Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007988.1 Hibiscus syriacus cultivar Beakdansim tig00110435_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 847207
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:5901 original size:20 final size:20
Alignment explanation
Indices: 5871--5930 Score: 75
Period size: 20 Copynumber: 2.9 Consensus size: 20
5861 TGATTTTGGG
5871 CAAGTGGAATCGGTACCCATT
1 CAAG-GGAATCGGTACCCATT
*
5892 CAAGGGAATCAGTACCCATT
1 CAAGGGAATCGGTACCCATT
*
5912 CAATGGGGAATCGATACCC
1 CAA--GGGAATCGGTACCC
5931 CTCAAGCGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.53
21 4 0.12
22 12 0.35
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.20
Consensus pattern (20 bp):
CAAGGGAATCGGTACCCATT
Found at i:6008 original size:23 final size:22
Alignment explanation
Indices: 5964--6008 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5954 AATCTCATAG
*
5964 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
5986 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
6009 AAAATGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:7477 original size:103 final size:103
Alignment explanation
Indices: 7298--7508 Score: 386
Period size: 103 Copynumber: 2.0 Consensus size: 103
7288 GTCTACGCGA
*
7298 TCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGTTGAGACACATACTTGATCC
1 TCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCC
* *
7363 TTGGCATATGTATATGATTCTTAAGGAATGATATGTGG
66 CTAGCATATGTATATGATTCTTAAGGAATGATATGTGG
7401 TCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCC
1 TCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCC
*
7466 CTAGTATATGTATATGATTCTTAAGGAATGATATGTGG
66 CTAGCATATGTATATGATTCTTAAGGAATGATATGTGG
7504 TCCTT
1 TCCTT
7509 ATGGACATTA
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCC
CTAGCATATGTATATGATTCTTAAGGAATGATATGTGG
Found at i:7561 original size:23 final size:23
Alignment explanation
Indices: 7525--7592 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
7515 ATTATTATAT
*
7525 GGCACTACGATGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
7548 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
7571 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
7593 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:7927 original size:13 final size:13
Alignment explanation
Indices: 7911--7954 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
7901 TATGAGAACA
7911 ATGTATGTGAT-AT
1 ATGTATGTG-TGAT
7924 ATGTATATGTGTGAT
1 ATG--TATGTGTGAT
7939 ATGTATGTGTGAT
1 ATGTATGTGTGAT
7952 ATG
1 ATG
7955 AATTGCATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 16 0.57
14 1 0.04
15 11 0.39
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (13 bp):
ATGTATGTGTGAT
Found at i:7934 original size:15 final size:15
Alignment explanation
Indices: 7914--7953 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
7904 GAGAACAATG
7914 TATGTGATATATGTA
1 TATGTGATATATGTA
7929 TATGTG-TGATATGTA
1 TATGTGAT-ATATGTA
*
7944 TGTGTGATAT
1 TATGTGATAT
7954 GAATTGCATG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (15 bp):
TATGTGATATATGTA
Found at i:19586 original size:98 final size:98
Alignment explanation
Indices: 19472--19648 Score: 302
Period size: 98 Copynumber: 1.8 Consensus size: 98
19462 TAAATAAGAT
* * * *
19472 TATTTTTTAACTTTTAATAATT-AGGAGACTTAATAAAGTAATGTGCTATAGTCGGGAGACTATT
1 TATTTTGTAACTTTTAATAATTAAGG-GAATTAACAAAGTAATGTACTATAGTCGGGAGACTATT
19536 TGTACTCCACCTATTTTATAAATAATCAGGAAAC
65 TGTACTCCACCTATTTTATAAATAATCAGGAAAC
19570 TATTTTGTAACTTTTAATAATTAAGGGAATTAACAAAGTAATGTACTATAGTCGGGAGACTATTT
1 TATTTTGTAACTTTTAATAATTAAGGGAATTAACAAAGTAATGTACTATAGTCGGGAGACTATTT
19635 GTACTCCACCTATT
66 GTACTCCACCTATT
19649 AAGATAATAC
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
98 71 0.96
99 3 0.04
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (98 bp):
TATTTTGTAACTTTTAATAATTAAGGGAATTAACAAAGTAATGTACTATAGTCGGGAGACTATTT
GTACTCCACCTATTTTATAAATAATCAGGAAAC
Found at i:24114 original size:21 final size:21
Alignment explanation
Indices: 24090--24130 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
24080 TTTTGGTAAA
*
24090 TTTCTACCGGTTTTATTATTT
1 TTTCTACCAGTTTTATTATTT
*
24111 TTTCTATCAGTTTTATTATT
1 TTTCTACCAGTTTTATTATT
24131 ATTGGTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTCTACCAGTTTTATTATTT
Found at i:24177 original size:21 final size:21
Alignment explanation
Indices: 24153--24193 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
24143 ATCGAAATAT
* *
24153 TAAAAATATTCATATTTTAAG
1 TAAAAATAATAATATTTTAAG
24174 TAAAAATAATAATATTTTAA
1 TAAAAATAATAATATTTTAA
24194 ATATTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAG
Found at i:28639 original size:24 final size:24
Alignment explanation
Indices: 28546--28655 Score: 80
Period size: 24 Copynumber: 4.5 Consensus size: 24
28536 GAATATTTTA
* * *
28546 TATGATTTCTGATTTGAATTCTGTT
1 TATGATATCTGATCTGAATTATG-T
* *
28571 TTTGACATCTGATCTGAAATT-TGT
1 TATGATATCTGATCTG-AATTATGT
* * * *
28595 TCTGAT-TCCTAACCTGGATTATGT
1 TATGATAT-CTGATCTGAATTATGT
28619 TATGATATCTGATCTGAATTATGT
1 TATGATATCTGATCTGAATTATGT
* *
28643 TTTGATTTCTGAT
1 TATGATATCTGAT
28656 ATCTCCGTTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
23 4 0.06
24 43 0.65
25 15 0.23
26 4 0.06
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.49
Consensus pattern (24 bp):
TATGATATCTGATCTGAATTATGT
Found at i:35714 original size:72 final size:73
Alignment explanation
Indices: 35566--35714 Score: 239
Period size: 72 Copynumber: 2.1 Consensus size: 73
35556 CGCTGGTCTT
* * *
35566 TCATTGTCAAGTCTTGTGCTGTTTCTGTTTTTCTGTCATGTAATAAATAATATCTCTTGGTTCTC
1 TCATTGTCAAGTCTTGTACTGTTTCTGTTTTTCTGTCATGTAATAAAAAATATCTCTTGGTTCTA
35631 ACCTAGAG
66 ACCTAGAG
35639 TCATTGTCAAGTCTTGTACTGTTTCTGTTTTTCTG-CATGTAA-AATAAAATATCTCTTGGTTCT
1 TCATTGTCAAGTCTTGTACTGTTTCTGTTTTTCTGTCATGTAATAA-AAAATATCTCTTGGTTCT
*
35702 AACCTAGGG
65 AACCTAGAG
35711 TCAT
1 TCAT
35715 GAAAATGCAA
Statistics
Matches: 71, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
71 2 0.03
72 35 0.49
73 34 0.48
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.44
Consensus pattern (73 bp):
TCATTGTCAAGTCTTGTACTGTTTCTGTTTTTCTGTCATGTAATAAAAAATATCTCTTGGTTCTA
ACCTAGAG
Found at i:43133 original size:32 final size:32
Alignment explanation
Indices: 43092--43155 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
43082 TTCCGAAGCA
43092 GTTGATGGAGGCGGTATTACTACCTTTTTCTC
1 GTTGATGGAGGCGGTATTACTACCTTTTTCTC
43124 GTTGATGGAGGCGGTATTACTACCTTTTTCTC
1 GTTGATGGAGGCGGTATTACTACCTTTTTCTC
43156 CATAACTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.16, C:0.19, G:0.25, T:0.41
Consensus pattern (32 bp):
GTTGATGGAGGCGGTATTACTACCTTTTTCTC
Found at i:50262 original size:20 final size:20
Alignment explanation
Indices: 50237--50327 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
50227 GATTTTTCCA
*
50237 AATTCGCATTGCGAATATGT
1 AATTCGCAATGCGAATATGT
50257 AATTCGCAATGCGAATA--T
1 AATTCGCAATGCGAATATGT
* *
50275 -ATTCGCAATGAGAATATGC
1 AATTCGCAATGCGAATATGT
* *
50294 AAATCGCAATGCGATTATG-
1 AATTCGCAATGCGAATATGT
*
50313 ACTATCGCAATGCGA
1 AAT-TCGCAATGCGA
50328 TTCTGACTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
17 15 0.25
18 1 0.02
19 1 0.02
20 42 0.71
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (20 bp):
AATTCGCAATGCGAATATGT
Found at i:50328 original size:20 final size:20
Alignment explanation
Indices: 50296--50383 Score: 122
Period size: 20 Copynumber: 4.4 Consensus size: 20
50286 GAATATGCAA
* *
50296 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
50316 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
50336 ATCGCAACGAGATTCTAACT
1 ATCGCAACGCGATTCTGACT
50356 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
50376 GTCGCAAC
1 ATCGCAAC
50384 ACTGAATTTC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:51465 original size:11 final size:12
Alignment explanation
Indices: 51449--51478 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
51439 AAAAGAAGAA
51449 GAAGAAA-TCCC
1 GAAGAAAGTCCC
51460 GAAGAAAGTCCC
1 GAAGAAAGTCCC
51472 GAAGAAA
1 GAAGAAA
51479 ATGCCACGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.50, C:0.20, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAGAAAGTCCC
Found at i:53531 original size:12 final size:12
Alignment explanation
Indices: 53516--53554 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
53506 AAGAAAAAGG
53516 CAATCAAAATCA
1 CAATCAAAATCA
53528 CAATCAAAATCA
1 CAATCAAAATCA
* **
53540 AAATCCCAATCA
1 CAATCAAAATCA
53552 CAA
1 CAA
53555 CCGGCTTCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATCAAAATCA
Found at i:53540 original size:18 final size:18
Alignment explanation
Indices: 53517--53551 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53507 AGAAAAAGGC
53517 AATCAAAATCACAATCAA
1 AATCAAAATCACAATCAA
*
53535 AATCAAAATCCCAATCA
1 AATCAAAATCACAATCA
53552 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (18 bp):
AATCAAAATCACAATCAA
Found at i:53863 original size:140 final size:140
Alignment explanation
Indices: 53611--53876 Score: 496
Period size: 140 Copynumber: 1.9 Consensus size: 140
53601 AAACGTTGTA
* *
53611 TTATGTGTAAACTTTTAATATTTTGAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
53676 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
53741 TATGTGTATT
131 TATGTGTATT
*
53751 TTATGTGTAAACTTTTAACATTTTCAGTTAGGTATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
*
53816 TGATATGTTCAGTTTTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGA
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGA
53877 TTATCACAAC
Statistics
Matches: 122, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 122 1.00
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:53918 original size:20 final size:20
Alignment explanation
Indices: 53893--54094 Score: 247
Period size: 20 Copynumber: 10.4 Consensus size: 20
53883 CAACTCAAAA
53893 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
53913 ATCGCAACGCGAATTTGTCT
1 ATCGCAACGCGAATTTGACT
53933 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
* * *
53953 ATCACAACTCGAATTTGATT
1 ATCGCAACGCGAATTTGACT
*
53973 ATCGCAACG-GTATTTGACT
1 ATCGCAACGCGAATTTGACT
*
53992 ATCGCAACGAGAA----A--
1 ATCGCAACGCGAATTTGACT
*
54006 ATCGCAACGCGAATTTGAGT
1 ATCGCAACGCGAATTTGACT
*
54026 ATCGCAACGCGAATTTGAGT
1 ATCGCAACGCGAATTTGACT
*
54046 ATCGCAACGCGAATTTGATT
1 ATCGCAACGCGAATTTGACT
* *
54066 ATCGCAACGGGTATTTGACT
1 ATCGCAACGCGAATTTGACT
*
54086 ATCACAACG
1 ATCGCAACG
54095 AGAAAATCGC
Statistics
Matches: 159, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
14 12 0.08
16 1 0.01
18 1 0.01
19 17 0.11
20 128 0.81
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:53948 original size:40 final size:39
Alignment explanation
Indices: 53851--54094 Score: 240
Period size: 40 Copynumber: 6.4 Consensus size: 39
53841 TTACACATTC
* * *
53851 ATTTGAATATCGCAACGCGAATTTGATTATCACAACTC-A
1 ATTTG-ATATCGCAACGCGAATTTGACTATCGCAACGCGA
*
53890 A----AAATCGCAACGCGAATTTGACTATCGCAACGCGA
1 ATTTGATATCGCAACGCGAATTTGACTATCGCAACGCGA
* * *
53925 ATTTGTCTATCGCAACGCGAATTTGACTATCACAACTCGA
1 ATTTG-ATATCGCAACGCGAATTTGACTATCGCAACGCGA
* *
53965 ATTTGATTATCGCAACG-GTATTTGACTATCGCAACGAGA
1 ATTTGA-TATCGCAACGCGAATTTGACTATCGCAACGCGA
*
54004 A----A-ATCGCAACGCGAATTTGAGTATCGCAACGCGA
1 ATTTGATATCGCAACGCGAATTTGACTATCGCAACGCGA
* * *
54038 ATTTGAGTATCGCAACGCGAATTTGATTATCGCAACGGGT
1 ATTTGA-TATCGCAACGCGAATTTGACTATCGCAACGCGA
*
54078 ATTTGACTATCACAACG
1 ATTTGA-TATCGCAACG
54095 AGAAAATCGC
Statistics
Matches: 170, Mismatches: 21, Indels: 27
0.78 0.10 0.12
Matches are distributed among these distances:
33 9 0.05
34 48 0.28
35 3 0.02
38 1 0.01
39 20 0.12
40 89 0.52
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (39 bp):
ATTTGATATCGCAACGCGAATTTGACTATCGCAACGCGA
Found at i:54029 original size:93 final size:94
Alignment explanation
Indices: 53913--54143 Score: 349
Period size: 93 Copynumber: 2.5 Consensus size: 94
53903 GAATTTGACT
* *
53913 ATCGCAACGCGAATTTGTCTATCGCAACGCGAATTTGACTATCACAACTCGAATTTGATTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGC
*
53978 AAC-GGTATTTGACTATCGCAACGAGAAA
66 AACGGGTATTTGACTATCACAACGAGAAA
* * *
54006 ATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGAGTATCGCAACGCGAATTTGATTATCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGC
54071 AACGGGTATTTGACTATCACAACGAGAAA
66 AACGGGTATTTGACTATCACAACGAGAAA
* * * * *
54100 ATCGCAAAGCGTATTAGACTATTGCAACGCGAA-TTGACTTTCAC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCAC
54144 GTTGCTATTT
Statistics
Matches: 123, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
93 71 0.58
94 52 0.42
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (94 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACGCGAATTTGATTATCGC
AACGGGTATTTGACTATCACAACGAGAAA
Found at i:54039 original size:73 final size:74
Alignment explanation
Indices: 53893--54074 Score: 231
Period size: 73 Copynumber: 2.4 Consensus size: 74
53883 CAACTCAAAA
* *
53893 ATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGTCTATCGCAACGCGAATTTGACTATCAC
1 ATCGCAACGCGAATTTGACTATCGCAACGAGAA------AATCGCAACGCGAATTTGACTATCAC
* *
53958 AACTCGAATTTGATT
60 AACGCGAATTTGAGT
* * *
53973 ATCGCAACG-GTATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGAGTATCGCAACGCG
1 ATCGCAACGCGAATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACTATCACAACGCG
54037 AATTTGAGT
66 AATTTGAGT
*
54046 ATCGCAACGCGAATTTGATTATCGCAACG
1 ATCGCAACGCGAATTTGACTATCGCAACG
54075 GGTATTTGAC
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
73 45 0.49
74 17 0.18
79 21 0.23
80 9 0.10
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGAGAAAATCGCAACGCGAATTTGACTATCACAACGCG
AATTTGAGT
Found at i:54050 original size:113 final size:114
Alignment explanation
Indices: 53851--54073 Score: 333
Period size: 113 Copynumber: 2.0 Consensus size: 114
53841 TTACACATTC
*
53851 ATTTGAATATCGCAACGCGAATTTGATTATCACAACTCAAAAATCGCAACGCGAATTTGACTATC
1 ATTTGAATATCGCAACGCGAATTTGACTATCACAACTCAAAAATCGCAACGCGAATTTGACTATC
*
53916 GCAACGCGAATTTGTCTATCGCAACGCGAATTTGACTATCACAACTCGA
66 GCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACTCGA
* * * * *
53965 ATTTGATTATCGCAACG-GTATTTGACTATCGCAAC-GAGAAAATCGCAACGCGAATTTGAGTAT
1 ATTTGAATATCGCAACGCGAATTTGACTATCACAACTCA-AAAATCGCAACGCGAATTTGACTAT
* * *
54028 CGCAACGCGAATTTGAGTATCGCAACGCGAATTTGATTATCGCAAC
65 CGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAAC
54074 GGGTATTTGA
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
112 1 0.01
113 81 0.83
114 16 0.16
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (114 bp):
ATTTGAATATCGCAACGCGAATTTGACTATCACAACTCAAAAATCGCAACGCGAATTTGACTATC
GCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATCACAACTCGA
Found at i:54162 original size:20 final size:20
Alignment explanation
Indices: 54137--54175 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54127 CGCGAATTGA
* *
54137 CTTTCACGTTGCTATTTTGT
1 CTTTCACATTGCGATTTTGT
54157 CTTTCACATTGCGATTTTG
1 CTTTCACATTGCGATTTTG
54176 AGTTTAGCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.21, G:0.15, T:0.51
Consensus pattern (20 bp):
CTTTCACATTGCGATTTTGT
Found at i:54349 original size:14 final size:14
Alignment explanation
Indices: 54289--54350 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
54279 CACAAATAAG
*
54289 AATTATTTACACATC
1 AATT-TTTACAAATC
**
54304 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
54319 AACTTTTACAAATC
1 AATTTTTACAAATC
*
54333 AATTTTTATAAATC
1 AATTTTTACAAATC
54347 AATT
1 AATT
54351 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:55842 original size:42 final size:42
Alignment explanation
Indices: 55763--55855 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
55753 CCTCTTCAAC
* * *
55763 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
55805 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGATC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
55847 GATGACAGG
1 GATGACAGG
55856 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.22, C:0.17, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:56365 original size:20 final size:20
Alignment explanation
Indices: 56342--56390 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
56332 GAAACTTAAA
56342 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
56362 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
56382 ATCGCAACG
1 ATCGCAACG
56391 AGAGAATCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.39, C:0.27, G:0.20, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:58397 original size:20 final size:20
Alignment explanation
Indices: 58374--58414 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
58364 TCTGAAACTT
58374 AAAATCACAACACGAAAATG
1 AAAATCACAACACGAAAATG
** *
58394 AAAATCGTAACATGAAAATG
1 AAAATCACAACACGAAAATG
58414 A
1 A
58415 CTATCGCAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.15, G:0.12, T:0.15
Consensus pattern (20 bp):
AAAATCACAACACGAAAATG
Found at i:59056 original size:20 final size:20
Alignment explanation
Indices: 59030--59167 Score: 204
Period size: 20 Copynumber: 6.9 Consensus size: 20
59020 GCACTTTGAA
*
59030 AATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
59050 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
59070 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
59090 AATCTCGTTGCAATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
59110 AATCTCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
59130 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
59150 AATCGCGTTGCGATAGTC
1 AATCGCGTTGCGATAGTC
59168 GGAAAATCGC
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 111 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:62139 original size:118 final size:119
Alignment explanation
Indices: 62017--62257 Score: 265
Period size: 118 Copynumber: 2.0 Consensus size: 119
62007 TAGGGTTAAA
* * * * *
62017 TTACACTATTAGTAATTATATTTTATAATATTTTA-AATTAAGACAATTAATTTAT-ATATTTTT
1 TTACACTAATAATAACTAGATTTCATAATA-TTTAGAATTAAGACAATTAATTT-TGATA-TTTT
* ** *
62080 ACAA-TTTAATCATTGAGGTTTAATATTTTAATTTTAAATAATA-TTTTAGGATTAT
63 ACAATTTTAATCATTGAGGTTTAAAATAATAATTTTAAATAATATTTTTAGAATTAT
* * ***
62135 TTACACTAATAATACCTAGATTTCATGATATTTAGAATTAAGATTTTTAATTTTGATATTTTACA
1 TTACACTAATAATAACTAGATTTCATAATATTTAGAATTAAGACAATTAATTTTGATATTTTACA
* * * *
62200 ATTTTAATCCTTTAGTTTTAAAATAATAATTTTAAATATTATTTTTAGAATTAT
66 ATTTTAATCATTGAGGTTTAAAATAATAATTTTAAATAATATTTTTAGAATTAT
62254 TTAC
1 TTAC
62258 TATTATAGTA
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
117 13 0.13
118 73 0.72
119 15 0.15
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (119 bp):
TTACACTAATAATAACTAGATTTCATAATATTTAGAATTAAGACAATTAATTTTGATATTTTACA
ATTTTAATCATTGAGGTTTAAAATAATAATTTTAAATAATATTTTTAGAATTAT
Found at i:63554 original size:46 final size:48
Alignment explanation
Indices: 63464--63560 Score: 112
Period size: 47 Copynumber: 2.1 Consensus size: 48
63454 CTTAATTTAC
* *
63464 TTTATTTTCCTAATAAATGCATGCAAACTAGAAATCATGCGGTTA-GA
1 TTTATTTTCCAAATAAATGCATGCAAACTAGAAATCATGAGGTTAGGA
* *
63511 TTTATTTCTCCAAATAAA-GCATG-GAACTAG-ATTACATGAGGTTAGGA
1 TTTATTT-TCCAAATAAATGCATGCAAACTAGAAAT-CATGAGGTTAGGA
63558 TTT
1 TTT
63561 TTATGATATT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
45 2 0.05
46 15 0.35
47 17 0.40
48 9 0.21
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (48 bp):
TTTATTTTCCAAATAAATGCATGCAAACTAGAAATCATGAGGTTAGGA
Found at i:65507 original size:97 final size:97
Alignment explanation
Indices: 65387--65578 Score: 341
Period size: 97 Copynumber: 2.0 Consensus size: 97
65377 GAAGTAATCG
*
65387 GAGACTGACCCATAGGTTTAAAAA-AGAATGGGGCAGATGTAACCCAGAATACACCTCAGACACC
1 GAGACTGACCCATAGGTTTAAAAAGA-AATGGGGCAGATGTAACCCAGAAGACACCTCAGACACC
65451 TATATCAGATTTTCTGAAAACAAGTGAGGTATT
65 TATATCAGATTTTCTGAAAACAAGTGAGGTATT
* *
65484 GAGACTGGCCCATAGGTTTAAAAAGAAATGGGGTAGATGTAACCCAGAAGACACCTCAGACACCT
1 GAGACTGACCCATAGGTTTAAAAAGAAATGGGGCAGATGTAACCCAGAAGACACCTCAGACACCT
65549 ATATCAGATTTTCTGAAAACAAGTGAGGTA
66 ATATCAGATTTTCTGAAAACAAGTGAGGTA
65579 GGGGGAAATT
Statistics
Matches: 91, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
97 90 0.99
98 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (97 bp):
GAGACTGACCCATAGGTTTAAAAAGAAATGGGGCAGATGTAACCCAGAAGACACCTCAGACACCT
ATATCAGATTTTCTGAAAACAAGTGAGGTATT
Found at i:70371 original size:136 final size:134
Alignment explanation
Indices: 70123--70378 Score: 318
Period size: 136 Copynumber: 1.9 Consensus size: 134
70113 AACAACTTTT
**
70123 CAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAAGATATTGAACTCAAATCAGTACAACCA
1 CAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAAGATATTGAACTCAAATCAACACAACCA
* * * *
70188 AAGATTGGATTTCAACTTCACAACAAATGATATCTAATTCAAAGCTCAACTTCACAGTAAAGGGG
66 AACATTGGATTTAAACTTCACAACAAAGGATATCCAATTCAAAGCTCAACTTCACAGTAAAGGGG
70253 TTTC
131 TTTC
* * * *
70257 CAGTTTCATTTAGAG-CTAATTTCAACTTCACGACGAAGGATATTGGACTCGAAA-CAACAGCAA
1 CAGTTTCATTCAGAGTC-AATTTCAACTTCACAACGAAAGATATTGAACTC-AAATCAACA-CAA
* * * * * *
70320 TGCAACCCTTGGATTTAAACTTCACGACAAAGGATATCCAATTCTAGGCTCAACTTCAC
63 -CCAAACATTGGATTTAAACTTCACAACAAAGGATATCCAATTCAAAGCTCAACTTCAC
70379 GACGAATGGG
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
133 1 0.01
134 47 0.46
135 6 0.06
136 48 0.47
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (134 bp):
CAGTTTCATTCAGAGTCAATTTCAACTTCACAACGAAAGATATTGAACTCAAATCAACACAACCA
AACATTGGATTTAAACTTCACAACAAAGGATATCCAATTCAAAGCTCAACTTCACAGTAAAGGGG
TTTC
Found at i:70652 original size:137 final size:137
Alignment explanation
Indices: 70485--71279 Score: 1103
Period size: 137 Copynumber: 5.8 Consensus size: 137
70475 TCGTGTCCAT
* * ** * * *
70485 CAACATCATCCTTAGATAGCCAGACGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCTTC
1 CAACATCATTCTTAGATAACCAGATATCCTCATCACGAAAGAACAGTGTTATCTCAAATATCTTT
* * *
70550 AAAGATGGCCAGACGTCCTCATCATGAAGGAACAATGTCATCCACCGATCATAACTCCTCATCAT
66 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
70615 GAAGGAG
131 GAAGGAG
* *
70622 CAACATCATTCTTAGATAACCAGATATCCTCATCATGAAAGAACGGTGTTATCTCAAATATCTTT
1 CAACATCATTCTTAGATAACCAGATATCCTCATCACGAAAGAACAGTGTTATCTCAAATATCTTT
*
70687 -AAGATGGCCAGACATCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
66 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
*
70751 GAAAGAG
131 GAAGGAG
* *
70758 CAACATCATTCTTAGATAACCAAATATCCTCATCATGAAAGAACAGTGTTATCTCAAATATCTTT
1 CAACATCATTCTTAGATAACCAGATATCCTCATCACGAAAGAACAGTGTTATCTCAAATATCTTT
* *
70823 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCGTCCACCGATTAGAACTCCTCATCAC
66 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
*
70888 AAAGGAG
131 GAAGGAG
** *
70895 CAACATCATTCTTAGATAACCAGATATCCTCATCGTGAAAGAACAATGTTATCTCAAATATCTTT
1 CAACATCATTCTTAGATAACCAGATATCCTCATCACGAAAGAACAGTGTTATCTCAAATATCTTT
*
70960 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAAAACTCCTCATCAC
66 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
71025 GAAGGAG
131 GAAGGAG
* * * * * *
71032 CAACATCATTCTTAGATAGCCAGATGTCCTCATCACGAAGGAACCGTGTTCTCTCAAATATATTT
1 CAACATCATTCTTAGATAACCAGATATCCTCATCACGAAAGAACAGTGTTATCTCAAATATCTTT
* * * * * *
71097 AAAGATGGCTAAACGTCCTCATCACGAAGGACCAATGTCATCCACTGACCATAACTCCTCATCAC
66 AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
*
71162 GTAGGAG
131 GAAGGAG
* * ** * **
71169 C--CGAGTCATCCTCAGATAACCAGACGTCTTCATCAC-AAAGGAACCTTGTTATCTCAAATATC
1 CAAC-A-TCATTCTTAGATAACCAGATATCCTCATCACGAAA-GAACAGTGTTATCTCAAATATC
* * ** *
71231 TTCAAAGATGGTCAGACGTCCTCATCGTGAAGGAACAATGTCATACACC
63 TTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACC
71280 AGTTTGATCT
Statistics
Matches: 593, Mismatches: 61, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
135 1 0.00
136 132 0.22
137 460 0.78
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.24
Consensus pattern (137 bp):
CAACATCATTCTTAGATAACCAGATATCCTCATCACGAAAGAACAGTGTTATCTCAAATATCTTT
AAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCAC
GAAGGAG
Found at i:71929 original size:76 final size:77
Alignment explanation
Indices: 71770--71979 Score: 291
Period size: 76 Copynumber: 2.8 Consensus size: 77
71760 CAAAGCCAAA
* * * **
71770 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
71834 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
*
71847 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
71912 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * * *
71923 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
71980 TGTATAACGG
Statistics
Matches: 120, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
75 19 0.16
76 62 0.52
77 39 0.32
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:77753 original size:19 final size:19
Alignment explanation
Indices: 77729--77766 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
77719 TTTTGGTGTA
*
77729 GAGGGAATCGATCCCCCCT
1 GAGGGAACCGATCCCCCCT
*
77748 GAGGGAACCGATTCCCCCT
1 GAGGGAACCGATCCCCCCT
77767 TTGAAGGGGA
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:0.21, C:0.37, G:0.26, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATCCCCCCT
Found at i:80046 original size:30 final size:30
Alignment explanation
Indices: 80012--80083 Score: 126
Period size: 30 Copynumber: 2.3 Consensus size: 30
80002 GGAGAAGAAT
80012 AGGTGTTAAATGTTTTACATAATAAATTGA
1 AGGTGTTAAATGTTTTACATAATAAATTGA
80042 AGGTGTTAAATGTTTTACATAATAAATTGA
1 AGGTGTTAAATGTTTTACATAATAAATTGA
80072 AGAAGTGTTAAA
1 AG--GTGTTAAA
80084 GTAAGGGGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 32 0.80
32 8 0.20
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.38
Consensus pattern (30 bp):
AGGTGTTAAATGTTTTACATAATAAATTGA
Found at i:80551 original size:76 final size:77
Alignment explanation
Indices: 80392--80598 Score: 287
Period size: 76 Copynumber: 2.7 Consensus size: 77
80382 CAAAGCCAAA
* * * **
80392 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
80456 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
*
80469 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
80534 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * *
80545 AATTCCAGTATGCTCGGAGGGAACCGA-TCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
80599 TTGTACAACG
Statistics
Matches: 118, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
74 17 0.14
75 8 0.07
76 54 0.46
77 39 0.33
ACGTcount: A:0.25, C:0.32, G:0.24, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:82301 original size:118 final size:119
Alignment explanation
Indices: 82179--82419 Score: 265
Period size: 118 Copynumber: 2.0 Consensus size: 119
82169 TAGGGTTAAA
* * * * *
82179 TTACACTATTAGTAATTATATTTTATAATATTTTA-AATTAAGACAATTAATTTAT-ATATTTTT
1 TTACACTAATAATAACTAGATTTCATAATA-TTTAGAATTAAGACAATTAATTT-TGATA-TTTT
* ** *
82242 ACAA-TTTAATCATTGAGGTTTAATATTTTAATTTTAAATAATA-TTTTAGGATTAT
63 ACAATTTTAATCATTGAGGTTTAAAATAATAATTTTAAATAATATTTTTAGAATTAT
* * ***
82297 TTACACTAATAATACCTAGATTTCATGATATTTAGAATTAAGATTTTTAATTTTGATATTTTACA
1 TTACACTAATAATAACTAGATTTCATAATATTTAGAATTAAGACAATTAATTTTGATATTTTACA
* * * *
82362 ATTTTAATCCTTTAGTTTTAAAATAATAATTTTAAATATTATTTTTAGAATTAT
66 ATTTTAATCATTGAGGTTTAAAATAATAATTTTAAATAATATTTTTAGAATTAT
82416 TTAC
1 TTAC
82420 TATTATAGTA
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
117 13 0.13
118 73 0.72
119 15 0.15
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (119 bp):
TTACACTAATAATAACTAGATTTCATAATATTTAGAATTAAGACAATTAATTTTGATATTTTACA
ATTTTAATCATTGAGGTTTAAAATAATAATTTTAAATAATATTTTTAGAATTAT
Found at i:83144 original size:11 final size:11
Alignment explanation
Indices: 83128--83158 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
83118 GCCACCAAGG
83128 ATGCTGGGCAT
1 ATGCTGGGCAT
83139 ATGCTGGGCAT
1 ATGCTGGGCAT
83150 ATGCTGGGC
1 ATGCTGGGC
83159 GGATTGCTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.19, G:0.39, T:0.26
Consensus pattern (11 bp):
ATGCTGGGCAT
Found at i:88484 original size:31 final size:31
Alignment explanation
Indices: 88441--88504 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
88431 CAGTTACGTC
88441 GGGGACCATATTGCAAACT-GACTAAATGTTG
1 GGGGACCATATTGCAAA-TGGACTAAATGTTG
*
88472 GGGGACCTTATTGCAAATGGACTAAATGTTG
1 GGGGACCATATTGCAAATGGACTAAATGTTG
88503 GG
1 GG
88505 TACCGTATTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (31 bp):
GGGGACCATATTGCAAATGGACTAAATGTTG
Found at i:90053 original size:31 final size:31
Alignment explanation
Indices: 90011--90085 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
90001 CAGTTACATC
* *
90011 AGGGACTATATTGCAAACT-GAATAAATGTTG
1 AGGGACCATATTGCAAA-TGGAATAAATCTTG
* *
90042 AGGGACCATATTACAAATGGACTAAATCTTG
1 AGGGACCATATTGCAAATGGAATAAATCTTG
*
90073 GGGGACCATATTG
1 AGGGACCATATTG
90086 TAAGTTTTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 1 0.03
31 36 0.97
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (31 bp):
AGGGACCATATTGCAAATGGAATAAATCTTG
Found at i:91243 original size:20 final size:20
Alignment explanation
Indices: 91218--91270 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
91208 ATCATATTCC
91218 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
91238 CTGGTAATCTTACATTCTCA
1 CTGGTAATCTTACATTCCCA
91258 CTGGTAATCTTAC
1 CTGGTAATCTTAC
91271 CTTTCGTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:93894 original size:14 final size:16
Alignment explanation
Indices: 93875--93906 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
93865 TCATATTATC
93875 TATTTAAA-TTAT-AA
1 TATTTAAAGTTATCAA
93889 TATTTAAAGTTATCAA
1 TATTTAAAGTTATCAA
93905 TA
1 TA
93907 GATGAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (16 bp):
TATTTAAAGTTATCAA
Found at i:94983 original size:5 final size:5
Alignment explanation
Indices: 94973--95000 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
94963 TTGGGTGACT
94973 TCATA TCATA TCATA TCATA TCATA TCA
1 TCATA TCATA TCATA TCATA TCATA TCA
95001 CACACACACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
TCATA
Found at i:96351 original size:2 final size:2
Alignment explanation
Indices: 96344--96374 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
96334 CTAACATGAA
96344 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
96375 ACAAAGACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:101389 original size:24 final size:23
Alignment explanation
Indices: 101362--101458 Score: 68
Period size: 24 Copynumber: 4.0 Consensus size: 23
101352 AAATATTTTA
*
101362 TCTGATTTTCGACTTGAATTATGT
1 TCTGATTTT-GACCTGAATTATGT
* **
101386 TCTGCTACATGACCTGAATTATGT
1 TCTGAT-TTTGACCTGAATTATGT
* * *
101410 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTT-TGACCTGAATTATGT
* * *
101434 TCTGATATCTGATCTGAATTCTGT
1 TCTGAT-TTTGACCTGAATTATGT
101458 T
1 T
101459 TTAATTTCTG
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
24 56 0.97
25 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.46
Consensus pattern (23 bp):
TCTGATTTTGACCTGAATTATGT
Found at i:101425 original size:12 final size:12
Alignment explanation
Indices: 101410--101470 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
101400 TGAATTATGT
101410 TCTGATTTCTGA
1 TCTGATTTCTGA
*
101422 TCTGGA-TTCTGT
1 TCT-GATTTCTGA
*
101434 TCTGATATCTGA
1 TCTGATTTCTGA
* *
101446 TCTGAATTCTGT
1 TCTGATTTCTGA
* *
101458 TTTAATTTCTGA
1 TCTGATTTCTGA
101470 T
1 T
101471 ATCTCTGTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.18, C:0.15, G:0.16, T:0.51
Consensus pattern (12 bp):
TCTGATTTCTGA
Found at i:101468 original size:24 final size:24
Alignment explanation
Indices: 101399--101470 Score: 99
Period size: 24 Copynumber: 3.0 Consensus size: 24
101389 GCTACATGAC
*
101399 CTGAATTATGTTCTGATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
101423 CTGGATTCTGTTCTGATATCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
* *
101447 CTGAATTCTGTTTTAATTTCTGAT
1 CTGAATTCTGTTCTGATTTCTGAT
101471 ATCTCTGTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTCTGATTTCTGAT
Found at i:104763 original size:11 final size:11
Alignment explanation
Indices: 104749--104780 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
104739 CAAGAATTAA
104749 TGAATGATGAT
1 TGAATGATGAT
*
104760 TGAAGGATGAT
1 TGAATGATGAT
104771 TGAATGATGA
1 TGAATGATGA
104781 ATAGATGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (11 bp):
TGAATGATGAT
Found at i:104908 original size:36 final size:35
Alignment explanation
Indices: 104808--104916 Score: 123
Period size: 35 Copynumber: 3.1 Consensus size: 35
104798 GGTGGTTATT
* * * *
104808 TAGGCGTGAAATGGTGATAGAAGATGGTAATGATA
1 TAGGCGTGAAATGGAGATGGAAGATGGTGATGTTA
* * *
104843 TAGGCGTGCAATGCTA-ATGAAAGATGGTGATGTTA
1 TAGGCGTGAAATG-GAGATGGAAGATGGTGATGTTA
104878 TAGGCGTGAAAATGGAGATGGAAGATGGTGATGTT-
1 TAGGCGTG-AAATGGAGATGGAAGATGGTGATGTTA
104913 TAGG
1 TAGG
104917 TAGTATCTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
35 40 0.66
36 21 0.34
ACGTcount: A:0.33, C:0.05, G:0.36, T:0.27
Consensus pattern (35 bp):
TAGGCGTGAAATGGAGATGGAAGATGGTGATGTTA
Found at i:109168 original size:21 final size:20
Alignment explanation
Indices: 109143--109184 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
109133 ATGGCTAATT
109143 AAGAAATGAAATAGAAATGAA
1 AAGAAATGAAATAGAAA-GAA
* *
109164 AAGAATTGAAATGGAAAGAA
1 AAGAAATGAAATAGAAAGAA
109184 A
1 A
109185 TGTTATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.14
Consensus pattern (20 bp):
AAGAAATGAAATAGAAAGAA
Found at i:109425 original size:36 final size:35
Alignment explanation
Indices: 109334--109442 Score: 132
Period size: 35 Copynumber: 3.1 Consensus size: 35
109324 GGTGGTTATT
* * * * *
109334 TAGGCGTGAAATGGTGATAGAAGATGGTAAAGATA
1 TAGGCGTGAAATGGAGATGGAAGATGGTGATGTTA
*
109369 TAGGCGTGCAATGGTA-ATGGAAGATGGTGATGTTA
1 TAGGCGTGAAATGG-AGATGGAAGATGGTGATGTTA
109404 TAGGCGTGAAAATGGAGATGGAAGATGGTGATGTT-
1 TAGGCGTG-AAATGGAGATGGAAGATGGTGATGTTA
109439 TAGG
1 TAGG
109443 TAGTATCTTA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
35 41 0.64
36 23 0.36
ACGTcount: A:0.33, C:0.04, G:0.38, T:0.26
Consensus pattern (35 bp):
TAGGCGTGAAATGGAGATGGAAGATGGTGATGTTA
Found at i:118058 original size:19 final size:20
Alignment explanation
Indices: 118034--118073 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
118024 ATAAATTAAA
118034 ATATTAATAAATTACA-TTT
1 ATATTAATAAATTACACTTT
*
118053 ATATTAATCAATTACACTTT
1 ATATTAATAAATTACACTTT
118073 A
1 A
118074 CCACCTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATTAATAAATTACACTTT
Found at i:120714 original size:18 final size:19
Alignment explanation
Indices: 120679--120715 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
120669 CACGGAATGT
120679 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
120699 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
120716 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:121931 original size:20 final size:20
Alignment explanation
Indices: 121895--121932 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
121885 AATCCTATTC
**
121895 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
121915 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
121933 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:123257 original size:17 final size:17
Alignment explanation
Indices: 123235--123270 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
123225 TTATTTTCTT
123235 TAATTACCAGCTCTCTA
1 TAATTACCAGCTCTCTA
123252 TAATTACCAGCTCTCTA
1 TAATTACCAGCTCTCTA
123269 TA
1 TA
123271 TCTCTGGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.36
Consensus pattern (17 bp):
TAATTACCAGCTCTCTA
Found at i:130315 original size:19 final size:21
Alignment explanation
Indices: 130291--130336 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
130281 TGTCGGGAAA
130291 ATATAA-T-ATCAAAATGT-AT
1 ATATAATTGATCAAAAT-TCAT
130310 ATATAATTGATCAAAATTCAT
1 ATATAATTGATCAAAATTCAT
130331 ATATAA
1 ATATAA
130337 CACGTTACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 16 0.67
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (21 bp):
ATATAATTGATCAAAATTCAT
Found at i:136961 original size:13 final size:15
Alignment explanation
Indices: 136912--136957 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
136902 TAATTTTAAA
*
136912 TATTTAAATAAAAAT
1 TATTTATATAAAAAT
136927 TATTTATATAAAAAT
1 TATTTATATAAAAAT
136942 TATTTATATAAAAAT
1 TATTTATATAAAAAT
136957 T
1 T
136958 TTATCTGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TATTTATATAAAAAT
Found at i:140820 original size:22 final size:22
Alignment explanation
Indices: 140777--140820 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
140767 TGTCTTCTGC
* *
140777 CACATGCCATGCAACTTCATTT
1 CACATGCAACGCAACTTCATTT
140799 CACATGCAACGCATACTT-ATTT
1 CACATGCAACGCA-ACTTCATTT
140821 TAGTGACATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (22 bp):
CACATGCAACGCAACTTCATTT
Found at i:141075 original size:2 final size:2
Alignment explanation
Indices: 141068--141097 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
141058 ACATAATTTG
141068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
141098 TTAACAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:142438 original size:15 final size:15
Alignment explanation
Indices: 142420--142474 Score: 65
Period size: 15 Copynumber: 3.3 Consensus size: 15
142410 GGTTAATGAT
142420 TTAATTGACATTTTA
1 TTAATTGACATTTTA
142435 TTAATTGACATTTTGAGGA
1 TTAATTGACATTTT----A
142454 TTTAATTGACATTTTA
1 -TTAATTGACATTTTA
142470 TTAAT
1 TTAAT
142475 GATTTTAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
15 19 0.54
16 1 0.03
19 1 0.03
20 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.51
Consensus pattern (15 bp):
TTAATTGACATTTTA
Found at i:145323 original size:27 final size:28
Alignment explanation
Indices: 145284--145337 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
145274 TTGAATCAAT
**
145284 ATAAATTTAATTTTTTATATA-ATATAA
1 ATAAATTTAATTTCATATATATATATAA
145311 ATAAATCTT-ATTTCATATATATATATA
1 ATAAAT-TTAATTTCATATATATATATA
145338 TAGATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (28 bp):
ATAAATTTAATTTCATATATATATATAA
Found at i:146420 original size:51 final size:51
Alignment explanation
Indices: 146329--146427 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
146319 TTTTCATTTA
* * *
146329 AAATCCCTAAATTCCCCGTGTTTCCCCTTTCTTCCACATTAGCTTCCATTG
1 AAATCCCTAAATTCACCATGTTTCCCCTTTCTTCCACATTAACTTCCATTG
* * *
146380 AAATCCCTAGATTCACCATGTTTCCCTTTTC-TCCTTCATTAACTTCCA
1 AAATCCCTAAATTCACCATGTTTCCCCTTTCTTCC-ACATTAACTTCCA
146428 ATTTCGCTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 3 0.07
51 38 0.93
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.38
Consensus pattern (51 bp):
AAATCCCTAAATTCACCATGTTTCCCCTTTCTTCCACATTAACTTCCATTG
Found at i:147601 original size:24 final size:24
Alignment explanation
Indices: 147574--147619 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
147564 CTCGTATAAA
147574 TGCACCGAAGTGCCACGTAGAATT
1 TGCACCGAAGTGCCACGTAGAATT
* *
147598 TGCACCGTAGTGCCGCGTAGAA
1 TGCACCGAAGTGCCACGTAGAA
147620 ATGCACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (24 bp):
TGCACCGAAGTGCCACGTAGAATT
Found at i:148069 original size:20 final size:21
Alignment explanation
Indices: 148022--148072 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
148012 TTTTGTGTCT
*
148022 TATCATATAACTTCTCTTTTA
1 TATCATATAACTTCTCTTTCA
148043 TATTCATATAA-TT-TCTTATCA
1 TA-TCATATAACTTCTCTT-TCA
148064 TATCATATA
1 TATCATATA
148073 GTTTATATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 11 0.41
21 8 0.30
22 8 0.30
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (21 bp):
TATCATATAACTTCTCTTTCA
Found at i:148572 original size:18 final size:17
Alignment explanation
Indices: 148549--148594 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
148539 TTTAAGGGGG
*
148549 TGCATCGATGCACTCAT
1 TGCATCGATGCACTAAT
148566 ATGCATCGATGCACTAAT
1 -TGCATCGATGCACTAAT
148584 TGCATTCGATG
1 TGCA-TCGATG
148595 TTTCCATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 4 0.15
18 22 0.85
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (17 bp):
TGCATCGATGCACTAAT
Found at i:148590 original size:63 final size:63
Alignment explanation
Indices: 148489--148639 Score: 171
Period size: 63 Copynumber: 2.4 Consensus size: 63
148479 TCGATGCATG
** * **
148489 TCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTTTA-TTTTAAGGGGGTGCA
1 TCGATGCACT-CATATGCATCGATGCACAAATCACATTCGATGTTTCCATTTTTAA-GGGGTGCA
* ** *
148553 TCGATGCACTCATATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGGGTGCA
1 TCGATGCACTCATATGCATCGATGCACAAATCACATTCGATGTTTCCATTTTTAAGGGGTGCA
*
148616 TCGATGCACTAAT-TGCATTCGATG
1 TCGATGCACTCATATGCA-TCGATG
148640 TTTCCATTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
62 4 0.05
63 55 0.73
64 16 0.21
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (63 bp):
TCGATGCACTCATATGCATCGATGCACAAATCACATTCGATGTTTCCATTTTTAAGGGGTGCA
Found at i:148617 original size:45 final size:45
Alignment explanation
Indices: 148567--148670 Score: 208
Period size: 45 Copynumber: 2.3 Consensus size: 45
148557 TGCACTCATA
148567 TGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGGG
1 TGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGGG
148612 TGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGGG
1 TGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGGG
148657 TGCATCGATGCACT
1 TGCATCGATGCACT
148671 TCTTGTGCAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.38
Consensus pattern (45 bp):
TGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGGG
Found at i:152467 original size:29 final size:29
Alignment explanation
Indices: 152425--152494 Score: 131
Period size: 29 Copynumber: 2.4 Consensus size: 29
152415 AACGTGTTTC
152425 ATATTTCTTTTGAGTGGGACTTCACTTTG
1 ATATTTCTTTTGAGTGGGACTTCACTTTG
152454 ATATTTCTTTTGAGTGGGACTTCACTTTG
1 ATATTTCTTTTGAGTGGGACTTCACTTTG
152483 ATATTTCATTTT
1 ATATTTC-TTTT
152495 TTTAAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 36 0.90
30 4 0.10
ACGTcount: A:0.19, C:0.13, G:0.17, T:0.51
Consensus pattern (29 bp):
ATATTTCTTTTGAGTGGGACTTCACTTTG
Found at i:153446 original size:216 final size:218
Alignment explanation
Indices: 153153--153587 Score: 831
Period size: 216 Copynumber: 2.0 Consensus size: 218
153143 TTGTAGGGGG
153153 CAACGTTATCTCATCGAAATAGTTAGACTAAGAAGAAAAGGATTGTACAAAATAATGAGAAGGAA
1 CAACGTTATCTCATCGAAATAGTTAGACTAAGAAGAAAA-GATTGTACAAAATAATGAGAAGGAA
153218 ACAAAAACAATGGTAAGAAAGAGAGCGAATAAAGTCGAGAGACCTGATGATCCAAAATTCAGGAG
65 ACAAAAACAATGGTAAGAAAGAGAGCGAATAAAGTCGAGAGACCTGATGATCCAAAATTCAGGAG
153283 AAAAAGCATTGGAGTTGTTGGAAAGGCACTAGTGGGGACACAACTGTTTAATTCACCAAAAGCTT
130 AAAAAGCATTGGAGTTGTTGGAAAGGCACTAGTGGGGACACAACTGTTTAATTCACCAAAAGCTT
153348 TAATAATAAACATAAAGGTCAATT
195 TAATAATAAACATAAAGGTCAATT
153372 CAACGTTATCTCATCGAAATAGTTAGACTAAGAAG-AAA-ATTGTACAAAATAATGA-AAGGAAA
1 CAACGTTATCTCATCGAAATAGTTAGACTAAGAAGAAAAGATTGTACAAAATAATGAGAAGG-AA
153434 ACAAAAACAATGGTAAGAAAGAGAGCGAATAAAGTCGAGAGACCTGATGATCCAAAATTCAGGAG
65 ACAAAAACAATGGTAAGAAAGAGAGCGAATAAAGTCGAGAGACCTGATGATCCAAAATTCAGGAG
153499 AAAAAGCATTGGAGTTGTTGGAAAGGCACTAGTGGGGACACAACTGTTTAATTCACCAAAAGCTT
130 AAAAAGCATTGGAGTTGTTGGAAAGGCACTAGTGGGGACACAACTGTTTAATTCACCAAAAGCTT
153564 TAATAATAAACATAAAGGTCAATT
195 TAATAATAAACATAAAGGTCAATT
153588 TGAGTTTTAC
Statistics
Matches: 215, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
215 4 0.02
216 173 0.80
218 3 0.01
219 35 0.16
ACGTcount: A:0.45, C:0.13, G:0.21, T:0.21
Consensus pattern (218 bp):
CAACGTTATCTCATCGAAATAGTTAGACTAAGAAGAAAAGATTGTACAAAATAATGAGAAGGAAA
CAAAAACAATGGTAAGAAAGAGAGCGAATAAAGTCGAGAGACCTGATGATCCAAAATTCAGGAGA
AAAAGCATTGGAGTTGTTGGAAAGGCACTAGTGGGGACACAACTGTTTAATTCACCAAAAGCTTT
AATAATAAACATAAAGGTCAATT
Found at i:162837 original size:15 final size:17
Alignment explanation
Indices: 162802--162838 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
162792 AATTCAAGGG
*
162802 TATAATTAAATATAGTA
1 TATAATTAAATAAAGTA
162819 TATAA-TAAATAAAGT-
1 TATAATTAAATAAAGTA
162834 TATAA
1 TATAA
162839 ATTGCTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 9 0.47
17 5 0.26
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
TATAATTAAATAAAGTA
Found at i:163338 original size:185 final size:187
Alignment explanation
Indices: 163007--163379 Score: 732
Period size: 185 Copynumber: 2.0 Consensus size: 187
162997 CAGGTTTTAA
163007 TTTCAAAATTGATTCCCTAACTTAATTAAGAGGAAAAGAATTGTAACAGCTTAATCAATTTCCGG
1 TTTCAAAATTGATTCCCTAACTTAATTAAGAGGAAAAGAATTGTAACAGCTTAATCAATTTCCGG
163072 TTTTTTTTCTTCATATAACTGTTAAATTCATTGATTTTTTATTTAACAGATTGAATTAATTAATT
66 TTTTTTTTCTTCATATAACTGTTAAATTCATTGATTTTTTATTTAACAGATTGAATTAATTAATT
163137 CAACTTAGTTTTTTAACTCATAAAACAATTAAAATAAATATAAATTACTAATAAATT
131 CAACTTAGTTTTTTAACTCATAAAACAATTAAAATAAATATAAATTACTAATAAATT
163194 TTTCAAAATTGATTCCCTAACTTAATTAAGAGGAAAAGAATTGTAACAGCTTAATCAATTTCCGG
1 TTTCAAAATTGATTCCCTAACTTAATTAAGAGGAAAAGAATTGTAACAGCTTAATCAATTTCCGG
163259 -TTTTTTT-TTCATATAACTGTTAAATTCATTGATTTTTTATTTAACAGATTGAATTAATTAATT
66 TTTTTTTTCTTCATATAACTGTTAAATTCATTGATTTTTTATTTAACAGATTGAATTAATTAATT
163322 CAACTTAGTTTTTTAACTCATAAAACAATTAAAATAAATATAAATTACTAATAAATT
131 CAACTTAGTTTTTTAACTCATAAAACAATTAAAATAAATATAAATTACTAATAAATT
163379 T
1 T
163380 AAAAGTTAAC
Statistics
Matches: 186, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
185 114 0.61
186 7 0.04
187 65 0.35
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (187 bp):
TTTCAAAATTGATTCCCTAACTTAATTAAGAGGAAAAGAATTGTAACAGCTTAATCAATTTCCGG
TTTTTTTTCTTCATATAACTGTTAAATTCATTGATTTTTTATTTAACAGATTGAATTAATTAATT
CAACTTAGTTTTTTAACTCATAAAACAATTAAAATAAATATAAATTACTAATAAATT
Found at i:177447 original size:22 final size:22
Alignment explanation
Indices: 177419--177462 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
177409 ATACTCCCCA
177419 GGCTGACAGACGAGGCTCACGT
1 GGCTGACAGACGAGGCTCACGT
177441 GGCTGACAGACGAGGCTCACGT
1 GGCTGACAGACGAGGCTCACGT
177463 CCAGGGGGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.27, G:0.36, T:0.14
Consensus pattern (22 bp):
GGCTGACAGACGAGGCTCACGT
Found at i:179239 original size:39 final size:39
Alignment explanation
Indices: 179185--179271 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
179175 CGGCTACGAC
179185 TTCTTTAGTAGTCAATGGCTCTTGCTATATTATAACAAA
1 TTCTTTAGTAGTCAATGGCTCTTGCTATATTATAACAAA
* *
179224 TTCTTTAGTAGTCAATGGCTCTTGTTATATTGTAACAAA
1 TTCTTTAGTAGTCAATGGCTCTTGCTATATTATAACAAA
179263 TTCTTTAGT
1 TTCTTTAGT
179272 TGCTATATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.45
Consensus pattern (39 bp):
TTCTTTAGTAGTCAATGGCTCTTGCTATATTATAACAAA
Found at i:181536 original size:23 final size:23
Alignment explanation
Indices: 181510--181584 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 23
181500 AACATGTTCA
181510 TGGACATTAAATGAACACATTCG
1 TGGACATTAAATGAACACATTCG
*
181533 TGGACATATAATATAGAAACAACACATTTG
1 TGGACAT-TAA-AT-G----AACACATTCG
* *
181563 CGAACATTAAATGAACACATTC
1 TGGACATTAAATGAACACATTC
181585 ACGAACAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
23 15 0.37
24 3 0.07
25 2 0.05
26 1 0.02
27 1 0.02
28 2 0.05
29 3 0.07
30 14 0.34
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (23 bp):
TGGACATTAAATGAACACATTCG
Found at i:181589 original size:23 final size:23
Alignment explanation
Indices: 181553--181597 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
181543 ATATAGAAAC
** *
181553 AACACATTTGCGAACATTAAATG
1 AACACATTCACGAACAATAAATG
181576 AACACATTCACGAACAATAAAT
1 AACACATTCACGAACAATAAAT
181598 AAGCGAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.49, C:0.20, G:0.09, T:0.22
Consensus pattern (23 bp):
AACACATTCACGAACAATAAATG
Found at i:181627 original size:30 final size:32
Alignment explanation
Indices: 181576--181644 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 32
181566 ACATTAAATG
**
181576 AACACATTCACGAACAATAAATAAGCGAACATA
1 AACACATTCAC-AACAATAAATAAAAGAACATA
*
181609 AACACATTCA-AA-AATAAATAAAAGAACATG
1 AACACATTCACAACAATAAATAAAAGAACATA
181639 AACACA
1 AACACA
181645 ATGTTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 21 0.64
31 2 0.06
33 10 0.30
ACGTcount: A:0.59, C:0.19, G:0.07, T:0.14
Consensus pattern (32 bp):
AACACATTCACAACAATAAATAAAAGAACATA
Found at i:185553 original size:12 final size:11
Alignment explanation
Indices: 185515--185561 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
185505 TAACCCCTAT
185515 CACA-CATATA
1 CACATCATATA
* *
185525 TCATATCATGTA
1 -CACATCATATA
185537 CACATCATATCA
1 CACATCATAT-A
185549 CACATCATATA
1 CACATCATATA
185560 CA
1 CA
185562 TATATCACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
11 14 0.47
12 16 0.53
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.28
Consensus pattern (11 bp):
CACATCATATA
Found at i:185920 original size:23 final size:23
Alignment explanation
Indices: 185894--185962 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
185884 CACCACAGCT
*
185894 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
185917 CGTAGAATTGCATCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
185940 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
185963 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:186159 original size:102 final size:103
Alignment explanation
Indices: 185978--186188 Score: 370
Period size: 102 Copynumber: 2.1 Consensus size: 103
185968 TAATGTCCAT
* * *
185978 AAGGACCACATATCATTCCTCAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACAACATATCATTCCTCAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
186043 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
186081 AAGGACAACATATCATTCCTTAAGAATCATATA-ATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACAACATATCATTCCTCAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
186145 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
186183 AAGGAC
1 AAGGAC
186189 CCCGTAGACC
Statistics
Matches: 103, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
102 72 0.70
103 31 0.30
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACAACATATCATTCCTCAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:187870 original size:13 final size:13
Alignment explanation
Indices: 187852--187876 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
187842 CATTAGATAC
187852 GTCCCGAAGGACT
1 GTCCCGAAGGACT
187865 GTCCCGAAGGAC
1 GTCCCGAAGGAC
187877 CACTATGTCC
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:0.32, G:0.32, T:0.12
Consensus pattern (13 bp):
GTCCCGAAGGACT
Found at i:189233 original size:64 final size:64
Alignment explanation
Indices: 189082--189235 Score: 175
Period size: 64 Copynumber: 2.4 Consensus size: 64
189072 TCTTTAACGG
* * **
189082 TGCATCGATGCACTACTTGTGTATCGGTGCATAAAATACATTCGATGTTTCAATATTAAGGTGA
1 TGCATCGATGCACTACTTGTGCATCGATGCATAAAATACATTCGATGTTTCAATATTAAGAAGA
* ** * * * * *
189146 TGCATCGATACACGCCTTATGCATCGATGCATTAATTGCATTCGATGTTTCTATTATTAAGAAG-
1 TGCATCGATGCACTACTTGTGCATCGATGCATAAAATACATTCGATGTTTC-AATATTAAGAAGA
*
189210 TTCATCGATGCACTACTTGTGCATCG
1 TGCATCGATGCACTACTTGTGCATCG
189236 GTACACCTTC
Statistics
Matches: 72, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
64 63 0.88
65 9 0.12
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (64 bp):
TGCATCGATGCACTACTTGTGCATCGATGCATAAAATACATTCGATGTTTCAATATTAAGAAGA
Found at i:193022 original size:18 final size:18
Alignment explanation
Indices: 192995--193029 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
192985 TTCAGTATTC
*
192995 GTCCCGAAGGACCACTAT
1 GTCCCAAAGGACCACTAT
193013 GTCCCAAAGGACCACTA
1 GTCCCAAAGGACCACTA
193030 GATATGTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.34, G:0.20, T:0.14
Consensus pattern (18 bp):
GTCCCAAAGGACCACTAT
Found at i:193038 original size:22 final size:22
Alignment explanation
Indices: 192994--193116 Score: 164
Period size: 22 Copynumber: 5.8 Consensus size: 22
192984 ATTCAGTATT
192994 CGTCCCGAAGGACCACT--AT-
1 CGTCCCGAAGGACCACTGGATA
* *
193013 -GTCCCAAAGGACCACTAGATA
1 CGTCCCGAAGGACCACTGGATA
* *
193034 TGTCCCGAATGACCACTGGATA
1 CGTCCCGAAGGACCACTGGATA
*
193056 CGTCCCGAAAGACCACTGGATA
1 CGTCCCGAAGGACCACTGGATA
*
193078 CGTCCCGAATGACCACTGGATA
1 CGTCCCGAAGGACCACTGGATA
193100 CGTCCCGAAGGACCACT
1 CGTCCCGAAGGACCACT
193117 ATGTCCCGAA
Statistics
Matches: 92, Mismatches: 8, Indels: 5
0.88 0.08 0.05
Matches are distributed among these distances:
18 15 0.16
20 2 0.02
22 75 0.82
ACGTcount: A:0.29, C:0.33, G:0.22, T:0.16
Consensus pattern (22 bp):
CGTCCCGAAGGACCACTGGATA
Found at i:193083 original size:44 final size:43
Alignment explanation
Indices: 192994--193130 Score: 164
Period size: 44 Copynumber: 3.3 Consensus size: 43
192984 ATTCAGTATT
*
192994 CGTCCCGAAGGACCACT--AT--GTCCC-AAAGGACCACTAGATA
1 CGTCCCGAATGACCACTGGATACGTCCCGAAA-GACCACT-GATA
*
193034 TGTCCCGAATGACCACTGGATACGTCCCGAAAGACCACTGGATA
1 CGTCCCGAATGACCACTGGATACGTCCCGAAAGACCACT-GATA
*
193078 CGTCCCGAATGACCACTGGATACGTCCCGAAGGACCACT-AT-
1 CGTCCCGAATGACCACTGGATACGTCCCGAAAGACCACTGATA
193119 -GTCCCGAATGAC
1 CGTCCCGAATGAC
193131 TAATATACCC
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
40 27 0.31
42 4 0.05
44 53 0.61
45 3 0.03
ACGTcount: A:0.29, C:0.32, G:0.22, T:0.17
Consensus pattern (43 bp):
CGTCCCGAATGACCACTGGATACGTCCCGAAAGACCACTGATA
Found at i:193265 original size:28 final size:27
Alignment explanation
Indices: 193214--193266 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
193204 TATGTTATCA
*
193214 CACTTTCACATATTCACATGTACATGT
1 CACTTTCACATATTCACATATACATGT
* *
193241 CACTTTCATATGATTCATATATACAT
1 CACTTTCACAT-ATTCACATATACAT
193267 CACATATCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.40
Consensus pattern (27 bp):
CACTTTCACATATTCACATATACATGT
Found at i:194484 original size:63 final size:62
Alignment explanation
Indices: 194333--194486 Score: 182
Period size: 63 Copynumber: 2.4 Consensus size: 62
194323 TTCTTTAACG
* **
194333 GTGCATCGATGCACTACTTGTGCATCGGTGCATAAAATACATTCGATGTTTCAATATTAAGGT
1 GTGCATCGATGCACTACTTGTGCATC-ATGCATAAAATACATTCGATGTTTCAATATTAAGAA
* ** * * * * *
194396 GATGCATTGATGCACGCCTTATGCATCATGCATTAATTGCATTCGATGTTTCTATTATTAAGAA
1 G-TGCATCGATGCACTACTTGTGCATCATGCATAAAATACATTCGATGTTTC-AATATTAAGAA
194460 GTGCATCGATGCACTACTTGTGCATCA
1 GTGCATCGATGCACTACTTGTGCATCA
194487 GTACACCTTC
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
63 44 0.59
64 30 0.41
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (62 bp):
GTGCATCGATGCACTACTTGTGCATCATGCATAAAATACATTCGATGTTTCAATATTAAGAA
Found at i:201709 original size:3 final size:3
Alignment explanation
Indices: 201701--201725 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
201691 TTGAAAGTCG
201701 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
201726 AAAAGATGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:203590 original size:51 final size:50
Alignment explanation
Indices: 203535--203725 Score: 134
Period size: 54 Copynumber: 3.6 Consensus size: 50
203525 ATGCTCTGAC
* *
203535 CAGCATAGTTCTCATTCTTACCTGCATTCTCATTGTTGGTGTTGATTTGAA
1 CAGCATAGTTCTCATTCTGACCTGCATTCTCATTGTTGGTG-TAATTTGAA
* * ** * *
203586 CAGCATTATTATTCTCATTCTGACTTGCATTCTCACCGTTGTTGTAATTCTGGGA
1 CAGCA-TA--GTTCTCATTCTGACCTGCATTCTCATTGTTGGTGTAATT-T-GAA
* ** * *
203641 -GGCATTCTTCTCATTCAT-ACCTGCTTTCTCATTGTTGGTGCCAATTTGAA
1 CAGCATAGTTCTCATTC-TGACCTGCATTCTCATTGTTGGTG-TAATTTGAA
* *
203691 CAGCATTGTTATTCTCATTCTGACTTGCATTCTCA
1 CAGCATAG---TTCTCATTCTGACCTGCATTCTCA
203726 CTGATATTGT
Statistics
Matches: 106, Mismatches: 22, Indels: 21
0.71 0.15 0.14
Matches are distributed among these distances:
50 2 0.02
51 37 0.35
52 7 0.07
53 6 0.06
54 52 0.49
55 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (50 bp):
CAGCATAGTTCTCATTCTGACCTGCATTCTCATTGTTGGTGTAATTTGAA
Found at i:203790 original size:111 final size:105
Alignment explanation
Indices: 203543--203767 Score: 306
Period size: 105 Copynumber: 2.1 Consensus size: 105
203533 ACCAGCATAG
* * ***
203543 TTCTCATTCTTACCTGCATTCTCATTGTTGGTGTTGATTTGAACAGCATTATTATTCTCATTCTG
1 TTCTCATTCATACCTGCTTTCTCATTGTTGGTGCCAATTTGAACAGCATTATTATTCTCATTCTG
* *
203608 ACTTGCATTCTCACCGTTGTTGTAATTCTGGGAGGCATTC
66 ACTTGCATTCTCACCGTTGTTGTAATTCTGGGAAGCATTA
*
203648 TTCTCATTCATACCTGCTTTCTCATTGTTGGTGCCAATTTGAACAGCATTGTTATTCTCATTCTG
1 TTCTCATTCATACCTGCTTTCTCATTGTTGGTGCCAATTTGAACAGCATTATTATTCTCATTCTG
* *
203713 ACTTGCATTCTCACTGATATTGTTGTTGTAGTTCTGGGAAGCATTA
66 ACTTGCATTCTCAC------CGTTGTTGTAATTCTGGGAAGCATTA
203759 TTCTCATTC
1 TTCTCATTC
203768 TGACTGGCTT
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
105 73 0.70
111 31 0.30
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (105 bp):
TTCTCATTCATACCTGCTTTCTCATTGTTGGTGCCAATTTGAACAGCATTATTATTCTCATTCTG
ACTTGCATTCTCACCGTTGTTGTAATTCTGGGAAGCATTA
Found at i:203931 original size:57 final size:57
Alignment explanation
Indices: 203805--204061 Score: 267
Period size: 57 Copynumber: 4.6 Consensus size: 57
203795 CCCTGAGCAG
* * * * * * * * *
203805 CATTGTTCTCATTCTCACTCGCGTTCTCATGGTTGTTAGTGTTGATCTGAACAGAAGT
1 CATTGTTCTCATTCTGACTTGCATTATCATTGTTGCTGGTATTGATCTGAACGGAA-T
* * * * *
203863 -TTTATTTTCATTCTGACTTGCATTCTCATTGTTGCTGGTATTGATCTGAACGGCAT
1 CATTGTTCTCATTCTGACTTGCATTATCATTGTTGCTGGTATTGATCTGAACGGAAT
* * *
203919 CATTGTTCTCATTCTGATTTGCATTATCATTGTTGCCGGTATTGATCTGAACGAAAT
1 CATTGTTCTCATTCTGACTTGCATTATCATTGTTGCTGGTATTGATCTGAACGGAAT
* * *
203976 CATTGTTCTCATTCTGACCTGCATTATCATTGTTG-T--TGTTGCTCTG---GGAAT
1 CATTGTTCTCATTCTGACTTGCATTATCATTGTTGCTGGTATTGATCTGAACGGAAT
*
204027 CATTATTCTCATTCTGACTTGCATTATCATTGTTG
1 CATTGTTCTCATTCTGACTTGCATTATCATTGTTG
204062 TTGTTGCTCT
Statistics
Matches: 170, Mismatches: 28, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
51 37 0.22
54 8 0.05
56 1 0.01
57 124 0.73
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (57 bp):
CATTGTTCTCATTCTGACTTGCATTATCATTGTTGCTGGTATTGATCTGAACGGAAT
Found at i:204050 original size:51 final size:52
Alignment explanation
Indices: 203864--204093 Score: 230
Period size: 57 Copynumber: 4.3 Consensus size: 52
203854 AACAGAAGTT
* * *
203864 TTATTTTCATTCTGACTTGCATTCTCATTGTTGCTGGTATTGATCTGAACGGCATCA
1 TTATTCTCATTCTGACTTGCATTATCATTGTTG-T--TATTGATCTG-A-GGAATCA
* * * *
203921 TTGTTCTCATTCTGATTTGCATTATCATTGTTGCCGGTATTGATCTGAACGAAATCA
1 TTATTCTCATTCTGACTTGCATTATCATTGTT---GTTATTGATCTG-A-GGAATCA
* * * *
203978 TTGTTCTCATTCTGACCTGCATTATCATTGTTGTTGTTGCTCTG-GGAATCA
1 TTATTCTCATTCTGACTTGCATTATCATTGTTGTTATTGATCTGAGGAATCA
* * *
204029 TTATTCTCATTCTGACTTGCATTATCATTGTTGTTGTTGCTCTG-GGAAGCA
1 TTATTCTCATTCTGACTTGCATTATCATTGTTGTTATTGATCTGAGGAATCA
204080 TTATTCTCATTCTG
1 TTATTCTCATTCTG
204094 TTCAGCATTC
Statistics
Matches: 154, Mismatches: 16, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
51 68 0.44
54 9 0.06
57 76 0.49
60 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.45
Consensus pattern (52 bp):
TTATTCTCATTCTGACTTGCATTATCATTGTTGTTATTGATCTGAGGAATCA
Found at i:204066 original size:57 final size:49
Alignment explanation
Indices: 203897--204093 Score: 110
Period size: 51 Copynumber: 3.7 Consensus size: 49
203887 CTCATTGTTG
* * *
203897 CTGGTATTGATCTGAACGGCATCATTGTTCTCATTCTGATTTGCATTATCA
1 CTGGTATTGATCTG-A-GGAATCATTATTCTCATTCTGACTTGCATTATCA
* * * *
203948 TTGTTGCCGGTATTGATCTGAACGAAATCATTGTTCTCATTCTGACCTGCATTATCA
1 ------CTGGTATTGATCTG-A-GGAATCATTATTCTCATTCTGACTTGCATTATCA
* * *
204005 TTGTTGTTGTTGCTCTG-GGAATCATTATTCTCATTCTGACTTGCATTATCA
1 CTG--G-TATTGATCTGAGGAATCATTATTCTCATTCTGACTTGCATTATCA
* * * *
204056 TTGTTGTTGTTGCTCTG-GGAAGCATTATTCTCATTCTG
1 CTG--G-TATTGATCTGAGGAATCATTATTCTCATTCTG
204094 TTCAGCATTC
Statistics
Matches: 124, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
51 69 0.56
53 1 0.01
54 8 0.06
57 46 0.37
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (49 bp):
CTGGTATTGATCTGAGGAATCATTATTCTCATTCTGACTTGCATTATCA
Found at i:204102 original size:51 final size:51
Alignment explanation
Indices: 203976--204172 Score: 214
Period size: 51 Copynumber: 3.9 Consensus size: 51
203966 TGAACGAAAT
* * *
203976 CATTGTTCTCATTCTGACCTGCATTATCATTGTTGTTGTTGCTCTGGGAAT
1 CATTATTCTCATTCTGACCAGCATTATCATTGTTGTTGTTGCTCTGGGAAG
**
204027 CATTATTCTCATTCTGACTTGCATTATCATTGTTGTTGTTGCTCTGGGAAG
1 CATTATTCTCATTCTGACCAGCATTATCATTGTTGTTGTTGCTCTGGGAAG
** * ** * **** * *
204078 CATTATTCTCATTCTGTTCAGCATTCTGGTTGTTGGTAACACTCTGAGCAG
1 CATTATTCTCATTCTGACCAGCATTATCATTGTTGTTGTTGCTCTGGGAAG
* * *
204129 CATTTTTCTCATTTTGACCAGCATTCTCATTGTTGTTGTTGCTC
1 CATTATTCTCATTCTGACCAGCATTATCATTGTTGTTGTTGCTC
204173 AGAACAGTAT
Statistics
Matches: 118, Mismatches: 28, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 118 1.00
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (51 bp):
CATTATTCTCATTCTGACCAGCATTATCATTGTTGTTGTTGCTCTGGGAAG
Found at i:208139 original size:3 final size:3
Alignment explanation
Indices: 208131--208165 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
208121 TATCCAACGT
208131 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
208166 ACATTATTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:214749 original size:31 final size:31
Alignment explanation
Indices: 214714--214781 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
214704 ATATAATAAA
*
214714 TTATAAAAAATGAAAAAATTTAATGATTATT
1 TTATAAAAAATGAAAAAATTTAATGACTATT
* * * *
214745 TTATAATAATTTAACAAATTTAATGACTATT
1 TTATAAAAAATGAAAAAATTTAATGACTATT
214776 TTATAA
1 TTATAA
214782 TATTTTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (31 bp):
TTATAAAAAATGAAAAAATTTAATGACTATT
Found at i:214782 original size:31 final size:30
Alignment explanation
Indices: 214727--214831 Score: 122
Period size: 31 Copynumber: 3.4 Consensus size: 30
214717 TAAAAAATGA
* *
214727 AAAAATTTAATGATTATTTTATAATAATTT
1 AAAAATTTAATGACTATTTTATAATATTTT
214757 AACAAATTTAATGACTATTTTATAATATTTT
1 AA-AAATTTAATGACTATTTTATAATATTTT
* * *
214788 AATAAAATTAAAGATCT-TTTCATAATATTTT
1 AA-AAATTTAATGA-CTATTTTATAATATTTT
*
214819 AAAATTTTAATGA
1 AAAAATTTAATGA
214832 TTAAAATGAC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
30 10 0.16
31 52 0.81
32 2 0.03
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (30 bp):
AAAAATTTAATGACTATTTTATAATATTTT
Found at i:218960 original size:18 final size:19
Alignment explanation
Indices: 218916--218961 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
218906 GATACTCGAT
*
218916 TTAATAATTTTTAATTAGA
1 TTAATAATTATTAATTAGA
*
218935 -TAAAAATTATTAATTA-A
1 TTAATAATTATTAATTAGA
218952 TTAATAATTA
1 TTAATAATTA
218962 ATGATATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TTAATAATTATTAATTAGA
Found at i:219853 original size:2 final size:2
Alignment explanation
Indices: 219848--219874 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
219838 AACTTTTTTA
219848 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
219875 CACTAATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:220721 original size:5 final size:5
Alignment explanation
Indices: 220711--220743 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
220701 TTCTACTTCT
220711 AACCA AACCA AACCA AACCA AACCA AACCA AAC
1 AACCA AACCA AACCA AACCA AACCA AACCA AAC
220744 TAAATTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.61, C:0.39, G:0.00, T:0.00
Consensus pattern (5 bp):
AACCA
Found at i:223481 original size:2 final size:2
Alignment explanation
Indices: 223474--223526 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
223464 GTAATGTACT
223474 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
223516 TA TA TA TA TA T
1 TA TA TA TA TA T
223527 GCCTTAATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:226618 original size:14 final size:14
Alignment explanation
Indices: 226599--226638 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
226589 AGTGCACCGC
226599 CGTCCTCCTCGACT
1 CGTCCTCCTCGACT
226613 CGTCCTCCTCGACT
1 CGTCCTCCTCGACT
*
226627 CGCCCTCCTCGA
1 CGTCCTCCTCGA
226639 TTCGATGCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.07, C:0.53, G:0.15, T:0.25
Consensus pattern (14 bp):
CGTCCTCCTCGACT
Found at i:226988 original size:35 final size:36
Alignment explanation
Indices: 226928--226996 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
226918 AAGTCTTTGC
*
226928 AGGTTCAGATCTGATCAAACTGGTAATTCCTTATAT
1 AGGTTCAGATCCGATCAAACTGGTAATTCCTTATAT
*
226964 AGGTTCAGA-CCGATCGAACTGGTAATTCCTTAT
1 AGGTTCAGATCCGATCAAACTGGTAATTCCTTAT
226997 GGACCTAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 22 0.71
36 9 0.29
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (36 bp):
AGGTTCAGATCCGATCAAACTGGTAATTCCTTATAT
Found at i:232453 original size:22 final size:22
Alignment explanation
Indices: 232425--232473 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
232415 AGTCAACTCA
232425 TTGACTTTGACCA-TAGTTGACT
1 TTGACTTTGACCAGT-GTTGACT
**
232447 TTGACTTTGATTAGTGTTGACT
1 TTGACTTTGACCAGTGTTGACT
232469 TTGAC
1 TTGAC
232474 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.45
Consensus pattern (22 bp):
TTGACTTTGACCAGTGTTGACT
Found at i:243239 original size:29 final size:27
Alignment explanation
Indices: 243181--243240 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 27
243171 ATTTAGTGAT
243181 TTATACAAATTAAAATTATATATATTA
1 TTATACAAATTAAAATTATATATATTA
243208 TTATACATAATTAAAATCTATATATCA-TA
1 TTATACA-AATTAAAAT-TATATAT-ATTA
243237 TTAT
1 TTAT
243241 GTATATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 7 0.23
28 9 0.30
29 13 0.43
30 1 0.03
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (27 bp):
TTATACAAATTAAAATTATATATATTA
Found at i:244095 original size:21 final size:21
Alignment explanation
Indices: 244066--244105 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
244056 TCGGTTATGA
244066 TTTTAATATT-TTCACTTAATT
1 TTTTAATATTGTT-ACTTAATT
*
244087 TTTTTATATTGTTACTTAA
1 TTTTAATATTGTTACTTAA
244106 CCCTTTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTTAATATTGTTACTTAATT
Found at i:247157 original size:22 final size:23
Alignment explanation
Indices: 247106--247157 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
247096 AAAATTGAAA
* *
247106 TTTCGAAATTTAATATTTTTTAT
1 TTTCAAAATTTAATAGTTTTTAT
* *
247129 TAT-AAAATTTAA-AGTTTTTGT
1 TTTCAAAATTTAATAGTTTTTAT
247150 TTTCAAAA
1 TTTCAAAA
247158 AACACATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
21 9 0.39
22 12 0.52
23 2 0.09
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.54
Consensus pattern (23 bp):
TTTCAAAATTTAATAGTTTTTAT
Found at i:249264 original size:18 final size:19
Alignment explanation
Indices: 249224--249264 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
249214 TGGTTCACAG
249224 AATGGAAGATTACCAGTGGC
1 AATGGAAGATTACCAG-GGC
249244 AATGGAAGATTACCA-GGC
1 AATGGAAGATTACCAGGGC
249262 AAT
1 AAT
249265 AGGATTACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 6 0.29
20 15 0.71
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.20
Consensus pattern (19 bp):
AATGGAAGATTACCAGGGC
Found at i:251771 original size:13 final size:13
Alignment explanation
Indices: 251753--251790 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
251743 ACTAAAGAGC
251753 AAATAAATTTTAG
1 AAATAAATTTTAG
*
251766 AAATAAATTTGAG
1 AAATAAATTTTAG
251779 AAA-AAATATTTA
1 AAATAAAT-TTTA
251791 ATTCAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (13 bp):
AAATAAATTTTAG
Found at i:255142 original size:59 final size:59
Alignment explanation
Indices: 255043--255159 Score: 164
Period size: 59 Copynumber: 2.0 Consensus size: 59
255033 CATTTGACAC
* * * * * *
255043 GATGCCTTCAAGTTCGAGGGGAGGCATTCAATTGTGAGCTTTTTCGACCTCAATGTCGA
1 GATGCCTTCAAGTTCAAGGGGAGGCATTCAACTATCAGCTTGTTCGACCTAAATGTCGA
255102 GATG-CTTCAAGTTCAAGGGGAAGGCATTCAACTATCAGCTTGTTCGACCTAAATGTCG
1 GATGCCTTCAAGTTCAAGGGG-AGGCATTCAACTATCAGCTTGTTCGACCTAAATGTCG
255160 TTATCTTGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
58 15 0.29
59 36 0.71
ACGTcount: A:0.25, C:0.21, G:0.26, T:0.29
Consensus pattern (59 bp):
GATGCCTTCAAGTTCAAGGGGAGGCATTCAACTATCAGCTTGTTCGACCTAAATGTCGA
Found at i:257178 original size:21 final size:21
Alignment explanation
Indices: 257129--257179 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
257119 ACTGCGGTGG
*
257129 CATCTGAAATAGTTGTGGTAT
1 CATCTGATATAGTTGTGGTAT
*
257150 CATCTGATATGGTTGTGGTGAT
1 CATCTGATATAGTTGTGGT-AT
257172 -ATCTGATA
1 CATCTGATA
257180 CGACTACGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.39
Consensus pattern (21 bp):
CATCTGATATAGTTGTGGTAT
Found at i:262624 original size:15 final size:15
Alignment explanation
Indices: 262604--262649 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 15
262594 TTGTAGTTTG
262604 CAATTTATATTTTTT
1 CAATTTATATTTTTT
262619 CAATTTATATTTATTTTTT
1 CAA-TT-TA--TATTTTTT
262638 CAATTTATATTT
1 CAATTTATATTT
262650 ATTTTTGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
15 8 0.30
16 2 0.07
17 4 0.15
18 2 0.07
19 11 0.41
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (15 bp):
CAATTTATATTTTTT
Found at i:262635 original size:19 final size:19
Alignment explanation
Indices: 262611--262655 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
262601 TTGCAATTTA
262611 TATTTTTTCAATTTATATT
1 TATTTTTTCAATTTATATT
262630 TATTTTTTCAATTTATATT
1 TATTTTTTCAATTTATATT
262649 TATTTTT
1 TATTTTT
262656 GTTTAAACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTTTTCAATTTATATT
Found at i:266171 original size:27 final size:26
Alignment explanation
Indices: 266133--266205 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
266123 TAAATTTATT
*
266133 AAAATATTTTATGTGAGAAAA-TAATC
1 AAAATATCTTATGT-AGAAAACTAATC
* * *
266159 AAAATATCATTATATATAAAACTTATC
1 AAAATATC-TTATGTAGAAAACTAATC
266186 AAAATATTCTTATGTAGAAA
1 AAAATA-TCTTATGTAGAAA
266206 TTACTAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
26 12 0.32
27 24 0.63
28 2 0.05
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (26 bp):
AAAATATCTTATGTAGAAAACTAATC
Found at i:271433 original size:21 final size:21
Alignment explanation
Indices: 271408--271452 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
271398 ATATTCTGAG
271408 GGCTTGTGGCCTGCCTCATTA
1 GGCTTGTGGCCTGCCTCATTA
**
271429 GGCTTGTGGCCTTTCTCATTA
1 GGCTTGTGGCCTGCCTCATTA
271450 GGC
1 GGC
271453 ATGTACCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.27, G:0.29, T:0.36
Consensus pattern (21 bp):
GGCTTGTGGCCTGCCTCATTA
Found at i:291864 original size:18 final size:18
Alignment explanation
Indices: 291835--291869 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
291825 AGTCGGTTTG
291835 TAATTATTTTC-TACATA
1 TAATTATTTTCTTACATA
291852 TAATTATTTTTCTTACAT
1 TAATTA-TTTTCTTACAT
291870 TAAAATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (18 bp):
TAATTATTTTCTTACATA
Found at i:294560 original size:204 final size:199
Alignment explanation
Indices: 294201--294603 Score: 761
Period size: 204 Copynumber: 2.0 Consensus size: 199
294191 ATTATTACCT
294201 CAAGAGATACCACAATCCCTTTCAACCACTTACACAACTTGATTGGTTAAAGGGTTTATAATAAA
1 CAAGAGATACCACAATCCCTTTCAACCACTTACACAACTTGATTGGTTAAAGGGTTTATAATAAA
294266 ATGATTAGTGATTAATATAAAAATGTTAATTAAATGTAAATTCGAAAATGAAGTTAATATAGTAC
66 ATGATTAGTGATTAATATAAAAATGTTAATTAAATGTAAATTCGAAAATGAAGTTAATATAGTAC
294331 CAGTCAGTGATATTAAGAGTAGGTGTAATATAGAAAAAGGACAACAAAAAGTCTCAAGAATAATT
131 CAGTCAGTGATATTAAGAGTAGGTGTAATATAGAAAAAGGACAACAAAAAGTCTCAAGAATAATT
294396 AAAA
196 AAAA
294400 CAAGAGATACCAACAATCCCTTTCAACCACTTACACAACTTGATTGGTTAAAGGGTTTATAATAA
1 CAAGAGATACC-ACAATCCCTTTCAACCACTTACACAACTTGATTGGTTAAAGGGTTTATAATAA
294465 ATATGATTAGTGATTAATATAAAAATGTTTAATTAAATGTTAAAATTCGAAAATGAAGTTAATAT
65 A-ATGATTAGTGATTAATATAAAAATG-TTAATTAAATG-T-AAATTCGAAAATGAAGTTAATAT
294530 AGTACCAGTCAGTGATATTAAGAGTAGGTGTAATATAGAAAAAGGACAACAAAAAGTCTCAAGAA
126 AGTACCAGTCAGTGATATTAAGAGTAGGTGTAATATAGAAAAAGGACAACAAAAAGTCTCAAGAA
294595 TAATTAAAA
191 TAATTAAAA
294604 ATCAATCTTC
Statistics
Matches: 199, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
199 11 0.06
200 54 0.27
201 25 0.13
202 11 0.06
203 1 0.01
204 97 0.49
ACGTcount: A:0.46, C:0.11, G:0.15, T:0.29
Consensus pattern (199 bp):
CAAGAGATACCACAATCCCTTTCAACCACTTACACAACTTGATTGGTTAAAGGGTTTATAATAAA
ATGATTAGTGATTAATATAAAAATGTTAATTAAATGTAAATTCGAAAATGAAGTTAATATAGTAC
CAGTCAGTGATATTAAGAGTAGGTGTAATATAGAAAAAGGACAACAAAAAGTCTCAAGAATAATT
AAAA
Found at i:296328 original size:31 final size:31
Alignment explanation
Indices: 296265--296329 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
296255 ACATTTCACT
* * * *
296265 TGTTCAAAGTGGTTACATGATACAAATAACA
1 TGTTCAAAGTGATGACATAACACAAATAACA
* *
296296 TGTTCAAAGTGATGACATAACACATATTACA
1 TGTTCAAAGTGATGACATAACACAAATAACA
296327 TGT
1 TGT
296330 ACGGAGGTGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (31 bp):
TGTTCAAAGTGATGACATAACACAAATAACA
Found at i:296486 original size:17 final size:18
Alignment explanation
Indices: 296442--296494 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
296432 CCAAACAAAG
296442 AATATTTTACATCAAAATAA
1 AATATTTTA-AT-AAAATAA
296462 AACGTATTTTAATAAAA-AA
1 AA--TATTTTAATAAAATAA
*
296481 AATATTTTATTAAA
1 AATATTTTAATAAA
296495 TGTTAGAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 11 0.37
19 4 0.13
20 6 0.20
21 2 0.07
22 7 0.23
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (18 bp):
AATATTTTAATAAAATAA
Done.