
TTCAACTTAAAACAAATGAATAATAGGTAAAGAAAATTCAACTTGAATAAGATCACAAGTAGAG
Found at i:355137 original size:27 final size:27
Alignment explanation
Indices: 355099--355152 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
355089 GACAAATAAT
355099 AAACCACCATTTTTGACAAACACAAAG
1 AAACCACCATTTTTGACAAACACAAAG
* *
355126 AAACCACTATTTTTGAGAAACACAAAG
1 AAACCACCATTTTTGACAAACACAAAG
355153 GGTGGCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.48, C:0.22, G:0.09, T:0.20
Consensus pattern (27 bp):
AAACCACCATTTTTGACAAACACAAAG
Found at i:357049 original size:132 final size:132
Alignment explanation
Indices: 356808--357077 Score: 504
Period size: 132 Copynumber: 2.0 Consensus size: 132
356798 TTTGCATTAC
356808 TTCTTGATAAGTGACAAGAATATCATCATCAACAACTGGAAGGGCATAGGCCACCATATCAGTAA
1 TTCTTGATAAGTGACAAGAATATCATCATCAACAACTGGAAGGGCATAGGCCACCATATCAGTAA
*
356873 ATCGAGCAGGTCTACGAATTTCTGTCCTTAGCCTAGTAACTGCAAGTGATTTTGGTGTCTCCAAT
66 ATCGAGCAGGTCTACGAATTTCTATCCTTAGCCTAGTAACTGCAAGTGATTTTGGTGTCTCCAAT
356938 GG
131 GG
356940 TTCTTGATAAGTGACAAGAATATCATCATCAACAACTGGAAGGGCATAGGCCACCATATCAGTAA
1 TTCTTGATAAGTGACAAGAATATCATCATCAACAACTGGAAGGGCATAGGCCACCATATCAGTAA
* * *
357005 ATCGAGCAGGTCTACGAATTTCTATCCTTGGCCTAGTAATTGCAAGTGGTTTTGGTGTCTCCAAT
66 ATCGAGCAGGTCTACGAATTTCTATCCTTAGCCTAGTAACTGCAAGTGATTTTGGTGTCTCCAAT
357070 GG
131 GG
357072 TTCTTG
1 TTCTTG
357078 GGTTTGAACC
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 134 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.29
Consensus pattern (132 bp):
TTCTTGATAAGTGACAAGAATATCATCATCAACAACTGGAAGGGCATAGGCCACCATATCAGTAA
ATCGAGCAGGTCTACGAATTTCTATCCTTAGCCTAGTAACTGCAAGTGATTTTGGTGTCTCCAAT
GG
Found at i:361267 original size:18 final size:18
Alignment explanation
Indices: 361246--361280 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
361236 TTAAATTAAA
361246 TATATATTTATCTATATC
1 TATATATTTATCTATATC
*
361264 TATATCTTTATCTATAT
1 TATATATTTATCTATAT
361281 TTTCATATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATATTTATCTATATC
Found at i:362198 original size:18 final size:18
Alignment explanation
Indices: 362175--362219 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
362165 TGGTTAAATA
362175 TAAATATAAACAAATTAT
1 TAAATATAAACAAATTAT
** *
362193 TAAATAT-ATTAAATTTT
1 TAAATATAAACAAATTAT
362210 TAAATATAAA
1 TAAATATAAA
362220 TACGATATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATATAAACAAATTAT
Found at i:362920 original size:2 final size:2
Alignment explanation
Indices: 362890--362943 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
362880 TCTACTACTG
* * * *
362890 TA TA CA TA TA CA TA TA CA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
362932 TA TA TA TA TA TA
1 TA TA TA TA TA TA
362944 AAAGATGAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:363536 original size:14 final size:14
Alignment explanation
Indices: 363519--363549 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
363509 TTTTAAAAAT
*
363519 TATTTTTATATTAA
1 TATTTATATATTAA
363533 TATTTATATATTAA
1 TATTTATATATTAA
363547 TAT
1 TAT
363550 AAACACAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTTATATATTAA
Found at i:363701 original size:2 final size:2
Alignment explanation
Indices: 363694--363722 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
363684 ATGTTGTATT
363694 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 T
363723 TTTAATGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:367897 original size:27 final size:27
Alignment explanation
Indices: 367859--367956 Score: 160
Period size: 27 Copynumber: 3.6 Consensus size: 27
367849 AAAGCCACCC
367859 TTTGTCAAAAATGGTGGTTACTTTGTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
*
367886 TTTGTCAAAAATGGTGGTTACTTTGTG
1 TTTGTCAAAAATGGTGGTTACTTTGTA
* * *
367913 TTTGTCAAAAATTGTGGTTTCTTTTTA
1 TTTGTCAAAAATGGTGGTTACTTTGTA
367940 TTTGTCAAAAATGGTGG
1 TTTGTCAAAAATGGTGG
367957 CATGTTGTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTACTTTGTA
Found at i:367989 original size:51 final size:54
Alignment explanation
Indices: 367859--367992 Score: 139
Period size: 54 Copynumber: 2.5 Consensus size: 54
367849 AAAGCCACCC
** * * * * *
367859 TTTGTCAAAAATGGTGGTTACTTTGTATTTGTCAAAAATGGTGGTTACTTTGTG
1 TTTGTCAAAAATTATGGCTAATTTTTATTTGTCAAAAATGGTGGTCACTGTGTG
* * **
367913 TTTGTCAAAAATTGTGGTTTCTTTTTATTTGTCAAAAATGGTGG-CA-TGT-TG
1 TTTGTCAAAAATTATGGCTAATTTTTATTTGTCAAAAATGGTGGTCACTGTGTG
*
367964 TTTGTCAAAATTTATGGCTAATTTTTATT
1 TTTGTCAAAAATTATGGCTAATTTTTATT
367993 ACAAAATGGG
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
51 26 0.37
52 2 0.03
53 1 0.01
54 41 0.59
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.48
Consensus pattern (54 bp):
TTTGTCAAAAATTATGGCTAATTTTTATTTGTCAAAAATGGTGGTCACTGTGTG
Found at i:368568 original size:11 final size:11
Alignment explanation
Indices: 368545--368586 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
368535 ATAATTTTTA
368545 ATAAAATAATTT
1 ATAAAA-AATTT
368557 ATAAAAAATTT
1 ATAAAAAATTT
*
368568 ATAAAAATTTT
1 ATAAAAAATTT
368579 A-AAAAAAT
1 ATAAAAAAT
368587 CACCCACCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 6 0.21
11 16 0.57
12 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAAAAAATTT
Found at i:369464 original size:20 final size:20
Alignment explanation
Indices: 369439--369476 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
369429 TATATTTATT
369439 AAAAAATTCACTTTTTTTAA
1 AAAAAATTCACTTTTTTTAA
369459 AAAAAATTCACTTTTTTT
1 AAAAAATTCACTTTTTTT
369477 TTTTTAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAAAATTCACTTTTTTTAA
Found at i:369700 original size:17 final size:18
Alignment explanation
Indices: 369666--369701 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
369656 ACATATTCTA
369666 GTTATTATATAAAATTTT
1 GTTATTATATAAAATTTT
*
369684 GTTATTA-ATAAAGTTTT
1 GTTATTATATAAAATTTT
369701 G
1 G
369702 ACTCATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (18 bp):
GTTATTATATAAAATTTT
Done.