Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2374
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: 50759
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:1603 original size:24 final size:22
Alignment explanation
Indices: 1562--1607 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1552 ATAATTAAAA
*
1562 TATAAAATAAAATATAATATAT
1 TATAAAAAAAAATATAATATAT
1584 TATAAAAAAATAATATTAATATAT
1 TATAAAAAAA-AATA-TAATATAT
1608 AAAATAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 4 0.19
24 8 0.38
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TATAAAAAAAAATATAATATAT
Found at i:1660 original size:27 final size:26
Alignment explanation
Indices: 1629--1683 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
1619 AAGAATATAT
*
1629 TAAAAT-TTATATATAATTATAATGTGA
1 TAAAATATTATA-ATAATT-TAATATGA
*
1656 TAAAATATTTTAATAATTTAATATGA
1 TAAAATATTATAATAATTTAATATGA
1682 TA
1 TA
1684 CATAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.36
27 12 0.48
28 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (26 bp):
TAAAATATTATAATAATTTAATATGA
Found at i:4625 original size:2 final size:2
Alignment explanation
Indices: 4618--4649 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4608 TTATTAATTA
4618 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
4650 GTATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5075 original size:29 final size:28
Alignment explanation
Indices: 5037--5092 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
5027 TTGATTAACC
* * *
5037 AATAATTCAAATTGAATTGAATTAAAAA
1 AATAATTCAAATTCAAATCAATTAAAAA
5065 AATATATTCAAATTCAAATCAATTAAAA
1 AATA-ATTCAAATTCAAATCAATTAAAA
5093 CCTTAAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.32
Consensus pattern (28 bp):
AATAATTCAAATTCAAATCAATTAAAAA
Found at i:5212 original size:3 final size:3
Alignment explanation
Indices: 5204--5243 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5194 AAAATGGTAG
5204 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5244 GGAATAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:7859 original size:2 final size:2
Alignment explanation
Indices: 7854--7888 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7844 CAGGGGGGGA
7854 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
7889 AGAATAACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9603 original size:108 final size:110
Alignment explanation
Indices: 9439--9734 Score: 364
Period size: 108 Copynumber: 2.7 Consensus size: 110
9429 TCATCGTCAC
* * * * * * * *
9439 CATCACGAATTCTTTCTCTTTCACGCCTTCTATCCCTA-TAGGCTCGCTTGTCTTCTTCTTCATC
1 CATCATGAATTCTCTCACTTTCTCGCCTCCTATCTCTACTA-GCACGATTGTCTTCTTCTTCATC
* * *
9503 ACCAGATCTAGAACGTTCTTCTCTCCGCCTATCCTTA-C-CATCAT
65 ACAAGATCTAGAACGTTCATCTCTCCGCCTATCCTTACCTCATCAG
* * *
9547 CATCATGAATTCTCTCACTTTCTCGCCTCCTATCTCTATTAGGAGGATTGTCTTCTTCTTCATCA
1 CATCATGAATTCTCTCACTTTCTCGCCTCCTATCTCTACTAGCACGATTGTCTTCTTCTTCATCA
* *
9612 GAAGATCTAGAATGTTCATCTCTCCGCCTATCCTTACCCTCATCAG
66 CAAGATCTAGAACGTTCATCTCTCCGCCTATCCTTA-CCTCATCAG
* * *
9658 CATCATGAATTCTCTCACTTTCTCGCCTCCTATCTCTACTAGCACGCTTGTCTTCCTCTTCATTA
1 CATCATGAATTCTCTCACTTTCTCGCCTCCTATCTCTACTAGCACGATTGTCTTCTTCTTCATCA
* *
9723 AAAGATCCAGAA
66 CAAGATCTAGAA
9735 TGCTCTCTCT
Statistics
Matches: 161, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
108 84 0.52
109 2 0.01
110 1 0.01
111 74 0.46
ACGTcount: A:0.20, C:0.33, G:0.10, T:0.37
Consensus pattern (110 bp):
CATCATGAATTCTCTCACTTTCTCGCCTCCTATCTCTACTAGCACGATTGTCTTCTTCTTCATCA
CAAGATCTAGAACGTTCATCTCTCCGCCTATCCTTACCTCATCAG
Found at i:10470 original size:21 final size:21
Alignment explanation
Indices: 10427--10469 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
10417 TGGTATTGGG
10427 ATTAAATTTAATTATTTTAAA
1 ATTAAATTTAATTATTTTAAA
10448 ATTAAA-TTAATTAAATTTTAAA
1 ATTAAATTTAATT--ATTTTAAA
10470 TAAAAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 6 0.30
22 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTAAATTTAATTATTTTAAA
Found at i:10582 original size:22 final size:21
Alignment explanation
Indices: 10557--10598 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
10547 AAAATAAAAA
10557 ATAT-TTTTAT-ATTAATATTT
1 ATATATTTTATAATTAA-ATTT
10577 ATATATTTTATAATTAAATTT
1 ATATATTTTATAATTAAATTT
10598 A
1 A
10599 AAGTAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATATTTTATAATTAAATTT
Found at i:11138 original size:16 final size:16
Alignment explanation
Indices: 11080--11138 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
11070 ATTAAATTTT
11080 ATATAAATATAAAATA
1 ATATAAATATAAAATA
* * * *
11096 TTTTAAATACAATAATG
1 ATATAAATATAA-AATA
11113 ATATAAATATAAAATA
1 ATATAAATATAAAATA
*
11129 ATAAAAATAT
1 ATATAAATAT
11139 GATACAAATA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
16 21 0.64
17 12 0.36
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (16 bp):
ATATAAATATAAAATA
Found at i:11206 original size:115 final size:114
Alignment explanation
Indices: 11005--11233 Score: 379
Period size: 115 Copynumber: 2.0 Consensus size: 114
10995 TTAATATGAT
* * * *
11005 ATATATAATAATATAAATATGATACAAATATATGTTTTAAATTATATAATATGAATTATTAATAT
1 ATATAAAATAATAAAAATATGATACAAATATATATTTTAAATTATATAATATAAATTATTAATAT
*
11070 ATTAAATTTTATATAAATATAAAATATTTTAAATACAATAATGATATAA
66 ATCAAATTTTATATAAATATAAAATATTTTAAATACAATAATGATATAA
11119 ATATAAAATAATAAAAATATGATACAAATATATATTTTAAATTTATATAATATAAATTATTAAT-
1 ATATAAAATAATAAAAATATGATACAAATATATATTTTAAA-TTATATAATATAAATTATTAATA
*
11183 TGATCAAATTTTATATAAATATAAAATATTTTAAATACAATGATGATATAA
65 T-ATCAAATTTTATATAAATATAAAATATTTTAAATACAATAATGATATAA
11234 TAAAATAAAT
Statistics
Matches: 107, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
114 39 0.36
115 68 0.64
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.41
Consensus pattern (114 bp):
ATATAAAATAATAAAAATATGATACAAATATATATTTTAAATTATATAATATAAATTATTAATAT
ATCAAATTTTATATAAATATAAAATATTTTAAATACAATAATGATATAA
Found at i:11218 original size:27 final size:27
Alignment explanation
Indices: 11065--11218 Score: 84
Period size: 33 Copynumber: 5.4 Consensus size: 27
11055 ATGAATTATT
*
11065 AATATATTAAATTTTATATAAATATAA
1 AATATTTTAAATTTTATATAAATATAA
*
11092 AATATTTTAAATACAATAATGATATAAATATAA
1 AATATTTTAAAT----T--TTATATAAATATAA
* ** * * *
11125 AATAATAAAAATATGATACAAATAT--
1 AATATTTTAAATTTTATATAAATATAA
11150 -ATATTTTAAA-TTTATAT-AATATAA
1 AATATTTTAAATTTTATATAAATATAA
*
11174 ATTATTAATTGATCAAATTTTATATAAATATAA
1 A--A-T-ATT--TTAAATTTTATATAAATATAA
11207 AATATTTTAAAT
1 AATATTTTAAAT
11219 ACAATGATGA
Statistics
Matches: 95, Mismatches: 15, Indels: 34
0.66 0.10 0.24
Matches are distributed among these distances:
22 5 0.05
23 4 0.04
24 7 0.07
27 28 0.29
28 1 0.01
29 6 0.06
30 1 0.01
31 6 0.06
32 7 0.07
33 30 0.32
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
AATATTTTAAATTTTATATAAATATAA
Found at i:12011 original size:5 final size:6
Alignment explanation
Indices: 11983--12020 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
11973 TAAAGTTTCG
* *
11983 ATAAAA A-AAAA AGAGAA ATAAAA ATAAAA ATAAAA ATA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATA
12021 CTCAAATCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (6 bp):
ATAAAA
Found at i:13794 original size:10 final size:11
Alignment explanation
Indices: 13769--13798 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
13759 AATTTTATGA
13769 ATCTTAATTAT
1 ATCTTAATTAT
13780 ATCTTAATT-T
1 ATCTTAATTAT
13790 ATCTTAATT
1 ATCTTAATT
13799 GAACATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (11 bp):
ATCTTAATTAT
Found at i:14642 original size:42 final size:41
Alignment explanation
Indices: 14582--14674 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
14572 TAGAATATAA
*
14582 ATATAAATTTAAATAATTAAATATTATT-TTTTAAAAATAATT
1 ATATAAATTTAAATAATTAAAT-TT-TTAGTTTAAAAATAATT
*
14624 ATATAAA-TTAATTAAATTAAATTTTTAGTTTAAAAAT-ATT
1 ATATAAATTTAAAT-AATTAAATTTTTAGTTTAAAAATAATT
* *
14664 AAAAAAATTTA
1 ATATAAATTTA
14675 GTTCAAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
40 10 0.23
41 19 0.43
42 15 0.34
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (41 bp):
ATATAAATTTAAATAATTAAATTTTTAGTTTAAAAATAATT
Found at i:15102 original size:21 final size:21
Alignment explanation
Indices: 15078--15121 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
15068 ATTAAATTTT
15078 TTTAAACAATTTTTAAATCAA
1 TTTAAACAATTTTTAAATCAA
** *
15099 TTTAATTAATTTTTAAATTAA
1 TTTAAACAATTTTTAAATCAA
15120 TT
1 TT
15122 AATTTATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTAAACAATTTTTAAATCAA
Found at i:15770 original size:2 final size:2
Alignment explanation
Indices: 15763--15797 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15753 TCTTGTAGAC
15763 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15798 ATTCTCATGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16290 original size:28 final size:28
Alignment explanation
Indices: 16254--16310 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
16244 TTTGATTATA
*
16254 AAATTTTAAAAAATTAAATAAATTAATT
1 AAATTTTAAAAAATTAAATAAACTAATT
16282 AAATTTTAAAAAATTAAATAAACTAATT
1 AAATTTTAAAAAATTAAATAAACTAATT
16310 A
1 A
16311 CACTCTCTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
AAATTTTAAAAAATTAAATAAACTAATT
Found at i:16917 original size:14 final size:14
Alignment explanation
Indices: 16900--16933 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
16890 TAAAATATAC
16900 TTAATTAAATT-AAA
1 TTAATT-AATTAAAA
16914 TTAATTAATTAAAA
1 TTAATTAATTAAAA
16928 TTAATT
1 TTAATT
16934 TGGCTGGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAATTAATTAAAA
Found at i:18950 original size:2 final size:2
Alignment explanation
Indices: 18943--18967 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18933 CATAGAAAGT
18943 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
18968 CTTGGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:22132 original size:4 final size:4
Alignment explanation
Indices: 22123--22159 Score: 56
Period size: 4 Copynumber: 8.8 Consensus size: 4
22113 CTTCCTGTAT
22123 ATAC ATAC ATAC ATATGC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATA--C ATAC ATAC ATAC ATAC ATA
22160 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 27 0.87
6 4 0.13
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:22164 original size:2 final size:2
Alignment explanation
Indices: 22157--22184 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22147 ACATACATAC
22157 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
22185 GATCCATTCC
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:22720 original size:27 final size:27
Alignment explanation
Indices: 22665--22715 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
22655 ATTTAAAAAA
*
22665 TAATTAAATATTAATTTATATATATTT
1 TAATTAAATATTAATATATATATATTT
22692 TAATTAAAT-TT-ATATATATA-ATTT
1 TAATTAAATATTAATATATATATATTT
22716 ATTTATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.17
25 8 0.35
26 2 0.09
27 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TAATTAAATATTAATATATATATATTT
Found at i:22723 original size:21 final size:19
Alignment explanation
Indices: 22673--22725 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
22663 AATAATTAAA
22673 TATTAATTTATATATATTT
1 TATTAATTTATATATATTT
22692 TAATTAAATTTATATATATAATT
1 T-ATT-AATTTATATATAT--TT
*
22715 TATTTATTTAT
1 TATTAATTTAT
22726 TAAATAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 1 0.03
20 3 0.10
21 19 0.66
22 3 0.10
23 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TATTAATTTATATATATTT
Found at i:28962 original size:27 final size:27
Alignment explanation
Indices: 28917--28969 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28907 TTATTTTAAA
*
28917 TATAAAAAATAATATAAATATGATATT
1 TATAAAAAATAATATAAATATAATATT
*
28944 TATAAAAAAT-ATTTAAAATATAATAT
1 TATAAAAAATAATAT-AAATATAATAT
28970 GAAAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 3 0.13
27 20 0.87
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (27 bp):
TATAAAAAATAATATAAATATAATATT
Found at i:29295 original size:13 final size:14
Alignment explanation
Indices: 29237--29297 Score: 54
Period size: 15 Copynumber: 4.4 Consensus size: 14
29227 TATAAATTTT
*
29237 TTTATTAAATAAAA
1 TTTAATAAATAAAA
*
29251 TTATAATTAATAAAA
1 TT-TAATAAATAAAA
* *
29266 TTTATTTAAA-AATA
1 TTTA-ATAAATAAAA
29280 TTTAATAAAT-AAA
1 TTTAATAAATAAAA
29293 TTTAA
1 TTTAA
29298 AATTTAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
13 11 0.30
14 11 0.30
15 15 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTAATAAATAAAA
Found at i:29354 original size:22 final size:21
Alignment explanation
Indices: 29310--29354 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
29300 TTTAAAATTA
* *
29310 AAAATATAAAAAAATTTATAT
1 AAAATATAAAAAAATTGACAT
*
29331 AAAATATAAGATAAATTGACAT
1 AAAATATAA-AAAAATTGACAT
29353 AA
1 AA
29355 TATAAACATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (21 bp):
AAAATATAAAAAAATTGACAT
Found at i:29813 original size:122 final size:123
Alignment explanation
Indices: 29667--29899 Score: 317
Period size: 122 Copynumber: 1.9 Consensus size: 123
29657 TTTTATGTAT
* ** *
29667 TTTTTATATTTTATTAAAATTTTATCTATAATTAATGAGATTTGAACTTTTAATTTCTAAATTTT
1 TTTTTATATTTTATTAAAATTTTATCTATAATTAATGAGATTTAAACTTTTAACCTCTAAATTCT
* *
29732 ATATT-AATGATCATATCATAAAATCAAATATATTTTTTTGTTAATTCAAGTATATATG
66 ATATTGAA-AATCATATCATAAAATCAAATATATTTTTTTATTAATTCAAGTATATATG
* * * * * *
29790 TTTTTAT-TTTTCTTAAAATTTTATTTATGATTAATGAGATTTAAATTTTTAACCTCTTACTTCT
1 TTTTTATATTTTATTAAAATTTTATCTATAATTAATGAGATTTAAACTTTTAACCTCTAAATTCT
* *
29854 ATATTGAAAATCATATCATAAAGTCAAATGTATTTTTTTATTAATT
66 ATATTGAAAATCATATCATAAAATCAAATATATTTTTTTATTAATT
29900 ATCAACTAAA
Statistics
Matches: 95, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
122 86 0.91
123 9 0.09
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.52
Consensus pattern (123 bp):
TTTTTATATTTTATTAAAATTTTATCTATAATTAATGAGATTTAAACTTTTAACCTCTAAATTCT
ATATTGAAAATCATATCATAAAATCAAATATATTTTTTTATTAATTCAAGTATATATG
Found at i:30530 original size:2 final size:2
Alignment explanation
Indices: 30523--30562 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
30513 TAGTATTGTA
30523 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30563 GAAATGAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32200 original size:2 final size:2
Alignment explanation
Indices: 32188--32218 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
32178 TTTCTTCCTG
*
32188 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32219 GTGTGTGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:33119 original size:20 final size:21
Alignment explanation
Indices: 33082--33123 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
33072 TTATTTAATT
33082 AAATTTTTTTGATAAAATTAA
1 AAATTTTTTTGATAAAATTAA
*
33103 AAATTTTTTTTAT-AAATTAA
1 AAATTTTTTTGATAAAATTAA
33123 A
1 A
33124 TAAATCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
AAATTTTTTTGATAAAATTAA
Found at i:33174 original size:16 final size:15
Alignment explanation
Indices: 33132--33177 Score: 60
Period size: 13 Copynumber: 3.1 Consensus size: 15
33122 AATAAATCTT
*
33132 ATTAATAATAAAAAA
1 ATTAATAATAATAAA
33147 ATTAA-AA-AATAAA
1 ATTAATAATAATAAA
33160 ATTAATAATATATAAA
1 ATTAATAATA-ATAAA
33176 AT
1 AT
33178 AACATGATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 10 0.37
14 4 0.15
15 6 0.22
16 7 0.26
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATTAATAATAATAAA
Found at i:33645 original size:48 final size:46
Alignment explanation
Indices: 33585--33684 Score: 128
Period size: 47 Copynumber: 2.1 Consensus size: 46
33575 AAACTTAAAT
* *
33585 TAAATCTATTAATGAAGGTATTTTAATAAAATTAAATTTTTTATTTA
1 TAAATTTATTAATCAAGGTATTTTAATAAAATTAAA-TTTTTATTTA
** * *
33632 TAAATTTATTTAATCAATTTTTTTTTATAAAATTAAATTTTTATTTA
1 TAAATTTA-TTAATCAAGGTATTTTAATAAAATTAAATTTTTATTTA
33679 TAAATT
1 TAAATT
33685 AAATAAAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 23 0.50
48 23 0.50
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (46 bp):
TAAATTTATTAATCAAGGTATTTTAATAAAATTAAATTTTTATTTA
Found at i:33672 original size:19 final size:19
Alignment explanation
Indices: 33647--33688 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
33637 TTATTTAATC
*
33647 AATTTTTTTTTATAAAATTA
1 AATTTTTATTTAT-AAATTA
33667 AATTTTTATTTATAAATTA
1 AATTTTTATTTATAAATTA
33686 AAT
1 AAT
33689 AAAATTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
AATTTTTATTTATAAATTA
Found at i:36286 original size:21 final size:21
Alignment explanation
Indices: 36260--36300 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
36250 TCAGCTTATA
36260 ATTGAACTAATAAAAAATCAG
1 ATTGAACTAATAAAAAATCAG
* *
36281 ATTGAATTAGTAAAAAATCA
1 ATTGAACTAATAAAAAATCA
36301 ATTATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.07, G:0.10, T:0.27
Consensus pattern (21 bp):
ATTGAACTAATAAAAAATCAG
Found at i:37135 original size:2 final size:2
Alignment explanation
Indices: 37128--37157 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
37118 TATTGTAACC
37128 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37158 AAAGAGACGA
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):
TA
Found at i:37240 original size:167 final size:168
Alignment explanation
Indices: 36973--37324 Score: 661
Period size: 167 Copynumber: 2.1 Consensus size: 168
36963 TAATAATGTA
36973 ATATATATATATATATAAAAGAGACAAAAGATTGCATCATTTGTGCACAGTTTAACTTGTAAAGT
1 ATATATATATATATATAAAAGAGACAAAAGATTGCATCATTTGTGCACAGTTTAACTTGTAAAGT
*
37038 GGAAATCTCGACCCACAGATTCATGATTTGTTAATAAAATGTTGGAATTGTAGTTTTTATAATTG
66 GAAAATCTCGACCCACAGATTCATGATTTGTTAATAAAATGTTGGAATTGTAGTTTTTATAATTG
37103 AAATTCTATCTCTTGTATTGTAACCTATATATATATAT
131 AAATTCTATCTCTTGTATTGTAACCTATATATATATAT
* *
37141 ATATATATATATATATAAAAGAGAC-GAAGATTGCATCATTTGTGCACAGTTTAGCTTGTAAAGT
1 ATATATATATATATATAAAAGAGACAAAAGATTGCATCATTTGTGCACAGTTTAACTTGTAAAGT
*
37205 GAAAATCTCGACCCACAGATTCATGATTTGTTAATAACATGTTGGAATTGTAGTTTTTATAATTG
66 GAAAATCTCGACCCACAGATTCATGATTTGTTAATAAAATGTTGGAATTGTAGTTTTTATAATTG
37270 AAATTCTATCTCTTGTATTGTAACCTATATATATATAT
131 AAATTCTATCTCTTGTATTGTAACCTATATATATATAT
37308 ATATATATATATATATA
1 ATATATATATATATATA
37325 TATATATATA
Statistics
Matches: 180, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
167 155 0.86
168 25 0.14
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (168 bp):
ATATATATATATATATAAAAGAGACAAAAGATTGCATCATTTGTGCACAGTTTAACTTGTAAAGT
GAAAATCTCGACCCACAGATTCATGATTTGTTAATAAAATGTTGGAATTGTAGTTTTTATAATTG
AAATTCTATCTCTTGTATTGTAACCTATATATATATAT
Found at i:37302 original size:2 final size:2
Alignment explanation
Indices: 37295--37346 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
37285 TATTGTAACC
37295 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37337 TA TA TA TA TA
1 TA TA TA TA TA
37347 AAAGAGACGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37445 original size:189 final size:189
Alignment explanation
Indices: 37128--37514 Score: 729
Period size: 189 Copynumber: 2.0 Consensus size: 189
37118 TATTGTAACC
37128 TATATATATATATATATATATATATATATAAAAGAGACGAAGATTGCATCATTTGTGCACAGTTT
1 TATATATATATATATATATATATATATATAAAAGAGACGAAGATTGCATCATTTGTGCACAGTTT
* * *
37193 AGCTTGTAAAGTGAAAATCTCGACCCACAGATTCATGATTTGTTAATAACATGTTGGAATTGTAG
66 AGCTTGTAAAGTGAAAATCTCGACCCACAGATTCATGATTTGTTAATAAAACGTTGCAATTGTAG
37258 TTTTTATAATTGAAATTCTATCTCTTGTATTGTAACCTATATATATATATATATATATA
131 TTTTTATAATTGAAATTCTATCTCTTGTATTGTAACCTATATATATATATATATATATA
37317 TATATATATATATATATATATATATATATAAAAGAGACGAAGATTGCATCATTTGTGCACAGTTT
1 TATATATATATATATATATATATATATATAAAAGAGACGAAGATTGCATCATTTGTGCACAGTTT
*
37382 AGCTTGTAAAGTGGAAATCTCGACCCACAGATTCATGATTTGTTAATAAAACGTTGCAATTGTAG
66 AGCTTGTAAAGTGAAAATCTCGACCCACAGATTCATGATTTGTTAATAAAACGTTGCAATTGTAG
*
37447 TTTTTATAATTGAAATTCTATCTCTTGTATTGTAATCTATATATATATATATATATATA
131 TTTTTATAATTGAAATTCTATCTCTTGTATTGTAACCTATATATATATATATATATATA
37506 TATATATAT
1 TATATATAT
37515 GAAATGAAAG
Statistics
Matches: 193, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
189 193 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (189 bp):
TATATATATATATATATATATATATATATAAAAGAGACGAAGATTGCATCATTTGTGCACAGTTT
AGCTTGTAAAGTGAAAATCTCGACCCACAGATTCATGATTTGTTAATAAAACGTTGCAATTGTAG
TTTTTATAATTGAAATTCTATCTCTTGTATTGTAACCTATATATATATATATATATATA
Found at i:37491 original size:2 final size:2
Alignment explanation
Indices: 37484--37514 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
37474 TATTGTAATC
37484 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37515 GAAATGAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37772 original size:3 final size:3
Alignment explanation
Indices: 37764--37788 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
37754 AATTGTAAAT
37764 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
37789 AAATTGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38762 original size:38 final size:37
Alignment explanation
Indices: 38719--38828 Score: 106
Period size: 38 Copynumber: 3.0 Consensus size: 37
38709 TTAATTTAAT
38719 TTAAATTATTATTTATATATAATAAAATAATATTTTTA
1 TTAAA-TATTATTTATATATAATAAAATAATATTTTTA
* *
38757 TTAAAT-TTAATTATAACTATTAATATAA-AATATTTTTA
1 TTAAATATTATTTAT-A-TA-TAATAAAATAATATTTTTA
*
38795 --AAATATTATTT-TAAATAATAAAATAA-ACTTTTTA
1 TTAAATATTATTTATATATAATAAAATAATA-TTTTTA
38829 AATCGACTCA
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
33 8 0.13
34 9 0.15
35 1 0.02
36 12 0.20
37 7 0.11
38 17 0.28
39 7 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (37 bp):
TTAAATATTATTTATATATAATAAAATAATATTTTTA
Found at i:39989 original size:2 final size:2
Alignment explanation
Indices: 39982--40007 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39972 ACTCAAATCT
39982 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
40008 ACCATAGATA
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):
TA
Found at i:40405 original size:2 final size:2
Alignment explanation
Indices: 40398--40433 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40388 ATTTCATGTG
40398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40434 TGCATTTGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41859 original size:2 final size:2
Alignment explanation
Indices: 41852--41891 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
41842 GGAAAGTATT
41852 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
41892 TGAAAGAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:42863 original size:2 final size:2
Alignment explanation
Indices: 42856--42897 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
42846 GGCTAATACT
42856 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42898 ATGCTCAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44229 original size:16 final size:16
Alignment explanation
Indices: 44210--44312 Score: 91
Period size: 16 Copynumber: 6.4 Consensus size: 16
44200 TTTTTAAAAT
*
44210 TTTAAATTATTTAAAA
1 TTTAAATTATTTTAAA
* * *
44226 TTTAAGTTATTTTGAT
1 TTTAAATTATTTTAAA
* *
44242 TTTAGATTATTTCAAA
1 TTTAAATTATTTTAAA
** * *
44258 TTTATGTCACTTT-AA
1 TTTAAATTATTTTAAA
44273 TTTAATATTATTTTAAA
1 TTTAA-ATTATTTTAAA
*
44290 TTTAAATTATTTTAAT
1 TTTAAATTATTTTAAA
44306 TTTAAAT
1 TTTAAAT
44313 CAATTAAGTT
Statistics
Matches: 66, Mismatches: 19, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
15 6 0.09
16 53 0.80
17 7 0.11
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:44244 original size:32 final size:31
Alignment explanation
Indices: 44208--44312 Score: 111
Period size: 32 Copynumber: 3.3 Consensus size: 31
44198 AATTTTTAAA
44208 ATTTTAAATTATTTAAAATTTAAGTTATTTT
1 ATTTTAAATTATTTAAAATTTAAGTTATTTT
* * * * *
44239 GATTTTAGATTATTTCAAATTTATGTCACTTT
1 -ATTTTAAATTATTTAAAATTTAAGTTATTTT
* * *
44271 AATTTAATATTATTTTAAATTTAAATTATTTT
1 ATTTTAA-ATTATTTAAAATTTAAGTTATTTT
44303 AATTTTAAAT
1 -ATTTTAAAT
44313 CAATTAAGTT
Statistics
Matches: 58, Mismatches: 13, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
31 5 0.09
32 47 0.81
33 6 0.10
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (31 bp):
ATTTTAAATTATTTAAAATTTAAGTTATTTT
Found at i:44293 original size:22 final size:22
Alignment explanation
Indices: 44268--44312 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
44258 TTTATGTCAC
*
44268 TTTAATTTAATATT-ATTTTAAA
1 TTTAAATT-ATATTAATTTTAAA
*
44290 TTTAAATTATTTTAATTTTAAA
1 TTTAAATTATATTAATTTTAAA
44312 T
1 T
44313 CAATTAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTAAATTATATTAATTTTAAA
Found at i:44399 original size:23 final size:23
Alignment explanation
Indices: 44362--44411 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
44352 TTTTATTCAG
*
44362 ATTATTTTTAGATTAATTATT-AAA
1 ATTATTTTTAAATT-ATT-TTCAAA
44386 ATTA-TTTTAAATTATTTTCAAA
1 ATTATTTTTAAATTATTTTCAAA
44408 ATTA
1 ATTA
44412 ATTGATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.08
22 10 0.42
23 8 0.33
24 4 0.17
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
ATTATTTTTAAATTATTTTCAAA
Found at i:45928 original size:2 final size:2
Alignment explanation
Indices: 45921--45951 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
45911 TGAAAAGTGC
45921 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
45952 GAAAATGGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46702 original size:22 final size:22
Alignment explanation
Indices: 46677--46718 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
46667 TAAAAAAATA
*
46677 TAAATTCAAATTTAAGCATAAT
1 TAAATTCAAAATTAAGCATAAT
*
46699 TAAATTTAAAATTAAGCATA
1 TAAATTCAAAATTAAGCATA
46719 TAATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (22 bp):
TAAATTCAAAATTAAGCATAAT
Found at i:47456 original size:36 final size:36
Alignment explanation
Indices: 47384--47466 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 36
47374 ATATATTTTG
* * * *
47384 ATAATTAAATTTAAATAATTTTTTATTAGTTAAATA
1 ATAATTTAAGTTAAATAATTTTTAATTAGTAAAATA
*
47420 ATAATTTAAGTTAAATTATTTTTAATTA-TAACAATA
1 ATAATTTAAGTTAAATAATTTTTAATTAGTAA-AATA
*
47456 AT-ATCTAAGTT
1 ATAATTTAAGTT
47467 GAATCTAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 10 0.25
36 30 0.75
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (36 bp):
ATAATTTAAGTTAAATAATTTTTAATTAGTAAAATA
Found at i:47682 original size:16 final size:16
Alignment explanation
Indices: 47661--47799 Score: 129
Period size: 16 Copynumber: 8.4 Consensus size: 16
47651 TGATTGATCA
47661 AAATTTAAAATAATTT
1 AAATTTAAAATAATTT
*
47677 AAATTTAAAATAATAT
1 AAATTTAAAATAATTT
*
47693 AAATCTAATTAATTTAAATATT
1 AAATTTAA--AA--T-AAT-TT
* *
47715 AAATTT-AATTAATTC
1 AAATTTAAAATAATTT
*
47730 AAAATTAAAATAATTT
1 AAATTTAAAATAATTT
47746 AAATTTAAAATAATTT
1 AAATTTAAAATAATTT
*
47762 AAA-ATAAAATAATTT
1 AAATTTAAAATAATTT
* *
47777 AAAATTAAAATTAATAT
1 AAATTTAAAA-TAATTT
47794 AAATTT
1 AAATTT
47800 TTTAAAAACC
Statistics
Matches: 100, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
15 20 0.20
16 55 0.55
17 11 0.11
18 2 0.02
19 1 0.01
20 1 0.01
21 4 0.04
22 6 0.06
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTTAAAATAATTT
Found at i:47706 original size:31 final size:31
Alignment explanation
Indices: 47668--47796 Score: 125
Period size: 31 Copynumber: 3.9 Consensus size: 31
47658 TCAAAATTTA
47668 AAATAATTTAAATTTAAAATAATAT-AAATCT
1 AAATAATTTAAATTTAAAATAATATAAAAT-T
* *
47699 AATTAATTTAAATATTAAATTTAATTAATTCAAAATT
1 AAATAATTTAAAT-TTAAA-ATAA-T-A-T-AAAATT
* *
47736 AAAATAATTTAAATTTAAAATAATTTAAAATA
1 -AAATAATTTAAATTTAAAATAATATAAAATT
*
47768 AAATAATTTAAAATTAAAATTAATATAAA
1 AAATAATTTAAATTTAAAA-TAATATAAA
47797 TTTTTTAAAA
Statistics
Matches: 81, Mismatches: 8, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
31 30 0.37
32 18 0.22
33 4 0.05
34 1 0.01
35 2 0.02
36 4 0.05
37 6 0.07
38 16 0.20
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (31 bp):
AAATAATTTAAATTTAAAATAATATAAAATT
Found at i:47719 original size:69 final size:69
Alignment explanation
Indices: 47641--47791 Score: 209
Period size: 69 Copynumber: 2.2 Consensus size: 69
47631 TAATTAATCT
* * * *
47641 ATATTAAATTTGATTGA-TCAAAATTTAAAATAATTTAAATTTAAAATAATAT-AAATCTAATTA
1 ATATTAAATTTAATTAATTCAAAA-TTAAAATAATTTAAATTTAAAATAATATAAAAT-AAAATA
47704 ATTTAA
64 ATTTAA
*
47710 ATATTAAATTTAATTAATTCAAAATTAAAATAATTTAAATTTAAAATAATTTAAAATAAAATAAT
1 ATATTAAATTTAATTAATTCAAAATTAAAATAATTTAAATTTAAAATAATATAAAATAAAATAAT
47775 TTAA
66 TTAA
*
47779 A-ATTAAAATTAAT
1 ATATTAAATTTAAT
47792 ATAAATTTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
68 11 0.15
69 53 0.72
70 10 0.14
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (69 bp):
ATATTAAATTTAATTAATTCAAAATTAAAATAATTTAAATTTAAAATAATATAAAATAAAATAAT
TTAA
Found at i:47741 original size:53 final size:55
Alignment explanation
Indices: 47661--47764 Score: 140
Period size: 53 Copynumber: 1.9 Consensus size: 55
47651 TGATTGATCA
* * *
47661 AAATTTAAAATAATTTAAATTTAAAATAATATAAATCT-AATTAATTTAAATATT
1 AAATTTAAAATAATTCAAAATTAAAATAATATAAATCTAAAATAATTTAAATATT
* * *
47715 AAATTT-AATTAATTCAAAATTAAAATAATTTAAATTTAAAATAATTTAAA
1 AAATTTAAAATAATTCAAAATTAAAATAATATAAATCTAAAATAATTTAAA
47765 ATAAAATAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 26 0.60
54 17 0.40
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (55 bp):
AAATTTAAAATAATTCAAAATTAAAATAATATAAATCTAAAATAATTTAAATATT
Done.