Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008645.1 Hibiscus syriacus cultivar Beakdansim tig00111621_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4138222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 22
Found at i:3770475 original size:32 final size:31
Alignment explanation
Indices: 3770427--3770515 Score: 90
Period size: 32 Copynumber: 2.8 Consensus size: 31
3770417 TCGCTTGAAG
* *
3770427 AAAGAAGAAATGAAAAAAAAAGAAAAAAATAAT
1 AAAGAA-AAATGAAAAAAAAA-AAAAAAAGAAA
* *
3770460 AATGAAAAATGAAAAAATAAAAAAAGAAGAAA
1 AAAGAAAAATGAAAAAA-AAAAAAAAAAGAAA
* *
3770492 AAAGAAAAA-GAAAAAGAAATAAAA
1 AAAGAAAAATGAAAAAAAAAAAAAA
3770516 GGAGGGTTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
30 6 0.13
31 6 0.13
32 27 0.57
33 8 0.17
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (31 bp):
AAAGAAAAATGAAAAAAAAAAAAAAAAGAAA
Found at i:3770499 original size:6 final size:6
Alignment explanation
Indices: 3770439--3770510 Score: 51
Period size: 6 Copynumber: 11.3 Consensus size: 6
3770429 AGAAGAAATG
*
3770439 AAAA-A AAAAGA AAAAAA TAATAATGA AAAATGA AAAA-A TAAAA-A AAGAAGAA
1 AAAAGA AAAAGA AAAAGA -AA-AA-GA AAAA-GA AAAAGA -AAAAGA AA-AAG-A
3770491 AAAAGA AAAAGA AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AA
3770511 TAAAAGGAGG
Statistics
Matches: 57, Mismatches: 2, Indels: 15
0.77 0.03 0.20
Matches are distributed among these distances:
5 7 0.12
6 28 0.49
7 14 0.25
8 7 0.12
9 1 0.02
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (6 bp):
AAAAGA
Found at i:3770515 original size:15 final size:14
Alignment explanation
Indices: 3770424--3770516 Score: 55
Period size: 15 Copynumber: 6.2 Consensus size: 14
3770414 ATTTCGCTTG
3770424 AAGAAAGAAGAAATGAA
1 AAGAAA-AAGAAA--AA
3770441 AA-AAAAAGAAAAA
1 AAGAAAAAGAAAAA
* *
3770454 AATAATAATG-AAAA
1 AAGAA-AAAGAAAAA
* *
3770468 ATGAAAAAATAAAAA
1 AAG-AAAAAGAAAAA
*
3770483 AAGAAGAAAAAAGAAA
1 AAGAA-AAAGAA-AAA
3770499 AAGAAAAAGAAATAA
1 AAGAAAAAGAAA-AA
3770514 AAG
1 AAG
3770517 GAGGGTTCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
13 4 0.07
14 12 0.20
15 32 0.52
16 11 0.18
17 2 0.03
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (14 bp):
AAGAAAAAGAAAAA
Found at i:3770562 original size:45 final size:45
Alignment explanation
Indices: 3770513--3770600 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
3770503 AAAAGAAATA
*
3770513 AAAGGAGGGT-TCAAGATGGAAACCCGAAAAGGGC-GTCTTGAAACC
1 AAAGGA-GGTCTCAAGATGAAAACCCGAAAAGGGCAG-CTTGAAACC
* * *
3770558 AAAGGAGGTCTCAAGTTGAAAACCTGTAAAGGGCAGCTTGAAA
1 AAAGGAGGTCTCAAGATGAAAACCCGAAAAGGGCAGCTTGAAA
3770601 TTTAAATTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 3 0.08
45 33 0.89
46 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.30, T:0.16
Consensus pattern (45 bp):
AAAGGAGGTCTCAAGATGAAAACCCGAAAAGGGCAGCTTGAAACC
Found at i:3771873 original size:36 final size:37
Alignment explanation
Indices: 3771784--3771893 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
3771774 TCAAAACAGG
* * *
3771784 TCAATCTTAAGCCTTCATGAAAGAGCAGTGAAGCAAT
1 TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
* *
3771821 TCAAACTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
3771858 TC-ATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
3771894 CTCGTTTGTT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
36 32 0.48
37 34 0.52
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
Found at i:3771979 original size:55 final size:55
Alignment explanation
Indices: 3771896--3772539 Score: 735
Period size: 55 Copynumber: 11.9 Consensus size: 55
3771886 GAAGCAAACT
*
3771896 CGTTTGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * *
3771947 AGTTCGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCAGACT
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
** *
3772002 CGTTTCATGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
3772057 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGAAATAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
3772112 CGTTT-TATGAAGATTGCTCGAGTTCTATACTCTCTGAAAGAATAGGGAGCGAACA
1 CGTTTGT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* *
3772167 CGTTTGTTAAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
3772218 AGTTCGTTGAAGA---TT-GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
3772269 AGTTCGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACA
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * *
3772324 CGTTT-TATGAAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGCGGACC
1 CGTTTGT-TGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * * *
3772379 CGTTTATTGAAGATTTTTCGAGTTCTATACTCTTTGAAGGAATAGAGAGCGGACC
1 CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
* * * ** **
3772434 CGTTTTATTGAAGATTGTTCAAG-TCTTATACTCCCTGACTGAATAGGGAGAAGACA
1 CG-TTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGGGAGCGGACA
** * * * *
3772490 CGTTTGCCGAATATTGTTTGAG-TCTTATACTCCCTGAAAGAATAGGGAGC
1 CGTTTGTTGAAGATTGTTCGAGTTC-TATACTCTCTGAAGGAATAGGGAGC
3772540 AGACCCGCCA
Statistics
Matches: 517, Mismatches: 62, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
51 105 0.20
52 1 0.00
54 6 0.01
55 361 0.70
56 44 0.09
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (55 bp):
CGTTTGTTGAAGATTGTTCGAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACA
Found at i:3785092 original size:21 final size:21
Alignment explanation
Indices: 3785068--3785124 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
3785058 TATTTAAAAA
3785068 AAATATTATCAAATTAGTAGT
1 AAATATTATCAAATTAGTAGT
* * *
3785089 AAATTATTA-AAAATTATTATT
1 AAA-TATTATCAAATTAGTAGT
3785110 AAATCATTATCAAAT
1 AAAT-ATTATCAAAT
3785125 CTTATAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
20 1 0.03
21 19 0.66
22 9 0.31
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (21 bp):
AAATATTATCAAATTAGTAGT
Found at i:3785328 original size:20 final size:20
Alignment explanation
Indices: 3785261--3785334 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
3785251 AAATCATTAG
*
3785261 ATTAATAATAATTATTAAA-A
1 ATTATTAATAA-TATTAAATA
*
3785281 CATTATTGATAATATT-AATA
1 -ATTATTAATAATATTAAATA
*
3785301 ATTAATTAATCATATTAAATA
1 ATT-ATTAATAATATTAAATA
*
3785322 ATTATTAGTAATA
1 ATTATTAATAATA
3785335 ATTCTCTATG
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
19 5 0.11
20 23 0.52
21 16 0.36
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (20 bp):
ATTATTAATAATATTAAATA
Found at i:3785468 original size:16 final size:18
Alignment explanation
Indices: 3785446--3785488 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
3785436 TTCGACTATT
*
3785446 TATAAATAAT-AATAAGA
1 TATAAATAATAAATAAAA
3785463 TA-AAAT-ATAAATAAAA
1 TATAAATAATAAATAAAA
3785479 TATAAATAAT
1 TATAAATAAT
3785489 TCAATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 2 0.09
16 12 0.55
17 6 0.27
18 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
TATAAATAATAAATAAAA
Found at i:3785476 original size:11 final size:11
Alignment explanation
Indices: 3785446--3785487 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
3785436 TTCGACTATT
3785446 TATAAATAATAA
1 TATAAATAA-AA
*
3785458 TA-AGATAAAA
1 TATAAATAAAA
3785468 TATAAATAAAA
1 TATAAATAAAA
3785479 TATAAATAA
1 TATAAATAA
3785488 TTCAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 4 0.15
11 21 0.78
12 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (11 bp):
TATAAATAAAA
Found at i:3786704 original size:29 final size:28
Alignment explanation
Indices: 3786662--3786746 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 28
3786652 AGGGACGAGA
3786662 TCGCACTGTCTCCATGGCGACCTACAAGG
1 TCGCAC-GTCTCCATGGCGACCTACAAGG
* *
3786691 TCGCACGATCTCCATGGCGGCCTATAAGG
1 TCGCACG-TCTCCATGGCGACCTACAAGG
* **
3786720 TCGCACGGCATATATGGCGACCTACAA
1 TCGCACGTC-TCCATGGCGACCTACAA
3786747 ATAATCTGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 2 0.04
29 45 0.96
ACGTcount: A:0.24, C:0.32, G:0.25, T:0.20
Consensus pattern (28 bp):
TCGCACGTCTCCATGGCGACCTACAAGG
Found at i:3790978 original size:21 final size:21
Alignment explanation
Indices: 3790948--3790987 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3790938 GGTAAAATAA
3790948 AAATATATTT-GTACTATTAT
1 AAATATATTTAGTACTATTAT
*
3790968 AAATCATATTTATTACTATT
1 AAAT-ATATTTAGTACTATT
3790988 TGAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 6 0.35
22 7 0.41
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (21 bp):
AAATATATTTAGTACTATTAT
Found at i:3811756 original size:2 final size:2
Alignment explanation
Indices: 3811751--3811783 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3811741 GAATAAGTAA
*
3811751 AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3811784 CTCAACTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3824079 original size:33 final size:33
Alignment explanation
Indices: 3824012--3824137 Score: 162
Period size: 33 Copynumber: 3.8 Consensus size: 33
3824002 TCCATTTCCA
* ** ***
3824012 TGTTAGAACAACTACCATCATCGGTGTCAACTC
1 TGTTAGAACAACTACCACCATCAATGTTGCCTC
* *
3824045 TGTTGGAACAAATACCACCATCAATGTTGCCTC
1 TGTTAGAACAACTACCACCATCAATGTTGCCTC
*
3824078 TGTTAGAACAACTACCACCATCAATGTTGCCTA
1 TGTTAGAACAACTACCACCATCAATGTTGCCTC
*
3824111 TGTTAGAACAACTACCAGCATCAATGT
1 TGTTAGAACAACTACCACCATCAATGT
3824138 CAGTTCCGTT
Statistics
Matches: 81, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 81 1.00
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (33 bp):
TGTTAGAACAACTACCACCATCAATGTTGCCTC
Found at i:3824676 original size:23 final size:24
Alignment explanation
Indices: 3824641--3824685 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
3824631 GTTTAATGTA
*
3824641 TATTTTATATATTTAA-TATTTTG
1 TATTTAATATATTTAAGTATTTTG
*
3824664 TATTTAATTTATTTAAGTATTT
1 TATTTAATATATTTAAGTATTT
3824686 AAATTATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (24 bp):
TATTTAATATATTTAAGTATTTTG
Found at i:3824685 original size:17 final size:17
Alignment explanation
Indices: 3824663--3824700 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
3824653 TTAATATTTT
*
3824663 GTATTTAATTTATTTAA
1 GTATTTAAATTATTTAA
3824680 GTATTTAAATTATTTAA
1 GTATTTAAATTATTTAA
3824697 -TATT
1 GTATT
3824701 GTATTTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (17 bp):
GTATTTAAATTATTTAA
Found at i:3827584 original size:28 final size:28
Alignment explanation
Indices: 3827553--3827627 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 28
3827543 GGTCGAGGTG
* *
3827553 ACCATATATCAATAAGGTGATATAACTA
1 ACCATATATCAATAAGGCGATATAACAA
3827581 ACCATATATCAATAAGGCGATATAACAA
1 ACCATATATCAATAAGGCGATATAACAA
* *
3827609 ATCATATATCAATCAGGCG
1 ACCATATATCAATAAGGCG
3827628 GCAGTGTCGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.25
Consensus pattern (28 bp):
ACCATATATCAATAAGGCGATATAACAA
Found at i:3828699 original size:24 final size:24
Alignment explanation
Indices: 3828667--3828722 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
3828657 CTATTCTTTC
3828667 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
*
3828691 GCTTCAATTGAGTTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
3828715 GCTTCAAT
1 GCTTCAAT
3828723 CAAACTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:3828984 original size:30 final size:30
Alignment explanation
Indices: 3828948--3829013 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
3828938 AGTGAACCGA
3828948 CGGTTCAAACCGGTTTTACCGATTTTCAGC
1 CGGTTCAAACCGGTTTTACCGATTTTCAGC
** * *
3828978 CGGTTCACCCCGGTTTTCCCGGTTTTCAGC
1 CGGTTCAAACCGGTTTTACCGATTTTCAGC
3829008 CGGTTC
1 CGGTTC
3829014 TTCCGGTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.12, C:0.32, G:0.23, T:0.33
Consensus pattern (30 bp):
CGGTTCAAACCGGTTTTACCGATTTTCAGC
Found at i:3834204 original size:168 final size:169
Alignment explanation
Indices: 3833921--3834227 Score: 429
Period size: 168 Copynumber: 1.8 Consensus size: 169
3833911 GGATTTGTTG
* * * * ** * *
3833921 CTTGAATCGATGTAATCATCGTCGTTAGTCGGAATCAATAAATTGTTGCAATTGTTGCTTGAAGC
1 CTTGAATCGATGGAATCATCATCATTAGTCGGAATCAATAAATTGATGCAATCATCGCTTGAAAC
* *
3833986 ATGGGCGTTCGGTCTTTGGGTGTTCGAGTGGTTGCACACCTTCAAA-TTTTTGGTCGATTGGCAG
66 ATGGGCGTTCGGTCTTTGGGTGTTCGAGTGGTTGCACACCTTCAAATTTTTTGGCCGATTGGCAA
3834050 CGGTTGTGATGGTCGATGGTGCTGAGGGGATTAAAATTA
131 CGGTTGTGATGGTCGATGGTGCTGAGGGGATTAAAATTA
* *
3834089 CTTGAATCGATGGAA-CTATCATCATTAGTCGGAATCAATAAGTTGATGCAATCATCGTTTGAAA
1 CTTGAATCGATGGAATC-ATCATCATTAGTCGGAATCAATAAATTGATGCAATCATCGCTTGAAA
* * ** **
3834153 CATGGGGGTTTGGTCTTTGGGTGTTCGAGTGGTTGTGCACCTTTGAATTTTTTGGCCGATTGGCA
65 CATGGGCGTTCGGTCTTTGGGTGTTCGAGTGGTTGCACACCTTCAAATTTTTTGGCCGATTGGCA
3834218 ACGGTTGTGA
130 ACGGTTGTGA
3834228 CAGTTGGTGG
Statistics
Matches: 119, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
167 1 0.01
168 93 0.78
169 25 0.21
ACGTcount: A:0.22, C:0.14, G:0.29, T:0.35
Consensus pattern (169 bp):
CTTGAATCGATGGAATCATCATCATTAGTCGGAATCAATAAATTGATGCAATCATCGCTTGAAAC
ATGGGCGTTCGGTCTTTGGGTGTTCGAGTGGTTGCACACCTTCAAATTTTTTGGCCGATTGGCAA
CGGTTGTGATGGTCGATGGTGCTGAGGGGATTAAAATTA
Found at i:3842443 original size:94 final size:94
Alignment explanation
Indices: 3842282--3842470 Score: 351
Period size: 94 Copynumber: 2.0 Consensus size: 94
3842272 ATTCCGGATG
* *
3842282 AGATGAAGCAGTGGTGCGGCGGAGAGGGTAGGTTTGGGGGAGAAAACATAGGAAAACAAGAGTAA
1 AGATGAAGCAGCGGTGCGGCGGAGAGGGTAGGTTTGGGGAAGAAAACATAGGAAAACAAGAGTAA
*
3842347 ATTAATATTTTATCCCTAAACTGGGTTTA
66 ATTAATATTTTATCCCTAAACTAGGTTTA
3842376 AGATGAAGCAGCGGTGCGGCGGAGAGGGTAGGTTTGGGGAAGAAAACATAGGAAAACAAGAGTAA
1 AGATGAAGCAGCGGTGCGGCGGAGAGGGTAGGTTTGGGGAAGAAAACATAGGAAAACAAGAGTAA
3842441 ATTAATATTTTATCCCTAAACTAGGTTTA
66 ATTAATATTTTATCCCTAAACTAGGTTTA
3842470 A
1 A
3842471 AAAAGAACCA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.37, C:0.10, G:0.31, T:0.23
Consensus pattern (94 bp):
AGATGAAGCAGCGGTGCGGCGGAGAGGGTAGGTTTGGGGAAGAAAACATAGGAAAACAAGAGTAA
ATTAATATTTTATCCCTAAACTAGGTTTA
Found at i:3844662 original size:18 final size:18
Alignment explanation
Indices: 3844636--3844680 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
3844626 TCACGGAATG
3844636 TAAGATTACCGGC-GAGAA
1 TAAGATTACCGGCTG-GAA
*
3844654 TATGATTACCGGCTGGAA
1 TAAGATTACCGGCTGGAA
3844672 TAAGATTAC
1 TAAGATTAC
3844681 TGTGAATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (18 bp):
TAAGATTACCGGCTGGAA
Found at i:3858475 original size:21 final size:22
Alignment explanation
Indices: 3858432--3858478 Score: 69
Period size: 24 Copynumber: 2.1 Consensus size: 22
3858422 TTTTTTATCC
3858432 TTATTCTATCATTGAATAATAAAT
1 TTATTCTATCATTG-A-AATAAAT
3858456 TTATTCTATCATTG-AATAAAT
1 TTATTCTATCATTGAAATAAAT
3858477 TT
1 TT
3858479 TTTACGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.39
24 14 0.61
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (22 bp):
TTATTCTATCATTGAAATAAAT
Found at i:3858642 original size:36 final size:33
Alignment explanation
Indices: 3858601--3858678 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 33
3858591 CATTAAACCT
* *
3858601 TTTTATATTTTCAATTTTGTAAAAAATATATATAAA
1 TTTTATAATTT-AAATTT-TAAAAAA-ATATATAAA
3858637 TTTTATGAATTTAAATTTTAAAAAAATATATAAA
1 TTTTAT-AATTTAAATTTTAAAAAAATATATAAA
3858671 TTTTATAA
1 TTTTATAA
3858679 AAATATATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
33 2 0.05
34 15 0.38
35 7 0.18
36 11 0.28
37 4 0.10
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (33 bp):
TTTTATAATTTAAATTTTAAAAAAATATATAAA
Found at i:3858672 original size:19 final size:19
Alignment explanation
Indices: 3858620--3858687 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
3858610 TTCAATTTTG
3858620 TAAAAAATATATATAAATTT
1 TAAAAAA-ATATATAAATTT
**
3858640 T--ATGAAT-T-TAAATTT
1 TAAAAAAATATATAAATTT
3858655 TAAAAAAATATATAAATTT
1 TAAAAAAATATATAAATTT
*
3858674 TATAAAAATATATA
1 TAAAAAAATATATA
3858688 TATAAATATT
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
15 8 0.21
16 1 0.03
17 6 0.15
18 3 0.08
19 20 0.51
20 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (19 bp):
TAAAAAAATATATAAATTT
Found at i:3858886 original size:20 final size:20
Alignment explanation
Indices: 3858850--3858887 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3858840 ATCCTATTCC
**
3858850 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
3858870 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
3858888 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:3870097 original size:25 final size:25
Alignment explanation
Indices: 3870048--3870097 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3870038 ATCCTTTTAT
* * *
3870048 CATCTTCCATTATCATTCTTTCAAC
1 CATCTTCCATTACCATTCATACAAC
*
3870073 CATCTTCCATTACCGTTCATACAAC
1 CATCTTCCATTACCATTCATACAAC
3870098 AACATCAAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.02, T:0.38
Consensus pattern (25 bp):
CATCTTCCATTACCATTCATACAAC
Found at i:3875034 original size:54 final size:54
Alignment explanation
Indices: 3874952--3875506 Score: 704
Period size: 54 Copynumber: 10.3 Consensus size: 54
3874942 ATTTGGGGTA
* * * * * *
3874952 CACACATAGTGCCGATACAGTCATTCATAAGCTCAGTATGAATTCAGTGGGTTG
1 CACACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTCTGTGGGTTG
* *
3875006 CACACTTAGTGTCGATACGGTCGTTCATAAACTTATTATGAATT-TCGTGGGTTG
1 CACACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTCT-GTGGGTTG
* * *
3875060 CACACTTAGTGCCAATACGGTCGTTCATAAACTTATTATAAATTCTGTGGGTTG
1 CACACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTCTGTGGGTTG
* * * * *
3875114 AACACTTAGTGCCAATACGGTCGTTCGTAAACTTATTATGAATTCCGTGGGTTG
1 CACACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTCTGTGGGTTG
* * * *
3875168 CACACTTAGTGCTGATACGGTCGTTCGTAAACTTATTATGAATTCAGTGGGTTG
1 CACACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTCTGTGGGTTG
*
3875222 CACACTTAGTGCCAATACGGTCATTCATAAACTTATTATGAATT-TCGTGGGTTG
1 CACACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTCT-GTGGGTTG
* ** * * *
3875276 CACAATTAGTATCGATACGATCATTCATTAACTTATTATGAATTTTGTGGGTTG
1 CACACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTCTGTGGGTTG
* * * *
3875330 CACACTTACTGCCGATATGGTCATTCATAATCTTATTATGAATTCTGTGGGTTT
1 CACACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTCTGTGGGTTG
* ** *
3875384 CA-ACTTAGTGCCGATATGGTTTTTCATAAACTTATTATGAATTTTGTGGGTTG
1 CACACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTCTGTGGGTTG
* * *
3875437 CACAGTTAGTGCCGATATGGTCATTCATAAACTTATTATGAATT-TCGTGGGCTG
1 CACACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTCT-GTGGGTTG
*
3875491 CACACTTAGTGTCGAT
1 CACACTTAGTGCCGAT
3875507 TCAGTAAATG
Statistics
Matches: 443, Mismatches: 52, Indels: 12
0.87 0.10 0.02
Matches are distributed among these distances:
53 48 0.11
54 393 0.89
55 2 0.00
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.36
Consensus pattern (54 bp):
CACACTTAGTGCCGATACGGTCATTCATAAACTTATTATGAATTCTGTGGGTTG
Found at i:3875093 original size:27 final size:27
Alignment explanation
Indices: 3875063--3875148 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
3875053 TGGGTTGCAC
3875063 ACTTAGTGCCAATACGGTCGTTCATAA
1 ACTTAGTGCCAATACGGTCGTTCATAA
* *** * * * * *
3875090 ACTTATTATAAATTCTGTGGGTTGA-AC
1 ACTTAGTGCCAATACGGT-CGTTCATAA
*
3875117 ACTTAGTGCCAATACGGTCGTTCGTAA
1 ACTTAGTGCCAATACGGTCGTTCATAA
3875144 ACTTA
1 ACTTA
3875149 TTATGAATTC
Statistics
Matches: 38, Mismatches: 19, Indels: 4
0.62 0.31 0.07
Matches are distributed among these distances:
26 3 0.08
27 31 0.82
28 4 0.11
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (27 bp):
ACTTAGTGCCAATACGGTCGTTCATAA
Found at i:3875174 original size:27 final size:27
Alignment explanation
Indices: 3875144--3875229 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
3875134 TCGTTCGTAA
*
3875144 ACTTATTATGAATTCCGTGGGTTGCAC
1 ACTTATTATGAATTCAGTGGGTTGCAC
** * * * * *
3875171 ACTTAGTGCTG-ATACGGT-CGTTCGTAA
1 ACTTA-TTATGAATTCAGTGGGTT-GCAC
3875198 ACTTATTATGAATTCAGTGGGTTGCAC
1 ACTTATTATGAATTCAGTGGGTTGCAC
3875225 ACTTA
1 ACTTA
3875230 GTGCCAATAC
Statistics
Matches: 41, Mismatches: 14, Indels: 8
0.65 0.22 0.13
Matches are distributed among these distances:
26 6 0.15
27 29 0.71
28 6 0.15
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (27 bp):
ACTTATTATGAATTCAGTGGGTTGCAC
Found at i:3875953 original size:20 final size:19
Alignment explanation
Indices: 3875928--3875978 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
3875918 TTTTCAGTAA
* *
3875928 TGGTATCGATACCTTCCTCT
1 TGGTATCGATACCCTACT-T
3875948 TGGTATCGATACCCTACTT
1 TGGTATCGATACCCTACTT
*
3875967 TAGTATCGATAC
1 TGGTATCGATAC
3875979 TACTTGCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (19 bp):
TGGTATCGATACCCTACTT
Found at i:3877504 original size:2 final size:2
Alignment explanation
Indices: 3877497--3877525 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3877487 ACAAATAAAC
3877497 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3877526 TAAAAAGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3902242 original size:27 final size:27
Alignment explanation
Indices: 3902210--3902262 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
3902200 TGTTGCTGAA
*
3902210 AATATCAATTCTGTGATGTTGAATATC
1 AATATCAATTCCGTGATGTTGAATATC
3902237 AATATCAATTCCGTGATGTTGAATAT
1 AATATCAATTCCGTGATGTTGAATAT
3902263 TGGCTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (27 bp):
AATATCAATTCCGTGATGTTGAATATC
Found at i:3904041 original size:39 final size:39
Alignment explanation
Indices: 3903965--3904041 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
3903955 ATGATTTTAT
* * *
3903965 CAAAACCATGATTAATAATATCATACACAATAGTCATAA
1 CAAAACCATGATAAACAATATCATACAAAATAGTCATAA
*
3904004 CAAAGCCATGATAAACAATATCATACATAAATA-TCATA
1 CAAAACCATGATAAACAATATCATACA-AAATAGTCATA
3904042 TTGTTTTACA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 29 0.88
40 4 0.12
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (39 bp):
CAAAACCATGATAAACAATATCATACAAAATAGTCATAA
Found at i:3904118 original size:19 final size:18
Alignment explanation
Indices: 3904092--3904127 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3904082 ATTTTTATCA
3904092 TTCAATTTCATATTCATT
1 TTCAATTTCATATTCATT
*
3904110 TTCACATTTCATTTTCAT
1 TTCA-ATTTCATATTCAT
3904128 AATCCGTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.25, C:0.19, G:0.00, T:0.56
Consensus pattern (18 bp):
TTCAATTTCATATTCATT
Found at i:3904120 original size:25 final size:26
Alignment explanation
Indices: 3904071--3904128 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
3904061 AATACAAAAC
*
3904071 TTTCATATCTCATTTTTATCATTCAA
1 TTTCATATCTCATTTTCATCATTCAA
*
3904097 TTTCATAT-TCATTTTCA-CATTTCAT
1 TTTCATATCTCATTTTCATCA-TTCAA
3904122 TTTCATA
1 TTTCATA
3904129 ATCCGTACTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 2 0.07
25 19 0.66
26 8 0.28
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTCATATCTCATTTTCATCATTCAA
Found at i:3905156 original size:172 final size:172
Alignment explanation
Indices: 3904870--3905209 Score: 554
Period size: 172 Copynumber: 2.0 Consensus size: 172
3904860 AATTATTCCG
*
3904870 TTTATACCAATGAAAACTATACTCGAATAAGAATCTAAAAATATAAGACACTCATTCTATTTCAT
1 TTTATACCAATGAAAACTATACTCGAATAAGAATCTAAAAATATAAGACAATCATTCTATTTCAT
* * *
3904935 CTTGTACAATTTATAGTGAATTTTCAAAATTGGCTTATAGAAGTTGTTTTGAGCAGAATCTGTTG
66 CTTGTACAATTTATAGTGAATTTTCAAAATTGACTTACAGAAGTTGTTTTGAGCAGAATCTGCTG
* *
3905000 CCTTATTTTCTGACCTATCCTCAATTAAAACTTCATATTTCA
131 CCCTATTTTCTGACCTATCCTCAATTAAAAATTCATATTTCA
* * * *
3905042 TTTATACCAATGGAAACTATACTCGAATAATAATCTAACAATATAAGACAATCTTTCTATTTCAT
1 TTTATACCAATGAAAACTATACTCGAATAAGAATCTAAAAATATAAGACAATCATTCTATTTCAT
* * *
3905107 CTTGTGCAATTTATAGTGAATTTTCAAATTTGACTTACAGAAGTTGTTTTGAGCAGAATTTGCTG
66 CTTGTACAATTTATAGTGAATTTTCAAAATTGACTTACAGAAGTTGTTTTGAGCAGAATCTGCTG
*
3905172 CCCTGTTTTCTGACCTATCCTCAATTAAAAATTCATAT
131 CCCTATTTTCTGACCTATCCTCAATTAAAAATTCATAT
3905210 CTTTTTTGTA
Statistics
Matches: 154, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
172 154 1.00
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (172 bp):
TTTATACCAATGAAAACTATACTCGAATAAGAATCTAAAAATATAAGACAATCATTCTATTTCAT
CTTGTACAATTTATAGTGAATTTTCAAAATTGACTTACAGAAGTTGTTTTGAGCAGAATCTGCTG
CCCTATTTTCTGACCTATCCTCAATTAAAAATTCATATTTCA
Found at i:3906149 original size:97 final size:97
Alignment explanation
Indices: 3905983--3906175 Score: 350
Period size: 97 Copynumber: 2.0 Consensus size: 97
3905973 AAATTTGCAG
*
3905983 CATCTAATTTCCAGTCCAATACCTAAAAAATTCCATTATTACCACTTAAGTCACTAACTTTCTCA
1 CATCTAATTTCCAGTCCAATACCTAAAAAATTCCATTATTACCACTTAAGTCACTAAATTTCTCA
3906048 ATATTTATCAGTTATTACTCAAACTTTGACAT
66 ATATTTATCAGTTATTACTCAAACTTTGACAT
* *
3906080 CATCTAATTTCCAGTCTAATACCTCAAAAATTCCATTATTACCACTTAAGTCACTAAATTTCTCA
1 CATCTAATTTCCAGTCCAATACCTAAAAAATTCCATTATTACCACTTAAGTCACTAAATTTCTCA
*
3906145 ATATTTATCATTTATTACTCAAACTTTGACA
66 ATATTTATCAGTTATTACTCAAACTTTGACA
3906176 ACTTCCCAAA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 92 1.00
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (97 bp):
CATCTAATTTCCAGTCCAATACCTAAAAAATTCCATTATTACCACTTAAGTCACTAAATTTCTCA
ATATTTATCAGTTATTACTCAAACTTTGACAT
Found at i:3908543 original size:15 final size:15
Alignment explanation
Indices: 3908523--3908552 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3908513 ATTTACAGTT
*
3908523 CTCTTAGCTTTCGTA
1 CTCTTAGCTTCCGTA
3908538 CTCTTAGCTTCCGTA
1 CTCTTAGCTTCCGTA
3908553 TGTCGACGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.30, G:0.13, T:0.43
Consensus pattern (15 bp):
CTCTTAGCTTCCGTA
Found at i:3909218 original size:37 final size:37
Alignment explanation
Indices: 3909165--3909269 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
3909155 CGTTTTCGTC
3909165 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
3909202 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
3909239 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
3909270 CCATAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:3913846 original size:183 final size:183
Alignment explanation
Indices: 3913538--3914074 Score: 934
Period size: 183 Copynumber: 2.9 Consensus size: 183
3913528 ATTAAATCCG
* *
3913538 TAAAGCTGAGCTTTTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAACCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
3913603 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
3913668 TTGTCAGGCTAAAGACTTTGTGATGAGATGAACTCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCTAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
3913721 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
3913786 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGTTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* * *
3913851 TTGTCAAGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCTAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
*
3913904 TAAAGCTGAGTTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** **
3913969 ATAGATTACATTCAAA-TCATGACTTTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
3914033 TTTGTCAGG-TCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCT-AAAGACTTTGTGATGAGATGAACCCTTCAGT
3914075 TAAACCTGAT
Statistics
Matches: 336, Mismatches: 16, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
182 1 0.00
183 335 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCTAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:3915310 original size:72 final size:76
Alignment explanation
Indices: 3915220--3915376 Score: 200
Period size: 72 Copynumber: 2.1 Consensus size: 76
3915210 TATGATTATC
* * * *
3915220 TCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTCGAAAG
1 TCACTCAAGATTTCTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTCGAAAG
*
3915282 AA-TA-TTCATT
65 AAGCATTTCATT
*
3915292 TCACTCAAGA-TTCTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGA
1 TCACTCAAGATTTCTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGAAAGA
3915356 AGGCATTTCATT
66 A-GCATTTCATT
3915368 TCACTCAAG
1 TCACTCAAG
3915377 GCTGTTTTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
71 1 0.01
72 45 0.62
73 11 0.15
75 1 0.01
76 15 0.21
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.39
Consensus pattern (76 bp):
TCACTCAAGATTTCTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGAAAGA
AGCATTTCATT
Found at i:3915450 original size:39 final size:39
Alignment explanation
Indices: 3915407--3915549 Score: 99
Period size: 39 Copynumber: 3.4 Consensus size: 39
3915397 TTTTATCTTG
*
3915407 CTTGAGATAGTTTCCCTCGAAATAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAATAGAAAATTTTGTCTCC
* * * *
3915446 CTTGAGACAGTTTCTCTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTC
1 CTTGAGACAGTTTCCCTCG--AA-A------TAG-AA--AATTTTGTCTC-C
* *
3915498 C-TGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAATAGAAAATTTTGTCTCC
3915536 CTTGAGACAGTTTC
1 CTTGAGACAGTTTC
3915550 TCTTGAAACA
Statistics
Matches: 78, Mismatches: 12, Indels: 28
0.66 0.10 0.24
Matches are distributed among these distances:
38 2 0.03
39 37 0.47
41 4 0.05
42 2 0.03
48 3 0.04
49 4 0.05
51 24 0.31
52 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (39 bp):
CTTGAGACAGTTTCCCTCGAAATAGAAAATTTTGTCTCC
Found at i:3915558 original size:39 final size:39
Alignment explanation
Indices: 3915485--3915559 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
3915475 CCTTGAAATT
* *
3915485 AATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAA
1 AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACAGAA
* *
3915524 AATTTTGTCTC-CCTTGAGACAGTTTCTCTTGAAACA
1 AATTTTGTCTCTCC-TGAGACAGTTTCCCTCGAAACA
3915560 TAAACATTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.06
39 29 0.94
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (39 bp):
AATTTTGTCTCTCCTGAGACAGTTTCCCTCGAAACAGAA
Found at i:3915576 original size:104 final size:104
Alignment explanation
Indices: 3915462--3915780 Score: 518
Period size: 105 Copynumber: 3.1 Consensus size: 104
3915452 ACAGTTTCTC
* *
3915462 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
3915527 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
3915566 TTGAAAACATTTCCCTTGAAATGATTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGA-ATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
*
3915631 TTTTGTCTCCATTGAGACAGTTTCTCTTGAAACATAAACA
65 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
3915671 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
** *
3915733 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
3915772 TTGAAAACA
1 TTGAAAACA
3915781 ATTTAACGAA
Statistics
Matches: 202, Mismatches: 12, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
101 47 0.23
103 1 0.00
104 53 0.26
105 101 0.50
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:3915727 original size:36 final size:36
Alignment explanation
Indices: 3915680--3915755 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
3915670 ATTGAAAACA
* * *
3915680 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
3915716 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
3915752 TTTC
1 TTTC
3915756 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:3916163 original size:105 final size:104
Alignment explanation
Indices: 3915955--3916480 Score: 736
Period size: 105 Copynumber: 5.0 Consensus size: 104
3915945 ATATCGTGAC
* * * * *
3915955 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
3916020 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AA-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
3916061 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
3916126 ATCTCAGAGCTAATTTCAACTTCACAACGAAGGATATTGG
66 AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
3916166 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
*
3916231 ACCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 A-TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
3916271 ACTCCAGACAATGCAAGTTCAACTCCACGACGAAGGGGCCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
* *
3916332 ATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
** * * * * *
3916371 ACTTGAGACAACACAAGTTCAACTTGACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCC
** * *
3916436 GGTTCTAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AATTC-AGAGCCAATTTCAACTTCACAACGAAGGATATTGG
3916477 ACTC
1 ACTC
3916481 GGAACAATGC
Statistics
Matches: 379, Mismatches: 33, Indels: 16
0.89 0.08 0.04
Matches are distributed among these distances:
100 78 0.21
101 3 0.01
102 3 0.01
103 4 0.01
104 4 0.01
105 204 0.54
106 83 0.22
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (104 bp):
ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCA
ATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:3917159 original size:37 final size:37
Alignment explanation
Indices: 3917106--3917210 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
3917096 CGTTTTCGTC
3917106 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
3917143 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
3917180 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
3917211 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:3921542 original size:47 final size:49
Alignment explanation
Indices: 3921460--3921556 Score: 144
Period size: 47 Copynumber: 2.0 Consensus size: 49
3921450 GAGTAGGATT
* *
3921460 GGGTTATTTTGGGTTTCGATTTTATTCGGGGTCTATAGTAAGTCAGGTC
1 GGGTCATTTCGGGTTTCGATTTTATTCGGGGTCTATAGTAAGTCAGGTC
* *
3921509 GGGTCATTTCGGGTTTC-ATTTTATT-TGGGTCTATAGTATGTCAGGTC
1 GGGTCATTTCGGGTTTCGATTTTATTCGGGGTCTATAGTAAGTCAGGTC
3921556 G
1 G
3921557 AGTCGGGATA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 21 0.48
48 8 0.18
49 15 0.34
ACGTcount: A:0.15, C:0.11, G:0.30, T:0.43
Consensus pattern (49 bp):
GGGTCATTTCGGGTTTCGATTTTATTCGGGGTCTATAGTAAGTCAGGTC
Found at i:3921622 original size:31 final size:31
Alignment explanation
Indices: 3921566--3921647 Score: 87
Period size: 31 Copynumber: 2.6 Consensus size: 31
3921556 GAGTCGGGAT
* *
3921566 AATATCAGATCGGTT-TATTTAAGGTCGGGTC
1 AATATCAGATCGATTAT-TTTAAGGTCAGGTC
*
3921597 AA-ATCAGATCGATTGATTTTCAGGTCAGGTC
1 AATATCAGATCGATT-ATTTTAAGGTCAGGTC
* *
3921628 AATATCCGATCAATTATTTT
1 AATATCAGATCGATTATTTT
3921648 TATTTGGGTC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
30 11 0.26
31 21 0.49
32 11 0.26
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (31 bp):
AATATCAGATCGATTATTTTAAGGTCAGGTC
Found at i:3921852 original size:47 final size:48
Alignment explanation
Indices: 3921796--3921887 Score: 123
Period size: 47 Copynumber: 1.9 Consensus size: 48
3921786 TCAAGTTACT
* * * * *
3921796 TTCGTTTCGGGTTGCTTTCGGTTTGG-TTAAATTTGGGTCGGTTTTGA
1 TTCGGTTCGGGTGGCTTTCAGTTTGGCTAAAATTCGGGTCGGTTTTGA
*
3921843 TTCGGTTCGGGTGGCTTTCAGTTTGGCTAAAATTCGGGTGGGTTT
1 TTCGGTTCGGGTGGCTTTCAGTTTGGCTAAAATTCGGGTCGGTTT
3921888 CAGTTCGATT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
47 23 0.61
48 15 0.39
ACGTcount: A:0.10, C:0.12, G:0.34, T:0.45
Consensus pattern (48 bp):
TTCGGTTCGGGTGGCTTTCAGTTTGGCTAAAATTCGGGTCGGTTTTGA
Found at i:3924815 original size:75 final size:75
Alignment explanation
Indices: 3924727--3924875 Score: 235
Period size: 75 Copynumber: 2.0 Consensus size: 75
3924717 TACCCATGGC
* * *
3924727 TCCATTTTGAGAAGCTTGCTGGTCAATTCTATTATCTTCTTGAAGCCAACTATTGGGAAATGAGA
1 TCCATTTTCAGAAGCTTGCCGGTCAATTCTATTATCATCTTGAAGCCAACTATTGGGAAATGAGA
3924792 CACCATTGGG
66 CACCATTGGG
* * * *
3924802 TCCATTTTCAGAAGCTTGCCGGTTAATTCTATTGTCATCTTGAAGCCAACTGTTGGGAAATGATA
1 TCCATTTTCAGAAGCTTGCCGGTCAATTCTATTATCATCTTGAAGCCAACTATTGGGAAATGAGA
3924867 CACCATTGG
66 CACCATTGG
3924876 CAGAAGCTTG
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 67 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (75 bp):
TCCATTTTCAGAAGCTTGCCGGTCAATTCTATTATCATCTTGAAGCCAACTATTGGGAAATGAGA
CACCATTGGG
Found at i:3927112 original size:20 final size:20
Alignment explanation
Indices: 3927083--3927122 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3927073 TTTGAATTAT
* * *
3927083 AGAAAGGAAATATTGTAAAA
1 AGAAAAGAAAGATAGTAAAA
3927103 AGAAAAGAAAGATAGTAAAA
1 AGAAAAGAAAGATAGTAAAA
3927123 TCATCATCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (20 bp):
AGAAAAGAAAGATAGTAAAA
Found at i:3927586 original size:163 final size:164
Alignment explanation
Indices: 3927378--3927699 Score: 434
Period size: 163 Copynumber: 2.0 Consensus size: 164
3927368 TTTAGCGGTG
* * * * *
3927378 TTTTTATACAAACGTATTAATAGGTTCATCTATAGTGGCGTTTTTTCAACAAACGTCGCAACAGA
1 TTTTTATACAAACGTATCAATAGGTTAATCTATAGTGACGTTTTTTCAACAAACGCCGCAACAAA
* * * * *
3927443 GTAGTACTTTAACGGTATTTTTATACAAACGCCG-TATAGGG-TCTTCTATAGTGGCATTTTTTC
66 GTAGTACTTTAACAGTATTTTTATAAAAACACCGCAATAGGGTTCATCTATAGTGGCATTTTTTC
* *
3927506 AACAAATGCCCCAATAGAGTAGTACTTTAACAAC
131 AACAAAGGCCCCAACAGAGTAGTACTTTAACAAC
*
3927540 TTTTTATACAAACGT-TGCAATAAGGTTAATCTATAGTGATGTTTTTTCAACAAACGCCGCAACA
1 TTTTTATACAAACGTAT-CAAT-AGGTTAATCTATAGTGACGTTTTTTCAACAAACGCCGCAACA
* * ** *
3927604 AAGTAGTACTTTAGCAGTGTTTTTATAAAAACATTGCAATAGGGTTCATCTATAGTGGCGTTTTT
64 AAGTAGTACTTTAACAGTATTTTTATAAAAACACCGCAATAGGGTTCATCTATAGTGGCATTTTT
*
3927669 TCAACAAAGGCCGCAACAGAGTAGTACTTTA
129 TCAACAAAGGCCCCAACAGAGTAGTACTTTA
3927700 GTATGTTTGT
Statistics
Matches: 137, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
161 1 0.01
162 18 0.13
163 66 0.48
164 6 0.04
165 46 0.34
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (164 bp):
TTTTTATACAAACGTATCAATAGGTTAATCTATAGTGACGTTTTTTCAACAAACGCCGCAACAAA
GTAGTACTTTAACAGTATTTTTATAAAAACACCGCAATAGGGTTCATCTATAGTGGCATTTTTTC
AACAAAGGCCCCAACAGAGTAGTACTTTAACAAC
Found at i:3927659 original size:83 final size:82
Alignment explanation
Indices: 3927328--3927700 Score: 398
Period size: 82 Copynumber: 4.5 Consensus size: 82
3927318 ATGGTAAGTT
* * * *
3927328 TAGTGGCG-TTTTT-ATACAAAACGCCGCGATAGATTAGTACTTTAGCGGTGTTTTTATACAAAC
1 TAGTGGCGTTTTTTCA-AC-AAACGCCGCAACAGAGTAGTACTTTAGCAGTGTTTTTATACAAAC
3927391 GTATT-AATA-GGTTCATCTA
64 --ATTGAATAGGGTTCATCTA
* * * * **
3927410 TAGTGGCGTTTTTTCAACAAACGTCGCAACAGAGTAGTACTTTAACGGTATTTTTATACAAACGC
1 TAGTGGCGTTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGCAGTGTTTTTATACAAACAT
* * *
3927475 CGTATAGGG-TCTTCTA
66 TGAATAGGGTTCATCTA
* * * * * ** *
3927491 TAGTGGCATTTTTTCAACAAATGCCCCAATAGAGTAGTACTTTAACA-ACTTTTTATACAAACGT
1 TAGTGGCGTTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGCAGTGTTTTTATACAAACAT
* *
3927555 TGCAATAAGGTTAATCTA
66 TG-AATAGGGTTCATCTA
** * *
3927573 TAGTGATGTTTTTTCAACAAACGCCGCAACAAAGTAGTACTTTAGCAGTGTTTTTATAAAAACAT
1 TAGTGGCGTTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGCAGTGTTTTTATACAAACAT
3927638 TGCAATAGGGTTCATCTA
66 TG-AATAGGGTTCATCTA
*
3927656 TAGTGGCGTTTTTTCAACAAAGGCCGCAACAGAGTAGTACTTTAG
1 TAGTGGCGTTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAG
3927701 TATGTTTGTG
Statistics
Matches: 241, Mismatches: 43, Indels: 13
0.81 0.14 0.04
Matches are distributed among these distances:
80 15 0.06
81 55 0.23
82 93 0.39
83 77 0.32
84 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (82 bp):
TAGTGGCGTTTTTTCAACAAACGCCGCAACAGAGTAGTACTTTAGCAGTGTTTTTATACAAACAT
TGAATAGGGTTCATCTA
Found at i:3931473 original size:21 final size:21
Alignment explanation
Indices: 3931447--3931493 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3931437 TGATTTATAA
3931447 TTATGGAGTTCAAGTTGGTTG
1 TTATGGAGTTCAAGTTGGTTG
* * *
3931468 TTATGGATTTTAAGTTTGTTG
1 TTATGGAGTTCAAGTTGGTTG
3931489 TTATG
1 TTATG
3931494 CATGTCAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.02, G:0.28, T:0.51
Consensus pattern (21 bp):
TTATGGAGTTCAAGTTGGTTG
Found at i:3931503 original size:21 final size:21
Alignment explanation
Indices: 3931456--3931505 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3931446 ATTATGGAGT
* * *
3931456 TCAAGTTGGTTGTTATGGATT
1 TCAAGTTTGTTGTTATGCATG
*
3931477 TTAAGTTTGTTGTTATGCATG
1 TCAAGTTTGTTGTTATGCATG
3931498 TCAAGTTT
1 TCAAGTTT
3931506 ATTGGATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.06, G:0.24, T:0.50
Consensus pattern (21 bp):
TCAAGTTTGTTGTTATGCATG
Found at i:3932095 original size:28 final size:30
Alignment explanation
Indices: 3932040--3932098 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
3932030 TTGTTATATT
*
3932040 TTTTTAAAAAATATGAATGTATTTATAATA
1 TTTTTAAAAAATATGAATGTATTAATAATA
* *
3932070 TTTTTAAAAAA-AT-TATTTATTAATAATA
1 TTTTTAAAAAATATGAATGTATTAATAATA
3932098 T
1 T
3932099 AGATGTATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 13 0.50
29 2 0.08
30 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
TTTTTAAAAAATATGAATGTATTAATAATA
Found at i:3932957 original size:225 final size:225
Alignment explanation
Indices: 3932566--3933017 Score: 888
Period size: 225 Copynumber: 2.0 Consensus size: 225
3932556 GGTGCTCGAG
3932566 ATCTTTGGTTGTCTGTCTCCCAATATACAACAATGAGATGATTAGCGCACAGTAGCACAACTGCC
1 ATCTTTGGTTGTCTGTCTCCCAATATACAACAATGAGATGATTAGCGCACAGTAGCACAACTGCC
3932631 GAGATCACGAACTATTCATTGTCTTTGCCTATCATAAAAAACTAGAGAAAAATAATTCCTTTGAA
66 GAGATCACGAACTATTCATTGTCTTTGCCTATCATAAAAAACTAGAGAAAAATAATTCCTTTGAA
3932696 TTGGTTTTTTGAGTTGTTTTGGATTGTGTTTAACCTAGTAGGTTTATGTAACACCCCAACCCGTA
131 TTGGTTTTTTGAGTTGTTTTGGATTGTGTTTAACCTAGTAGGTTTATGTAACACCCCAACCCGTA
3932761 TCCGATCCGGATACGAGTCCGAGATGTCAC
196 TCCGATCCGGATACGAGTCCGAGATGTCAC
3932791 ATCTTTGGTTGTCTGTCTCCCAATATACAACAATGAGATGATTAGCGCACAGTAGCACAACTGCC
1 ATCTTTGGTTGTCTGTCTCCCAATATACAACAATGAGATGATTAGCGCACAGTAGCACAACTGCC
3932856 GAGATCACGAACTATTCATTGTCTTTGCCTATCATAAAAAACTAGAGAAAAATAATTCCTTTGAA
66 GAGATCACGAACTATTCATTGTCTTTGCCTATCATAAAAAACTAGAGAAAAATAATTCCTTTGAA
3932921 TTGG-TTTTTGAGTTGTTTTTGGATTGTGTTTAACCTAGTAGGTTTATGTAACACCCCAACCCGT
131 TTGGTTTTTTGAGTTG-TTTTGGATTGTGTTTAACCTAGTAGGTTTATGTAACACCCCAACCCGT
3932985 ATCCGATCCGGATACGAGTCCGAGATGTCAC
195 ATCCGATCCGGATACGAGTCCGAGATGTCAC
3933016 AT
1 AT
3933018 TGACATTTAA
Statistics
Matches: 226, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
224 11 0.05
225 215 0.95
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (225 bp):
ATCTTTGGTTGTCTGTCTCCCAATATACAACAATGAGATGATTAGCGCACAGTAGCACAACTGCC
GAGATCACGAACTATTCATTGTCTTTGCCTATCATAAAAAACTAGAGAAAAATAATTCCTTTGAA
TTGGTTTTTTGAGTTGTTTTGGATTGTGTTTAACCTAGTAGGTTTATGTAACACCCCAACCCGTA
TCCGATCCGGATACGAGTCCGAGATGTCAC
Found at i:3933174 original size:12 final size:12
Alignment explanation
Indices: 3933156--3933186 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3933146 AAAATACGGT
3933156 ATGAACAGTACC
1 ATGAACAGTACC
*
3933168 GTGAACAGTACC
1 ATGAACAGTACC
3933180 ATGAACA
1 ATGAACA
3933187 ATGAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:3933979 original size:24 final size:24
Alignment explanation
Indices: 3933952--3934017 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
3933942 AGCTCGTATA
3933952 AATTTGCACCGTAGTGCCACGTAG
1 AATTTGCACCGTAGTGCCACGTAG
* * **
3933976 AATTTGCACCGAAGCGCTGCGTAG
1 AATTTGCACCGTAGTGCCACGTAG
* *
3934000 AA-ATGCACTGTAGTGCCA
1 AATTTGCACCGTAGTGCCA
3934018 TTTAAGATTG
Statistics
Matches: 32, Mismatches: 10, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
23 10 0.31
24 22 0.69
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (24 bp):
AATTTGCACCGTAGTGCCACGTAG
Found at i:3937614 original size:17 final size:16
Alignment explanation
Indices: 3937583--3937633 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
3937573 TGTCATGTCC
*
3937583 ATATTTTTTAAAATAT
1 ATATTTTTAAAAATAT
3937599 ATATTTTTAAATAATATT
1 ATATTTTTAAA-AATA-T
* *
3937617 TTATTTTAAAAAATAT
1 ATATTTTTAAAAATAT
3937633 A
1 A
3937634 AATGTGACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 11 0.38
17 8 0.28
18 10 0.34
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTTTTAAAAATAT
Found at i:3938342 original size:96 final size:98
Alignment explanation
Indices: 3938201--3938388 Score: 222
Period size: 96 Copynumber: 1.9 Consensus size: 98
3938191 TTTTCAAAAT
** * * *
3938201 AGAATCATACTTGATTCTCAAGAAAATAAATCCAATCCACCGATTTATTTTATTTTA-CAAATAA
1 AGAATCATACAAGATTCCCAAGAAAATAAATCCAAT----CGATTTATTTCATTTTATAAAATAA
* *
3938265 TGAAAAT-AATTCCAATGCTTTATTTCATCTTACAGACA
62 -GAAAATAAATT-CAACGATTTATTTCATCTTACAGACA
*
3938303 AGAATCATACAAGATTCCCAA-AAAATAAATCCAAT-GATTTATTTCCTTTTATAAAATAAGAAA
1 AGAATCATACAAGATTCCCAAGAAAATAAATCCAATCGATTTATTTCATTTTATAAAATAAGAAA
3938366 ATAAATTCAACGATTTATTTCAT
66 ATAAATTCAACGATTTATTTCAT
3938389 TTTATAAAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
96 34 0.45
97 10 0.13
101 14 0.18
102 18 0.24
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.35
Consensus pattern (98 bp):
AGAATCATACAAGATTCCCAAGAAAATAAATCCAATCGATTTATTTCATTTTATAAAATAAGAAA
ATAAATTCAACGATTTATTTCATCTTACAGACA
Found at i:3938381 original size:39 final size:39
Alignment explanation
Indices: 3938324--3938548 Score: 197
Period size: 39 Copynumber: 5.8 Consensus size: 39
3938314 AGATTCCCAA
* * *
3938324 AAAATAAATCCAATGATTTATTTCCTTTTATAAAATAAG
1 AAAATAAATTCAACGATTTATTTCCTTTTATAAAATAGG
*
3938363 AAAATAAATTCAACGATTTATTTCATTTTATAAAATAGG
1 AAAATAAATTCAACGATTTATTTCCTTTTATAAAATAGG
* * * *
3938402 AAACTAAATCCAACAATTTATTTACTTTT-TACAAACTAGG
1 AAAATAAATTCAACGATTTATTTCCTTTTATA-AAA-TAGG
* * * **
3938442 AAAACAAA-TCTAACGAATTATTTTCTTTTATAAACCAGG
1 AAAATAAATTC-AACGATTTATTTCCTTTTATAAAATAGG
* ** * * *
3938481 AAACTAAATTTTATGATTTATTTGCTTTT-CAAAATAGG
1 AAAATAAATTCAACGATTTATTTCCTTTTATAAAATAGG
* *
3938519 AAAATAAA-TCTAGCAATTTATTTCCTTTTA
1 AAAATAAATTC-AACGATTTATTTCCTTTTA
3938549 CATATCAGAG
Statistics
Matches: 145, Mismatches: 34, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
37 1 0.01
38 28 0.19
39 86 0.59
40 28 0.19
41 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.39
Consensus pattern (39 bp):
AAAATAAATTCAACGATTTATTTCCTTTTATAAAATAGG
Found at i:3938500 original size:79 final size:78
Alignment explanation
Indices: 3938328--3938548 Score: 227
Period size: 79 Copynumber: 2.8 Consensus size: 78
3938318 TCCCAAAAAA
* * *
3938328 TAAATCCAATGATTTATTTCCTTTTATA-AAATAAGAAAATAAAT-TCAACGATTTA-TTTCATT
1 TAAATCCAATGATTTATTTACTTTT-TACAAATAGGAAAATAAATCT-AACGAATTATTTTC-TT
*
3938390 TTATAAAATAGGAAAC
63 TTATAAAACAGGAAAC
** *
3938406 TAAATCCAACAATTTATTTACTTTTTACAAACTAGGAAAACAAATCTAACGAATTATTTTCTTTT
1 TAAATCCAATGATTTATTTACTTTTTACAAA-TAGGAAAATAAATCTAACGAATTATTTTCTTTT
*
3938471 ATAAACCAGGAAAC
65 ATAAAACAGGAAAC
*** * * * *
3938485 TAAATTTTATGATTTATTTGCTTTTCA-AAATAGGAAAATAAATCTAGC-AATTTATTTCCTTTT
1 TAAATCCAATGATTTATTTACTTTTTACAAATAGGAAAATAAATCTAACGAA-TTATTTTCTTTT
3938548 A
65 A
3938549 CATATCAGAG
Statistics
Matches: 120, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
76 2 0.02
77 30 0.25
78 28 0.23
79 55 0.46
80 5 0.04
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (78 bp):
TAAATCCAATGATTTATTTACTTTTTACAAATAGGAAAATAAATCTAACGAATTATTTTCTTTTA
TAAAACAGGAAAC
Found at i:3938669 original size:97 final size:96
Alignment explanation
Indices: 3938477--3938707 Score: 241
Period size: 97 Copynumber: 2.4 Consensus size: 96
3938467 TTTTATAAAC
* ** * *
3938477 CAGGAAACTAAATTTTATGATTTATTTGC-TTTTCAAAATAGGAAAATAAATCTAGCAATTTATT
1 CAGGAAAATAAATTCAACGATTTATTTTCTTTTTCAAAATAGGAAAATAAATCTAG-AATTTATT
3938541 TCCTTTTACATATCAGAGTCATACAAGATTCT
65 TCCTTTTACATATCAGAGTCATACAAGATTCT
* * * * *
3938573 TAGGAGAATAAATTTACCGATTTATTTTCTTTTTCAAAATAGGAAAATAATTTCTA-AGATTTAT
1 CAGGAAAATAAATTCAACGATTTATTTTCTTTTTCAAAATAGGAAAATAA-ATCTAGA-ATTTAT
* * * *** *
3938637 TTTCTTTTACATATTAGTGTCATGTGATATTCT
64 TTCCTTTTACATATCAGAGTCATACAAGATTCT
* * *
3938670 CGGGAAAATAAATTCAACAATTTATTTTCTTTTACAAA
1 CAGGAAAATAAATTCAACGATTTATTTTCTTTTTCAAA
3938708 TACAATTATA
Statistics
Matches: 110, Mismatches: 22, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
96 23 0.21
97 83 0.75
98 4 0.04
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.42
Consensus pattern (96 bp):
CAGGAAAATAAATTCAACGATTTATTTTCTTTTTCAAAATAGGAAAATAAATCTAGAATTTATTT
CCTTTTACATATCAGAGTCATACAAGATTCT
Found at i:3938816 original size:58 final size:55
Alignment explanation
Indices: 3938751--3939082 Score: 231
Period size: 58 Copynumber: 5.7 Consensus size: 55
3938741 ATTTCTTTAT
*
3938751 TTAAGATTCCCAAGAAAATAAAGTT-AACAATTTATTTCCTTTAACAAAATAAAATCA
1 TTAAGATTCTCAA-AAAATAAA-TTCAACAATTTATTTCCTTTAA-AAAATAAAATCA
* * * * * * *
3938808 CTTAAGATTTTCAAGAAAACAAATTTAATAATTTATTAACTTTTATAAAATAAAATCA
1 -TTAAGATTCTCAA-AAAATAAATTCAACAATTTATT-TCCTTTAAAAAATAAAATCA
* * * ** **
3938866 TTTAAGATTATCAATAAATGAAATTGAACAATTTATTTATTTTTAAAGGATAAAATCA
1 -TTAAGATTCTCAAAAAAT-AAATTCAACAATTTATTT-CCTTTAAAAAATAAAATCA
* * * **
3938924 TCCACTG-TTCTCAAAAAATTAAATTCAACAATTTATTT-TTCTTACAAAGTTAAAATCA
1 T-TA-AGATTCTCAAAAAA-TAAATTCAACAATTTATTTCCT-TTA-AAAAATAAAATCA
* * *
3938982 TTCAAGATT-TCCAAGAAAATAAATTCAACAATTTATTTTCTTTAGAAAATTAGAATCA
1 TT-AAGATTCT-CAA-AAAATAAATTCAACAATTTATTTCCTTTA-AAAAATAAAATCA
*
3939040 TTTAAGATTCTCAAAGAAATAAATTCAACAATCTATTTTCCTT
1 -TTAAGATTCTCAAA-AAATAAATTCAACAATTTA-TTTCCTT
3939083 ACAAATTTAG
Statistics
Matches: 223, Mismatches: 33, Indels: 35
0.77 0.11 0.12
Matches are distributed among these distances:
56 2 0.01
57 12 0.05
58 188 0.84
59 21 0.09
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.37
Consensus pattern (55 bp):
TTAAGATTCTCAAAAAATAAATTCAACAATTTATTTCCTTTAAAAAATAAAATCA
Found at i:3939039 original size:116 final size:116
Alignment explanation
Indices: 3938858--3939107 Score: 269
Period size: 116 Copynumber: 2.1 Consensus size: 116
3938848 TTTTATAAAA
* * * * *
3938858 TAAAATCATTTAAGATTATCAATAAATGAAATTGAACAATTTATTTATTTTTAAAGGATAAAATC
1 TAAAATCATTCAAGATTATCAAAAAATGAAATTCAACAATTTATTTATCTTTAAAGAATAAAATC
* * *
3938923 ATCCACTG-TTCTCAAA-AAATTAAATTCAACAATTTATTTTTCTTACAAAGT
66 ATCCA-AGATTCTCAAAGAAA-TAAATTCAACAATCTATTTTCCTTACAAAGT
*
3938974 TAAAATCATTCAAGATT-TCCAAGAAAAT-AAATTCAACAATTTATTT-TCTTTAGAA-AATTAG
1 TAAAATCATTCAAGATTAT-CAA-AAAATGAAATTCAACAATTTATTTATCTTTA-AAGAA-TAA
** *
3939035 AATCATTTAAGATTCTCAAAGAAATAAATTCAACAATCTATTTTCCTTACAAATT
62 AATCATCCAAGATTCTCAAAGAAATAAATTCAACAATCTATTTTCCTTACAAAGT
* *
3939090 TAGAATCAATGCAAGATT
1 TAAAATC-ATTCAAGATT
3939108 CTAACAATGA
Statistics
Matches: 113, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
115 8 0.07
116 89 0.79
117 16 0.14
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.37
Consensus pattern (116 bp):
TAAAATCATTCAAGATTATCAAAAAATGAAATTCAACAATTTATTTATCTTTAAAGAATAAAATC
ATCCAAGATTCTCAAAGAAATAAATTCAACAATCTATTTTCCTTACAAAGT
Found at i:3939093 original size:58 final size:58
Alignment explanation
Indices: 3938931--3939124 Score: 230
Period size: 58 Copynumber: 3.3 Consensus size: 58
3938921 TCATCCACTG
* * *
3938931 TTCTCAAA-AAATTAAATTCAACAATTTATTTTTCTTACAAAGTTAAAATCATTCAAGA
1 TTCTCAAAGAAA-TAAATTCAACAATTTATTTTCCTTACAAAATTAGAATCATTCAAGA
* * * *
3938989 TT-TCCAAGAAAATAAATTCAACAATTTATTTTCTTTAGAAAATTAGAATCATTTAAGA
1 TTCTCAAAG-AAATAAATTCAACAATTTATTTTCCTTACAAAATTAGAATCATTCAAGA
* * *
3939047 TTCTCAAAGAAATAAATTCAACAATCTATTTTCCTTACAAATTTAGAATCAATGCAAGA
1 TTCTCAAAGAAATAAATTCAACAATTTATTTTCCTTACAAAATTAGAATC-ATTCAAGA
*
3939106 TTCTAACAATGAAATAAAT
1 TTCT--CAAAGAAATAAAT
3939125 CTAGTAATTT
Statistics
Matches: 115, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
57 4 0.03
58 81 0.70
59 18 0.16
61 12 0.10
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (58 bp):
TTCTCAAAGAAATAAATTCAACAATTTATTTTCCTTACAAAATTAGAATCATTCAAGA
Found at i:3939300 original size:45 final size:45
Alignment explanation
Indices: 3939236--3939355 Score: 136
Period size: 45 Copynumber: 2.7 Consensus size: 45
3939226 TGAATTTATC
*
3939236 TTTTAATTTT-ACCTATCCAATAATCAAAAGGAACTAATCATATAA
1 TTTTAATTTTGA-CAATCCAATAATCAAAAGGAACTAATCATATAA
* * * * *
3939281 TTTTAATTTTCGA-AATCCAATAATCTAAAGGAACTGATCTTTTGA
1 TTTTAATTTT-GACAATCCAATAATCAAAAGGAACTAATCATATAA
* *
3939326 TTTTACTTTTGACAAACCAATAATCAAAAG
1 TTTTAATTTTGACAATCCAATAATCAAAAG
3939356 CCTTGGATTA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
44 2 0.03
45 60 0.95
47 1 0.02
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (45 bp):
TTTTAATTTTGACAATCCAATAATCAAAAGGAACTAATCATATAA
Found at i:3939573 original size:14 final size:14
Alignment explanation
Indices: 3939554--3939585 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3939544 TTTATATGGT
3939554 AATAATATCATAAC
1 AATAATATCATAAC
*
3939568 AATAATATCATGAC
1 AATAATATCATAAC
3939582 AATA
1 AATA
3939586 TCATGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.28
Consensus pattern (14 bp):
AATAATATCATAAC
Found at i:3940814 original size:21 final size:21
Alignment explanation
Indices: 3940785--3940824 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3940775 ACATTTTTTG
*
3940785 AAAAGATATGCTC-TATTTGAA
1 AAAAAATAT-CTCATATTTGAA
3940806 AAAAAATATCTCATATTTG
1 AAAAAATATCTCATATTTG
3940825 GGTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (21 bp):
AAAAAATATCTCATATTTGAA
Found at i:3941681 original size:20 final size:23
Alignment explanation
Indices: 3941628--3941682 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 23
3941618 AAGAAAAAAC
3941628 ATGTCACAAAGACAAAGATAAAT
1 ATGTCACAAAGACAAAGATAAAT
* *
3941651 GTGTCATAAAGAC-AA-AT-AAT
1 ATGTCACAAAGACAAAGATAAAT
3941671 ATGTCACAAAGA
1 ATGTCACAAAGA
3941683 TATAATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 13 0.46
21 2 0.07
22 2 0.07
23 11 0.39
ACGTcount: A:0.53, C:0.13, G:0.15, T:0.20
Consensus pattern (23 bp):
ATGTCACAAAGACAAAGATAAAT
Found at i:3950497 original size:16 final size:16
Alignment explanation
Indices: 3950474--3950516 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
3950464 CTTAATATCT
3950474 AAATTAAATTAATAAC
1 AAATTAAATTAATAAC
*
3950490 ATATTAAATTAATAAC
1 AAATTAAATTAATAAC
3950506 AAATTAAATTA
1 AAATTAAATTA
3950517 GTTTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTAAATTAATAAC
Found at i:3951325 original size:17 final size:17
Alignment explanation
Indices: 3951290--3951335 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
3951280 ACAAAAACTT
*
3951290 ATATATATATATATATA
1 ATATATATATTTATATA
* *
3951307 ATATATATATTTGTTTA
1 ATATATATATTTATATA
3951324 ATATA-ATATTTA
1 ATATATATATTTA
3951336 AATTATCTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 6 0.24
17 19 0.76
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
ATATATATATTTATATA
Found at i:3951774 original size:37 final size:40
Alignment explanation
Indices: 3951733--3951843 Score: 122
Period size: 42 Copynumber: 2.8 Consensus size: 40
3951723 ACTATTATAT
3951733 TTTATTAAAATAAAT-TT-T-TTATAAATTATATTAATTA
1 TTTATTAAAATAAATATTATATTATAAATTATATTAATTA
* *
3951770 TTTATTATAATAAAAATATTATATTATTAATTATATTAATTA
1 TTTATTA-AA-ATAAATATTATATTATAAATTATATTAATTA
* *
3951812 CTTATTAAAATAAA-AATATTATTATAATATTA
1 TTTATTAAAATAAATATTA-TATTATAA-ATTA
3951844 AAATTATAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
37 7 0.11
38 2 0.03
39 8 0.13
40 13 0.21
41 7 0.11
42 24 0.39
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (40 bp):
TTTATTAAAATAAATATTATATTATAAATTATATTAATTA
Found at i:3951776 original size:16 final size:15
Alignment explanation
Indices: 3951757--3951818 Score: 51
Period size: 16 Copynumber: 4.3 Consensus size: 15
3951747 TTTTTTATAA
3951757 ATTATATTAATTATTT
1 ATTATATTAATTA-TT
* * *
3951773 ATTATAATAA-AAAT
1 ATTATATTAATTATT
3951787 ATTATATT-ATTA--
1 ATTATATTAATTATT
3951799 ATTATATTAATTACTT
1 ATTATATTAATTA-TT
3951815 ATTA
1 ATTA
3951819 AAATAAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
12 8 0.22
13 5 0.14
14 9 0.25
15 1 0.03
16 13 0.36
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTATATTAATTATT
Found at i:3951777 original size:23 final size:23
Alignment explanation
Indices: 3951746--3951822 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 23
3951736 ATTAAAATAA
*
3951746 ATTTTTTATAAATTATATTAATT
1 ATTTATTATAAATTATATTAATT
*
3951769 ATTTATTAT-AA-TA-A--AAAT
1 ATTTATTATAAATTATATTAATT
*
3951787 ATTATATTATTAATTATATTAATT
1 ATT-TATTATAAATTATATTAATT
*
3951811 ACTTATTA-AAAT
1 ATTTATTATAAAT
3951823 AAAAATATTA
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
18 6 0.14
19 6 0.14
20 3 0.07
21 4 0.09
22 6 0.14
23 13 0.30
24 5 0.12
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTATTATAAATTATATTAATT
Found at i:3951802 original size:42 final size:42
Alignment explanation
Indices: 3951751--3951833 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
3951741 AATAAATTTT
* *
3951751 TTATAAATTATATTAATTATTTATTATAATAAAAATATTATA
1 TTATAAATTATATTAATTACTTATTAAAATAAAAATATTATA
*
3951793 TTATTAATTATATTAATTACTTATTAAAATAAAAATATTAT
1 TTATAAATTATATTAATTACTTATTAAAATAAAAATATTAT
3951834 TATAATATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (42 bp):
TTATAAATTATATTAATTACTTATTAAAATAAAAATATTATA
Found at i:3951830 original size:25 final size:25
Alignment explanation
Indices: 3951802--3951876 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 25
3951792 ATTATTAATT
3951802 ATATTAATTACT-TATTAAAATAAAA
1 ATATTAATTA-TATATTAAAATAAAA
* *
3951827 ATATT-ATTATAATATTAAAATTATA
1 ATATTAATTAT-ATATTAAAATAAAA
*
3951852 ATATTAAATTATATTTTGAAAATAA
1 ATATT-AATTATATATT-AAAATAA
3951877 TTAATAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
23 1 0.02
24 4 0.10
25 21 0.51
26 4 0.10
27 11 0.27
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (25 bp):
ATATTAATTATATATTAAAATAAAA
Found at i:3951849 original size:14 final size:13
Alignment explanation
Indices: 3951832--3951864 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
3951822 TAAAAATATT
3951832 ATTATAATATTAAA
1 ATTATAATATT-AA
3951846 ATTATAATATTAA
1 ATTATAATATTAA
3951859 ATTATA
1 ATTATA
3951865 TTTTGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTATAATATTAA
Found at i:3951887 original size:22 final size:22
Alignment explanation
Indices: 3951856--3951905 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 22
3951846 ATTATAATAT
3951856 TAAATTATATTTTGAAAATAATTAA
1 TAAA-TATA-TTT-AAAATAATTAA
* *
3951881 TAAATATATTTTAAATATTTAA
1 TAAATATATTTAAAATAATTAA
3951903 TAA
1 TAA
3951906 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 12 0.52
23 3 0.13
24 4 0.17
25 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
TAAATATATTTAAAATAATTAA
Found at i:3952002 original size:10 final size:10
Alignment explanation
Indices: 3951984--3952076 Score: 50
Period size: 10 Copynumber: 9.0 Consensus size: 10
3951974 AAAGTAAAAC
3951984 TATAATATTA
1 TATAATATTA
*
3951994 TATATTATTA
1 TATAATATTA
3952004 TA-ATATAATTTAA
1 TATA-AT-A-TT-A
3952017 TATAATATTA
1 TATAATATTA
3952027 TCA-AAT-TTA
1 T-ATAATATTA
*
3952036 -AAAATATTA
1 TATAATATTA
*
3952045 TATTATATTA
1 TATAATATTA
* *
3952055 TTAAAATAATA
1 -TATAATATTA
3952066 TATTAATATTA
1 TA-TAATATTA
3952077 AATATATAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 21
0.68 0.10 0.23
Matches are distributed among these distances:
7 1 0.02
8 3 0.05
9 7 0.11
10 26 0.41
11 17 0.27
12 3 0.05
13 5 0.08
14 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (10 bp):
TATAATATTA
Found at i:3952054 original size:54 final size:53
Alignment explanation
Indices: 3951953--3952076 Score: 132
Period size: 54 Copynumber: 2.4 Consensus size: 53
3951943 TAATTTTACT
* * *
3951953 AATAATTTACTAT-ATATTATTAAAGTAAAACTATAATATTATATATTATTATA
1 AATAATTTAATATAATATTATCAAAGTAAAAATATAATATTATATATTATTA-A
* *
3952006 ATATAATTTAATATAATATTATCAAATTTAAAAATATTATA-T-TATATTATTAA
1 A-ATAATTTAATATAATATTATCAAA-GTAAAAATATAATATTATATATTATTAA
*
3952059 AATAATAT-AT-TAATATTA
1 AATAATTTAATATAATATTA
3952077 AATATATAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
50 8 0.13
51 2 0.03
52 6 0.10
53 3 0.05
54 21 0.34
55 11 0.18
56 11 0.18
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (53 bp):
AATAATTTAATATAATATTATCAAAGTAAAAATATAATATTATATATTATTAA
Found at i:3952078 original size:41 final size:42
Alignment explanation
Indices: 3951965--3952097 Score: 112
Period size: 41 Copynumber: 3.2 Consensus size: 42
3951955 TAATTTACTA
* * * * *
3951965 TATATTATTAAAGTAAAACTA-TAATATTATATATTATTATAA
1 TATATTATTAAAATAATACTATTAATATTA-AAAATATTATAT
* * * *
3952007 TATAAT-TTAATATAATATTATCAA-ATTTAAAAATATTATAT
1 TATATTATTAAAATAATACTATTAATA-TTAAAAATATTATAT
* * *
3952048 TATATTATTAAAATAATA-TATTAATATTAAATATATAAAAT
1 TATATTATTAAAATAATACTATTAATATTAAAAATATTATAT
3952089 TATATTATT
1 TATATTATT
3952098 TTAAGTATTT
Statistics
Matches: 72, Mismatches: 15, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
41 51 0.71
42 21 0.29
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.47
Consensus pattern (42 bp):
TATATTATTAAAATAATACTATTAATATTAAAAATATTATAT
Found at i:3952086 original size:27 final size:26
Alignment explanation
Indices: 3952039--3952101 Score: 69
Period size: 27 Copynumber: 2.5 Consensus size: 26
3952029 AAATTTAAAA
*
3952039 ATATTATATTATATTATTAAAATAAT
1 ATATTATATTAAATTATTAAAATAAT
3952065 ATATTAATATTAAA-TATATAAAAT--T
1 ATATT-ATATTAAATTAT-TAAAATAAT
*
3952090 ATATTATTTTAA
1 ATATTATATTAA
3952102 GTATTTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 6 0.18
25 6 0.18
26 8 0.24
27 13 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATATTATATTAAATTATTAAAATAAT
Found at i:3962499 original size:50 final size:53
Alignment explanation
Indices: 3962417--3962521 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 53
3962407 CACAAGATGG
* * *
3962417 GGCACATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACAA
1 GGCACATA-AAATAGGAAACTAGCCTAGAGTTAGAGAATTACAACTAATCACAA
*
3962471 GGCACAT-AAATAGGAGA-TAG-CTAGAGTTAGAGAATTACAACTAATCACAA
1 GGCACATAAAATAGGAAACTAGCCTAGAGTTAGAGAATTACAACTAATCACAA
3962521 G
1 G
3962522 AATATTATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
50 28 0.60
51 3 0.06
52 9 0.19
54 7 0.15
ACGTcount: A:0.44, C:0.14, G:0.22, T:0.20
Consensus pattern (53 bp):
GGCACATAAAATAGGAAACTAGCCTAGAGTTAGAGAATTACAACTAATCACAA
Found at i:3963377 original size:2 final size:2
Alignment explanation
Indices: 3963370--3963394 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3963360 TAAATGTGGC
3963370 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3963395 CATTGTTATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3967282 original size:26 final size:26
Alignment explanation
Indices: 3967243--3967292 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3967233 TTTTATAATA
**
3967243 ATAAATTTTTTATAATTTT-AAAAATT
1 ATAAATTTCATAT-ATTTTGAAAAATT
3967269 ATAAATTTCATATATTTTGAAAAA
1 ATAAATTTCATATATTTTGAAAAA
3967293 AATATTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
ATAAATTTCATATATTTTGAAAAATT
Found at i:3967963 original size:343 final size:333
Alignment explanation
Indices: 3967289--3968099 Score: 1257
Period size: 343 Copynumber: 2.4 Consensus size: 333
3967279 TATATTTTGA
* * ** *
3967289 AAAAAATATTGAATAATAATTCATTTGATCAATCAATTGTATTTAAAAGTTTA-TTT--TA----
1 AAAAATTAATGAATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTT
* *
3967347 -ATATTTTTAAACAATTAATTTTAAAAGGCAATATTTTTTTCAAAAATATATGAAATTTATAATT
66 TATATTTTTAAACAATTAATTTTAAAAGGAAATAATTTTTTCAAAAATATATGAAATTTATAATT
*
3967411 TTTTAAATTAT-AAAATATTTATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTT
131 TTTAAAATTATAAAAATATTTATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTT
* * * *
3967475 TTATAAAATTATTCATATTTTAAATATTTACCCTCAAAGTTTTTATATACTAGATTATATGTATT
196 TTATAAAATTATTCATATTTTAAATACTTACCCTCAAAGTTTTCATATAATAGATTATACGTATT
*** *
3967540 GTGTAATTTTAATGCAAAAATTTGAATAATTTTATTAAAAATGAATAAACATTATTAATTGTTGT
261 GTGTAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAAATGTTGT
*
3967605 TAAAAATT
326 TAAAAACT
3967613 AAAAATTAATGAATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTT
1 AAAAATTAATGAATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATA-TTT
*
3967678 TTATATTTTTAAACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTATAAT
65 TTATATTTTTAAACAATTAATTTTAAAAGGAAATAATTTTTTCAAAAATATATGAAATTTATAAT
*
3967743 TTTTAAAATTATAAAATATTTATTATTATCATCATCACCATCATTTTGTAAAAGAAATATTAGTT
130 TTTTAAAATTATAAAA-A--TA-T-TTATCATCAT---CATCATTTTGTAAAAGAAATACTAGTT
*
3967808 ATAAAACTTTTATAAAATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATAATAGAT
187 ATAAAACTTTTATAAAATTATTCATATTTT-AAATACTTACCCTCAAAGTTTTCATATAATAGAT
3967873 TATACGTATTGTGTAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTAT
251 TATACGTATTGTGTAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTAT
3967938 TAAATGTTGTTAAAAACT
316 TAAATGTTGTTAAAAACT
*
3967956 AAAAATTAATGAATAATAATTCATTTGATCCCTTAATTGTAATTAAAAGTTTATTTTAATATTTT
1 AAAAATTAATGAATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTT
*
3968021 TATATTTTTAAACAATTAATTTTAAAAGAAAAT-ATTTTTTC-AAAATATATGAAATTTATAATT
66 TATATTTTTAAACAATTAATTTTAAAAGGAAATAATTTTTTCAAAAATATATGAAATTTATAATT
3968084 TTTAAAATTATAAAAA
131 TTTAAAATTATAAAAA
3968100 ATAAACTTGT
Statistics
Matches: 446, Mismatches: 22, Indels: 23
0.91 0.04 0.05
Matches are distributed among these distances:
324 48 0.11
325 3 0.01
327 2 0.00
333 72 0.16
334 3 0.01
335 1 0.00
337 2 0.00
338 1 0.00
339 11 0.02
340 37 0.08
341 8 0.02
342 91 0.20
343 167 0.37
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.44
Consensus pattern (333 bp):
AAAAATTAATGAATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGTTTATTTTAATATTTT
TATATTTTTAAACAATTAATTTTAAAAGGAAATAATTTTTTCAAAAATATATGAAATTTATAATT
TTTAAAATTATAAAAATATTTATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAAAACTT
TTATAAAATTATTCATATTTTAAATACTTACCCTCAAAGTTTTCATATAATAGATTATACGTATT
GTGTAATTTTAATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATTAAATGTTGT
TAAAAACT
Found at i:3968382 original size:37 final size:37
Alignment explanation
Indices: 3968335--3968407 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
3968325 GCCCCCGGGG
*
3968335 GCGCCTTCGACCACGTGGCGTAAAGCACGGTGCAGGC
1 GCGCCTTCGACCACGTGGCATAAAGCACGGTGCAGGC
**
3968372 GCGCCTTCGACCACGTGGCATAAAGTGCGGTGCAGG
1 GCGCCTTCGACCACGTGGCATAAAGCACGGTGCAGG
3968408 GGGAGCGTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.19, C:0.30, G:0.36, T:0.15
Consensus pattern (37 bp):
GCGCCTTCGACCACGTGGCATAAAGCACGGTGCAGGC
Found at i:3968945 original size:35 final size:35
Alignment explanation
Indices: 3968899--3968974 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
3968889 AAAACAGACC
* *
3968899 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
3968934 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
3968969 TCAATT
1 TCAATT
3968975 GAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:3969517 original size:130 final size:130
Alignment explanation
Indices: 3969371--3969618 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
3969361 TATTTATATA
**
3969371 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
3969436 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
3969501 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
3969566 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
3969619 GAATAAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:3969649 original size:130 final size:129
Alignment explanation
Indices: 3969385--3969649 Score: 327
Period size: 130 Copynumber: 2.0 Consensus size: 129
3969375 ATTTGGTCCT
** *
3969385 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * * * **** *
3969450 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAATAAAATAAGCTATCAAAGAAGT-CA
3969515 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
3969580 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAATAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AATAAAA-TAAGCTATCAAAGAAGT
3969644 -A
128 CA
3969645 AAATT
1 AAATT
3969650 TGGGTCTTGG
Statistics
Matches: 115, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
130 101 0.88
132 9 0.08
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAATAAAATAAGCTATCAAAGAAGTCA
Found at i:3969884 original size:25 final size:25
Alignment explanation
Indices: 3969855--3969919 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
3969845 TAAATGATGG
3969855 GAAAATATTATATTTTTTTACAATA
1 GAAAATATTATATTTTTTTACAATA
3969880 GAAAATATTATATTTTTTTACAATA
1 GAAAATATTATATTTTTTTACAATA
*
3969905 AAAAATATTATATTT
1 GAAAATATTATATTT
3969920 GATAAATTGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (25 bp):
GAAAATATTATATTTTTTTACAATA
Found at i:3971910 original size:20 final size:20
Alignment explanation
Indices: 3971885--3971923 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3971875 TGTCTTTTGA
3971885 TTCATGTTTTTTGATTTGGG
1 TTCATGTTTTTTGATTTGGG
*
3971905 TTCATGTTTTTTTATTTGG
1 TTCATGTTTTTTGATTTGG
3971924 CAGAACCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.10, C:0.05, G:0.21, T:0.64
Consensus pattern (20 bp):
TTCATGTTTTTTGATTTGGG
Found at i:3976075 original size:33 final size:31
Alignment explanation
Indices: 3976038--3976112 Score: 98
Period size: 33 Copynumber: 2.4 Consensus size: 31
3976028 TATAAATTTA
*
3976038 AAAAACGTTTTCAAACTATATGT-TATAGTTTTC
1 AAAAACGTTTTAAAACTATAT-TATAT-G-TTTC
3976071 AAAAACGTTTTAAAACTATATTATATGTTTC
1 AAAAACGTTTTAAAACTATATTATATGTTTC
*
3976102 AAAAATGTTTT
1 AAAAACGTTTT
3976113 TTTAACTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
31 14 0.36
32 2 0.05
33 23 0.59
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (31 bp):
AAAAACGTTTTAAAACTATATTATATGTTTC
Found at i:3976102 original size:31 final size:33
Alignment explanation
Indices: 3976038--3976112 Score: 102
Period size: 31 Copynumber: 2.3 Consensus size: 33
3976028 TATAAATTTA
*
3976038 AAAAACGTTTTCAAACTATATGTTATAGTTTTC
1 AAAAACGTTTTAAAACTATATGTTATAGTTTTC
3976071 AAAAACGTTTTAAAACTATA--TTATA-TGTTTC
1 AAAAACGTTTTAAAACTATATGTTATAGT-TTTC
*
3976102 AAAAATGTTTT
1 AAAAACGTTTT
3976113 TTTAACTATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
30 1 0.03
31 19 0.49
33 19 0.49
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (33 bp):
AAAAACGTTTTAAAACTATATGTTATAGTTTTC
Found at i:3976155 original size:35 final size:35
Alignment explanation
Indices: 3975967--3976294 Score: 203
Period size: 35 Copynumber: 9.3 Consensus size: 35
3975957 TATATGATAA
* * *
3975967 AAAAATGTTTTAAAACTTTATATAATATATATTTC
1 AAAAATGTTTTAAAACTATATATTATATAAATTTC
* * *
3976002 AAAGATATTTTCAAAA-TCATATATTATATAAATTTA
1 AAAAATGTTTT-AAAACT-ATATATTATATAAATTTC
* * *
3976038 AAAAACGTTTTCAAACTATATGTTATAGT---TTTC
1 AAAAATGTTTTAAAACTATATATTATA-TAAATTTC
* *
3976071 AAAAACGTTTTAAAAC--TATATTATAT--GTTTC
1 AAAAATGTTTTAAAACTATATATTATATAAATTTC
**
3976102 AAAAATGTTTTTTTAACTATATATTATATAAATTT-
1 AAAAATG-TTTTAAAACTATATATTATATAAATTTC
*
3976137 TAAAATGATTTTAAAACTATATATTATATAAATTTTC
1 AAAAATG-TTTTAAAACTATATATTATATAAA-TTTC
* **
3976174 -AAAATGGTTTTAAAAACTATATAATATATATGGTTTC
1 AAAAAT-GTTTT-AAAACTATATATTATATA-AATTTC
** ** * * **
3976211 AAAAAAAATTCAAAAATTATATAATATATATGTTTTC
1 -AAAAATGTTTTAAAACTATATATTATATA-AATTTC
* *
3976248 AAAAAATGTTTTCAAAAACCATATATTATAT-ATTTTC
1 -AAAAATGTTTT--AAAACTATATATTATATAAATTTC
3976285 -AAAATGTTTT
1 AAAAATGTTTT
3976295 CTTTTTAGAA
Statistics
Matches: 235, Mismatches: 39, Indels: 38
0.75 0.12 0.12
Matches are distributed among these distances:
30 1 0.00
31 18 0.08
32 7 0.03
33 18 0.08
34 10 0.04
35 60 0.26
36 43 0.18
37 58 0.25
38 2 0.01
39 18 0.08
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (35 bp):
AAAAATGTTTTAAAACTATATATTATATAAATTTC
Found at i:3976190 original size:37 final size:36
Alignment explanation
Indices: 3975968--3976294 Score: 184
Period size: 37 Copynumber: 9.3 Consensus size: 36
3975958 ATATGATAAA
* * *
3975968 AAAATGTTTT-AAAACTTTATATAATATATA-TTTC
1 AAAATGTTTTAAAAACTATATATTATATAAATTTTC
* * **
3976002 AAAGATATTTTCAAAA-TCATATATTATATAAATTTAA
1 AAA-ATGTTTTAAAAACT-ATATATTATATAAATTTTC
* * * *
3976039 AAAACGTTTT-CAAACTATAT-GT-TAT-AGTTTTC
1 AAAATGTTTTAAAAACTATATATTATATAAATTTTC
* *
3976071 AAAAACGTTTT-AAAAC--TATATTATAT---GTTTC
1 -AAAATGTTTTAAAAACTATATATTATATAAATTTTC
***
3976102 AAAAATGTTTTTTTAACTATATATTATATAAATTTT-
1 -AAAATGTTTTAAAAACTATATATTATATAAATTTTC
3976138 AAAATGATTTT-AAAACTATATATTATATAAATTTTC
1 AAAATG-TTTTAAAAACTATATATTATATAAATTTTC
* ***
3976174 AAAATGGTTTTAAAAACTATATAATATATATGGTTTC
1 AAAAT-GTTTTAAAAACTATATATTATATAAATTTTC
*** * * * **
3976211 AAAAAAAATTCAAAAATTATATAATATATATGTTTTC
1 -AAAATGTTTTAAAAACTATATATTATATAAATTTTC
*
3976248 AAAAAATGTTTTCAAAAACCATATATTATAT--ATTTTC
1 --AAAATGTTTT-AAAAACTATATATTATATAAATTTTC
3976285 AAAATGTTTT
1 AAAATGTTTT
3976295 CTTTTTAGAA
Statistics
Matches: 232, Mismatches: 40, Indels: 41
0.74 0.13 0.13
Matches are distributed among these distances:
31 17 0.07
32 8 0.03
33 20 0.09
34 14 0.06
35 52 0.22
36 34 0.15
37 61 0.26
38 11 0.05
39 15 0.06
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (36 bp):
AAAATGTTTTAAAAACTATATATTATATAAATTTTC
Found at i:3976258 original size:13 final size:13
Alignment explanation
Indices: 3976240--3976265 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3976230 TATAATATAT
3976240 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
3976253 ATGTTTTCAAAAA
1 ATGTTTTCAAAAA
3976266 CCATATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ATGTTTTCAAAAA
Found at i:3977032 original size:84 final size:84
Alignment explanation
Indices: 3976906--3977790 Score: 888
Period size: 84 Copynumber: 10.7 Consensus size: 84
3976896 CTTGCTTTGG
* * * *
3976906 GCTATGTTGTAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
1 GCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
*
3976970 ATAACCCTTCTAGACTTGA
66 ATAACCCTTCTAGACTTAA
* ** * * * * * **
3976989 GTTATGCTGTGAATGATATACCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCTTT-G-GA-AG
1 GCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* * **
3977051 ATAGCTCTTCTCTACTTAA
66 ATAACCCTTCTAGACTTAA
* * * * * *
3977070 GCTATGCTGCAAATGATGTGTCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCA
1 GCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACA
*
3977134 GACAACCCTTCTAGACTTAA
65 GATAACCCTTCTAGACTTAA
* * * * * *
3977154 GTTGTGATGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
1 GCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
*
3977218 ATAACCCTTCTAGACTTGA
66 ATAACCCTTCTAGACTTAA
* ** * * * **
3977237 GTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G-G-CAG
1 GCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* * * *
3977299 ATAGCTCTTCTCGAATTAA
66 ATAACCCTTCTAGACTTAA
* * * *
3977318 GCTATGCTGCAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCA
1 GCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACA
*
3977382 GATAACCCTTCTCGACTTAA
65 GATAACCCTTCTAGACTTAA
* * * *
3977402 GTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT-G-G-CAG
1 GCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* *
3977464 ATAGCCCTTCTCGACTTAA
66 ATAACCCTTCTAGACTTAA
* * * *
3977483 GCTATACTGCAAATGATGTGCCTTAG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTGACA
1 GCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACA
* *
3977547 GATAACCCTTCTAGCCTTGA
65 GATAACCCTTCTAGACTTAA
* * * * **
3977567 GCTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCTTT-G-G-CAG
1 GCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* *
3977629 ATAGCCCTTCTTGACTTAA
66 ATAACCCTTCTAGACTTAA
* *
3977648 GCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACA
1 GCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACA
* *
3977712 GATAACCCTTCTAGCCTTGA
65 GATAACCCTTCTAGACTTAA
* * * * **
3977732 GTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG
1 GCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
3977791 CAGATAGCCT
Statistics
Matches: 649, Mismatches: 131, Indels: 43
0.79 0.16 0.05
Matches are distributed among these distances:
80 95 0.15
81 161 0.25
82 7 0.01
83 68 0.10
84 244 0.38
85 74 0.11
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.30
Consensus pattern (84 bp):
GCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
ATAACCCTTCTAGACTTAA
Found at i:3977354 original size:248 final size:248
Alignment explanation
Indices: 3976916--3977806 Score: 1188
Period size: 248 Copynumber: 3.6 Consensus size: 248
3976906 GCTATGTTGT
3976916 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
* * *
3976981 AGACTTGAGTTATGCTGTGAATGATATACCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCTTT
66 AGACTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
* * *
3977046 GGAAGATAGCTCTTCTCTACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCG
131 GGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCG
* * *
3977111 AACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGATGC
196 AACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
*
3977164 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
*
3977229 AGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
66 AGACTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
*
3977294 GGCAGATAGCTCTTCTCGAATTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCG
131 GGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCG
* *
3977359 AACTCAAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
196 AACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * * * * *
3977412 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT-G-G-CAGATAGCCCTTC
1 AAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTC
* * * * * * * * * * ***
3977474 TCGACTTAAGCTATACTGCAAATGATGTGCCTTAG-AGCTGAGCGTAGTCGAACTCAAAGGTCTT
65 TAGACTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-T
* * * * * * * * *
3977538 TTGGTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
129 TT-G-G-CAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG-AGCTGAGCG
* * *** * * *
3977603 TAATCAAACTCGGGGGTC---T-TTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTGC
190 TAGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
3977658 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTC
1 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTC
* *
3977723 TAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
65 TAGACTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTT
3977788 TGGCAGATAGC-CTTCTCGA
130 TGGCAGATAGCTCTTCTCGA
3977807 GTTGGATATC
Statistics
Matches: 558, Mismatches: 74, Indels: 25
0.85 0.11 0.04
Matches are distributed among these distances:
245 56 0.10
246 94 0.17
247 4 0.01
248 249 0.45
249 112 0.20
250 43 0.08
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (248 bp):
AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCT
AGACTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT
GGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCG
AACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
Found at i:3977446 original size:165 final size:165
Alignment explanation
Indices: 3977128--3977806 Score: 1087
Period size: 165 Copynumber: 4.1 Consensus size: 165
3977118 AGGTCTTTTG
* * * * * * *
3977128 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGATGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* * *
3977193 CGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGTGAATGATATG
66 CGAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATGTG
3977257 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
131 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
* *
3977292 TTGGCAGATAGCTCTTCTCGAATTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAG
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAG
* * * *
3977356 TCGAACTCAAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
65 TCGAACTCAAAGGTCTTTTGG-TGACAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATG
*
3977420 TGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCT
129 TGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
* *
3977457 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTAGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* *
3977522 CGAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTG
66 CGAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATGTG
*
3977587 CCCTCGAAGCTGAGTGTAATCAAACTCGGGGGTCT
131 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
*
3977622 TTGGCAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* *
3977687 CGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
66 CGAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATGTG
3977752 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
131 CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
3977787 TTGGCAGATAG-CCTTCTCGA
1 TTGGCAGATAGCCCTTCTCGA
3977807 GTTGGATATC
Statistics
Matches: 476, Mismatches: 35, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
164 81 0.17
165 390 0.82
166 5 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (165 bp):
TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
CGAACTCAAAGGTCTTTTGGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATGTG
CCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCT
Found at i:3985088 original size:15 final size:15
Alignment explanation
Indices: 3985068--3985097 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3985058 TGTTGAAGGC
3985068 GGGGCTGTGTATATT
1 GGGGCTGTGTATATT
*
3985083 GGGGCTGTGTTTATT
1 GGGGCTGTGTATATT
3985098 CGGCTACATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.07, G:0.40, T:0.43
Consensus pattern (15 bp):
GGGGCTGTGTATATT
Found at i:3994912 original size:6 final size:6
Alignment explanation
Indices: 3994903--3994937 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
3994893 AACAGCAAAA
*
3994903 GAAGAA GAAGAG GAAGAG GAAGAG GAAGAG GAAGA
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGA
3994938 CGTGGTTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:3996166 original size:10 final size:10
Alignment explanation
Indices: 3996153--3996263 Score: 62
Period size: 10 Copynumber: 10.2 Consensus size: 10
3996143 AACACAAATG
3996153 AACGAACATA
1 AACGAACATA
3996163 AACGAACGGATGTA
1 AACGAAC--A--TA
3996177 AACGAACAT-
1 AACGAACATA
3996186 AACGAACACAATA
1 AACG-A-AC-ATA
*
3996199 AACGAACTTA
1 AACGAACATA
* * *
3996209 AACAAATACA
1 AACGAACATA
*
3996219 AACGAACGTA
1 AACGAACATA
*
3996229 AACAAACATAATA
1 AACGAAC---ATA
*
3996242 AATGAACATA
1 AACGAACATA
3996252 AACGAACATA
1 AACGAACATA
3996262 AA
1 AA
3996264 TGACAAAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
9 4 0.05
10 43 0.57
11 4 0.05
12 5 0.07
13 11 0.14
14 9 0.12
ACGTcount: A:0.59, C:0.18, G:0.11, T:0.13
Consensus pattern (10 bp):
AACGAACATA
Found at i:3996848 original size:60 final size:60
Alignment explanation
Indices: 3996729--3996853 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 60
3996719 TAAAATATAT
* * * *
3996729 AAATGGTCCTCTGATTATATGGTATTTTTTATTGAGTCGATCGACTATTAAAAAATTACA
1 AAATGGTCCCCTAATTATATGATATTTTTTATTGAGTCGATCAACTATTAAAAAATTACA
* *
3996789 AAATGGTCCCCTAATTATATGATATTATTTGT-TTGAGTC-CTCTAACTATT-AAAAGTTACA
1 AAATGGTCCCCTAATTATATGATATT-TTT-TATTGAGTCGATC-AACTATTAAAAAATTACA
3996849 AAATG
1 AAATG
3996854 ATCATCCGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
60 39 0.70
61 16 0.29
62 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (60 bp):
AAATGGTCCCCTAATTATATGATATTTTTTATTGAGTCGATCAACTATTAAAAAATTACA
Found at i:3997418 original size:3 final size:3
Alignment explanation
Indices: 3997410--3997472 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
3997400 ACTCATATGC
*
3997410 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3997458 ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA
3997473 GGAATGGGGG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3998177 original size:6 final size:6
Alignment explanation
Indices: 3998166--3998201 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
3998156 TTAACTTAGC
3998166 GGGGAA GGGGAA GGGGAA GGGGGAA GGGGGAA GGGG
1 GGGGAA GGGGAA GGGGAA -GGGGAA -GGGGAA GGGG
3998202 GAAGTGGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 16 0.55
7 13 0.45
ACGTcount: A:0.28, C:0.00, G:0.72, T:0.00
Consensus pattern (6 bp):
GGGGAA
Found at i:3998190 original size:7 final size:7
Alignment explanation
Indices: 3998166--3998205 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
3998156 TTAACTTAGC
3998166 GGGGAA-
1 GGGGAAG
3998172 GGGGAA-
1 GGGGAAG
3998178 GGGGAAG
1 GGGGAAG
3998185 GGGGAAG
1 GGGGAAG
3998192 GGGGAAG
1 GGGGAAG
3998199 GGGGAAG
1 GGGGAAG
3998206 TGGAAAAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 12 0.36
7 21 0.64
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (7 bp):
GGGGAAG
Found at i:4014280 original size:58 final size:60
Alignment explanation
Indices: 4014203--4014318 Score: 157
Period size: 59 Copynumber: 2.0 Consensus size: 60
4014193 AAGGTTAAAG
*
4014203 TATACAAATGGTCCCCGATTATA-GATATTATTTTATTGAGT-TTCCAACTATTAAAAAT
1 TATACAAATGGCCCCCGATTATAGGATATTATTTTATTGAGTCTTCCAACTATTAAAAAT
* * * *
4014261 TATA-AAATGGCCCCTCGATTGTAGGATGTTATTTTGTTGAGTCTTCCGACTATTAAAA
1 TATACAAATGGCCCC-CGATTATAGGATATTATTTTATTGAGTCTTCCAACTATTAAAA
4014319 GTTACGAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
57 9 0.18
58 11 0.22
59 16 0.32
60 14 0.28
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (60 bp):
TATACAAATGGCCCCCGATTATAGGATATTATTTTATTGAGTCTTCCAACTATTAAAAAT
Found at i:4017818 original size:25 final size:24
Alignment explanation
Indices: 4017796--4017852 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 24
4017786 GCTTAAAAAT
4017796 AAAACTT-AAAATGAAAATGAAAAGA
1 AAAACTTGAAAA-GAAAA-GAAAAGA
4017821 AAAACTTGAAAAGAAAAGAAAAGA
1 AAAACTTGAAAAGAAAAGAAAAGA
4017845 AATAACTT
1 AA-AACTT
4017853 TATAAAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.30
25 17 0.57
26 4 0.13
ACGTcount: A:0.67, C:0.05, G:0.12, T:0.16
Consensus pattern (24 bp):
AAAACTTGAAAAGAAAAGAAAAGA
Found at i:4020099 original size:16 final size:16
Alignment explanation
Indices: 4020078--4020110 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4020068 AAAAAAATAG
*
4020078 AGAAAATTTG-GAGAA
1 AGAAAAATTGAGAGAA
4020093 AGAAAAATTGAGAGAA
1 AGAAAAATTGAGAGAA
4020109 AG
1 AG
4020111 CAAAGAGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (16 bp):
AGAAAAATTGAGAGAA
Found at i:4026134 original size:37 final size:36
Alignment explanation
Indices: 4026088--4026422 Score: 261
Period size: 36 Copynumber: 8.9 Consensus size: 36
4026078 ATAAAAATAT
* * *
4026088 TTTTTAAAACTATATAATATATATGTTTAAAAAATAA
1 TTTTAAAAACTATATAATATATATGTTTCAAAAAT-G
* *
4026125 TTTTCAAAACTATATAATTTATAT-TTTCAAAAATTG
1 TTTTAAAAACTATATAATATATATGTTTCAAAAA-TG
* *
4026161 TTTTAAAAACTTATATATTATATATATTTTTCAAAAACG
1 TTTTAAAAAC-TATATA--ATATATATGTTTCAAAAATG
* * **
4026200 TTTTAAAAATTATAATATATAAATATTTTTGTTTTTTAAAATG
1 TTTTAAAAACTAT-ATA-AT--ATA--TATG-TTTCAAAAATG
4026243 TTTTAAAAACTATATAATATATATGTTTTC-AAAATG
1 TTTTAAAAACTATATAATATATATG-TTTCAAAAATG
*
4026279 TTTTAAAAACTATATAATATATATACGTTTTCAAAAATA
1 TTTTAAAAACTATATAATATATAT--G-TTTCAAAAATG
* * * * *
4026318 CTTTAAAAATTACATATTATATAT-TTTC-GAAATG
1 TTTTAAAAACTATATAATATATATGTTTCAAAAATG
* *
4026352 TTTTAAAAAACCATATATTATACATAT-TTTC-AAAATG
1 TTTT-AAAAA-C-TATATAATATATATGTTTCAAAAATG
4026389 TTTTAAAAACTATATATCATATATAT-TTTCAAAA
1 TTTTAAAAACTATATA--ATATATATGTTTCAAAA
4026423 TTATATATCA
Statistics
Matches: 246, Mismatches: 32, Indels: 40
0.77 0.10 0.13
Matches are distributed among these distances:
34 12 0.05
35 10 0.04
36 63 0.26
37 62 0.25
38 12 0.05
39 48 0.20
40 12 0.05
41 2 0.01
42 5 0.02
43 20 0.08
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (36 bp):
TTTTAAAAACTATATAATATATATGTTTCAAAAATG
Found at i:4026293 original size:110 final size:110
Alignment explanation
Indices: 4026193--4026411 Score: 243
Period size: 110 Copynumber: 2.0 Consensus size: 110
4026183 TATATTTTTC
* * * *
4026193 AAAAACGTTTT-AAAAAT-TAT-AATATATAAATATT-TTTGTTTTTTAAAATGTTTT-AAAAAC
1 AAAAACGTTTTCAAAAATATATAAAAAT-TAAATATTATAT-ATTTTCAAAATGTTTTAAAAAAC
* * *
4026253 TATATAATATATATGTTTTCAAAATGTTTTAAAAACTATATA-ATAT
64 CATATAATATACATATTTTCAAAATGTTTTAAAAACTATATATATAT
* * * * *
4026299 ATATACGTTTTCAAAAATACTTTAAAAATTACATATTATATATTTTCGAAATGTTTTAAAAAACC
1 AAAAACGTTTTCAAAAATA-TATAAAAATTAAATATTATATATTTTCAAAATGTTTTAAAAAACC
*
4026364 ATATATTATACATATTTTCAAAATGTTTTAAAAACTATATATCATAT
65 ATATAATATACATATTTTCAAAATGTTTTAAAAACTATATAT-ATAT
4026411 A
1 A
4026412 TATTTTCAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
106 9 0.10
107 6 0.07
109 22 0.24
110 50 0.54
112 5 0.05
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (110 bp):
AAAAACGTTTTCAAAAATATATAAAAATTAAATATTATATATTTTCAAAATGTTTTAAAAAACCA
TATAATATACATATTTTCAAAATGTTTTAAAAACTATATATATAT
Found at i:4026439 original size:36 final size:34
Alignment explanation
Indices: 4026364--4026481 Score: 80
Period size: 36 Copynumber: 3.4 Consensus size: 34
4026354 TTAAAAAACC
* * * *
4026364 ATATATTATACATATTTTCAAAATGT-TTTAAAAACT
1 ATATATCATATATATTTTCAAAAT-TATAT-AATA-T
4026400 ATATATCATATATATTTTCAAAATTATATATCATAT
1 ATATATCATATATATTTTCAAAATTATATA--ATAT
* * * *
4026436 ATATTTTCA-AAATGTTTTTAAAATTATATAATAT
1 ATA-TATCATATATATTTTCAAAATTATATAATAT
*
4026470 ATACAT-ATATAT
1 ATATATCATATAT
4026482 TATAAATAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 13
0.73 0.12 0.14
Matches are distributed among these distances:
32 1 0.02
33 4 0.06
34 7 0.11
35 2 0.03
36 46 0.70
37 6 0.09
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (34 bp):
ATATATCATATATATTTTCAAAATTATATAATAT
Found at i:4026448 original size:25 final size:25
Alignment explanation
Indices: 4026389--4026448 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
4026379 TTTCAAAATG
* *
4026389 TTTTAAAAACTATATATCATATATA
1 TTTTCAAAATTATATATCATATATA
4026414 TTTTCAAAATTATATATCATATATA
1 TTTTCAAAATTATATATCATATATA
4026439 TTTTCAAAAT
1 TTTTCAAAAT
4026449 GTTTTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTTCAAAATTATATATCATATATA
Found at i:4030285 original size:22 final size:23
Alignment explanation
Indices: 4030260--4030308 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
4030250 TTATTACAAA
4030260 TATTAAAT-ATAATAA-TTAATAT
1 TATTAAATCATAA-AACTTAATAT
*
4030282 TATT-TATCATAAAACTTAATAT
1 TATTAAATCATAAAACTTAATAT
4030304 TATTA
1 TATTA
4030309 TTTTTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTAAATCATAAAACTTAATAT
Found at i:4030421 original size:31 final size:29
Alignment explanation
Indices: 4030353--4030422 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
4030343 AATATTATTT
*
4030353 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
4030383 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
4030416 TTATATT
1 TTATATT
4030423 AATTGTTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Done.