Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 11 of 163
Found at i:3624564 original size:3 final size:3
Alignment explanation
Indices: 3624552--3624589 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
3624542 ATGGTGATGA
* *
3624552 TGG TGA TGG TGG TGG TGA TGG TGG TGG TGG TGG TGG TG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TG
3624590 ATGATGATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.05, C:0.00, G:0.61, T:0.34
Consensus pattern (3 bp):
TGG
Found at i:3624569 original size:12 final size:12
Alignment explanation
Indices: 3624552--3624595 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
3624542 ATGGTGATGA
3624552 TGGTGATGGTGG
1 TGGTGATGGTGG
3624564 TGGTGATGGTGG
1 TGGTGATGGTGG
*
3624576 TGGTGGTGGTGG
1 TGGTGATGGTGG
*
3624588 TGATGATG
1 TGGTGATG
3624596 ATTACTGTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.09, C:0.00, G:0.57, T:0.34
Consensus pattern (12 bp):
TGGTGATGGTGG
Found at i:3625915 original size:169 final size:169
Alignment explanation
Indices: 3625723--3626040 Score: 453
Period size: 169 Copynumber: 1.9 Consensus size: 169
3625713 ATAAATAACT
* *
3625723 ACAACAATTATTATATGAATGCAGAGATTAATAACCAAGTTGATACATCAAAAATAATTCTCAAA
1 ACAACAATGATTATATGAATGCAGAGATCAATAACCAAGTTGATACATCAAAAATAATTCTCAAA
* ** ** *
3625788 CCAATACCGATGACAGGTACTT-ATATGC-ACTATACGTGACATAACATCCAATAATAATTGATC
66 CCAACACCGACAACACATA-TTCATATACAAC-ATACGTGACATAACATCCAATAATAA-TGATC
3625851 TATGAAATGTTGAAC-AATTCAGTCAGAAAACCGTATAAACA
128 TATGAAATGTTGAACAAATTCAGTCAGAAAACCGTATAAACA
* * *
3625892 ACAACAATGGTTATATGAATGCAGAGATCAATAACCAAGTTGATACATCAAATATAATTCTGAAA
1 ACAACAATGATTATATGAATGCAGAGATCAATAACCAAGTTGATACATCAAAAATAATTCTCAAA
* **
3625957 CCAACACCGACAACACATATTCATATACAACGTACGTGACATAACATCCAATGCTAATGATCTAT
66 CCAACACCGACAACACATATTCATATACAACATACGTGACATAACATCCAATAATAATGATCTAT
*
3626022 GAAATGTTTAACAAATTCA
131 GAAATGTTGAACAAATTCA
3626041 ATGGTATACA
Statistics
Matches: 131, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
168 21 0.16
169 108 0.82
170 2 0.02
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (169 bp):
ACAACAATGATTATATGAATGCAGAGATCAATAACCAAGTTGATACATCAAAAATAATTCTCAAA
CCAACACCGACAACACATATTCATATACAACATACGTGACATAACATCCAATAATAATGATCTAT
GAAATGTTGAACAAATTCAGTCAGAAAACCGTATAAACA
Found at i:3626686 original size:23 final size:22
Alignment explanation
Indices: 3626650--3626697 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
3626640 AGTTACCAAA
*
3626650 TTTATTTATCTTTTGTGGAAAT
1 TTTATTTATCTTTTATGGAAAT
*
3626672 TTTATCTTATTTTTTATGGAAAT
1 TTTAT-TTATCTTTTATGGAAAT
3626695 TTT
1 TTT
3626698 TTATGGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.62
Consensus pattern (22 bp):
TTTATTTATCTTTTATGGAAAT
Found at i:3626698 original size:13 final size:13
Alignment explanation
Indices: 3626680--3626710 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3626670 ATTTTATCTT
3626680 ATTTTTTATGGAA
1 ATTTTTTATGGAA
3626693 ATTTTTTATGGAA
1 ATTTTTTATGGAA
3626706 ATTTT
1 ATTTT
3626711 ATCTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (13 bp):
ATTTTTTATGGAA
Found at i:3627520 original size:13 final size:12
Alignment explanation
Indices: 3627496--3627528 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
3627486 TTTTTTGGGA
3627496 TTTTT-TTTATT
1 TTTTTATTTATT
3627507 TTTTTATTTAATT
1 TTTTTATTT-ATT
3627520 TTTTTATTT
1 TTTTTATTT
3627529 TTACAGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 5 0.25
12 3 0.15
13 12 0.60
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTATTTATT
Found at i:3627538 original size:21 final size:21
Alignment explanation
Indices: 3627497--3627538 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3627487 TTTTTGGGAT
** *
3627497 TTTTTTTATTTTTTTATTTAA
1 TTTTTTTATTTTTACAGTTAA
3627518 TTTTTTTATTTTTACAGTTAA
1 TTTTTTTATTTTTACAGTTAA
3627539 AGACAATGAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTTTTATTTTTACAGTTAA
Found at i:3635478 original size:25 final size:25
Alignment explanation
Indices: 3635432--3635480 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
3635422 TTATTAGATT
*
3635432 TTTTATATTTTATAATACTTTTAAG
1 TTTTATATTTTATAATAATTTTAAG
* *
3635457 TTTTATATTTTTTTATAATTTTAA
1 TTTTATATTTTATAATAATTTTAA
3635481 TAAATTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTTATATTTTATAATAATTTTAAG
Found at i:3635541 original size:10 final size:9
Alignment explanation
Indices: 3635431--3635534 Score: 56
Period size: 9 Copynumber: 11.7 Consensus size: 9
3635421 ATTATTAGAT
3635431 TTTTTAT-A
1 TTTTTATAA
3635439 -TTTTATAA
1 TTTTTATAA
*
3635447 TACTTT-TAA
1 T-TTTTATAA
* *
3635456 GTTTTATATT
1 TTTTTATA-A
3635466 TTTTTATAA
1 TTTTTATAA
*
3635475 TTTTAATAAA
1 TTTTTAT-AA
*
3635485 TTTATATCAA
1 TTTTTAT-AA
*
3635495 TTTTAAT-A
1 TTTTTATAA
*
3635503 TTTTTCT-A
1 TTTTTATAA
* *
3635511 TTTTTCTGA
1 TTTTTATAA
3635520 TTTTTATAA
1 TTTTTATAA
3635529 TTTTTA
1 TTTTTA
3635535 ATCATTTCTT
Statistics
Matches: 73, Mismatches: 16, Indels: 13
0.72 0.16 0.13
Matches are distributed among these distances:
7 6 0.08
8 18 0.25
9 25 0.34
10 24 0.33
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3638041 original size:25 final size:25
Alignment explanation
Indices: 3637995--3638043 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
3637985 TTATTAGATT
*
3637995 TTTTATATTTTATAATACTTTTAAG
1 TTTTATATTTTATAATAATTTTAAG
* *
3638020 TTTTATATTTTTTTATAATTTTAA
1 TTTTATATTTTATAATAATTTTAA
3638044 TAAATTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTTATATTTTATAATAATTTTAAG
Found at i:3638104 original size:10 final size:9
Alignment explanation
Indices: 3637994--3638097 Score: 56
Period size: 9 Copynumber: 11.7 Consensus size: 9
3637984 ATTATTAGAT
3637994 TTTTTAT-A
1 TTTTTATAA
3638002 -TTTTATAA
1 TTTTTATAA
*
3638010 TACTTT-TAA
1 T-TTTTATAA
* *
3638019 GTTTTATATT
1 TTTTTATA-A
3638029 TTTTTATAA
1 TTTTTATAA
*
3638038 TTTTAATAAA
1 TTTTTAT-AA
*
3638048 TTTATATCAA
1 TTTTTAT-AA
*
3638058 TTTTAAT-A
1 TTTTTATAA
*
3638066 TTTTTCT-A
1 TTTTTATAA
* *
3638074 TTTTTCTGA
1 TTTTTATAA
3638083 TTTTTATAA
1 TTTTTATAA
3638092 TTTTTA
1 TTTTTA
3638098 ATCATTTCTT
Statistics
Matches: 73, Mismatches: 16, Indels: 13
0.72 0.16 0.13
Matches are distributed among these distances:
7 6 0.08
8 18 0.25
9 25 0.34
10 24 0.33
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3647699 original size:84 final size:84
Alignment explanation
Indices: 3647553--3647707 Score: 222
Period size: 84 Copynumber: 1.8 Consensus size: 84
3647543 ACACAGACAC
** ** *
3647553 ATATAGGGCTCAAATTTGGTACACTAGCAATGGAATTTTTTAACTCCATAACAGAGTAAAAAAAA
1 ATATAGGGCTCAAATTCAGTACACTAGCAATACAATTTTTTAACTCCACAACAGAGTAAAAAAAA
*
3647618 CTGCCAAATTGCTTCATAT
66 ATGCCAAATTGCTTCATAT
* *
3647637 ATATAGGGTTCAAATTCAGTACACTAGCAATACAATTTTTTAACTCCACAA-AGGAGTTAAAAAA
1 ATATAGGGCTCAAATTCAGTACACTAGCAATACAATTTTTTAACTCCACAACA-GAGTAAAAAAA
3647701 AATGCCA
65 AATGCCA
3647708 CATGTCCTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
83 1 0.02
84 61 0.98
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (84 bp):
ATATAGGGCTCAAATTCAGTACACTAGCAATACAATTTTTTAACTCCACAACAGAGTAAAAAAAA
ATGCCAAATTGCTTCATAT
Found at i:3648908 original size:19 final size:19
Alignment explanation
Indices: 3648884--3648922 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3648874 CTCATTAGCA
3648884 TGCAGTAGAAGTAGAGGTG
1 TGCAGTAGAAGTAGAGGTG
3648903 TGCAGTAGAAGTAGAGGTG
1 TGCAGTAGAAGTAGAGGTG
3648922 T
1 T
3648923 TTAGGTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.41, T:0.23
Consensus pattern (19 bp):
TGCAGTAGAAGTAGAGGTG
Found at i:3650022 original size:57 final size:57
Alignment explanation
Indices: 3649929--3650037 Score: 137
Period size: 57 Copynumber: 1.9 Consensus size: 57
3649919 TGTTATTTGT
* * * *
3649929 ATTTGACTTCAATATTTAATTTAATACTTGAGTTTTTTTTCTCAATTAAGTATCTAA
1 ATTTGACTTCAATATTCAATTTAATACTTAAGTTTTTTGTCCCAATTAAGTATCTAA
* ** * *
3649986 ATTTGACTTCAATGTTCAATTTGGTACTTAATTTTTTTGTCCCTATTAAGTA
1 ATTTGACTTCAATATTCAATTTAATACTTAAGTTTTTTGTCCCAATTAAGTA
3650038 CTTTATGTTC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
57 43 1.00
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.50
Consensus pattern (57 bp):
ATTTGACTTCAATATTCAATTTAATACTTAAGTTTTTTGTCCCAATTAAGTATCTAA
Found at i:3650183 original size:16 final size:16
Alignment explanation
Indices: 3650162--3650213 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
3650152 TTTGGTTCGC
3650162 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
3650178 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * *
3650194 TGTAATAGAATAGAGG
1 TGTATTGGATTAGAGG
3650210 TGTA
1 TGTA
3650214 ATAGCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:3650260 original size:45 final size:44
Alignment explanation
Indices: 3650194--3650291 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
3650184 GGATTAGAGG
*
3650194 TGTAATAGAATAGAGGTGTAATAGCAAATCAAATGTTTGGTTGAA
1 TGTAATAGAATAGAGGCGTAATAG-AAATCAAATGTTTGGTTGAA
* * ***
3650239 TGTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAA
1 TGTAATAGAATAGAGGCGTAATAGAAATCAAATGTTTGGTTGAA
*
3650283 TGGAATAGA
1 TGTAATAGA
3650292 GGTGTAATAG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 23 0.51
45 22 0.49
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.33
Consensus pattern (44 bp):
TGTAATAGAATAGAGGCGTAATAGAAATCAAATGTTTGGTTGAA
Found at i:3650470 original size:18 final size:17
Alignment explanation
Indices: 3650449--3650483 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3650439 TTATTATTAA
*
3650449 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3650467 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3650484 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3654876 original size:23 final size:23
Alignment explanation
Indices: 3654837--3654902 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
3654827 TGTTTTGTTA
* *
3654837 TTTTAAATTCATGATGTA-CATTC
1 TTTTAAATT-ATTATGTATAATTC
*
3654860 TTTTAAATCTATTATGTATAATTG
1 TTTTAAAT-TATTATGTATAATTC
*
3654884 TTTTAATTTTATTATGTAT
1 TTTTAA-ATTATTATGTAT
3654903 TGTTGTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 15 0.42
24 20 0.56
25 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.08, T:0.56
Consensus pattern (23 bp):
TTTTAAATTATTATGTATAATTC
Found at i:3654896 original size:24 final size:24
Alignment explanation
Indices: 3654860--3654937 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
3654850 ATGTACATTC
3654860 TTTTAAATCTATTATGTATAATTG
1 TTTTAAATCTATTATGTATAATTG
* * **
3654884 TTTTAATTTTATTATGTATTGTTG
1 TTTTAAATCTATTATGTATAATTG
* * * *
3654908 TTTTAAAGCTATTAGGTATTATTA
1 TTTTAAATCTATTATGTATAATTG
3654932 TTTTAA
1 TTTTAA
3654938 GTTATCTTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (24 bp):
TTTTAAATCTATTATGTATAATTG
Found at i:3657128 original size:24 final size:24
Alignment explanation
Indices: 3657068--3657145 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
3657058 ATGTACATTC
3657068 TTTTAAATCTATTATGTATAATTG
1 TTTTAAATCTATTATGTATAATTG
* * *
3657092 TTTTAATTTTATTATGTACT-GTTG
1 TTTTAAATCTATTATGTA-TAATTG
* * * *
3657116 TTTTAAAGCTATTAGGTATTATTA
1 TTTTAAATCTATTATGTATAATTG
3657140 TTTTAA
1 TTTTAA
3657146 GTTATCTCAT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
23 1 0.02
24 41 0.95
25 1 0.02
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.56
Consensus pattern (24 bp):
TTTTAAATCTATTATGTATAATTG
Found at i:3662326 original size:154 final size:154
Alignment explanation
Indices: 3662138--3662878 Score: 796
Period size: 154 Copynumber: 4.9 Consensus size: 154
3662128 TCAAAAAAAA
* * * * *
3662138 TTAGTAAAAAATCTTTATTTCGGTCATTTATTCGTACTATTTTCCCGAATTTTATTACTTTCAAT
1 TTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTATTTTCCCGAATTTTATTACTTTCAAT
*
3662203 AAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAGTGTAT
66 AAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
*
3662268 TAATTATTTCTGTTTTTTTTAAAT
131 TAATTATTTCTGTTTTTTATAAAT
*
3662292 TTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTATTTTCCTGAATTTTATTACTTTCAAT
1 TTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTATTTTCCCGAATTTTATTACTTTCAAT
* * *** *
3662357 CAAAATATATTATTTTCGCATTTTATTATTTTGTTTTATTTTAGTACATTATGTTTGAAGTGTAT
66 AAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
3662422 TAATTATTTC---------TAAAT
131 TAATTATTTCTGTTTTTTATAAAT
* * * *
3662437 TT-TTAAAAAACTCTTACTTCGGCCATTTGTTCGTATT-TTTTCTCCGCATTTTATTACTTT--A
1 TTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTATTTTC-CCGAATTTTATTACTTTCAA
* *
3662498 -AAAAATATCA-TA-TTTC-TAATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAAATT
65 TAAAAATAT-ATTATTTTCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATG
* *
3662559 TATTAATT-TAGTGTGTTTTTTGAATAAAT
128 TATTAATTAT-TTCTGTTTTTT--ATAAAT
* * *
3662588 TT--TAAAAAACCCTTATTTCTGTCC-TTTGCTCGCATTATTTTCCCGAATTTTATTACTTTCAA
1 TTAGTAAAAAACCCTTATTTC-GGCCATTTGTTCGTATTATTTTCCCGAATTTTATTACTTTCAA
* * *
3662650 TAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATT
65 TAAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTG-AA-A--
* *
3662715 TGTATTAATTATTTCTGAATTTTTAAAAAAT
126 TGTATTAATTATTTCTG--TTTTTTATAAAT
** * * * * *
3662746 TTAGTAAAAAACTTTTACTTCGGCCCTTTGTTCGTATTTTTTTCTTCGCATTTTATTACTTT--A
1 TTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTATTTTC-CCGAATTTTATTACTTTCAA
* * *
3662809 -AAAAATATCA-TATTTT-ATAATTTTATTATTTTACATTATTTTAGTACATTAAGTTTGAAATT
65 TAAAAATAT-ATTATTTTCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATG
3662871 TATTAATT
128 TATTAATT
3662879 TAGTGTGTTT
Statistics
Matches: 497, Mismatches: 54, Indels: 72
0.80 0.09 0.12
Matches are distributed among these distances:
139 1 0.00
140 50 0.10
141 9 0.02
142 2 0.00
143 5 0.01
144 47 0.09
145 7 0.01
150 41 0.08
151 15 0.03
152 2 0.00
153 10 0.02
154 178 0.36
155 3 0.01
156 2 0.00
157 3 0.01
158 67 0.13
159 6 0.01
160 34 0.07
161 15 0.03
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (154 bp):
TTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTATTTTCCCGAATTTTATTACTTTCAAT
AAAAATATATTATTTTCGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTAT
TAATTATTTCTGTTTTTTATAAAT
Found at i:3662638 original size:150 final size:149
Alignment explanation
Indices: 3662432--3662893 Score: 547
Period size: 158 Copynumber: 3.0 Consensus size: 149
3662422 TAATTATTTC
*
3662432 TAAATTTTTAAAAAACTCTTACTTCGGCCATTTGTTCGTATTTTTTCTCCGCATTTTATTACTTT
1 TAAA-TTTTAAAAAACTCTTACTTC-GCCCTTTGTTCGTATTTTTTCTCCGCATTTTATTACTTT
3662497 AAAAAATATCATA-TTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAAATTTA
64 AAAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAAATTTA
3662561 TTAATTTAGTGTGTTTTTTGAA
129 TTAATTTAGTGTGTTTTTT-AA
* * * * * *
3662583 TAAATTTTAAAAAACCCTTATTTCTGTCCTTTGCTCGCATTATTTTC-CCGAATTTTATTACTTT
1 TAAATTTTAAAAAACTCTTACTTC-GCCCTTTGTTCGTATT-TTTTCTCCGCATTTTATTACTTT
* *
3662647 CAATAAAAATAT-ATTATTTTCGT-ATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAA
64 --A-AAAAATATCA-TATTTTC-TAATTTTATTATTTTACATTATTTCAGTACATTATGTTTG-A
* * *
3662710 ATATTTGTATTAA-TTATTTCTGAATTTTTAA
123 A-A-TT-TATTAATTTA-GTGTG-TTTTTTAA
* * *
3662741 AAAATTTAGTAAAAAACTTTTACTTCGGCCCTTTGTTCGTATTTTTTTCTTCGCATTTTATTACT
1 TAAATTT--TAAAAAACTCTTACTTC-GCCCTTTGTTCGTA-TTTTTTCTCCGCATTTTATTACT
* * *
3662806 TTAAAAAATATCATATTTTATAATTTTATTATTTTACATTATTTTAGTACATTAAGTTTGAAATT
62 TTAAAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAAATT
3662871 TATTAATTTAGTGTGTTTTTTAA
127 TATTAATTTAGTGTGTTTTTTAA
3662894 ATATACAATT
Statistics
Matches: 260, Mismatches: 31, Indels: 38
0.79 0.09 0.12
Matches are distributed among these distances:
150 46 0.18
151 9 0.03
152 2 0.01
153 17 0.07
154 49 0.19
155 8 0.03
156 2 0.01
157 8 0.03
158 65 0.25
159 7 0.03
160 30 0.12
161 17 0.07
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (149 bp):
TAAATTTTAAAAAACTCTTACTTCGCCCTTTGTTCGTATTTTTTCTCCGCATTTTATTACTTTAA
AAAATATCATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAAATTTATT
AATTTAGTGTGTTTTTTAA
Found at i:3663243 original size:8 final size:9
Alignment explanation
Indices: 3663232--3663325 Score: 54
Period size: 10 Copynumber: 10.1 Consensus size: 9
3663222 TTACCTTTAC
3663232 TTCTTT-TT
1 TTCTTTCTT
3663240 TTCTTTCTTT
1 TTCTTTC-TT
*
3663250 TTCCTTCCTT
1 TT-CTTTCTT
**
3663260 CCCTCTTCTT
1 TTCT-TTCTT
3663270 CTTC-TT-TT
1 -TTCTTTCTT
3663278 TTCTTTCTT
1 TTCTTTCTT
3663287 TT-TTT-TT
1 TTCTTTCTT
3663294 TCTCCTTTCCTT
1 T-T-CTTT-CTT
3663306 TTCTTTCTTT
1 TTCTTTC-TT
3663316 TTCTTTCTT
1 TTCTTTCTT
3663325 T
1 T
3663326 CTTCTCCTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 25
0.68 0.06 0.26
Matches are distributed among these distances:
7 6 0.09
8 14 0.21
9 12 0.18
10 26 0.39
11 6 0.09
12 3 0.04
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (9 bp):
TTCTTTCTT
Found at i:3663285 original size:14 final size:13
Alignment explanation
Indices: 3663268--3663328 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 13
3663258 TTCCCTCTTC
3663268 TTCTTCTTTTTTCT
1 TTCTT-TTTTTTCT
3663282 TTCTTTTTTTT-T
1 TTCTTTTTTTTCT
*
3663294 TCTCCTTTCCTTTTCT
1 T-T-CTTT-TTTTTCT
3663310 TTCTTTTTCTTTCT
1 TTCTTTTT-TTTCT
3663324 TTCTT
1 TTCTT
3663329 CTCCTTTCCC
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
12 2 0.05
13 8 0.20
14 23 0.57
15 5 0.12
16 2 0.05
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTCTTTTTTTTCT
Found at i:3663296 original size:28 final size:28
Alignment explanation
Indices: 3663265--3663335 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
3663255 TCCTTCCCTC
* *
3663265 TTCTTCTTCT-TTTTTCTTTCTTTTTTTT
1 TTCTTCTTCTCCTTTTCTTTC-TTTTTCT
*
3663293 TTCTCCTT-TCCTTTTCTTTCTTTTTCT
1 TTCTTCTTCTCCTTTTCTTTCTTTTTCT
3663320 TTCTTTCTTCTCCTTT
1 TTC-TTCTTCTCCTTT
3663336 CCCTCTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 10 0.28
28 20 0.56
29 6 0.17
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (28 bp):
TTCTTCTTCTCCTTTTCTTTCTTTTTCT
Found at i:3663310 original size:38 final size:38
Alignment explanation
Indices: 3663225--3663325 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 38
3663215 AAAAAAATTA
*
3663225 CCTTTACTTCTTTTTTTCTTTCTTTTTCCTTCCTTCCCT
1 CCTTTTCTTC-TTTTTTCTTTCTTTTTCCTTCCTTCCCT
** * *
3663264 -CTTCTTCTTCTTTTTTCTTTCTTTTTTTTTTC-TCCTTT
1 CCTT-TTCTTCTTTTTTCTTTCTTTTTCCTTCCTTCC-CT
3663302 CCTTTTCTT-TCTTTTTCTTTCTTT
1 CCTTTTCTTCT-TTTTTCTTTCTTT
3663326 CTTCTCCTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
37 4 0.08
38 41 0.77
39 8 0.15
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (38 bp):
CCTTTTCTTCTTTTTTCTTTCTTTTTCCTTCCTTCCCT
Found at i:3663955 original size:4 final size:4
Alignment explanation
Indices: 3663946--3663970 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3663936 CTTTAAAATT
3663946 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
3663971 GTTGATCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:3664705 original size:21 final size:20
Alignment explanation
Indices: 3664675--3664713 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3664665 TTAGCGCTGC
* *
3664675 CTTTATTTAGATTTTGGGTAA
1 CTTTAATTAG-TTTAGGGTAA
3664696 CTTTAATTAGTTTAGGGT
1 CTTTAATTAGTTTAGGGT
3664714 TCTCTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.51
Consensus pattern (20 bp):
CTTTAATTAGTTTAGGGTAA
Found at i:3670165 original size:104 final size:104
Alignment explanation
Indices: 3670036--3670259 Score: 416
Period size: 104 Copynumber: 2.2 Consensus size: 104
3670026 TTTATAATAC
*
3670036 ATATATTT-TTTA-TAATGTAAAAGAAATTATATCTAAAATAGTGAATATGACTTAAAACATTCA
1 ATATATTTATTTATTTATGTAAAAGAAATTATATCTAAAATAGTGAATATGACTTAAAACATTCA
3670099 TATAATAATTTATCAAAAAATATTATATAAGGTTTATTG
66 TATAATAATTTATCAAAAAATATTATATAAGGTTTATTG
3670138 ATATATTTATTTATTTATGTAAAAGAAATTATATCTAAAATAGTGAATATGACTTAAAACATTCA
1 ATATATTTATTTATTTATGTAAAAGAAATTATATCTAAAATAGTGAATATGACTTAAAACATTCA
3670203 TATAATAATTTATCAAAAAATATTATATAAGGTTTATTG
66 TATAATAATTTATCAAAAAATATTATATAAGGTTTATTG
3670242 ATATATTTTATTTATTTA
1 ATATA-TTTATTTATTTA
3670260 AAATTTAATT
Statistics
Matches: 118, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
102 8 0.07
103 4 0.03
104 94 0.80
105 12 0.10
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (104 bp):
ATATATTTATTTATTTATGTAAAAGAAATTATATCTAAAATAGTGAATATGACTTAAAACATTCA
TATAATAATTTATCAAAAAATATTATATAAGGTTTATTG
Found at i:3675513 original size:14 final size:14
Alignment explanation
Indices: 3675470--3675513 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
3675460 TACATATTTT
3675470 ATATTTTAAAGAGA
1 ATATTTTAAAGAGA
* * *
3675484 TTTTTTTAAA-ATA
1 ATATTTTAAAGAGA
3675497 ATATTTTAAAGAGA
1 ATATTTTAAAGAGA
3675511 ATA
1 ATA
3675514 AAATATTTGG
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (14 bp):
ATATTTTAAAGAGA
Found at i:3682590 original size:24 final size:23
Alignment explanation
Indices: 3682534--3682599 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
3682524 TAGATAAGAA
3682534 ATTTTAATAAATAAAAAATATATT
1 ATTTTAA-AAATAAAAAATATATT
**
3682558 AAATT-AAAATAATATAAATATA-T
1 ATTTTAAAAATAA-A-AAATATATT
*
3682581 ATTTTAAAAATTAAAAATA
1 ATTTTAAAAATAAAAAATA
3682600 ACATGGGTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
22 11 0.32
23 7 0.21
24 16 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTTTAAAAATAAAAAATATATT
Found at i:3703253 original size:23 final size:23
Alignment explanation
Indices: 3703223--3703269 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3703213 TAAGTGACCG
3703223 TTTGTGATGGCCTACTTTGTTTA
1 TTTGTGATGGCCTACTTTGTTTA
3703246 TTTGTGATGGCCTACTTTGTTTA
1 TTTGTGATGGCCTACTTTGTTTA
3703269 T
1 T
3703270 ACACTTGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.53
Consensus pattern (23 bp):
TTTGTGATGGCCTACTTTGTTTA
Found at i:3703473 original size:17 final size:17
Alignment explanation
Indices: 3703441--3703474 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3703431 AGTTTGTGAG
*
3703441 TTTTATCAAATTTTTTA
1 TTTTATCAAATATTTTA
*
3703458 TTTTATCATATATTTTA
1 TTTTATCAAATATTTTA
3703475 AATATTTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTATCAAATATTTTA
Found at i:3718564 original size:55 final size:55
Alignment explanation
Indices: 3718499--3718605 Score: 178
Period size: 55 Copynumber: 1.9 Consensus size: 55
3718489 CACTACTAAT
* * *
3718499 CGACCCACTAACTCTCAACTACCCCAGAATTTCACTTTCACCGAACCTCTATAAC
1 CGACCCACTAACTCTCAACTACACCAGAATTTCACTTCCACCGAAACTCTATAAC
*
3718554 CGACCCACTAACTCTCAACTACACCAGAATTTCACTTCCACTGAAACTCTAT
1 CGACCCACTAACTCTCAACTACACCAGAATTTCACTTCCACCGAAACTCTAT
3718606 CACACAATCG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.32, C:0.38, G:0.06, T:0.24
Consensus pattern (55 bp):
CGACCCACTAACTCTCAACTACACCAGAATTTCACTTCCACCGAAACTCTATAAC
Found at i:3723942 original size:18 final size:18
Alignment explanation
Indices: 3723919--3723956 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3723909 AGTTTTTAAT
3723919 AATATTATCTAAAAAATA
1 AATATTATCTAAAAAATA
3723937 AATATTATCTAAAAAATA
1 AATATTATCTAAAAAATA
3723955 AA
1 AA
3723957 ATTGACTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
AATATTATCTAAAAAATA
Found at i:3725216 original size:301 final size:302
Alignment explanation
Indices: 3724674--3725277 Score: 1201
Period size: 301 Copynumber: 2.0 Consensus size: 302
3724664 TGATTTAACG
3724674 TGCCACGTCAGCTTATCGTTACACTGTTAATAGCAATTAACGGCTCAGTGACTAAAATGTTACAA
1 TGCCACGTCAGCTTATCGTTACACTGTTAATAGCAATTAACGGCTCAGTGACTAAAATGTTACAA
3724739 CGCGATAACGTAAGTGACTAAAAAATAATATTTCAAATATAACTGACTAAAATGTAACTCGAGGT
66 CGCGATAACGTAAGTGACTAAAAAATAATATTTCAAATATAACTGACTAAAATGTAACTCGAGGT
3724804 AAACAAAATGACTATTTTAATAGTTTACCCTTTTTTTAACTATTATAATATCATATATAATATCC
131 AAACAAAATGACTATTTTAATAGTTTACCCTTTTTTTAACTATTATAATATCATATATAATATCC
3724869 ATAACATACCTTTTTTATATTAAAAATTTTAACAATAATTTAAGACAATATTTTTTTAATCTTTA
196 ATAACATACCTTTTTTATATTAAAAATTTTAACAATAATTTAAGACAATATTTTTTTAATCTTTA
3724934 TTTAAAAACATCTTAATTATAACTTTTAAA-TTAATAAATAT
261 TTTAAAAACATCTTAATTATAACTTTTAAATTTAATAAATAT
3724975 TGCCACGTCAGCTTATCGTTACACTGTTAATAGCAATTAACGGCTCAGTGACTAAAATGTTACAA
1 TGCCACGTCAGCTTATCGTTACACTGTTAATAGCAATTAACGGCTCAGTGACTAAAATGTTACAA
3725040 CGCGATAACGTAAGTGACTAAAAAATAATATTTCAAATATAACTGACTAAAATGTAACTCGAGGT
66 CGCGATAACGTAAGTGACTAAAAAATAATATTTCAAATATAACTGACTAAAATGTAACTCGAGGT
3725105 AAACAAAATGACTATTTTAATAGTTTACCCTTTTTTTAACTATTATAATATCATATATAATATCC
131 AAACAAAATGACTATTTTAATAGTTTACCCTTTTTTTAACTATTATAATATCATATATAATATCC
3725170 ATAACATACCTTTTTTATATTAAAAATTTTAACAATAATTTAAGACAATATTTTTTTAATCTTTA
196 ATAACATACCTTTTTTATATTAAAAATTTTAACAATAATTTAAGACAATATTTTTTTAATCTTTA
3725235 TTTAAAAACATCTTAATTATAACTTTTAAATTTAATAAATAT
261 TTTAAAAACATCTTAATTATAACTTTTAAATTTAATAAATAT
3725277 T
1 T
3725278 TTCATTTAAA
Statistics
Matches: 302, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
301 290 0.96
302 12 0.04
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (302 bp):
TGCCACGTCAGCTTATCGTTACACTGTTAATAGCAATTAACGGCTCAGTGACTAAAATGTTACAA
CGCGATAACGTAAGTGACTAAAAAATAATATTTCAAATATAACTGACTAAAATGTAACTCGAGGT
AAACAAAATGACTATTTTAATAGTTTACCCTTTTTTTAACTATTATAATATCATATATAATATCC
ATAACATACCTTTTTTATATTAAAAATTTTAACAATAATTTAAGACAATATTTTTTTAATCTTTA
TTTAAAAACATCTTAATTATAACTTTTAAATTTAATAAATAT
Found at i:3730417 original size:17 final size:16
Alignment explanation
Indices: 3730386--3730431 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
3730376 AAAAATTAAA
3730386 AAGAA-AAAG-AAAAG
1 AAGAAGAAAGAAAAAG
3730400 AACGAAGAAAGAAAAAG
1 AA-GAAGAAAGAAAAAG
*
3730417 AAGGAGAAGAGAAAA
1 AAGAAGAA-AGAAAA
3730432 CTAAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.07
15 3 0.11
16 9 0.33
17 13 0.48
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (16 bp):
AAGAAGAAAGAAAAAG
Found at i:3731288 original size:19 final size:19
Alignment explanation
Indices: 3731242--3731280 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3731232 ATATTATTCA
3731242 ATATATAAAAATCTAAAAG
1 ATATATAAAAATCTAAAAG
3731261 ATATATAAAAATCTAAAAG
1 ATATATAAAAATCTAAAAG
3731280 A
1 A
3731281 GTATTAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (19 bp):
ATATATAAAAATCTAAAAG
Found at i:3731313 original size:20 final size:20
Alignment explanation
Indices: 3731300--3731339 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3731290 ATTATAGAAT
3731300 ATTGTTAAAAATTACTAAAA
1 ATTGTTAAAAATTACTAAAA
*
3731320 ATTTTTAAAAA-TA-TAAAA
1 ATTGTTAAAAATTACTAAAA
3731338 AT
1 AT
3731340 AATTATAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 2 0.11
20 10 0.53
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
ATTGTTAAAAATTACTAAAA
Found at i:3731714 original size:69 final size:68
Alignment explanation
Indices: 3731481--3731730 Score: 266
Period size: 69 Copynumber: 3.6 Consensus size: 68
3731471 GTGAACTCCA
* * * * * * * *
3731481 TATGCTGCCATAGCCAAGTTATGGTTTTACACATCATGCCTCATGTTTAATATCTTGACAGACTC
1 TATGTTGCCATAGCCAAGCTATGGTCTTACACATTATTCCTCATG-TTAATGTCCTGGCAGACTC
*
3731546 TTTC
65 TCTC
*** * * * * * *
3731550 TATGTTGCCATAGTTGAGTTATGGTCTTAGACATTATTCCCCATGTTAATGACCTAGTAGACTCT
1 TATGTTGCCATAGCCAAGCTATGGTCTTACACATTATTCCTCATGTTAATGTCCTGGCAGACTCT
3731615 CTC
66 CTC
* *
3731618 TATGTTGCCATAGCCGAGCTATGGTCTTACACATTATTCCTCATGTTGAATGTCCTGGCAAACTC
1 TATGTTGCCATAGCCAAGCTATGGTCTTACACATTATTCCTCATGTT-AATGTCCTGGCAGACTC
3731683 TCTC
65 TCTC
* * * *
3731687 TATATTTCCATAGTCAAGCTATAGTCTTACACATTATTCCTCAT
1 TATGTTGCCATAGCCAAGCTATGGTCTTACACATTATTCCTCAT
3731731 TACAGCTTAT
Statistics
Matches: 150, Mismatches: 30, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
68 58 0.39
69 92 0.61
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (68 bp):
TATGTTGCCATAGCCAAGCTATGGTCTTACACATTATTCCTCATGTTAATGTCCTGGCAGACTCT
CTC
Found at i:3738135 original size:7 final size:7
Alignment explanation
Indices: 3738123--3738148 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3738113 GCAGAGGAAA
3738123 TGTCAAT
1 TGTCAAT
3738130 TGTCAAT
1 TGTCAAT
3738137 TGTCAAT
1 TGTCAAT
3738144 TGTCA
1 TGTCA
3738149 TTGACACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (7 bp):
TGTCAAT
Found at i:3739376 original size:24 final size:24
Alignment explanation
Indices: 3739349--3739455 Score: 76
Period size: 23 Copynumber: 4.2 Consensus size: 24
3739339 TCTCATTTCA
3739349 ATCAAAATTATATTTAATTTTTAT
1 ATCAAAATTATATTTAATTTTTAT
* * *
3739373 ATC-AAATTTTAATAAATTTATTAGT
1 ATCAAAATTATATTTAATTT-TTA-T
* *
3739398 ATCATGAATACCTCATAATTTAA-TTTCA-
1 ATCA--AA-A--TTAT-ATTTAATTTTTAT
3739426 ATCAAAATTATATTTAATTTTTAT
1 ATCAAAATTATATTTAATTTTTAT
3739450 ATCAAA
1 ATCAAA
3739456 TTTTAATATA
Statistics
Matches: 62, Mismatches: 10, Indels: 22
0.66 0.11 0.23
Matches are distributed among these distances:
22 6 0.10
23 20 0.32
24 12 0.19
25 5 0.08
26 2 0.03
28 6 0.10
29 1 0.02
30 2 0.03
31 4 0.06
32 4 0.06
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (24 bp):
ATCAAAATTATATTTAATTTTTAT
Found at i:3739428 original size:77 final size:77
Alignment explanation
Indices: 3739343--3739500 Score: 307
Period size: 77 Copynumber: 2.1 Consensus size: 77
3739333 CAATTTTCTC
3739343 ATTTCAATCAAAATTATATTTAATTTTTATATCAAATTTTAATAAATTTATTAGTATCATGAATA
1 ATTTCAATCAAAATTATATTTAATTTTTATATCAAATTTTAATAAATTTATTAGTATCATGAATA
3739408 CCTCATAATTTA
66 CCTCATAATTTA
*
3739420 ATTTCAATCAAAATTATATTTAATTTTTATATCAAATTTTAATATATTTATTAGTATCATGAATA
1 ATTTCAATCAAAATTATATTTAATTTTTATATCAAATTTTAATAAATTTATTAGTATCATGAATA
3739485 CCTCATAATTTA
66 CCTCATAATTTA
3739497 ATTT
1 ATTT
3739501 TCAGTGCTTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 80 1.00
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.48
Consensus pattern (77 bp):
ATTTCAATCAAAATTATATTTAATTTTTATATCAAATTTTAATAAATTTATTAGTATCATGAATA
CCTCATAATTTA
Found at i:3753747 original size:31 final size:31
Alignment explanation
Indices: 3753654--3753808 Score: 88
Period size: 31 Copynumber: 5.1 Consensus size: 31
3753644 TAACATTAAG
* *
3753654 TTTTGGTCGGTCTAAT-TAAAATTTAAAAAA
1 TTTTGGTAGGTCTAATAAAAAATTTAAAAAA
** *
3753684 AATT-G-AGGTTTAATAAAAAATTTAAAAAA
1 TTTTGGTAGGTCTAATAAAAAATTTAAAAAA
* * * *
3753713 TTTTGGTAGGTCTAATGAAAACTTTCAAATA
1 TTTTGGTAGGTCTAATAAAAAATTTAAAAAA
* * *
3753744 TTTTAG-AGGTTTAAT-AGAAATTTACAAAAAA
1 TTTTGGTAGGTCTAATAAAAAATTT--AAAAAA
* * * * *
3753775 ATTT-GAAGAGTCTAATTAAAATTTTTAAAAA
1 TTTTGGTAG-GTCTAATAAAAAATTTAAAAAA
3753806 TTT
1 TTT
3753809 CCAAATATTT
Statistics
Matches: 93, Mismatches: 24, Indels: 15
0.70 0.18 0.11
Matches are distributed among these distances:
28 7 0.08
29 22 0.24
30 12 0.13
31 40 0.43
32 6 0.06
33 6 0.06
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (31 bp):
TTTTGGTAGGTCTAATAAAAAATTTAAAAAA
Found at i:3754407 original size:19 final size:19
Alignment explanation
Indices: 3754385--3754427 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
3754375 TAAAAATCAA
*
3754385 TAAAATTT-ATAAAATTTAT
1 TAAAATTTAAT-AAATATAT
*
3754404 TAAACTTTAATAAATATAT
1 TAAAATTTAATAAATATAT
3754423 TAAAA
1 TAAAA
3754428 AATTACTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
TAAAATTTAATAAATATAT
Found at i:3754753 original size:10 final size:10
Alignment explanation
Indices: 3754740--3754803 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
3754730 CTTTATAAAA
3754740 TTTTATATATT
1 TTTTATATA-T
*
3754751 TTTTCTATAT
1 TTTTATATAT
* *
3754761 CTCTATATA-
1 TTTTATATAT
3754770 TTTTATA-AT
1 TTTTATATAT
3754779 ATTTTAT-TAT
1 -TTTTATATAT
3754789 TTTTATAATAT
1 TTTTAT-ATAT
3754800 TTTT
1 TTTT
3754804 CTAAATTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
8 1 0.02
9 11 0.26
10 15 0.36
11 15 0.36
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTATATAT
Found at i:3754792 original size:9 final size:10
Alignment explanation
Indices: 3754731--3754873 Score: 61
Period size: 9 Copynumber: 14.5 Consensus size: 10
3754721 TTCTTACGAC
*
3754731 TTTATAAAAT
1 TTTATAATAT
3754741 TTTAT-ATAT
1 TTTATAATAT
* *
3754750 TTTTTCTATAT
1 TTTAT-AATAT
*
3754761 CTCTAT-ATAT
1 -TTTATAATAT
3754771 TTTATAATAT
1 TTTATAATAT
*
3754781 TTTATTAT-T
1 TTTATAATAT
3754790 TTTATAATATT
1 TTTATAATA-T
*
3754801 TTTCTAA-AT
1 TTTATAATAT
*
3754810 TTTAATAA-AA
1 TTT-ATAATAT
*
3754820 ATTA-AATAT
1 TTTATAATAT
*
3754829 TTCT-TAAATTT
1 TT-TAT-AATAT
*
3754840 TTTAGTAAAAT
1 TTTA-TAATAT
*
3754851 TTAATAAT-T
1 TTTATAATAT
3754860 TTTATAAT-T
1 TTTATAATAT
3754869 TTTAT
1 TTTAT
3754874 TGGTTTTTAT
Statistics
Matches: 101, Mismatches: 19, Indels: 27
0.69 0.13 0.18
Matches are distributed among these distances:
8 2 0.02
9 40 0.40
10 32 0.32
11 23 0.23
12 4 0.04
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (10 bp):
TTTATAATAT
Found at i:3754792 original size:19 final size:19
Alignment explanation
Indices: 3754731--3754802 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
3754721 TTCTTACGAC
*
3754731 TTTATAAAATTTTATATATT
1 TTTATAATATTTTAT-TATT
* *
3754751 TTT-TCTATATCTCTA-TATAT
1 TTTAT-AATAT-TTTATTAT-T
3754771 TTTATAATATTTTATTATT
1 TTTATAATATTTTATTATT
3754790 TTTATAATATTTT
1 TTTATAATATTTT
3754803 TCTAAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
19 21 0.50
20 17 0.40
21 4 0.10
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATAATATTTTATTATT
Found at i:3754811 original size:10 final size:11
Alignment explanation
Indices: 3754765--3754817 Score: 51
Period size: 10 Copynumber: 5.1 Consensus size: 11
3754755 CTATATCTCT
3754765 ATATATTTTATA
1 ATAT-TTTTATA
3754777 ATA-TTTTAT-
1 ATATTTTTATA
3754786 -TATTTTTATA
1 ATATTTTTATA
*
3754796 ATATTTTTCTA
1 ATATTTTTATA
*
3754807 A-ATTTTAATA
1 ATATTTTTATA
3754817 A
1 A
3754818 AAATTAAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
8 2 0.06
9 6 0.17
10 14 0.40
11 10 0.29
12 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (11 bp):
ATATTTTTATA
Found at i:3754841 original size:29 final size:27
Alignment explanation
Indices: 3754795--3754872 Score: 68
Period size: 29 Copynumber: 2.7 Consensus size: 27
3754785 TTATTTTTAT
3754795 AATATTTTTCTAAA-TTTTAATAAAAATTA
1 AATA-TTTT-TAAATTTTTAAT-AAAATTA
* *
3754824 AATATTTCTTAAATTTTTTAGTAAAATTT
1 AATATTT-TTAAA-TTTTTAATAAAATTA
3754853 AATAATTTTTATAATTTTTA
1 AAT-ATTTTTA-AATTTTTA
3754873 TTGGTTTTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
28 7 0.17
29 23 0.55
30 12 0.29
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (27 bp):
AATATTTTTAAATTTTTAATAAAATTA
Found at i:3754849 original size:30 final size:30
Alignment explanation
Indices: 3754809--3754871 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
3754799 TTTTTCTAAA
3754809 TTTTAATAAAAATTAAAT-ATTTCTTA-AATT
1 TTTTAAT-AAAATTAAATAATTT-TTATAATT
* *
3754839 TTTTAGTAAAATTTAATAATTTTTATAATT
1 TTTTAATAAAATTAAATAATTTTTATAATT
3754869 TTT
1 TTT
3754872 ATTGGTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTTAATAAAATTAAATAATTTTTATAATT
Found at i:3754987 original size:20 final size:20
Alignment explanation
Indices: 3754958--3755002 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3754948 ACTGTTAGCT
*
3754958 TTAACGGTCAACCGTAAAAG
1 TTAACAGTCAACCGTAAAAG
* *
3754978 TTAACAGTCAATCGTTAAAG
1 TTAACAGTCAACCGTAAAAG
3754998 TTAAC
1 TTAAC
3755003 GGTAAAATGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.27
Consensus pattern (20 bp):
TTAACAGTCAACCGTAAAAG
Found at i:3755223 original size:88 final size:86
Alignment explanation
Indices: 3755060--3755223 Score: 197
Period size: 88 Copynumber: 1.9 Consensus size: 86
3755050 AAGCAGGGAC
* ** * *
3755060 TTAATTGCTTTTTTGAAAAATTTTGAGGGCCTTTTTGATGTATTTTGGCAATTCAAGTACCCAAT
1 TTAATTGCTTTTTTGAAAAAGTTTGAGGGCCTTTTTGATACACTTTGGAAATTCAAGTACCCAAT
**
3755125 TGAGTGAAAAAAAACAATGGG
66 TGAGAAAAAAAAAACAATGGG
**
3755146 TTAATTGCTTTTTCTTGAAAAAGTTTGAGGGCCTTTTTGATACACTTT-GAAAGTTCAAGTATTC
1 TTAATTGC-TTTT-TTGAAAAAGTTTGAGGGCCTTTTTGATACACTTTGGAAA-TTCAAGTACCC
*
3755210 AA-TGTGAAAAAAAA
63 AATTGAGAAAAAAAA
3755224 TAGAGACTTA
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
86 8 0.12
87 16 0.25
88 41 0.63
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (86 bp):
TTAATTGCTTTTTTGAAAAAGTTTGAGGGCCTTTTTGATACACTTTGGAAATTCAAGTACCCAAT
TGAGAAAAAAAAAACAATGGG
Found at i:3766703 original size:17 final size:18
Alignment explanation
Indices: 3766681--3766721 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3766671 ATATAAATTC
3766681 ATTTATATTATT-TTTAA-
1 ATTTATATT-TTATTTAAT
3766698 ATTTAT-TTTTATTTAAT
1 ATTTATATTTTATTTAAT
3766715 ATTTATA
1 ATTTATA
3766722 AATAATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.10
16 7 0.33
17 12 0.57
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTATATTTTATTTAAT
Found at i:3767503 original size:13 final size:12
Alignment explanation
Indices: 3767485--3767527 Score: 61
Period size: 12 Copynumber: 3.5 Consensus size: 12
3767475 TAAGCTTCCA
3767485 TTTTTTTCTAATT
1 TTTTTTTC-AATT
3767498 TTTTTTTCCAA-T
1 TTTTTTT-CAATT
3767510 TTTTTTTCAATT
1 TTTTTTTCAATT
3767522 TTTTTT
1 TTTTTT
3767528 GGAGTGGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.11
12 15 0.54
13 9 0.32
14 1 0.04
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:3767527 original size:11 final size:11
Alignment explanation
Indices: 3767485--3767527 Score: 59
Period size: 11 Copynumber: 3.6 Consensus size: 11
3767475 TAAGCTTCCA
3767485 TTTTTTTCTAATT
1 TTTTTTTC-AA-T
3767498 TTTTTTTCCAAT
1 TTTTTTT-CAAT
3767510 TTTTTTTCAAT
1 TTTTTTTCAAT
3767521 TTTTTTT
1 TTTTTTT
3767528 GGAGTGGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.38
12 8 0.28
13 9 0.31
14 1 0.03
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTTCAAT
Found at i:3785784 original size:17 final size:18
Alignment explanation
Indices: 3785753--3785786 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3785743 CATAAACATA
3785753 ATTTAGGTATATATAATT
1 ATTTAGGTATATATAATT
*
3785771 ATTTA-GTATGTATAAT
1 ATTTAGGTATATATAAT
3785787 GAGGGGCGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (18 bp):
ATTTAGGTATATATAATT
Found at i:3789309 original size:30 final size:30
Alignment explanation
Indices: 3789250--3789310 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
3789240 TTATTTTATG
*
3789250 GTTAATTTTGTTATTATTTTAAATACATTT
1 GTTAATTTTGTTATTATTTTAAAGACATTT
* *
3789280 GTTAATTTTGTTATTATTTTAGAGGCATTT
1 GTTAATTTTGTTATTATTTTAAAGACATTT
3789310 G
1 G
3789311 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
GTTAATTTTGTTATTATTTTAAAGACATTT
Found at i:3794037 original size:5 final size:5
Alignment explanation
Indices: 3794029--3794056 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3794019 TTAATTTAAT
3794029 TATTA TATTA TATTA TATTA TATTA TAT
1 TATTA TATTA TATTA TATTA TATTA TAT
3794057 ACTTCACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATTA
Found at i:3795556 original size:17 final size:17
Alignment explanation
Indices: 3795524--3795568 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3795514 ACGAAATATT
*
3795524 ATAAAAATTAAATAAATTC
1 ATAAAAA-T-AATAAATAC
3795543 ATAAAAATAATAAATAC
1 ATAAAAATAATAAATAC
3795560 A-AAAAATAA
1 ATAAAAATAA
3795569 ACTTCCCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 8 0.32
17 9 0.36
18 1 0.04
19 7 0.28
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (17 bp):
ATAAAAATAATAAATAC
Found at i:3798114 original size:237 final size:238
Alignment explanation
Indices: 3797699--3798173 Score: 943
Period size: 237 Copynumber: 2.0 Consensus size: 238
3797689 TTAAATTGAA
3797699 CAATTAACATTTAAAAGACAGTACAACTACAATTATACTATTGATCCAAAAGTACCCCTCCCCCC
1 CAATTAACATTTAAAAGACAGTACAACTACAATTATACTATTGATCCAAAAGTACCCCTCCCCCC
3797764 CCTTCACTACTCTCTTAATGAGACTTAAACTTAACAATATTAACTAATCTCTCATTGGTTGTGGT
66 CCTTCACTACTCTCTTAATGAGACTTAAACTTAACAATATTAACTAATCTCTCATTGGTTGTGGT
3797829 GGACATAAATTATGAATTATATATAAAGATATTTATGATAAATTATATATATCACATTACTATAA
131 GGACATAAATTATGAATTATATATAAAGATATTTATGATAAATTATATATATCACATTACTATAA
3797894 GGGTAAGAAGAAAAAGTAATTTGTAAAAATAT-TAATTTAAAT
196 GGGTAAGAAGAAAAAGTAATTTGTAAAAATATATAATTTAAAT
3797936 CAATTAACATTTAAAAGACAGTACAACTACAATTATACTATTGATCCAAAAGTACCCCTCCCCCC
1 CAATTAACATTTAAAAGACAGTACAACTACAATTATACTATTGATCCAAAAGTACCCCTCCCCCC
3798001 CCTTCACTACTCTCTTAATGAGACTTAAACTTAACAATATTAACTAATCTCTCATTGGTTGTGGT
66 CCTTCACTACTCTCTTAATGAGACTTAAACTTAACAATATTAACTAATCTCTCATTGGTTGTGGT
3798066 GGACATAAATTATGAATTATATATAAAGATATTTATGATAAATTATATATATCACATTACTATAA
131 GGACATAAATTATGAATTATATATAAAGATATTTATGATAAATTATATATATCACATTACTATAA
3798131 GGGTAAGAAGAAAAAGTAATTTGTAAAAATATATAATTTAAAT
196 GGGTAAGAAGAAAAAGTAATTTGTAAAAATATATAATTTAAAT
3798174 AAATAATAAT
Statistics
Matches: 237, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
237 227 0.96
238 10 0.04
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (238 bp):
CAATTAACATTTAAAAGACAGTACAACTACAATTATACTATTGATCCAAAAGTACCCCTCCCCCC
CCTTCACTACTCTCTTAATGAGACTTAAACTTAACAATATTAACTAATCTCTCATTGGTTGTGGT
GGACATAAATTATGAATTATATATAAAGATATTTATGATAAATTATATATATCACATTACTATAA
GGGTAAGAAGAAAAAGTAATTTGTAAAAATATATAATTTAAAT
Found at i:3800117 original size:21 final size:21
Alignment explanation
Indices: 3800093--3800163 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
3800083 TTAACTCATA
3800093 TGAGTTTCAGTTTAACCCTTC
1 TGAGTTTCAGTTTAACCCTTC
* *
3800114 TGAGTTTCAGTTTAGCTCTTC
1 TGAGTTTCAGTTTAACCCTTC
* * *
3800135 TAAGCTTCAGTTTAACCCTTA
1 TGAGTTTCAGTTTAACCCTTC
*
3800156 TGGGTTTC
1 TGAGTTTC
3800164 CGTTCAGCTC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.44
Consensus pattern (21 bp):
TGAGTTTCAGTTTAACCCTTC
Found at i:3800183 original size:42 final size:42
Alignment explanation
Indices: 3800091--3800209 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
3800081 AGTTAACTCA
* * * * * *
3800091 TATGAGTTTCAGTTTAACCCTTCTGAGTTTCAGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCC
* *
3800133 TCTAAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCC
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCC
* *
3800175 TATGAGCTTCCA-TTCAA-CCTCTACGGGTTTCCGTT
1 TATGAGCTT-CAGTTTAACCCT-TATGGGTTTCCGTT
3800210 TAGCACTTAT
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
41 3 0.05
42 58 0.92
43 2 0.03
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTATGGGTTTCCGTTCAGCTCC
Found at i:3805273 original size:21 final size:21
Alignment explanation
Indices: 3805209--3805273 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
3805199 TAAAATAAAG
3805209 ATGAACGTCAAGAACTTGTTT
1 ATGAACGTCAAGAACTTGTTT
** **
3805230 ATGCAA--TTTAGAATCTT-CCT
1 ATG-AACGTCAAGAA-CTTGTTT
3805250 ATGAACGTCAAGAACTTGTTT
1 ATGAACGTCAAGAACTTGTTT
3805271 ATG
1 ATG
3805274 CAATTTAAAC
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
19 2 0.06
20 12 0.39
21 15 0.48
22 2 0.06
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (21 bp):
ATGAACGTCAAGAACTTGTTT
Found at i:3807298 original size:100 final size:101
Alignment explanation
Indices: 3807124--3807319 Score: 331
Period size: 100 Copynumber: 2.0 Consensus size: 101
3807114 TCGTTAAAAA
*
3807124 TTTCATCTATTTCTATTATTAAAAACTAACATGACTAATAAAACAACCAAATAGTAACATGTGGT
1 TTTCATCTATTTCTACTATTAAAAACTAACATGACTAATAAAACAACCAAATAGTAACATGTGGT
*
3807189 ATGTCATGTGTATCTCATACTTACGTACATGGAAAG
66 ATGTCATGTGTATCTCATACTGACGTACATGGAAAG
* * *
3807225 TTTCATCTATTTTTACTATT-AAAACTAGCATGACTAATAAAACAACCAACTAGTAACATGTGGT
1 TTTCATCTATTTCTACTATTAAAAACTAACATGACTAATAAAACAACCAAATAGTAACATGTGGT
*
3807289 ATGTCATGTGTATCTCATGCTGACGTACATG
66 ATGTCATGTGTATCTCATACTGACGTACATG
3807320 AATTAGTTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
100 71 0.80
101 18 0.20
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (101 bp):
TTTCATCTATTTCTACTATTAAAAACTAACATGACTAATAAAACAACCAAATAGTAACATGTGGT
ATGTCATGTGTATCTCATACTGACGTACATGGAAAG
Found at i:3813226 original size:16 final size:16
Alignment explanation
Indices: 3813207--3813237 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3813197 GAGTTAGGTC
3813207 GTTTTGAGTTTGGGTT
1 GTTTTGAGTTTGGGTT
*
3813223 GTTTTGATTTTGGGT
1 GTTTTGAGTTTGGGT
3813238 CATTCAAGTT
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:0.06, C:0.00, G:0.35, T:0.58
Consensus pattern (16 bp):
GTTTTGAGTTTGGGTT
Found at i:3814847 original size:43 final size:43
Alignment explanation
Indices: 3814790--3814877 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
3814780 GTTGAAATAA
* * * * *
3814790 AATAGAACTTGTGATAATTATACATTTAAAATAATTACAATTT
1 AATAGAACTCGTGATAATTACAAATTAAAAAAAATTACAATTT
* *
3814833 AATAGAAGTCGTGATAATTACAAATTAAAAAAAATTAGAATTT
1 AATAGAACTCGTGATAATTACAAATTAAAAAAAATTACAATTT
3814876 AA
1 AA
3814878 ATTACAATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (43 bp):
AATAGAACTCGTGATAATTACAAATTAAAAAAAATTACAATTT
Found at i:3815163 original size:85 final size:86
Alignment explanation
Indices: 3815020--3815190 Score: 335
Period size: 85 Copynumber: 2.0 Consensus size: 86
3815010 AAAAATTGTG
3815020 CTAATTTTATTGATGTAAAATAGAGTTTTTAATTGAATAGAATTCTAAATATCTTAATTATCACT
1 CTAATTTTATTGATGTAAAATAGAGTTTTTAATTGAATAGAATTCTAAATATCTTAATTATCACT
3815085 TAATTATGTTAA-TAATTATT
66 TAATTATGTTAATTAATTATT
3815105 CTAATTTTATTGATGTAAAATAGAGTTTTTAATTGAATAGAATTCTAAATATCTTAATTATCACT
1 CTAATTTTATTGATGTAAAATAGAGTTTTTAATTGAATAGAATTCTAAATATCTTAATTATCACT
3815170 TAATTATGTTAATTAATTATT
66 TAATTATGTTAATTAATTATT
3815191 ATTTAGAATA
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 77 0.91
86 8 0.09
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (86 bp):
CTAATTTTATTGATGTAAAATAGAGTTTTTAATTGAATAGAATTCTAAATATCTTAATTATCACT
TAATTATGTTAATTAATTATT
Found at i:3815556 original size:15 final size:16
Alignment explanation
Indices: 3815531--3815564 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
3815521 AAGTCTAACT
3815531 ATTTCTAGGTTTATTA
1 ATTTCTAGGTTTATTA
3815547 ATTT-TAGGTTTATTA
1 ATTTCTAGGTTTATTA
3815562 ATT
1 ATT
3815565 GTTTAAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.26, C:0.03, G:0.12, T:0.59
Consensus pattern (16 bp):
ATTTCTAGGTTTATTA
Found at i:3823337 original size:33 final size:33
Alignment explanation
Indices: 3823278--3823343 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
3823268 GAAAAAAAAA
* * * *
3823278 TTCGAGTTAATCGAATCGAGTTATTTGATTTTT
1 TTCGAGTCAATCGAATCAAGTAATTTGAGTTTT
3823311 TTCGAGTCAACTCGAAT-AAGTAATTTGAGTTTT
1 TTCGAGTCAA-TCGAATCAAGTAATTTGAGTTTT
3823344 GAGTTCGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 22 0.79
34 6 0.21
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (33 bp):
TTCGAGTCAATCGAATCAAGTAATTTGAGTTTT
Found at i:3823510 original size:18 final size:18
Alignment explanation
Indices: 3823471--3823513 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
3823461 AATTACAAAA
3823471 AAAAATCAAAATAGTTTTT
1 AAAAATCAAAATA-TTTTT
*
3823490 AAAATTCAAAAT-TTTTAT
1 AAAAATCAAAATATTTT-T
3823508 AAAAAT
1 AAAAAT
3823514 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 6 0.29
19 11 0.52
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (18 bp):
AAAAATCAAAATATTTTT
Found at i:3827467 original size:31 final size:32
Alignment explanation
Indices: 3827412--3827478 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
3827402 GAAATTAATA
* * * *
3827412 TTAAAAAATGATTTAGATTAAATTATTTACTT
1 TTAAAAAAGGATTTAAATTAAATTATTGAATT
*
3827444 TTAAAAAAGGA-TTAAATTGAATTATTGAATT
1 TTAAAAAAGGATTTAAATTAAATTATTGAATT
3827475 TTAA
1 TTAA
3827479 TAGGGAGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.46, C:0.01, G:0.09, T:0.43
Consensus pattern (32 bp):
TTAAAAAAGGATTTAAATTAAATTATTGAATT
Found at i:3831456 original size:14 final size:14
Alignment explanation
Indices: 3831433--3831466 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3831423 TATCATTTCG
*
3831433 TTATTATATTGCTA
1 TTATTTTATTGCTA
*
3831447 TTATTTTATTGTTA
1 TTATTTTATTGCTA
3831461 TTATTT
1 TTATTT
3831467 GGATATTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.68
Consensus pattern (14 bp):
TTATTTTATTGCTA
Found at i:3831753 original size:99 final size:96
Alignment explanation
Indices: 3831646--3832021 Score: 457
Period size: 99 Copynumber: 3.8 Consensus size: 96
3831636 CCACGCTTCA
* * *
3831646 AGTTGGTCACTATTTGAACTTTGGGATATTATCGAAGGGAGAGCCCACTCCACCATCTGCCCTTG
1 AGTTGGTCACGATTTAAACTTTGGGATATTA-CGAAGGGAGAGCCCACTCCACCATCTGCCCCTG
3831711 GAAAACGTATAAATACACCACCACCACCGTCGCT
65 GAAAACGTATAAATACACCACCACCACCG-C-CT
* * * * * *
3831745 AGTTGGTCACAATTTGAACTTTGGGATATTACGAAAGGGAGGGCCCACTCCACTATTTTCCCCTG
1 AGTTGGTCACGATTTAAACTTTGGGATATTACG-AAGGGAGAGCCCACTCCACCATCTGCCCCTG
*
3831810 GAAAACGTATAAATACGCCACCACCACCGCCTT
65 GAAAACGTATAAATACACCACCACCACCGCC-T
* ** * **
3831843 AAGGTT-GTCACGGTTTAAACTTCAGGATATTACCAAAGGGAGAGCCCACTCCACCATCTGCTTC
1 -A-GTTGGTCACGATTTAAACTTTGGGATATTA-CGAAGGGAGAGCCCACTCCACCATCTGCCCC
* * *
3831907 TAGAAAACGTATAAATACACCAGCACCATCGCCT
63 TGGAAAACGTATAAATACACCACCACCACCGCCT
*
3831941 CAAGTTGGTCACGGTTTAAACTTTGGGATATTACTGAAGGGAGAGCCCACTCCACCATCTGCCCC
1 --AGTTGGTCACGATTTAAACTTTGGGATATTAC-GAAGGGAGAGCCCACTCCACCATCTGCCCC
*
3832006 TGGAAAAGGTATAAAT
63 TGGAAAACGTATAAAT
3832022 CAAGTTCCGC
Statistics
Matches: 239, Mismatches: 30, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
97 1 0.00
98 9 0.04
99 225 0.94
100 4 0.02
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.24
Consensus pattern (96 bp):
AGTTGGTCACGATTTAAACTTTGGGATATTACGAAGGGAGAGCCCACTCCACCATCTGCCCCTGG
AAAACGTATAAATACACCACCACCACCGCCT
Found at i:3832195 original size:107 final size:108
Alignment explanation
Indices: 3831940--3832214 Score: 353
Period size: 108 Copynumber: 2.6 Consensus size: 108
3831930 CACCATCGCC
* * *
3831940 TCAAGTTGGTCAC-GGTTTAAACTTTGGGATATTACTGAAGGGAGAGCCCACTCCACCATCTGCC
1 TCAAGTTGGTC-CTGGTTTGAACATTGGGATATTACTGAAGGAAGAGCCCACTCCACCATCTGCC
*
3832004 CCTGGAAAAGGTATAAATCAAGTTCCGCCTCCATCTCAAGTAAG
65 CCTGGAAAAGGTAGAAATCAAGTTCCGCCTCCATCTCAAGTAAG
* * * *
3832048 TCAAGTTGGTCCTGGTTTGAACATTGGGATGTTACCGAAGGAAGGGTCCACTCCACCATCTGCCC
1 TCAAGTTGGTCCTGGTTTGAACATTGGGATATTACTGAAGGAAGAGCCCACTCCACCATCTGCCC
* * * *
3832113 TTGGAAAAGGTGGAAATCAAGTTCTGCC-GCATCTCATAG-AAG
66 CTGGAAAAGGTAGAAATCAAGTTCCGCCTCCATCTCA-AGTAAG
* * *
3832155 TCAAGTTGGTCCTGGTTTGAACACTGGGATATTATTGAAGGGACGA-CCCACT-CACCATCT
1 TCAAGTTGGTCCTGGTTTGAACATTGGGATATTACTGAA-GGAAGAGCCCACTCCACCATCT
3832215 ATTTTTGAAA
Statistics
Matches: 145, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
106 8 0.06
107 51 0.35
108 86 0.59
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.26
Consensus pattern (108 bp):
TCAAGTTGGTCCTGGTTTGAACATTGGGATATTACTGAAGGAAGAGCCCACTCCACCATCTGCCC
CTGGAAAAGGTAGAAATCAAGTTCCGCCTCCATCTCAAGTAAG
Found at i:3837144 original size:14 final size:15
Alignment explanation
Indices: 3837124--3837161 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
3837114 ATCATAGTAA
3837124 AATTAACAATTACTT
1 AATTAACAATTACTT
3837139 -ATTAAC-ATTACTT
1 AATTAACAATTACTT
3837152 AATTAACAAT
1 AATTAACAAT
3837162 AATGTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 7 0.33
14 12 0.57
15 2 0.10
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (15 bp):
AATTAACAATTACTT
Found at i:3841531 original size:23 final size:23
Alignment explanation
Indices: 3841501--3841546 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
3841491 CAAAGCTGTA
*
3841501 TTTAATTT-TTAAATTAATTTTT
1 TTTAATTTGTTAAATAAATTTTT
*
3841523 TTTACATTTGTTACATAAATTTTT
1 TTTA-ATTTGTTAAATAAATTTTT
3841547 CACCAACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 4 0.20
24 12 0.60
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (23 bp):
TTTAATTTGTTAAATAAATTTTT
Found at i:3842796 original size:29 final size:31
Alignment explanation
Indices: 3842743--3842802 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
3842733 CAAAATTAAA
* * *
3842743 GCACCACAATTATAGTTTTATGTATATAATT
1 GCACCACAATTAAAGTTTCATGTATAAAATT
3842774 GCACCA-AATTAAAG-TTCATGTATAAAATT
1 GCACCACAATTAAAGTTTCATGTATAAAATT
3842803 ATATATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.50
30 7 0.27
31 6 0.23
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (31 bp):
GCACCACAATTAAAGTTTCATGTATAAAATT
Found at i:3842820 original size:18 final size:18
Alignment explanation
Indices: 3842797--3842831 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3842787 GTTCATGTAT
3842797 AAAATT-ATATATTAAATC
1 AAAATTCATATA-TAAATC
3842815 AAAATTCATATATAAAT
1 AAAATTCATATATAAAT
3842832 TTAAGATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (18 bp):
AAAATTCATATATAAATC
Found at i:3844616 original size:127 final size:124
Alignment explanation
Indices: 3844452--3844680 Score: 282
Period size: 125 Copynumber: 1.8 Consensus size: 124
3844442 TGTTTTAATT
** * *
3844452 TTAAAAGGATATTTGATTATTTAGGATCAACGCGAAAAAATCGA-AGCCCAGTAAGTTAGGGCAC
1 TTAAAAGGATATTTGACCATTGAGGATCAA--CGAGAAAATCGAGA-CCCAGTAAGTTAGGGCAC
* * * * * *
3844516 GATTTCTCGAATTTTCTAAATATAGAATATTACCTTTATTTTTGAAATTTTGTGTTTGGAAAA
63 AATTTCTCAAATTTCCAAAATACAAAATATTACC-TTATTTTTGAAATTTTGTGTTTGGAAAA
* * *
3844579 TTAAAAGGATATTTCG-CCATTGAGGATTAACGAGAAAATCGAGACCTAGTAAGTTAGGGTACAA
1 TTAAAAGGATATTT-GACCATTGAGGATCAACGAGAAAATCGAGACCCAGTAAGTTAGGGCACAA
3844643 TTTCTCAAATTTCCAAAATACAAAATATTACCTTATTT
65 TTTCTCAAATTTCCAAAATACAAAATATTACCTTATTT
3844681 GAAATTATGA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
124 6 0.07
125 55 0.63
126 1 0.01
127 24 0.28
128 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (124 bp):
TTAAAAGGATATTTGACCATTGAGGATCAACGAGAAAATCGAGACCCAGTAAGTTAGGGCACAAT
TTCTCAAATTTCCAAAATACAAAATATTACCTTATTTTTGAAATTTTGTGTTTGGAAAA
Found at i:3845971 original size:13 final size:13
Alignment explanation
Indices: 3845955--3845979 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3845945 ACCGACTTGC
3845955 AAAAGAAATAAAT
1 AAAAGAAATAAAT
3845968 AAAAGAAATAAA
1 AAAAGAAATAAA
3845980 AGAGGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (13 bp):
AAAAGAAATAAAT
Found at i:3850054 original size:21 final size:21
Alignment explanation
Indices: 3850028--3850071 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3850018 AGTCCCTTTA
* * *
3850028 AAAATTTTGAAATTATAAGTT
1 AAAATTATGAAATAATAAATT
3850049 AAAATTATGAAATAATAAATT
1 AAAATTATGAAATAATAAATT
3850070 AA
1 AA
3850072 TTCAATGATA
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:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (21 bp):
AAAATTATGAAATAATAAATT
Found at i:3853186 original size:8 final size:8
Alignment explanation
Indices: 3853173--3853197 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
3853163 TAAATAAATT
3853173 ATTTTAAA
1 ATTTTAAA
3853181 ATTTTAAA
1 ATTTTAAA
3853189 ATTTTAAA
1 ATTTTAAA
3853197 A
1 A
3853198 AATGTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTTAAA
Found at i:3853915 original size:155 final size:157
Alignment explanation
Indices: 3853752--3854049 Score: 343
Period size: 161 Copynumber: 1.9 Consensus size: 157
3853742 GGATTAGAGT
3853752 TATGAAGAGGATTCGGTCCTCCCAG-AGTGTCTCTCTTAACAAAGATATTAAAACCACCAGGTG-
1 TATGAAGAGGATTCGGTCCTCCCAGTA-TGTCTCTCTTAACAAAGATATTAAAACCACCA-GTGC
* * * * **
3853815 T-C-TATTAGAGTTATGAAAAGGATTTGGTCCTCCTGGAGTTTCTTTCTTCGTGATGATATTAAG
64 TACAGATTAGAGTTATGAAAAGGATTTGGCCCTCCTAGAGTTTCTTTCGTCACGATGATATTAAG
3853878 ACCACTAGGTGATAATAGAGGATTAAAAC
129 ACCACTAGGTGATAATAGAGGATTAAAAC
* * * * * * * * *
3853907 TATGAAGAGTATTTGGTCCTTCCGGTATTTGTCTCTTCACGATGATATTAAAACCACCAGTGCCT
1 TATGAAGAGGATTCGGTCCTCCCAGTATGTCTCTCTTAACAAAGATATTAAAACCACCAGTG-CT
* * * *
3853972 ACAAAGGATTGGAGTTATGAAGAGGATTTGGCCCTCCTAGAGTTTTTTTCGTCACGATGGTATTA
65 AC--A-GATTAGAGTTATGAAAAGGATTTGGCCCTCCTAGAGTTTCTTTCGTCACGATGATATTA
3854037 AGACCACTAGGTG
127 AGACCACTAGGTG
3854050 CCAGTGAGAG
Statistics
Matches: 116, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
154 3 0.03
155 48 0.41
156 2 0.02
157 1 0.01
161 62 0.53
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (157 bp):
TATGAAGAGGATTCGGTCCTCCCAGTATGTCTCTCTTAACAAAGATATTAAAACCACCAGTGCTA
CAGATTAGAGTTATGAAAAGGATTTGGCCCTCCTAGAGTTTCTTTCGTCACGATGATATTAAGAC
CACTAGGTGATAATAGAGGATTAAAAC
Found at i:3856772 original size:81 final size:81
Alignment explanation
Indices: 3856637--3857105 Score: 706
Period size: 81 Copynumber: 5.8 Consensus size: 81
3856627 GGAGCTAGCA
* * *
3856637 GAGGATTAGAGTTGTGAAGAGGATTTGGTCCTCCCGGAGTTTCCCGCTTCACAATGACATTAAAA
1 GAGGATTAGAATTGTGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGACATTAAAA
*
3856702 CCACTAGGTGTCTGCG
66 CCACTAGGTGCCTGCG
* ** *
3856718 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCTTGGAGTTTCTCTCTTCACAATGACAGTAAAA
1 GAGGATTAGAATTGTGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGACATTAAAA
*
3856783 CCACTAGGTGCCTGTG
66 CCACTAGGTGCCTGCG
* * *
3856799 GAGGATTATG-GTTGTGAATAGGATTTGGTCCTCCTGGAGTTTCTCTCTTCACAATGACATTAAA
1 GAGGATTA-GAATTGTGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGACATTAAA
*
3856863 ACCACTAGGTGCCAGCG
65 ACCACTAGGTGCCTGCG
*
3856880 GAGGATTAGAATGGTGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGACATTAAAA
1 GAGGATTAGAATTGTGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGACATTAAAA
*
3856945 CCACTAGGTGCCTGCA
66 CCACTAGGTGCCTGCG
* *
3856961 GAGGATTAGAATCGTGAAGAGGATTTGGTCCTCCTGGAGTTTCTCTCTTCACAATGACATTAAAA
1 GAGGATTAGAATTGTGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGACATTAAAA
*
3857026 CCACTAGGTGCATGCG
66 CCACTAGGTGCCTGCG
* **
3857042 GAGGATTAGAATTGTGAAGAGGATAATTTGATCCTCCCGGAGTTTCTCTCTTCATGATGACATT
1 GAGGATTAGAATTGTGAAGAGG---ATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGACATT
3857106 TTTAATGATA
Statistics
Matches: 352, Mismatches: 31, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
80 1 0.00
81 315 0.89
82 1 0.00
84 35 0.10
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (81 bp):
GAGGATTAGAATTGTGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGACATTAAAA
CCACTAGGTGCCTGCG
Found at i:3862945 original size:81 final size:81
Alignment explanation
Indices: 3862803--3863437 Score: 806
Period size: 81 Copynumber: 7.8 Consensus size: 81
3862793 TGGAGGCGGA
* * * *
3862803 GCTAGCAGAGGATTAGAGTTGTGAAGAGGATTTGGTCCTCCCGGAGTTTCCCGCTTCACAATGAC
1 GCTAGCAGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGAC
3862868 ATTAAAACCACTAGGT
66 ATTAAAACCACTAGGT
* **
3862884 GTCT-GCGGAGGATTAGAATTATGAAGAGGATTTGGTCCTCTTGGAGTTTCTCTCTTCACAATGA
1 G-CTAGCAGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGA
3862948 CATTAAAACCACTAGGT
65 CATTAAAACCACTAGGT
* *
3862965 GCTAGCAGAGGATTAGAATTTTGAATAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGAC
1 GCTAGCAGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGAC
*
3863030 ATTAAAACCACTAAGT
66 ATTAAAACCACTAGGT
* * * * * *
3863046 GCTAGCAGAGGATTAGAATTTTGAATAGGATTTGGTCCTCCTGGAGCTTCTCTCTTCACGATGAT
1 GCTAGCAGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGAC
* *
3863111 GTTTAAACCACTAGGT
66 ATTAAAACCACTAGGT
* * *** * * * *
3863127 ACCAATGGAGGATTAGAATTATGAAGAGGA-TTGGACCTCCTGGAGCTTCTCTCTTCACAATGAT
1 GCTAGCAGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGAC
* *
3863191 ATTAAAACCAGTAGAT
66 ATTAAAACCACTAGGT
* * * *
3863207 GCTAGCAGAGGATTAGAGTTATGAAGAGGATTTGGTCCTCCTGGAGTTTCTCTCTTCACGATGAT
1 GCTAGCAGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGAC
* *
3863272 GTTTAAACCACTAGGT
66 ATTAAAACCACTAGGT
* * ** * * * *
3863288 GCCAACAGAATATTAGAATTATGAAGAGGATTTGGACATCTCGGAGTTTCTCTCTTCACAATGAT
1 GCTAGCAGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGAC
3863353 ATTAAAACCACTAGGT
66 ATTAAAACCACTAGGT
* * * **
3863369 GCTAGCGGAGGATTAGAGTTATGAAGAGGATTTGGTCCCTCCCGGAGTTTCTTTCTTCATGATGA
1 GCTAGCAGAGGATTAGAATTATGAAGAGGATTTGGT-CCTCCCGGAGTTTCTCTCTTCACAATGA
3863434 CATT
65 CATT
3863438 TTTTTAATGG
Statistics
Matches: 479, Mismatches: 71, Indels: 7
0.86 0.13 0.01
Matches are distributed among these distances:
80 70 0.15
81 381 0.80
82 28 0.06
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (81 bp):
GCTAGCAGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACAATGAC
ATTAAAACCACTAGGT
Found at i:3865111 original size:26 final size:28
Alignment explanation
Indices: 3865042--3865122 Score: 148
Period size: 28 Copynumber: 3.0 Consensus size: 28
3865032 CTCCTTTCTG
3865042 GAAAGAGAAACACAAAATCAGATAAACT
1 GAAAGAGAAACACAAAATCAGATAAACT
3865070 GAAAGAGAAACACAAAATCAGATAAACT
1 GAAAGAGAAACACAAAATCAGATAAACT
3865098 G-AA-AGAAACACAAAATCAGATAAAC
1 GAAAGAGAAACACAAAATCAGATAAAC
3865123 ATTTTTGTAC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
26 22 0.42
27 2 0.04
28 29 0.55
ACGTcount: A:0.62, C:0.15, G:0.14, T:0.10
Consensus pattern (28 bp):
GAAAGAGAAACACAAAATCAGATAAACT
Found at i:3870530 original size:16 final size:15
Alignment explanation
Indices: 3870499--3870529 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3870489 AAATAAAAAA
3870499 TGGGTCTGGTTTTTT
1 TGGGTCTGGTTTTTT
3870514 TGGGTCTGGTTTTTT
1 TGGGTCTGGTTTTTT
3870529 T
1 T
3870530 TTTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.06, G:0.32, T:0.61
Consensus pattern (15 bp):
TGGGTCTGGTTTTTT
Found at i:3874306 original size:14 final size:15
Alignment explanation
Indices: 3874279--3874307 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3874269 GGAATAACTC
3874279 TGTAATTAAATAAGT
1 TGTAATTAAATAAGT
3874294 TGTAATT-AATAAGT
1 TGTAATTAAATAAGT
3874308 GGAGAGCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (15 bp):
TGTAATTAAATAAGT
Found at i:3876496 original size:30 final size:32
Alignment explanation
Indices: 3876457--3876534 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 32
3876447 ACTTCAAATT
*
3876457 ATTAAAATTATA-TTTGTATTAAATAAT-A-AA
1 ATTATAATTATATTTTG-ATTAAATAATAATAA
*
3876487 ATTATAATTACATTTTGATTAAATAATAATAA
1 ATTATAATTATATTTTGATTAAATAATAATAA
*
3876519 ATTTATATTTATATTT
1 A-TTATAATTATATTT
3876535 AATATATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 20 0.50
31 5 0.12
32 3 0.08
33 12 0.30
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (32 bp):
ATTATAATTATATTTTGATTAAATAATAATAA
Found at i:3877637 original size:82 final size:83
Alignment explanation
Indices: 3877500--3877664 Score: 323
Period size: 82 Copynumber: 2.0 Consensus size: 83
3877490 TACCATTACA
3877500 CTAAATACTTGATAAAGAAAAATAATTTTGAATATTGTTTTGGGTTAATTTATTTAGCTATATAA
1 CTAAATACTTGATAAAGAAAAATAATTTTGAATATTGTTTTGGGTTAATTTATTTAGCTATATAA
3877565 GATAAAA-TTTATATATT
66 GATAAAATTTTATATATT
3877582 CTAAATACTTGATAAAGAAAAATAATTTTGAATATTGTTTTGGGTTAATTTATTTAGCTATATAA
1 CTAAATACTTGATAAAGAAAAATAATTTTGAATATTGTTTTGGGTTAATTTATTTAGCTATATAA
3877647 GATAAAATTTTATATATT
66 GATAAAATTTTATATATT
3877665 TATATTTGTA
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 72 0.88
83 10 0.12
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (83 bp):
CTAAATACTTGATAAAGAAAAATAATTTTGAATATTGTTTTGGGTTAATTTATTTAGCTATATAA
GATAAAATTTTATATATT
Found at i:3878592 original size:26 final size:26
Alignment explanation
Indices: 3878563--3878623 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
3878553 CCATTTTTTT
* * *
3878563 AATAAACACCAAAAAATTATTTTAAA
1 AATAAAAACAAAAAAAGTATTTTAAA
*
3878589 AATAAAAAATAAAAAAAGTATTTTAAA
1 AAT-AAAAACAAAAAAAGTATTTTAAA
3878616 AATAAAAA
1 AATAAAAA
3878624 AATATATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.25
Consensus pattern (26 bp):
AATAAAAACAAAAAAAGTATTTTAAA
Found at i:3878596 original size:20 final size:21
Alignment explanation
Indices: 3878593--3878632 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3878583 TTTAAAAATA
3878593 AAAAATAAAAAAAG-TATTTT
1 AAAAATAAAAAAAGATATTTT
*
3878613 AAAAATAAAAAAATATATTT
1 AAAAATAAAAAAAGATATTT
3878633 ATTAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (21 bp):
AAAAATAAAAAAAGATATTTT
Found at i:3878627 original size:28 final size:27
Alignment explanation
Indices: 3878573--3878624 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
3878563 AATAAACACC
*
3878573 AAAAAATTATTTTAAAAATAAAAAATA
1 AAAAAAGTATTTTAAAAATAAAAAATA
3878600 AAAAAAGTATTTTAAAAATAAAAAA
1 AAAAAAGTATTTTAAAAATAAAAAA
3878625 ATATATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (27 bp):
AAAAAAGTATTTTAAAAATAAAAAATA
Found at i:3879161 original size:88 final size:88
Alignment explanation
Indices: 3879069--3879242 Score: 235
Period size: 88 Copynumber: 2.0 Consensus size: 88
3879059 AGGGTTATAG
* * * *
3879069 ATTTGACTGAAATATAGGGATCAAAACT-AATATTTAACCATAAAAATTTGAATG-ATTAGAATT
1 ATTTGACTGAAATATAAGGATCAAAACTGAA-ATTTAACCATAAAAACTAG-AGGAATTAGAATT
3879132 GAAATTTAGCAATTATCTTCTCAAA
64 GAAATTTAGCAATTATCTTCTCAAA
* * *
3879157 ATTTGAGTGATATATAAGGATCAAAACTGAAATTTAACCATAGAAACTAGAGGAATTAGAATTGA
1 ATTTGACTGAAATATAAGGATCAAAACTGAAATTTAACCATAAAAACTAGAGGAATTAGAATTGA
**
3879222 AATTTAGTTATTATCTTCTCA
66 AATTTAGCAATTATCTTCTCA
3879243 TATTAAAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
87 2 0.03
88 71 0.95
89 2 0.03
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (88 bp):
ATTTGACTGAAATATAAGGATCAAAACTGAAATTTAACCATAAAAACTAGAGGAATTAGAATTGA
AATTTAGCAATTATCTTCTCAAA
Found at i:3891659 original size:82 final size:83
Alignment explanation
Indices: 3891561--3891730 Score: 333
Period size: 82 Copynumber: 2.1 Consensus size: 83
3891551 AAATTAGTGT
3891561 TTAAAATCAATTATTTGACGAGTTAAAATCTTATTATAAGTGAATTTTTATTGATTTTAATATAA
1 TTAAAATCAATTATTTGACGAGTTAAAATCTTATTATAAGTGAATTTTTATTGATTTTAATATAA
3891626 AATAT-AAAATATTTTAA
66 AATATAAAAATATTTTAA
3891643 TTAAAATCAATTATTTGACGAGTTAAAATCTTATTATAAGTGAATTTTTATTGATTTTAATATAA
1 TTAAAATCAATTATTTGACGAGTTAAAATCTTATTATAAGTGAATTTTTATTGATTTTAATATAA
3891708 AATATAAAAATATTTTAA
66 AATATAAAAATATTTTAA
3891726 TTAAA
1 TTAAA
3891731 TTAATATTTA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 70 0.80
83 17 0.20
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.45
Consensus pattern (83 bp):
TTAAAATCAATTATTTGACGAGTTAAAATCTTATTATAAGTGAATTTTTATTGATTTTAATATAA
AATATAAAAATATTTTAA
Found at i:3901412 original size:4 final size:4
Alignment explanation
Indices: 3901403--3901429 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3901393 GAATTTAATG
3901403 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
3901430 CACATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:3907678 original size:61 final size:60
Alignment explanation
Indices: 3907584--3907700 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 60
3907574 TGAGTCCGGA
* * *
3907584 TGGTAATGGATATGCCCGATGCTGTTGGCTTCCTGTGATCATACCACACTTACAATACAT
1 TGGTAATGGACATGCCAGATGCTGTTGGCTTCCTGTGATCAGACCACACTTACAATACAT
*
3907644 TGGTAATGGACCATGCCAGATGCTGTTGGCTTCCTGTGATCAGACCACGCTTACAAT
1 TGGTAATGGA-CATGCCAGATGCTGTTGGCTTCCTGTGATCAGACCACACTTACAAT
3907701 GCAATCAGCT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 10 0.19
61 42 0.81
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (60 bp):
TGGTAATGGACATGCCAGATGCTGTTGGCTTCCTGTGATCAGACCACACTTACAATACAT
Found at i:3910983 original size:32 final size:32
Alignment explanation
Indices: 3910947--3911012 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
3910937 ATTAGGGAAA
3910947 AATCAAGAAGAAGAAAAAGAAGAGAAAGATGG
1 AATCAAGAAGAAGAAAAAGAAGAGAAAGATGG
3910979 AATCAAGAAGAAGAAAAAGAAGAGAAAGATGG
1 AATCAAGAAGAAGAAAAAGAAGAGAAAGATGG
3911011 AA
1 AA
3911013 AAACTCAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.64, C:0.03, G:0.27, T:0.06
Consensus pattern (32 bp):
AATCAAGAAGAAGAAAAAGAAGAGAAAGATGG
Found at i:3911650 original size:21 final size:21
Alignment explanation
Indices: 3911624--3911667 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
3911614 CCTCTCTGAA
3911624 CAGCAAGCCATCACACCTTAC
1 CAGCAAGCCATCACACCTTAC
*
3911645 CAGCAAGCCATCACACTTTAC
1 CAGCAAGCCATCACACCTTAC
3911666 CA
1 CA
3911668 TCAGAAATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.41, G:0.09, T:0.16
Consensus pattern (21 bp):
CAGCAAGCCATCACACCTTAC
Found at i:3916977 original size:44 final size:43
Alignment explanation
Indices: 3916874--3916993 Score: 131
Period size: 44 Copynumber: 2.8 Consensus size: 43
3916864 ACAACGCCAT
* *
3916874 TGTCCCAGATGTGGTCTTACATGTAATCACATATCGATGCCAC
1 TGTCCCAGATGTGGTCTTACACGTAATCACATATCGATGCAAC
*
3916917 TGTCCCAGACAG-GGTCTTACACGTAAGTCACA-AGTCGATGTCAAC
1 TGTCCCAGA-TGTGGTCTTACACGTAA-TCACATA-TCGATG-CAAC
*
3916962 -GTCTCAGATGTGGTCTTACACGATAA-CACATA
1 TGTCCCAGATGTGGTCTTACACG-TAATCACATA
3916994 ACAAAATTAT
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
43 28 0.43
44 31 0.48
45 6 0.09
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (43 bp):
TGTCCCAGATGTGGTCTTACACGTAATCACATATCGATGCAAC
Found at i:3922848 original size:24 final size:24
Alignment explanation
Indices: 3922812--3922859 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3922802 TTAACTTCAA
* *
3922812 ATTTTTTTCTTTT-TTTCATTTATT
1 ATTTTGTTATTTTATTT-ATTTATT
3922836 ATTTTGTTATTTTATTTATTTATT
1 ATTTTGTTATTTTATTTATTTATT
3922860 TTCAACTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (24 bp):
ATTTTGTTATTTTATTTATTTATT
Found at i:3924647 original size:19 final size:20
Alignment explanation
Indices: 3924608--3924655 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
3924598 TACAAAAAAG
3924608 AATTCAAAATAATTTTCAAA
1 AATTCAAAATAATTTTCAAA
3924628 AATTCAAAAT-ATTTAT-AAA
1 AATTCAAAATAATTT-TCAAA
3924647 AATTTCAAA
1 AA-TTCAAA
3924656 TTTTATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTCAAAATAATTTTCAAA
Found at i:3924656 original size:19 final size:18
Alignment explanation
Indices: 3924625--3924662 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
3924615 AATAATTTTC
3924625 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAAT-TTTAT
3924644 AAAAATTTC-AAATTTTAT
1 AAAAA-TTCAAAATTTTAT
3924662 A
1 A
3924663 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 9 0.50
20 3 0.17
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATTCAAAATTTTAT
Found at i:3924674 original size:18 final size:19
Alignment explanation
Indices: 3924653--3924692 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3924643 TAAAAATTTC
*
3924653 AAATTTT-ATATTTTTAAA
1 AAATTTTAAAATTTTTAAA
3924671 AAATTTTAAAATTTTTAAA
1 AAATTTTAAAATTTTTAAA
3924690 AAA
1 AAA
3924693 AAATTCTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTTTAAAATTTTTAAA
Found at i:3925862 original size:5 final size:5
Alignment explanation
Indices: 3925852--3925885 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
3925842 GACTTAATCT
*
3925852 TTTTA TTTTA TTTTA TTTTA TTTTA TTCTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
3925886 TCCCAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:3930697 original size:20 final size:20
Alignment explanation
Indices: 3930668--3930706 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3930658 ATATTTTCCT
*
3930668 GTAAATCATTTTACAGAAAA
1 GTAAAACATTTTACAGAAAA
*
3930688 GTAAAACATTTTCCAGAAA
1 GTAAAACATTTTACAGAAA
3930707 TCATTTTACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (20 bp):
GTAAAACATTTTACAGAAAA
Found at i:3930710 original size:34 final size:35
Alignment explanation
Indices: 3930655--3930721 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
3930645 CAAACACCAG
* *
3930655 AAAATATTTTCCTGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3930690 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
3930722 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:3932602 original size:6 final size:6
Alignment explanation
Indices: 3932591--3932627 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
3932581 AAAATTTACC
3932591 ATTATA ATTATA ATTAT- ATTATA ATTATA ATTATA AT
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTATA AT
3932628 GGCTAGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
ATTATA
Found at i:3932613 original size:17 final size:17
Alignment explanation
Indices: 3932591--3932625 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
3932581 AAAATTTACC
3932591 ATTATAATTATAATTAT
1 ATTATAATTATAATTAT
3932608 ATTATAATTATAATTAT
1 ATTATAATTATAATTAT
3932625 A
1 A
3932626 ATGGCTAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATAATTATAATTAT
Found at i:3934457 original size:14 final size:14
Alignment explanation
Indices: 3934438--3934467 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3934428 GAGATATGGT
*
3934438 ATATATGTATTATC
1 ATATATGTAATATC
3934452 ATATATGTAATATC
1 ATATATGTAATATC
3934466 AT
1 AT
3934468 GTCAATTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
ATATATGTAATATC
Found at i:3935796 original size:24 final size:24
Alignment explanation
Indices: 3935758--3936057 Score: 144
Period size: 24 Copynumber: 12.8 Consensus size: 24
3935748 TGAATTGGAT
* *
3935758 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
3935783 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
3935807 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
* * **
3935827 AATTCTAGAATAATCATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** * *
3935852 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
*
3935876 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* * *
3935897 ATTTTGAAATAA-ATATACATGATA
1 AATTTAAAATAATA-ATATATGATA
** * *
3935921 AATTTAAAATAATGTTA-ACGATG
1 AATTTAAAATAATAATATATGATA
3935944 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
3935967 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
* **
3935991 AATCTAAAATAATAATATACAATA
1 AATTTAAAATAATAATATATGATA
* * * * *
3936015 CACTT-AGATAATATTA-ATGATT
1 AATTTAAAATAATAATATATGATA
3936037 AATTTAATAATAATAAGTATA
1 AATTTAA-AATAATAA-TATA
3936058 AACATTCAAA
Statistics
Matches: 201, Mismatches: 52, Indels: 43
0.68 0.18 0.15
Matches are distributed among these distances:
20 5 0.02
21 12 0.06
22 26 0.13
23 59 0.29
24 82 0.41
25 16 0.08
26 1 0.00
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:3935830 original size:69 final size:67
Alignment explanation
Indices: 3935755--3936043 Score: 190
Period size: 69 Copynumber: 4.1 Consensus size: 67
3935745 AAATGAATTG
* * * *
3935755 GATAATTTACAATAAATAATATATAATAAATTTGAAATAATAATACAT-ATAAAATTTAAAAATT
1 GATAATTTA-AATAAAT-ATACATGATAAATTTAAAATAATAATACATAAT-AAATTTAAAAATA
*
3935819 TTGAT
63 TTAAT
* ** * *
3935824 GATAATTCTAGAAT-AATCATACGTGATAAATCCAAAATAATAGTATATAATAAATTTAAAAATA
1 GATAATT-TA-AATAAAT-ATACATGATAAATTTAAAATAATAATACATAATAAATTTAAAAATA
3935888 TTAAT
63 TTAAT
** ** *
3935893 GATAATTTTGAAATAAATATACATGATAAATTTAAAATAATGTTA-ACGATGAATTTAAAATAAT
1 GATAA-TTT-AAATAAATATACATGATAAATTTAAAATAATAATACATAATAAATTT-AAA-AAT
* *
3935957 AATATT
62 ATTAAT
* * * * * * * *
3935963 GATAAATTACAA-ATAATAAAACATGATAAATCTAAAATAATAATATACAATACACTTAGATAAT
1 GATAATTTA-AATA-AAT-ATACATGATAAATTTAAAATAATAATACATAATAAATTTA-AAAAT
3936027 ATTAAT
62 ATTAAT
3936033 GATTAATTTAA
1 GA-TAATTTAA
3936044 TAATAATAAG
Statistics
Matches: 172, Mismatches: 35, Indels: 25
0.74 0.15 0.11
Matches are distributed among these distances:
68 10 0.06
69 89 0.52
70 59 0.34
71 14 0.08
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (67 bp):
GATAATTTAAATAAATATACATGATAAATTTAAAATAATAATACATAATAAATTTAAAAATATTA
AT
Found at i:3936620 original size:19 final size:19
Alignment explanation
Indices: 3936596--3936633 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3936586 TATCAAGGAA
3936596 AAAAAACTAAACCCTCTCT
1 AAAAAACTAAACCCTCTCT
3936615 AAAAAACTAAACCCTCTCT
1 AAAAAACTAAACCCTCTCT
3936634 GCCCTCTGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAAACTAAACCCTCTCT
Found at i:3943888 original size:9 final size:9
Alignment explanation
Indices: 3943870--3943907 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
3943860 ATTAGGTCGG
3943870 TTAACCGAA
1 TTAACCGAA
*
3943879 TTAACTGAA
1 TTAACCGAA
3943888 TTAACCGAA
1 TTAACCGAA
*
3943897 TTACCCGAA
1 TTAACCGAA
3943906 TT
1 TT
3943908 GAATCACTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (9 bp):
TTAACCGAA
Found at i:3943937 original size:17 final size:17
Alignment explanation
Indices: 3943915--3943971 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
3943905 ATTGAATCAC
3943915 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
3943932 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
3943952 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
3943969 TAC
1 TAC
3943972 GTAAGTCTTG
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
17 16 0.55
20 13 0.45
ACGTcount: A:0.49, C:0.16, G:0.04, T:0.32
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:3943953 original size:37 final size:37
Alignment explanation
Indices: 3943906--3943980 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
3943896 ATTACCCGAA
3943906 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
*
3943943 TTGAATCACTACATAATTAAAAACATTACGTAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
3943980 T
1 T
3943981 GAAATTAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:3943994 original size:37 final size:37
Alignment explanation
Indices: 3943906--3943997 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
3943896 ATTACCCGAA
*
3943906 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
* *
3943943 TTGAATCACTACATAATTAAAAACATTACGTAAGTC-
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
3943979 TTGAAATTAAC-ACATAATT
1 TTG-AA-TAACTACATAATT
3943998 GAAATGTAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 3 0.06
37 45 0.88
38 3 0.06
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.33
Consensus pattern (37 bp):
TTGAATAACTACATAATTAAAAACATTACATAAGTCT
Found at i:3944158 original size:41 final size:42
Alignment explanation
Indices: 3944111--3944195 Score: 127
Period size: 41 Copynumber: 2.0 Consensus size: 42
3944101 GACTTAGAGT
* *
3944111 TAGACTTTAGTTTTATTTTTATT-ATTGGGTTGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGATTGGGTTGGCAATTGGG
*
3944152 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTTGGCAATTGGG
1 TAGACTTTAGTTTTAGTTTTATT-GATTGGGTTGGCAATTGGG
3944195 T
1 T
3944196 TGGGTAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
41 22 0.56
43 17 0.44
ACGTcount: A:0.18, C:0.04, G:0.28, T:0.51
Consensus pattern (42 bp):
TAGACTTTAGTTTTAGTTTTATTGATTGGGTTGGCAATTGGG
Found at i:3958238 original size:23 final size:23
Alignment explanation
Indices: 3958212--3958257 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3958202 AGAAAAATCA
3958212 GAAAAACTTATTGATACAAAACT
1 GAAAAACTTATTGATACAAAACT
3958235 GAAAAACTTATTGATACAAAACT
1 GAAAAACTTATTGATACAAAACT
3958258 AAGTACTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.13, G:0.09, T:0.26
Consensus pattern (23 bp):
GAAAAACTTATTGATACAAAACT
Done.