Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold89
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: 5168001
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 33045 characters in sequence are not A, C, G, or T
File 19 of 27
Found at i:3150080 original size:7 final size:7
Alignment explanation
Indices: 3150038--3150117 Score: 53
Period size: 7 Copynumber: 11.9 Consensus size: 7
3150028 TATATTATAA
3150038 TTATATT
1 TTATATT
*
3150045 TTAAATT
1 TTATATT
* *
3150052 TTTTAAAT
1 TTAT-ATT
3150060 TTATA--
1 TTATATT
3150065 TTA-ATT
1 TTATATT
3150071 TTATATT
1 TTATATT
3150078 TTATA--
1 TTATATT
3150083 TTATATT
1 TTATATT
3150090 TTATATT
1 TTATATT
* *
3150097 TAAAATAT
1 TTATAT-T
3150105 TTATATT
1 TTATATT
*
3150112 ATATAT
1 TTATAT
3150118 AAATTTAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
4 1 0.02
5 8 0.14
6 3 0.05
7 34 0.61
8 10 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTATATT
Found at i:3150099 original size:51 final size:52
Alignment explanation
Indices: 3150028--3150156 Score: 140
Period size: 51 Copynumber: 2.5 Consensus size: 52
3150018 TCCATTTTAA
* * * * *
3150028 TATATTATA-ATTATATTTTAAATTTTTTAAATT-TATATTAATTTTATATTT
1 TATATTATATTTTATA-TTTAAATTTTTTAAATTATATATAAATTTAAAATAT
* * *
3150079 TATATTATATTTTATATTTAAAATATTTATATTATATATAAATTTAAAATAT
1 TATATTATATTTTATATTTAAATTTTTTAAATTATATATAAATTTAAAATAT
*
3150131 T-TATT-TATTTTATATTTTAATTTTTT
1 TATATTATATTTTATATTTAAATTTTTT
3150157 TTATTAACTA
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
50 18 0.28
51 27 0.42
52 20 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (52 bp):
TATATTATATTTTATATTTAAATTTTTTAAATTATATATAAATTTAAAATAT
Found at i:3150107 original size:45 final size:47
Alignment explanation
Indices: 3150021--3150112 Score: 118
Period size: 45 Copynumber: 2.0 Consensus size: 47
3150011 TTTTTTATCC
**
3150021 ATTTTAATATATTATAATTATATTTTAAATTTTTTAAATTTATATTA
1 ATTTTAATATATTATAATTATATTTTAAATTTTAAAAATTTATATTA
* *
3150068 ATTTT-ATATTTTAT-ATTATATTTTATA-TTTAAAATATTTATATTA
1 ATTTTAATATATTATAATTATATTTTAAATTTTAAAA-ATTTATATTA
3150113 TATATAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
44 5 0.12
45 22 0.55
46 8 0.20
47 5 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (47 bp):
ATTTTAATATATTATAATTATATTTTAAATTTTAAAAATTTATATTA
Found at i:3150130 original size:26 final size:27
Alignment explanation
Indices: 3150077--3150144 Score: 95
Period size: 26 Copynumber: 2.6 Consensus size: 27
3150067 AATTTTATAT
* *
3150077 TTTATATTATATTTTATATTTAAAATA
1 TTTATATTATATTATAAATTTAAAATA
3150104 TTTATATTATA-TATAAATTTAAAATA
1 TTTATATTATATTATAAATTTAAAATA
*
3150130 TTTAT-TTATTTTATA
1 TTTATATTATATTATA
3150145 TTTTAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.11
26 22 0.59
27 11 0.30
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTATATTATATTATAAATTTAAAATA
Found at i:3150508 original size:32 final size:31
Alignment explanation
Indices: 3150457--3150530 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 31
3150447 AAATATTTTT
* * *
3150457 TATTTATCTTTATGTAAATTTTAATATAATAA
1 TATTTAT-ATTATATAAATTTTAAAATAATAA
* *
3150489 TAATTTATATTATATAAATTTTAAAATATTTA
1 T-ATTTATATTATATAAATTTTAAAATAATAA
3150521 TATTTATATT
1 TATTTATATT
3150531 TTTTATCAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 9 0.25
32 21 0.58
33 6 0.17
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (31 bp):
TATTTATATTATATAAATTTTAAAATAATAA
Found at i:3155988 original size:16 final size:16
Alignment explanation
Indices: 3155969--3156004 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3155959 CAAATATGAT
*
3155969 AAAAGAAAAA-AAAAG
1 AAAAAAAAAAGAAAAG
3155984 AAAAAAAAAAGAAAAG
1 AAAAAAAAAAGAAAAG
3156000 AAAAA
1 AAAAA
3156005 TCTTACTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAGAAAAG
Found at i:3155990 original size:11 final size:11
Alignment explanation
Indices: 3155969--3156004 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
3155959 CAAATATGAT
3155969 AAAAG-AAAAA
1 AAAAGAAAAAA
3155979 AAAAGAAAAAA
1 AAAAGAAAAAA
3155990 AAAAGAAAAGAA
1 AAAAGAAAA-AA
3156002 AAA
1 AAA
3156005 TCTTACTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.21
11 14 0.58
12 5 0.21
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:3157344 original size:15 final size:16
Alignment explanation
Indices: 3157316--3157365 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
3157306 AAATTTTATT
* *
3157316 TAAATTTATATTTTAA
1 TAAAATTATTTTTTAA
3157332 -AAAATTATTTTTTAA
1 TAAAATTATTTTTTAA
* *
3157347 TATAA-TATTTTTTAT
1 TAAAATTATTTTTTAA
3157362 TAAA
1 TAAA
3157366 TTTTAGAATA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 25 0.89
16 3 0.11
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TAAAATTATTTTTTAA
Found at i:3158089 original size:16 final size:16
Alignment explanation
Indices: 3158068--3158103 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3158058 TCTTATTTTA
*
3158068 AAATATTTAATTAATT
1 AAATATTAAATTAATT
*
3158084 AAATATTAAATTATTT
1 AAATATTAAATTAATT
3158100 AAAT
1 AAAT
3158104 TTTTTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATTAAATTAATT
Found at i:3162395 original size:16 final size:17
Alignment explanation
Indices: 3162374--3162414 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
3162364 GTTATTCAAA
3162374 ATTTATTAAAT-ATTAT
1 ATTTATTAAATAATTAT
3162390 ATTTATT-AATAATTAT
1 ATTTATTAAATAATTAT
*
3162406 ATTAATTAA
1 ATTTATTAA
3162415 TTAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 18 0.82
17 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTATTAAATAATTAT
Found at i:3163483 original size:17 final size:19
Alignment explanation
Indices: 3163439--3163483 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
3163429 ATTTTTAATA
3163439 AAAATTAAA-AAAATATAT
1 AAAATTAAACAAAATATAT
* *
3163457 AAAATCAAACAAAA-GTAT
1 AAAATTAAACAAAATATAT
3163475 -AAATTAAAC
1 AAAATTAAAC
3163484 GGAAGTTGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 8 0.35
18 11 0.48
19 4 0.17
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAATTAAACAAAATATAT
Found at i:3163887 original size:20 final size:20
Alignment explanation
Indices: 3163855--3163892 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3163845 TTTTTTAATT
3163855 AAATTGAATTAAGTTAAAAA
1 AAATTGAATTAAGTTAAAAA
3163875 AAATTCGAA-TAAGTTAAA
1 AAATT-GAATTAAGTTAAA
3163893 CGAGTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.58, C:0.03, G:0.11, T:0.29
Consensus pattern (20 bp):
AAATTGAATTAAGTTAAAAA
Found at i:3165541 original size:2 final size:2
Alignment explanation
Indices: 3165536--3165562 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3165526 ATTTGAAGTC
3165536 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 A
3165563 GCACATTTTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3166923 original size:21 final size:21
Alignment explanation
Indices: 3166879--3166923 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3166869 CGTTAAAAAG
* *
3166879 TATTATTTTATTTATATAATT
1 TATTATTTTATTTATAGAAGT
3166900 TATTATTATTATTT-TAGAAGT
1 TATTATT-TTATTTATAGAAGT
3166921 TAT
1 TAT
3166924 GAAAATCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TATTATTTTATTTATAGAAGT
Found at i:3168194 original size:13 final size:13
Alignment explanation
Indices: 3168166--3168199 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3168156 AAAAATAAAA
3168166 AAATTATAAATATT
1 AAATT-TAAATATT
*
3168180 AAATTTAAATTTT
1 AAATTTAAATATT
3168193 AAATTTA
1 AAATTTA
3168200 TTAAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTTAAATATT
Found at i:3170465 original size:2 final size:2
Alignment explanation
Indices: 3170458--3170512 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
3170448 TCAAAGGCTG
**
3170458 AT AT AT AT CC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3170500 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
3170513 CACACACAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3173825 original size:13 final size:14
Alignment explanation
Indices: 3173798--3173826 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3173788 TAACACATTA
3173798 AAAATGTTAAATTT
1 AAAATGTTAAATTT
3173812 AAAATGTT-AATTT
1 AAAATGTTAAATTT
3173825 AA
1 AA
3173827 TTATCGACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (14 bp):
AAAATGTTAAATTT
Found at i:3175061 original size:2 final size:2
Alignment explanation
Indices: 3175054--3175079 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3175044 TCGAAATCAA
3175054 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3175080 TAAAATACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3178108 original size:12 final size:12
Alignment explanation
Indices: 3178091--3178182 Score: 60
Period size: 12 Copynumber: 7.7 Consensus size: 12
3178081 ATCAACATTT
*
3178091 CCAGGCATCCCA
1 CCAGGCATACCA
* *
3178103 CCAGGCATGCTA
1 CCAGGCATACCA
* *
3178115 CCAGGGAAACCA
1 CCAGGCATACCA
*
3178127 CCAGGCATACCT
1 CCAGGCATACCA
* * *
3178139 CCAGGAAAACCT
1 CCAGGCATACCA
*
3178151 CCAGGCATTCCA
1 CCAGGCATACCA
* *
3178163 CCTGG-AAACCCA
1 CCAGGCATA-CCA
3178175 CCAGGCAT
1 CCAGGCAT
3178183 GCCTCCAGGT
Statistics
Matches: 58, Mismatches: 20, Indels: 3
0.72 0.25 0.04
Matches are distributed among these distances:
11 1 0.02
12 56 0.97
13 1 0.02
ACGTcount: A:0.30, C:0.39, G:0.20, T:0.11
Consensus pattern (12 bp):
CCAGGCATACCA
Found at i:3178127 original size:24 final size:24
Alignment explanation
Indices: 3178100--3178184 Score: 84
Period size: 24 Copynumber: 3.5 Consensus size: 24
3178090 TCCAGGCATC
3178100 CCACCAGGCATGCTACCAGGGAAA
1 CCACCAGGCATGCTACCAGGGAAA
* *
3178124 CCACCAGGCATACCT-CCAGGAAAA
1 CCACCAGGCAT-GCTACCAGGGAAA
* * * *
3178148 CCTCCAGGCATTCCACC-TGGAAA
1 CCACCAGGCATGCTACCAGGGAAA
3178171 CCCACCAGGCATGC
1 -CCACCAGGCATGC
3178185 CTCCAGGTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
23 5 0.10
24 42 0.86
25 2 0.04
ACGTcount: A:0.31, C:0.39, G:0.20, T:0.11
Consensus pattern (24 bp):
CCACCAGGCATGCTACCAGGGAAA
Found at i:3179529 original size:40 final size:40
Alignment explanation
Indices: 3179485--3179567 Score: 112
Period size: 40 Copynumber: 2.1 Consensus size: 40
3179475 ATCTATCTCA
* *
3179485 AAAAACTAAACCAAACAGAGCATGTAACGGGCTAAATAAC
1 AAAAACTAAACAAAACAGAGCATGTAACAGGCTAAATAAC
* ** *
3179525 AAAAACTAATCAAAAGGGAGCATGTAACAGGCTAAATAGC
1 AAAAACTAAACAAAACAGAGCATGTAACAGGCTAAATAAC
3179565 AAA
1 AAA
3179568 CGCTAACCTC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.53, C:0.17, G:0.17, T:0.13
Consensus pattern (40 bp):
AAAAACTAAACAAAACAGAGCATGTAACAGGCTAAATAAC
Found at i:3181396 original size:2 final size:2
Alignment explanation
Indices: 3181389--3181433 Score: 56
Period size: 2 Copynumber: 22.0 Consensus size: 2
3181379 CCTAATCTGA
*
3181389 AT AT AT AT AT AT AT AT CACC AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT -A-T AT AT AT AT AT AT AT AT AT AT AT AT
3181432 AT
1 AT
3181434 CATCTTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3181442 original size:29 final size:29
Alignment explanation
Indices: 3181389--3181445 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
3181379 CCTAATCTGA
3181389 ATATATATATATATATCACCATAATATAT
1 ATATATATATATATATCACCATAATATAT
* *
3181418 ATATATATATATATATCATCTTAATATA
1 ATATATATATATATATCACCATAATATA
3181446 GTGCTATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (29 bp):
ATATATATATATATATCACCATAATATAT
Found at i:3182511 original size:22 final size:22
Alignment explanation
Indices: 3182492--3182535 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3182482 ATACTATATT
3182492 TAATATGG-AATATAATTATAAA
1 TAATATGGTAAT-TAATTATAAA
*
3182514 TAATATGGTAATTAATTTTAAA
1 TAATATGGTAATTAATTATAAA
3182536 ATATTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (22 bp):
TAATATGGTAATTAATTATAAA
Found at i:3182552 original size:11 final size:10
Alignment explanation
Indices: 3182528--3182570 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
3182518 ATGGTAATTA
3182528 ATTTTAAAAT
1 ATTTTAAAAT
3182538 ATTTTAAAGAT
1 ATTTTAAA-AT
*
3182549 ATTTTTAAAT
1 ATTTTAAAAT
*
3182559 AATTTATAAAT
1 ATTTTA-AAAT
3182570 A
1 A
3182571 ATAAAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
10 14 0.50
11 14 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:3182696 original size:3 final size:3
Alignment explanation
Indices: 3182688--3182714 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3182678 TTGGTGTTTG
3182688 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
3182715 GCAGTTGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3183134 original size:15 final size:16
Alignment explanation
Indices: 3183104--3183139 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
3183094 ATCCAGATTA
3183104 AATTATTTTAAATTTT
1 AATTATTTTAAATTTT
3183120 AATTATTTT-AATTTT
1 AATTATTTTAAATTTT
3183135 AATTA
1 AATTA
3183140 AATTAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTATTTTAAATTTT
Found at i:3183145 original size:15 final size:15
Alignment explanation
Indices: 3183114--3183148 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3183104 AATTATTTTA
**
3183114 AATTTTAATTATTTT
1 AATTTTAATTAAATT
3183129 AATTTTAATTAAATT
1 AATTTTAATTAAATT
3183144 AATTT
1 AATTT
3183149 AGATATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
AATTTTAATTAAATT
Found at i:3183438 original size:26 final size:26
Alignment explanation
Indices: 3183388--3183435 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
3183378 ATATTTTTAA
3183388 ATTTATCATAATAATTATTTTTATTC
1 ATTTATCATAATAATTATTTTTATTC
*
3183414 ATTTAT-A-AATAATTACTTTTAT
1 ATTTATCATAATAATTATTTTTAT
3183436 ATTAATACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 1 0.05
26 6 0.29
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (26 bp):
ATTTATCATAATAATTATTTTTATTC
Found at i:3188856 original size:2 final size:2
Alignment explanation
Indices: 3188849--3188893 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3188839 GCAAACTCAG
3188849 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3188891 CT C
1 CT C
3188894 ACACACACAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:3188898 original size:2 final size:2
Alignment explanation
Indices: 3188893--3188918 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3188883 CTCTCTCTCT
3188893 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
3188919 AACAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3189466 original size:6 final size:6
Alignment explanation
Indices: 3189455--3189490 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
3189445 AGCTGTTACG
*
3189455 ATTATA ATTATA ATTATA ATTATA ATTACA ATTATA
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA
3189491 GAGTAGTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (6 bp):
ATTATA
Found at i:3195056 original size:19 final size:20
Alignment explanation
Indices: 3194983--3195065 Score: 70
Period size: 21 Copynumber: 4.3 Consensus size: 20
3194973 AAAATTAAAA
* *
3194983 TTAAATAAAAAATATTTTTT
1 TTAAATAAATAATATTATTT
3195003 ATTAAATAAATAATA--A--T
1 -TTAAATAAATAATATTATTT
3195020 TTAAATTAAATCAA-ATTATTT
1 TTAAA-TAAAT-AATATTATTT
*
3195041 TTAAATAAA-AATATTATAT
1 TTAAATAAATAATATTATTT
3195060 TTAAAT
1 TTAAAT
3195066 TTAATTTAAT
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
16 5 0.10
17 7 0.13
18 4 0.08
19 13 0.25
20 4 0.08
21 19 0.37
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAATAAATAATATTATTT
Found at i:3195177 original size:21 final size:19
Alignment explanation
Indices: 3195151--3195213 Score: 71
Period size: 18 Copynumber: 3.4 Consensus size: 19
3195141 TATTTTTAAA
3195151 ATTAAATTAAATTAAATATAT
1 ATTAAATTAAA-TAAATA-AT
3195172 ATTAAA-TAAAT-AATAAT
1 ATTAAATTAAATAAATAAT
*
3195189 -TTAATTTAAATAAA-AAT
1 ATTAAATTAAATAAATAAT
3195206 ATTAAATT
1 ATTAAATT
3195214 TTAATTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
16 4 0.11
17 10 0.27
18 12 0.32
19 1 0.03
20 4 0.11
21 6 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTAAATTAAATAAATAAT
Found at i:3195217 original size:20 final size:21
Alignment explanation
Indices: 3195173--3195214 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3195163 TAAATATATA
*
3195173 TTAAATAAATAATAATTTAAT
1 TTAAATAAATAATAATTAAAT
3195194 TTAAATAAA-AAT-ATTAAAT
1 TTAAATAAATAATAATTAAAT
3195213 TT
1 TT
3195215 TAATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTAAATAAATAATAATTAAAT
Found at i:3196088 original size:19 final size:19
Alignment explanation
Indices: 3196064--3196103 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3196054 ATAAAATAAT
3196064 ATAATAAAAAGATATAAAA
1 ATAATAAAAAGATATAAAA
** *
3196083 ATAATATGAATATATAAAA
1 ATAATAAAAAGATATAAAA
3196102 AT
1 AT
3196104 TTATATGTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (19 bp):
ATAATAAAAAGATATAAAA
Found at i:3196127 original size:32 final size:32
Alignment explanation
Indices: 3196060--3196154 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 32
3196050 AAGTATAAAA
**
3196060 TAATATAATAAAAAGATATAAAA-ATA-A-TAT
1 TAATAT-ATAAAAATTTATAAAATATATATTAT
* ***
3196090 GAATATATAAAAATTTATATGTTATATATTAT
1 TAATATATAAAAATTTATAAAATATATATTAT
3196122 TAATATATAAAAATTTATAAAATATATATTAT
1 TAATATATAAAAATTTATAAAATATATATTAT
3196154 T
1 T
3196155 TTAAATATAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 11 0.21
30 8 0.15
31 1 0.02
32 32 0.62
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (32 bp):
TAATATATAAAAATTTATAAAATATATATTAT
Found at i:3199479 original size:21 final size:20
Alignment explanation
Indices: 3199454--3199507 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
3199444 ATTATTTTTA
*
3199454 AATATTTTAATATTTTATTT
1 AATATTTTAATATTTAATTT
3199474 AGATATATTTTAA-ATTTAATTT
1 --A-ATATTTTAATATTTAATTT
3199496 AAT-TTTTAATAT
1 AATATTTTAATAT
3199508 ATTTTTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 4 0.14
20 1 0.03
22 9 0.31
23 9 0.31
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
AATATTTTAATATTTAATTT
Found at i:3199575 original size:26 final size:26
Alignment explanation
Indices: 3199537--3199589 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
3199527 TTAAAAAATT
* * *
3199537 TAATTTAATTTAAATTTAAACATAAA
1 TAATTAAACTTAAATTTAAACACAAA
3199563 TAATTAAACTTAAATTTAAACACAAA
1 TAATTAAACTTAAATTTAAACACAAA
3199589 T
1 T
3199590 TAAATTTACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.38
Consensus pattern (26 bp):
TAATTAAACTTAAATTTAAACACAAA
Found at i:3199589 original size:12 final size:12
Alignment explanation
Indices: 3199547--3199590 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
3199537 TAATTTAATT
3199547 TAAATTTAAACA
1 TAAATTTAAACA
*
3199559 TAAATAATTAAACT
1 TAAAT--TTAAACA
3199573 TAAATTTAAACA
1 TAAATTTAAACA
*
3199585 CAAATT
1 TAAATT
3199591 AAATTTACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 16 0.59
14 11 0.41
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAATTTAAACA
Found at i:3203537 original size:16 final size:16
Alignment explanation
Indices: 3203516--3203547 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3203506 TTGTGTCTTG
3203516 ATATAATTGCTGCTTT
1 ATATAATTGCTGCTTT
3203532 ATATAATTGCTGCTTT
1 ATATAATTGCTGCTTT
3203548 TGATCTTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (16 bp):
ATATAATTGCTGCTTT
Found at i:3205151 original size:6 final size:6
Alignment explanation
Indices: 3205140--3205172 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
3205130 AAATAAAAAC
3205140 AATTAA AATTAA AATTAA AATTAA AATATAA AA
1 AATTAA AATTAA AATTAA AATTAA AAT-TAA AA
3205173 CAAATGTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AATTAA
Found at i:3207047 original size:17 final size:18
Alignment explanation
Indices: 3207025--3207059 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3207015 TTTAAAGATG
3207025 TAATTATAAT-TTTATTT
1 TAATTATAATATTTATTT
*
3207042 TAATTATATTATTTATTT
1 TAATTATAATATTTATTT
3207060 ATTAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TAATTATAATATTTATTT
Found at i:3212394 original size:2 final size:2
Alignment explanation
Indices: 3212387--3212417 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3212377 TAACAATTAT
*
3212387 TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3212418 TTAGCAAGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3212928 original size:23 final size:24
Alignment explanation
Indices: 3212894--3212950 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
3212884 ATTTATATTT
3212894 AATAT-ATATTTTAAAAATATAAA
1 AATATAATATTTTAAAAATATAAA
**
3212917 AATATAAT-TTTTAATTATATAAA
1 AATATAATATTTTAAAAATATAAA
*
3212940 AA-ATAAAATTT
1 AATATAATATTT
3212951 AAATGTATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 4 0.14
23 23 0.79
24 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
AATATAATATTTTAAAAATATAAA
Found at i:3212959 original size:22 final size:23
Alignment explanation
Indices: 3212894--3212959 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
3212884 ATTTATATTT
* * *
3212894 AATATATATTTTAAAAATATAAA
1 AATATAAAATTTAAATATATAAA
** *
3212917 AATATAATTTTTAATTATATAAA
1 AATATAAAATTTAAATATATAAA
*
3212940 AA-ATAAAATTTAAATGTATA
1 AATATAAAATTTAAATATATA
3212960 CATATCAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
AATATAAAATTTAAATATATAAA
Found at i:3214678 original size:22 final size:22
Alignment explanation
Indices: 3214653--3214711 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 22
3214643 ATAACTTTTG
3214653 ATATATTAATA-ATTTATATAAT
1 ATATATTAATATATTT-TATAAT
* *
3214675 ATATTTTTATATATTTTATAAT
1 ATATATTAATATATTTTATAAT
3214697 -TA-ATT-ATATTATTTT
1 ATATATTAATA-TATTTT
3214712 TTTATATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.09
20 8 0.25
21 2 0.06
22 15 0.47
23 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
ATATATTAATATATTTTATAAT
Found at i:3214687 original size:30 final size:31
Alignment explanation
Indices: 3214648--3214733 Score: 84
Period size: 32 Copynumber: 2.7 Consensus size: 31
3214638 TTTATATAAC
*
3214648 TTTTGATATATTAATAATTTA-TATAATATA
1 TTTTTATATATTAATAATTTATTATAATATA
* * * *
3214678 TTTTTATATATTTTATAATTAATTATATTATT
1 TTTTTATATA-TTAATAATTTATTATAATATA
3214710 TTTTTATATTATATACATAATTTA
1 TTTTTATA-TAT-TA-ATAATTTA
3214734 AATATATCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
30 9 0.20
31 9 0.20
32 16 0.36
33 3 0.07
34 7 0.16
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (31 bp):
TTTTTATATATTAATAATTTATTATAATATA
Found at i:3215716 original size:21 final size:21
Alignment explanation
Indices: 3215702--3215743 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3215692 TCATAAATTT
3215702 ATTTTTCTAATTCATATAAATA
1 ATTTTT-TAATTCATATAAATA
* *
3215724 ATTTTTTAATTAATTTAAAT
1 ATTTTTTAATTCATATAAAT
3215744 TTAAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTTTAATTCATATAAATA
Found at i:3215721 original size:23 final size:22
Alignment explanation
Indices: 3215694--3215782 Score: 65
Period size: 22 Copynumber: 3.9 Consensus size: 22
3215684 AGAAACTATC
*
3215694 ATAAATTTATTTTTCTAATTCAT
1 ATAAATTTATTTTT-TAATTAAT
*
3215717 ATAAA-TAATTTTTTAATTAAT
1 ATAAATTTATTTTTTAATTAAT
* ** *
3215738 TTAAATTTAAATTTTAA-TATTT
1 ATAAATTTATTTTTTAATTA-AT
3215760 ATAATTATTTATTTATTTAATTA
1 ATAA--ATTTATTT-TTTAATTA
3215783 GTGTTTATGT
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
21 13 0.26
22 19 0.38
23 5 0.10
24 6 0.12
25 5 0.10
26 2 0.04
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATAAATTTATTTTTTAATTAAT
Found at i:3217506 original size:19 final size:18
Alignment explanation
Indices: 3217482--3217531 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
3217472 AATATTAAAT
3217482 TAAATTTAATTTAAAATAA
1 TAAATTTAATTTAAAA-AA
3217501 TAAATTATTAATTT-AAAAA
1 TAAA-T-TTAATTTAAAAAA
3217520 TAAA-TTAATTTA
1 TAAATTTAATTTA
3217532 TTTTATGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 7 0.25
19 10 0.36
20 4 0.14
21 7 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATTTAATTTAAAAAA
Found at i:3217513 original size:21 final size:19
Alignment explanation
Indices: 3217487--3217526 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 19
3217477 TAAATTAAAT
3217487 TTAATTTAAAATAATAAATTA
1 TTAATTT-AAA-AATAAATTA
3217508 TTAATTTAAAAATAAATTA
1 TTAATTTAAAAATAAATTA
3217527 ATTTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 3 0.16
21 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAATTTAAAAATAAATTA
Found at i:3217536 original size:21 final size:22
Alignment explanation
Indices: 3217472--3217536 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 22
3217462 TTTAACTCAT
* *
3217472 AATATTAAATTAAATTTAATTTAA
1 AATAATAAATT-AATTT-ATTTTA
*
3217496 AATAATAAATT-A-TTAATTTA
1 AATAATAAATTAATTTATTTTA
3217516 AA-AATAAATTAATTTATTTTA
1 AATAATAAATTAATTTATTTTA
3217537 TGATAAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
19 8 0.23
20 7 0.20
21 9 0.26
22 1 0.03
24 10 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATAATAAATTAATTTATTTTA
Found at i:3220810 original size:2 final size:2
Alignment explanation
Indices: 3220762--3220793 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3220752 TTTACATCTC
3220762 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3220794 GTTTTAAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3223911 original size:16 final size:17
Alignment explanation
Indices: 3223890--3223924 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3223880 TATTATTTTT
*
3223890 ATTTATATATTA-TATA
1 ATTTATATAATATTATA
3223906 ATTTATATAATATTATA
1 ATTTATATAATATTATA
3223923 AT
1 AT
3223925 ATGAACATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTATATAATATTATA
Found at i:3224129 original size:10 final size:10
Alignment explanation
Indices: 3224030--3224095 Score: 55
Period size: 10 Copynumber: 6.4 Consensus size: 10
3224020 AATTAAAAAA
*
3224030 TAAATAAACT
1 TAAATAAATT
3224040 TAAATAAATT
1 TAAATAAATT
3224050 TAAATTATATATT
1 TAAA-TA-A-ATT
* *
3224063 T-AA-GAATA
1 TAAATAAATT
3224071 TAAATAAATT
1 TAAATAAATT
3224081 TAAATAAAATT
1 TAAAT-AAATT
3224092 TAAA
1 TAAA
3224096 ATTAACTTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
8 3 0.07
9 3 0.07
10 21 0.47
11 11 0.24
12 3 0.07
13 4 0.09
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (10 bp):
TAAATAAATT
Found at i:3224499 original size:2 final size:2
Alignment explanation
Indices: 3224492--3224518 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3224482 AACGCAACAA
3224492 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 A
3224519 AAAGGAATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3225863 original size:17 final size:16
Alignment explanation
Indices: 3225838--3225903 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 16
3225828 TTATATAAAT
*
3225838 TTTAAAATATTTATCTA
1 TTTATAATATTTAT-TA
3225855 TTTATAATA--TATTA
1 TTTATAATATTTATTA
* *
3225869 TTTATATTATTTTTATA
1 TTTATAATATTTAT-TA
*
3225886 TTTAT-ATAATTA-TA
1 TTTATAATATTTATTA
3225900 TTTA
1 TTTA
3225904 ATATTATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 16 0.40
15 3 0.08
16 6 0.15
17 15 0.38
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATAATATTTATTA
Found at i:3225866 original size:33 final size:32
Alignment explanation
Indices: 3225784--3225866 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 32
3225774 TTATATTTAA
* *
3225784 AATAATTTTTATATATATAAATTTTAATATTTT
1 AATAATTTATA-ATATATAAATTTTAAAATTTT
* *
3225817 AATAACTTATATTATATAAATTTTAAAATATTT
1 AATAATTTATAATATATAAATTTTAAAAT-TTT
*
3225850 -ATCTATTTATAATATAT
1 AAT-AATTTATAATATAT
3225867 TATTTATATT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
32 18 0.44
33 23 0.56
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (32 bp):
AATAATTTATAATATATAAATTTTAAAATTTT
Found at i:3225885 original size:20 final size:22
Alignment explanation
Indices: 3225862--3225911 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
3225852 CTATTTATAA
3225862 TATATTATTTAT-ATTAT-TTT
1 TATATTATTTATAATTATATTT
*
3225882 TATATT-TATATAATTATATTT
1 TATATTATTTATAATTATATTT
*
3225903 AATATTATT
1 TATATTATT
3225912 AAATATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 8 0.33
22 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATATTATTTATAATTATATTT
Found at i:3225902 original size:31 final size:31
Alignment explanation
Indices: 3225747--3225911 Score: 84
Period size: 32 Copynumber: 5.5 Consensus size: 31
3225737 TAATGATATC
3225747 ATATTTAT-TTA-TTTTAT-TTTATTATAATT
1 ATATTTATATTATTTTTATATTTA-TATAATT
* *
3225776 ATATTTAAAATAATTTTTATA--TATATAA--
1 ATATTT-ATATTATTTTTATATTTATATAATT
* * *
3225804 AT-TTTA-A-TATTTTAATAACTTATATTATAT
1 ATATTTATATTATTTTTAT-ATTTATATAAT-T
* ** * *
3225834 AAATTT-TAAAATATTTATCTATT-TATAATAT
1 ATATTTATATTATTTTTATAT-TTATATAAT-T
3225865 ATTATTTATATTATTTTTATATTTATATAATT
1 A-TATTTATATTATTTTTATATTTATATAATT
3225897 ATATTTAATATTATT
1 ATATTT-ATATTATT
3225912 AAATATAAAT
Statistics
Matches: 101, Mismatches: 17, Indels: 33
0.67 0.11 0.22
Matches are distributed among these distances:
24 7 0.07
25 2 0.02
26 1 0.01
27 9 0.09
28 2 0.02
29 6 0.06
30 7 0.07
31 21 0.21
32 30 0.30
33 16 0.16
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (31 bp):
ATATTTATATTATTTTTATATTTATATAATT
Found at i:3225955 original size:17 final size:17
Alignment explanation
Indices: 3225888--3225956 Score: 52
Period size: 17 Copynumber: 4.0 Consensus size: 17
3225878 TTTTTATATT
*
3225888 TATATAATTATATTTAATA
1 TATATAA-TATA-TAAATA
3225907 T-TATTAA-ATATAAATA
1 TATA-TAATATATAAATA
* * * *
3225923 TAAATAACAAAAAAATA
1 TATATAATATATAAATA
3225940 TATATAATATATAAATA
1 TATATAATATATAAATA
3225957 AATAAAAGAC
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
16 9 0.23
17 24 0.62
18 2 0.05
19 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (17 bp):
TATATAATATATAAATA
Found at i:3225959 original size:21 final size:21
Alignment explanation
Indices: 3225891--3225960 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 21
3225881 TTATATTTAT
* *
3225891 ATAATTATATTTAATATTATTAA
1 ATAAATATATATAATA-TA-TAA
*
3225914 ATATAA-ATATA-AATA-ACAA
1 ATA-AATATATATAATATATAA
*
3225933 AAAAATATATATAATATATAA
1 ATAAATATATATAATATATAA
3225954 ATAAATA
1 ATAAATA
3225961 AAAGACGAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
18 2 0.05
19 9 0.24
20 5 0.14
21 9 0.24
22 4 0.11
23 7 0.19
24 1 0.03
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAAATATATATAATATATAA
Found at i:3226272 original size:5 final size:5
Alignment explanation
Indices: 3226262--3226336 Score: 55
Period size: 5 Copynumber: 14.4 Consensus size: 5
3226252 GAATCATACG
* * *
3226262 ATAAT ATAAT ATAA- AAAGATT AAAAT ATAAT ATAAT ATAAAA ATAAT
1 ATAAT ATAAT ATAAT ATA-A-T ATAAT ATAAT ATAAT AT-AAT ATAAT
*
3226309 ATGATAT ATAAT ATAAT -TATT ATAAT AT
1 AT-A-AT ATAAT ATAAT ATAAT ATAAT AT
3226337 TAAATTTTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
4 5 0.09
5 38 0.67
6 7 0.12
7 7 0.12
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:3226307 original size:16 final size:17
Alignment explanation
Indices: 3226282--3226398 Score: 68
Period size: 16 Copynumber: 7.2 Consensus size: 17
3226272 ATAAAAAGAT
3226282 TAAAATATAATATAATA
1 TAAAATATAATATAATA
*
3226299 TAAAA-ATAATATGATA
1 TAAAATATAATATAATA
* *
3226315 TATAATATAAT-TATTA
1 TAAAATATAATATAATA
* **
3226331 TAATAT-TAA-ATTTTA
1 TAAAATATAATATAATA
* * *
3226346 TTTAAATATAAAAT-ATT
1 -TAAAATATAATATAATA
*
3226363 TTAAATATAAT-T-ATA
1 TAAAATATAATATAATA
*
3226378 AAAAATATAAATATAATA
1 TAAAATAT-AATATAATA
3226396 TAA
1 TAA
3226399 CACAAAATCT
Statistics
Matches: 76, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
15 16 0.21
16 38 0.50
17 15 0.20
18 7 0.09
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (17 bp):
TAAAATATAATATAATA
Found at i:3226309 original size:21 final size:24
Alignment explanation
Indices: 3226262--3226324 Score: 69
Period size: 23 Copynumber: 2.6 Consensus size: 24
3226252 GAATCATACG
3226262 ATAATATAATATAAAAAGATTAAAAT
1 ATAATATAATAT-AAAAGATT-AAAT
3226288 ATAATATAATATAAAA-A-T-AAT
1 ATAATATAATATAAAAGATTAAAT
3226309 ATGATATATAATATAA
1 AT-A-ATATAATATAA
3226325 TTATTATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.14
22 1 0.03
23 12 0.34
24 1 0.03
25 4 0.11
26 12 0.34
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (24 bp):
ATAATATAATATAAAAGATTAAAT
Found at i:3226398 original size:26 final size:25
Alignment explanation
Indices: 3226262--3226398 Score: 86
Period size: 26 Copynumber: 5.4 Consensus size: 25
3226252 GAATCATACG
3226262 ATAATATAATATAAAAAGAT-TAAAAT
1 ATAATATAATATAAAAA-ATAT-AAAT
*
3226288 ATAATATAATATAAAAATAATATGATAT
1 ATAATATAATAT-AAAA-AATAT-AAAT
* *
3226316 ATAATATAAT-TATTATAATATTAAAT
1 ATAATATAATATA-AAAAATA-TAAAT
* * * * **
3226342 TTTATTTAA-ATATAAAATAT-TTT
1 ATAATATAATATAAAAAATATAAAT
3226365 A-AATATAATTATAAAAAATATAAAT
1 ATAATATAA-TATAAAAAATATAAAT
3226390 ATAATATAA
1 ATAATATAA
3226399 CACAAAATCT
Statistics
Matches: 84, Mismatches: 17, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
22 5 0.06
23 1 0.01
24 11 0.13
25 8 0.10
26 35 0.42
27 9 0.11
28 15 0.18
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (25 bp):
ATAATATAATATAAAAAATATAAAT
Found at i:3226867 original size:26 final size:26
Alignment explanation
Indices: 3226830--3226887 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
3226820 CATATGTATG
**
3226830 ATTTTCACGTC-ATTAAAATATTTTC
1 ATTTTCACGTCAAAAAAAATATTTTC
*
3226855 ATTTTACAGGTCAAAAAAAATATTTTC
1 ATTTT-CACGTCAAAAAAAATATTTTC
3226882 ACTTTT
1 A-TTTT
3226888 TTTTTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 5 0.19
26 5 0.19
27 13 0.48
28 4 0.15
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (26 bp):
ATTTTCACGTCAAAAAAAATATTTTC
Found at i:3236698 original size:2 final size:2
Alignment explanation
Indices: 3236691--3236725 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3236681 GGATGTAGCG
*
3236691 TA 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 TA T
3236726 GAGAAAGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3243853 original size:2 final size:2
Alignment explanation
Indices: 3243846--3243885 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3243836 AAATCTACCC
3243846 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3243886 CTTTGAAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3244219 original size:30 final size:30
Alignment explanation
Indices: 3244162--3244248 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
3244152 TTTTTAAAAA
3244162 AATTAAATTAATATTGATTATAAATTTGATG
1 AATTAAATTAAT-TTGATTATAAATTTGATG
* * *
3244193 AATTAGATTAATTTGATTGTACATTTGATG
1 AATTAAATTAATTTGATTATAAATTTGATG
*
3244223 AATTATATGTAA-TT-ACTTATAAATTT
1 AATTAAAT-TAATTTGA-TTATAAATTT
3244249 AATAAGTATT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
29 1 0.02
30 33 0.69
31 14 0.29
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.47
Consensus pattern (30 bp):
AATTAAATTAATTTGATTATAAATTTGATG
Found at i:3244310 original size:32 final size:33
Alignment explanation
Indices: 3244232--3244315 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 33
3244222 GAATTATATG
* *
3244232 TAATTACTTATAAATTTAATAAGTATTTAAATA
1 TAATTATTTATAAATTTAATAAATATTTAAATA
* * *
3244265 AAATTATTCATAAATTTAATAAATA-TTAGATA
1 TAATTATTTATAAATTTAATAAATATTTAAATA
3244297 TAATTATTTATAAATTTAA
1 TAATTATTTATAAATTTAA
3244316 CGGTCATTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 23 0.52
33 21 0.48
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (33 bp):
TAATTATTTATAAATTTAATAAATATTTAAATA
Found at i:3248890 original size:18 final size:17
Alignment explanation
Indices: 3248857--3248890 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3248847 TATTTTTGAA
*
3248857 TTTTTAATATTTTTATT
1 TTTTTAATATTCTTATT
3248874 TTTTTAATATGTCTTAT
1 TTTTTAATAT-TCTTAT
3248891 AATTTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTTAATATTCTTATT
Found at i:3249039 original size:17 final size:18
Alignment explanation
Indices: 3249017--3249054 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
3249007 GCTATTATAT
3249017 AAAAAT-TAAAAATTAAG
1 AAAAATCTAAAAATTAAG
* *
3249034 AAAAATCTAAAGATTATG
1 AAAAATCTAAAAATTAAG
3249052 AAA
1 AAA
3249055 GTAAGAAGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.24
Consensus pattern (18 bp):
AAAAATCTAAAAATTAAG
Found at i:3250400 original size:2 final size:2
Alignment explanation
Indices: 3250369--3250422 Score: 56
Period size: 2 Copynumber: 26.5 Consensus size: 2
3250359 GCGTGTGATG
* * *
3250369 AT AT AC AT AC AT AT AT AC AT AT AGT CAT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT AT AT AT AT AT AT
3250413 -T AT AT AT AT A
1 AT AT AT AT AT A
3250423 AGCAGTTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
1 1 0.02
2 39 0.91
3 2 0.05
4 1 0.02
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3251987 original size:17 final size:17
Alignment explanation
Indices: 3251967--3251999 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3251957 ATCATTTTAT
3251967 TATTT-TTTATAATAAAA
1 TATTTATTTA-AATAAAA
3251984 TATTTATTTAAATAAA
1 TATTTATTTAAATAAA
3252000 TTATATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTTATTTAAATAAAA
Found at i:3253402 original size:2 final size:2
Alignment explanation
Indices: 3253395--3253441 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
3253385 ATCAAGTAAA
* * *
3253395 AT AT AT AT AT AT AT GT AT AT AT AC AT -T AG AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3253436 AT AT AT
1 AT AT AT
3253442 GCTAAGTAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3254041 original size:57 final size:56
Alignment explanation
Indices: 3253971--3254086 Score: 214
Period size: 57 Copynumber: 2.1 Consensus size: 56
3253961 ATATATTTAC
*
3253971 TTATAGTTGACACTTTGTATACAAAAATTTTAAATTATCAAAATATAAAATTTACTT
1 TTATAGTTGACACTTCGTATACAAAAATTTTAAATTATCAAAATATAAAATTTA-TT
3254028 TTATAGTTGACACTTCGTATACAAAAATTTTAAATTATCAAAATATAAAATTTATT
1 TTATAGTTGACACTTCGTATACAAAAATTTTAAATTATCAAAATATAAAATTTATT
3254084 TTA
1 TTA
3254087 AATTTATTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
56 5 0.09
57 53 0.91
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (56 bp):
TTATAGTTGACACTTCGTATACAAAAATTTTAAATTATCAAAATATAAAATTTATT
Found at i:3254113 original size:23 final size:20
Alignment explanation
Indices: 3254072--3254121 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
3254062 TTATCAAAAT
3254072 ATAAAATTTATTTTAAATTTA
1 ATAAAATTTATTTTAAA-TTA
* *
3254093 TTAAAATTTAAATTTTTAATTA
1 ATAAAATTT--ATTTTAAATTA
3254115 ATAAAAT
1 ATAAAAT
3254122 ATTACATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 8 0.33
22 9 0.38
23 7 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATAAAATTTATTTTAAATTA
Found at i:3261149 original size:2 final size:2
Alignment explanation
Indices: 3261142--3261167 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3261132 CAGAAACTTT
3261142 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
3261168 ATGGAAACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3262742 original size:13 final size:14
Alignment explanation
Indices: 3262718--3262749 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
3262708 CCCATGTTAC
3262718 TATTACATTTTATA
1 TATTACATTTTATA
3262732 TATTA-ATTTTATA
1 TATTACATTTTATA
3262745 TATTA
1 TATTA
3262750 TATAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTACATTTTATA
Found at i:3264302 original size:21 final size:20
Alignment explanation
Indices: 3264278--3264342 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 20
3264268 TAACTCATTT
3264278 ATTAGAATAATAAAAAATTAA
1 ATTA-AATAATAAAAAATTAA
3264299 ATTAATATAATAATATAAA-TAA
1 ATTAA-ATAATAA-A-AAATTAA
* *
3264321 ATAAAAATATATTAAAAATTAA
1 AT-TAAATA-ATAAAAAATTAA
3264343 TTTTTTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
20 1 0.03
21 14 0.39
22 13 0.36
23 8 0.22
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (20 bp):
ATTAAATAATAAAAAATTAA
Found at i:3264317 original size:18 final size:16
Alignment explanation
Indices: 3264290--3264331 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
3264280 TAGAATAATA
3264290 AAAAAT-TAAATTAATAT
1 AAAAATATAAA-TAA-AT
*
3264307 AATAATATAAATAAAT
1 AAAAATATAAATAAAT
3264323 AAAAATATA
1 AAAAATATA
3264332 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 10 0.45
17 8 0.36
18 4 0.18
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAATATAAATAAAT
Found at i:3268146 original size:16 final size:16
Alignment explanation
Indices: 3268127--3268168 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3268117 AAATAAAATT
*
3268127 TTATTTATATTATTTG
1 TTATTAATATTATTTG
*
3268143 TTATTAATATTATTTA
1 TTATTAATATTATTTG
*
3268159 ATATTAATAT
1 TTATTAATAT
3268169 ATATATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TTATTAATATTATTTG
Found at i:3270204 original size:17 final size:18
Alignment explanation
Indices: 3270154--3270250 Score: 69
Period size: 18 Copynumber: 6.2 Consensus size: 18
3270144 TCTAAAATTT
*
3270154 ATTATTTTATTTAAATAA
1 ATTATTATATTTAAATAA
*
3270172 ATTATTATATTCAAATAA
1 ATTATTATATTTAAATAA
3270190 A-TATTA-ATTT---TAA
1 ATTATTATATTTAAATAA
3270203 A-T-TTAT-TTTAAATAA
1 ATTATTATATTTAAATAA
*
3270218 ATT-TTAAATTT---TAA
1 ATTATTATATTTAAATAA
3270232 A-T-TTATATTTAAATAA
1 ATTATTATATTTAAATAA
3270248 ATT
1 ATT
3270251 TTTAACATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 21
0.71 0.06 0.23
Matches are distributed among these distances:
12 6 0.09
13 13 0.20
14 4 0.06
15 4 0.06
16 11 0.17
17 9 0.14
18 17 0.27
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATTATATTTAAATAA
Found at i:3270208 original size:29 final size:30
Alignment explanation
Indices: 3270176--3270322 Score: 117
Period size: 30 Copynumber: 4.9 Consensus size: 30
3270166 AAATAAATTA
*
3270176 TTATATTCAAATAAATATT-AATTTTAAAT
1 TTATATTTAAATAAATATTAAATTTTAAAT
*
3270205 TTAT-TTTAAATAAATTTTAAATTTTAAAT
1 TTATATTTAAATAAATATTAAATTTTAAAT
*
3270234 TTATATTTAAATAAATTTTTAACA-TTT-AAT
1 TTATATTTAAATAAA-TATTAA-ATTTTAAAT
** ** *
3270264 TTATACATAAATAAAATACTTGCATAATTAAAT
1 TTATATTTAAAT-AAATA-TTAAAT-TTTAAAT
* *
3270297 TTCTATTT-AA-AAATATTATATTTTAA
1 TTATATTTAAATAAATATTAAATTTTAA
3270323 TATAAATTAA
Statistics
Matches: 95, Mismatches: 14, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
28 16 0.17
29 22 0.23
30 30 0.32
31 14 0.15
32 5 0.05
33 8 0.08
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (30 bp):
TTATATTTAAATAAATATTAAATTTTAAAT
Found at i:3270245 original size:30 final size:30
Alignment explanation
Indices: 3270176--3270278 Score: 124
Period size: 30 Copynumber: 3.5 Consensus size: 30
3270166 AAATAAATTA
* *
3270176 TTATATTCAAATAAATATT-AATTTTAAAT
1 TTATATTTAAATAAATTTTAAATTTTAAAT
3270205 TTAT-TTTAAATAAATTTTAAATTTTAAAT
1 TTATATTTAAATAAATTTTAAATTTTAAAT
3270234 TTATATTTAAATAAATTTTTAACA-TTT-AAT
1 TTATATTTAAATAAA-TTTTAA-ATTTTAAAT
**
3270264 TTATACATAAATAAA
1 TTATATTTAAATAAA
3270279 ATACTTGCAT
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
28 12 0.18
29 18 0.27
30 26 0.39
31 9 0.14
32 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.50
Consensus pattern (30 bp):
TTATATTTAAATAAATTTTAAATTTTAAAT
Found at i:3270253 original size:24 final size:26
Alignment explanation
Indices: 3270222--3270275 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
3270212 AAATAAATTT
3270222 TAAA-TTTTAA-ATTTATATTTA-A-A
1 TAAATTTTTAACATTTA-ATTTATACA
3270245 TAAATTTTTAACATTTAATTTATACA
1 TAAATTTTTAACATTTAATTTATACA
3270271 TAAAT
1 TAAAT
3270276 AAAATACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.15
24 11 0.41
25 6 0.22
26 6 0.22
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (26 bp):
TAAATTTTTAACATTTAATTTATACA
Found at i:3270434 original size:22 final size:21
Alignment explanation
Indices: 3270399--3270439 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3270389 TAATATATAA
*
3270399 ATTTTTATAAATTTTAATTTT
1 ATTTTAATAAATTTTAATTTT
3270420 ATTTTAATATAATTTTAATT
1 ATTTTAATA-AATTTTAATT
3270440 ATCATTCGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTTTAATAAATTTTAATTTT
Found at i:3270531 original size:22 final size:23
Alignment explanation
Indices: 3270496--3270556 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
3270486 ATATAAATAT
* *
3270496 AAAAT-ATTAATAAATATATT-A
1 AAAATAATAAATAAAAATATTAA
3270517 AAAATAATAAATAAAAATATTAA
1 AAAATAATAAATAAAAATATTAA
*
3270540 AAAATAATGAAAGAAAA
1 AAAATAAT-AAATAAAA
3270557 CTTAATCCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.15
22 13 0.38
23 9 0.26
24 7 0.21
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.26
Consensus pattern (23 bp):
AAAATAATAAATAAAAATATTAA
Found at i:3270534 original size:24 final size:24
Alignment explanation
Indices: 3270511--3270556 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
3270501 ATTAATAAAT
*
3270511 ATATT-AAAAATAAT-AAATAAAA
1 ATATTAAAAAATAATGAAAGAAAA
3270533 ATATTAAAAAATAATGAAAGAAAA
1 ATATTAAAAAATAATGAAAGAAAA
3270557 CTTAATCCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.24
23 9 0.43
24 7 0.33
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (24 bp):
ATATTAAAAAATAATGAAAGAAAA
Found at i:3284023 original size:62 final size:65
Alignment explanation
Indices: 3283909--3284039 Score: 171
Period size: 62 Copynumber: 2.1 Consensus size: 65
3283899 TAATACAAAA
* * * *
3283909 CTTTCAAATACTTTTATTAGGATACTTTTTTAAAAATATCATTAACACATTATTCT-ATAATTGA
1 CTTTCAAATACTTTGATTAGGATACGTCTTTAAAAATAACATTAACACATTATT-TGATAATTGA
3283973 T
65 T
* *
3283974 CTTTC-AA-ACTTTGATTAGGATA-GTCTTTAAAAATAACATTGACATATTATTTGATAATTGAT
1 CTTTCAAATACTTTGATTAGGATACGTCTTTAAAAATAACATTAACACATTATTTGATAATTGAT
3284036 CTTT
1 CTTT
3284040 TAAAAATATT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
61 1 0.02
62 37 0.63
63 14 0.24
64 2 0.03
65 5 0.08
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (65 bp):
CTTTCAAATACTTTGATTAGGATACGTCTTTAAAAATAACATTAACACATTATTTGATAATTGAT
Found at i:3294473 original size:2 final size:2
Alignment explanation
Indices: 3294468--3294507 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3294458 AAAGTCTCTT
3294468 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3294508 ATCCATGCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3304946 original size:5 final size:5
Alignment explanation
Indices: 3304936--3304969 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
3304926 TAATAATAAT
* *
3304936 ATTAA ATTAA ATTAA ATTAA AATAA ATTAG ATTA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTA
3304970 CTATACTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (5 bp):
ATTAA
Found at i:3305106 original size:20 final size:18
Alignment explanation
Indices: 3305083--3305121 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
3305073 AATATATACA
3305083 AAATTAAAAATAATTTATAT
1 AAATTAAAAAT--TTTATAT
*
3305103 AAATTTAAAATTTTATAT
1 AAATTAAAAATTTTATAT
3305121 A
1 A
3305122 TTTTTATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTAAAAATTTTATAT
Found at i:3305110 original size:21 final size:20
Alignment explanation
Indices: 3305065--3305112 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
3305055 TAAATATCAC
3305065 ATTT-AAAAAATATATACAA
1 ATTTAAAAAAATATATACAA
* * *
3305084 AATTAAAAATAATTTATATAA
1 ATTTAAAAA-AATATATACAA
3305105 ATTTAAAA
1 ATTTAAAA
3305113 TTTTATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 3 0.13
20 4 0.17
21 16 0.70
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTTAAAAAAATATATACAA
Found at i:3305127 original size:18 final size:18
Alignment explanation
Indices: 3305096--3305196 Score: 71
Period size: 18 Copynumber: 5.6 Consensus size: 18
3305086 TTAAAAATAA
**
3305096 TTTATATAAATTTAAAAT
1 TTTATATATTTTTAAAAT
* *
3305114 TTTATATATTTTTATCATT
1 TTTATATATTTTTA-AAAT
* *
3305133 TTTATATATTTTTTATAT
1 TTTATATATTTTTAAAAT
*
3305151 ATTATAATTATTTTTAAAAT
1 TTTAT-A-TATTTTTAAAAT
* * *
3305171 ATTACATA--TTTATAAT
1 TTTATATATTTTTAAAAT
3305187 TTTATATATT
1 TTTATATATT
3305197 AATATTTTAT
Statistics
Matches: 63, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
16 13 0.21
18 19 0.30
19 17 0.27
20 14 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATATATTTTTAAAAT
Found at i:3305147 original size:11 final size:10
Alignment explanation
Indices: 3305113--3305166 Score: 58
Period size: 9 Copynumber: 5.5 Consensus size: 10
3305103 AAATTTAAAA
3305113 TTTTATATAT
1 TTTTATATAT
*
3305123 TTTTAT-CAT
1 TTTTATATAT
3305132 TTTTATATATT
1 TTTTATATA-T
3305143 TTTTATATAT
1 TTTTATATAT
* *
3305153 TATAAT-TAT
1 TTTTATATAT
3305162 TTTTA
1 TTTTA
3305167 AAATATTACA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
9 14 0.39
10 12 0.33
11 10 0.28
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTATATAT
Found at i:3305200 original size:29 final size:30
Alignment explanation
Indices: 3305168--3305226 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
3305158 TTATTTTTAA
3305168 AATATTACATATT-TAT-AATTTTATATATT
1 AATATTACATATTATATAAATTTTAT-TATT
**
3305197 AATATTTTATATTATATAAATTTTATTATT
1 AATATTACATATTATATAAATTTTATTATT
3305227 TTTGTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.42
30 7 0.27
31 8 0.31
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (30 bp):
AATATTACATATTATATAAATTTTATTATT
Found at i:3305205 original size:15 final size:14
Alignment explanation
Indices: 3305184--3305226 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 14
3305174 ACATATTTAT
3305184 AATTTTATATATTA
1 AATTTTATATATTA
3305198 ATATTTTATATTATATA
1 A-ATTTTATA-TAT-TA
3305215 AATTTTAT-TATT
1 AATTTTATATATT
3305227 TTTGTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 1 0.04
14 4 0.15
15 8 0.31
16 10 0.38
17 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
AATTTTATATATTA
Found at i:3305589 original size:18 final size:19
Alignment explanation
Indices: 3305566--3305602 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3305556 TGTTAGGTAA
3305566 AAAGTTCAATT-ATTGATT
1 AAAGTTCAATTGATTGATT
*
3305584 AAAGTTCCATTGATTGATT
1 AAAGTTCAATTGATTGATT
3305603 TTTTTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (19 bp):
AAAGTTCAATTGATTGATT
Found at i:3306625 original size:2 final size:2
Alignment explanation
Indices: 3306620--3306645 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3306610 TCTTTCTCTC
3306620 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3306646 TGGGGGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3308608 original size:26 final size:25
Alignment explanation
Indices: 3308562--3308620 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 25
3308552 TAAATTATTC
3308562 ATATATTTATAAATATTTAA-TAATAA
1 ATAT-TTTATAAATATTTAATTAAT-A
3308588 ATATTTTA-AAATTATTATAATTAATA
1 ATATTTTATAAA-TATT-TAATTAATA
3308614 ATATTTT
1 ATATTTT
3308621 CATTTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
24 3 0.10
25 8 0.27
26 15 0.50
27 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATATTTTATAAATATTTAATTAATA
Found at i:3308697 original size:17 final size:16
Alignment explanation
Indices: 3308645--3308701 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
3308635 AAAATAATAA
3308645 ATTAAT-TAATTATTAT
1 ATTAATATAATTA-TAT
*
3308661 ATTTAATATAATAATAAT
1 A-TTAATATAATTAT-AT
*
3308679 ATTATTATAAATTATAT
1 ATTAATAT-AATTATAT
3308696 ATTAAT
1 ATTAAT
3308702 TAAACCTAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
16 1 0.03
17 19 0.58
18 13 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTAATATAATTATAT
Found at i:3309640 original size:2 final size:2
Alignment explanation
Indices: 3309627--3309659 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3309617 AGTGCCCTCA
*
3309627 AT AT AC 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
3309660 ATACTCAGGG
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:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3310646 original size:28 final size:27
Alignment explanation
Indices: 3310615--3310670 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
3310605 AATATATTTA
3310615 TATATTCTT-ATTATGTTTATTCTTATAT
1 TATATT-TTAATTATGTTTATT-TTATAT
*
3310643 TATATTTTAATTATTTTTATTTTATAT
1 TATATTTTAATTATGTTTATTTTATAT
3310670 T
1 T
3310671 TGAGTCGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.68
Consensus pattern (27 bp):
TATATTTTAATTATGTTTATTTTATAT
Found at i:3310655 original size:11 final size:12
Alignment explanation
Indices: 3310598--3310671 Score: 52
Period size: 11 Copynumber: 6.5 Consensus size: 12
3310588 AAATTTATAC
3310598 ATATTTTA-A-T
1 ATATTTTATATT
3310608 ATATTTATATATT
1 ATATTT-TATATT
* * *
3310621 CT-TATTATGTT
1 ATATTTTATATT
3310632 -TATTCTTATATT
1 ATATT-TTATATT
3310644 ATATTTTA-ATT
1 ATATTTTATATT
*
3310655 AT-TTTTATTTT
1 ATATTTTATATT
3310666 ATATTT
1 ATATTT
3310672 GAGTCGTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
10 12 0.24
11 17 0.34
12 15 0.30
13 6 0.12
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (12 bp):
ATATTTTATATT
Found at i:3311097 original size:20 final size:21
Alignment explanation
Indices: 3311073--3311144 Score: 71
Period size: 20 Copynumber: 3.5 Consensus size: 21
3311063 TATAAAAAGT
3311073 ATTTAATTAAATAATAATTT-
1 ATTTAATTAAATAATAATTTA
*
3311093 ATTTAA-TATAAT-TTAATTTA
1 ATTTAATTA-AATAATAATTTA
* *
3311113 ATTTAAATTATATAAT-TTTTA
1 ATTT-AATTAAATAATAATTTA
3311134 ATTTAATTAAA
1 ATTTAATTAAA
3311145 ATTCATAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
19 8 0.19
20 19 0.45
21 12 0.29
22 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAATTAAATAATAATTTA
Found at i:3311100 original size:15 final size:15
Alignment explanation
Indices: 3311073--3311114 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
3311063 TATAAAAAGT
*
3311073 ATTTAATTAAATAATA
1 ATTTAATTTAAT-ATA
3311089 ATTT-ATTTAATATA
1 ATTTAATTTAATATA
3311103 ATTTAATTTAAT
1 ATTTAATTTAAT
3311115 TTAAATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 7 0.29
15 13 0.54
16 4 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATTTAATTTAATATA
Found at i:3311109 original size:5 final size:5
Alignment explanation
Indices: 3311073--3311141 Score: 52
Period size: 5 Copynumber: 13.6 Consensus size: 5
3311063 TATAAAAAGT
* * * *
3311073 ATTTA ATTAA ATAATA ATTT- ATTTA ATATA ATTTA ATTTA ATTTA AATT-
1 ATTTA ATTTA AT-TTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
*
3311122 ATATA ATTTTTA ATTTA ATT
1 ATTTA A--TTTA ATTTA ATT
3311142 AAAATTCATA
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
4 6 0.12
5 36 0.73
6 3 0.06
7 4 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
ATTTA
Found at i:3311152 original size:25 final size:26
Alignment explanation
Indices: 3311104--3311152 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
3311094 TTTAATATAA
* *
3311104 TTTAATTTAATTTAAATTATATAATT
1 TTTAATTTAATTAAAATTACATAATT
3311130 TTTAATTTAATTAAAATT-CATAA
1 TTTAATTTAATTAAAATTACATAA
3311153 ATATTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTAATTTAATTAAAATTACATAATT
Found at i:3311640 original size:4 final size:4
Alignment explanation
Indices: 3311633--3311658 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3311623 TGATAGATAC
3311633 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
3311659 TTACTATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:3314966 original size:2 final size:2
Alignment explanation
Indices: 3314959--3314988 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3314949 GAATTTATGA
3314959 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3314989 GCTATGGCCG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3316384 original size:2 final size:2
Alignment explanation
Indices: 3316377--3316408 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3316367 CATGAACAAT
*
3316377 TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3316409 ATTCCTCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3324713 original size:25 final size:27
Alignment explanation
Indices: 3324664--3324721 Score: 88
Period size: 25 Copynumber: 2.3 Consensus size: 27
3324654 TGAAAGATTT
3324664 TTAAT-ATTTATAAATATTTAATTAAA
1 TTAATAATTTATAAATATTTAATTAAA
3324690 TTAATAATTTAT-AA-ATTTAATTAAA
1 TTAATAATTTATAAATATTTAATTAAA
3324715 TT-ATAAT
1 TTAATAAT
3324722 ACATAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 5 0.16
25 13 0.42
26 7 0.23
27 6 0.19
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TTAATAATTTATAAATATTTAATTAAA
Found at i:3324826 original size:18 final size:17
Alignment explanation
Indices: 3324803--3324904 Score: 60
Period size: 16 Copynumber: 6.1 Consensus size: 17
3324793 TAATTATTAT
3324803 ATAAATTATAACATATAA
1 ATAAATTATAA-ATATAA
3324821 ATAAA-TA-AAATATAA
1 ATAAATTATAAATATAA
3324836 A-AAATATATATAA-A-AA
1 ATAAAT-TATA-AATATAA
3324852 AT-AATTA-AAATAT-A
1 ATAAATTATAAATATAA
* *
3324866 ATACGA-TATAAAAATAA
1 ATA-AATTATAAATATAA
3324883 TATAAATATATATAATATAA
1 -ATAAAT-TATA-AATATAA
3324903 AT
1 AT
3324905 TTATCAAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 29
0.66 0.04 0.30
Matches are distributed among these distances:
13 2 0.03
14 8 0.12
15 11 0.17
16 16 0.25
17 6 0.09
18 10 0.15
19 6 0.09
20 6 0.09
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (17 bp):
ATAAATTATAAATATAA
Found at i:3324835 original size:11 final size:11
Alignment explanation
Indices: 3324803--3324903 Score: 61
Period size: 11 Copynumber: 9.5 Consensus size: 11
3324793 TAATTATTAT
*
3324803 ATAAATTATAA
1 ATAAAATATAA
*
3324814 CATATAA-ATAA
1 -ATAAAATATAA
3324825 ATAAAATAT-A
1 ATAAAATATAA
*
3324835 A-AAAATATAT
1 ATAAAATATAA
*
3324845 ATAAAAAATAA
1 ATAAAATATAA
*
3324856 TTAAAATAT-A
1 ATAAAATATAA
**
3324866 ATACGATATAA
1 ATAAAATATAA
3324877 A-AATAATATAA
1 ATAA-AATATAA
*
3324888 AT-ATATATAA
1 ATAAAATATAA
3324898 TATAAA
1 -ATAAA
3324904 TTTATCAAAA
Statistics
Matches: 66, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
9 7 0.11
10 22 0.33
11 32 0.48
12 5 0.08
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (11 bp):
ATAAAATATAA
Found at i:3324848 original size:24 final size:24
Alignment explanation
Indices: 3324815--3324927 Score: 72
Period size: 24 Copynumber: 4.6 Consensus size: 24
3324805 AAATTATAAC
*
3324815 ATATAAATAAATAAAATATAAAAA
1 ATATATATAAATAAAATATAAAAA
* *
3324839 ATATATATAAAAAATAAT-TAAAAT
1 ATATATATAAATAA-AATATAAAAA
* *
3324863 ATA-ATACGATATAAAA-ATAATATAA
1 ATATATA-TAAATAAAATATAA-A-AA
* *
3324888 ATATATATAATATAAATTTATCAAAA
1 ATATATATAA-ATAAA-ATATAAAAA
*
3324914 TTATATA-AAATAAA
1 ATATATATAAATAAA
3324928 TTATTAATAT
Statistics
Matches: 68, Mismatches: 12, Indels: 18
0.69 0.12 0.18
Matches are distributed among these distances:
23 8 0.12
24 30 0.44
25 10 0.15
26 16 0.24
27 1 0.01
28 3 0.04
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.32
Consensus pattern (24 bp):
ATATATATAAATAAAATATAAAAA
Found at i:3324868 original size:27 final size:27
Alignment explanation
Indices: 3324801--3324903 Score: 83
Period size: 27 Copynumber: 3.8 Consensus size: 27
3324791 ATTAATTATT
* *
3324801 ATATAAATTATAACATATA-AATAAATAAA
1 ATATAAA-TATAATATATATAA-AAA-ATA
3324830 ATATAAA-A-AATATATATAAAAAATA
1 ATATAAATATAATATATATAAAAAATA
*
3324855 AT-TAAAATATAATACGATAT-AAAAATA
1 ATAT-AAATATAATA-TATATAAAAAATA
3324882 ATATAAATAT-ATATAATATAAA
1 ATATAAATATAATAT-ATATAAA
3324904 TTTATCAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
24 1 0.02
25 7 0.11
26 18 0.29
27 24 0.39
28 5 0.08
29 7 0.11
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.31
Consensus pattern (27 bp):
ATATAAATATAATATATATAAAAAATA
Found at i:3324945 original size:15 final size:16
Alignment explanation
Indices: 3324906--3324950 Score: 60
Period size: 14 Copynumber: 3.0 Consensus size: 16
3324896 AATATAAATT
3324906 TATCAAAATTATATAA
1 TATCAAAATTATATAA
*
3324922 AAT--AAATTAT-TAA
1 TATCAAAATTATATAA
3324935 TATCAAAATTATATAA
1 TATCAAAATTATATAA
3324951 ATTTATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
13 5 0.21
14 7 0.29
15 7 0.29
16 5 0.21
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (16 bp):
TATCAAAATTATATAA
Done.