Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 202 of 444
Found at i:56559477 original size:24 final size:24
Alignment explanation
Indices: 56559386--56559475 Score: 144
Period size: 24 Copynumber: 3.8 Consensus size: 24
56559376 GAAATGACTT
*
56559386 TGGCACTATGTGAGCGGACTTGTA
1 TGGCACTATGTGTGCGGACTTGTA
56559410 TGGCACTATGTGTGCGGACTTGTA
1 TGGCACTATGTGTGCGGACTTGTA
* * *
56559434 TGGCACTATGTGTACGGATTTATA
1 TGGCACTATGTGTGCGGACTTGTA
56559458 TGGCACTATGTGTGCGGA
1 TGGCACTATGTGTGCGGA
56559476 TTGGAATGTC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.20, C:0.16, G:0.32, T:0.32
Consensus pattern (24 bp):
TGGCACTATGTGTGCGGACTTGTA
Found at i:56559491 original size:24 final size:23
Alignment explanation
Indices: 56559386--56559492 Score: 115
Period size: 24 Copynumber: 4.5 Consensus size: 23
56559376 GAAATGACTT
* *
56559386 TGGCACTATGTGAGCGGACTTGTA
1 TGGCACTATGTGTGCGGA-TTGAA
*
56559410 TGGCACTATGTGTGCGGACTTGTA
1 TGGCACTATGTGTGCGGA-TTGAA
* *
56559434 TGGCACTATGTGTACGGATTTATA
1 TGGCACTATGTGTGCGGATTGA-A
56559458 TGGCACTATGTGTGCGGATTGGAA
1 TGGCACTATGTGTGCGGATT-GAA
* *
56559482 TGTCAATATGT
1 TGGCACTATGT
56559493 ATGTGAATTA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
23 2 0.03
24 70 0.96
25 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.34
Consensus pattern (23 bp):
TGGCACTATGTGTGCGGATTGAA
Found at i:56564390 original size:33 final size:33
Alignment explanation
Indices: 56564343--56564408 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
56564333 AACATCAGCA
* *
56564343 CACCATACAGTGAAGTCATTCATGCATGTACCT
1 CACCATACAGTGAAGCCATCCATGCATGTACCT
* * *
56564376 CACCATGCATTGAAGCCGTCCATGCATGTACCT
1 CACCATACAGTGAAGCCATCCATGCATGTACCT
56564409 TTGCATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.26
Consensus pattern (33 bp):
CACCATACAGTGAAGCCATCCATGCATGTACCT
Found at i:56566984 original size:14 final size:14
Alignment explanation
Indices: 56566965--56567006 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
56566955 AAGAAGCAAC
56566965 TCATTAAATTAAAT
1 TCATTAAATTAAAT
*
56566979 TCATTAAA-TAAAC
1 TCATTAAATTAAAT
56566992 TCAATT-AATTAAAT
1 TC-ATTAAATTAAAT
56567006 T
1 T
56567007 AAGATGAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (14 bp):
TCATTAAATTAAAT
Found at i:56567416 original size:30 final size:30
Alignment explanation
Indices: 56567378--56567479 Score: 84
Period size: 30 Copynumber: 3.4 Consensus size: 30
56567368 GAGTTTAAAT
56567378 TAAA-ATGAGCTAAGCTTTAGCTCGTGAGC
1 TAAAGATGAGCTAAGCTTTAGCTCGTGAGC
* * * * *
56567407 TAAAGATGAGCTGAGGC-TAAACTCCTAAGC
1 TAAAGATGAGCT-AAGCTTTAGCTCGTGAGC
* * * *
56567437 TGAAGTTGAGCTAAGGTTTAGCTCGTGAGT
1 TAAAGATGAGCTAAGCTTTAGCTCGTGAGC
56567467 TGAAAG-TGAGCTA
1 T-AAAGATGAGCTA
56567480 GGAGTGAGCT
Statistics
Matches: 54, Mismatches: 15, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
29 6 0.11
30 42 0.78
31 6 0.11
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.26
Consensus pattern (30 bp):
TAAAGATGAGCTAAGCTTTAGCTCGTGAGC
Found at i:56567739 original size:28 final size:28
Alignment explanation
Indices: 56567692--56567757 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
56567682 CTTTAAACTT
*
56567692 AGACACATT-AATAACATGTAACTAAGA-A
1 AGACACATTAAATAACATGT-A-TAAAATA
*
56567720 AGACACATTAAAT-ACTTGTATAAAATA
1 AGACACATTAAATAACATGTATAAAATA
56567747 AGACACATTAA
1 AGACACATTAA
56567758 TTCGGATGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 4 0.12
27 13 0.38
28 14 0.41
29 3 0.09
ACGTcount: A:0.53, C:0.14, G:0.09, T:0.24
Consensus pattern (28 bp):
AGACACATTAAATAACATGTATAAAATA
Found at i:56573326 original size:30 final size:30
Alignment explanation
Indices: 56573255--56573337 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
56573245 CTTTTGTTTC
* *
56573255 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
56573286 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
56573315 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
56573338 GCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:56573337 original size:18 final size:18
Alignment explanation
Indices: 56573288--56573343 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
56573278 CACTCTCAAA
* *
56573288 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
56573305 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
56573323 TTTCATTTTCTTTTTGCTT
1 TTTCATTTTCATTTT-CTT
56573342 TT
1 TT
56573344 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.07, C:0.20, G:0.04, T:0.70
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:56573344 original size:12 final size:12
Alignment explanation
Indices: 56573313--56573337 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56573303 TTTTTCAATC
56573313 TCATTTTCTTTT
1 TCATTTTCTTTT
56573325 TCATTTTCTTTT
1 TCATTTTCTTTT
56573337 T
1 T
56573338 GCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:56573433 original size:6 final size:6
Alignment explanation
Indices: 56573419--56573468 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
56573409 TCTCTTTTTA
*
56573419 TTTCAT TTTCTT TTTCTT TTTCTTCT TTTACTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTC-T-T TTT-CTT TTTCTT TTTCTT TTTCTT
56573468 T
1 T
56573469 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 18 0.46
7 5 0.13
8 5 0.13
9 1 0.03
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:56573438 original size:21 final size:21
Alignment explanation
Indices: 56573428--56573468 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
56573418 ATTTCATTTT
56573428 CTTTTTCTTTTTCTTCTTTTA
1 CTTTTTCTTTTTCTTCTTTTA
*
56573449 CTTTTTCTTTTCTTTTCTTT
1 CTTTTTCTTTT-TCTTCTTT
56573469 GTTTTCTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (21 bp):
CTTTTTCTTTTTCTTCTTTTA
Found at i:56573444 original size:15 final size:15
Alignment explanation
Indices: 56573426--56573468 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
56573416 TTATTTCATT
56573426 TTCTTTTTCTTTTTC
1 TTCTTTTTCTTTTTC
*
56573441 TTCTTTTACTTTTTC
1 TTCTTTTTCTTTTTC
*
56573456 TTTTCTTTTCTTT
1 TTCT-TTTTCTTT
56573469 GTTTTCTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (15 bp):
TTCTTTTTCTTTTTC
Found at i:56587265 original size:30 final size:30
Alignment explanation
Indices: 56587180--56587276 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
56587170 TAAACTAAAA
* *
56587180 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
56587210 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
56587240 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
56587269 ATGAGCTA
1 -TGAGCTA
56587277 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:56587602 original size:20 final size:22
Alignment explanation
Indices: 56587579--56587621 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
56587569 TTTTGTTGTC
56587579 TTTCCTCTCTTT-T-TCTCATT
1 TTTCCTCTCTTTCTCTCTCATT
* *
56587599 TTTCTTTTCTTTCTCTCTCATT
1 TTTCCTCTCTTTCTCTCTCATT
56587621 T
1 T
56587622 GATCTACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTCCTCTCTTTCTCTCTCATT
Found at i:56591784 original size:15 final size:16
Alignment explanation
Indices: 56591738--56591786 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
56591728 TAACCCCATA
*
56591738 AAGTGAAAAGAGAAGA
1 AAGTGAAAAGAGAAGT
*
56591754 AAGTCAAAAGCAAGAAGT
1 AAGTGAAAAG--AGAAGT
56591772 AAG-GAAAAGAGAAGT
1 AAGTGAAAAGAGAAGT
56591787 CAAGAGAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 5 0.18
18 8 0.29
ACGTcount: A:0.59, C:0.04, G:0.29, T:0.08
Consensus pattern (16 bp):
AAGTGAAAAGAGAAGT
Found at i:56595848 original size:15 final size:17
Alignment explanation
Indices: 56595820--56595853 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
56595810 TTATTAATTT
56595820 TAAAAGGTTAAAT-ATA
1 TAAAAGGTTAAATAATA
56595836 TAAAAGG-TAAATAATA
1 TAAAAGGTTAAATAATA
56595852 TA
1 TA
56595854 TATGATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (17 bp):
TAAAAGGTTAAATAATA
Found at i:56596806 original size:43 final size:41
Alignment explanation
Indices: 56596746--56596851 Score: 122
Period size: 43 Copynumber: 2.5 Consensus size: 41
56596736 TAGGATTTTG
* * *
56596746 ATATGTGTTCTCATGTAAAACCACGTCTGGGACGTTGGCATC
1 ATATGTGAT-TCATGTAAAACCACGTCTGGGACATCGGCATC
* * *
56596788 GATATGTGATTACGTGTAAGACCATGTCTGGGACATCGGCATC
1 -ATATGTGATT-CATGTAAAACCACGTCTGGGACATCGGCATC
*
56596831 ATATTTGATTCATGTAAAACC
1 ATATGTGATTCATGTAAAACC
56596852 CTATCTTGGA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
41 9 0.17
42 10 0.19
43 34 0.64
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (41 bp):
ATATGTGATTCATGTAAAACCACGTCTGGGACATCGGCATC
Found at i:56596863 original size:41 final size:41
Alignment explanation
Indices: 56596745--56596874 Score: 120
Period size: 43 Copynumber: 3.1 Consensus size: 41
56596735 ATAGGATTTT
* *
56596745 GATATGTGTTCTCATGTAAAACCAC-GTCTGGGACGTTGGCATC
1 GATATGTGAT-TCATGTAAAACC-CTGTCTGGGAC-ATGGCATC
* * *
56596788 GATATGTGATTACGTGTAAGACCATGTCTGGGACATCGGCATC
1 GATATGTGATT-CATGTAAAACCCTGTCTGGGACAT-GGCATC
* * *
56596831 -ATATTTGATTCATGTAAAACCCTATCTTGGACAGTGGCATC
1 GATATGTGATTCATGTAAAACCCTGTCTGGGACA-TGGCATC
56596872 GAT
1 GAT
56596875 TTATCAATAT
Statistics
Matches: 71, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
41 24 0.34
42 14 0.20
43 33 0.46
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (41 bp):
GATATGTGATTCATGTAAAACCCTGTCTGGGACATGGCATC
Found at i:56597667 original size:17 final size:18
Alignment explanation
Indices: 56597645--56597686 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
56597635 CATGTTTACA
56597645 TGGTTGAGTA-AATGA-TG
1 TGGTTGA-TATAATGATTG
*
56597662 TGGTTGATATATTGATTG
1 TGGTTGATATAATGATTG
56597680 TGGTTGA
1 TGGTTGA
56597687 CATATTCGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 2 0.09
17 11 0.50
18 9 0.41
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (18 bp):
TGGTTGATATAATGATTG
Found at i:56601992 original size:12 final size:11
Alignment explanation
Indices: 56601975--56602026 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
56601965 AGTAAGTGAA
56601975 AAAAAAGTTTC
1 AAAAAAGTTTC
56601986 GAAAAAAG-TTC
1 -AAAAAAGTTTC
56601997 AAAAAAAAGTTTC
1 --AAAAAAGTTTC
**
56602010 AAAAAAAATTC
1 AAAAAAGTTTC
56602021 AAAAAA
1 AAAAAA
56602027 AAATTGAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 18 0.51
12 14 0.40
13 3 0.09
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (11 bp):
AAAAAAGTTTC
Found at i:56602005 original size:24 final size:24
Alignment explanation
Indices: 56601973--56602028 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
56601963 CAAGTAAGTG
* *
56601973 AAAAAAAAGTTTCGAAAAAAGTTC
1 AAAAAAAAGTTTCAAAAAAAATTC
56601997 AAAAAAAAGTTTCAAAAAAAATTC
1 AAAAAAAAGTTTCAAAAAAAATTC
56602021 AAAAAAAA
1 AAAAAAAA
56602029 ATTGAAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (24 bp):
AAAAAAAAGTTTCAAAAAAAATTC
Found at i:56602027 original size:12 final size:12
Alignment explanation
Indices: 56601987--56602031 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
56601977 AAAAGTTTCG
*
56601987 AAAAAAGTTCAA
1 AAAAAAATTCAA
*
56601999 AAAAAAGTTTC-A
1 AAAAAA-ATTCAA
56602011 AAAAAAATTCAA
1 AAAAAAATTCAA
56602023 AAAAAAATT
1 AAAAAAATT
56602032 GAAACTAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
11 3 0.10
12 23 0.79
13 3 0.10
ACGTcount: A:0.69, C:0.07, G:0.04, T:0.20
Consensus pattern (12 bp):
AAAAAAATTCAA
Found at i:56610718 original size:27 final size:26
Alignment explanation
Indices: 56610656--56610767 Score: 116
Period size: 27 Copynumber: 4.2 Consensus size: 26
56610646 AGCATGGCTG
* * *
56610656 CCAGAACAGATAATGAGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
56610682 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
* *
56610710 CTAGAACAGATATATGTGGCGGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
56610737 CCAGATCAGACAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
56610764 CCAG
1 CCAG
56610768 GACGTTTCCT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 6 0.08
27 51 0.71
28 15 0.21
ACGTcount: A:0.37, C:0.23, G:0.25, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:56610756 original size:54 final size:54
Alignment explanation
Indices: 56610658--56610764 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
56610648 CATGGCTGCC
* *
56610658 AGAACAGATAATGAGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCACT
1 AGAACAGATAATGAGACAGAGCCACCAGATACAGACAATCGTGGCAGAGCCACT
* * * * *
56610712 AGAACAGATATATGTGGCGGAGCCACCAGAT-CAGACAATTGTGGCATAGCCAC
1 AGAACAGATA-ATGAGACAGAGCCACCAGATACAGACAATCGTGGCAGAGCCAC
56610765 CAGGACGTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
54 29 0.64
55 16 0.36
ACGTcount: A:0.37, C:0.21, G:0.25, T:0.16
Consensus pattern (54 bp):
AGAACAGATAATGAGACAGAGCCACCAGATACAGACAATCGTGGCAGAGCCACT
Found at i:56612904 original size:30 final size:30
Alignment explanation
Indices: 56612870--56612966 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
56612860 TAAACTAAAA
56612870 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
56612900 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
56612930 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
56612960 TGAGCTA
1 TGAGCTA
56612967 GGAGTGACCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:56613663 original size:16 final size:16
Alignment explanation
Indices: 56613638--56613669 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56613628 GCTAAAAAAA
56613638 AAGAAAAGATGAGCAG
1 AAGAAAAGATGAGCAG
*
56613654 AAGAAGAGATGAGCAG
1 AAGAAAAGATGAGCAG
56613670 GGAGTTCGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.34, T:0.06
Consensus pattern (16 bp):
AAGAAAAGATGAGCAG
Found at i:56623229 original size:18 final size:18
Alignment explanation
Indices: 56623206--56623247 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
56623196 GTCCTTTGTA
*
56623206 GGAAAAGTGATTAATTTT
1 GGAAAAATGATTAATTTT
56623224 GGAAAAATGATTAATTTT
1 GGAAAAATGATTAATTTT
56623242 GGAAAA
1 GGAAAA
56623248 CTATTTTCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.33
Consensus pattern (18 bp):
GGAAAAATGATTAATTTT
Found at i:56623872 original size:27 final size:26
Alignment explanation
Indices: 56623835--56623946 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
56623825 TGCATGGCTG
* *
56623835 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
56623861 CCAGATACAGATAATCGTGGTAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
* *
56623889 CCAGAATAGATATATGTGGCGGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
56623916 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
56623943 CCAG
1 CCAG
56623947 GACGCTTCCT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 6 0.08
27 50 0.69
28 16 0.22
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:56623900 original size:54 final size:54
Alignment explanation
Indices: 56623835--56623946 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
56623825 TGCATGGCTG
* *
56623835 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGTAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * * *
56623889 CCAGAATAGATATATGTGGCGGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
56623943 CCAG
1 CCAG
56623947 GACGCTTCCT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
54 33 0.66
55 17 0.34
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:56625150 original size:16 final size:16
Alignment explanation
Indices: 56625125--56625157 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
56625115 CTAAAAGAAA
56625125 AAGAAAAGATGAGCAG
1 AAGAAAAGATGAGCAG
*
56625141 AAGAAGAGATGAGCAG
1 AAGAAAAGATGAGCAG
56625157 A
1 A
56625158 GAATTTGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.06, G:0.33, T:0.06
Consensus pattern (16 bp):
AAGAAAAGATGAGCAG
Found at i:56631232 original size:42 final size:43
Alignment explanation
Indices: 56631152--56631235 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
56631142 AATTCATACA
* **
56631152 ATGCCAACGTCCCAGACATGGTCTTACATGTAGCCACATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCG
*
56631195 ATGCC-ACTGTCCCAGACA-GTTCTTACACGTAAACACATATC
1 ATGCCAAC-GTCCCAGACATGGTCTTACACGTAAACACATATC
56631236 AAAATCACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 21 0.58
43 15 0.42
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATCG
Found at i:56634080 original size:26 final size:27
Alignment explanation
Indices: 56634017--56634088 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 27
56634007 CCCAAATTAA
* *
56634017 TAAAATGACTGTTTTTCCCTTATATGG
1 TAAAATGACTGTTTTGCCCTTACATGG
* *
56634044 TAAAATCACTGTTATGCCC-TACATGG
1 TAAAATGACTGTTTTGCCCTTACATGG
*
56634070 TAAATTGACTGTTTTGCCC
1 TAAAATGACTGTTTTGCCC
56634089 CTATGTGAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 22 0.58
27 16 0.42
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (27 bp):
TAAAATGACTGTTTTGCCCTTACATGG
Found at i:56639854 original size:16 final size:17
Alignment explanation
Indices: 56639818--56639854 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
56639808 CAGCAAATCT
56639818 AGAAATGCCAAAAAGTC
1 AGAAATGCCAAAAAGTC
*
56639835 -GAAATGCCGAAAAG-C
1 AGAAATGCCAAAAAGTC
56639850 AGAAA
1 AGAAA
56639855 GTCCAGCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 1 0.06
16 17 0.94
ACGTcount: A:0.54, C:0.16, G:0.22, T:0.08
Consensus pattern (17 bp):
AGAAATGCCAAAAAGTC
Found at i:56641703 original size:64 final size:64
Alignment explanation
Indices: 56641623--56641806 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
56641613 AGACATTATG
* * * *
56641623 ATGTAGCTAGGTCGCATGGGCGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
56641687 ATGTAGCTAGGTCGCATGTGTGGTTCCAGGTGAAGGATACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
56641752 AA
63 AA
* * *
56641754 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAG-ACAAGAGAGC
56641807 CAAAATTATG
Statistics
Matches: 96, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
62 1 0.01
63 18 0.19
64 24 0.25
66 21 0.22
67 30 0.31
68 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:56643254 original size:28 final size:29
Alignment explanation
Indices: 56643193--56643261 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 29
56643183 TTCAGGCCAG
*
56643193 ATGGGCCATATGAATGTGATTTGGGACTA
1 ATGGGCCATATGAATGAGATTTGGGACTA
* *
56643222 ATGGGCTATATGAATGAGA-TTGGGCCTA
1 ATGGGCCATATGAATGAGATTTGGGACTA
*
56643250 GTGGGCCATATG
1 ATGGGCCATATG
56643262 CATGTATGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
28 18 0.51
29 17 0.49
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.29
Consensus pattern (29 bp):
ATGGGCCATATGAATGAGATTTGGGACTA
Found at i:56645006 original size:12 final size:12
Alignment explanation
Indices: 56644989--56645015 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
56644979 TTGGGATCGG
56644989 TTAGAAGGCGGC
1 TTAGAAGGCGGC
56645001 TTAGAAGGCGGC
1 TTAGAAGGCGGC
56645013 TTA
1 TTA
56645016 AATAACTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (12 bp):
TTAGAAGGCGGC
Found at i:56647802 original size:18 final size:17
Alignment explanation
Indices: 56647774--56647816 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
56647764 CTCTCCCTTA
*
56647774 CTTTTTCCTTTCCTTTTT
1 CTTTTT-CTTTCCTTTCT
*
56647792 CATTTTTCTTTTCTTTCT
1 C-TTTTTCTTTCCTTTCT
56647810 CTTTTTC
1 CTTTTTC
56647817 AATCTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 6 0.27
18 11 0.50
19 5 0.23
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (17 bp):
CTTTTTCTTTCCTTTCT
Found at i:56647827 original size:24 final size:22
Alignment explanation
Indices: 56647775--56647853 Score: 72
Period size: 24 Copynumber: 3.5 Consensus size: 22
56647765 TCTCCCTTAC
* *
56647775 TTTTTCCTTTCCTTTTTCATTT
1 TTTTTTCTTTCCTTTTTCATCT
56647797 TTCTTTTCTTTCTCTTTTTCAATCT
1 TT-TTTTCTTTC-CTTTTTC-ATCT
*
56647822 TTTTTTCTTGTACTTTTTC-T-T
1 TTTTTTCTT-TCCTTTTTCATCT
*
56647843 TGTTTTCTTTC
1 TTTTTTCTTTC
56647854 AATTCAATTG
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
20 1 0.02
21 9 0.19
22 3 0.06
23 8 0.17
24 21 0.44
25 6 0.12
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.72
Consensus pattern (22 bp):
TTTTTTCTTTCCTTTTTCATCT
Found at i:56650421 original size:50 final size:50
Alignment explanation
Indices: 56650302--56650595 Score: 275
Period size: 50 Copynumber: 5.8 Consensus size: 50
56650292 AACCGAAGCT
* * * * *
56650302 ATCTGGTACGCATATTAGCCTGCACTTAGTACTACACATGCGACC-AACA
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACC
* * * * *
56650351 ATCTGGTAGACGTAGTAGCCTGTACTTAGTACTACACAAGTGATCTAGCC
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACC
* * * * **
56650401 ATCTGATACATGTAGTAGCCTGCACTTAGTACTACACATGTGATCGAAGTT
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAA-CC
* *** * * *
56650452 GTCTGGTACGTATAGTAGCCCGCACTTAGTACTACACATGCGACCTAACT
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACC
* * *
56650502 ATCTGGTACACGTAGTAGCCTGCACTTAATACTATACACGTGACCTACAACC
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCT--AACC
*** * *
56650554 ATCTTAAACACCTAGTAGCCTGCACATAGTACTACACATGTG
1 ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTG
56650596 TTCTTACAAT
Statistics
Matches: 195, Mismatches: 46, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
49 37 0.19
50 81 0.42
51 40 0.21
52 37 0.19
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (50 bp):
ATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACATGTGACCTAACC
Found at i:56650506 original size:101 final size:98
Alignment explanation
Indices: 56650317--56650551 Score: 256
Period size: 101 Copynumber: 2.4 Consensus size: 98
56650307 GTACGCATAT
* * *
56650317 TAGCCTGCACTTAGTACTACACATGCGACCAACAATCTGGTAGACGTAGTAGCCTGTACTTAGTA
1 TAGCCTGCACTTAGTACTACACATGTGACCAACAATCTGGTAGAC-TAGTAGCCCGCACTTAGTA
* * * *
56650382 CTACACAAGTGATCTAGCCATCTGATACATGTAG
65 CTACACAAGCGACCTAACCATCTGATACACGTAG
* ***
56650416 TAGCCTGCACTTAGTACTACACATGTGATCGAAGTTGTCTGGTACGTA-TAGTAGCCCGCACTTA
1 TAGCCTGCACTTAGTACTACACATGTGA-CCAA-CAATCTGGTA-G-ACTAGTAGCCCGCACTTA
* * *
56650480 GTACTACACATGCGACCTAACTATCTGGTACACGTAG
62 GTACTACACAAGCGACCTAACCATCTGATACACGTAG
* * * *
56650517 TAGCCTGCACTTAATACTATACACGTGACCTACAA
1 TAGCCTGCACTTAGTACTACACATGTGACCAACAA
56650552 CCATCTTAAA
Statistics
Matches: 110, Mismatches: 22, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
99 27 0.25
100 5 0.05
101 76 0.69
102 1 0.01
103 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (98 bp):
TAGCCTGCACTTAGTACTACACATGTGACCAACAATCTGGTAGACTAGTAGCCCGCACTTAGTAC
TACACAAGCGACCTAACCATCTGATACACGTAG
Found at i:56653625 original size:46 final size:46
Alignment explanation
Indices: 56653558--56653729 Score: 206
Period size: 46 Copynumber: 3.7 Consensus size: 46
56653548 AACCCGCCCC
* *
56653558 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTTTCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTACATCCA
* *
56653604 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C-ATTTACATCCA
* * * *
56653652 TCA-TGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTACATCCA
*
56653697 TAAGTGAACTCGGACTCAACTCAATGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
56653730 ATGCTCAACC
Statistics
Matches: 106, Mismatches: 13, Indels: 14
0.80 0.10 0.11
Matches are distributed among these distances:
43 6 0.06
44 1 0.01
45 2 0.02
46 59 0.56
47 28 0.26
48 3 0.03
49 1 0.01
50 6 0.06
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCATTTACATCCA
Found at i:56653670 original size:93 final size:93
Alignment explanation
Indices: 56653562--56653733 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
56653552 CGCCCCTAAG
* * *
56653562 TGAACTCGGACTCAACTCAACGAGCTCGGGCATTTTCATCCATAAGTGAACTCGGACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGCTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
56653627 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATTTCA
*
56653655 TGAACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 TGAACTCGGACTCAACTCAACGAGCTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
*
56653720 ATGAGTTCGGATGC
66 ACGAGTTCGGATGC
56653734 TCAACCATCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (93 bp):
TGAACTCGGACTCAACTCAACGAGCTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATTTCA
Found at i:56653906 original size:15 final size:15
Alignment explanation
Indices: 56653886--56653933 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
56653876 TCAAAGATGG
56653886 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
56653901 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
56653916 -TTTATGGATATAAA
1 GTTTATGGATATGAA
56653930 GTTT
1 GTTT
56653934 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:56653913 original size:29 final size:29
Alignment explanation
Indices: 56653880--56653939 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
56653870 AAGGATTCAA
* *
56653880 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
56653909 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
56653938 AG
1 AG
56653940 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:56654843 original size:30 final size:30
Alignment explanation
Indices: 56654809--56654905 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
56654799 AGCTCACTCC
56654809 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
56654839 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * * *
56654869 CAGCTCAACTTTAGCTCACAAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
56654899 TAGCTCA
1 TAGCTCA
56654906 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:56657494 original size:5 final size:5
Alignment explanation
Indices: 56657484--56657534 Score: 52
Period size: 5 Copynumber: 10.2 Consensus size: 5
56657474 AAGAGAAAAT
* *
56657484 AAAGA AAAGA AAAGA AAA-A GAAGAA AAAGA AAA-A GAAATA AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAG-A AAAGA AAAGA -AAAGA AAAGA AAAGA
56657534 A
1 A
56657535 GAGGCAAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 4 0.10
5 30 0.77
6 5 0.13
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:56657513 original size:15 final size:16
Alignment explanation
Indices: 56657493--56657536 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
56657483 TAAAGAAAAG
56657493 AAAAGAAAAAGAAGA-
1 AAAAGAAAAAGAAGAT
56657508 AAAAGAAAAAGAA-AT
1 AAAAGAAAAAGAAGAT
56657523 AAAAG-AAAAGAAGA
1 AAAAGAAAAAGAAGA
56657537 GGCAAGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.30
15 19 0.70
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAAGAAGAT
Found at i:56657551 original size:30 final size:30
Alignment explanation
Indices: 56657474--56657551 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 30
56657464 CATTCTTGTA
*
56657474 AAGAGAAAATAAAGA-AAAGAAAAGAAAAAG
1 AAGA-AAAAGAAAGAGAAAGAAAAGAAAAAG
* *
56657504 AAGAAAAAGAAAAAGAAATAAAAG-AAAAG
1 AAGAAAAAGAAAGAGAAAGAAAAGAAAAAG
**
56657533 AAGAGGCAAGAAAGAGAAA
1 AAGA-AAAAGAAAGAGAAA
56657552 ATGAGAATCT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 17 0.43
30 23 0.57
ACGTcount: A:0.74, C:0.01, G:0.22, T:0.03
Consensus pattern (30 bp):
AAGAAAAAGAAAGAGAAAGAAAAGAAAAAG
Found at i:56657599 original size:12 final size:12
Alignment explanation
Indices: 56657591--56657615 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56657581 TTTGAAAAGC
56657591 AAAAAGAAAATG
1 AAAAAGAAAATG
56657603 AAAAAGAAAATG
1 AAAAAGAAAATG
56657615 A
1 A
56657616 GATTGAGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:56659810 original size:30 final size:30
Alignment explanation
Indices: 56659775--56659871 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
56659765 GAGCTCACTC
56659775 TAGCTCATA-TTCAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTCAGCTCACGAGCTAAACCT
* * * * *
56659805 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
* * *
56659835 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTCAGCTCACGAGCTAAACCT
56659865 TAGCTCA
1 TAGCTCA
56659872 TTTTAGTTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 1 0.02
30 51 0.98
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (30 bp):
TAGCTCAACTTCAGCTCACGAGCTAAACCT
Found at i:56661638 original size:14 final size:14
Alignment explanation
Indices: 56661596--56661640 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
56661586 TTAAAGAAGC
56661596 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
56661610 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
56661623 AACTCATTTAATTA
1 AACTCATTAAATTA
56661637 AACT
1 AACT
56661641 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:56664056 original size:14 final size:14
Alignment explanation
Indices: 56664037--56664081 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
56664027 AACTCATCTT
*
56664037 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
56664051 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
56664064 AATTTAATTTAATG
1 AGTTTAATTTAATG
56664078 AGTT
1 AGTT
56664082 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:56665088 original size:29 final size:29
Alignment explanation
Indices: 56665055--56665114 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
56665045 ATAACCAAAC
* *
56665055 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
* *
56665084 CTACATAAACTTCATATCTATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
56665113 CT
1 CT
56665115 TTGAATCCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.32
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:56665416 original size:18 final size:18
Alignment explanation
Indices: 56665393--56665429 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
56665383 AAAATTTGAA
56665393 CATAGTTTTACTTCTTCT
1 CATAGTTTTACTTCTTCT
56665411 CATAGTTTTACTTCTTCT
1 CATAGTTTTACTTCTTCT
56665429 C
1 C
56665430 CATTTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.24, G:0.05, T:0.54
Consensus pattern (18 bp):
CATAGTTTTACTTCTTCT
Found at i:56666471 original size:18 final size:19
Alignment explanation
Indices: 56666422--56666473 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 19
56666412 AGAAATCGAG
*
56666422 AGAA-GTGAAAAAG-AGAA
1 AGAATGTGAAAAAGAAAAA
*
56666439 AGAATGTGAACAAGAAAAA
1 AGAATGTGAAAAAGAAAAA
*
56666458 AGAGTG-GAAAAAGAAA
1 AGAATGTGAAAAAGAAA
56666474 TTGAGATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 4 0.14
18 17 0.59
19 8 0.28
ACGTcount: A:0.63, C:0.02, G:0.27, T:0.08
Consensus pattern (19 bp):
AGAATGTGAAAAAGAAAAA
Found at i:56668244 original size:30 final size:30
Alignment explanation
Indices: 56668210--56668269 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
56668200 ATTTAATACG
56668210 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
56668240 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
56668270 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:56670402 original size:30 final size:30
Alignment explanation
Indices: 56670321--56670403 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
56670311 TAGCTCTCAA
*
56670321 CTCACGAGCTAAACCTTAGCTCAACTTCAG
1 CTCACGAGCTAAAGCTTAGCTCAACTTCAG
* * ** * *
56670351 CTTAGGAG-TTTAGCCTCAGCTCAACTTTAG
1 CTCACGAGCTAAAG-CTTAGCTCAACTTCAG
56670381 CTCACGAGCTAAAGCTTAGCTCA
1 CTCACGAGCTAAAGCTTAGCTCA
56670404 TTTTAGTTTA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 34 0.87
31 3 0.08
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.27
Consensus pattern (30 bp):
CTCACGAGCTAAAGCTTAGCTCAACTTCAG
Found at i:56672929 original size:5 final size:5
Alignment explanation
Indices: 56672919--56672974 Score: 53
Period size: 5 Copynumber: 11.0 Consensus size: 5
56672909 AAGAGAAAAC
* *
56672919 AAAGA AAAGA AAAGAA AAAGC AAAGA AGA-A AAAGA AAACGA AATA-A
1 AAAGA AAAGA AAAG-A AAAGA AAAGA AAAGA AAAGA AAA-GA AA-AGA
56672965 AAAGA AAAGA
1 AAAGA AAAGA
56672975 GAGGCAAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 4 0.10
5 28 0.67
6 9 0.21
7 1 0.02
ACGTcount: A:0.77, C:0.04, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:56672968 original size:25 final size:24
Alignment explanation
Indices: 56672923--56672970 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
56672913 GAAAACAAAG
56672923 AAAAGAAAAGAAAAAGCAAAGAAGA
1 AAAAGAAAAGAAAAA-CAAAGAAGA
56672948 AAAAGAAAACGAAATAA-AAAGAA
1 AAAAGAAAA-GAAA-AACAAAGAA
56672971 AAGAGAGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
25 15 0.71
26 4 0.19
27 2 0.10
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (24 bp):
AAAAGAAAAGAAAAACAAAGAAGA
Found at i:56673054 original size:11 final size:12
Alignment explanation
Indices: 56673022--56673052 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
56673012 TTGAGAGAAC
56673022 TTGAAAAAGCCT
1 TTGAAAAAGCCT
56673034 TTGAAAAAGCCT
1 TTGAAAAAGCCT
56673046 TTGAAAA
1 TTGAAAA
56673053 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:56673063 original size:12 final size:12
Alignment explanation
Indices: 56673055--56673079 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56673045 TTTGAAAAGC
56673055 AAAAAGAAAATG
1 AAAAAGAAAATG
56673067 AAAAAGAAAATG
1 AAAAAGAAAATG
56673079 A
1 A
56673080 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:56673076 original size:18 final size:18
Alignment explanation
Indices: 56673049--56673104 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
56673039 AAAGCCTTTG
56673049 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
56673068 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
56673086 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
56673103 AA
1 AA
56673105 TCTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:56673089 original size:30 final size:31
Alignment explanation
Indices: 56673055--56673136 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
56673045 TTTGAAAAGC
*
56673055 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
56673085 AAAAAGAGAACG-AAAAGAAATCTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
56673115 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
56673137 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.02, G:0.22, T:0.11
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:56675374 original size:30 final size:31
Alignment explanation
Indices: 56675340--56675436 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 31
56675330 AGCTCACTCC
*
56675340 TAGCTC-ACTTTCAACTCACGAGCTAAACCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* * * * *
56675370 TAGCTCAAC-TTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
* *
56675400 CAGCTCAACTTT-AGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTCAGCTCACGAGCTAAACCT
56675430 TAGCTCA
1 TAGCTCA
56675437 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
30 47 0.92
31 4 0.08
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (31 bp):
TAGCTCAACTTTCAGCTCACGAGCTAAACCT
Found at i:56681068 original size:14 final size:14
Alignment explanation
Indices: 56681046--56681093 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
56681036 ACCTAAACCG
* *
56681046 ACCAATTTGTTCAT
1 ACCATTTTGTTCCT
56681060 ACCATTTTGTTCCT
1 ACCATTTTGTTCCT
* *
56681074 ACCCTTTCGTTCCT
1 ACCATTTTGTTCCT
56681088 ACCATT
1 ACCATT
56681094 CCATTCGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.06, T:0.44
Consensus pattern (14 bp):
ACCATTTTGTTCCT
Found at i:56683435 original size:30 final size:30
Alignment explanation
Indices: 56683401--56683460 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
56683391 ATTTAATACG
56683401 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
*** *
56683431 AACTTTTTCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
56683461 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:56684832 original size:43 final size:43
Alignment explanation
Indices: 56684785--56684866 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
56684775 AAGACACGAG
* *
56684785 CGTGTGTCTTAGCCATGTGTGACACACGGCTAGGTGACATGGT
1 CGTGTGTCTCAGCCATGTGTGACACACGGCCAGGTGACATGGT
* *
56684828 CGTGTGTCTCAGCCGTGTGTGACACATGGCCAGGTGACA
1 CGTGTGTCTCAGCCATGTGTGACACACGGCCAGGTGACA
56684867 CGGTTATGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.18, C:0.23, G:0.33, T:0.26
Consensus pattern (43 bp):
CGTGTGTCTCAGCCATGTGTGACACACGGCCAGGTGACATGGT
Found at i:56684877 original size:43 final size:43
Alignment explanation
Indices: 56684787--56684878 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
56684777 GACACGAGCG
* * * *
56684787 TGTGTCTTAGCCATGTGTGACACACGGCTAGGTGACATGGTCG
1 TGTGTCTCAGCCATGTGTGACACACGGCCAGGTGACACGGTCA
* * *
56684830 TGTGTCTCAGCCGTGTGTGACACATGGCCAGGTGACACGGTTA
1 TGTGTCTCAGCCATGTGTGACACACGGCCAGGTGACACGGTCA
56684873 TGTGTC
1 TGTGTC
56684879 CCCTATAGCT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (43 bp):
TGTGTCTCAGCCATGTGTGACACACGGCCAGGTGACACGGTCA
Found at i:56685914 original size:19 final size:20
Alignment explanation
Indices: 56685866--56685919 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
56685856 TAATGAGAGA
*
56685866 AAATGAGTGAAAAATAAAAG
1 AAATGAGAGAAAAATAAAAG
* *
56685886 AAATTTAGAGAAGAA-AAAAG
1 AAA-TGAGAGAAAAATAAAAG
56685906 AAATGAGAGAAAAA
1 AAATGAGAGAAAAA
56685920 GAAATTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 9 0.32
20 11 0.39
21 8 0.29
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (20 bp):
AAATGAGAGAAAAATAAAAG
Found at i:56685918 original size:16 final size:17
Alignment explanation
Indices: 56685881--56685958 Score: 70
Period size: 18 Copynumber: 4.5 Consensus size: 17
56685871 AGTGAAAAAT
56685881 AAAAGAAATTTAGAGAAGAA
1 AAAAGAAA-TT-GA-AAGAA
*
56685901 AAAAGAAA-TGAGAG-A
1 AAAAGAAATTGAAAGAA
56685916 AAAAGAAATTGAAAGAA
1 AAAAGAAATTGAAAGAA
**
56685933 AAAGAGAGCTTGAAAGAA
1 AAA-AGAAATTGAAAGAA
*
56685951 AAGAGAAA
1 AAAAGAAA
56685959 GAAAAAGAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
15 9 0.19
16 7 0.15
17 9 0.19
18 15 0.31
20 8 0.17
ACGTcount: A:0.65, C:0.01, G:0.23, T:0.10
Consensus pattern (17 bp):
AAAAGAAATTGAAAGAA
Found at i:56685920 original size:15 final size:16
Alignment explanation
Indices: 56685881--56685958 Score: 68
Period size: 16 Copynumber: 4.5 Consensus size: 16
56685871 AGTGAAAAAT
56685881 AAAAGAAATTTAGAGAAGAA
1 AAAAGAAA-TT-GA-AAG-A
*
56685901 AAAAGAAA-TGAGAGA
1 AAAAGAAATTGAAAGA
56685916 AAAAGAAATTGAAAGA
1 AAAAGAAATTGAAAGA
*
56685932 AAAAGAGAGCTTGAAAGA
1 AAAAGA-A-ATTGAAAGA
56685950 AAAGAGAAA
1 AAA-AGAAA
56685959 GAAAAAGAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
15 9 0.18
16 14 0.28
17 3 0.06
18 13 0.26
19 3 0.06
20 8 0.16
ACGTcount: A:0.65, C:0.01, G:0.23, T:0.10
Consensus pattern (16 bp):
AAAAGAAATTGAAAGA
Found at i:56687707 original size:13 final size:13
Alignment explanation
Indices: 56687689--56687713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56687679 AGCACATAGG
56687689 CATGTGTCCAAGT
1 CATGTGTCCAAGT
56687702 CATGTGTCCAAG
1 CATGTGTCCAAG
56687714 CCGTGTAGCT
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:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (13 bp):
CATGTGTCCAAGT
Found at i:56691669 original size:24 final size:24
Alignment explanation
Indices: 56691625--56691676 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
56691615 CTCACACCCC
*
56691625 AATCTCTCCCCTATTTCCTCCTAA
1 AATCTCTCCCCTATCTCCTCCTAA
*
56691649 AATCTCTCCCCTTATCT-CTCCTCA
1 AATCTCTCCCC-TATCTCCTCCTAA
56691673 AATC
1 AATC
56691677 CCTCAAACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (24 bp):
AATCTCTCCCCTATCTCCTCCTAA
Found at i:56693801 original size:46 final size:47
Alignment explanation
Indices: 56693640--56694003 Score: 191
Period size: 46 Copynumber: 7.7 Consensus size: 47
56693630 TTTGTGTGCT
* *
56693640 AGTGTAAGA-CATGTCTGGGACATGCATCGGCCAC-ATTATG-AGAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGA-GATGTA-AGCC
* * * * ** * * ** *
56693686 AATGAAAGACCATGTCTAGGACATGGCAACAACATTGAGA-CAAGAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGATGTA-AGCC
*
56693734 AGTGTAAGA-CATGTCTAGGACATGCATCGGCCTCGAGATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATGTAAGCC
* * * *
56693780 AGTGTAAGA-CATGTTTGGGACATGCATTGG-CTATGAGATGT--GTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCCT-CGAGATGTAAGCC
* * *
56693824 AATGTAAGACCATCTCTGGGACATGGCATCGGCAC-GGAGATGTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGC-CTCGAGATGT-A-AGCC
* * * *
56693874 AGTGTAAAACCATGTCTGGGACATGGCCGTCGGCCTC-A-ATTTTGATAGTC
1 AGTGTAAGACCATGTCTGGGACAT-G-CATCGGCCTCGAGA-TGT-A-AGCC
* * * * *
56693924 AGTGTAAGGCCATGTCTAGGATATGACATC-GACTTGATGGATG--AGCC
1 AGTGTAAGACCATGTCTGGGACATG-CATCGGCCTCGA--GATGTAAGCC
56693971 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGC
56694004 ATTACACCCT
Statistics
Matches: 240, Mismatches: 55, Indels: 44
0.71 0.16 0.13
Matches are distributed among these distances:
44 10 0.04
45 14 0.06
46 67 0.28
47 56 0.23
48 24 0.10
49 7 0.03
50 54 0.22
51 7 0.03
52 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATGTAAGCC
Found at i:56697646 original size:40 final size:39
Alignment explanation
Indices: 56697591--56697792 Score: 255
Period size: 39 Copynumber: 5.1 Consensus size: 39
56697581 TGAATGATAC
* * * *
56697591 CCGGGCTAAGCCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTG-TTATAT
*
56697631 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
56697671 CCGGGTTAAGA-CCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAG-TGTTATAT
* *
56697710 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGT-TGTATAC
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTGT-TATAT
* **
56697749 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGT-GTTATAT
56697789 CCGG
1 CCGG
56697793 CTAAATTCCG
Statistics
Matches: 144, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
38 1 0.01
39 70 0.49
40 70 0.49
41 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (39 bp):
CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTGTTATAT
Found at i:56697697 original size:39 final size:40
Alignment explanation
Indices: 56697591--56697792 Score: 275
Period size: 40 Copynumber: 5.1 Consensus size: 40
56697581 TGAATGATAC
* * * *
56697591 CCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATAT
*
56697631 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
56697671 CCGGGTTAAGA-CCGAAGGCATTTGTGCGAGTTGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* *
56697710 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-TATAC
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
* ** *
56697749 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
56697789 CCGG
1 CCGG
56697793 CTAAATTCCG
Statistics
Matches: 145, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
39 70 0.48
40 73 0.50
41 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.27
Consensus pattern (40 bp):
CCGGGTTAAGACCCGAAGGCATTTGTGCGAGTTGTTATAT
Found at i:56697734 original size:79 final size:79
Alignment explanation
Indices: 56697587--56697796 Score: 300
Period size: 79 Copynumber: 2.7 Consensus size: 79
56697577 CAATTGAATG
* * * *
56697587 ATACCCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATATCCGGGTTAAGACCCGAAGGC
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTTG-TTATATCCGGGCTAAGACCCGAAGGC
56697651 ATTTGTGCGAGTTGCT
65 ATTTGTGCGAGTTG-T
* *
56697667 ATATCCGGGTTAAGA-CCGAAGGCATTTGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCA
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTTGTTATATCCGGGCTAAGACCCGAAGGCA
56697731 TTTGTGCGAGTTGT
66 TTTGTGCGAGTTGT
* * *
56697745 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC-GGCTAA
1 ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTTGTTATATCCGGGCTAA
56697797 ATTCCGAAGA
Statistics
Matches: 117, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
78 21 0.18
79 82 0.70
80 14 0.12
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (79 bp):
ATACCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTTGTTATATCCGGGCTAAGACCCGAAGGCA
TTTGTGCGAGTTGT
Found at i:56705745 original size:40 final size:40
Alignment explanation
Indices: 56705690--56705856 Score: 189
Period size: 40 Copynumber: 4.2 Consensus size: 40
56705680 TGAATGATAC
* *
56705690 CCGGGCTAAGCCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCTG-TTATAT
* **
56705730 CCGGGTTAAGACCCGAAGGCATTTGTGAGAGCTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCTGTTATAT
* * *
56705770 CCGGGCTAAGACCCGAAGGCATTTGTGC-AGTTGCTATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCTGTTATAT
* * *
56705809 CCGGGTTAAGACCCGAAGGCAATTGTGCTTG-TGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCT-GTTATAT
56705849 CC-GGCTAA
1 CCGGGCTAA
56705857 ATTCCGAAGA
Statistics
Matches: 108, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
39 40 0.37
40 66 0.61
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGCTGTTATAT
Found at i:56707308 original size:10 final size:10
Alignment explanation
Indices: 56707290--56707323 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
56707280 AACCACATTT
*
56707290 ATACCAAAAC
1 ATACTAAAAC
56707300 ATACTAAAAC
1 ATACTAAAAC
*
56707310 ATACTAAAAT
1 ATACTAAAAC
56707320 ATAC
1 ATAC
56707324 CATATATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.21
Consensus pattern (10 bp):
ATACTAAAAC
Found at i:56707772 original size:70 final size:70
Alignment explanation
Indices: 56707659--56707825 Score: 244
Period size: 70 Copynumber: 2.4 Consensus size: 70
56707649 CAGTGTCAAA
* * * * * *
56707659 TACTCAATGTTTCGCGCATTAATTGCCATCGCATAGCCGAAGCTATTATAATTCTGCACACTAAG
1 TACTCAATGTTTCGCACACTAAGTGCCATCACATAGCCGAAGCTATTAGAATTCCGCACACTAAG
*
56707724 TGTCT
66 TGCCT
**
56707729 TACTCAATGTTTCATACACTAAGTGCCATCACATAGCCGAAGCTATTAGAATTCCGCACACTAAG
1 TACTCAATGTTTCGCACACTAAGTGCCATCACATAGCCGAAGCTATTAGAATTCCGCACACTAAG
56707794 TGCCT
66 TGCCT
*
56707799 TACTCGATGTTTCGCACACTAAGTGCC
1 TACTCAATGTTTCGCACACTAAGTGCC
56707826 TTACTCAATG
Statistics
Matches: 85, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
70 85 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (70 bp):
TACTCAATGTTTCGCACACTAAGTGCCATCACATAGCCGAAGCTATTAGAATTCCGCACACTAAG
TGCCT
Found at i:56707823 original size:28 final size:28
Alignment explanation
Indices: 56707783--56707853 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
56707773 ATTAGAATTC
*
56707783 CGCACACTAAGTGCCTTACTCGATGTTT
1 CGCACACTAAGTGCCTTACTCAATGTTT
56707811 CGCACACTAAGTGCCTTACTCAATGTTT
1 CGCACACTAAGTGCCTTACTCAATGTTT
* *
56707839 CACATACTAAGTGCC
1 CGCACACTAAGTGCC
56707854 ATATATAGTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.25, C:0.30, G:0.15, T:0.30
Consensus pattern (28 bp):
CGCACACTAAGTGCCTTACTCAATGTTT
Found at i:56710711 original size:30 final size:30
Alignment explanation
Indices: 56710677--56710737 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
56710667 TCCTTAACTC
56710677 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
56710707 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
56710737 A
1 A
56710738 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:56714138 original size:46 final size:45
Alignment explanation
Indices: 56714082--56714253 Score: 177
Period size: 46 Copynumber: 3.7 Consensus size: 45
56714072 TGGGCATCCA
*
56714082 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCCG
* *** * *
56714128 AACTCCTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-TCCG
1 AACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAGTCCG
* *
56714175 AGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTCCG
* *
56714221 AGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
56714254 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 63 0.61
47 30 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (45 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGTCCG
Found at i:56714233 original size:93 final size:93
Alignment explanation
Indices: 56714074--56714245 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
56714064 GGGATATTTG
* * * *
56714074 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCCTTGAG
1 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
56714139 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
56714167 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG
1 GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
56714232 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
56714246 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GGCATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:56721439 original size:46 final size:46
Alignment explanation
Indices: 56721386--56721561 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
56721376 TATTTGGGCA
*
56721386 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
56721432 TCCGAACTCCTTGAGTTGAGTCCGAGTTCA---A-GAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G
*
56721477 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
56721525 CCCGAGCTCGTTGATTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
56721562 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
42 3 0.03
43 6 0.05
45 1 0.01
46 64 0.57
47 28 0.25
48 1 0.01
50 6 0.05
51 3 0.03
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:56721544 original size:93 final size:93
Alignment explanation
Indices: 56721382--56721554 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
56721372 GGGATATTTG
*
56721382 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCCTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCCTTGAG
56721447 TTGAGTCCGAGTTCAAGAGATGTAACTA
66 TTGAGTCCGAGTTCAAGAGATGTAACTA
* * * * *
56721475 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAGCTCGTTGAT
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCCTTGAG
56721540 TTGAGTCCGAGTTCA
66 TTGAGTCCGAGTTCA
56721555 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCCTTGAG
TTGAGTCCGAGTTCAAGAGATGTAACTA
Found at i:56725635 original size:24 final size:24
Alignment explanation
Indices: 56725585--56725636 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
56725575 GTGTAATAAC
* **
56725585 AAAAGTCGAAAAGCTGAAAAGTTA
1 AAAAGTCGAAAAGCCGAAAAGCCA
* *
56725609 AAAAGTCGAAAAGCCGGAAGGCCA
1 AAAAGTCGAAAAGCCGAAAAGCCA
56725633 AAAA
1 AAAA
56725637 TTGGGATGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.13, G:0.23, T:0.10
Consensus pattern (24 bp):
AAAAGTCGAAAAGCCGAAAAGCCA
Found at i:56731592 original size:29 final size:29
Alignment explanation
Indices: 56731555--56731614 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
56731545 AAGGATTCAA
* *
56731555 AGATAGGTTTATGGATATGAAGTTTATGT
1 AGATAGGTTTATAGATATAAAGTTTATGT
* *
56731584 AGATGGGTTTATAGATATAAAGTTTTTGT
1 AGATAGGTTTATAGATATAAAGTTTATGT
56731613 AG
1 AG
56731615 GTTTGGTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.27, T:0.42
Consensus pattern (29 bp):
AGATAGGTTTATAGATATAAAGTTTATGT
Found at i:56732634 original size:14 final size:14
Alignment explanation
Indices: 56732592--56732636 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
56732582 TTAAAGAAGC
56732592 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
56732606 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
56732619 AACTCATTTAATTA
1 AACTCATTAAATTA
56732633 AACT
1 AACT
56732637 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:56735938 original size:17 final size:17
Alignment explanation
Indices: 56735911--56735943 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
56735901 TATGTTCAAA
56735911 TTTTCAGATTTTGTTTTT
1 TTTTCAGATTTT-TTTTT
56735929 TTTTCA-ATTTTTTTT
1 TTTTCAGATTTTTTTT
56735944 GAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTCAGATTTTTTTTT
Found at i:56735941 original size:12 final size:12
Alignment explanation
Indices: 56735924--56735970 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
56735914 TCAGATTTTG
56735924 TTTTTTTTTCAA
1 TTTTTTTTTCAA
*
56735936 -TTTTTTTTGAA
1 TTTTTTTTTCAA
**
56735947 TTTTTTTTTTGA
1 TTTTTTTTTCAA
56735959 TTTTTTTTTCAA
1 TTTTTTTTTCAA
56735971 ACTTACTTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTCAA
Found at i:56735962 original size:11 final size:11
Alignment explanation
Indices: 56735919--56735967 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
56735909 AATTTTCAGA
56735919 TTTTG-TTTTT
1 TTTTGATTTTT
* *
56735929 TTTTCAATTTT
1 TTTTGATTTTT
56735940 TTTTGAATTTTTT
1 TTTTG-A-TTTTT
56735953 TTTTGATTTTT
1 TTTTGATTTTT
56735964 TTTT
1 TTTT
56735968 CAAACTTACT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 4 0.12
11 17 0.53
12 2 0.06
13 9 0.28
ACGTcount: A:0.10, C:0.02, G:0.06, T:0.82
Consensus pattern (11 bp):
TTTTGATTTTT
Found at i:56736209 original size:15 final size:15
Alignment explanation
Indices: 56736189--56736236 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
56736179 TCAAAGATAG
56736189 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
56736204 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
56736218 GTTTATGGATATAAA
1 GTTTATGGATATGAA
56736233 GTTT
1 GTTT
56736237 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:56736252 original size:29 final size:29
Alignment explanation
Indices: 56736183--56736242 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
56736173 AAGGATTCAA
* *
56736183 AGATAGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
56736212 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
56736241 AG
1 AG
56736243 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:56738162 original size:30 final size:30
Alignment explanation
Indices: 56738128--56738223 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
56738118 TAAACTAAAA
*
56738128 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTGAAGT
* * * * *
56738158 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTGAAGT
* *
56738188 TGAGCTAAGGTTTAGCTCGTGAGTTGAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCTGAAGT
56738217 TGAGCTA
1 TGAGCTA
56738224 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
29 9 0.18
30 39 0.76
31 3 0.06
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTGAAGT
Found at i:56739161 original size:9 final size:10
Alignment explanation
Indices: 56739154--56739210 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
56739144 AAGAGAAAAC
56739154 AAAGAAAAGA
1 AAAGAAAAGA
56739164 AAAGAAAAAGCA
1 AAAG-AAAAG-A
*
56739176 AAAGAAGA-A
1 AAAGAAAAGA
56739185 AAAGAAAATGA
1 AAAGAAAA-GA
56739196 AATA-AAAAGA
1 AA-AGAAAAGA
56739206 AAAGA
1 AAAGA
56739211 GAGGCAAGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
9 9 0.23
10 9 0.23
11 15 0.38
12 6 0.15
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:56739177 original size:21 final size:20
Alignment explanation
Indices: 56739143--56739210 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 20
56739133 ACATTCTTGT
56739143 AAAGAGAAAA-CAAAGAAAAGA
1 AAAGA-AAAAGCAAA-AAAAGA
*
56739164 AAAGAAAAAGCAAAAGAAGAA
1 AAAGAAAAAGCAAAAAAAG-A
* *
56739185 AAAGAAAATGAAATAAAAAGA
1 AAAGAAAAAGCAA-AAAAAGA
56739206 AAAGA
1 AAAGA
56739211 GAGGCAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 8 0.20
21 27 0.68
22 5 0.12
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAAGAAAAAGCAAAAAAAGA
Found at i:56739178 original size:6 final size:5
Alignment explanation
Indices: 56739154--56739210 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
56739144 AAGAGAAAAC
*
56739154 AAAGA AAAGA AAAGAA AAAGCA AAAGA AGA-A AAAGA AAATGA AATA-A
1 AAAGA AAAGA AAAG-A AAAG-A AAAGA AAAGA AAAGA AAA-GA AA-AGA
56739201 AAAGA AAAGA
1 AAAGA AAAGA
56739211 GAGGCAAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 4 0.09
5 25 0.57
6 14 0.32
7 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAGA
Found at i:56739185 original size:15 final size:14
Alignment explanation
Indices: 56739154--56739210 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
56739144 AAGAGAAAAC
56739154 AAAGAAAAGAAAAGAA
1 AAAGAAAAG--AAGAA
56739170 AAAGCAAAAGAAGAA
1 AAAG-AAAAGAAGAA
*
56739185 AAAGAAAATGAAATAA
1 AAAGAAAA-G-AAGAA
56739201 AAAGAAAAGA
1 AAAGAAAAGA
56739211 GAGGCAAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 5 0.14
15 11 0.30
16 16 0.43
17 5 0.14
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAAAAGAAGAA
Found at i:56739287 original size:12 final size:12
Alignment explanation
Indices: 56739279--56739303 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56739269 TTTGAAAAGC
56739279 AAAAAGAAAATG
1 AAAAAGAAAATG
56739291 AAAAAGAAAATG
1 AAAAAGAAAATG
56739303 A
1 A
56739304 GATTGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:56739300 original size:18 final size:18
Alignment explanation
Indices: 56739273--56739328 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
56739263 AAAGCCTTTG
56739273 AAAAGCAAAAAGAAAATGA
1 AAAAG-AAAAAGAAAATGA
* * *
56739292 AAAAGAAAATGAGATTGA
1 AAAAGAAAAAGAAAATGA
* *
56739310 AAAAGAGAACGAAAA-GA
1 AAAAGAAAAAGAAAATGA
56739327 AA
1 AA
56739329 TTTGAGAGTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 21 0.70
19 5 0.17
ACGTcount: A:0.70, C:0.04, G:0.20, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAATGA
Found at i:56739313 original size:30 final size:31
Alignment explanation
Indices: 56739279--56739360 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 31
56739269 TTTGAAAAGC
*
56739279 AAAAAGAAAATGAAAAAGAAA-ATGAGATTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
* * *
56739309 AAAAAGAGAACG-AAAAGAAATTTGAGAGTG
1 AAAAAGAAAATGAAAAAGAAATATGAGAGTG
*
56739339 AAAAAGAAGATGAAAAAGAAAT
1 AAAAAGAAAATGAAAAAGAAAT
56739361 TGAAACAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 26 0.60
31 9 0.21
ACGTcount: A:0.65, C:0.01, G:0.22, T:0.12
Consensus pattern (31 bp):
AAAAAGAAAATGAAAAAGAAATATGAGAGTG
Found at i:56741350 original size:27 final size:26
Alignment explanation
Indices: 56741313--56741427 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
56741303 AGCATGGCTG
* *
56741313 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
56741339 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
56741367 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
56741394 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
56741421 CCAGAAC
1 CCAGAAC
56741428 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:56741372 original size:54 final size:54
Alignment explanation
Indices: 56741313--56741427 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
56741303 AGCATGGCTG
*
56741313 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
56741367 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
56741421 CCAGAAC
1 CCAGAAC
56741428 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:56743080 original size:26 final size:26
Alignment explanation
Indices: 56743044--56743153 Score: 193
Period size: 26 Copynumber: 4.2 Consensus size: 26
56743034 CATGAAATTC
56743044 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
56743070 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
56743096 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
56743122 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
56743148 TTATCA
1 TTATCA
56743154 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:56748691 original size:26 final size:26
Alignment explanation
Indices: 56748655--56748790 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
56748645 CATGAAATTC
56748655 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
56748681 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
56748707 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
56748733 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
56748759 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
56748785 TTATCA
1 TTATCA
56748791 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:56749223 original size:6 final size:6
Alignment explanation
Indices: 56749212--56749303 Score: 71
Period size: 6 Copynumber: 15.0 Consensus size: 6
56749202 AATCAGGTGA
* * * *
56749212 CAGAAT CAGAAT CAAAAT CAGAAT CAGAAT CAAAAT TAG-CT GACAGAAT
1 CAGAAT CAGAAT CAGAAT CAGAAT CAGAAT CAGAAT CAGAAT --CAGAAT
* * *
56749261 TAGAAT CAGAAT CAGTAT CAGGTAA- CAGAAT CAAAAT CAGAAT
1 CAGAAT CAGAAT CAGAAT CA-G-AAT CAGAAT CAGAAT CAGAAT
56749304 GTGAATGCAA
Statistics
Matches: 66, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
5 3 0.05
6 56 0.85
7 5 0.08
8 2 0.03
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (6 bp):
CAGAAT
Found at i:56749230 original size:25 final size:25
Alignment explanation
Indices: 56749228--56749300 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 25
56749218 CAGAATCAAA
*
56749228 ATCAGAATCAGAATCAAAATTAGCT
1 ATCAGAATCAGAATCAAAATCAGCT
* *
56749253 GA-CAGAATTAGAATCAGAATCAG-T
1 -ATCAGAATCAGAATCAAAATCAGCT
56749277 ATCAGGTAA-CAGAATCAAAATCAG
1 ATCA-G-AATCAGAATCAAAATCAG
56749301 AATGTGAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 1 0.03
24 3 0.08
25 32 0.82
26 3 0.08
ACGTcount: A:0.48, C:0.15, G:0.16, T:0.21
Consensus pattern (25 bp):
ATCAGAATCAGAATCAAAATCAGCT
Found at i:56749289 original size:31 final size:31
Alignment explanation
Indices: 56749227--56749303 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
56749217 TCAGAATCAA
* *
56749227 AATCAGAATCAGAATCAAAATTAGCTGACAG
1 AATCAGAATCAGAATCAAAATCAGCTAACAG
* ** *
56749258 AATTAGAATCAGAATCAGTATCAGGTAACAG
1 AATCAGAATCAGAATCAAAATCAGCTAACAG
*
56749289 AATCAAAATCAGAAT
1 AATCAGAATCAGAAT
56749304 GTGAATGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (31 bp):
AATCAGAATCAGAATCAAAATCAGCTAACAG
Found at i:56749772 original size:27 final size:27
Alignment explanation
Indices: 56749742--56750070 Score: 406
Period size: 27 Copynumber: 12.2 Consensus size: 27
56749732 AACACCCTAG
* * *
56749742 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
*
56749769 GGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
* **
56749796 GAGTAAAATAGTAATTCTGTAAATCGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
* * * *
56749823 GGGTAAAACGATAATTTTTTAAATTGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
*
56749850 GGGTAAAACGGTAATTCTATAAATCGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
* *
56749877 GGGTAAAACAGTAATTCTGTAAATTGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
* *
56749904 GGGTAAAATGGTAATTCTGTAAATTGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
* *
56749931 GTGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
*
56749958 GGGTAAAATGGTAATTCTGTAAATCGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
* ** *
56749985 AGGTAAAATAGTAATTCTATAAATCGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
* *
56750012 TGGTAAAACAGTAATTCTGTAAATCGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
* * *
56750039 GGGTAAAACGATAATTCTATAAATTGA
1 GGGTAAAACGGTAATTCTGTAAATCGA
56750066 GGGTA
1 GGGTA
56750071 CTTTGGTAAT
Statistics
Matches: 262, Mismatches: 40, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 262 1.00
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.30
Consensus pattern (27 bp):
GGGTAAAACGGTAATTCTGTAAATCGA
Found at i:56750108 original size:81 final size:82
Alignment explanation
Indices: 56749742--56750097 Score: 459
Period size: 81 Copynumber: 4.4 Consensus size: 82
56749732 AACACCCTAG
* *
56749742 GGGTAAAATGGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGAGTAAAA-TA
1 GGGTAAAATGGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAACGA
56749806 GTAATTCTGTAAATCGA
66 GTAATTCTGTAAATCGA
* * * * * *
56749823 GGGTAAAACGATAATTTTTTAAATTGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAAC-A
1 GGGTAAAATGGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAACGA
*
56749887 GTAATTCTGTAAATTGA
66 GTAATTCTGTAAATCGA
* * * * *
56749904 GGGTAAAATGGTAATTCTGTAAATTGAGTGTAAAACAGTAATTCTGTAAATCGAGGGTAAAATG-
1 GGGTAAAATGGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAACGA
56749968 GTAATTCTGTAAATCGA
66 GTAATTCTGTAAATCGA
* * * *
56749985 AGGTAAAATAGTAATTCTATAAATCGATGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAACGA
1 GGGTAAAATGGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAACGA
* *
56750050 -TAATTCTATAAATTGA
66 GTAATTCTGTAAATCGA
*** * *
56750066 GGGTACTTTGGTAATTTTACAAGTCGAGGGTA
1 GGGTAAAATGGTAATTTTATAAATCGAGGGTA
56750098 TTTCAGTAAT
Statistics
Matches: 237, Mismatches: 35, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
81 237 1.00
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (82 bp):
GGGTAAAATGGTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCGAGGGTAAAACGA
GTAATTCTGTAAATCGA
Found at i:56756729 original size:2 final size:2
Alignment explanation
Indices: 56756722--56756746 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56756712 GTTTGTCATT
56756722 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 T
56756747 GCCAACAATA
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:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56761411 original size:30 final size:30
Alignment explanation
Indices: 56761340--56761422 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
56761330 CTTTTGTTTC
* *
56761340 AATTTCTTTTTCATCTTCTTTTTCACTCTCA
1 AATTTCTTTTTCTTC-TCTTTTTCAATCTCA
56761371 AATTTC-TTTTCGTTCTCTTTTTCAATCTC-
1 AATTTCTTTTTC-TTCTCTTTTTCAATCTCA
* *
56761400 ATTTTCTTTTTCATTTTCTTTTT
1 AATTTCTTTTTC-TTCTCTTTTT
56761423 TCTTTTCAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
29 5 0.11
30 32 0.71
31 8 0.18
ACGTcount: A:0.13, C:0.22, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTCTTTTTCTTCTCTTTTTCAATCTCA
Found at i:56761422 original size:18 final size:18
Alignment explanation
Indices: 56761373--56761428 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
56761363 CACTCTCAAA
* *
56761373 TTTC-TTTTCGTTCTCTT
1 TTTCATTTTCATTTTCTT
* *
56761390 TTTCAATCTCATTTTCTT
1 TTTCATTTTCATTTTCTT
*
56761408 TTTCATTTTCTTTTTTCTT
1 TTTCATTTTC-ATTTTCTT
56761427 TT
1 TT
56761429 CAAAGGCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 4 0.13
18 17 0.57
19 9 0.30
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTCATTTTCATTTTCTT
Found at i:56761429 original size:12 final size:12
Alignment explanation
Indices: 56761398--56761422 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56761388 TTTTTCAATC
56761398 TCATTTTCTTTT
1 TCATTTTCTTTT
56761410 TCATTTTCTTTT
1 TCATTTTCTTTT
56761422 T
1 T
56761423 TCTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:56761440 original size:12 final size:12
Alignment explanation
Indices: 56761425--56761455 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
56761415 TTCTTTTTTC
56761425 TTTTCAAAGGCT
1 TTTTCAAAGGCT
56761437 TTTTCAAAGGCT
1 TTTTCAAAGGCT
56761449 TTTTCAA
1 TTTTCAA
56761456 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:56761513 original size:5 final size:5
Alignment explanation
Indices: 56761503--56761559 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
56761493 CTCTTGCCTC
*
56761503 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-C-TTT TCTTT
56761550 TCTTT TCTTT
1 TCTTT TCTTT
56761560 GTTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 6 0.14
7 5 0.11
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:56761543 original size:15 final size:14
Alignment explanation
Indices: 56761503--56761559 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 14
56761493 CTCTTGCCTC
*
56761503 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-CT
56761518 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTCT
56761533 TCTTTTGCTTTTTCTTT
1 TCTTTT-CTTTTTC--T
56761550 TCTTTTCTTT
1 TCTTTTCTTT
56761560 GTTTTCTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
14 4 0.11
15 12 0.32
16 14 0.38
17 7 0.19
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (14 bp):
TCTTTTCTTTTTCT
Found at i:56761560 original size:21 final size:21
Alignment explanation
Indices: 56761503--56761570 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
56761493 CTCTTGCCTC
* *
56761503 TCTTTTCTTTT-TATTTCATTT
1 TCTTTTCTTTTCT-TTGCTTTT
*
56761524 TCTTTT-TCTTCTTTTGCTTTT
1 TCTTTTCTTTTC-TTTGCTTTT
56761545 TCTTTTCTTTTCTTTG-TTTT
1 TCTTTTCTTTTCTTTGCTTTT
56761565 CTCTTT
1 -TCTTT
56761571 ACAAGAATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
20 7 0.18
21 27 0.69
22 5 0.13
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (21 bp):
TCTTTTCTTTTCTTTGCTTTT
Found at i:56780563 original size:27 final size:26
Alignment explanation
Indices: 56780487--56780593 Score: 83
Period size: 27 Copynumber: 3.9 Consensus size: 26
56780477 GGAGGAAGCA
*
56780487 TTCTGGTTGCTCTGCCAGAAATATCTG-
1 TTCTGG-TGCTCTGCCA-CAATATCTGT
** * *
56780514 AACTAGTGGCTCTACCACAAATATCTGT
1 TTCTGGT-GCTCTGCCAC-AATATCTGT
56780542 TTCTGGTAGCTCTGCCACAATATCTGT
1 TTCTGGT-GCTCTGCCACAATATCTGT
*
56780569 ATT-TGGTGACTCTGTCACAATATCT
1 -TTCTGGTG-CTCTGCCACAATATCT
56780594 ATTCTGGCAG
Statistics
Matches: 64, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
26 2 0.03
27 47 0.73
28 15 0.23
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (26 bp):
TTCTGGTGCTCTGCCACAATATCTGT
Done.