Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 18 of 125
Found at i:3143914 original size:11 final size:11
Alignment explanation
Indices: 3143900--3143981 Score: 60
Period size: 11 Copynumber: 7.5 Consensus size: 11
3143890 TATCAATGAT
3143900 TTATTATTAAA
1 TTATTATTAAA
*
3143911 TTATTA-AAAA
1 TTATTATTAAA
3143921 TTTATTATTAAA
1 -TTATTATTAAA
* * *
3143933 TTATCAATAAT
1 TTATTATTAAA
*
3143944 TTATCATTAAA
1 TTATTATTAAA
* * *
3143955 TTATAAAT-GA
1 TTATTATTAAA
*
3143965 TTATTATTAAG
1 TTATTATTAAA
3143976 TTATTA
1 TTATTA
3143982 ATGATTTCTA
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
10 10 0.19
11 41 0.76
12 3 0.06
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (11 bp):
TTATTATTAAA
Found at i:3144011 original size:65 final size:66
Alignment explanation
Indices: 3143883--3144058 Score: 171
Period size: 65 Copynumber: 2.7 Consensus size: 66
3143873 TGGATAGACA
* * ** * *
3143883 ACTAAGTTATCAATGATTTATTATTAAATTATTAAAAATTTATTATTAAATTATCAATAATTTAT
1 ACTAAATTATAAATGATTTATTATTAAATTATTAATGATTTACTATTAAATTATCAATAATTTAG
3143948 C
66 C
* * *** *
3143949 ATTAAATTATAAATGA-TTATTATTAAGTTATTAATGATTT-CTATTAAAATTATTTTTTATTTA
1 ACTAAATTATAAATGATTTATTATTAAATTATTAATGATTTACTATT-AAATTATCAATAATTTA
3144012 GC
65 GC
* *
3144014 ACTAAGTTATTAATGATTTATTA-TAAATT-TATAATTGATTTACTA
1 ACTAAATTATAAATGATTTATTATTAAATTAT-TAA-TGATTTACTA
3144059 CTATTTTTTT
Statistics
Matches: 89, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
64 5 0.06
65 56 0.63
66 25 0.28
67 3 0.03
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (66 bp):
ACTAAATTATAAATGATTTATTATTAAATTATTAATGATTTACTATTAAATTATCAATAATTTAG
C
Found at i:3144045 original size:22 final size:22
Alignment explanation
Indices: 3143889--3144055 Score: 135
Period size: 22 Copynumber: 7.6 Consensus size: 22
3143879 GACAACTAAG
*
3143889 TTATCAATGATTTATTATTAAA
1 TTATTAATGATTTATTATTAAA
**
3143911 TTATTAAAAATTTATTATTAAA
1 TTATTAATGATTTATTATTAAA
* * *
3143933 TTATCAATAATTTATCATTAAA
1 TTATTAATGATTTATTATTAAA
* *
3143955 TTATAAATGA-TTATTATTAAG
1 TTATTAATGATTTATTATTAAA
*
3143976 TTATTAATGATTT-CTATTAAAA
1 TTATTAATGATTTATTATT-AAA
** * ** * *
3143998 TTATTTTTTATTTAGCACTAAG
1 TTATTAATGATTTATTATTAAA
3144020 TTATTAATGATTTATTA-TAAA
1 TTATTAATGATTTATTATTAAA
3144041 TT-TATAATTGATTTA
1 TTAT-TAA-TGATTTA
3144056 CTACTATTTT
Statistics
Matches: 114, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
20 1 0.01
21 30 0.26
22 81 0.71
23 2 0.02
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.51
Consensus pattern (22 bp):
TTATTAATGATTTATTATTAAA
Found at i:3144399 original size:17 final size:17
Alignment explanation
Indices: 3144372--3144413 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
3144362 ATTTTTCTTA
3144372 TATTT-TTTATTATTTT
1 TATTTATTTATTATTTT
3144388 TATTTATTTATTATTTT
1 TATTTATTTATTATTTT
*
3144405 TCTTTATTT
1 TATTTATTT
3144414 TTTCCAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (17 bp):
TATTTATTTATTATTTT
Found at i:3145307 original size:15 final size:15
Alignment explanation
Indices: 3145285--3145319 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3145275 TAACAGGGTC
3145285 TTTT-TTTTTTTTTT
1 TTTTCTTTTTTTTTT
3145299 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
*
3145314 GTTTCT
1 TTTTCT
3145320 AGCAAGGTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (15 bp):
TTTTCTTTTTTTTTT
Found at i:3145526 original size:11 final size:11
Alignment explanation
Indices: 3145505--3145535 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
3145495 TCTAATAATA
3145505 ATTATTATTATT
1 ATTA-TATTATT
3145517 ATTATATTATT
1 ATTATATTATT
3145528 ATTATATT
1 ATTATATT
3145536 TAATATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATTATATTATT
Found at i:3145548 original size:20 final size:21
Alignment explanation
Indices: 3145503--3145560 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
3145493 TTTCTAATAA
*
3145503 TAATTATTAT-TATTATTATAT
1 TAATTATTATAT-TTAATATAT
3145524 T-ATTATTATATTTAATAT-T
1 TAATTATTATATTTAATATAT
3145543 TAATTATTA-ATTTTAATA
1 TAATTATTATA-TTTAATA
3145561 AAATTAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 3 0.09
20 28 0.85
21 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAATTATTATATTTAATATAT
Found at i:3146480 original size:20 final size:20
Alignment explanation
Indices: 3146447--3146489 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3146437 CAAAAAAAAA
*
3146447 AGAATAATTTAATACA-ATTG
1 AGAATAATTAAATA-AGATTG
*
3146467 AGAATGATTAAATAAGATTG
1 AGAATAATTAAATAAGATTG
3146487 AGA
1 AGA
3146490 TTAAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.51, C:0.02, G:0.16, T:0.30
Consensus pattern (20 bp):
AGAATAATTAAATAAGATTG
Found at i:3147495 original size:21 final size:20
Alignment explanation
Indices: 3147474--3147513 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3147464 TTAATTAATA
3147474 AAAATTA-TATATTTAAAAAT
1 AAAATTATTA-ATTTAAAAAT
*
3147494 AAATTTATTAATTTAAAAAT
1 AAAATTATTAATTTAAAAAT
3147514 TCATAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATTATTAATTTAAAAAT
Found at i:3150608 original size:16 final size:16
Alignment explanation
Indices: 3150587--3150617 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3150577 CTAATGGGAT
3150587 TTGAACCCATGACTTC
1 TTGAACCCATGACTTC
*
3150603 TTGAACCTATGACTT
1 TTGAACCCATGACTT
3150618 TTTTGGCCCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (16 bp):
TTGAACCCATGACTTC
Found at i:3158799 original size:5 final size:5
Alignment explanation
Indices: 3158791--3158820 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
3158781 ATCAAATATG
3158791 TTTTA TTTTA TTTTA TTTTA TTTT- TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
3158821 CAAAGGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:3159832 original size:21 final size:22
Alignment explanation
Indices: 3159797--3159847 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
3159787 TTTTATTGGA
3159797 AAAGAAAAAAGAAGAAT-GAAGG
1 AAAGAAAAAAGAAGAATGGAA-G
3159819 AAAGAAAAAA-AAGAATGGAAG
1 AAAGAAAAAAGAAGAATGGAAG
3159840 -AAGAAAAA
1 AAAGAAAAA
3159848 TGGAAGAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.29
21 7 0.25
22 13 0.46
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.04
Consensus pattern (22 bp):
AAAGAAAAAAGAAGAATGGAAG
Found at i:3159851 original size:14 final size:14
Alignment explanation
Indices: 3159832--3159893 Score: 51
Period size: 14 Copynumber: 4.6 Consensus size: 14
3159822 GAAAAAAAAG
3159832 AATGGAAGAAGAAA
1 AATGGAAGAAGAAA
**
3159846 AATGGAAG-AG-TT
1 AATGGAAGAAGAAA
*
3159858 AATGGTAGGAAGAAGA
1 AATGG-AAGAAGAA-A
3159874 AA--GAAGAAGAAA
1 AATGGAAGAAGAAA
3159886 AATGGAAG
1 AATGGAAG
3159894 TGTTTGTTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
12 8 0.22
13 11 0.31
14 15 0.42
16 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.32, T:0.11
Consensus pattern (14 bp):
AATGGAAGAAGAAA
Found at i:3159854 original size:22 final size:20
Alignment explanation
Indices: 3159793--3159847 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
3159783 ATAGTTTTAT
3159793 TGGAA-AAGAAAAAAGAAGAA
1 TGGAAGAAG-AAAAAGAAGAA
*
3159813 T-GAAGGAAAGAAAAAAAAGAA
1 TGGAA-G-AAGAAAAAGAAGAA
3159834 TGGAAGAAGAAAAA
1 TGGAAGAAGAAAAA
3159848 TGGAAGAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 3 0.10
20 9 0.30
21 12 0.40
22 6 0.20
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (20 bp):
TGGAAGAAGAAAAAGAAGAA
Found at i:3159910 original size:41 final size:39
Alignment explanation
Indices: 3159830--3159928 Score: 94
Period size: 40 Copynumber: 2.5 Consensus size: 39
3159820 AAGAAAAAAA
*
3159830 AGAATGGAAGAAGAAAAATGGAAGAGTTAATGGTAGGAAG
1 AGAATAGAAGAAGAAAAATGGAAGAGTT-ATGGTAGGAAG
* *
3159870 AAGAA-AGAAGAAGAAAAATGGAAGTGTT-TGTTGACTGGAAG
1 -AGAATAGAAGAAGAAAAATGGAAGAGTTATGGT-A--GGAAG
* *
3159911 AGAATAAAAAAAGAAAAA
1 AGAATAGAAGAAGAAAAA
3159929 AAAAAGAAGG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
38 3 0.06
39 1 0.02
40 25 0.51
41 20 0.41
ACGTcount: A:0.55, C:0.01, G:0.29, T:0.15
Consensus pattern (39 bp):
AGAATAGAAGAAGAAAAATGGAAGAGTTATGGTAGGAAG
Found at i:3167437 original size:2 final size:2
Alignment explanation
Indices: 3167430--3167455 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3167420 TCAATGGTAA
3167430 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
3167456 TTTCAGTTAG
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:3171039 original size:6 final size:6
Alignment explanation
Indices: 3171028--3171057 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3171018 TTTGGGGTTT
*
3171028 CTTTTG CTTTTG CTTTTG CTTTTG TTTTTG
1 CTTTTG CTTTTG CTTTTG CTTTTG CTTTTG
3171058 GTTTCCTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.13, G:0.17, T:0.70
Consensus pattern (6 bp):
CTTTTG
Found at i:3180652 original size:2 final size:2
Alignment explanation
Indices: 3180639--3180676 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
3180629 TGTCAACAAA
* *
3180639 AT AT AA AT AT AT AT AT AC 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
3180677 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3182229 original size:23 final size:22
Alignment explanation
Indices: 3182203--3182249 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
3182193 TATGAAAATA
3182203 TAAAATATAATTTTTTATTTTAT
1 TAAAA-ATAATTTTTTATTTTAT
* *
3182226 T-AAACTAATTTTTTATTTTTT
1 TAAAAATAATTTTTTATTTTAT
3182247 TAA
1 TAA
3182250 TTTTTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
21 16 0.76
22 4 0.19
23 1 0.05
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TAAAAATAATTTTTTATTTTAT
Found at i:3182234 original size:21 final size:21
Alignment explanation
Indices: 3182210--3182249 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3182200 ATATAAAATA
3182210 TAATTTTTTATTTTATTAAAC
1 TAATTTTTTATTTTATTAAAC
*
3182231 TAATTTTTTATTTTTTTAA
1 TAATTTTTTATTTTATTAA
3182250 TTTTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (21 bp):
TAATTTTTTATTTTATTAAAC
Found at i:3183629 original size:7 final size:8
Alignment explanation
Indices: 3183593--3183626 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
3183583 AATTCATATG
3183593 AAATTTTA
1 AAATTTTA
3183601 AAATTTTA
1 AAATTTTA
* *
3183609 AAATCTTG
1 AAATTTTA
3183617 AAATTTTA
1 AAATTTTA
3183625 AA
1 AA
3183627 TTTAAGTATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (8 bp):
AAATTTTA
Found at i:3184687 original size:10 final size:10
Alignment explanation
Indices: 3184672--3184710 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
3184662 TTATAATTAT
3184672 TTTATATATA
1 TTTATATATA
3184682 TTTATATATA
1 TTTATATATA
*
3184692 TTTAATTTTATA
1 TTT-A-TATATA
3184704 TTTATAT
1 TTTATAT
3184711 TAAAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 15 0.60
11 2 0.08
12 8 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTATATATA
Found at i:3185404 original size:53 final size:54
Alignment explanation
Indices: 3185311--3185419 Score: 184
Period size: 53 Copynumber: 2.0 Consensus size: 54
3185301 CATACCGTTA
* *
3185311 ATTTTATTTATGTAATTAAAAAAATTACACTGATAATATATTTAATAATTTCTC
1 ATTTTATTTATGTAATTAAAAAAATTACACTCATAATATATTTAATAACTTCTC
*
3185365 ATTTTATTTTTGTAATT-AAAAAATTACACTCATAATATATTTAATAACTTCTC
1 ATTTTATTTATGTAATTAAAAAAATTACACTCATAATATATTTAATAACTTCTC
3185418 AT
1 AT
3185420 ATATATAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
53 36 0.69
54 16 0.31
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (54 bp):
ATTTTATTTATGTAATTAAAAAAATTACACTCATAATATATTTAATAACTTCTC
Found at i:3187209 original size:23 final size:24
Alignment explanation
Indices: 3187160--3187211 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
3187150 TTAAAATTTA
* *
3187160 TTTTTCAATCATAATTATAATATT
1 TTTTTAAATCATAATTACAATATT
3187184 TTTTTAAATCATAATTACAATATT
1 TTTTTAAATCATAATTACAATATT
3187208 TTTT
1 TTTT
3187212 ATTATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTTAAATCATAATTACAATATT
Found at i:3189319 original size:3 final size:3
Alignment explanation
Indices: 3189306--3189348 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
3189296 TTTATTTACT
* *
3189306 TAA TTA TAA TAA TAA TTA TAA TAAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
3189349 AAGATAATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3189334 original size:16 final size:16
Alignment explanation
Indices: 3189313--3189345 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3189303 ACTTAATTAT
*
3189313 AATAATAATTATAATA
1 AATAATAATAATAATA
3189329 AATAATAATAATAATA
1 AATAATAATAATAATA
3189345 A
1 A
3189346 TAAAAGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATAATAATAATA
Found at i:3189357 original size:19 final size:19
Alignment explanation
Indices: 3189311--3189349 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3189301 TTACTTAATT
*
3189311 ATAATAATAATTATAATAA
1 ATAATAATAATAATAATAA
3189330 ATAATAATAATAATAATAA
1 ATAATAATAATAATAATAA
3189349 A
1 A
3189350 AGATAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATAATAATAATAATAA
Found at i:3189937 original size:2 final size:2
Alignment explanation
Indices: 3189930--3189957 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3189920 TAGAACTTTA
3189930 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
3189958 TTGGGTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3197096 original size:16 final size:16
Alignment explanation
Indices: 3197072--3197106 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3197062 ATTGATGACA
*
3197072 TATCTTTAACAATTGG
1 TATCATTAACAATTGG
3197088 TATCATTAACAATTGG
1 TATCATTAACAATTGG
3197104 TAT
1 TAT
3197107 GAGCTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (16 bp):
TATCATTAACAATTGG
Found at i:3202684 original size:16 final size:16
Alignment explanation
Indices: 3202663--3202693 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3202653 AAAGAAAATT
3202663 TTAAAATTTTATTATG
1 TTAAAATTTTATTATG
3202679 TTAAAATTTTATTAT
1 TTAAAATTTTATTAT
3202694 TTGTGAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
TTAAAATTTTATTATG
Found at i:3212063 original size:29 final size:30
Alignment explanation
Indices: 3212004--3212071 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
3211994 CCCACAAGAG
*
3212004 TAATTTAAAATTTTTATTCCTTAATAAGGA
1 TAATTTAAAATTTTTATCCCTTAATAAGGA
* *
3212034 TAATTTTAAATTTATT-TCCCTTAA-CAGGA
1 TAATTTAAAATTT-TTATCCCTTAATAAGGA
*
3212063 TACTTTAAA
1 TAATTTAAA
3212072 CCAATAAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 11 0.34
30 19 0.59
31 2 0.06
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (30 bp):
TAATTTAAAATTTTTATCCCTTAATAAGGA
Found at i:3222251 original size:9 final size:10
Alignment explanation
Indices: 3222230--3222277 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
3222220 AATTGATTTT
3222230 ATTTCATAAAA
1 ATTT-ATAAAA
3222241 ATTTA-AAAA
1 ATTTATAAAA
*
3222250 ATATATAAAA
1 ATTTATAAAA
*
3222260 ATTAATAAAA
1 ATTTATAAAA
*
3222270 ATATATAA
1 ATTTATAA
3222278 TTCGATGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
9 8 0.26
10 19 0.61
11 4 0.13
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (10 bp):
ATTTATAAAA
Found at i:3222259 original size:10 final size:10
Alignment explanation
Indices: 3222235--3222277 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
3222225 ATTTTATTTC
*
3222235 ATAAAAATTT
1 ATAAAAATAT
3222245 A-AAAAATAT
1 ATAAAAATAT
3222254 ATAAAAAT-T
1 ATAAAAATAT
3222263 AATAAAAATAT
1 -ATAAAAATAT
3222274 ATAA
1 ATAA
3222278 TTCGATGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
9 9 0.31
10 19 0.66
11 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:3222260 original size:20 final size:20
Alignment explanation
Indices: 3222235--3222277 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
3222225 ATTTTATTTC
*
3222235 ATAAAAATTTA-AAAAATAT
1 ATAAAAATTAATAAAAATAT
3222254 ATAAAAATTAATAAAAATAT
1 ATAAAAATTAATAAAAATAT
3222274 ATAA
1 ATAA
3222278 TTCGATGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAAAAATTAATAAAAATAT
Found at i:3222359 original size:24 final size:24
Alignment explanation
Indices: 3222314--3222359 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
3222304 AAATTTAATT
* *
3222314 TAAAATTAATATATATTTAATATC
1 TAAAATTAATATAAATTAAATATC
* *
3222338 TAAATTTAATCTAAATTAAATA
1 TAAAATTAATATAAATTAAATA
3222360 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAAATTAATATAAATTAAATATC
Found at i:3229181 original size:12 final size:12
Alignment explanation
Indices: 3229164--3229189 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3229154 AAGCAAACCT
3229164 TCAATGTTGATG
1 TCAATGTTGATG
3229176 TCAATGTTGATG
1 TCAATGTTGATG
3229188 TC
1 TC
3229190 GATCCTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (12 bp):
TCAATGTTGATG
Found at i:3230280 original size:23 final size:23
Alignment explanation
Indices: 3230242--3230299 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
3230232 AATTCAAAAG
*
3230242 ATAT-TTATA-ATCAATT-TAAT
1 ATATATTATATATTAATTATAAT
3230262 ATGAT-TTGATATATTAATTATAAT
1 AT-ATATT-ATATATTAATTATAAT
3230286 ATATATTATATATT
1 ATATATTATATATT
3230300 TTTAAATATG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.06
21 4 0.12
22 3 0.09
23 15 0.47
24 8 0.25
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (23 bp):
ATATATTATATATTAATTATAAT
Found at i:3235454 original size:17 final size:17
Alignment explanation
Indices: 3235428--3235482 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
3235418 ATTATTAAAA
*
3235428 TTTTAAATTATATTATT
1 TTTTATATTATATTATT
3235445 TTTTATATTATA-TATT
1 TTTTATATTATATTATT
*
3235461 TATATTATATTTATATCATT
1 T-T-TTATA-TTATATTATT
3235481 TT
1 TT
3235483 ATCATATCGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 5 0.16
17 12 0.38
18 5 0.16
19 6 0.19
20 4 0.12
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTATATTATATTATT
Found at i:3235489 original size:19 final size:18
Alignment explanation
Indices: 3235435--3235489 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
3235425 AAATTTTAAA
3235435 TTATATTATTTT-TTATA-
1 TTATA-TATTTTATTATAT
3235452 TTATATATTTATATTATAT
1 TTATATATTT-TATTATAT
*
3235471 TTATATCATTTTATCATAT
1 TTATAT-ATTTTATTATAT
3235490 CGTATTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 5 0.15
17 6 0.18
18 5 0.15
19 13 0.39
20 4 0.12
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATATATTTTATTATAT
Found at i:3238191 original size:29 final size:30
Alignment explanation
Indices: 3238142--3238210 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 30
3238132 ATTTTTTATG
* * *
3238142 AAAA-TCAATAAAATTAAAAATACAATGAT
1 AAAATTCAATAAAACTAAAAATACAATAAC
*
3238171 AAAATTCAATAAAACT-AAAATATAATAAC
1 AAAATTCAATAAAACTAAAAATACAATAAC
3238200 AAAATTCAATA
1 AAAATTCAATA
3238211 GTCAATCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 25 0.71
30 10 0.29
ACGTcount: A:0.65, C:0.09, G:0.01, T:0.25
Consensus pattern (30 bp):
AAAATTCAATAAAACTAAAAATACAATAAC
Found at i:3238663 original size:12 final size:12
Alignment explanation
Indices: 3238646--3238671 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3238636 TCCTCAATCC
3238646 ACTCACAAACAA
1 ACTCACAAACAA
3238658 ACTCACAAACAA
1 ACTCACAAACAA
3238670 AC
1 AC
3238672 ATATACAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.35, G:0.00, T:0.08
Consensus pattern (12 bp):
ACTCACAAACAA
Found at i:3247499 original size:18 final size:17
Alignment explanation
Indices: 3247476--3247509 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3247466 TAAGTTTTGC
3247476 TTTTGAGTAAATAATTAA
1 TTTTGA-TAAATAATTAA
*
3247494 TTTTGATTAATAATTA
1 TTTTGATAAATAATTA
3247510 TTTAATTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (17 bp):
TTTTGATAAATAATTAA
Found at i:3251574 original size:2 final size:2
Alignment explanation
Indices: 3251567--3251594 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3251557 CTAGACATTC
3251567 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
3251595 GTTGTGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3254264 original size:20 final size:20
Alignment explanation
Indices: 3254224--3254269 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
3254214 TTTTATTAAA
*
3254224 TTTAATATTTAATTTTAATT
1 TTTAATATATAATTTTAATT
3254244 TTTACATATATAATTTT-ATT
1 TTTA-ATATATAATTTTAATT
3254264 TTTAAT
1 TTTAAT
3254270 TTTTATATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 11 0.46
21 11 0.46
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTAATATATAATTTTAATT
Found at i:3254267 original size:27 final size:27
Alignment explanation
Indices: 3254226--3254284 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
3254216 TTATTAAATT
3254226 TAATATTTAATTTTAATTTTTACATATA
1 TAAT-TTTAATTTTAATTTTTACATATA
* *
3254254 TAATTTTATTTTTAATTTTTATATATA
1 TAATTTTAATTTTAATTTTTACATATA
3254281 -AATT
1 TAATT
3254285 AAATATAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.14
27 21 0.72
28 4 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATTTTAATTTTAATTTTTACATATA
Found at i:3254455 original size:20 final size:20
Alignment explanation
Indices: 3254432--3254470 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3254422 CGAATTGAAT
3254432 TTAAT-TAAATATATAAATTA
1 TTAATATAAA-ATATAAATTA
*
3254452 TTAATATCAAATATAAATT
1 TTAATATAAAATATAAATT
3254471 TAATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATATAAAATATAAATTA
Found at i:3255372 original size:21 final size:22
Alignment explanation
Indices: 3255347--3255391 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
3255337 TATTTTTAAA
3255347 ATATTTT-AAAAATAATATTTT
1 ATATTTTAAAAAATAATATTTT
3255368 ATATTTTAAAAAATAATATTTT
1 ATATTTTAAAAAATAATATTTT
3255390 AT
1 AT
3255392 TAATTTCGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATTTTAAAAAATAATATTTT
Found at i:3256058 original size:26 final size:27
Alignment explanation
Indices: 3256028--3256080 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
3256018 GTTAATAAAA
*
3256028 TAAAATATTAAAA-AAATTATTTTTAT
1 TAAAATATTAAAATAAATTAGTTTTAT
* *
3256054 TAAAATTTTAAAATATATTAGTTTTAT
1 TAAAATATTAAAATAAATTAGTTTTAT
3256081 ATGGCGTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
TAAAATATTAAAATAAATTAGTTTTAT
Found at i:3257482 original size:14 final size:15
Alignment explanation
Indices: 3257463--3257500 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
3257453 AAATAATATT
3257463 AATATA-ATTATTAA
1 AATATATATTATTAA
3257477 AATATATTTATTATTAA
1 AATATA--TATTATTAA
3257494 AATATAT
1 AATATAT
3257501 TAAATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 1 0.05
17 14 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATATATTATTAA
Found at i:3257489 original size:26 final size:26
Alignment explanation
Indices: 3257459--3257527 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 26
3257449 TTTCAAATAA
* *
3257459 TATTAATATAATTATTAAAATATATT
1 TATTATTAAAATTATTAAAATATATT
*
3257485 TATTATTAAAATATATT-AAATTTATT
1 TATTATTAAAAT-TATTAAAATATATT
3257511 TATTATTAAAATTATTA
1 TATTATTAAAATTATTA
3257528 TATATTTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 4 0.11
26 30 0.79
27 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TATTATTAAAATTATTAAAATATATT
Found at i:3257491 original size:17 final size:17
Alignment explanation
Indices: 3257469--3257501 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3257459 TATTAATATA
3257469 ATTATTAAAATATATTT
1 ATTATTAAAATATATTT
3257486 ATTATTAAAATATATT
1 ATTATTAAAATATATT
3257502 AAATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTATTAAAATATATTT
Found at i:3257522 original size:43 final size:44
Alignment explanation
Indices: 3257469--3257552 Score: 113
Period size: 43 Copynumber: 1.9 Consensus size: 44
3257459 TATTAATATA
3257469 ATTATTAAAATATATT-TAT-TATT-AAAATATATTA-AATTTATTT
1 ATTATTAAAAT-TATTATATAT-TTAAAAATA-ATTATAATTTATTT
3257512 ATTATTAAAATTATTATATATTTAAAAATAATTATAATTTA
1 ATTATTAAAATTATTATATATTTAAAAATAATTATAATTTA
3257553 ATAATAATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
42 4 0.11
43 20 0.54
44 13 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (44 bp):
ATTATTAAAATTATTATATATTTAAAAATAATTATAATTTATTT
Found at i:3257536 original size:17 final size:17
Alignment explanation
Indices: 3257495--3257553 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 17
3257485 TATTATTAAA
*
3257495 ATATA-TTAAATTTATT
1 ATATATTTAAAATTATT
3257511 -TAT-TATTAAAATTATT
1 ATATAT-TTAAAATTATT
*
3257527 ATATATTTAAAAATAATT
1 ATATATTT-AAAATTATT
3257545 ATA-ATTTAA
1 ATATATTTAA
3257554 TAATAATACT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
15 3 0.08
16 12 0.33
17 9 0.25
18 12 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATTTAAAATTATT
Found at i:3257558 original size:17 final size:18
Alignment explanation
Indices: 3257518--3257560 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
3257508 ATTTATTATT
*
3257518 AAAATTATTATATATTTA
1 AAAATAATTATATATTTA
3257536 AAAATAATTATA-ATTTA
1 AAAATAATTATATATTTA
*
3257553 ATAATAAT
1 AAAATAAT
3257561 ACTTAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATAATTATATATTTA
Found at i:3257633 original size:15 final size:15
Alignment explanation
Indices: 3257622--3257696 Score: 60
Period size: 15 Copynumber: 4.6 Consensus size: 15
3257612 TTATTATTTT
3257622 TATATTATTTATTAA
1 TATATTATTTATTAA
3257637 TATATTATAATATTATTTATA
1 TATA-T-T-AT-TTA-TTA-A
* *
3257658 AATAATATTTATTAA
1 TATATTATTTATTAA
*
3257673 TATATTTTTTATTAA
1 TATATTATTTATTAA
*
3257688 TATAATATT
1 TATATTATT
3257697 ATTTATAAGT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
15 24 0.51
16 4 0.09
17 4 0.09
18 4 0.09
19 4 0.09
20 3 0.06
21 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATATTATTTATTAA
Found at i:3257671 original size:28 final size:29
Alignment explanation
Indices: 3257621--3257704 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 29
3257611 TTTATTATTT
*
3257621 TTATATTATTTAT-TAATA-TATTATAATA
1 TTAT-TTATTAATATAATATTATTATAATA
3257649 TTATTTA-TAA-ATAATATTTATTA-ATATA
1 TTATTTATTAATATAATA-TTATTATA-ATA
*
3257677 TTTTTTATTAATATAATATTATTTATAA
1 TTATTTATTAATATAATATTA-TTATAA
3257705 GTAAAATTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
26 7 0.15
27 4 0.09
28 18 0.39
29 6 0.13
30 10 0.22
31 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TTATTTATTAATATAATATTATTATAATA
Found at i:3257690 original size:13 final size:13
Alignment explanation
Indices: 3257613--3257690 Score: 76
Period size: 13 Copynumber: 6.2 Consensus size: 13
3257603 TAAAACTATT
3257613 TATTATTT-TT-A
1 TATTATTTATTAA
3257624 TATTATTTATTAA
1 TATTATTTATTAA
3257637 TA-TA-TTA-TAA
1 TATTATTTATTAA
*
3257647 TATTATTTATAAA
1 TATTATTTATTAA
*
3257660 TAATATTTATTAATA
1 TATTATTTATT-A-A
*
3257675 TATTTTTTATTAA
1 TATTATTTATTAA
3257688 TAT
1 TAT
3257691 AATATTATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
10 5 0.09
11 13 0.24
12 7 0.13
13 18 0.33
14 2 0.04
15 10 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTATTTATTAA
Found at i:3257890 original size:15 final size:14
Alignment explanation
Indices: 3257855--3257881 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3257845 ATACTTATTT
3257855 CAAAAATTATTTTA
1 CAAAAATTATTTTA
3257869 CAAAAATTATTTT
1 CAAAAATTATTTT
3257882 TCACGAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
CAAAAATTATTTTA
Found at i:3258413 original size:31 final size:32
Alignment explanation
Indices: 3258378--3258467 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 32
3258368 AATATTTTAT
* *
3258378 ATTTTTATATTAATATA-AAT-TATAATATATA
1 ATTTTTATATTAAAATATAATATA-AATATAAA
3258409 ATTTTTATA-TAAAATATAATATAAATATAAA
1 ATTTTTATATTAAAATATAATATAAATATAAA
* ** *
3258440 ATTTTAATATT-TTATATGATATAAATAT
1 ATTTTTATATTAAAATATAATATAAATAT
3258468 TTAAATCATC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
30 6 0.12
31 41 0.82
32 3 0.06
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
ATTTTTATATTAAAATATAATATAAATATAAA
Found at i:3258436 original size:18 final size:18
Alignment explanation
Indices: 3258388--3258441 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
3258378 ATTTTTATAT
*
3258388 TAATATAAATTATAATATA
1 TAATATAAA-TATAAAATA
* **
3258407 TAATTTTTATATAAAATA
1 TAATATAAATATAAAATA
3258425 TAATATAAATATAAAAT
1 TAATATAAATATAAAAT
3258442 TTTAATATTT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATATAAATATAAAATA
Found at i:3264992 original size:75 final size:75
Alignment explanation
Indices: 3264902--3265048 Score: 240
Period size: 75 Copynumber: 2.0 Consensus size: 75
3264892 GCTCAATTTT
** *
3264902 ATCATCAATCTTGCTGCATATTGTACAGGAGTTTGATAGCCAGCATATAGCATCTGGTCTAGTTT
1 ATCATCAATCTTGCTGCATATTGTACAGGAGTTTGATAGCCAAAATATAGCATCTGGTCTAGCTT
3264967 TGATTCTTTA
66 TGATTCTTTA
* * *
3264977 ATCATGAATCTTGCTGCCTATTGTACAGTAGTTTGATAGCCAAAATATAGCATCTGGTCTAGCTT
1 ATCATCAATCTTGCTGCATATTGTACAGGAGTTTGATAGCCAAAATATAGCATCTGGTCTAGCTT
3265042 TGATTCT
66 TGATTCT
3265049 GTTGAAGCTA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 66 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (75 bp):
ATCATCAATCTTGCTGCATATTGTACAGGAGTTTGATAGCCAAAATATAGCATCTGGTCTAGCTT
TGATTCTTTA
Found at i:3267104 original size:3 final size:3
Alignment explanation
Indices: 3267096--3267124 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3267086 TTTTCTTTCT
3267096 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3267125 TTGGTTTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3268511 original size:26 final size:26
Alignment explanation
Indices: 3268482--3268540 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
3268472 TATTAAAAAA
* *
3268482 TTAAACTATTAATCTTTCAAAATTTT
1 TTAAACTATTAATCTTTAAAAAATTT
* *
3268508 TTAATA-TTTTAATTTTTAAAAAATTT
1 TTAA-ACTATTAATCTTTAAAAAATTT
3268534 TTAAACT
1 TTAAACT
3268541 TCTTAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
25 1 0.04
26 25 0.93
27 1 0.04
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.53
Consensus pattern (26 bp):
TTAAACTATTAATCTTTAAAAAATTT
Found at i:3269191 original size:13 final size:13
Alignment explanation
Indices: 3269161--3269190 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3269151 ATACAAAACA
3269161 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
3269174 TTTTTCTTTTTT-
1 TTTTTCTTTTTTC
3269186 TTTTT
1 TTTTT
3269191 TAATTTGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:3269811 original size:23 final size:21
Alignment explanation
Indices: 3269774--3269819 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
3269764 TACATAGGGG
**
3269774 AAGCAATTCGGCAACAGACATTC
1 AAGCAATTCAACAACA-A-ATTC
3269797 AAGCAATTCAACAACAAATTC
1 AAGCAATTCAACAACAAATTC
3269818 AA
1 AA
3269820 TTAGCCTCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 1 0.05
23 14 0.67
ACGTcount: A:0.48, C:0.24, G:0.11, T:0.17
Consensus pattern (21 bp):
AAGCAATTCAACAACAAATTC
Found at i:3271234 original size:10 final size:10
Alignment explanation
Indices: 3271219--3271293 Score: 73
Period size: 10 Copynumber: 7.5 Consensus size: 10
3271209 CACTTTAGCA
3271219 TAAAAAAATT
1 TAAAAAAATT
3271229 TAAAAAAA-T
1 TAAAAAAATT
* *
3271238 CAAAAAATTT
1 TAAAAAAATT
* *
3271248 TAAAAGATTT
1 TAAAAAAATT
3271258 TAAAAAAA-T
1 TAAAAAAATT
*
3271267 TAAAAAAGTT
1 TAAAAAAATT
3271277 CTAAAAAAATAT
1 -TAAAAAAAT-T
3271289 TAAAA
1 TAAAA
3271294 CTTTTTTTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
9 15 0.28
10 24 0.45
11 13 0.25
12 1 0.02
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (10 bp):
TAAAAAAATT
Found at i:3271262 original size:20 final size:19
Alignment explanation
Indices: 3271219--3271485 Score: 101
Period size: 19 Copynumber: 13.7 Consensus size: 19
3271209 CACTTTAGCA
* **
3271219 TAAAAAAATTTAAAAAAAT
1 TAAAAAATTTTAAAAATTT
*
3271238 CAAAAAATTTTAAAAGATTT
1 TAAAAAATTTTAAAA-ATTT
* *
3271258 TAAAAAAATTAAAAAAGTTCT
1 TAAAAAATTTTAAAAA-TT-T
* * *
3271279 AAAAAAATATTAAAACTTTTT
1 TAAAAAATTTTAAAA--ATTT
* *
3271300 TTAAAAATTCT-AAAATTT
1 TAAAAAATTTTAAAAATTT
** ** *
3271318 TAAAATTTTTTTTAAATTC
1 TAAAAAATTTTAAAAATTT
* * *
3271337 T-AACAATTTTAAAAAACTC
1 TAAAAAATTTT-AAAAATTT
*
3271356 TAAAAAATTTTAAAAACTT
1 TAAAAAATTTTAAAAATTT
* * *
3271375 CAAAAAATTTTAAAAACTA
1 TAAAAAATTTTAAAAATTT
* *
3271394 TAAAAAA-TTCAAAACAATT
1 TAAAAAATTTTAAAA-ATTT
* ** *
3271413 CAAAATTTTTTTAAAATTAT
1 TAAAAAATTTTAAAAATT-T
* *
3271433 GAAAAAATTCTAAAAATATTT
1 TAAAAAATT-TTAAAA-ATTT
* **
3271454 TTAAAAATTTT-CTAATTT
1 TAAAAAATTTTAAAAATTT
3271472 ATAAAAAATTTTAA
1 -TAAAAAATTTTAA
3271486 TTTAAAATTA
Statistics
Matches: 178, Mismatches: 55, Indels: 29
0.68 0.21 0.11
Matches are distributed among these distances:
18 26 0.15
19 75 0.42
20 40 0.22
21 32 0.18
22 5 0.03
ACGTcount: A:0.55, C:0.06, G:0.01, T:0.37
Consensus pattern (19 bp):
TAAAAAATTTTAAAAATTT
Found at i:3271344 original size:28 final size:29
Alignment explanation
Indices: 3271282--3271350 Score: 97
Period size: 28 Copynumber: 2.4 Consensus size: 29
3271272 AAGTTCTAAA
*
3271282 AAAATATTAAAACTTTTTTTAAAAATTCT
1 AAAATTTTAAAACTTTTTTTAAAAATTCT
*
3271311 AAAATTTTAAAA-TTTTTTT-TAAATTCT
1 AAAATTTTAAAACTTTTTTTAAAAATTCT
3271338 AACAATTTTAAAA
1 AA-AATTTTAAAA
3271351 AACTCTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 9 0.24
28 17 0.46
29 11 0.30
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (29 bp):
AAAATTTTAAAACTTTTTTTAAAAATTCT
Found at i:3271361 original size:10 final size:10
Alignment explanation
Indices: 3271344--3271400 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 10
3271334 TTCTAACAAT
3271344 TTTAAAAAAC
1 TTTAAAAAAC
*
3271354 TCTAAAAAA-
1 TTTAAAAAAC
*
3271363 TTTTAAAAAC
1 TTTAAAAAAC
*
3271373 TTCAAAAAA-
1 TTTAAAAAAC
*
3271382 TTTTAAAAAC
1 TTTAAAAAAC
*
3271392 TATAAAAAA
1 TTTAAAAAA
3271401 TTCAAAACAA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
9 14 0.39
10 22 0.61
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (10 bp):
TTTAAAAAAC
Found at i:3271415 original size:38 final size:37
Alignment explanation
Indices: 3271331--3271449 Score: 112
Period size: 38 Copynumber: 3.1 Consensus size: 37
3271321 AATTTTTTTT
* * * *
3271331 AAATTCTAACAATTTTAAAAAACTCTAAAAAATTTTAAA
1 AAATTCAAAAAATTTT-AAAAACTATAAAAAA-TTCAAA
*
3271370 AACTTCAAAAAATTTTAAAAACTATAAAAAATTCAAA
1 AAATTCAAAAAATTTTAAAAACTATAAAAAATTCAAA
** * * *
3271407 ACAATTCAAAATTTTTTTAAAATTATGAAAAAATTCTAA
1 A-AATTCAAAAAATTTTAAAAACTAT-AAAAAATTCAAA
3271446 AAAT
1 AAAT
3271450 ATTTTTAAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
37 6 0.09
38 36 0.54
39 25 0.37
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.33
Consensus pattern (37 bp):
AAATTCAAAAAATTTTAAAAACTATAAAAAATTCAAA
Found at i:3271486 original size:17 final size:18
Alignment explanation
Indices: 3271450--3271489 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3271440 TTCTAAAAAT
* *
3271450 ATTTTTAAAAATTTTCTA
1 ATTTATAAAAAATTTCTA
3271468 ATTTATAAAAAATTT-TA
1 ATTTATAAAAAATTTCTA
3271485 ATTTA
1 ATTTA
3271490 AAATTATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTATAAAAAATTTCTA
Found at i:3271549 original size:21 final size:20
Alignment explanation
Indices: 3271512--3271559 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
3271502 ATAAAAAATG
3271512 TTTTAAATATTTGAAATTTT
1 TTTTAAATATTTGAAATTTT
* *
3271532 TTTTAAAATTTTTTAAA-TTT
1 TTTT-AAATATTTGAAATTTT
3271552 TTTTAAAT
1 TTTTAAAT
3271560 TTGTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 11 0.44
21 10 0.40
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTAAATATTTGAAATTTT
Found at i:3271559 original size:10 final size:10
Alignment explanation
Indices: 3271529--3271561 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3271519 TATTTGAAAT
3271529 TTTTTTTAAA
1 TTTTTTTAAA
*
3271539 ATTTTTTAAA
1 TTTTTTTAAA
3271549 TTTTTTTAAA
1 TTTTTTTAAA
3271559 TTT
1 TTT
3271562 GTAAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:3271753 original size:10 final size:10
Alignment explanation
Indices: 3271738--3271774 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
3271728 ATTACTTTTG
3271738 AATTTTTAAA
1 AATTTTTAAA
3271748 AATTTTTAAA
1 AATTTTTAAA
*
3271758 ATTTTTTTAAA
1 A-ATTTTTAAA
3271769 AATTTT
1 AATTTT
3271775 ATTGTTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
AATTTTTAAA
Found at i:3271758 original size:9 final size:9
Alignment explanation
Indices: 3271738--3271819 Score: 51
Period size: 9 Copynumber: 8.8 Consensus size: 9
3271728 ATTACTTTTG
3271738 AATTTTTAAA
1 AATTTTT-AA
3271748 AATTTTTAA
1 AATTTTTAA
3271757 AATTTTTTTAA
1 AA--TTTTTAA
* *
3271768 AAATTTTAT
1 AATTTTTAA
**
3271777 TGTTTTTAA
1 AATTTTTAA
3271786 AA--TTTAA
1 AATTTTTAA
* *
3271793 ATTTTATTTAG
1 A-ATT-TTTAA
3271804 AATTTTTAA
1 AATTTTTAA
3271813 AATTTTT
1 AATTTTT
3271820 TCAAAAATTC
Statistics
Matches: 54, Mismatches: 12, Indels: 13
0.68 0.15 0.16
Matches are distributed among these distances:
7 6 0.11
9 25 0.46
10 9 0.17
11 14 0.26
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (9 bp):
AATTTTTAA
Found at i:3271769 original size:20 final size:20
Alignment explanation
Indices: 3271740--3272193 Score: 83
Period size: 20 Copynumber: 23.1 Consensus size: 20
3271730 TACTTTTGAA
*
3271740 TTTTTAAAAATTTTTAAAAT
1 TTTTTTAAAATTTTTAAAAT
*
3271760 TTTTTTAAAAATTTT---AT
1 TTTTTTAAAATTTTTAAAAT
3271777 TGTTTTTAAAA--TTT-AAAT
1 T-TTTTTAAAATTTTTAAAAT
*
3271795 TTTATTTAGAATTTTTAAAAT
1 TTT-TTTAAAATTTTTAAAAT
* * * *
3271816 TTTTTCAAAAATTCT--CA-
1 TTTTTTAAAATTTTTAAAAT
* **
3271833 --TTTTAAACTTTTTTGAA-
1 TTTTTTAAAATTTTTAAAAT
* * *
3271850 TTCTCTAAAATCTTTTGAAAT
1 TTTTTTAAAAT-TTTTAAAAT
*
3271871 TATTTTAGAAA-TTTTAGAAAT
1 TTTTTTA-AAATTTTTA-AAAT
* *
3271892 TTTTATT--AATTGTTAGAAT
1 TTTT-TTAAAATTTTTAAAAT
* *** * *
3271911 TCTGAAAAAAATTTTAGAATT
1 TTTTTTAAAATTTTTA-AAAT
* * *
3271932 TTTTTTACAATATTTAGAAT
1 TTTTTTAAAATTTTTAAAAT
* * *
3271952 TTTTTTATAACTTTTAAAAA
1 TTTTTTAAAATTTTTAAAAT
* * *
3271972 TTTTTTAAAATATTCTAGATT
1 TTTTTTAAAAT-TTTTAAAAT
* * * *
3271993 TTTTCTTTAAGTTTTTGAAGT
1 TTTT-TTAAAATTTTTAAAAT
3272014 TTTTTT--AATTTTATAAAA-
1 TTTTTTAAAATTTT-TAAAAT
*** * ***
3272032 AAATTTAAATTATTTTATGTT
1 TTTTTTAAAAT-TTTTAAAAT
* *
3272053 TTTTTTGAAA-TTTTAAAAA
1 TTTTTTAAAATTTTTAAAAT
* *
3272072 TTGTTTAGAATTTCTT-AAAT
1 TTTTTTAAAATTT-TTAAAAT
* * * **
3272092 ATGTTTAGAATTTTT-TTAT
1 TTTTTTAAAATTTTTAAAAT
3272111 ATTTTTTAAAACTTTTT-AAAT
1 -TTTTTTAAAA-TTTTTAAAAT
* * *
3272132 TTTTTTGAATTTTTTATAA-
1 TTTTTTAAAATTTTTAAAAT
*
3272151 TTTTTAAAAATTTTTAGAAA-
1 TTTTTTAAAATTTTTA-AAAT
** *
3272171 TTTTGAAAAATTTTAAAAAT
1 TTTTTTAAAATTTTTAAAAT
3272191 TTT
1 TTT
3272194 ATAGATTTTT
Statistics
Matches: 301, Mismatches: 99, Indels: 68
0.64 0.21 0.15
Matches are distributed among these distances:
15 9 0.03
16 3 0.01
17 6 0.02
18 27 0.09
19 53 0.18
20 129 0.43
21 64 0.21
22 10 0.03
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTTTTAAAATTTTTAAAAT
Found at i:3271967 original size:41 final size:42
Alignment explanation
Indices: 3271922--3272021 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 42
3271912 CTGAAAAAAA
* *
3271922 TTTTAGAATTTTTTTTACAATATT-TAGAATTTTTT-TATAAC
1 TTTTAGAAATTTTTTTAAAATATTCTAG-ATTTTTTCTATAAC
* * *
3271963 TTTTA-AAAATTTTTTAAAATATTCTAGATTTTTTCTTTAAG
1 TTTTAGAAATTTTTTTAAAATATTCTAGATTTTTTCTATAAC
* *
3272004 TTTTTGAAGTTTTTTTAA
1 TTTTAGAAATTTTTTTAA
3272022 TTTTATAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
40 22 0.46
41 16 0.33
42 10 0.21
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (42 bp):
TTTTAGAAATTTTTTTAAAATATTCTAGATTTTTTCTATAAC
Found at i:3272116 original size:10 final size:9
Alignment explanation
Indices: 3272053--3272166 Score: 66
Period size: 10 Copynumber: 11.8 Consensus size: 9
3272043 ATTTTATGTT
3272053 TTTTTTGAAA
1 TTTTTT-AAA
**
3272063 TTTTAAAAA
1 TTTTTTAAA
*
3272072 TTGTTTAGAA
1 TTTTTTA-AA
*
3272082 TTTCTTAAA
1 TTTTTTAAA
*
3272091 TATGTTTAGAA
1 T-TTTTTA-AA
*
3272102 TTTTTTTATA
1 -TTTTTTAAA
3272112 TTTTTTAAAA
1 TTTTTT-AAA
*
3272122 CTTTTTAAA
1 TTTTTTAAA
*
3272131 TTTTTTTGAA
1 -TTTTTTAAA
3272141 TTTTTTATAA
1 TTTTTTA-AA
*
3272151 TTTTTAAAA
1 TTTTTTAAA
*
3272160 ATTTTTA
1 TTTTTTA
3272167 GAAATTTTGA
Statistics
Matches: 78, Mismatches: 19, Indels: 15
0.70 0.17 0.13
Matches are distributed among these distances:
9 32 0.41
10 38 0.49
11 7 0.09
12 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:3272126 original size:19 final size:19
Alignment explanation
Indices: 3272104--3272166 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
3272094 GTTTAGAATT
*
3272104 TTTTTATATTTTTTAAAAC
1 TTTTTATATTTTTTAAAAA
* ** *
3272123 TTTTTAAATTTTTTTGAAT
1 TTTTTATATTTTTTAAAAA
*
3272142 TTTTTATAATTTTTAAAAA
1 TTTTTATATTTTTTAAAAA
3272161 TTTTTA
1 TTTTTA
3272167 GAAATTTTGA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTTATATTTTTTAAAAA
Found at i:3272133 original size:29 final size:28
Alignment explanation
Indices: 3272004--3272187 Score: 102
Period size: 29 Copynumber: 6.3 Consensus size: 28
3271994 TTTCTTTAAG
* *
3272004 TTTTTGAAGTTTTTTT-AATTTTATAAAAA
1 TTTTT-AAATTTTTTTGAATTTT-TTAAAA
** ** *
3272033 AATTTAAATTATTTTATGTTTTTTTTGAAA
1 TTTTTAAATT-TTTT-TGAATTTTTTAAAA
* * * *
3272063 TTTTAAAAATTGTTTAGAATTTCTTAAATA
1 TTTT-TAAATTTTTTTGAATTTTTTAAA-A
*
3272093 TGTTTAGAATTTTTTT-ATATTTTTTAAAA
1 TTTTTA-AATTTTTTTGA-ATTTTTTAAAA
*
3272122 CTTTTTAAATTTTTTTGAATTTTTTATAA
1 -TTTTTAAATTTTTTTGAATTTTTTAAAA
* * * *
3272151 TTTTTAAAAATTTTTAGAAATTTTGAAAA
1 TTTTT-AAATTTTTTTGAATTTTTTAAAA
*
3272180 ATTTTAAA
1 TTTTTAAA
3272188 AATTTTATAG
Statistics
Matches: 116, Mismatches: 29, Indels: 21
0.70 0.17 0.13
Matches are distributed among these distances:
28 12 0.10
29 59 0.51
30 36 0.31
31 9 0.08
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (28 bp):
TTTTTAAATTTTTTTGAATTTTTTAAAA
Found at i:3272164 original size:9 final size:9
Alignment explanation
Indices: 3272152--3272194 Score: 59
Period size: 10 Copynumber: 4.6 Consensus size: 9
3272142 TTTTTATAAT
3272152 TTTTAAAAA
1 TTTTAAAAA
*
3272161 TTTTTAGAAA
1 -TTTTAAAAA
3272171 TTTTGAAAAA
1 TTTT-AAAAA
3272181 TTTTAAAAA
1 TTTTAAAAA
3272190 TTTTA
1 TTTTA
3272195 TAGATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
9 14 0.47
10 16 0.53
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:3272171 original size:10 final size:9
Alignment explanation
Indices: 3272054--3272194 Score: 75
Period size: 9 Copynumber: 14.7 Consensus size: 9
3272044 TTTTATGTTT
*
3272054 TTTTTGAAA
1 TTTTTAAAA
*
3272063 TTTTAAAAA
1 TTTTTAAAA
*
3272072 TTGTTTAGAA
1 TT-TTTAAAA
3272082 TTTCTTAAATA
1 TTT-TTAAA-A
* *
3272093 TGTTTAGAATT
1 TTTTTA-AA-A
* *
3272104 TTTTTATAT
1 TTTTTAAAA
3272113 TTTTTAAAA
1 TTTTTAAAA
*
3272122 CTTTTTAAATT
1 -TTTTTAAA-A
* *
3272133 TTTTTGAAT
1 TTTTTAAAA
*
3272142 TTTTTATAA
1 TTTTTAAAA
3272151 TTTTTAAAAA
1 TTTTT-AAAA
3272161 TTTTTAGAAA
1 TTTTTA-AAA
*
3272171 TTTTGAAAA
1 TTTTTAAAA
*
3272180 ATTTTAAAA
1 TTTTTAAAA
*
3272189 ATTTTA
1 TTTTTA
3272195 TAGATTTTTT
Statistics
Matches: 104, Mismatches: 20, Indels: 16
0.74 0.14 0.11
Matches are distributed among these distances:
9 47 0.45
10 46 0.44
11 11 0.11
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:3272174 original size:19 final size:19
Alignment explanation
Indices: 3272053--3272198 Score: 69
Period size: 19 Copynumber: 7.4 Consensus size: 19
3272043 ATTTTATGTT
*
3272053 TTTTTTGAAATTTTAAAAA
1 TTTTTAGAAATTTTAAAAA
* *
3272072 TTGTTTAGAATTTCTTAAATA
1 TT-TTTAGAAATT-TTAAAAA
* * * * *
3272093 TGTTTAGAATTTTTTTATAT
1 TTTTTAGAA-ATTTTAAAAA
* *
3272113 TTTTTA-AAACTTTTTAAAT
1 TTTTTAGAAA-TTTTAAAAA
* * * *
3272132 TTTTTTGAATTTTTTATAA
1 TTTTTAGAAATTTTAAAAA
* *
3272151 TTTTTAAAAATTTTTAGAAA
1 TTTTTAGAAA-TTTTAAAAA
* *
3272171 TTTTGAAAAATTTTAAAAA
1 TTTTTAGAAATTTTAAAAA
3272190 TTTTATAGA
1 TTTT-TAGA
3272199 TTTTTTTTTA
Statistics
Matches: 95, Mismatches: 25, Indels: 13
0.71 0.19 0.10
Matches are distributed among these distances:
19 43 0.45
20 42 0.44
21 10 0.11
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.55
Consensus pattern (19 bp):
TTTTTAGAAATTTTAAAAA
Found at i:3272384 original size:26 final size:27
Alignment explanation
Indices: 3272355--3272411 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
3272345 ATAACGATTT
3272355 AAAA-TTTTAAGTATCAATATAACAAA
1 AAAATTTTTAAGTATCAATATAACAAA
* * *
3272381 AAAATTTTTTAAGTCTTAATTTAACAAA
1 AAAA-TTTTTAAGTATCAATATAACAAA
3272409 AAA
1 AAA
3272412 TTTAAAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.15
28 22 0.85
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (27 bp):
AAAATTTTTAAGTATCAATATAACAAA
Found at i:3278984 original size:16 final size:15
Alignment explanation
Indices: 3278958--3278987 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3278948 AAGGTAGTTT
3278958 AATGAAAATCCTGGC
1 AATGAAAATCCTGGC
3278973 AATGAGAAATCCTGG
1 AATGA-AAATCCTGG
3278988 AATTGTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (15 bp):
AATGAAAATCCTGGC
Found at i:3281422 original size:19 final size:18
Alignment explanation
Indices: 3281398--3281441 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3281388 TTGTGTGGTG
*
3281398 ATTTAGGATTGTGAGTTGA
1 ATTTAGGATT-TGAGTTAA
* *
3281417 ATTTAGGGTTTGGGTTAA
1 ATTTAGGATTTGAGTTAA
3281435 ATTTAGG
1 ATTTAGG
3281442 GTCTTTGTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.43
Consensus pattern (18 bp):
ATTTAGGATTTGAGTTAA
Found at i:3281486 original size:8 final size:8
Alignment explanation
Indices: 3281473--3281598 Score: 73
Period size: 8 Copynumber: 15.8 Consensus size: 8
3281463 TTAGGGTCTT
3281473 GTTTTAGG
1 GTTTTAGG
3281481 GTTTTA-G
1 GTTTTAGG
3281488 GTTATT-GTG
1 GTT-TTAG-G
*
3281497 ATTTTAGG
1 GTTTTAGG
3281505 GTTTT-GG
1 GTTTTAGG
* *
3281512 AGTTTTTGA
1 -GTTTTAGG
3281521 GTTTTAGG
1 GTTTTAGG
3281529 G-TTT-GG
1 GTTTTAGG
*
3281535 TGTTTTAGT
1 -GTTTTAGG
*
3281544 GTTTTAGC
1 GTTTTAGG
* *
3281552 ATTATAGG
1 GTTTTAGG
*
3281560 GTTTTGGG
1 GTTTTAGG
*
3281568 GTTTTTGG
1 GTTTTAGG
* *
3281576 ACTTTGAGG
1 -GTTTTAGG
3281585 GTTTTAGG
1 GTTTTAGG
3281593 GTTTTA
1 GTTTTA
3281599 AATTTTAAGG
Statistics
Matches: 89, Mismatches: 19, Indels: 20
0.70 0.15 0.16
Matches are distributed among these distances:
6 2 0.02
7 10 0.11
8 66 0.74
9 11 0.12
ACGTcount: A:0.13, C:0.02, G:0.33, T:0.52
Consensus pattern (8 bp):
GTTTTAGG
Found at i:3281539 original size:23 final size:24
Alignment explanation
Indices: 3281473--3281550 Score: 81
Period size: 23 Copynumber: 3.3 Consensus size: 24
3281463 TTAGGGTCTT
*
3281473 GTTTTAGGGTTTTAGGT-TATTGTGA
1 GTTTTAGGGTTTT-GGTGT-TTTTGA
*
3281498 -TTTTAGGGTTTTGGAGTTTTTGA
1 GTTTTAGGGTTTTGGTGTTTTTGA
* *
3281521 GTTTTAGGG-TTTGGTGTTTTAGT
1 GTTTTAGGGTTTTGGTGTTTTTGA
3281544 GTTTTAG
1 GTTTTAG
3281551 CATTATAGGG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
23 25 0.54
24 21 0.46
ACGTcount: A:0.13, C:0.00, G:0.32, T:0.55
Consensus pattern (24 bp):
GTTTTAGGGTTTTGGTGTTTTTGA
Found at i:3281636 original size:16 final size:16
Alignment explanation
Indices: 3281586--3281636 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
3281576 ACTTTGAGGG
* *
3281586 TTTTAGGGTTTTAA-A
1 TTTTAAGGTTTCAAGA
*
3281601 TTTTAAGGTTTCGAGA
1 TTTTAAGGTTTCAAGA
*
3281617 TTTTAAGGTTTCAAGG
1 TTTTAAGGTTTCAAGA
3281633 TTTT
1 TTTT
3281637 GTGGTTCTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.51
Consensus pattern (16 bp):
TTTTAAGGTTTCAAGA
Found at i:3281755 original size:16 final size:16
Alignment explanation
Indices: 3281736--3281780 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
3281726 TAAATTTATA
3281736 GTTTTAGGATTTCAAG
1 GTTTTAGGATTTCAAG
* * *
3281752 GTTTTAGGGTTTTAAT
1 GTTTTAGGATTTCAAG
3281768 GTTTTAGGATTTC
1 GTTTTAGGATTTC
3281781 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.20, C:0.04, G:0.24, T:0.51
Consensus pattern (16 bp):
GTTTTAGGATTTCAAG
Found at i:3283015 original size:17 final size:17
Alignment explanation
Indices: 3282982--3283013 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3282972 CTCAACCCGG
3282982 TTCTCCCTTTCTTTTTC
1 TTCTCCCTTTCTTTTTC
3282999 TTCT-CCTTTCTTTTT
1 TTCTCCCTTTCTTTTT
3283014 TCCTTTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCTCCCTTTCTTTTTC
Found at i:3285053 original size:54 final size:54
Alignment explanation
Indices: 3284974--3285098 Score: 223
Period size: 54 Copynumber: 2.3 Consensus size: 54
3284964 CACTCATAAT
*
3284974 ACACATAATTATATATACCATAAGTTACTTAAAATCTTACAACAGTCTGCACTC
1 ACACATAATTATATATACCAGAAGTTACTTAAAATCTTACAACAGTCTGCACTC
3285028 ACACATAATTATATATACCAGAAGTTACTTAAAATCTTACAACAGTCTGCACTC
1 ACACATAATTATATATACCAGAAGTTACTTAAAATCTTACAACAGTCTGCACTC
* *
3285082 ACAAATATTTATATATA
1 ACACATAATTATATATA
3285099 GCAGCTAAGA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.32
Consensus pattern (54 bp):
ACACATAATTATATATACCAGAAGTTACTTAAAATCTTACAACAGTCTGCACTC
Found at i:3289482 original size:24 final size:25
Alignment explanation
Indices: 3289433--3289489 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
3289423 ATATATTTTT
*
3289433 TATAAAAAAAATCATAATTTAATAA
1 TATATAAAAAATCATAATTTAATAA
* *
3289458 TATATAAAAAATTATAA-TTATTAA
1 TATATAAAAAATCATAATTTAATAA
*
3289482 TATTTAAA
1 TATATAAA
3289490 TTATAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
TATATAAAAAATCATAATTTAATAA
Found at i:3294909 original size:15 final size:16
Alignment explanation
Indices: 3294881--3294918 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
3294871 AGTCGGTCGC
3294881 TTTTTTAGGATTTTAA
1 TTTTTTAGGATTTTAA
* *
3294897 TTTTTTA-GTTTTTCA
1 TTTTTTAGGATTTTAA
3294912 TTTTTTA
1 TTTTTTA
3294919 TAGAATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.18, C:0.03, G:0.08, T:0.71
Consensus pattern (16 bp):
TTTTTTAGGATTTTAA
Found at i:3295130 original size:29 final size:29
Alignment explanation
Indices: 3295096--3295152 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
3295086 TATTTAAAAT
3295096 AAAGTTTTTAAAATAAAAAAGAAAGAAAG
1 AAAGTTTTTAAAATAAAAAAGAAAGAAAG
*
3295125 AAAGTTTTTAAAATAAAAAATAAAGAAA
1 AAAGTTTTTAAAATAAAAAAGAAAGAAA
3295153 TACAAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.23
Consensus pattern (29 bp):
AAAGTTTTTAAAATAAAAAAGAAAGAAAG
Found at i:3295146 original size:7 final size:7
Alignment explanation
Indices: 3295134--3295179 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
3295124 GAAAGTTTTT
3295134 AAAATAA
1 AAAATAA
3295141 AAAATAA
1 AAAATAA
3295148 AGAAATACA
1 A-AAATA-A
*
3295157 AAAACAA
1 AAAATAA
3295164 AAAA-AA
1 AAAATAA
3295170 AAAA-AA
1 AAAATAA
3295176 AAAA
1 AAAA
3295180 AAGTTAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
6 12 0.33
7 13 0.36
8 9 0.25
9 2 0.06
ACGTcount: A:0.87, C:0.04, G:0.02, T:0.07
Consensus pattern (7 bp):
AAAATAA
Found at i:3295820 original size:9 final size:10
Alignment explanation
Indices: 3295804--3295834 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
3295794 AAAAAGTTTT
3295804 GAAAAAAAAA
1 GAAAAAAAAA
3295814 GAAAAAAAAA
1 GAAAAAAAAA
3295824 GAAAAAAAAA
1 GAAAAAAAAA
3295834 G
1 G
3295835 GAGCAATATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:3296691 original size:2 final size:2
Alignment explanation
Indices: 3296684--3296713 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3296674 ATTTAATAGA
3296684 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
3296714 TGGGTTTGCG
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:3312110 original size:52 final size:51
Alignment explanation
Indices: 3311958--3312114 Score: 179
Period size: 52 Copynumber: 3.0 Consensus size: 51
3311948 TATAACCATA
* * * *
3311958 CAAACTTGCCCATTAAGAATCACTTTTCTCTTAGAATTCTTCTCTTGTAAGT
1 CAAACTTACCTATTAAGAATTAC-TTTCTCTTAGAATTCTTCTCTTGCAAGT
** * *
3312010 CAAACTTACCTATTAAGAATCCCTTTCCCCTTAAAATTCTTCTCTTGCAAGT
1 CAAACTTACCTATTAAGAATTACTTT-CTCTTAGAATTCTTCTCTTGCAAGT
* * * *
3312062 CAAATTTACCTATTAAGAATTATCTTTCTTTTAGAATTTTTCTTTTGCAAGT
1 CAAACTTACCTATTAAGAATTA-CTTTCTCTTAGAATTCTTCTCTTGCAAGT
3312114 C
1 C
3312115 TTCTTGTCCA
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
51 3 0.03
52 82 0.92
53 4 0.04
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (51 bp):
CAAACTTACCTATTAAGAATTACTTTCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:3313992 original size:15 final size:16
Alignment explanation
Indices: 3313960--3314000 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
3313950 TTGAAAAATC
3313960 TGAACTCAAACTGATT
1 TGAACTCAAACTGATT
*
3313976 TGAACTCAATC-GATT
1 TGAACTCAAACTGATT
*
3313991 TGAATTCAAA
1 TGAACTCAAA
3314001 AAAATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (16 bp):
TGAACTCAAACTGATT
Found at i:3316271 original size:55 final size:55
Alignment explanation
Indices: 3316187--3316300 Score: 187
Period size: 55 Copynumber: 2.1 Consensus size: 55
3316177 ACATGACATT
*
3316187 TCATGTGCATTTTTTAGCATAACTTTTTTCAGA-GAAAGTTGAAAAAGTGATTCAG
1 TCATGTGCATTTTTTAGCATAACTCTTTTCAGACGAAAG-TGAAAAAGTGATTCAG
*
3316242 TCATGTGCATTTTTTAGCCTAACTCTTTTCAGACGAAAGTGAAAAAGTGATTCAG
1 TCATGTGCATTTTTTAGCATAACTCTTTTCAGACGAAAGTGAAAAAGTGATTCAG
3316297 -CATG
1 TCATG
3316301 GATGGGATCC
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
54 4 0.07
55 47 0.84
56 5 0.09
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (55 bp):
TCATGTGCATTTTTTAGCATAACTCTTTTCAGACGAAAGTGAAAAAGTGATTCAG
Found at i:3319032 original size:16 final size:14
Alignment explanation
Indices: 3319001--3319056 Score: 51
Period size: 16 Copynumber: 3.7 Consensus size: 14
3318991 GTGGATTCAT
3319001 AAATTTATTTTG-AA
1 AAATTT-TTTTGAAA
3319015 AAATTTTCATTTGAAA
1 AAATTTT--TTTGAAA
3319031 AAGATTATTTTTGAAA
1 AA-ATT-TTTTTGAAA
*
3319047 GAATTTTTTT
1 AAATTTTTTT
3319057 TTTTTGTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 1 0.03
14 11 0.31
15 7 0.19
16 12 0.33
17 3 0.08
18 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.09, T:0.50
Consensus pattern (14 bp):
AAATTTTTTTGAAA
Found at i:3319237 original size:16 final size:16
Alignment explanation
Indices: 3319202--3319251 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
3319192 TTAAATAAAT
** *
3319202 AAAATAAAAACTTAAC
1 AAAATAAAAACAAAAA
3319218 AAAATAAAAACAAAAAA
1 AAAATAAAAAC-AAAAA
*
3319235 AAAATAAAATCAAAAA
1 AAAATAAAAACAAAAA
3319251 A
1 A
3319252 TAAAATGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 17 0.59
17 12 0.41
ACGTcount: A:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAATAAAAACAAAAA
Found at i:3319249 original size:13 final size:13
Alignment explanation
Indices: 3319233--3319262 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3319223 AAAAACAAAA
3319233 AAAAAATAAAATC
1 AAAAAATAAAATC
*
3319246 AAAAAATAAAATG
1 AAAAAATAAAATC
3319259 AAAA
1 AAAA
3319263 TAGAAAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.13
Consensus pattern (13 bp):
AAAAAATAAAATC
Found at i:3319269 original size:19 final size:18
Alignment explanation
Indices: 3319218--3319276 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
3319208 AAAACTTAAC
*
3319218 AAAATAAAAAC-AAAAAA
1 AAAATAAAATCAAAAAAA
*
3319235 AAAATAAAATCAAAAAAT
1 AAAATAAAATCAAAAAAA
3319253 AAAATGAAAAT-AGAAAAGAA
1 AAAAT-AAAATCA-AAAA-AA
3319273 AAAA
1 AAAA
3319277 CCTGCGATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 10 0.29
18 11 0.31
19 9 0.26
20 5 0.14
ACGTcount: A:0.81, C:0.03, G:0.05, T:0.10
Consensus pattern (18 bp):
AAAATAAAATCAAAAAAA
Found at i:3320158 original size:3 final size:3
Alignment explanation
Indices: 3320145--3320187 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
3320135 AAGAAAGAAA
3320145 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3320188 CCCTAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3320818 original size:120 final size:118
Alignment explanation
Indices: 3320466--3320831 Score: 351
Period size: 119 Copynumber: 3.1 Consensus size: 118
3320456 ATGAAACCAC
** *
3320466 AAGTCAAAAATGAAGCAATTAGGA-TCGAGTTGAGGTCGAAAATAAATGACAAGGATG-AACCAC
1 AAGTCAAAAATGAAGCAACCAGGACT-GAGTTGAGGTCGAAAATAAATGAC-AGGATGAAACCAT
** * * * * * * *
3320529 GAGTTGTAAGAAGCGATCTGGATTGAGCTAAGATCAAGTGACGGGGATGAAACCAC
64 GAGTCATAAGAAGTGATCTGGATTGAGCAAAGATCAAGTGACCGAGA-CAAATCAT
* * * * ** * *
3320585 AAATCAAAAATGAAGTAACCAAGACTAAGTTGAGGTAAAAAATGAATGACCA-GATAAAACCATG
1 AAGTCAAAAATGAAGCAACCAGGACTGAGTTGAGGTCGAAAATAAATGA-CAGGATGAAACCATG
* ** *
3320649 AGTCATAAGAAGTGATCTGGATTGAGCCAAGATCAAGTGATTGAAACAAAATCAT
65 AGTCATAAGAAGTGATCTGGATTGAGCAAAGATCAAGTGACCGAGAC-AAATCAT
* * * * *
3320704 AAGTCAAAAATGAAGCAACCAGGACTGAGTCGAGGTCGACAATAAATAACTGGGATGAAACCATA
1 AAGTCAAAAATGAAGCAACCAGGACTGAGTTGAGGTCGAAAATAAATGAC-AGGATGAAACCATG
* * *
3320769 AGTCATAATAAATGATCTGGACTGAGCAAAGATCAAGTGACCGAGACAAATCCAT
65 AGTCATAAGAAGTGATCTGGATTGAGCAAAGATCAAGTGACCGAGACAAAT-CAT
*
3320824 AGGTCAAA
1 AAGTCAAA
3320832 TAAAGTTCAA
Statistics
Matches: 197, Mismatches: 43, Indels: 13
0.78 0.17 0.05
Matches are distributed among these distances:
118 4 0.02
119 131 0.66
120 62 0.31
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (118 bp):
AAGTCAAAAATGAAGCAACCAGGACTGAGTTGAGGTCGAAAATAAATGACAGGATGAAACCATGA
GTCATAAGAAGTGATCTGGATTGAGCAAAGATCAAGTGACCGAGACAAATCAT
Found at i:3321037 original size:35 final size:34
Alignment explanation
Indices: 3320998--3321065 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
3320988 GCAAAGGTTC
* *
3320998 TAGATTCACAA-AGATACAAGATTCACAAAGATTTT
1 TAGATTCACAAGA-AAAAAAGATTCAC-AAGATTTT
3321033 TAGATTCACAAGAAAAAAAGATTCACAAGATTT
1 TAGATTCACAAGAAAAAAAGATTCACAAGATTT
3321066 CAAGTTTCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
34 7 0.23
35 22 0.73
36 1 0.03
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.26
Consensus pattern (34 bp):
TAGATTCACAAGAAAAAAAGATTCACAAGATTTT
Found at i:3321039 original size:18 final size:17
Alignment explanation
Indices: 3320997--3321043 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
3320987 CGCAAAGGTT
3320997 CTAGATTCACAAAGATA
1 CTAGATTCACAAAGATA
* *
3321014 CAAGATTCACAAAGATTT
1 CTAGATTCACAAAGA-TA
*
3321032 TTAGATTCACAA
1 CTAGATTCACAA
3321044 GAAAAAAAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.28
Consensus pattern (17 bp):
CTAGATTCACAAAGATA
Found at i:3325737 original size:16 final size:16
Alignment explanation
Indices: 3325716--3325771 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
3325706 ATTCCATAAA
3325716 TTTATTTTGAAAGATT
1 TTTATTTTGAAAGATT
*
3325732 TTTA-TTTGAAAAATAT
1 TTTATTTTGAAAGAT-T
*
3325748 TTT-TTTTCAAAGGATT
1 TTTATTTTGAAA-GATT
*
3325764 TTTCTTTT
1 TTTATTTT
3325772 TTGTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
15 9 0.27
16 18 0.55
17 6 0.18
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.59
Consensus pattern (16 bp):
TTTATTTTGAAAGATT
Found at i:3325966 original size:16 final size:16
Alignment explanation
Indices: 3325916--3325960 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
3325906 GAAATTAAGT
* *
3325916 AAATAAAGTAAAAACT
1 AAATAAAATAAAAACA
* *
3325932 TAAGAAAATAAAAACA
1 AAATAAAATAAAAACA
3325948 AAATAAAATAAAA
1 AAATAAAATAAAA
3325961 TAAAAAGTGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (16 bp):
AAATAAAATAAAAACA
Found at i:3326844 original size:3 final size:3
Alignment explanation
Indices: 3326836--3326887 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
3326826 GAAAAGAAAT
3326836 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3326884 ATA A
1 ATA A
3326888 CCCTATTGAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3328582 original size:298 final size:287
Alignment explanation
Indices: 3328032--3328604 Score: 790
Period size: 298 Copynumber: 2.0 Consensus size: 287
3328022 AAATAGGTAG
* * *
3328032 TTGTTTGAATTAAAAATTTGAGTGATATGTCTAGTTAATATTAAGTAATAATTTAAGAGAATTAA
1 TTGTTTGAATTAAAAATTTGAGTGATATGTATAGTTAATATAAAGTAACAATTTAAGAGAATTAA
* * * *
3328097 TATTTATGACTAAATATCTCGGATATTCTCTTTTCTAAATCAAAGCTATTCTTCTTTTCAGGAAT
66 CATTTATGACTAAATATCTCAGATATACTCTTTTCTAAATCAAAGCTATTCTTCTTTTCAGGAAC
* * * * *
3328162 TTGAAATTGTCTGTAGCAAAAGAAGTTATTAACCAAAATCACTGTTCAAATAAAACTAAGCAGCA
131 TTGAAATTATCTGTAGCAAAAGAAATTAGTAACCAAAATCACTGTTAAAATAAAACAAAGCAGCA
* * *
3328227 TGTTGAGTAGCATACGAAGATAGATTTTTTCTAACCATAAACCAAACTAATTTAACCATCATATA
196 TGTTGAGTAGCATACAAAGACAGACTTTTTCTAACCATAAACCAAACTAATTTAACCATCATATA
3328292 CATATATATATATATTTAAATTGATAT
261 CATATATATATATATTTAAATTGATAT
*
3328319 TTGTTTGAATTAAAAGTTTGAGTGATATGTATAGTTAATATAAAGTAACAATTTAAGAGAAAGTT
1 TTGTTTGAATTAAAAATTTGAGTGATATGTATAGTTAATATAAAGTAACAATTTAAGAG-AA-TT
* * *
3328384 AACATTTATGACTAAATATCTCAGATATAC-CTTTCTTTAAATTAGAGCTACTT-TTCTTTTCAC
64 AACATTTATGACTAAATATCTCAGATATACTCTTT-TCTAAATCAAAGCTA-TTCTTCTTTT--C
* *
3328447 TTGATGTGGAACTTGAAATTATTTGTAGCAAAAGAAATTAGTAACCAAAATCATTGTTAAAATAA
125 ---A---GGAACTTGAAATTATCTGTAGCAAAAGAAATTAGTAACCAAAATCACTGTTAAAAT-A
* * *
3328512 AAACAAAGCAGCATGTTGAGTAGCATGCAAAGACAGACTTTTTCTCATCATAAACCAAACTAATT
183 AAACAAAGCAGCATGTTGAGTAGCATACAAAGACAGACTTTTTCTAACCATAAACCAAACTAATT
*
3328577 TAACCATCATATATATATATATATATAT
248 TAACCATCATATACATATATATATATAT
3328605 ATAACTAATC
Statistics
Matches: 248, Mismatches: 25, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
287 55 0.22
288 6 0.02
289 48 0.19
290 2 0.01
291 1 0.00
294 1 0.00
297 49 0.20
298 86 0.35
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (287 bp):
TTGTTTGAATTAAAAATTTGAGTGATATGTATAGTTAATATAAAGTAACAATTTAAGAGAATTAA
CATTTATGACTAAATATCTCAGATATACTCTTTTCTAAATCAAAGCTATTCTTCTTTTCAGGAAC
TTGAAATTATCTGTAGCAAAAGAAATTAGTAACCAAAATCACTGTTAAAATAAAACAAAGCAGCA
TGTTGAGTAGCATACAAAGACAGACTTTTTCTAACCATAAACCAAACTAATTTAACCATCATATA
CATATATATATATATTTAAATTGATAT
Found at i:3328853 original size:55 final size:55
Alignment explanation
Indices: 3328786--3328898 Score: 199
Period size: 55 Copynumber: 2.1 Consensus size: 55
3328776 CCAATCATAA
*
3328786 TTAAATAAGTTCAACTTAGTGAACTAAACAATTATAACTAAAACATGAAAATGCC
1 TTAAATAAGTTCAACTTAGTGAACTAAACAATTATAACTAAAACATGAAAATACC
* *
3328841 TTAAATAAGTTCAACTTAGTGAACTAAACAGTTATAACTAAAACATGAACATACC
1 TTAAATAAGTTCAACTTAGTGAACTAAACAATTATAACTAAAACATGAAAATACC
3328896 TTA
1 TTA
3328899 TTTAAATGAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.48, C:0.15, G:0.09, T:0.28
Consensus pattern (55 bp):
TTAAATAAGTTCAACTTAGTGAACTAAACAATTATAACTAAAACATGAAAATACC
Found at i:3331185 original size:10 final size:10
Alignment explanation
Indices: 3331172--3331204 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3331162 AAATAGGTTA
3331172 AAAATCAAAT
1 AAAATCAAAT
3331182 AAAATCAAAT
1 AAAATCAAAT
3331192 AAAAT-AAA-
1 AAAATCAAAT
3331200 AAAAT
1 AAAAT
3331205 GAAAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 5 0.22
9 3 0.13
10 15 0.65
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAATCAAAT
Found at i:3332049 original size:17 final size:17
Alignment explanation
Indices: 3332027--3332065 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3332017 AGATTTGAGC
*
3332027 AAAAAAGGAAAA-AAATA
1 AAAAAAAGAAAAGAAA-A
3332044 AAAAAAAGAAAAGAAAA
1 AAAAAAAGAAAAGAAAA
3332061 AAAAA
1 AAAAA
3332066 TAATAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAAAAGAAAA
Found at i:3332070 original size:3 final size:3
Alignment explanation
Indices: 3332064--3332111 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
3332054 AAGAAAAAAA
3332064 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3332112 TTATAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3332251 original size:26 final size:25
Alignment explanation
Indices: 3332203--3332261 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
3332193 ATGTCAGCGA
** *
3332203 GCCTAATCGGGCTTGGATATCAATAG
1 GCCTAATCGGGCCCGGACATCAAT-G
*
3332229 GCCTAATCGGGCCCGGACCTCAATG
1 GCCTAATCGGGCCCGGACATCAATG
3332254 GACCTAAT
1 G-CCTAAT
3332262 TAGGCCTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 2 0.07
26 26 0.93
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.22
Consensus pattern (25 bp):
GCCTAATCGGGCCCGGACATCAATG
Found at i:3332517 original size:54 final size:54
Alignment explanation
Indices: 3332436--3332575 Score: 147
Period size: 54 Copynumber: 2.6 Consensus size: 54
3332426 TGAAAGTAAA
* * * * *
3332436 ATGATCTGACTTGAGTCGAGGTTAAATGATTGGGACAATGCCGCAAGTCGAAAG
1 ATGATCTGACTGGAGTTGAGATCAAATGATTGGGACAATGCCGCAAGTCAAAAG
* * * * * * *
3332490 ATGATCTGACTGGAGTTAAGATCAAATGACTAGGACGATGCCTCGAGTTAAAAG
1 ATGATCTGACTGGAGTTGAGATCAAATGATTGGGACAATGCCGCAAGTCAAAAG
*
3332544 ATGATCTAAAC-GGAGTTGAGATCAAATGATTG
1 ATGATCT-GACTGGAGTTGAGATCAAATGATTG
3332576 AAATGATGCC
Statistics
Matches: 69, Mismatches: 16, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
54 67 0.97
55 2 0.03
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (54 bp):
ATGATCTGACTGGAGTTGAGATCAAATGATTGGGACAATGCCGCAAGTCAAAAG
Found at i:3332674 original size:114 final size:113
Alignment explanation
Indices: 3332541--3333204 Score: 500
Period size: 114 Copynumber: 5.8 Consensus size: 113
3332531 CTCGAGTTAA
* * * * * * * ** *
3332541 AAGATGATCTAAACGGAGTTGAGATCAAATGATTGAAATGATGCCT-TAAGTTTGAAA-GTGGCC
1 AAGATGATCTGACCTGAGTCGAGATCAAATGACTGAGATGATG-CTGTGAG-TCAAAAGGTGACC
* * * *
3332604 AAGACTGAGTCGAGATCATAAATAAATGACTGGACTGATGTTGCAAGTCTG
64 AAGACTGAGTCAAG-TCAAAAATAAATGACCGAACTGATGTTGCAAGTCTG
* * * *
3332655 AAGATGATCTGACCTGAGTTGAGATCAAATGACTGGGATGATGTTGTGAGTCAAAAGGTGACTAA
1 AAGATGATCTGACCTGAGTCGAGATCAAATGACTGAGATGATGCTGTGAGTCAAAAGGTGACCAA
* *
3332720 GA-TCGAGTCAAGGTTAAAAATAAATGACCGAACTGATG-T-CATGAGTCTT
66 GACT-GAGTCAA-GTCAAAAATAAATGACCGAACTGATGTTGCA--AGTCTG
* * * * * * ** * *
3332769 AAGATGATTTGACCTGAGTCAAGATCAAATAATTGGGACGATGCCATGAGTCAAAAGATGACTAA
1 AAGATGATCTGACCTGAGTCGAGATCAAATGACTGAGATGATGCTGTGAGTCAAAAGGTGACCAA
* *
3332834 GATTGAGTTAAGTCAAAAATAAATGACCGAACTGATGTTGCAAGTCTG
66 GACTGAGTCAAGTCAAAAATAAATGACCGAACTGATGTTGCAAGTCTG
* * * *
3332882 -AGATGATCTGACTTGAGTCAAGATCAAATGACTGAGATGATGTTGTGAGTCAAAATGTGACCAA
1 AAGATGATCTGACCTGAGTCGAGATCAAATGACTGAGATGATGCTGTGAGTCAAAAGGTGACCAA
** * ** *
3332946 GACTGAGTCAAGGTTGAAAATAAATGACC-AGACTAATGTCACAAGTTTG
66 GACTGAGTCAA-GTCAAAAATAAATGACCGA-ACTGATGTTGCAAGTCTG
* * ** * ** *
3332995 AAGATTATCTGACCTAAGTCGAGATCAAATGACTGAGACAATGTTACGAGTCAAAATAAAGTGAC
1 AAGATGATCTGACCTGAGTCGAGATCAAATGACTGAGATGATGCTGTGAGTC--AA-AAGGTGAC
* * * * * ** * *
3333060 CAA-AATCAAGTCAAGGTTAAAAATAAATTATCGAACTGATGTCACGAGTC-C
63 CAAGACT-GAGTCAA-GTCAAAAATAAATGACCGAACTGATGTTGCAAGTCTG
* * * * *
3333111 ACAAATGATCTTACCTGAGTCGAGATCAAATGACTGGGATGATGCTATGAGTCAAAATAAAGTGA
1 A-AGATGATCTGACCTGAGTCGAGATCAAATGACTGAGATGATGCTGTGAGTC--AA-AAGGTGA
* *
3333176 TCAAAACTGAGTCAAGGTCAAAAATAAAT
62 CCAAGACTGAGTCAA-GTCAAAAATAAAT
3333205 AATCAAGATT
Statistics
Matches: 449, Mismatches: 82, Indels: 35
0.79 0.14 0.06
Matches are distributed among these distances:
112 64 0.14
113 66 0.15
114 187 0.42
115 4 0.01
116 5 0.01
117 120 0.27
118 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.23, T:0.25
Consensus pattern (113 bp):
AAGATGATCTGACCTGAGTCGAGATCAAATGACTGAGATGATGCTGTGAGTCAAAAGGTGACCAA
GACTGAGTCAAGTCAAAAATAAATGACCGAACTGATGTTGCAAGTCTG
Done.