Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 18 of 235
Found at i:5397020 original size:22 final size:21
Alignment explanation
Indices: 5396995--5397036 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
5396985 GTCAAAAAGG
5396995 CCACACGGGCGTGTCGCCCCTT
1 CCACACGGGCGTGT-GCCCCTT
* *
5397017 CCACATGGGTGTGTGCCCCT
1 CCACACGGGCGTGTGCCCCT
5397037 ATTTTAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.10, C:0.40, G:0.29, T:0.21
Consensus pattern (21 bp):
CCACACGGGCGTGTGCCCCTT
Found at i:5398615 original size:14 final size:14
Alignment explanation
Indices: 5398596--5398622 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5398586 AGATCAAGAG
5398596 AACTTTGTTATAAT
1 AACTTTGTTATAAT
5398610 AACTTTGTTATAA
1 AACTTTGTTATAA
5398623 CGTTAATCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.48
Consensus pattern (14 bp):
AACTTTGTTATAAT
Found at i:5399041 original size:27 final size:27
Alignment explanation
Indices: 5399003--5399061 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
5398993 TATCCTAGTC
**
5399003 TTAATGATAATCCAAATGGTCTTGGTG
1 TTAATGATAATCCAAATGGTCAAGGTG
*
5399030 TTAATGATAATCCAAATGTTCAAGGTG
1 TTAATGATAATCCAAATGGTCAAGGTG
5399057 TTAAT
1 TTAAT
5399062 CCTCCTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (27 bp):
TTAATGATAATCCAAATGGTCAAGGTG
Found at i:5402069 original size:12 final size:12
Alignment explanation
Indices: 5402052--5402081 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
5402042 CTTACCTTGG
5402052 AATAACTTAAGC
1 AATAACTTAAGC
5402064 AATAACTTAAGC
1 AATAACTTAAGC
5402076 AATAAC
1 AATAAC
5402082 ATATCACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.07, T:0.23
Consensus pattern (12 bp):
AATAACTTAAGC
Found at i:5402695 original size:53 final size:52
Alignment explanation
Indices: 5402632--5402790 Score: 237
Period size: 53 Copynumber: 3.0 Consensus size: 52
5402622 TAGTACACTC
*
5402632 GAAGTGTATGATTCAATAATCCGTCAATTCCTTTTTCAAGCGTACCCATTAGG
1 GAAGTGTATGATTTAATAATCCGTCAATTCCTTTTTCAAG-GTACCCATTAGG
* *
5402685 GAAGTGTATGATTTAATAATCCGTCAATTCCTTTTTCAAGGGTGCCCATTAGA
1 GAAGTGTATGATTTAATAATCCGTCAATTCCTTTTTCAA-GGTACCCATTAGG
* * * *
5402738 GAAGCGTATGATTTAATAATCTGTCAATTCCTTTTTAAAGGTTCCCATTAGG
1 GAAGTGTATGATTTAATAATCCGTCAATTCCTTTTTCAAGGTACCCATTAGG
5402790 G
1 G
5402791 CACTTAACCA
Statistics
Matches: 97, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
52 12 0.12
53 84 0.87
54 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
GAAGTGTATGATTTAATAATCCGTCAATTCCTTTTTCAAGGTACCCATTAGG
Found at i:5403564 original size:20 final size:20
Alignment explanation
Indices: 5403522--5403566 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5403512 AGCACATGTA
* **
5403522 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACAT
*
5403542 TTCATCAAATTTTACAACAT
1 TTCATAAAATTTTACAACAT
5403562 TTCAT
1 TTCAT
5403567 TTTAGTCCCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.02, T:0.47
Consensus pattern (20 bp):
TTCATAAAATTTTACAACAT
Found at i:5409822 original size:71 final size:71
Alignment explanation
Indices: 5409706--5409848 Score: 286
Period size: 71 Copynumber: 2.0 Consensus size: 71
5409696 ATTCATCTTC
5409706 TATCAAAATTTTGTGGGTGCAAAAAGAAGGGTTGATTCCTTTAATGTTAGAAATTTTCCAAGCTA
1 TATCAAAATTTTGTGGGTGCAAAAAGAAGGGTTGATTCCTTTAATGTTAGAAATTTTCCAAGCTA
5409771 TGGCCT
66 TGGCCT
5409777 TATCAAAATTTTGTGGGTGCAAAAAGAAGGGTTGATTCCTTTAATGTTAGAAATTTTCCAAGCTA
1 TATCAAAATTTTGTGGGTGCAAAAAGAAGGGTTGATTCCTTTAATGTTAGAAATTTTCCAAGCTA
5409842 TGGCCT
66 TGGCCT
5409848 T
1 T
5409849 TTTATGTTCT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.36
Consensus pattern (71 bp):
TATCAAAATTTTGTGGGTGCAAAAAGAAGGGTTGATTCCTTTAATGTTAGAAATTTTCCAAGCTA
TGGCCT
Found at i:5415094 original size:30 final size:31
Alignment explanation
Indices: 5415021--5415102 Score: 114
Period size: 30 Copynumber: 2.7 Consensus size: 31
5415011 CAATCTCAAT
*
5415021 ATAT-ACTGGGCCAAAGCCTTTGCATTATTC
1 ATATCACTGGGCCGAAGCCTTTGCATTATTC
* *
5415051 ATGTCACTGGGCCGAAGCCTTTTCATTA-TC
1 ATATCACTGGGCCGAAGCCTTTGCATTATTC
*
5415081 ATATCACTAGGCCGAAGCCTTT
1 ATATCACTGGGCCGAAGCCTTT
5415103 ACTGTAAACG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 25 0.54
31 21 0.46
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (31 bp):
ATATCACTGGGCCGAAGCCTTTGCATTATTC
Found at i:5415393 original size:26 final size:25
Alignment explanation
Indices: 5415323--5415393 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
5415313 CTCTTTTAAT
*
5415323 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
* *
5415348 AACTAGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
5415373 AACTGGGGCAAAAGCCCTTTT
1 AACTGGGGC-AAAGCCCTTTT
5415394 GCACTTCCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
25 30 0.73
26 11 0.27
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:5415628 original size:30 final size:31
Alignment explanation
Indices: 5415588--5415648 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
5415578 TATAAGGGTA
*
5415588 ATTTCATAATTTTACC-AAATATTAGGGTTT
1 ATTTCATAATTTTACCAAAATATCAGGGTTT
*
5415618 ATTTCGTAATTTTACCAAAATATCAGGGTTT
1 ATTTCATAATTTTACCAAAATATCAGGGTTT
5415649 CCATGTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (31 bp):
ATTTCATAATTTTACCAAAATATCAGGGTTT
Found at i:5417612 original size:5 final size:5
Alignment explanation
Indices: 5417602--5417626 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5417592 AATAATAAAA
5417602 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
5417627 CCATGAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:5421089 original size:24 final size:24
Alignment explanation
Indices: 5421016--5421089 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
5421006 CACTTCCCGA
5421016 TATGATGCCATAGTGTCTTTCAAC
1 TATGATGCCATAGTGTCTTTCAAC
* * *
5421040 CATG--GTCTTA-T-TCATTTTCCAA-
1 TATGATGCCATAGTGTC--TTT-CAAC
5421062 TATGATGCCATAGTGTCTTTCAAC
1 TATGATGCCATAGTGTCTTTCAAC
5421086 TATG
1 TATG
5421090 GTCTTATTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 16
0.62 0.10 0.28
Matches are distributed among these distances:
20 2 0.06
21 1 0.03
22 10 0.28
23 6 0.17
24 14 0.39
25 1 0.03
26 2 0.06
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (24 bp):
TATGATGCCATAGTGTCTTTCAAC
Found at i:5421133 original size:45 final size:44
Alignment explanation
Indices: 5420928--5421417 Score: 467
Period size: 45 Copynumber: 10.9 Consensus size: 44
5420918 ATGATTGAAG
* *
5420928 GATGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCGACT-T
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATT-TCGA-TAT
* * * * *
5420973 AATGCTATAATGTCTTTCAACCATGGTCTTATTCACTTCCCGATAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCA-TT-TCGATAT
* *
5421019 GATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCCAATAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCA-TTT-CGATAT
5421065 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATATTCGATA-
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCAT-TTCGATAT
* * *
5421109 GAATGTCATATTGTCTTTCAACTATAGTCTTATTCACTTTCCGATAT
1 G-ATGCCATAGTGTCTTTCAACTATGGTCTTATTCA-TTT-CGATAT
* * *
5421156 GATGCCAT-GTGTCTTTCAACTATGGTCTTATCCATCTTCGGTAG
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCAT-TTCGATAT
*
5421200 GTTGCCATAGTGTCTTT-AACTATGGTCTTATAT-ACTTTCCGATAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTAT-TCA-TTT-CGATAT
*
5421245 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCGTTTTCGAT-T
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTC-ATTTCGATAT
* *
5421289 GGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATCT-GAATCAT
1 -GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCG-AT-AT
** * * * *
5421335 GATGCCATAGCATCTTTCAGCTATGATATTACTT-GTTT-GAATAAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTA-TTCATTTCG-AT-AT
** * *
5421380 GATGCCATAGCATCTTTCAGCTATGGTCTTACTCATTT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTT
5421418 GAATAATGAT
Statistics
Matches: 379, Mismatches: 44, Indels: 44
0.81 0.09 0.09
Matches are distributed among these distances:
43 1 0.00
44 36 0.09
45 228 0.60
46 113 0.30
47 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.41
Consensus pattern (44 bp):
GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCGATAT
Found at i:5421269 original size:24 final size:24
Alignment explanation
Indices: 5421242--5421314 Score: 57
Period size: 22 Copynumber: 3.2 Consensus size: 24
5421232 TACTTTCCGA
5421242 TATGATGCCATAGTGTCTTTCAAC
1 TATGATGCCATAGTGTCTTTCAAC
* * * *
5421266 TATG--GTCTTATTCGT-TTTCGA-
1 TATGATGCCATAGT-GTCTTTCAAC
5421287 T-TGGATGCCATAGTGTCTTTCAAC
1 TAT-GATGCCATAGTGTCTTTCAAC
5421311 TATG
1 TATG
5421315 GTCTTACTCA
Statistics
Matches: 34, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
20 1 0.03
21 2 0.06
22 12 0.35
23 12 0.35
24 6 0.18
25 1 0.03
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (24 bp):
TATGATGCCATAGTGTCTTTCAAC
Found at i:5421353 original size:180 final size:181
Alignment explanation
Indices: 5420926--5421359 Score: 522
Period size: 180 Copynumber: 2.4 Consensus size: 181
5420916 TAATGATTGA
* * * * * *
5420926 AGGATGCCATAGTGTCTTTCAACCATGGTCTTATTTATTCTCGA-CTTAATGCTATAATGTCTTT
1 AGGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTCT-GATCATGATGCCATAGTGTCTTT
* * * *
5420990 CAACCATGGTCTTATTCACTTCCCGATATGATGCCATAGTGTCTTTCAACCATGGTCTTATTCAT
65 CAACTATGGTCTTATCCACTT-CCGATAGGATGCCATAGTGTCTTTCAACCATGGTCTTATTCAC
5421055 TTTCCAATATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATATTCGAT
129 TTTCCAATATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATATTCGAT
* * * * *
5421108 AGAATGTCATATTGTCTTTCAACTATAGTCTTATTCACTTTCCGAT-ATGATGCCAT-GTGTCTT
1 AGGATGCCATAGTGTCTTTCAACTATGGTCTTATTCA--TTCTGATCATGATGCCATAGTGTCTT
* * *
5421171 TCAACTATGGTCTTATCCATCTT-CGGTAGGTTGCCATAGTGTCTTT-AACTATGGTCTTATAT-
64 TCAACTATGGTCTTATCCA-CTTCCGATAGGATGCCATAGTGTCTTTCAACCATGGTCTTAT-TC
* * *
5421233 ACTTTCCGATATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCGTTTTCGAT
127 ACTTTCCAATATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATATTCGAT
* * **
5421288 TGGATGCCATAGTGTCTTTCAACTATGGTCTTACTCA-TCTGAATCATGATGCCATAGCATCTTT
1 AGGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTCTG-ATCATGATGCCATAGTGTCTTT
*
5421352 CAGCTATG
65 CAACTATG
5421360 ATATTACTTG
Statistics
Matches: 213, Mismatches: 31, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
177 3 0.01
178 2 0.01
179 10 0.05
180 108 0.51
181 21 0.10
182 54 0.25
183 12 0.06
184 3 0.01
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.41
Consensus pattern (181 bp):
AGGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTCTGATCATGATGCCATAGTGTCTTTC
AACTATGGTCTTATCCACTTCCGATAGGATGCCATAGTGTCTTTCAACCATGGTCTTATTCACTT
TCCAATATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATATTCGAT
Found at i:5424845 original size:43 final size:43
Alignment explanation
Indices: 5424744--5424914 Score: 170
Period size: 43 Copynumber: 4.0 Consensus size: 43
5424734 ACAAAAGCTC
* * *
5424744 ATACAATGCC-ATATCCTAGATATGGTCTTACATGTCAAT-GC-
1 ATACAATGCCAATGTCCTAGACATGGTCTTACATGT-AATCACA
* * * * * *
5424785 ATATCGATGCTACTGTCCTAGACAAGGTCTTACACGAAATCACA
1 ATA-CAATGCCAATGTCCTAGACATGGTCTTACATGTAATCACA
* * *
5424829 ATACAATGCCAATGTCCCAGACATGGTCTTATATGTAATCTCA
1 ATACAATGCCAATGTCCTAGACATGGTCTTACATGTAATCACA
*
5424872 ATACAATGCCAATGT-CTCAGACATGGTCGTACATGTAATCACA
1 ATACAATGCCAATGTCCT-AGACATGGTCTTACATGTAATCACA
5424915 TCTCGATAAC
Statistics
Matches: 103, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
41 3 0.03
42 9 0.09
43 88 0.85
44 3 0.03
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.28
Consensus pattern (43 bp):
ATACAATGCCAATGTCCTAGACATGGTCTTACATGTAATCACA
Found at i:5430711 original size:17 final size:18
Alignment explanation
Indices: 5430684--5430717 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5430674 AATTAAATAT
5430684 ATGCATATTAAATTATTA
1 ATGCATATTAAATTATTA
*
5430702 ATGC-TATTAATTTATT
1 ATGCATATTAAATTATT
5430718 TAAACAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
ATGCATATTAAATTATTA
Found at i:5430868 original size:23 final size:23
Alignment explanation
Indices: 5430842--5430888 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
5430832 TAATTGAAAA
5430842 AAAAACTTATCAAATAAAATATG
1 AAAAACTTATCAAATAAAATATG
5430865 AAAAACTTATCAAATAAAATATG
1 AAAAACTTATCAAATAAAATATG
5430888 A
1 A
5430889 TTAAATAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.62, C:0.09, G:0.04, T:0.26
Consensus pattern (23 bp):
AAAAACTTATCAAATAAAATATG
Found at i:5443751 original size:13 final size:13
Alignment explanation
Indices: 5443733--5443761 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5443723 GGTTGTTCAT
5443733 TAAACTAATTAAC
1 TAAACTAATTAAC
5443746 TAAACTAATTAAC
1 TAAACTAATTAAC
5443759 TAA
1 TAA
5443762 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:5453550 original size:21 final size:21
Alignment explanation
Indices: 5453526--5453576 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
5453516 AGAGAGGAGA
*
5453526 GAGTGATGAATGATAAGGGAT
1 GAGTGATGAAGGATAAGGGAT
* *
5453547 GAGTGATGAGGGATGAGGGAT
1 GAGTGATGAAGGATAAGGGAT
*
5453568 GAGGGATGA
1 GAGTGATGA
5453577 GTAGAAATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.47, T:0.20
Consensus pattern (21 bp):
GAGTGATGAAGGATAAGGGAT
Found at i:5453553 original size:14 final size:14
Alignment explanation
Indices: 5453530--5453578 Score: 71
Period size: 14 Copynumber: 3.5 Consensus size: 14
5453520 AGGAGAGAGT
* *
5453530 GATGAATGATAAGG
1 GATGAGTGATGAGG
5453544 GATGAGTGATGAGG
1 GATGAGTGATGAGG
*
5453558 GATGAGGGATGAGG
1 GATGAGTGATGAGG
5453572 GATGAGT
1 GATGAGT
5453579 AGAAATGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.47, T:0.20
Consensus pattern (14 bp):
GATGAGTGATGAGG
Found at i:5453554 original size:7 final size:7
Alignment explanation
Indices: 5453541--5453577 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
5453531 ATGAATGATA
5453541 AGGGATG
1 AGGGATG
*
5453548 AGTGATG
1 AGGGATG
5453555 AGGGATG
1 AGGGATG
5453562 AGGGATG
1 AGGGATG
5453569 AGGGATG
1 AGGGATG
5453576 AG
1 AG
5453578 TAGAAATGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.54, T:0.16
Consensus pattern (7 bp):
AGGGATG
Found at i:5455715 original size:21 final size:21
Alignment explanation
Indices: 5455668--5455720 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
5455658 TCTCAGTTTT
* *
5455668 AGCAACTTCTTCTACTTCAAC
1 AGCAACTTCCTCTACTGCAAC
* * *
5455689 AACAACTTCCTCTTCTGCAGC
1 AGCAACTTCCTCTACTGCAAC
5455710 AGCAACTTCCT
1 AGCAACTTCCT
5455721 TCTCAACAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.36, G:0.08, T:0.30
Consensus pattern (21 bp):
AGCAACTTCCTCTACTGCAAC
Found at i:5466228 original size:46 final size:44
Alignment explanation
Indices: 5466119--5466512 Score: 364
Period size: 45 Copynumber: 8.7 Consensus size: 44
5466109 ATGATTGAAG
* * * *
5466119 GATGCCACAGTGTCTTTCAACCATGGTCTTATTTATTCTCGACT-T
1 GATGCCATAGTGTCTTTCAA-CATGGTCTTATTCATTTTTGA-TAT
* *
5466164 GATGCCATAATATCTTTCAATCATGGTCTTATTCACTTTTTGATAT
1 GATGCCATAGTGTCTTTCAA-CATGGTCTTATTCA-TTTTTGATAT
* *
5466210 GATGCCATAGTGTCTTTCAACCATAGTCTTATGCAGTTTTTGATAT
1 GATGCCATAGTGTCTTTCAA-CATGGTCTTATTCA-TTTTTGATAT
* * * * * *
5466256 AATGCCATAGTGTCTTTTAAATATAGTCTTATCCATTTTTGATAG
1 GATGCCATAGTGTC-TTTCAACATGGTCTTATTCATTTTTGATAT
*
5466301 GATGCAATAGTGTCTTTCAACTATGGTCTTATTCATTTTTTGATAT
1 GATGCCATAGTGTCTTTCAAC-ATGGTCTTATTCA-TTTTTGATAT
* * *
5466347 GATGCCATAGTGTCTTTCAACTATGGCCTTATCCATTTTTGATAG
1 GATGCCATAGTGTCTTTCAAC-ATGGTCTTATTCATTTTTGATAT
* * ***
5466392 GATTCCATAGTGTCTCT-AACTATGGTCTTATTCACTTTCCAATAT
1 GATGCCATAGTGTCTTTCAAC-ATGGTCTTATTCA-TTTTTGATAT
* * *
5466437 GATGCCATAGTGTCTTTCAACTATGGTATTACTCA--TCTGAATCAT
1 GATGCCATAGTGTCTTTCAAC-ATGGTCTTATTCATTTTTG-AT-AT
**
5466482 GATGCCATAGCATCTTTCAACTATGGTCTTA
1 GATGCCATAGTGTCTTTCAAC-ATGGTCTTA
5466513 CTCGATTGAA
Statistics
Matches: 294, Mismatches: 46, Indels: 18
0.82 0.13 0.05
Matches are distributed among these distances:
43 2 0.01
44 22 0.07
45 138 0.47
46 127 0.43
47 5 0.02
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (44 bp):
GATGCCATAGTGTCTTTCAACATGGTCTTATTCATTTTTGATAT
Found at i:5466295 original size:91 final size:90
Alignment explanation
Indices: 5466113--5466463 Score: 386
Period size: 91 Copynumber: 3.9 Consensus size: 90
5466103 ATAGTAATGA
* * * * *
5466113 TTGA-AGGATGCCACAGTGTCTTTCAACCATGGTCTTATTTATTCTCGACT-TGATGCCATAATA
1 TTGATAGGATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCGA-TATGATGCCATAGTG
* *
5466176 TC-TTTCAATCATGGTCTTATTCACTTT
65 TCTTTTAAAT-ATGGTCTTATCCA-TTT
* * * * *
5466203 TTGATATGATGCCATAGTGTCTTTCAACCATAGTCTTATGCAGTTTTTGATATAATGCCATAGTG
1 TTGATAGGATGCCATAGTGTCTTTCAACCATGGTCTTATTCA-TTTTCGATATGATGCCATAGTG
*
5466268 TCTTTTAAATATAGTCTTATCCATTT
65 TCTTTTAAATATGGTCTTATCCATTT
* * *
5466294 TTGATAGGATGCAATAGTGTCTTTCAACTATGGTCTTATTCATTTTTTGATATGATGCCATAGTG
1 TTGATAGGATGCCATAGTGTCTTTCAACCATGGTCTTATTCA-TTTTCGATATGATGCCATAGTG
* * *
5466359 TCTTTCAACTATGGCCTTATCCATTT
65 TCTTTTAAATATGGTCTTATCCATTT
* * * * *
5466385 TTGATAGGATTCCATAGTGTCTCT-AACTATGGTCTTATTCACTTTCCAATATGATGCCATAGTG
1 TTGATAGGATGCCATAGTGTCTTTCAACCATGGTCTTATTCA-TTTTCGATATGATGCCATAGTG
* *
5466449 TCTTTCAACTATGGT
65 TCTTTTAAATATGGT
5466464 ATTACTCATC
Statistics
Matches: 225, Mismatches: 32, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
90 54 0.24
91 137 0.61
92 28 0.12
93 6 0.03
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (90 bp):
TTGATAGGATGCCATAGTGTCTTTCAACCATGGTCTTATTCATTTTCGATATGATGCCATAGTGT
CTTTTAAATATGGTCTTATCCATTT
Found at i:5466490 original size:90 final size:90
Alignment explanation
Indices: 5466117--5466512 Score: 322
Period size: 91 Copynumber: 4.4 Consensus size: 90
5466107 TAATGATTGA
* * * * * * *
5466117 AGGATGCCACAGTGTCTTTCAACCATGGTCTTATTTA-TTCTCGACT-TGATGCCATAATATCTT
1 AGGATGCCATAGTGTCTTTCAACTATGGTCTTATTCACTT-TCCAATATGATGCCATAGTGTCTT
* *
5466180 TCAA-TCATGGTC-TTATTCACTTTTTGAT
65 TCAACT-ATGG-CATTA-TC-CATTCTGAT
* * * * * *** *
5466208 ATGATGCCATAGTGTCTTTCAACCATAGTCTTATGCAGTTTTTGATATAATGCCATAGTGTCTTT
1 AGGATGCCATAGTGTCTTTCAACTATGGTCTTATTCACTTTCCAATATGATGCCATAGTGTCTTT
* * * *
5466273 TAAATATAGTC-TTATCCATTTTTGAT
66 CAACTAT-GGCATTATCCA-TTCTGAT
* * ***
5466299 AGGATGCAATAGTGTCTTTCAACTATGGTCTTATTCATTTTTTGATATGATGCCATAGTGTCTTT
1 AGGATGCCATAGTGTCTTTCAACTATGGTCTTATTCACTTTCCAATATGATGCCATAGTGTCTTT
* *
5466364 CAACTATGGCCTTATCCATTTTTGAT
66 CAACTATGGCATTATCCA-TTCTGAT
* *
5466390 AGGATTCCATAGTGTCTCT-AACTATGGTCTTATTCACTTTCCAATATGATGCCATAGTGTCTTT
1 AGGATGCCATAGTGTCTTTCAACTATGGTCTTATTCACTTTCCAATATGATGCCATAGTGTCTTT
*
5466454 CAACTATGGTATTA-CTCA-TCTGAAT
66 CAACTATGGCATTATC-CATTCTG-AT
* **
5466479 CATGATGCCATAGCATCTTTCAACTATGGTCTTA
1 -AGGATGCCATAGTGTCTTTCAACTATGGTCTTA
5466513 CTCGATTGAA
Statistics
Matches: 255, Mismatches: 40, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
88 3 0.01
89 3 0.01
90 72 0.28
91 150 0.59
92 25 0.10
93 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.42
Consensus pattern (90 bp):
AGGATGCCATAGTGTCTTTCAACTATGGTCTTATTCACTTTCCAATATGATGCCATAGTGTCTTT
CAACTATGGCATTATCCATTCTGAT
Found at i:5466514 original size:45 final size:43
Alignment explanation
Indices: 5466313--5466535 Score: 157
Period size: 45 Copynumber: 4.9 Consensus size: 43
5466303 TGCAATAGTG
* **
5466313 TCTTTCAACTATGGTCTTATTCATTTTTTG-ATATGATGCCATAGTG
1 TCTTTCAACTATGGTCTTACTCA----TTGAATATGATGCCATAGCA
* * * **
5466359 TCTTTCAACTATGGCCTTA-TCCATTTTTG-ATAGGATTCCATAGTG
1 TCTTTCAACTATGGTCTTACT-CA---TTGAATATGATGCCATAGCA
* * * **
5466404 TCTCT-AACTATGGTCTTATTCACTTTCCAATATGATGCCATAGTG
1 TCTTTCAACTATGGTCTTACTCA--TT-GAATATGATGCCATAGCA
*
5466449 TCTTTCAACTATGGTATTACTCATCTGAATCATGATGCCATAGCA
1 TCTTTCAACTATGGTCTTACTCAT-TGAAT-ATGATGCCATAGCA
5466494 TCTTTCAACTATGGTCTTACTCGATTGAATAATGATGCCATA
1 TCTTTCAACTATGGTCTTACTC-ATTGAAT-ATGATGCCATA
5466536 TCATGTAACA
Statistics
Matches: 152, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
43 3 0.02
44 18 0.12
45 94 0.62
46 37 0.24
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (43 bp):
TCTTTCAACTATGGTCTTACTCATTGAATATGATGCCATAGCA
Found at i:5470278 original size:80 final size:81
Alignment explanation
Indices: 5470107--5470304 Score: 256
Period size: 80 Copynumber: 2.5 Consensus size: 81
5470097 TTTAGTTTAC
** * *
5470107 TAAAATTACCGAAA-TACCCTTAGTTTGTAAAATTACTGAAATACCCTCGATTTGTAAAATTACT
1 TAAAATTACC-AAAGTACCCTCGGTTTATAAAATTACCGAAATACCCTCGATTTGTAAAATTACT
*
5470171 GAAATACCTTCAACTTG
65 GAAATACCCTCAACTTG
* * *
5470188 TAAAATTACCAAAGTACCCCCGGTTTATAAAATTACCGAAATATCGTCGA-TTGTAAAATTACTG
1 TAAAATTACCAAAGTACCCTCGGTTTATAAAATTACCGAAATACCCTCGATTTGTAAAATTACTG
* *
5470252 AAATGCCCTCAATTTG
66 AAATACCCTCAACTTG
* * *
5470268 TAAAATTACCAAAGTACCCTCGATTTACAGAATTACC
1 TAAAATTACCAAAGTACCCTCGGTTTATAAAATTACC
5470305 ATTTTAGCCT
Statistics
Matches: 102, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
80 63 0.62
81 39 0.38
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (81 bp):
TAAAATTACCAAAGTACCCTCGGTTTATAAAATTACCGAAATACCCTCGATTTGTAAAATTACTG
AAATACCCTCAACTTG
Found at i:5470288 original size:27 final size:26
Alignment explanation
Indices: 5470107--5470597 Score: 191
Period size: 27 Copynumber: 18.2 Consensus size: 26
5470097 TTTAGTTTAC
*
5470107 TAAAATTACCGAAATACCCT-TAGTTTG
1 TAAAATTACC-AAATACCCTCGA-TTTG
*
5470134 TAAAATTACTGAAATACCCTCGATTTG
1 TAAAATTAC-CAAATACCCTCGATTTG
* * * *
5470161 TAAAATTACTGAAATACCTTCAACTTG
1 TAAAATTAC-CAAATACCCTCGATTTG
* * *
5470188 TAAAATTACCAAAGTACCCCCGGTTTA
1 TAAAATTACCAAA-TACCCTCGATTTG
* *
5470215 TAAAATTACCGAAATATCGTCGA-TTG
1 TAAAATTACC-AAATACCCTCGATTTG
* * *
5470241 TAAAATTACTGAAATGCCCTCAATTTG
1 TAAAATTAC-CAAATACCCTCGATTTG
*
5470268 TAAAATTACCAAAGTACCCTCGATTTA
1 TAAAATTACCAAA-TACCCTCGATTTG
* * ** * *
5470295 CAGAATTACCATTTTAGCCTCGATTTA
1 TAAAATTACCA-AATACCCTCGATTTG
* ** *
5470322 TAGAATTACCATTTTACCCTCGATTTA
1 TAAAATTACCA-AATACCCTCGATTTG
* *** ** *
5470349 TAGAATTACCGTTTTACCCTTAATTTA
1 TAAAATTACC-AAATACCCTCGATTTG
* * * ** * *
5470376 CAGAATTATCATTTTACCCTCAATTTA
1 TAAAATTACCA-AATACCCTCGATTTG
* * * * *
5470403 CAGAATT-GCAATTTTACCCTCGATTTA
1 TAAAATTACCAA--ATACCCTCGATTTG
* * * * *
5470430 CAAAATTACTAAAATACCCTTGGTTTA
1 TAAAATTAC-CAAATACCCTCGATTTG
*
5470457 TAAAATTACCAAAATACCCTCGATTAG
1 TAAAATTACC-AAATACCCTCGATTTG
* * *
5470484 TAAAATTACGAAAATACCCCTTG-TTTA
1 TAAAATTAC-CAAATA-CCCTCGATTTG
* * *
5470511 TAAAATTACTAAAATACTCCT-GGTTTA
1 TAAAATTAC-CAAATAC-CCTCGATTTG
* *
5470538 TAAAATTACCAAAATACCCCCGATTTA
1 TAAAATTACC-AAATACCCTCGATTTG
* * * *
5470565 TGAAATTATCGAAATACTCTCAATTTG
1 TAAAATTA-CCAAATACCCTCGATTTG
5470592 TAAAAT
1 TAAAAT
5470598 ATTGAAATAC
Statistics
Matches: 372, Mismatches: 70, Indels: 44
0.77 0.14 0.09
Matches are distributed among these distances:
26 31 0.08
27 329 0.88
28 10 0.03
29 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.09, T:0.34
Consensus pattern (26 bp):
TAAAATTACCAAATACCCTCGATTTG
Found at i:5470464 original size:81 final size:81
Alignment explanation
Indices: 5470269--5470467 Score: 227
Period size: 81 Copynumber: 2.5 Consensus size: 81
5470259 CTCAATTTGT
* * * * * *
5470269 AAAATTACCAAAGTACCCTCGATTTACAGAATTACCATTTTAGCCTCGATTTATAGAATTACCAT
1 AAAATTACCAAAATACCCTTGATTTACAGAATTACCATTTTACCCTCAATTTACAGAATTACAAT
*
5470334 TTTACCCTCGATTTAT
66 TTTACCCTCGATTTAC
* **** * * *
5470350 AGAATTACCGTTTTACCCTTAATTTACAGAATTATCATTTTACCCTCAATTTACAGAATTGCAAT
1 AAAATTACCAAAATACCCTTGATTTACAGAATTACCATTTTACCCTCAATTTACAGAATTACAAT
5470415 TTTACCCTCGATTTAC
66 TTTACCCTCGATTTAC
* * * *
5470431 AAAATTACTAAAATACCCTTGGTTTATAAAATTACCA
1 AAAATTACCAAAATACCCTTGATTTACAGAATTACCA
5470468 AAATACCCTC
Statistics
Matches: 93, Mismatches: 25, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
81 93 1.00
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (81 bp):
AAAATTACCAAAATACCCTTGATTTACAGAATTACCATTTTACCCTCAATTTACAGAATTACAAT
TTTACCCTCGATTTAC
Found at i:5470571 original size:81 final size:82
Alignment explanation
Indices: 5470426--5470578 Score: 240
Period size: 81 Copynumber: 1.9 Consensus size: 82
5470416 TTACCCTCGA
*
5470426 TTTACAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCTCGATTAGTAAAATT
1 TTTACAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCCGATTAGTAAAATT
5470491 A-CGAAAATACCCCTTG
66 ATCGAAAATACCCCTTG
* *
5470507 TTTATAAAATTACTAAAATACTCC-TGGTTTATAAAATTACCAAAATACCCCCGATTTA-TGAAA
1 TTTACAAAATTACTAAAATAC-CCTTGGTTTATAAAATTACCAAAATACCCCCGA-TTAGTAAAA
5470570 TTATCGAAA
64 TTATCGAAA
5470579 TACTCTCAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
81 56 0.85
82 10 0.15
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.32
Consensus pattern (82 bp):
TTTACAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCCGATTAGTAAAATT
ATCGAAAATACCCCTTG
Found at i:5470643 original size:27 final size:27
Alignment explanation
Indices: 5470601--5470781 Score: 290
Period size: 27 Copynumber: 6.7 Consensus size: 27
5470591 GTAAAATATT
5470601 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* *
5470628 GAAATACCCCTATAGGGTAAAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
*
5470655 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
*
5470682 GAAATACCCCTGTAGGGTAGAATTACT
1 GAAATACCCCTGTAGGGTAGAATTACC
5470709 GAAATACCCCTGTAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
*
5470736 GAAATACCCCTATAGGGTAGAATTACC
1 GAAATACCCCTGTAGGGTAGAATTACC
* * *
5470763 GAGATACCCTTGTGGGGTA
1 GAAATACCCCTGTAGGGTA
5470782 AAATACCATT
Statistics
Matches: 143, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 143 1.00
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (27 bp):
GAAATACCCCTGTAGGGTAGAATTACC
Found at i:5471785 original size:27 final size:27
Alignment explanation
Indices: 5471747--5471807 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
5471737 TATAACTGGA
*
5471747 GTATTTCGATAATTCTACCCTACAGGG
1 GTATTTCGATAATTCTACACTACAGGG
5471774 GTATTTCGATAATTCTACACTACAGGG
1 GTATTTCGATAATTCTACACTACAGGG
5471801 GTATTTC
1 GTATTTC
5471808 AATTATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (27 bp):
GTATTTCGATAATTCTACACTACAGGG
Found at i:5472244 original size:27 final size:27
Alignment explanation
Indices: 5471812--5472234 Score: 367
Period size: 27 Copynumber: 15.6 Consensus size: 27
5471802 TATTTCAATT
* ***
5471812 ATTTTATAAATCGAGGGTAAAATGGTA
1 ATTTTACAAATCGAGGGTATTTTGGTA
* ** * *
5471839 ATTCTGTAAATCGGGGGTACTTTGGTA
1 ATTTTACAAATCGAGGGTATTTTGGTA
* ***
5471866 ATTTTTACAAGTCGAGGGTATTTCAATA
1 A-TTTTACAAATCGAGGGTATTTTGGTA
* ***
5471894 ATTTTACAAATCGACGGTATTTCAATA
1 ATTTTACAAATCGAGGGTATTTTGGTA
* *
5471921 ATTTTTCAAA-CTGAGGGTATTTCGGTA
1 ATTTTACAAATC-GAGGGTATTTTGGTA
*
5471948 ATTTCACAAATC-AGGGGTATTTTGGTA
1 ATTTTACAAATCGA-GGGTATTTTGGTA
*
5471975 ATTTTACAAA-CCAGGGGTATTTTGGTA
1 ATTTTACAAATCGA-GGGTATTTTGGTA
** * *
5472002 ATTTTGTAAACCAAGGGTATTTTGGTA
1 ATTTTACAAATCGAGGGTATTTTGGTA
* **
5472029 ATTTTACAAGTCGAGGGTATTTCAGTA
1 ATTTTACAAATCGAGGGTATTTTGGTA
*
5472056 ATTTCACAAATC-AGTGGTATTTTGGTA
1 ATTTTACAAATCGAG-GGTATTTTGGTA
*
5472083 ATTTTACAAGTCGAGGGTATTTTGGTA
1 ATTTTACAAATCGAGGGTATTTTGGTA
* *
5472110 ATTTCACAAAT-TAGGGGTATTTTGGTA
1 ATTTTACAAATCGA-GGGTATTTTGGTA
* * *
5472137 ATTTCACAAA-CTAAAGGTATTTTGGTA
1 ATTTTACAAATC-GAGGGTATTTTGGTA
*
5472164 ATTTTACAAA-CTAGGGGTATTTTGGTA
1 ATTTTACAAATCGA-GGGTATTTTGGTA
* *
5472191 ATTTTACAAA-CCAGGGGTATTTTAGTA
1 ATTTTACAAATCGA-GGGTATTTTGGTA
5472218 ATTTTACAAATCGAGGG
1 ATTTTACAAATCGAGGG
5472235 CATCTTAGTA
Statistics
Matches: 331, Mismatches: 52, Indels: 26
0.81 0.13 0.06
Matches are distributed among these distances:
26 7 0.02
27 298 0.90
28 26 0.08
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (27 bp):
ATTTTACAAATCGAGGGTATTTTGGTA
Found at i:5472256 original size:81 final size:80
Alignment explanation
Indices: 5471770--5472257 Score: 366
Period size: 81 Copynumber: 6.0 Consensus size: 80
5471760 TCTACCCTAC
* * * * * * * * ***
5471770 AGGGGTATTTCGATAATTCTAC-ACTACAGGGGTATTTCAATTATTTTATAAATCGAGGGTAAAA
1 AGGGGTATTTTGGTAATTTTACAAAT-CAGGGGTATTTTAGTAATTTTACAAATCGAGGGTATTT
5471834 TGGTAATTCTGTAAA-T
65 TGGTAATT-TGTAAACT
* * * * * *
5471850 CGGGGGTACTTTGGTAATTTTTACAAGTC-GAGGGTATTTCAATAATTTTACAAATCGACGGTAT
1 -AGGGGTATTTTGGTAA-TTTTACAAATCAG-GGGTATTTTAGTAATTTTACAAATCGAGGGTAT
*** *
5471914 TTCAATAATTTTTCAAACT
63 TTTGGTAATTTGT-AAACT
* * * *
5471933 -GAGGGTATTTCGGTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAA-CCAGGGGTATT
1 AG-GGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTAGTAATTTTACAAATCGA-GGGTATT
*
5471996 TTGGTAATTTTGTAAACC
64 TTGGTAA-TTTGTAAACT
* * * *
5472014 AAGGGTATTTTGGTAATTTTACAAGTC-GAGGGTATTTCAGTAATTTCACAAATC-AGTGGTATT
1 AGGGGTATTTTGGTAATTTTACAAATCAG-GGGTATTTTAGTAATTTTACAAATCGAG-GGTATT
*
5472077 TTGGTAATTT-TACAAGT
64 TTGGTAATTTGTA-AACT
* * * * * * *
5472094 CGAGGGTATTTTGGTAATTTCACAAATTAGGGGTATTTTGGTAATTTCACAAA-CTAAAGGTATT
1 AG-GGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTAGTAATTTTACAAATC-GAGGGTATT
5472158 TTGGTAATTT-TACAAACT
64 TTGGTAATTTGT--AAACT
* * *
5472176 AGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGTAATTTTACAAATCGAGGGCATCTT
1 AGGGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTAGTAATTTTACAAATCGAGGGTATTTT
* *
5472241 AGTACTTTGGTAAACT
66 GGTAATTT-GTAAACT
5472257 A
1 A
5472258 AAGTATTCTA
Statistics
Matches: 324, Mismatches: 60, Indels: 46
0.75 0.14 0.11
Matches are distributed among these distances:
79 2 0.01
80 10 0.03
81 239 0.74
82 68 0.21
83 5 0.02
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.38
Consensus pattern (80 bp):
AGGGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTAGTAATTTTACAAATCGAGGGTATTTT
GGTAATTTGTAAACT
Found at i:5473244 original size:25 final size:25
Alignment explanation
Indices: 5473210--5473303 Score: 118
Period size: 25 Copynumber: 3.8 Consensus size: 25
5473200 AGGAAGTGCT
*
5473210 AAAAGGGCTTTGCCCCAGGTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
5473235 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
*** * *
5473260 AAAAGGG-AAAGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCG
*
5473284 AAAAGGGCTTTTCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
5473304 ATTAAAAGAG
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
24 19 0.33
25 39 0.67
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:5476615 original size:93 final size:93
Alignment explanation
Indices: 5476453--5476624 Score: 247
Period size: 93 Copynumber: 1.8 Consensus size: 93
5476443 GTTTCTAGTG
* * *
5476453 ACCAAGAGAAGACAACTTTCACTTGTCCATATGGTACTATTGCGTTTAGACGAATGTCATTCGAG
1 ACCAAGAAAAGACAACTTTCACTTGTCCATATGGTACTATTGCGTTTAGACGAATGTCATTCAAC
*
5476518 TTATGTAATTCCCCCATTGCTCTCAATA
66 TTATGTAATGCCCCCATTGCTCTCAATA
* * * * *
5476546 ACCAAGAAAAGATAACTTTCA-TGTGTCCATATGGTACTTTTGTGTTTAGACGATTGTCGTTCAA
1 ACCAAGAAAAGACAACTTTCACT-TGTCCATATGGTACTATTGCGTTTAGACGAATGTCATTCAA
5476610 CTTATGTAATGCCCC
65 CTTATGTAATGCCCC
5476625 TATAACTTTT
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
92 1 0.01
93 68 0.99
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (93 bp):
ACCAAGAAAAGACAACTTTCACTTGTCCATATGGTACTATTGCGTTTAGACGAATGTCATTCAAC
TTATGTAATGCCCCCATTGCTCTCAATA
Found at i:5482815 original size:40 final size:39
Alignment explanation
Indices: 5482717--5482979 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
5482707 TCCTCGTTCA
* * * *
5482717 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
5482756 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
5482795 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
5482835 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
5482875 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
5482915 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
5482956 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
5482980 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:5482939 original size:120 final size:119
Alignment explanation
Indices: 5482717--5482979 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
5482707 TCCTCGTTCA
* * *
5482717 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
5482782 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
5482835 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
5482900 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
5482956 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
5482980 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:5482988 original size:41 final size:41
Alignment explanation
Indices: 5482911--5482988 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
5482901 TTTGTATCTC
* * *
5482911 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
5482952 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
5482989 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:5491214 original size:31 final size:31
Alignment explanation
Indices: 5491178--5491239 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
5491168 TAAATCTCTT
5491178 ACATTTGTGATTTCTTTATCTTCAACCTTTA
1 ACATTTGTGATTTCTTTATCTTCAACCTTTA
5491209 ACATTTGTGATTTCTTTATCTTCAACCTTTA
1 ACATTTGTGATTTCTTTATCTTCAACCTTTA
5491240 CTCTAGTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.19, G:0.06, T:0.52
Consensus pattern (31 bp):
ACATTTGTGATTTCTTTATCTTCAACCTTTA
Found at i:5491578 original size:140 final size:140
Alignment explanation
Indices: 5491326--5491599 Score: 431
Period size: 140 Copynumber: 2.0 Consensus size: 140
5491316 AAAATTGCAG
* ** *
5491326 AGTCATCATGCACAGACATTTCTCAACCAAATACATTCTTCAACTCTACTGTGGCTACAAGGTAC
1 AGTCATCATGCACAGACATTTCTCAACCAAAGACATTCTTCAACTCTACTGTGAATACAAAGTAC
* *
5491391 TCAAATAATATTCTAAAGCATCCCTTTTGTTTTGAGTAGGGATTCTTATTTAAGGATGAACCCTA
66 TCAAATAATATTCTAAAGCATCCCTTTTGTTTTGAGCAGGGATTCTTATTTAAGGATGAACCATA
5491456 TATATCACGA
131 TATATCACGA
* ** * **
5491466 AGTCATCATGCACTGATGTTTCTCAACGAAAGACATTCTTCAACTCTGTTGTGAATACAAAGTAC
1 AGTCATCATGCACAGACATTTCTCAACCAAAGACATTCTTCAACTCTACTGTGAATACAAAGTAC
*
5491531 TCAAATGATATTCTAAAGCATCCCTTTTGTTTTGAGCAGGGATTCTTATTTAAGGATGAACCATA
66 TCAAATAATATTCTAAAGCATCCCTTTTGTTTTGAGCAGGGATTCTTATTTAAGGATGAACCATA
5491596 TATA
131 TATA
5491600 GGGTATGATG
Statistics
Matches: 121, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
140 121 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (140 bp):
AGTCATCATGCACAGACATTTCTCAACCAAAGACATTCTTCAACTCTACTGTGAATACAAAGTAC
TCAAATAATATTCTAAAGCATCCCTTTTGTTTTGAGCAGGGATTCTTATTTAAGGATGAACCATA
TATATCACGA
Found at i:5503955 original size:41 final size:40
Alignment explanation
Indices: 5503828--5503972 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
5503818 CTCGCACAAG
* * * * *
5503828 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
*
5503868 GCCTTCGGGACTTAGCCCGGATATAGTCTCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
5503908 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
5503949 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
5503973 CATTCGAGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.03
40 58 0.64
41 27 0.30
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:5505880 original size:70 final size:70
Alignment explanation
Indices: 5505767--5505902 Score: 263
Period size: 70 Copynumber: 1.9 Consensus size: 70
5505757 GTTTCCCAAA
5505767 TAGCTTCCTCGATCCCGTGTTTGAGCCATAACACCTTTACTAACGGAACCCTTTTGTTTCGCAAC
1 TAGCTTCCTCGATCCCGTGTTTGAGCCATAACACCTTTACTAACGGAACCCTTTTGTTTCGCAAC
5505832 TCAAG
66 TCAAG
*
5505837 TAGCTTTCTCGATCCCGTGTTTGAGCCATAACACCTTTACTAACGGAACCCTTTTGTTTCGCAAC
1 TAGCTTCCTCGATCCCGTGTTTGAGCCATAACACCTTTACTAACGGAACCCTTTTGTTTCGCAAC
5505902 T
66 T
5505903 TTTTCACTTC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.33
Consensus pattern (70 bp):
TAGCTTCCTCGATCCCGTGTTTGAGCCATAACACCTTTACTAACGGAACCCTTTTGTTTCGCAAC
TCAAG
Found at i:5512079 original size:41 final size:40
Alignment explanation
Indices: 5511952--5512096 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
5511942 CTCGCACAAG
* * * * *
5511952 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
*
5511992 GCCTTCGGGACTTAGCCCGGATATAGTCTCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
5512032 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
5512073 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
5512097 CATTCGAGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.03
40 58 0.64
41 27 0.30
42 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:5513386 original size:38 final size:38
Alignment explanation
Indices: 5513330--5513405 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
5513320 AAAAGGATGA
5513330 ACAAATTTTCTTTCTTTCTTTTCTTCACTCACGGCAAT
1 ACAAATTTTCTTTCTTTCTTTTCTTCACTCACGGCAAT
*
5513368 ACAAATTTTCTTTTTTTCTTTTCTTCACTCACGGCAAT
1 ACAAATTTTCTTTCTTTCTTTTCTTCACTCACGGCAAT
5513406 GGGGGGGGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.21, C:0.25, G:0.05, T:0.49
Consensus pattern (38 bp):
ACAAATTTTCTTTCTTTCTTTTCTTCACTCACGGCAAT
Found at i:5515035 original size:8 final size:8
Alignment explanation
Indices: 5515022--5515067 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
5515012 TTGGCAAATC
5515022 CCGAAAAG
1 CCGAAAAG
5515030 CCGAAATA-
1 CCGAAA-AG
5515038 CCGAAAAG
1 CCGAAAAG
* *
5515046 CTGAAATG
1 CCGAAAAG
5515054 CCGAAAAG
1 CCGAAAAG
5515062 CCGAAA
1 CCGAAA
5515068 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 1 0.03
8 30 0.94
9 1 0.03
ACGTcount: A:0.48, C:0.24, G:0.22, T:0.07
Consensus pattern (8 bp):
CCGAAAAG
Found at i:5515041 original size:16 final size:16
Alignment explanation
Indices: 5515017--5515067 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
5515007 GTAGATTGGC
*
5515017 AAATCCCGAAAAGCCG
1 AAATACCGAAAAGCCG
*
5515033 AAATACCGAAAAGCTG
1 AAATACCGAAAAGCCG
*
5515049 AAATGCCGAAAAGCCG
1 AAATACCGAAAAGCCG
5515065 AAA
1 AAA
5515068 GTTTGGCTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.49, C:0.24, G:0.20, T:0.08
Consensus pattern (16 bp):
AAATACCGAAAAGCCG
Found at i:5515360 original size:27 final size:29
Alignment explanation
Indices: 5515290--5515365 Score: 102
Period size: 27 Copynumber: 2.7 Consensus size: 29
5515280 TGTAAAAGTG
* *
5515290 ATTGGGCCTAGTGGGCCATATAGATGTGA
1 ATTGGGCCTAGTGGGCCATATAGATATAA
* *
5515319 TTTGGGCCTAATGGGCCATAT-GA-ATAA
1 ATTGGGCCTAGTGGGCCATATAGATATAA
5515346 ATTGGGCCTAGTGGGCCATA
1 ATTGGGCCTAGTGGGCCATA
5515366 AGCATGTATG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 20 0.49
28 2 0.05
29 19 0.46
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.28
Consensus pattern (29 bp):
ATTGGGCCTAGTGGGCCATATAGATATAA
Found at i:5517069 original size:34 final size:34
Alignment explanation
Indices: 5517026--5517094 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
5517016 CTCTACTTGC
5517026 ACTAGATAAATCTTCCTAGAAAATATGAGAAGAT
1 ACTAGATAAATCTTCCTAGAAAATATGAGAAGAT
5517060 ACTAGATAAATCTTCCTAGAAAATATGAGAAGAT
1 ACTAGATAAATCTTCCTAGAAAATATGAGAAGAT
5517094 A
1 A
5517095 AATCTTGGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (34 bp):
ACTAGATAAATCTTCCTAGAAAATATGAGAAGAT
Found at i:5518554 original size:180 final size:180
Alignment explanation
Indices: 5518252--5518602 Score: 558
Period size: 180 Copynumber: 1.9 Consensus size: 180
5518242 ACGGAACTCC
* * * *
5518252 AAATTAAGATCTGTTAATTTTCTCAGAAACTATACTCACATATATTCTTACCATAAAATTTGCAG
1 AAATTAAGAACTGCTAATTTTCCCAGAAACTAGACTCACATATATTCTTACCATAAAATTTGCAG
** *
5518317 AATTTTTGGTTTAGCCAATTAGTACAGTTTATTCATTAAAGGTACCCCTATTTCACTGTCCAATA
66 AATTTTTGGTTTAGCCAATTAGTACAGTTTATTCATTAAAAATACCCCTATTTCACTGTCCAACA
*
5518382 GTTCCAACCTCTCTTCACTAAAAATTATTTATCTCATGGTAAGGAAATTG
131 GTTCCAACATCTCTTCACTAAAAATTATTTATCTCATGGTAAGGAAATTG
**
5518432 AAATTAAGAACTGCTAATTTTCCCAGAAACTAGACTCACATATATTCTTACCATAAAATTTTTAG
1 AAATTAAGAACTGCTAATTTTCCCAGAAACTAGACTCACATATATTCTTACCATAAAATTTGCAG
** **
5518497 AATTTTTGGTTTAGCCAATTAGTACAGTTTATTGGTTAAAAATACCCCTATTTCACTGTCTGACA
66 AATTTTTGGTTTAGCCAATTAGTACAGTTTATTCATTAAAAATACCCCTATTTCACTGTCCAACA
* *
5518562 GTTCCAATATTTCTTCACTAAAAATTATTTATCTCATGGTA
131 GTTCCAACATCTCTTCACTAAAAATTATTTATCTCATGGTA
5518603 CAGATCTTGG
Statistics
Matches: 155, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
180 155 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (180 bp):
AAATTAAGAACTGCTAATTTTCCCAGAAACTAGACTCACATATATTCTTACCATAAAATTTGCAG
AATTTTTGGTTTAGCCAATTAGTACAGTTTATTCATTAAAAATACCCCTATTTCACTGTCCAACA
GTTCCAACATCTCTTCACTAAAAATTATTTATCTCATGGTAAGGAAATTG
Found at i:5519340 original size:51 final size:51
Alignment explanation
Indices: 5519273--5519606 Score: 246
Period size: 51 Copynumber: 6.6 Consensus size: 51
5519263 CTGATACATG
5519273 TAGTAGCCTACACTTAGTACTACACATGTGATCGAAGTTAACGGGTACGCA
1 TAGTAGCCTACACTTAGTACTACACATGTGATCGAAGTTAACGGGTACGCA
* *
5519324 TAGTAGCCTATACTTAGTACTACACACGTGATCGAAGTTAACGGGTACGCA
1 TAGTAGCCTACACTTAGTACTACACATGTGATCGAAGTTAACGGGTACGCA
* ** * * * *
5519375 TAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAATCCGGTACACG
1 TAGTAGCCTACACTTAGTACTACACATGTGATCGAAGTTAA-CGGGTACGCA
* ** * * ** *** * * *
5519425 TAGTTGCCTACACTTAGTACTACACACATGACCTAA-ACATTTGATACACG
1 TAGTAGCCTACACTTAGTACTACACATGTGATCGAAGTTAACGGGTACGCA
* * * * ** *
5519475 TAGTAGCTTGCACTTAGTACTACACACGTGATCAAAACTATCGGGTACGCA
1 TAGTAGCCTACACTTAGTACTACACATGTGATCGAAGTTAACGGGTACGCA
** * * * * * * * *
5519526 TAGTAGCCTGTACTTAGTACTAGACATGCGACCTAA--CAATCTGGTACACG
1 TAGTAGCCTACACTTAGTACTACACATGTGATCGAAGTTAA-CGGGTACGCA
* *
5519576 TAGTAGCCTGCACTTAGTACTACACACGTGA
1 TAGTAGCCTACACTTAGTACTACACATGTGA
5519607 CCTAAAATTG
Statistics
Matches: 228, Mismatches: 51, Indels: 9
0.79 0.18 0.03
Matches are distributed among these distances:
49 4 0.02
50 107 0.47
51 117 0.51
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (51 bp):
TAGTAGCCTACACTTAGTACTACACATGTGATCGAAGTTAACGGGTACGCA
Found at i:5519522 original size:202 final size:201
Alignment explanation
Indices: 5519165--5519610 Score: 597
Period size: 202 Copynumber: 2.2 Consensus size: 201
5519155 GAAGCTCTAT
* * *
5519165 GGTACGCATAGTAGCCTTCACTTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCCGGTACACGTAGTAGC
* * * ** *
5519230 ATGCACTTAGTACTACACACGTGACTTATCCATCTGATACATGTAGTAGCCTACACTTAGTACTA
66 ATACACTTAGTACTACACACATGACCTAAACATCTGATACACGTAGTAGCCTACACTTAGTACTA
* * ** * *
5519295 CACATGTGATCGAAGTTAACGGGTACGCATAGTAGCCTATACTTAGTACTACACACGTGATCGAA
131 CACACGTGATCAAAACTAACGGGTACGCATAGTAGCCTATACTTAGTACTACACACGCGACCGAA
*
5519360 GTTAA-CG
196 --CAATCG
*
5519367 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCCGGTACACGTAGTTGC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCCGGTACACGTAGTAGC
* * * *
5519432 CTACACTTAGTACTACACACATGACCTAAACATTTGATACACGTAGTAGCTTGCACTTAGTACTA
66 ATACACTTAGTACTACACACATGACCTAAACATCTGATACACGTAGTAGCCTACACTTAGTACTA
* * * * *
5519497 CACACGTGATCAAAACTATCGGGTACGCATAGTAGCCTGTACTTAGTACTAGACATGCGACCTAA
131 CACACGTGATCAAAACTAACGGGTACGCATAGTAGCCTATACTTAGTACTACACACGCGACCGAA
*
5519562 CAATCT
196 CAATCG
* * *
5519568 GGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTA
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTA
5519611 AAATTGTCTT
Statistics
Matches: 213, Mismatches: 30, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
200 2 0.01
201 41 0.19
202 170 0.80
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (201 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCCGGTACACGTAGTAGC
ATACACTTAGTACTACACACATGACCTAAACATCTGATACACGTAGTAGCCTACACTTAGTACTA
CACACGTGATCAAAACTAACGGGTACGCATAGTAGCCTATACTTAGTACTACACACGCGACCGAA
CAATCG
Found at i:5519535 original size:151 final size:151
Alignment explanation
Indices: 5519171--5519612 Score: 483
Period size: 151 Copynumber: 2.9 Consensus size: 151
5519161 CTATGGTACG
* * * ** * * * * *
5519171 CATAGTAGCCTTCACTTAGTACTACACATGCGA-CCTATC-AATCTGGTACACGTAGTAGCATGC
1 CATAGTAGCCTACACTTAGTACTACACACGTGATCAAAACTAA-CGGGTACGCATAGTAGCCTGC
* * * * *
5519234 ACTTAGTACTACACACGTGACTTATCCATCTGATACATGTAGTAGCCTACACTTAGTACTACACA
65 ACTTAGTACTACACATGTGACCTATCAATCTGGTACACGTAGTAGCCTACACTTAGTACTACACA
* * * ** * *
5519299 TGTGATCGAAGTTAACGGGTACG
130 CGTGACCTAA-ACAACGGATACA
* * **
5519322 CATAGTAGCCTATACTTAGTACTACACACGTGATCGAAGTTAACGGGTACGCATAGTAGCCTGCA
1 CATAGTAGCCTACACTTAGTACTACACACGTGATCAAAACTAACGGGTACGCATAGTAGCCTGCA
* *
5519387 CTTAGTACTACACATGTGACCTATCAATCCGGTACACGTAGTTGCCTACACTTAGTACTACACAC
66 CTTAGTACTACACATGTGACCTATCAATCTGGTACACGTAGTAGCCTACACTTAGTACTACACAC
* ***
5519452 ATGACCTAAACATTTGATACA
131 GTGACCTAAACAACGGATACA
* * * * *
5519473 CGTAGTAGCTTGCACTTAGTACTACACACGTGATCAAAACTATCGGGTACGCATAGTAGCCTGTA
1 CATAGTAGCCTACACTTAGTACTACACACGTGATCAAAACTAACGGGTACGCATAGTAGCCTGCA
* * * *
5519538 CTTAGTACTAGACATGCGACCTAACAATCTGGTACACGTAGTAGCCTGCACTTAGTACTACACAC
66 CTTAGTACTACACATGTGACCTATCAATCTGGTACACGTAGTAGCCTACACTTAGTACTACACAC
5519603 GTGACCTAAA
131 GTGACCTAAA
5519613 ATTGTCTTAA
Statistics
Matches: 243, Mismatches: 46, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
151 158 0.65
152 83 0.34
153 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (151 bp):
CATAGTAGCCTACACTTAGTACTACACACGTGATCAAAACTAACGGGTACGCATAGTAGCCTGCA
CTTAGTACTACACATGTGACCTATCAATCTGGTACACGTAGTAGCCTACACTTAGTACTACACAC
GTGACCTAAACAACGGATACA
Found at i:5519611 original size:50 final size:50
Alignment explanation
Indices: 5519164--5519611 Score: 398
Period size: 50 Copynumber: 8.9 Consensus size: 50
5519154 CGAAGCTCTA
* * * * * *
5519164 TGGTACGCATAGTAGCCTTCACTTAGTACTACACATGCGACCTATCAATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATC
* * * *
5519214 TGGTACACGTAGTAGCATGCACTTAGTACTACACACGTGACTTATCCATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATC
* * * * * * *
5519264 TGATACATGTAGTAGCCTACACTTAGTACTACACATGTGATCGAAGTTAA-C
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA--CAATC
* * * ** * * *
5519315 GGGTACGCATAGTAGCCTATACTTAGTACTACACACGTGATCGAAGTTAA-C
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA--CAATC
* * * * *
5519366 GGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATC
* * * * *
5519416 CGGTACACGTAGTTGCCTACACTTAGTACTACACACATGACCTAA-ACATT
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACA-ATC
* * ** *
5519466 TGATACACGTAGTAGCTTGCACTTAGTACTACACACGTGATCAAAACTATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGA-CCTAACAATC
* * * * * * *
5519517 GGGTACGCATAGTAGCCTGTACTTAGTACTAGACATGCGACCTAACAATC
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATC
5519567 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
1 TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAA
5519612 AATTGTCTTA
Statistics
Matches: 321, Mismatches: 71, Indels: 12
0.79 0.18 0.03
Matches are distributed among these distances:
49 3 0.01
50 197 0.61
51 120 0.37
52 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (50 bp):
TGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACAATC
Found at i:5521013 original size:15 final size:15
Alignment explanation
Indices: 5520993--5521034 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
5520983 AAGAAATCTT
5520993 TAAAAA-ATAATTCCA
1 TAAAAATATAA-TCCA
5521008 TAAAAATATAGA-CCA
1 TAAAAATATA-ATCCA
5521023 TAAAAATATAAT
1 TAAAAATATAAT
5521035 AAAACACATT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 1 0.04
15 19 0.79
16 3 0.12
17 1 0.04
ACGTcount: A:0.62, C:0.10, G:0.02, T:0.26
Consensus pattern (15 bp):
TAAAAATATAATCCA
Found at i:5526738 original size:180 final size:180
Alignment explanation
Indices: 5526464--5526822 Score: 524
Period size: 180 Copynumber: 2.0 Consensus size: 180
5526454 TAGATCTACA
* * *
5526464 GAACTCCAAATTAAGATCCGTTAATTTTCACAGAAACTAGACTCAAATATATTCTTTCCATAAAA
1 GAACTCCAAATTAAGAACCGCTAATTTTCACAGAAACTAGACTCAAATATATTCTTACCATAAAA
* * * * *
5526529 TTTTCAGAATTTTTTGTTTATCCAATTAGTACAGTTTATTCATTAAAGTTACCCCTATTTTACTA
66 TTTTCAAAAATTTTTGTTTAGCCAATTAGTACAGTTTATTCATTAAAGATACCCCTATTTCACTA
5526594 TCTAACAGTTCCTAA-CTCTCTTCACTAAAAATTATATATCTCATGGTACG
131 TCTAACAGTTCC-AATCTCTCTTCACTAAAAATTATATATCTCATGGTACG
* * *
5526644 GAACTCCAAATTAAGAACCGCTAATTTTCCCTGAAACTAGACTCACATATATTCTTACCATAAAA
1 GAACTCCAAATTAAGAACCGCTAATTTTCACAGAAACTAGACTCAAATATATTCTTACCATAAAA
* * * *
5526709 TTTT-AAAAATTTTTGATTTAGCTAATTAGTACAGTTTATTCATTGAAGATACCCTTGTTTCACT
66 TTTTCAAAAATTTTTG-TTTAGCCAATTAGTACAGTTTATTCATTAAAGATACCCCTATTTCACT
* * *
5526773 GTCTAACAGTTCCAATCTTTCTTCACTAAAAATTATTTATCTCATGGTAC
130 ATCTAACAGTTCCAATCTCTCTTCACTAAAAATTATATATCTCATGGTAC
5526823 AGATCTCGGG
Statistics
Matches: 159, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
179 11 0.07
180 148 0.93
ACGTcount: A:0.34, C:0.19, G:0.08, T:0.38
Consensus pattern (180 bp):
GAACTCCAAATTAAGAACCGCTAATTTTCACAGAAACTAGACTCAAATATATTCTTACCATAAAA
TTTTCAAAAATTTTTGTTTAGCCAATTAGTACAGTTTATTCATTAAAGATACCCCTATTTCACTA
TCTAACAGTTCCAATCTCTCTTCACTAAAAATTATATATCTCATGGTACG
Found at i:5527456 original size:50 final size:50
Alignment explanation
Indices: 5527381--5527821 Score: 375
Period size: 50 Copynumber: 8.7 Consensus size: 50
5527371 ACTGAAGGTC
* * * *
5527381 TCTGGTACGCATAGTAGCTTGCACTTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * *
5527431 TCTGGTACACATAGCAGCCTGCACTTAGTACTACACACGTGACTTATCCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * ** *
5527481 TCTGATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAGTTAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCTA-TCAA
* * * * * *
5527533 -CGGGTACGCATAGTAGCCTGGAATTAGTACTACACATGCGACCTATCAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * * * * * * *
5527582 TCCGGTACACGTAGTAGCTTGTAATTAATACTACACACGTGACCTAACCA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * * * ** * *
5527632 TCTGATACACGTAGTAGCTTGCACTTAGTACTACACATGTGATCGAAACTA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-CCTATCAA
* ** * * **
5527683 TCGGGTATGCATAGTAGCCTGCATTTAGTACTACACAAGTGACCTAAAAA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* *
5527733 TCTGGTACACGTAGCAGCCTGCACTTAGTACTACACACGTGACCTA--AA
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
* * * *
5527781 ACTGTCTTAAACACATAGTATCCTGCACATAGTACTACACA
1 TCTG--GT--ACACATAGTAGCCTGCACTTAGTACTACACA
5527822 TGTGTTCTCG
Statistics
Matches: 314, Mismatches: 69, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
48 5 0.02
49 3 0.01
50 203 0.65
51 74 0.24
52 29 0.09
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (50 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTATCAA
Found at i:5527658 original size:151 final size:151
Alignment explanation
Indices: 5527384--5527821 Score: 581
Period size: 151 Copynumber: 2.9 Consensus size: 151
5527374 GAAGGTCTCT
* * *
5527384 GGTACGCATAGTAGCTTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACATAGCAGC
1 GGTACGCATAGTAGCCTGCAATTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGCAGC
* *
5527449 CTGCACTTAGTACTACACACGTGACTTATCCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
66 CTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
*
5527514 CACACGTGATC-AAAGTTAACG
131 CACACGTGATCGAAA-CTAACG
* * *
5527535 GGTACGCATAGTAGCCTGGAATTAGTACTACACATGCGACCTATCAATCCGGTACACGTAGTAGC
1 GGTACGCATAGTAGCCTGCAATTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGCAGC
* * * * *
5527600 TTGTAATTAATACTACACACGTGACCTAACCATCTGATACACGTAGTAGCTTGCACTTAGTACTA
66 CTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
* *
5527665 CACATGTGATCGAAACTATCG
131 CACACGTGATCGAAACTAACG
* * * * **
5527686 GGTATGCATAGTAGCCTGCATTTAGTACTACACAAGTGACCTAAAAATCTGGTACACGTAGCAGC
1 GGTACGCATAGTAGCCTGCAATTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGCAGC
** * * * * *
5527751 CTGCACTTAGTACTACACACGTGACCTAAAACTGTCTTAAACACATAGTATCCTGCACATAGTAC
66 CTGCACTTAGTACTACACACGTGACCT--AACCATCTGATACACGTAGTAGCCTGCACTTAGTAC
5527816 TACACA
129 TACACA
5527822 TGTGTTCTCG
Statistics
Matches: 247, Mismatches: 37, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
151 210 0.85
152 3 0.01
153 34 0.14
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (151 bp):
GGTACGCATAGTAGCCTGCAATTAGTACTACACATGCGACCTATCAATCTGGTACACGTAGCAGC
CTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTTAGTACTA
CACACGTGATCGAAACTAACG
Found at i:5527698 original size:101 final size:101
Alignment explanation
Indices: 5527384--5527774 Score: 268
Period size: 101 Copynumber: 3.9 Consensus size: 101
5527374 GAAGGTCTCT
* * * * * * ** * *
5527384 GGTACGCATAGTAGCTTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACATAGCAGC
1 GGTATGCATAGTAGCCTGCAATTAATACTACACAAGTGACCTAAAAATCTGATACACGTAGCAGC
** * * *
5527449 CTGCACTTAGTACTACACACGTGA-CTTATCCATCT
66 CTGCACTTAGTACTACACACGTGATCGAAACTATCG
* ** * * * * * * * * * *
5527484 GATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATC-AAAGTTAA-CGGGTACGCATAGT
1 GGTATGCATAGTAGCCTGCAATTAATACTACACAAGTGACCTAAA---AATCTGATACACGTAGC
* * * * ** * * *
5527547 AGCCTGGAATTAGTACTACACATGCGA-CCTATCAATCC
63 AGCCTGCACTTAGTACTACACACGTGATCGAAACTATCG
** * * * * ** *
5527585 GGTACACGTAGTAGCTTGTAATTAATACTACACACGTGACCTAACCATCTGATACACGTAGTAGC
1 GGTATGCATAGTAGCCTGCAATTAATACTACACAAGTGACCTAAAAATCTGATACACGTAGCAGC
* *
5527650 TTGCACTTAGTACTACACATGTGATCGAAACTATCG
66 CTGCACTTAGTACTACACACGTGATCGAAACTATCG
* * *
5527686 GGTATGCATAGTAGCCTGCATTTAGTACTACACAAGTGACCTAAAAATCTGGTACACGTAGCAGC
1 GGTATGCATAGTAGCCTGCAATTAATACTACACAAGTGACCTAAAAATCTGATACACGTAGCAGC
5527751 CTGCACTTAGTACTACACACGTGA
66 CTGCACTTAGTACTACACACGTGA
5527775 CCTAAAACTG
Statistics
Matches: 231, Mismatches: 54, Indels: 11
0.78 0.18 0.04
Matches are distributed among these distances:
99 2 0.01
100 67 0.29
101 158 0.68
102 4 0.02
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.26
Consensus pattern (101 bp):
GGTATGCATAGTAGCCTGCAATTAATACTACACAAGTGACCTAAAAATCTGATACACGTAGCAGC
CTGCACTTAGTACTACACACGTGATCGAAACTATCG
Found at i:5528233 original size:31 final size:31
Alignment explanation
Indices: 5528195--5528253 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
5528185 TAAAAATCAT
*
5528195 ACTTTTACAAATTTGCATTTTGACCCCTTAA
1 ACTTTTACAAATTTGCACTTTGACCCCTTAA
* * *
5528226 ACTTTTACATATTTTCACTTTGGCCCCT
1 ACTTTTACAAATTTGCACTTTGACCCCT
5528254 AGGCTCGTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.24, C:0.25, G:0.07, T:0.44
Consensus pattern (31 bp):
ACTTTTACAAATTTGCACTTTGACCCCTTAA
Found at i:5529192 original size:27 final size:27
Alignment explanation
Indices: 5529160--5529213 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
5529150 AAGTAGGCCA
5529160 CTTTAGAACTCTTCTGAGCAGTAGGTT
1 CTTTAGAACTCTTCTGAGCAGTAGGTT
* *
5529187 CTTTAGAACTGTTCTGAGTAGTAGGTT
1 CTTTAGAACTCTTCTGAGCAGTAGGTT
5529214 AAGTATGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (27 bp):
CTTTAGAACTCTTCTGAGCAGTAGGTT
Found at i:5530685 original size:40 final size:40
Alignment explanation
Indices: 5530616--5530694 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
5530606 CTTGTATGGG
* **
5530616 ATTGCACTTTGGTGCCTCTGTTTGTACTTC-AGTGCCTCTA
1 ATTGCACTTTGGTGCCTCTGTCTACACTTCGA-TGCCTCTA
5530656 ATTGCACATTT-GTGCCTCTGTCTACACTTCGATGCCTCT
1 ATTGCAC-TTTGGTGCCTCTGTCTACACTTCGATGCCTCT
5530695 GTTATGCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 30 0.88
41 4 0.12
ACGTcount: A:0.14, C:0.28, G:0.18, T:0.41
Consensus pattern (40 bp):
ATTGCACTTTGGTGCCTCTGTCTACACTTCGATGCCTCTA
Found at i:5534335 original size:27 final size:27
Alignment explanation
Indices: 5534280--5534347 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
5534270 AACACGTCAG
* *
5534280 GAAATGAAAGCCTTTGTGGAGAATCAT
1 GAAATGAAAGCCTTTATGGAAAATCAT
*
5534307 GAAATGAATGCCTTTATGGAAAAGT-AT
1 GAAATGAAAGCCTTTATGGAAAA-TCAT
*
5534334 GAAAAGAACAGCCT
1 GAAATGAA-AGCCT
5534348 CTGTGGTGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (27 bp):
GAAATGAAAGCCTTTATGGAAAATCAT
Found at i:5539368 original size:13 final size:13
Alignment explanation
Indices: 5539352--5539376 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5539342 TGATTTTGTG
5539352 AAAATTTCACGAA
1 AAAATTTCACGAA
5539365 AAAATTTCACGA
1 AAAATTTCACGA
5539377 CATGATTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAATTTCACGAA
Found at i:5540573 original size:49 final size:50
Alignment explanation
Indices: 5540483--5540675 Score: 192
Period size: 49 Copynumber: 3.9 Consensus size: 50
5540473 ATCTATTGTG
** * *
5540483 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAAATTATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* * * * *
5540533 -GGTCGCATGTGTAGTACTAAATGCAGGCTACTATGCGTACCCGATAACTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAA-TT
* * * * * **
5540583 CGATCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTATCAGATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
* *
5540633 AGG-CAACGTGTGTAGTACTAACTGCAGGCTACTATGCGTACCA
1 AGGTC-ACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCA
5540676 TATAGCTTTA
Statistics
Matches: 113, Mismatches: 27, Indels: 6
0.77 0.18 0.04
Matches are distributed among these distances:
49 39 0.35
50 38 0.34
51 36 0.32
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.28
Consensus pattern (50 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATT
Found at i:5547126 original size:39 final size:41
Alignment explanation
Indices: 5547072--5547211 Score: 225
Period size: 40 Copynumber: 3.5 Consensus size: 41
5547062 AACCCAAGTA
* *
5547072 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATG
*
5547111 CCTTCGGGACTTAGCCCGAATATAGTC-ACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATG
5547151 CCTTCGGGACTTAGCCCGGATATAGTCAA-TAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATG
5547191 CCTTCGGGACTTAGCCCGGAT
1 CCTTCGGGACTTAGCCCGGAT
5547212 GTCATCCAAA
Statistics
Matches: 94, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
39 13 0.14
40 79 0.84
41 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (41 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAACTAGCACAAATG
Found at i:5549569 original size:11 final size:11
Alignment explanation
Indices: 5549553--5549577 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5549543 GTGTGTAGTA
5549553 CTAAGTGCAGG
1 CTAAGTGCAGG
5549564 CTAAGTGCAGG
1 CTAAGTGCAGG
5549575 CTA
1 CTA
5549578 CTACGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.20
Consensus pattern (11 bp):
CTAAGTGCAGG
Found at i:5549573 original size:62 final size:61
Alignment explanation
Indices: 5549502--5549627 Score: 162
Period size: 61 Copynumber: 2.0 Consensus size: 61
5549492 GTGTGTAGTA
** * *
5549502 CTAAGTGCAGGCTACTTTGCGTACCCGATAACTTCGATCACGTGTGTAGTACTAAGTGCAGG
1 CTAAGTGCAGGCTACTACGCGTACCAGAT-ACTTAGATCACGTGTGTAGTACTAAGTGCAGG
* * ** *
5549564 CTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGTGCAGG
1 CTAAGTGCAGGCTACTACGCGTACCAGATACTTAGATCACGTGTGTAGTACTAAGTGCAGG
5549625 CTA
1 CTA
5549628 CTACGTATAC
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
61 31 0.56
62 24 0.44
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (61 bp):
CTAAGTGCAGGCTACTACGCGTACCAGATACTTAGATCACGTGTGTAGTACTAAGTGCAGG
Found at i:5549692 original size:49 final size:50
Alignment explanation
Indices: 5549564--5549692 Score: 161
Period size: 49 Copynumber: 2.6 Consensus size: 50
5549554 TAAGTGCAGG
* ** *
5549564 CTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACGTGTGTAGTA
1 CTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCACATGTGTAGTA
* * *
5549614 CTAAGTGCAGGCTACTACGTATACTAGATAATT-GGTCGCATGTGTAGTA
1 CTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCACATGTGTAGTA
* * *
5549663 CTAAGTGCAAGCTACTATGCGTACCAGATA
1 CTAAGTGCAGGCTACTACGTGTACCAGATA
5549693 GCTTTGGCTA
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
49 39 0.58
50 28 0.42
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.29
Consensus pattern (50 bp):
CTAAGTGCAGGCTACTACGTGTACCAGATAATTAGGTCACATGTGTAGTA
Found at i:5553805 original size:50 final size:49
Alignment explanation
Indices: 5553683--5553871 Score: 234
Period size: 50 Copynumber: 3.8 Consensus size: 49
5553673 TGAGGTCGCA
* * *
5553683 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAA-TT-GGTCACG
* * **
5553734 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATT-GGTCACG
* ** *
5553784 TGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAGATAATTGGTTGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCACG
* *
5553833 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA
5553872 GCTTTGGCTA
Statistics
Matches: 119, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
49 40 0.34
50 45 0.38
51 34 0.29
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCACG
Found at i:5553856 original size:49 final size:49
Alignment explanation
Indices: 5553680--5553871 Score: 215
Period size: 49 Copynumber: 3.9 Consensus size: 49
5553670 TTGTGAGGTC
* * *
5553680 GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCGAT
1 GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA-TTGGTT
* * * ** *
5553730 -CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTC
1 GCA--TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATT-GGTT
* * * *
5553781 ACGTGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAGATAATTGGTT
1 GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTT
*
5553830 GCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA
1 GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
5553872 GCTTTGGCTA
Statistics
Matches: 117, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
49 42 0.36
50 39 0.33
51 35 0.30
52 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
GCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATTGGTT
Found at i:5562857 original size:46 final size:46
Alignment explanation
Indices: 5562804--5562979 Score: 193
Period size: 46 Copynumber: 3.8 Consensus size: 46
5562794 TATTTGGGCA
5562804 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
5562850 TCCGAACTCGTTGAGTTGAGTCCGAGTT---TGA-GAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGCGAA-T--G
* * *
5562895 CATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
5562943 CCCGAGA-TCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGA-ACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5562980 GCGGGGTACA
Statistics
Matches: 108, Mismatches: 10, Indels: 24
0.76 0.07 0.17
Matches are distributed among these distances:
42 3 0.03
43 7 0.06
45 1 0.01
46 61 0.56
47 26 0.24
48 1 0.01
50 6 0.06
51 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5562959 original size:93 final size:93
Alignment explanation
Indices: 5562800--5562970 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
5562790 AGGATATTTG
* *
5562800 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
5562865 TTGAGTCCGAGTTTGAGAGATGTAACTA
66 TTGAGTCCGAGTTTGAGAGATGTAACTA
* *
5562893 GGCATCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGA-TCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGA-ACTCGTTGA
5562957 GTTGAGTCCGAGTT
65 GTTGAGTCCGAGTT
5562971 CACTTATGGG
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
93 72 0.99
94 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTTGAGAGATGTAACTA
Found at i:5568343 original size:46 final size:46
Alignment explanation
Indices: 5568276--5568404 Score: 188
Period size: 46 Copynumber: 2.8 Consensus size: 46
5568266 TATTTGGCCA
* *
5568276 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAGTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
5568322 TCCGAACTCGTTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
5568368 CCCGAGCGT-GTTGAGTTGAGTCTGAGTTCACTTATGG
1 TCCGAAC-TCGTTGAGTTGAGTCCGAGTTCACTTATGG
5568405 GCGGGTTACA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
46 74 0.99
47 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:5571153 original size:14 final size:14
Alignment explanation
Indices: 5571134--5571160 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5571124 ATATTTGACT
5571134 TGTTCTTAATTATG
1 TGTTCTTAATTATG
5571148 TGTTCTTAATTAT
1 TGTTCTTAATTAT
5571161 TGCCTTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.59
Consensus pattern (14 bp):
TGTTCTTAATTATG
Found at i:5572646 original size:27 final size:27
Alignment explanation
Indices: 5572616--5572668 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
5572606 ACCCCTAACC
5572616 GATAAAATGACT-ATTATGCCCCTATGT
1 GATAAAATGACTGA-TATGCCCCTATGT
*
5572643 GATAAATTGACTGATATGCCCCTATG
1 GATAAAATGACTGATATGCCCCTATG
5572669 AGAAGTATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (27 bp):
GATAAAATGACTGATATGCCCCTATGT
Found at i:5578844 original size:16 final size:16
Alignment explanation
Indices: 5578820--5578877 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
5578810 TACATATTTA
*
5578820 ATTATTATAATAAATT
1 ATTAATATAATAAATT
**
5578836 ATTAATATAATTTATT
1 ATTAATATAATAAATT
*
5578852 ATT-TTAATAATAAATT
1 ATTAAT-ATAATAAATT
5578868 -TTAA-ATAATA
1 ATTAATATAATA
5578878 TTTTTCACAT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 24 0.73
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAATATAATAAATT
Found at i:5578906 original size:47 final size:48
Alignment explanation
Indices: 5578854--5578961 Score: 127
Period size: 48 Copynumber: 2.3 Consensus size: 48
5578844 AATTTATTAT
5578854 TTTAATAATAAATTTT-A-AAT-AATATTT-TTCACATATTATTAAAAATA
1 TTTAATAATAAATTTTAATAATAAATATTTATT-ACA-ATTA-TAAAAATA
* *
5578901 TTTAATATTAATATTTTAATAATAAATATTTATTACAATTATAAATATA
1 TTTAATAATAA-ATTTTAATAATAAATATTTATTACAATTATAAAAATA
5578950 -TTAATAATAAAT
1 TTTAATAATAAAT
5578962 GTTTTGTAAT
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
47 12 0.23
48 14 0.26
49 8 0.15
50 7 0.13
51 10 0.19
52 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (48 bp):
TTTAATAATAAATTTTAATAATAAATATTTATTACAATTATAAAAATA
Found at i:5578930 original size:15 final size:15
Alignment explanation
Indices: 5578896--5578966 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
5578886 ATATTATTAA
5578896 AAATA-TTTAAT-AT
1 AAATATTTTAATAAT
*
5578909 TAATATTTTAATAAT
1 AAATATTTTAATAAT
*
5578924 AAATATTTATTACAATTAT
1 AAATA-TT-TT--AATAAT
*
5578943 AAATATATTAATAAT
1 AAATATTTTAATAAT
*
5578958 AAATGTTTT
1 AAATATTTT
5578967 GTAATATAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
13 4 0.09
14 6 0.13
15 18 0.40
16 2 0.04
17 4 0.09
18 1 0.02
19 10 0.22
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:5579521 original size:23 final size:23
Alignment explanation
Indices: 5579490--5579578 Score: 69
Period size: 23 Copynumber: 4.0 Consensus size: 23
5579480 AGCAATCCTA
*
5579490 AAATTTTAATATATAATAATTTT
1 AAATATTAATATATAATAATTTT
* * **
5579513 AAATATTAAGT-TATGATAGTAAT
1 AAATATTAA-TATATAATAATTTT
**
5579536 AAATATTAAGGTATAATAATTTT
1 AAATATTAATATATAATAATTTT
*
5579559 AAATA--AATA-ATCATAATTTT
1 AAATATTAATATATAATAATTTT
5579579 TAAAATTTTA
Statistics
Matches: 51, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
20 10 0.20
21 2 0.04
23 38 0.75
24 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (23 bp):
AAATATTAATATATAATAATTTT
Found at i:5585938 original size:22 final size:22
Alignment explanation
Indices: 5585913--5585955 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5585903 ATCCATTTTT
* *
5585913 ATTTTTATTTTTATTACAATTA
1 ATTTTAATTTTAATTACAATTA
*
5585935 ATTTTAATTTTAATTTCAATT
1 ATTTTAATTTTAATTACAATT
5585956 TTTGTTTACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (22 bp):
ATTTTAATTTTAATTACAATTA
Found at i:5588755 original size:43 final size:42
Alignment explanation
Indices: 5588708--5588828 Score: 104
Period size: 43 Copynumber: 2.8 Consensus size: 42
5588698 CCTCGGTTGA
5588708 GATTTATGTATAAGACCATGTCTGGGACATCGGCATCG-TATCT
1 GATTTATGT-TAAGACCATGTCTGGGACATCGGCATCGATAT-T
* * **
5588751 GATTTCATG-TAAGACCTTGCCTGGGACAGAGGCATCGATATT
1 GATTT-ATGTTAAGACCATGTCTGGGACATCGGCATCGATATT
* * * *
5588793 GAATTACATG-TAAGACCACGTCCGGGACGTCGGCAT
1 G-ATT-TATGTTAAGACCATGTCTGGGACATCGGCAT
5588829 TGTACTTGTT
Statistics
Matches: 62, Mismatches: 12, Indels: 8
0.76 0.15 0.10
Matches are distributed among these distances:
42 26 0.42
43 33 0.53
44 3 0.05
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (42 bp):
GATTTATGTTAAGACCATGTCTGGGACATCGGCATCGATATT
Found at i:5588777 original size:42 final size:43
Alignment explanation
Indices: 5588718--5588810 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 43
5588708 GATTTATGTA
* ** *
5588718 TAAGACCATGTCTGGGACATCGGCATCG-TATCTG-ATTTCATG
1 TAAGACCATGCCTGGGACAGAGGCATCGATAT-TGAATTACATG
*
5588760 TAAGACCTTGCCTGGGACAGAGGCATCGATATTGAATTACATG
1 TAAGACCATGCCTGGGACAGAGGCATCGATATTGAATTACATG
5588803 TAAGACCA
1 TAAGACCA
5588811 CGTCCGGGAC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
42 26 0.60
43 17 0.40
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (43 bp):
TAAGACCATGCCTGGGACAGAGGCATCGATATTGAATTACATG
Found at i:5591174 original size:20 final size:20
Alignment explanation
Indices: 5591145--5591182 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5591135 GGGCACAGGC
*
5591145 GTGTCTCAAGCCACACGGGT
1 GTGTCCCAAGCCACACGGGT
5591165 GTGTCCCAAGCCACACGG
1 GTGTCCCAAGCCACACGG
5591183 CCGTGTGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.34, G:0.29, T:0.16
Consensus pattern (20 bp):
GTGTCCCAAGCCACACGGGT
Found at i:5591188 original size:20 final size:20
Alignment explanation
Indices: 5591144--5591188 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5591134 AGGGCACAGG
* *
5591144 CGTGTCTCAAGCCACACGGG
1 CGTGTCCCAAGCCACACGGC
*
5591164 TGTGTCCCAAGCCACACGGC
1 CGTGTCCCAAGCCACACGGC
5591184 CGTGT
1 CGTGT
5591189 GTGACCACAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.18
Consensus pattern (20 bp):
CGTGTCCCAAGCCACACGGC
Found at i:5594401 original size:19 final size:19
Alignment explanation
Indices: 5594354--5594401 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
5594344 CTTATTTAGA
* * *
5594354 TAATTTTATTTCTTTTATT
1 TAATATTATTTCTATTAAT
* *
5594373 TATTACTATTTCTATTAAT
1 TAATATTATTTCTATTAAT
5594392 TAATATTATT
1 TAATATTATT
5594402 ATCATTATTC
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (19 bp):
TAATATTATTTCTATTAAT
Found at i:5594421 original size:4 final size:4
Alignment explanation
Indices: 5594412--5594438 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5594402 ATCATTATTC
5594412 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
5594439 TTGTTTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:5596050 original size:6 final size:6
Alignment explanation
Indices: 5596049--5596101 Score: 106
Period size: 6 Copynumber: 8.8 Consensus size: 6
5596039 TCTTTATGTT
5596049 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA
5596097 TATTT
1 TATTT
5596102 TTCTTTTCCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:5596055 original size:16 final size:16
Alignment explanation
Indices: 5596034--5596101 Score: 82
Period size: 18 Copynumber: 4.0 Consensus size: 16
5596024 CATTGAGTCC
* *
5596034 ATTTATCTTTATGTTT
1 ATTTATATTTATATTT
5596050 ATTTATATTTATATTTAT
1 ATTTATATTTATA-TT-T
5596068 ATTTATATTTATATTTAT
1 ATTTATATTTATA-TT-T
5596086 ATTTATATTTATATTT
1 ATTTATATTTATATTT
5596102 TTCTTTTCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
16 12 0.25
17 4 0.08
18 32 0.67
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (16 bp):
ATTTATATTTATATTT
Found at i:5602905 original size:12 final size:12
Alignment explanation
Indices: 5602888--5602912 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5602878 TCACACACGC
5602888 TCGTGTGCTAGG
1 TCGTGTGCTAGG
5602900 TCGTGTGCTAGG
1 TCGTGTGCTAGG
5602912 T
1 T
5602913 TGTGCCAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.40, T:0.36
Consensus pattern (12 bp):
TCGTGTGCTAGG
Found at i:5607305 original size:29 final size:29
Alignment explanation
Indices: 5607231--5607349 Score: 107
Period size: 29 Copynumber: 4.2 Consensus size: 29
5607221 TACATACATG
* *
5607231 CATATGGCCTACTAGGCCC-AATCTTATT
1 CATATGGCCCACTAGGCCCAAATCATATT
* * * * **
5607259 CAAATGGCCTATTTGGCCCAGTTCATATT
1 CATATGGCCCACTAGGCCCAAATCATATT
* * * *
5607288 CTTATGGCCCACTAGGCCTAATTCACATT
1 CATATGGCCCACTAGGCCCAAATCATATT
*
5607317 CATATGGCCCATTAGGCCCAAATCATATT
1 CATATGGCCCACTAGGCCCAAATCATATT
5607346 -ATAT
1 CATAT
5607350 TCATGCTCAC
Statistics
Matches: 71, Mismatches: 19, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
28 20 0.28
29 51 0.72
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (29 bp):
CATATGGCCCACTAGGCCCAAATCATATT
Found at i:5607335 original size:58 final size:57
Alignment explanation
Indices: 5607233--5607345 Score: 136
Period size: 58 Copynumber: 2.0 Consensus size: 57
5607223 CATACATGCA
* ** * * **
5607233 TATGGCCTACTAGGCCCAATCTTATTCAAATGGCCTATTTGGCCCAGTTCATATTCT
1 TATGGCCCACTAGGCCCAATCACATTCAAATGGCCCATTAGGCCCAAATCATATTCT
* *
5607290 TATGGCCCACTAGGCCTAATTCACATTCATATGGCCCATTAGGCCCAAATCATATT
1 TATGGCCCACTAGGCCCAA-TCACATTCAAATGGCCCATTAGGCCCAAATCATATT
5607346 ATATTCATGC
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
57 17 0.37
58 29 0.63
ACGTcount: A:0.26, C:0.27, G:0.15, T:0.32
Consensus pattern (57 bp):
TATGGCCCACTAGGCCCAATCACATTCAAATGGCCCATTAGGCCCAAATCATATTCT
Found at i:5611725 original size:369 final size:369
Alignment explanation
Indices: 5611046--5611784 Score: 1478
Period size: 369 Copynumber: 2.0 Consensus size: 369
5611036 AGGGGGTGAG
5611046 TTCTCACAAAATCAGTATGTACAACCCTCGAAGAAAAACAAGCATTCAAAGAGAAATCATCAAAC
1 TTCTCACAAAATCAGTATGTACAACCCTCGAAGAAAAACAAGCATTCAAAGAGAAATCATCAAAC
5611111 ATGCAATGCAATCCCATCCAAATTATCCATCCGCTACACACCAGCTCTGTCCCCCGTCACACCAT
66 ATGCAATGCAATCCCATCCAAATTATCCATCCGCTACACACCAGCTCTGTCCCCCGTCACACCAT
5611176 GTGGGGATATAAATATCGACCCACCCAGCCCACACACCAATGGTAGCCTAGTTGCAGAACTGCCT
131 GTGGGGATATAAATATCGACCCACCCAGCCCACACACCAATGGTAGCCTAGTTGCAGAACTGCCT
5611241 TCATTTACATATTGGGCTTTAAAAGCCGTCGGTGGATCCATGATTGTCAAGCAACCATGCGAATC
196 TCATTTACATATTGGGCTTTAAAAGCCGTCGGTGGATCCATGATTGTCAAGCAACCATGCGAATC
5611306 CTCATATACTTCCTCCATTCCATAATTCCCACCCCATACGCAACCTAAGCAGAATGCCATATGTA
261 CTCATATACTTCCTCCATTCCATAATTCCCACCCCATACGCAACCTAAGCAGAATGCCATATGTA
5611371 TGCATGTCACATCCATAAAACTTACATTCAACACCTAGGGGTAT
326 TGCATGTCACATCCATAAAACTTACATTCAACACCTAGGGGTAT
5611415 TTCTCACAAAATCAGTATGTACAACCCTCGAAGAAAAACAAGCATTCAAAGAGAAATCATCAAAC
1 TTCTCACAAAATCAGTATGTACAACCCTCGAAGAAAAACAAGCATTCAAAGAGAAATCATCAAAC
5611480 ATGCAATGCAATCCCATCCAAATTATCCATCCGCTACACACCAGCTCTGTCCCCCGTCACACCAT
66 ATGCAATGCAATCCCATCCAAATTATCCATCCGCTACACACCAGCTCTGTCCCCCGTCACACCAT
5611545 GTGGGGATATAAATATCGACCCACCCAGCCCACACACCAATGGTAGCCTAGTTGCAGAACTGCCT
131 GTGGGGATATAAATATCGACCCACCCAGCCCACACACCAATGGTAGCCTAGTTGCAGAACTGCCT
5611610 TCATTTACATATTGGGCTTTAAAAGCCGTCGGTGGATCCATGATTGTCAAGCAACCATGCGAATC
196 TCATTTACATATTGGGCTTTAAAAGCCGTCGGTGGATCCATGATTGTCAAGCAACCATGCGAATC
5611675 CTCATATACTTCCTCCATTCCATAATTCCCACCCCATACGCAACCTAAGCAGAATGCCATATGTA
261 CTCATATACTTCCTCCATTCCATAATTCCCACCCCATACGCAACCTAAGCAGAATGCCATATGTA
5611740 TGCATGTCACATCCATAAAACTTACATTCAACACCTAGGGGTAT
326 TGCATGTCACATCCATAAAACTTACATTCAACACCTAGGGGTAT
5611784 T
1 T
5611785 CTGGTCATTC
Statistics
Matches: 370, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
369 370 1.00
ACGTcount: A:0.33, C:0.30, G:0.14, T:0.23
Consensus pattern (369 bp):
TTCTCACAAAATCAGTATGTACAACCCTCGAAGAAAAACAAGCATTCAAAGAGAAATCATCAAAC
ATGCAATGCAATCCCATCCAAATTATCCATCCGCTACACACCAGCTCTGTCCCCCGTCACACCAT
GTGGGGATATAAATATCGACCCACCCAGCCCACACACCAATGGTAGCCTAGTTGCAGAACTGCCT
TCATTTACATATTGGGCTTTAAAAGCCGTCGGTGGATCCATGATTGTCAAGCAACCATGCGAATC
CTCATATACTTCCTCCATTCCATAATTCCCACCCCATACGCAACCTAAGCAGAATGCCATATGTA
TGCATGTCACATCCATAAAACTTACATTCAACACCTAGGGGTAT
Found at i:5612133 original size:297 final size:296
Alignment explanation
Indices: 5611600--5612192 Score: 1141
Period size: 297 Copynumber: 2.0 Consensus size: 296
5611590 GCCTAGTTGC
5611600 AGAACTGCCTTCATTTACATATTGGGCTTTAAAAGCCGTCGGTGGATCCATGATTGTCAAGCAAC
1 AGAACTGCCTTCATTTACATATTGGGCTTTAAAAGCCGTCGGTGGATCCATGATTGTCAAGCAAC
* *
5611665 CATGCGAATCCTCATATACTTCCTCCATTCCATAATTCCCACCCCATACGCAACCTAAGCAGAAT
66 CATGCGAATCCTCATATACTTCCTCCATTCCATAATTCCCACCCCATACACAACCTAAGCAGAAC
5611730 GCCATATGTATGCATGTCACATCCATAAAACTTACATTCAACACCTAGGGGTATTCTGGTCATTC
131 GCCATATGTATGCATGTCACATCCATAAAACTTACATTCAACACCTAGGGGTATTCTGGTCATTC
5611795 TCGCCCTTAGTGGCATTTCGATAATTTTCTCTTAATTACAGTTTTGACTTACCTTGGCCCATGAA
196 TCGCCCTTAGTGGCATTTCGATAATTTTCTCTTAATTACAGTTTTGACTTACCTTGGCCCATGAA
5611860 CAAGTCCCGCAAGCTAAGATGAACGAATACTATGCA
261 CAAGTCCCGCAAGCTAAGATGAACGAATACTATGCA
5611896 AGAACTGCCTTCATTTACATATTGGGCTTTAAAAGCCGTCGGTGGATCCATGATTGTCAAGCAAC
1 AGAACTGCCTTCATTTACATATTGGGCTTTAAAAGCCGTCGGTGGATCCATGATTGTCAAGCAAC
*
5611961 CATGCGAATCCTCATATACTTCCTCCATTCCATAATTCCCACCCCCATATACAACCTAAGCAGAA
66 CATGCGAATCCTCATATACTTCCTCCATTCCATAATTCCCA-CCCCATACACAACCTAAGCAGAA
*
5612026 CGTCATATGTATGCATGTCACATCCATAAAACTTACATTCAACACCTAGGGGTATTCTGGTCATT
130 CGCCATATGTATGCATGTCACATCCATAAAACTTACATTCAACACCTAGGGGTATTCTGGTCATT
5612091 CTCGCCCTTAGTGGCATTTCGATAATTTTCTCTTAATTACAGTTTTGACTTACCTTGGCCCATGA
195 CTCGCCCTTAGTGGCATTTCGATAATTTTCTCTTAATTACAGTTTTGACTTACCTTGGCCCATGA
5612156 ACAAGTCCCGCAAGCTAAGATGAACGAATACTATGCA
260 ACAAGTCCCGCAAGCTAAGATGAACGAATACTATGCA
5612193 CCAGGTAGGA
Statistics
Matches: 292, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
296 106 0.36
297 186 0.64
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (296 bp):
AGAACTGCCTTCATTTACATATTGGGCTTTAAAAGCCGTCGGTGGATCCATGATTGTCAAGCAAC
CATGCGAATCCTCATATACTTCCTCCATTCCATAATTCCCACCCCATACACAACCTAAGCAGAAC
GCCATATGTATGCATGTCACATCCATAAAACTTACATTCAACACCTAGGGGTATTCTGGTCATTC
TCGCCCTTAGTGGCATTTCGATAATTTTCTCTTAATTACAGTTTTGACTTACCTTGGCCCATGAA
CAAGTCCCGCAAGCTAAGATGAACGAATACTATGCA
Found at i:5612448 original size:29 final size:30
Alignment explanation
Indices: 5612384--5612502 Score: 124
Period size: 29 Copynumber: 4.2 Consensus size: 30
5612374 TACATACATG
* *
5612384 CATATGGCCTA-CTAGGCCCAA-TCTTATT
1 CATATGGCCCATCTAGGCCCAATTCATATT
* *
5612412 CAAATGGCCCATCT-GGCCCAGTTCATATT
1 CATATGGCCCATCTAGGCCCAATTCATATT
* *
5612441 CTTATGGCCCA-CTAGGCCCAATTCACATT
1 CATATGGCCCATCTAGGCCCAATTCATATT
* *
5612470 CATATTGCCCAT-TAGGCCCAAATCATATT
1 CATATGGCCCATCTAGGCCCAATTCATATT
5612499 -ATAT
1 CATAT
5612503 TCATGCTCAC
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
28 21 0.28
29 54 0.72
ACGTcount: A:0.27, C:0.29, G:0.13, T:0.30
Consensus pattern (30 bp):
CATATGGCCCATCTAGGCCCAATTCATATT
Found at i:5612496 original size:58 final size:57
Alignment explanation
Indices: 5612386--5612498 Score: 138
Period size: 58 Copynumber: 2.0 Consensus size: 57
5612376 CATACATGCA
* ** **
5612386 TATGGCCTACTAGGCCCAATCTTATTCAAATGGCCCATCTGGCCCAGTTCATATTCT
1 TATGGCCCACTAGGCCCAATCACATTCAAATGGCCCATCTGGCCCAAATCATATTCT
* *
5612443 TATGGCCCACTAGGCCCAATTCACATTCATATTGCCCAT-TAGGCCCAAATCATATT
1 TATGGCCCACTAGGCCCAA-TCACATTCAAATGGCCCATCT-GGCCCAAATCATATT
5612499 ATATTCATGC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
57 19 0.40
58 28 0.60
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (57 bp):
TATGGCCCACTAGGCCCAATCACATTCAAATGGCCCATCTGGCCCAAATCATATTCT
Found at i:5612604 original size:19 final size:19
Alignment explanation
Indices: 5612580--5612617 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5612570 CAGCCTATCA
*
5612580 GGCCCATTTAGCCCATTCT
1 GGCCCATTTAGCCAATTCT
*
5612599 GGCCCATTTGGCCAATTCT
1 GGCCCATTTAGCCAATTCT
5612618 CAACCTAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.16, C:0.34, G:0.18, T:0.32
Consensus pattern (19 bp):
GGCCCATTTAGCCAATTCT
Found at i:5612738 original size:16 final size:16
Alignment explanation
Indices: 5612714--5612772 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
5612704 GTAGCCCAAC
* * *
5612714 TTTCGGCTTTTTGACA
1 TTTCAGCTTTTCGGCA
*
5612730 TTTCAGCTTTTCGGCT
1 TTTCAGCTTTTCGGCA
*
5612746 TTTCGGCTTTTCGGCA
1 TTTCAGCTTTTCGGCA
5612762 TTTCAGCTTTT
1 TTTCAGCTTTT
5612773 GTCAATTCAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.08, C:0.22, G:0.19, T:0.51
Consensus pattern (16 bp):
TTTCAGCTTTTCGGCA
Found at i:5612746 original size:8 final size:8
Alignment explanation
Indices: 5612714--5612772 Score: 64
Period size: 8 Copynumber: 7.4 Consensus size: 8
5612704 GTAGCCCAAC
5612714 TTTCGGCT
1 TTTCGGCT
* * *
5612722 TTTTGACA
1 TTTCGGCT
*
5612730 TTTCAGCT
1 TTTCGGCT
5612738 TTTCGGCT
1 TTTCGGCT
5612746 TTTCGGCT
1 TTTCGGCT
*
5612754 TTTCGGCA
1 TTTCGGCT
*
5612762 TTTCAGCT
1 TTTCGGCT
5612770 TTT
1 TTT
5612773 GTCAATTCAT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 40 1.00
ACGTcount: A:0.08, C:0.22, G:0.19, T:0.51
Consensus pattern (8 bp):
TTTCGGCT
Found at i:5619260 original size:32 final size:31
Alignment explanation
Indices: 5619205--5619268 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
5619195 CTTATAAGTG
* * *
5619205 ATTACTTTAATTTAATTATTCATAATAAATTA
1 ATTAATTTAATTTAATAACTCATAAT-AATTA
* *
5619237 ATTAATTTAATTTGATAACTCATACTAATTA
1 ATTAATTTAATTTAATAACTCATAATAATTA
5619268 A
1 A
5619269 AGAAATTTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.47
Consensus pattern (31 bp):
ATTAATTTAATTTAATAACTCATAATAATTA
Found at i:5622966 original size:4 final size:4
Alignment explanation
Indices: 5622949--5623001 Score: 63
Period size: 4 Copynumber: 12.8 Consensus size: 4
5622939 ATTATTACAT
*
5622949 TTTA TTTGA TTTA TTTA -TTA TTTCA TTTCT TTTA TTTA TTTA TTTA TTTA
1 TTTA TTT-A TTTA TTTA TTTA TTT-A TTT-A TTTA TTTA TTTA TTTA TTTA
5622999 TTT
1 TTT
5623002 CGCTTTCTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
3 3 0.07
4 29 0.66
5 12 0.27
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:5622976 original size:21 final size:20
Alignment explanation
Indices: 5622949--5623001 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
5622939 ATTATTACAT
5622949 TTTATTTGATTTATTTA-TTA
1 TTTATTT-ATTTATTTATTTA
*
5622969 TTTCATTTCTTTTATTTATTTA
1 TTT-ATTT-ATTTATTTATTTA
5622991 TTTATTTATTT
1 TTTATTTATTT
5623002 CGCTTTCTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 6 0.21
21 16 0.57
22 6 0.21
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTATTTATTTATTTATTTA
Found at i:5624878 original size:19 final size:20
Alignment explanation
Indices: 5624854--5624892 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5624844 TTTCCTTTCC
5624854 CCTCTCCC-TCCTCTCTCTT
1 CCTCTCCCTTCCTCTCTCTT
*
5624873 CCTCTCCCTTCTTCTCTCTT
1 CCTCTCCCTTCCTCTCTCTT
5624893 TTGTTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (20 bp):
CCTCTCCCTTCCTCTCTCTT
Found at i:5634441 original size:100 final size:100
Alignment explanation
Indices: 5634268--5634465 Score: 306
Period size: 100 Copynumber: 2.0 Consensus size: 100
5634258 CCATTGAAGC
* * * * *
5634268 CAGAATGCAAACCCATTCAACAAAAGCTAAGACGGATGAGACCTGAGATGTTGTTGAAAATAAAA
1 CAGAATGCAAACCCATCCAACAAAAACTAAGACGGATGAGACCCGAAATGCTGTTGAAAATAAAA
*
5634333 GAGGAAGTCAAGAAGCAATTTGATGCTGGCTTCCT
66 GAGGAAGTCAAGAAGCAATTTGACGCTGGCTTCCT
* * * *
5634368 CAGAATGCAAGCCCATCCAGCAAAAATTAAGACGGATGAGGCCCGAAATGCTGTTGAAAATAAAA
1 CAGAATGCAAACCCATCCAACAAAAACTAAGACGGATGAGACCCGAAATGCTGTTGAAAATAAAA
5634433 GAGGAAGTCAAGAAGCAATTTGACGCTGGCTTC
66 GAGGAAGTCAAGAAGCAATTTGACGCTGGCTTC
5634466 TTACAGGCCT
Statistics
Matches: 88, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 88 1.00
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (100 bp):
CAGAATGCAAACCCATCCAACAAAAACTAAGACGGATGAGACCCGAAATGCTGTTGAAAATAAAA
GAGGAAGTCAAGAAGCAATTTGACGCTGGCTTCCT
Found at i:5634618 original size:92 final size:92
Alignment explanation
Indices: 5634461--5634644 Score: 325
Period size: 92 Copynumber: 2.0 Consensus size: 92
5634451 TTTGACGCTG
* *
5634461 GCTTCTTACAGGCCTCCAAATATCCAGAATGGGTGGCTAACATAGTCCCGGTACCAAAGAAAGAC
1 GCTTCCTACAAGCCTCCAAATATCCAGAATGGGTGGCTAACATAGTCCCGGTACCAAAGAAAGAC
*
5634526 GGA-AAAGTACGAATGTGCGTGGATTAT
66 -GACAAAGTACGAATGTACGTGGATTAT
5634553 GCTTCCTACAAGCCTCCAAATATCCAGAATGGGTGGCTAACATAGTCCCGGTACCAAAGAAAGAC
1 GCTTCCTACAAGCCTCCAAATATCCAGAATGGGTGGCTAACATAGTCCCGGTACCAAAGAAAGAC
5634618 GACAAAGTACGAATGTACGTGGATTAT
66 GACAAAGTACGAATGTACGTGGATTAT
5634645 CGTGACCTGA
Statistics
Matches: 88, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
91 2 0.02
92 86 0.98
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (92 bp):
GCTTCCTACAAGCCTCCAAATATCCAGAATGGGTGGCTAACATAGTCCCGGTACCAAAGAAAGAC
GACAAAGTACGAATGTACGTGGATTAT
Found at i:5638548 original size:14 final size:14
Alignment explanation
Indices: 5638510--5638541 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5638500 CGCTGAGGTA
*
5638510 TTTTCAATTTCTTC
1 TTTTCAATTTCTGC
5638524 TTTTCAATTTCTGC
1 TTTTCAATTTCTGC
5638538 TTTT
1 TTTT
5638542 AAGTTTCAGA
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:0.12, C:0.19, G:0.03, T:0.66
Consensus pattern (14 bp):
TTTTCAATTTCTGC
Found at i:5638896 original size:75 final size:75
Alignment explanation
Indices: 5638707--5638926 Score: 241
Period size: 75 Copynumber: 2.9 Consensus size: 75
5638697 AATTCTTTAA
* * * * *
5638707 AAAAAAATCAACTCATATTGCAAGAAATGAGTTGAACTTCAGGGTACACTGAGGAATTTTCAATT
1 AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGAGTACACTGAGGAATTTTCAATT
*
5638772 TCTGCTTTTC
66 TCTACTTTTC
* * *
5638782 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA-AG-ACACGTTGAGGTATTTTTAA
1 AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGAGTACAC--TGAGGAATTTTCAA
*
5638845 TTTTTACTTTTC
64 TTTCTACTTTTC
* *
5638857 -AAAAAATCAACTCATATTGCGAGAAGTGAGTTGGGGCCTCAG-GTCACATGCTGAGGTATTTTC
1 AAAAAAATCAACTCATATTGCGAGAAGTGAGTT-GAGCCTCAGAGT-ACA--CTGAGGAATTTTC
*
5638920 AAATTCT
62 AATTTCT
5638927 GTGTTCAAAT
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
73 4 0.03
74 32 0.26
75 66 0.54
77 19 0.16
79 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (75 bp):
AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGAGTACACTGAGGAATTTTCAATT
TCTACTTTTC
Found at i:5638935 original size:13 final size:13
Alignment explanation
Indices: 5638917--5638941 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5638907 CTGAGGTATT
5638917 TTCAAATTCTGTG
1 TTCAAATTCTGTG
5638930 TTCAAATTCTGT
1 TTCAAATTCTGT
5638942 CTTTAATTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
TTCAAATTCTGTG
Found at i:5638988 original size:102 final size:100
Alignment explanation
Indices: 5638840--5639023 Score: 289
Period size: 102 Copynumber: 1.8 Consensus size: 100
5638830 TTGAGGTATT
* * *
5638840 TTTAATTTTTACTTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGGGGCCTCAGGTCACA
1 TTTAATTTCTACTTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTT-GAGCCTCAAG--ACA
5638905 TGCTGAGGTATTTTCAAATTCTGTGTTCAAATTCTGTC
63 TGCTGAGGTATTTTCAAATTCTGTGTTCAAATTCTGTC
* *
5638943 TTTAATTTCTACTTTTC-CAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATGC
1 TTTAATTTCTACTTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACATGC
5639007 TGAGGTATTTTCAAATT
66 TGAGGTATTTTCAAATT
5639024 TTGTTTAATT
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
99 23 0.30
101 8 0.11
102 29 0.38
103 16 0.21
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (100 bp):
TTTAATTTCTACTTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACATGC
TGAGGTATTTTCAAATTCTGTGTTCAAATTCTGTC
Found at i:5640933 original size:22 final size:22
Alignment explanation
Indices: 5640906--5640951 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5640896 TTTTGTTTCT
5640906 TTATTAAATATTGTTATTATTA
1 TTATTAAATATTGTTATTATTA
5640928 TTATTAAATATTGTTATTATTA
1 TTATTAAATATTGTTATTATTA
5640950 TT
1 TT
5640952 CTAATATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (22 bp):
TTATTAAATATTGTTATTATTA
Found at i:5641392 original size:20 final size:20
Alignment explanation
Indices: 5641342--5641413 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
5641332 ATATTCTTGC
* *
5641342 ATTATGTATATTATTCTTTTT
1 ATTATGTATATT-TTCTATAT
*
5641363 AAATAT-TATATTTTCTATAT
1 -ATTATGTATATTTTCTATAT
*
5641383 ATTATGTATACATTT-TATAT
1 ATTATGTATA-TTTTCTATAT
5641403 ATTATGTATAT
1 ATTATGTATAT
5641414 ATCTTTTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
19 4 0.10
20 25 0.60
21 9 0.21
22 4 0.10
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (20 bp):
ATTATGTATATTTTCTATAT
Found at i:5641456 original size:58 final size:61
Alignment explanation
Indices: 5641342--5641456 Score: 139
Period size: 58 Copynumber: 1.9 Consensus size: 61
5641332 ATATTCTTGC
* ** *
5641342 ATTATGTATATTATTCTTTTTAAATATTATATTTTCTATATATTATGTATACATTTTATAT
1 ATTATGTATATTATTCTTTTTAAATATTATATTTTATATATACCATGTACACATTTTATAT
* *
5641403 ATTATGTATA-TA-TC-TTTT-AATATTGTACTTTTATATATACCATGTACATATTTT
1 ATTATGTATATTATTCTTTTTAAATATTATA-TTTTATATATACCATGTACACATTTT
5641457 GAATACTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
57 8 0.17
58 25 0.53
59 2 0.04
60 2 0.04
61 10 0.21
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (61 bp):
ATTATGTATATTATTCTTTTTAAATATTATATTTTATATATACCATGTACACATTTTATAT
Found at i:5649505 original size:1 final size:1
Alignment explanation
Indices: 5649490--5649567 Score: 84
Period size: 1 Copynumber: 78.0 Consensus size: 1
5649480 TTCAATGATG
* * * * * * * *
5649490 TTTTGTTTTTCTTTTTCTTTTTTTTGTTTTTTTGTTTTGTTTTGTTTTGTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5649555 TTTTTTTTTTTTT
1 TTTTTTTTTTTTT
5649568 GCATTCAGTT
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.00, C:0.03, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:5649544 original size:39 final size:36
Alignment explanation
Indices: 5649488--5649568 Score: 112
Period size: 39 Copynumber: 2.2 Consensus size: 36
5649478 TCTTCAATGA
5649488 TGTTTTGTTTTTCTTTTTCTTTTTTTTGTTTTTTTGTTT
1 TGTTTTGTTTTTCTTTTT-TTTTTTTT-TTTTTTT-TTT
5649527 TGTTTTGTTTTGT-TTTTTTTTTTTTTTTTTTTTTTT
1 TGTTTTGTTTT-TCTTTTTTTTTTTTTTTTTTTTTTT
5649563 T-TTTTG
1 TGTTTTG
5649569 CATTCAGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
35 5 0.12
36 4 0.10
37 7 0.17
38 8 0.20
39 16 0.39
40 1 0.02
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (36 bp):
TGTTTTGTTTTTCTTTTTTTTTTTTTTTTTTTTTTT
Found at i:5652292 original size:21 final size:21
Alignment explanation
Indices: 5652261--5652301 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
5652251 TCTTGATTTA
*
5652261 TTTATTTATTACTTTTTTTTGT
1 TTTATTTATTA-TTTATTTTGT
5652283 TTTA-TTATTATTTATTTTG
1 TTTATTTATTATTTATTTTG
5652302 AATTTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTATTTATTATTTATTTTGT
Found at i:5662971 original size:50 final size:50
Alignment explanation
Indices: 5662896--5663072 Score: 248
Period size: 50 Copynumber: 3.5 Consensus size: 50
5662886 CCATGGAAAC
*
5662896 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
5662946 AAGTGATAAGTAATAGCTTCGGCTACACTTATTTGATCAAGGACAACTGA
1 AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
5662996 AAATGATAAGTGAA-AGCTTCGACTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGT-AATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* ** *
5663046 CAAGTGAAAAGTGGTAGCTTCTGCTAC
1 -AAGTGATAAGTAATAGCTTCGGCTAC
5663073 CTGATCAGTG
Statistics
Matches: 111, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
50 90 0.81
51 21 0.19
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (50 bp):
AAGTGATAAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:5663086 original size:31 final size:31
Alignment explanation
Indices: 5663048--5663190 Score: 223
Period size: 31 Copynumber: 4.6 Consensus size: 31
5663038 ACAAATGACA
5663048 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
5663079 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
* * *
5663110 AGTGAAAAGGGGTAGCTCCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
* * *
5663141 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
*
5663172 AGTGAATAGTGGTAGCTTC
1 AGTGAAAAGTGGTAGCTTC
5663191 AACTACATGT
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 103 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
Found at i:5663269 original size:47 final size:46
Alignment explanation
Indices: 5663214--5663378 Score: 160
Period size: 47 Copynumber: 3.7 Consensus size: 46
5663204 AAGTGATTTC
* *
5663214 CGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
** * *
5663260 CTGTATAAGACCATATCTGGGATATGGCATTAGTGAGATATGTGATT
1 C-GTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
* * *
5663307 CGTGTAAGACCATAGCTGGGCTATGGCATC-----GATATATGAATA
1 CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATG-ATA
* * * *
5663349 TGTGTAAGACCATAGCTGGGCTATGGCATC
1 CGTATAAGACCATATCTGGGATATGGCATC
5663379 ATTATGTGAA
Statistics
Matches: 104, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
41 7 0.07
42 31 0.30
46 26 0.25
47 40 0.38
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (46 bp):
CGTATAAGACCATATCTGGGATATGGCATCGGTGAGATATATGATA
Found at i:5663366 original size:42 final size:43
Alignment explanation
Indices: 5663308--5663422 Score: 171
Period size: 42 Copynumber: 2.7 Consensus size: 43
5663298 TATGTGATTC
*
5663308 GTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
*
5663350 GTGTAAGACCATAGCTGGGCTATGGCATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
* **
5663392 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
5663423 GAAAACGAAG
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 1 0.02
42 64 0.97
43 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
Done.