Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold653
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: 38497
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:706 original size:28 final size:28
Alignment explanation
Indices: 687--840 Score: 231
Period size: 28 Copynumber: 5.5 Consensus size: 28
677 TAATTAAGTC
* *
687 CGCACACTCAGTGCTATATAATCAA-CT
1 CGCACACTTAGTGCTACATAATCAATCT
* *
714 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAATCT
*
742 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAATCT
770 CGCACACTTAGTGCTACATAATCAAAT-T
1 CGCACACTTAGTGCTACATAATC-AATCT
*
798 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAATCT
826 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
841 GTACAATTTA
Statistics
Matches: 120, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
27 26 0.22
28 92 0.77
29 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAATCT
Found at i:791 original size:56 final size:56
Alignment explanation
Indices: 687--840 Score: 256
Period size: 56 Copynumber: 2.8 Consensus size: 56
677 TAATTAAGTC
* * *
687 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAACT
*
742 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAACT
*
798 CGCACACTTAGTGCTACATAATCAAGCTCGCACACTTAGTGCT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCT
841 GTACAATTTA
Statistics
Matches: 93, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
55 21 0.23
56 72 0.77
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (56 bp):
CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:8955 original size:28 final size:28
Alignment explanation
Indices: 8892--9045 Score: 256
Period size: 28 Copynumber: 5.5 Consensus size: 28
8882 AAATTAAGTC
* *
8892 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
8919 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
8947 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
8975 CGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACT
*
9003 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
9031 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9046 GTACAATTTA
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
27 22 0.18
28 99 0.82
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:8982 original size:56 final size:56
Alignment explanation
Indices: 8892--9070 Score: 261
Period size: 56 Copynumber: 3.2 Consensus size: 56
8882 AAATTAAGTC
* *
8892 CGCACACTCAGTGCTATATAATC-AACTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
* *
8947 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAATCAAATT
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
9003 CGCACACTTAGTGCTACATAATCAAGCTCGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTATATAA-TCAAACT
9060 CGCACACTTAG
1 CGCACACTTAG
9071 CGCCAATCTC
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
55 21 0.19
56 75 0.68
57 15 0.14
ACGTcount: A:0.34, C:0.28, G:0.12, T:0.26
Consensus pattern (56 bp):
CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTATATAATCAAACT
Found at i:22452 original size:68 final size:68
Alignment explanation
Indices: 22379--22530 Score: 170
Period size: 67 Copynumber: 2.2 Consensus size: 68
22369 CATCATGTGT
* * * *
22379 ACAAGAGAGCTACGAGACATTATGATGTAGCTAGGTTGCATAG-GTGATACTA-TG-TGTACACC
1 ACAAGAGAGCTACGAGACA-TAT-ATGTAGCTAGGTCGCAT-GCATGATACTAGTGAAGGACACC
22441 ATGTAG
63 ATGTAG
* * *
22447 ACAAGAGAGCTACG-G-GATATATGTAGCTAGGTCGCATGCATGGTTCTAGGTGAAGGACACCAT
1 ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGCATGATACTA-GTGAAGGACACCAT
22510 GTAG
65 GTAG
22514 ACAAGAGAGCTACGAGA
1 ACAAGAGAGCTACGAGA
22531 TAAACTAGCT
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
63 1 0.01
64 22 0.31
65 3 0.04
66 3 0.04
67 27 0.38
68 15 0.21
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.22
Consensus pattern (68 bp):
ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCGCATGCATGATACTAGTGAAGGACACCATG
TAG
Found at i:26048 original size:6 final size:6
Alignment explanation
Indices: 26037--26063 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
26027 AGTTAGGCCA
26037 TCATGT TCATGT TCATGT TCATGT TCA
1 TCATGT TCATGT TCATGT TCATGT TCA
26064 CCCCCCACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
TCATGT
Found at i:26478 original size:6 final size:6
Alignment explanation
Indices: 26469--26501 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
26459 AATAAAATTG
*
26469 AAATGA AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
26502 GATAAGAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:30230 original size:29 final size:28
Alignment explanation
Indices: 30195--30272 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
30185 TCATGAGATT
30195 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
30225 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
30252 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
30273 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:36414 original size:17 final size:18
Alignment explanation
Indices: 36394--36435 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
36384 TTACTTTCTG
*
36394 TAATAATATAATAT-ATT
1 TAATAATACAATATAATT
*
36411 TAATATTACAATATAATT
1 TAATAATACAATATAATT
*
36429 TTATAAT
1 TAATAAT
36436 TTATTTATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATAATACAATATAATT
Found at i:36780 original size:17 final size:16
Alignment explanation
Indices: 36747--36794 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
36737 TAATATTTTC
*
36747 TATT-ATTTTATTTTT
1 TATTAATTTTATTATT
36762 TATTAATTTTAATTATT
1 TATTAATTTT-ATTATT
*
36779 TATTATTATTTATTAT
1 TATTAAT-TTTATTAT
36795 ATATATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 4 0.14
16 5 0.18
17 16 0.57
18 3 0.11
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTAATTTTATTATT
Found at i:36888 original size:24 final size:25
Alignment explanation
Indices: 36845--36894 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
36835 TTTTATTACA
* *
36845 ATATATTTGAATTTTTTATTAGTTT
1 ATATATTTGAATTATGTATTAGTTT
*
36870 ATATATTT-AATTATGTATTATTTT
1 ATATATTTGAATTATGTATTAGTTT
36894 A
1 A
36895 AAATTATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (25 bp):
ATATATTTGAATTATGTATTAGTTT
Found at i:36906 original size:13 final size:13
Alignment explanation
Indices: 36888--36937 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
36878 AATTATGTAT
*
36888 TATTTTAAAATTA
1 TATTTTATAATTA
*
36901 TATTTTATATTTAAA
1 TATTTTATAATT--A
*
36916 TATTTTATTATTA
1 TATTTTATAATTA
36929 TATTTTATA
1 TATTTTATA
36938 TTTTTATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 19 0.63
15 11 0.37
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTTATAATTA
Found at i:36920 original size:15 final size:15
Alignment explanation
Indices: 36900--36956 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
36890 TTTTAAAATT
36900 ATATTTTATATTTAA
1 ATATTTTATATTTAA
36915 ATATTTTAT-TATT--
1 ATATTTTATAT-TTAA
36928 ATATTTTATATTTTTATA
1 ATATTTTATA--TTTA-A
36946 ATATTTTATAT
1 ATATTTTATAT
36957 AATTTATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.26
14 1 0.03
15 13 0.37
16 2 0.06
18 10 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATATTTTATATTTAA
Found at i:36944 original size:18 final size:19
Alignment explanation
Indices: 36923--36966 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
36913 AAATATTTTA
*
36923 TTATTATATTTTATAT-TT
1 TTATTATATTTTATATAAT
*
36941 TTATAATATTTTATATAAT
1 TTATTATATTTTATATAAT
36960 TTATTAT
1 TTATTAT
36967 TAATTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTATATTTTATATAAT
Found at i:36956 original size:7 final size:7
Alignment explanation
Indices: 36898--36941 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
36888 TATTTTAAAA
36898 TTATATT
1 TTATATT
36905 TTATATT
1 TTATATT
*
36912 TAAATATT
1 T-TATATT
*
36920 TTAT-TA
1 TTATATT
36926 TTATATT
1 TTATATT
36933 TTATATT
1 TTATATT
36940 TT
1 TT
36942 TATAATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
6 5 0.16
7 20 0.65
8 6 0.19
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
TTATATT
Found at i:36961 original size:28 final size:28
Alignment explanation
Indices: 36888--36954 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 28
36878 AATTATGTAT
**
36888 TATTTTAAAATTATATTTTATATTTAAA
1 TATTTTATTATTATATTTTATATTTAAA
36916 TATTTTATTATTATATTTTATATTTTTATAA
1 TATTTTATTATTATATTTTATA--TTTA-AA
36947 TATTTTAT
1 TATTTTAT
36955 ATAATTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 20 0.59
30 4 0.12
31 10 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TATTTTATTATTATATTTTATATTTAAA
Found at i:36987 original size:22 final size:23
Alignment explanation
Indices: 36915--37017 Score: 76
Period size: 22 Copynumber: 4.6 Consensus size: 23
36905 TTATATTTAA
36915 ATATT-TT-ATTATTATATT-TT
1 ATATTATTAATTATTATATTATT
* * *
36935 ATATTTTTATAATATTTTATATAATT
1 ATA-TTAT-TAAT-TATTATATTATT
*
36961 -TATTATTAATTATTTTGATT-TT
1 ATATTATTAATTATTAT-ATTATT
*
36983 A-ATTATTCATTA-TATATTATT
1 ATATTATTAATTATTATATTATT
37004 ATATTATTAATTAT
1 ATATTATTAATTAT
37018 ATTTAATAAT
Statistics
Matches: 63, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
20 6 0.10
21 7 0.11
22 27 0.43
23 7 0.11
24 5 0.08
25 9 0.14
26 2 0.03
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (23 bp):
ATATTATTAATTATTATATTATT
Found at i:36995 original size:29 final size:26
Alignment explanation
Indices: 36922--37039 Score: 79
Period size: 29 Copynumber: 4.5 Consensus size: 26
36912 TAAATATTTT
* *
36922 ATTATTATATTTT-A-TATTTTTATA
1 ATTATTTTATTTTAATTATTATTATA
*
36946 A-TATTTTA-TATAA-T-TTATTATTA
1 ATTATTTTATTTTAATTATTATTA-TA
36969 ATTATTTTGATTTTAATTATTCATTATA
1 ATTATTTT-ATTTTAATTATT-ATTATA
*
36997 TATTATTATATTATTAATTA-TATTTAATA
1 -ATTATTTTATT-TTAATTATTA-TT-ATA
*
37026 ATTATTTTTTTTTA
1 ATTATTTTATTTTA
37040 TGTAATAATT
Statistics
Matches: 75, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
22 7 0.09
23 11 0.15
24 7 0.09
25 1 0.01
26 4 0.05
27 5 0.07
28 19 0.25
29 21 0.28
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.64
Consensus pattern (26 bp):
ATTATTTTATTTTAATTATTATTATA
Found at i:37071 original size:37 final size:37
Alignment explanation
Indices: 37030--37101 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
37020 TTAATAATTA
* *
37030 TTTTTTT-TTATGTAATAATTTATATATAATTTTTTAT
1 TTTTTTTATTATAT-ATAATATATATATAATTTTTTAT
* *
37067 TTTTTTTATTATATATTATATATATTTAATTTTTT
1 TTTTTTTATTATATATAATATATATATAATTTTTT
37102 TTATAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 25 0.83
38 5 0.17
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.69
Consensus pattern (37 bp):
TTTTTTTATTATATATAATATATATATAATTTTTTAT
Found at i:37113 original size:64 final size:63
Alignment explanation
Indices: 37015--37142 Score: 152
Period size: 64 Copynumber: 2.0 Consensus size: 63
37005 TATTATTAAT
* * **
37015 TATATTTAATAATTATTTTTTTTTATGTAATAATTTATATATAATTT-TTTATTTTTTTTATTA
1 TATATTTAATAATTAATTTTTTTTATGAAATAATTTATATAT-ATTTATTTAAATTTTTTATTA
* * *
37078 TATATTATATATATTTAATTTTTTTTAT-AAATAATTTATCTATTTTTATTTAAATTTTTTATTA
1 TATATT-TA-ATAATTAATTTTTTTTATGAAATAATTTATATATATTTATTTAAATTTTTTATTA
37142 T
1 T
37143 TATGTTATTA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
63 9 0.16
64 30 0.55
65 16 0.29
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.66
Consensus pattern (63 bp):
TATATTTAATAATTAATTTTTTTTATGAAATAATTTATATATATTTATTTAAATTTTTTATTA
Found at i:37233 original size:23 final size:24
Alignment explanation
Indices: 37174--37293 Score: 72
Period size: 23 Copynumber: 5.0 Consensus size: 24
37164 TGTTAATGTA
* *
37174 TTATTTTATTATTATAATT-TTTATT
1 TTATTTAATTA-TAT-ATTATTTAAT
*
37199 TTATTTAATTATCTA-TATTTAAT
1 TTATTTAATTATATATTATTTAAT
**
37222 TTATTTCTTTATATATTATTTAAT
1 TTATTTAATTATATATTATTTAAT
*
37246 ATT-TTATAA-TAAAT-TTATTTTAAT
1 -TTATT-TAATTATATATTA-TTTAAT
* * *
37270 ATA-TTATTTATTTATTATTTAAT
1 TTATTTAATTATATATTATTTAAT
37293 T
1 T
37294 AATGTTTTAT
Statistics
Matches: 73, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
22 3 0.04
23 32 0.44
24 25 0.34
25 13 0.18
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATTTAATTATATATTATTTAAT
Found at i:37234 original size:19 final size:18
Alignment explanation
Indices: 37087--37307 Score: 55
Period size: 19 Copynumber: 12.4 Consensus size: 18
37077 ATATATTATA
37087 TATATTTAA-TT-TTTTT
1 TATATTTAATTTATTTTT
**
37103 TATAAATAATTTATCTATTT
1 TATATTTAATTTAT-T-TTT
*
37123 T-TATTTAAATTT-TTTAT
1 TATATTT-AATTTATTTTT
37140 TATTATGTT-A-TTATTTTAGT
1 TA-TAT-TTAATTTATTTT--T
* *
37160 AATATGTTAATGTATTATTT
1 TATAT-TTAATTTATT-TTT
*
37180 TATTATTATAATTT-TTATT
1 TA-TATT-TAATTTATTTTT
*
37199 T-TATTTAA-TTA---TC
1 TATATTTAATTTATTTTT
37212 TATATTTAATTTATTTCTT
1 TATATTTAATTTATTT-TT
*
37231 TATATATT-ATTTAATATTT
1 TATAT-TTAATTT-ATTTTT
* *
37250 TATAATAAATTTA-TTTT
1 TATATTTAATTTATTTTT
* *
37267 AATATATT-ATTTA-TTTA
1 TATAT-TTAATTTATTTTT
* *
37284 T-TATTTAATTAATGTTT
1 TATATTTAATTTATTTTT
37301 TAT-TTTA
1 TATATTTA
37308 TTAATTATTA
Statistics
Matches: 150, Mismatches: 25, Indels: 59
0.64 0.11 0.25
Matches are distributed among these distances:
13 2 0.01
14 7 0.05
15 7 0.05
16 17 0.11
17 32 0.21
18 10 0.07
19 37 0.25
20 24 0.16
21 12 0.08
22 2 0.01
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (18 bp):
TATATTTAATTTATTTTT
Found at i:37241 original size:38 final size:36
Alignment explanation
Indices: 37199--37284 Score: 93
Period size: 38 Copynumber: 2.3 Consensus size: 36
37189 AATTTTTATT
* * *
37199 TTATTTAATTATCTATATTTAATTTATTTCTTTATATA
1 TTATTTAATTATCTATAATAAATTTA-TT-TTAATATA
*
37237 TTATTTAA-TATTTTATAATAAATTTATTTTAATATA
1 TTATTTAATTA-TCTATAATAAATTTATTTTAATATA
*
37273 TTATTTATTTAT
1 TTATTTAATTAT
37285 TATTTAATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
36 15 0.37
37 6 0.15
38 20 0.49
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (36 bp):
TTATTTAATTATCTATAATAAATTTATTTTAATATA
Found at i:37289 original size:28 final size:29
Alignment explanation
Indices: 37245--37378 Score: 70
Period size: 28 Copynumber: 4.8 Consensus size: 29
37235 TATTATTTAA
*
37245 TATTTTA-TAATAAATTTATTTTAATATAT
1 TATTTTATTAAT-TATTTATTTTAATATAT
* * * *
37274 TA-TTTATTTATTATTTA-ATTAATGTTT
1 TATTTTATTAATTATTTATTTTAATATAT
*
37301 TATTTTATTAATTA-TTATTTCT-TTATAT
1 TATTTTATTAATTATTTATTT-TAATATAT
* *
37329 TA-ATTATT-ATCTATTAATTTATAAT-T-T
1 TATTTTATTAAT-TATTTATTT-TAATATAT
* *
37356 AATTTTATAAATATATTTATTTT
1 TATTTTATTAAT-TATTTATTTT
37379 TTATAGAATA
Statistics
Matches: 77, Mismatches: 19, Indels: 19
0.67 0.17 0.17
Matches are distributed among these distances:
26 2 0.03
27 21 0.27
28 37 0.48
29 17 0.22
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (29 bp):
TATTTTATTAATTATTTATTTTAATATAT
Found at i:37328 original size:55 final size:56
Alignment explanation
Indices: 37246--37383 Score: 142
Period size: 55 Copynumber: 2.5 Consensus size: 56
37236 ATTATTTAAT
* * * * *
37246 ATTTTAT-AATAAATTTATTTTAATATATTATTTATTTAT-TATTTAATTAAT-GTTTT
1 ATTTTATAAATATATTTATTTT-TTATATTAATTA-TTATCTA-TTAATTAATAATTTA
* *
37302 ATTTTATTAAT-TA-TTATTTCTTTATATTAATTATTATCTATTAATTTATAATTTA
1 ATTTTATAAATATATTTATTT-TTTATATTAATTATTATCTATTAATTAATAATTTA
37357 ATTTTATAAATATATTTATTTTTTATA
1 ATTTTATAAATATATTTATTTTTTATA
37384 GAATATTTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
54 12 0.17
55 31 0.45
56 17 0.25
57 9 0.13
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (56 bp):
ATTTTATAAATATATTTATTTTTTATATTAATTATTATCTATTAATTAATAATTTA
Found at i:37329 original size:20 final size:20
Alignment explanation
Indices: 37258--37343 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
37248 TTTATAATAA
*
37258 ATTTATTTTAATATATTATTT
1 ATTTATATTAAT-TATTATTT
37279 ATTTATTATTTAATTAATGT-TTT
1 ATTTA-TA-TTAATT-AT-TATTT
37302 ATTT-TATTAATTATTATTT
1 ATTTATATTAATTATTATTT
* *
37321 CTTTATATTAATTATTATCT
1 ATTTATATTAATTATTATTT
37341 ATT
1 ATT
37344 AATTTATAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
18 1 0.02
19 8 0.15
20 22 0.40
21 7 0.13
22 2 0.04
23 14 0.25
24 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (20 bp):
ATTTATATTAATTATTATTT
Found at i:37379 original size:18 final size:17
Alignment explanation
Indices: 37352--37394 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
37342 TTAATTTATA
*
37352 ATTTAATTTTATAAATAT
1 ATTTATTTTTATAAA-AT
*
37370 ATTTATTTTTTATAGAAT
1 ATTTA-TTTTTATAAAAT
37388 ATTTATT
1 ATTTATT
37395 ATTTTAGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 12 0.55
19 8 0.36
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTTATTTTTATAAAAT
Found at i:37380 original size:19 final size:19
Alignment explanation
Indices: 37357--37400 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
37347 TTATAATTTA
37357 ATTTTATAAATATATTTATT
1 ATTTTATAAA-ATATTTATT
*
37377 -TTTTATAGAATATTTATT
1 ATTTTATAAAATATTTATT
37395 ATTTTA
1 ATTTTA
37401 GTATCATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
ATTTTATAAAATATTTATT
Found at i:37465 original size:16 final size:15
Alignment explanation
Indices: 37414--37497 Score: 62
Period size: 16 Copynumber: 5.3 Consensus size: 15
37404 TCATTAAAGA
37414 TTTTAATTATATATAT
1 TTTTAA-TATATATAT
* * *
37430 TATTATTATATAATAA
1 TTTTAATATAT-ATAT
37446 TTTTAATATATATGAT
1 TTTTAATATATAT-AT
*
37462 TTTTAAT-TTTATTAT
1 TTTTAATATATA-TAT
* *
37477 TTTATAATATAAATTT
1 TTT-TAATATATATAT
37493 TTTTA
1 TTTTA
37498 TTGTATTTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
15 17 0.32
16 34 0.64
17 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (15 bp):
TTTTAATATATATAT
Found at i:37610 original size:13 final size:13
Alignment explanation
Indices: 37594--37619 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
37584 AATTTTTAAA
37594 TTATTTTATTTTT
1 TTATTTTATTTTT
37607 TTATTTTATTTTT
1 TTATTTTATTTTT
37620 AATTTTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTATTTTATTTTT
Found at i:37619 original size:19 final size:19
Alignment explanation
Indices: 37581--37634 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
37571 AAATTATATA
* *
37581 TTAAATTTTTAAATTA-TT
1 TTAATTTTTTATATTATTT
* *
37599 TTATTTTTTTATTTTATTT
1 TTAATTTTTTATATTATTT
37618 TTAATTTTTTATATTAT
1 TTAATTTTTTATATTAT
37635 ATTATTATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
18 12 0.41
19 17 0.59
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTAATTTTTTATATTATTT
Found at i:37634 original size:24 final size:23
Alignment explanation
Indices: 37607--37663 Score: 71
Period size: 24 Copynumber: 2.5 Consensus size: 23
37597 TTTTATTTTT
* *
37607 TTATTTTATTTTTAATTTTTTATA
1 TTATTTTATTATTAATTTTATA-A
*
37631 TTATATTATTATTAATTTTATAA
1 TTATTTTATTATTAATTTTATAA
37654 TT-TTTTATTA
1 TTATTTTATTA
37664 ATATAAGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 7 0.24
23 3 0.10
24 19 0.66
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTATTTTATTATTAATTTTATAA
Found at i:37743 original size:63 final size:63
Alignment explanation
Indices: 37620--37754 Score: 150
Period size: 63 Copynumber: 2.1 Consensus size: 63
37610 TTTTATTTTT
* *
37620 AATTTTTTATATTATATTATTATTAATTTTATAATTTTTTATTAATATAAGATTAGTAATA-TA
1 AATTTTTTAAATTATATTATTATT-ATTTTATAATTTTTTAATAATATAAGATTAGTAATATTA
* * * * *
37683 TATTTTTTAAATTAATATTTTTATT-TTTTATTTATTTTTTAATAATATTA-ATTAATTAATATT
1 AATTTTTTAAATT-ATATTATTATTATTTTA-TAATTTTTTAATAATATAAGATT-AGTAATATT
37746 A
63 A
37747 AATTTTTT
1 AATTTTTT
37755 TTATTATTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
62 8 0.13
63 33 0.55
64 19 0.32
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (63 bp):
AATTTTTTAAATTATATTATTATTATTTTATAATTTTTTAATAATATAAGATTAGTAATATTA
Found at i:37772 original size:28 final size:27
Alignment explanation
Indices: 37728--37791 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
37718 TTTTTAATAA
37728 TATTAATT-AATTAATATTAAATTTTTTT
1 TATT-ATTAAATTAATATTAAA-TTTTTT
* **
37756 TATTATTAAATTTATATTTTATTTTTT
1 TATTATTAAATTAATATTAAATTTTTT
37783 TATTTATTA
1 TA-TTATTA
37792 TGTATATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 11 0.35
28 20 0.65
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TATTATTAAATTAATATTAAATTTTTT
Found at i:37797 original size:26 final size:27
Alignment explanation
Indices: 37750--37811 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
37740 AATATTAAAT
*
37750 TTTTTTTATTATTAAATTTATATTTT-A
1 TTTTTTTATTATT-AATGTATATTTTAA
37777 TTTTTTTATTTATT-ATGTATATTTTAA
1 TTTTTTTA-TTATTAATGTATATTTTAA
*
37804 TTATTTTA
1 TTTTTTTA
37812 AGATTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 10 0.32
27 16 0.52
28 5 0.16
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTTTTTATTATTAATGTATATTTTAA
Found at i:37831 original size:29 final size:29
Alignment explanation
Indices: 37799--37857 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
37789 TTATGTATAT
37799 TTTAATTATTT-TAAGATTTT-TATTTTTTA
1 TTTAATT-TTTATAA-ATTTTATATTTTTTA
*
37828 TTTAATTTTTATTAATTTTATATTTTTTA
1 TTTAATTTTTATAAATTTTATATTTTTTA
37857 T
1 T
37858 ATTATCATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (29 bp):
TTTAATTTTTATAAATTTTATATTTTTTA
Found at i:37852 original size:43 final size:46
Alignment explanation
Indices: 37751--37853 Score: 106
Period size: 49 Copynumber: 2.2 Consensus size: 46
37741 ATATTAAATT
* * *
37751 TTTTTTATTATTAAATTTATATTTTATTTTTTTATTTATTATGTATA
1 TTTTATATT-TTAAATTTATATTTTATTATTTAATTTATTATGTATA
*
37798 TTTTAATTATTTTAAGATTTTTATTTT-TTATTTAATTT-TTAT-TA-A
1 TTTT-A-TATTTTAA-ATTTATATTTTATTATTTAATTTATTATGTATA
37843 TTTTATATTTT
1 TTTTATATTTT
37854 TTATATTATC
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
43 6 0.12
44 1 0.02
45 5 0.10
46 2 0.04
47 8 0.16
48 13 0.27
49 14 0.29
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (46 bp):
TTTTATATTTTAAATTTATATTTTATTATTTAATTTATTATGTATA
Found at i:37853 original size:35 final size:35
Alignment explanation
Indices: 37734--37862 Score: 101
Period size: 35 Copynumber: 3.8 Consensus size: 35
37724 ATAATATTAA
* * *
37734 TTAATTAATATTAAATTTTT-TTTATTAT-TA-AAT
1 TTAATT-ATTTTATATTTTTATTTATTATGTATATT
*
37767 TT-A-TATTTTATTTTTTTATTTATTATGTATATT
1 TTAATTATTTTATATTTTTATTTATTATGTATATT
* * *
37800 TTAATTATTTTAAGATTTTTATTTTTTATTTA-ATT
1 TTAATTATTTT-ATATTTTTATTTATTATGTATATT
* *
37835 TTTATTAATTTTATATTTTT-TATATTAT
1 TTAATT-ATTTTATATTTTTATTTATTAT
37863 CATATAATTT
Statistics
Matches: 77, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
30 10 0.13
31 9 0.12
32 3 0.04
33 6 0.08
34 7 0.09
35 21 0.27
36 21 0.27
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (35 bp):
TTAATTATTTTATATTTTTATTTATTATGTATATT
Found at i:37854 original size:18 final size:17
Alignment explanation
Indices: 37766--37880 Score: 62
Period size: 18 Copynumber: 6.5 Consensus size: 17
37756 TATTATTAAA
*
37766 TTTA-TATTTTAT-TTT
1 TTTATTATTTTATAATT
37781 TTTATTTATTATGTAT-ATT
1 TTTA-TTATT-T-TATAATT
*
37800 TTAATTATTTTA-AGATT
1 TTTATTATTTTATA-ATT
37817 TTTATT-TTTTATTTAATT
1 TTTATTATTTTA--TAATT
*
37835 TTTATTAATTTTATATTT
1 TTTATT-ATTTTATAATT
37853 TTTA-TATTATCATATAATT
1 TTTATTATT-T--TATAATT
37872 TATTATTAT
1 T-TTATTAT
37881 AATTCATTTT
Statistics
Matches: 79, Mismatches: 5, Indels: 26
0.72 0.05 0.24
Matches are distributed among these distances:
15 4 0.05
16 10 0.13
17 15 0.19
18 23 0.29
19 16 0.20
20 8 0.10
21 3 0.04
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTATTATTTTATAATT
Found at i:37855 original size:36 final size:36
Alignment explanation
Indices: 37694--37862 Score: 104
Period size: 36 Copynumber: 4.7 Consensus size: 36
37684 ATTTTTTAAA
* * *
37694 TTAA-TATTTT-TATTTTTTATTTATTTTTTAATAATA
1 TTAATTATTTTATATTTTTTATTTATTATGT-AT-ATT
* * * *
37730 TTAATTAATTAATATTAAATTTTTTTTATTAT-TA-AAT
1 TTAATTATTTTATATT---TTTTATTTATTATGTATATT
37767 TT-A-TATTTTAT-TTTTTTATTTATTATGTATATT
1 TTAATTATTTTATATTTTTTATTTATTATGTATATT
* * *
37800 TTAATTATTTTA-AGATTTTTATTTTTTATTTA-ATT
1 TTAATTATTTTATA-TTTTTTATTTATTATGTATATT
*
37835 TTTATTAATTTTATATTTTTTATATTAT
1 TTAATT-ATTTTATATTTTTTAT-TTAT
37863 CATATAATTT
Statistics
Matches: 103, Mismatches: 16, Indels: 27
0.71 0.11 0.18
Matches are distributed among these distances:
31 12 0.12
32 2 0.02
33 4 0.04
34 3 0.03
35 21 0.20
36 33 0.32
37 11 0.11
38 4 0.04
39 1 0.01
40 1 0.01
41 11 0.11
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (36 bp):
TTAATTATTTTATATTTTTTATTTATTATGTATATT
Found at i:37948 original size:19 final size:21
Alignment explanation
Indices: 37870--37945 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 21
37860 TATCATATAA
* *
37870 TTTATTATTATAATTCAT-TT
1 TTTATTATTATTATTAATATT
*
37890 TTAATAATATATATATATTAATATT
1 TT--TATTAT-TAT-TATTAATATT
*
37915 TTTATTATTTATTATTAATTTT
1 TTTATTA-TTATTATTAATATT
37937 TTTATTATT
1 TTTATTATT
37946 TATATATTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
20 2 0.04
21 2 0.04
22 21 0.47
23 10 0.22
24 6 0.13
25 4 0.09
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTATTATTATTATTAATATT
Found at i:38005 original size:21 final size:21
Alignment explanation
Indices: 37966--38005 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
37956 AATATTATAT
*
37966 AATTTAATTAATTTCTATTTA
1 AATTTAAATAATTTCTATTTA
37987 AATTTAAATATATTT-TATT
1 AATTTAAATA-ATTTCTATT
38006 ATTTTTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
AATTTAAATAATTTCTATTTA
Found at i:38169 original size:11 final size:11
Alignment explanation
Indices: 38130--38245 Score: 62
Period size: 11 Copynumber: 10.4 Consensus size: 11
38120 ATAATTTTAT
38130 TTTTAATATATA
1 TTTT-ATATATA
38142 TTATT-TATA-A
1 TT-TTATATATA
*
38152 TTCTATATATA
1 TTTTATATATA
38163 TTTTATATATA
1 TTTTATATATA
* *
38174 TATTATATTTA
1 TTTTATATATA
*
38185 TTTTAATTTATTTA
1 TTTT-A--TATATA
38199 TTTT-TATATA
1 TTTTATATATA
* *
38209 ATTTATTTTATA
1 TTTTA-TATATA
*
38221 TTTT-TTTATTA
1 TTTTATATA-TA
*
38232 TTTT-TTTATA
1 TTTTATATATA
38242 TTTT
1 TTTT
38246 TATTTTTATT
Statistics
Matches: 86, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
9 1 0.01
10 25 0.29
11 37 0.43
12 11 0.13
13 2 0.02
14 10 0.12
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTATATATA
Found at i:38198 original size:14 final size:14
Alignment explanation
Indices: 38179--38230 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
38169 ATATATATTA
38179 TATTTATTTTAATT
1 TATTTATTTTAATT
*
38193 TATTTATTTTTATAT
1 TATTTATTTTAAT-T
*
38208 AATTTATTTTATATT
1 TATTTATTTTA-ATT
*
38223 TTTTTATT
1 TATTTATT
38231 ATTTTTTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 12 0.39
15 17 0.55
16 2 0.06
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTATTTTAATT
Found at i:38208 original size:69 final size:68
Alignment explanation
Indices: 38125--38281 Score: 160
Period size: 69 Copynumber: 2.3 Consensus size: 68
38115 ATTTTATAAT
38125 TTTATTTTTAATATATATTA-TTTATAATTCTATATATATTTTATATATATATTATATTTATT-T
1 TTTATTTTT-ATATATATTATTTTATAATTCTATAT-TATTTT-TATATAT-TTATATTT-TTAT
38188 TAATTTA-
61 TAATTTAC
* * * * * *
38195 TTTATTTTTATATA-ATTTATTTTATATTTTTTTATTATTTTTTTATATTTTTATTTTTATTCAT
1 TTTATTTTTATATATA-TTATTTTATAATTCTATATTATTTTTATATATTTATATTTTTATTAAT
38259 TTACC
65 TTA-C
*
38264 TTTATTTTTATATCTATT
1 TTTATTTTTATATATATT
38282 CATATTTACA
Statistics
Matches: 74, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
66 2 0.03
67 14 0.19
68 7 0.09
69 29 0.39
70 22 0.30
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (68 bp):
TTTATTTTTATATATATTATTTTATAATTCTATATTATTTTTATATATTTATATTTTTATTAATT
TAC
Found at i:38229 original size:10 final size:10
Alignment explanation
Indices: 38176--38246 Score: 67
Period size: 11 Copynumber: 7.0 Consensus size: 10
38166 TATATATATA
38176 TTATATTTATT
1 TTATATTT-TT
*
38187 TTA-A-TTTA
1 TTATATTTTT
38195 TT-TATTTTT
1 TTATATTTTT
*
38204 ATATAATTTATT
1 TTAT-ATTT-TT
38216 TTATATTTTT
1 TTATATTTTT
38226 TTATTATTTTT
1 TTA-TATTTTT
38237 TTATATTTTT
1 TTATATTTTT
38247 ATTTTTATTC
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
8 4 0.08
9 6 0.12
10 14 0.28
11 21 0.42
12 5 0.10
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TTATATTTTT
Found at i:38229 original size:34 final size:36
Alignment explanation
Indices: 38125--38276 Score: 133
Period size: 34 Copynumber: 4.4 Consensus size: 36
38115 ATTTTATAAT
* * *
38125 TTTATTTTTA-ATATATATTA-TTTATAATTCTATA
1 TTTATTTTTATATATATATTATTTTATATTTATTTA
*
38159 TATA-TTTTATATATATATTATATTTAT-TTTAATTTA
1 TTTATTTTTATATATATATTAT-TTTATATTT-ATTTA
*
38195 TTTATTTTTATATA-AT-TTATTTTATATTTTTTTA
1 TTTATTTTTATATATATATTATTTTATATTTATTTA
* * *
38229 -TTATTTTTTTATAT-TTTTATTTT-TATTCATTTA
1 TTTATTTTTATATATATATTATTTTATATTTATTTA
38262 CCTTTATTTTTATAT
1 --TTTATTTTTATAT
38277 CTATTCATAT
Statistics
Matches: 97, Mismatches: 10, Indels: 20
0.76 0.08 0.16
Matches are distributed among these distances:
33 26 0.27
34 29 0.30
35 9 0.09
36 24 0.25
37 9 0.09
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (36 bp):
TTTATTTTTATATATATATTATTTTATATTTATTTA
Found at i:38234 original size:22 final size:22
Alignment explanation
Indices: 38197--38260 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
38187 TTAATTTATT
* *
38197 TATTTTTATATAATTTATTTTA
1 TATTTTTTTATTATTTATTTTA
38219 TATTTTTTTATTATTT-TTTTA
1 TATTTTTTTATTATTTATTTTA
* *
38240 TATTTTTATTTTTATTCATTT
1 TATTTTT-TTATTATTTATTT
38261 ACCTTTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 12 0.33
22 21 0.58
23 3 0.08
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (22 bp):
TATTTTTTTATTATTTATTTTA
Found at i:38238 original size:35 final size:35
Alignment explanation
Indices: 38149--38276 Score: 104
Period size: 33 Copynumber: 3.6 Consensus size: 35
38139 ATATTATTTA
*
38149 TAATTCTATATATATTTTATATATATATTATATTTAT-TT
1 TAATT-TATTTAT-TTTTATATA-AT-TTAT-TTTATATT
38188 TAATTTATTTATTTTTATATAATTTATTTTATATT
1 TAATTTATTTATTTTTATATAATTTATTTTATATT
* * *
38223 T-TTTTA-TTATTTTTTTATATTTTTATTTT-TA-T
1 TAATTTATTTATTTTTATATA-ATTTATTTTATATT
*
38255 TCATTTACCTTTATTTTTATAT
1 TAATTTA--TTTATTTTTATAT
38277 CTATTCATAT
Statistics
Matches: 77, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
32 2 0.03
33 18 0.23
34 17 0.22
35 7 0.09
36 13 0.17
37 9 0.12
38 6 0.08
39 5 0.06
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (35 bp):
TAATTTATTTATTTTTATATAATTTATTTTATATT
Found at i:38245 original size:19 final size:19
Alignment explanation
Indices: 38176--38249 Score: 62
Period size: 19 Copynumber: 3.7 Consensus size: 19
38166 TATATATATA
*
38176 TTATATTTATT-TTAATTTAT
1 TTATATTT-TTATT-ATTTTT
*
38196 TTAT-TTTTATATAATTTATT
1 TTATATTTT-TATTATTT-TT
38216 TTATATTTTTTTATTATTTTT
1 TTATA--TTTTTATTATTTTT
38237 TTATATTTTTATT
1 TTATATTTTTATT
38250 TTTATTCATT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
18 1 0.02
19 16 0.36
20 10 0.22
21 7 0.16
22 7 0.16
23 4 0.09
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTATATTTTTATTATTTTT
Found at i:38261 original size:14 final size:13
Alignment explanation
Indices: 38086--38274 Score: 74
Period size: 14 Copynumber: 14.2 Consensus size: 13
38076 GTCCTAATTA
*
38086 ATTTTATATTAATT
1 ATTTT-TATTATTT
*
38100 ATTTTTAATT-TGT
1 ATTTTT-ATTATTT
*
38113 ATATTTTATAATTTT
1 AT-TTTTATTA-TTT
* *
38128 ATTTTTAATATAT
1 ATTTTTATTATTT
*
38141 ATTATTTATAATTCT
1 ATT-TTTATTATT-T
*
38156 ATATATATT-TTATAT
1 AT-T-T-TTATTATTT
*
38171 ATATATTA-TATTT
1 AT-TTTTATTATTT
*
38184 ATTTTAATTTATTT
1 ATTTTTA-TTATTT
38198 ATTTTTATATAATTT
1 ATTTTTAT-T-ATTT
38213 A-TTTTA-TA-TT
1 ATTTTTATTATTT
38223 -TTTTTATTATTT
1 ATTTTTATTATTT
38235 -TTTTATATT-TTT
1 ATTTT-TATTATTT
38247 ATTTTTATTCATTT
1 ATTTTTATT-ATTT
**
38261 ACCTTTATT-TTT
1 ATTTTTATTATTT
38273 AT
1 AT
38275 ATCTATTCAT
Statistics
Matches: 135, Mismatches: 20, Indels: 42
0.69 0.10 0.21
Matches are distributed among these distances:
10 7 0.05
11 3 0.02
12 21 0.16
13 28 0.21
14 51 0.38
15 17 0.13
16 6 0.04
17 2 0.01
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.68
Consensus pattern (13 bp):
ATTTTTATTATTT
Found at i:38477 original size:30 final size:30
Alignment explanation
Indices: 38382--38477 Score: 90
Period size: 35 Copynumber: 3.1 Consensus size: 30
38372 AAATTATATA
*
38382 ATTTAATT-TATTCTAAAAT-TCTAGTTTTT
1 ATTTAATTATATT-TAAAATATATAGTTTTT
38411 ATTTAATTATATTTAAAATATATAGTTATTTTTTT
1 ATTTAATTATATTTAAAATATATAG-----TTTTT
*
38446 ATTTAATTATTATTTATAA-ATATAGTTTTT
1 ATTTAATTA-TATTTAAAATATATAGTTTTT
38476 AT
1 AT
38478 AATAATTTAA
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
29 14 0.25
30 15 0.26
35 20 0.35
36 8 0.14
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.59
Consensus pattern (30 bp):
ATTTAATTATATTTAAAATATATAGTTTTT
Done.