Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 109 of 182
Found at i:35455969 original size:18 final size:18
Alignment explanation
Indices: 35455915--35455973 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
35455905 TCCTCCATGA
*
35455915 GGAGGATATCCTGCAGGT
1 GGAGGATATCCCGCAGGT
* *
35455933 -G-GG-TAT-CCGCCATGA
1 GGAGGATATCCCG-CAGGT
35455948 GGAGGATATCCCGCAGGT
1 GGAGGATATCCCGCAGGT
35455966 GGAGGATA
1 GGAGGATA
35455974 ACCAGCCGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
14 2 0.06
15 6 0.19
16 3 0.10
17 3 0.10
18 14 0.45
19 3 0.10
ACGTcount: A:0.24, C:0.19, G:0.39, T:0.19
Consensus pattern (18 bp):
GGAGGATATCCCGCAGGT
Found at i:35455984 original size:18 final size:18
Alignment explanation
Indices: 35455948--35455986 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
35455938 TCCGCCATGA
* *
35455948 GGAGGATATCCCGCAGGT
1 GGAGGATAACCAGCAGGT
*
35455966 GGAGGATAACCAGCCGGT
1 GGAGGATAACCAGCAGGT
35455984 GGA
1 GGA
35455987 TAGCCTTGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.41, T:0.13
Consensus pattern (18 bp):
GGAGGATAACCAGCAGGT
Found at i:35456002 original size:15 final size:15
Alignment explanation
Indices: 35455984--35456030 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
35455974 ACCAGCCGGT
* *
35455984 GGATAGCCTTGTGGC
1 GGATATCCTTGTGGA
*
35455999 GGATATCCTTGAGGA
1 GGATATCCTTGTGGA
35456014 GGATATCCTTGTGGA
1 GGATATCCTTGTGGA
35456029 GG
1 GG
35456031 GTAGGATCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.19, C:0.15, G:0.38, T:0.28
Consensus pattern (15 bp):
GGATATCCTTGTGGA
Found at i:35466100 original size:19 final size:17
Alignment explanation
Indices: 35466057--35466105 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
35466047 TTCTATTGAA
*
35466057 AATAATTTTTGAAAAAT
1 AATATTTTTTGAAAAAT
35466074 AATTTATTTTTATGAAAAATT
1 AA--TATTTTT-TGAAAAA-T
35466095 AATATTTTTTG
1 AATATTTTTTG
35466106 GTATTTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 2 0.07
18 2 0.07
19 13 0.48
20 7 0.26
21 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (17 bp):
AATATTTTTTGAAAAAT
Found at i:35466103 original size:20 final size:19
Alignment explanation
Indices: 35466062--35466105 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
35466052 TTGAAAATAA
*
35466062 TTTTTGAAAAATAATTTAT
1 TTTTTGAAAAATAATATAT
*
35466081 TTTTATGAAAAATTA-ATAT
1 TTTT-TGAAAAATAATATAT
35466100 TTTTTG
1 TTTTTG
35466106 GTATTTAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 11 0.50
20 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (19 bp):
TTTTTGAAAAATAATATAT
Found at i:35466573 original size:15 final size:15
Alignment explanation
Indices: 35466553--35466604 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
35466543 ACTATAAAAC
35466553 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
35466568 ATTTATAATTATAATAAAT
1 ATTTATTA-T-TAAT--AT
*
35466587 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
35466602 ATT
1 ATT
35466605 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:35466590 original size:19 final size:19
Alignment explanation
Indices: 35466566--35466602 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35466556 TATTATTAAT
*
35466566 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
35466585 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
35466603 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:35466716 original size:29 final size:30
Alignment explanation
Indices: 35466677--35466734 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
35466667 ATAAATTTAA
35466677 ATATTAAATAATTTATTAAAATAATAAATT
1 ATATTAAATAATTTATTAAAATAATAAATT
* *
35466707 ATATT-AATAATTTATTATAATACTAAAT
1 ATATTAAATAATTTATTAAAATAATAAAT
35466735 ATAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (30 bp):
ATATTAAATAATTTATTAAAATAATAAATT
Found at i:35466723 original size:16 final size:16
Alignment explanation
Indices: 35466677--35466725 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
35466667 ATAAATTTAA
35466677 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
**
35466694 A-A--AATAATAAATT
1 ATATTAATAATTTATT
35466707 ATATTAATAATTTATT
1 ATATTAATAATTTATT
35466723 ATA
1 ATA
35466726 ATACTAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 7
0.69 0.11 0.19
Matches are distributed among these distances:
13 10 0.40
14 1 0.04
16 13 0.52
17 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:35466743 original size:29 final size:29
Alignment explanation
Indices: 35466683--35466743 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
35466673 TTAAATATTA
*
35466683 AATAATTTATTAAAATAATAAATTATATT
1 AATAATTTATTAAAATAATAAATTATAAT
* *
35466712 AATAATTTATTATAATACTAAA-TATAAAT
1 AATAATTTATTAAAATAATAAATTAT-AAT
35466741 AAT
1 AAT
35466744 TAAATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 3 0.11
29 25 0.89
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (29 bp):
AATAATTTATTAAAATAATAAATTATAAT
Found at i:35466770 original size:23 final size:23
Alignment explanation
Indices: 35466742--35466799 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 23
35466732 AATATAAATA
35466742 ATTAAATAT-ATATGTTTAATAAT
1 ATTAAATATAATAT-TTTAATAAT
35466765 ATTAAAAAATATAATATTTTAATAAT
1 ATT---AAATATAATATTTTAATAAT
*
35466791 TTTAAATAT
1 ATTAAATAT
35466800 TTTTAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
23 9 0.30
26 17 0.57
27 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTAAATATAATATTTTAATAAT
Found at i:35466774 original size:26 final size:26
Alignment explanation
Indices: 35466745--35466796 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
35466735 ATAAATAATT
35466745 AAATAT-ATATGTTTAATAATATTAAA
1 AAATATAATAT-TTTAATAATATTAAA
*
35466771 AAATATAATATTTTAATAATTTTAAA
1 AAATATAATATTTTAATAATATTAAA
35466797 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (26 bp):
AAATATAATATTTTAATAATATTAAA
Found at i:35473820 original size:19 final size:19
Alignment explanation
Indices: 35473796--35473834 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
35473786 ATCAGTCAGA
35473796 AATTAACACCGTTACCGAC
1 AATTAACACCGTTACCGAC
*
35473815 AATTAACACCGTTACTGAC
1 AATTAACACCGTTACCGAC
35473834 A
1 A
35473835 GGTACCAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.23
Consensus pattern (19 bp):
AATTAACACCGTTACCGAC
Found at i:35474677 original size:172 final size:167
Alignment explanation
Indices: 35474396--35474704 Score: 467
Period size: 172 Copynumber: 1.8 Consensus size: 167
35474386 TAGGGGGAAA
**
35474396 GATTTTAAATTGAAAGTGTGGTGTGCGTTTACAAAAATTACACAAAAGCATAATCATGGTAATGA
1 GATTTTAAATTGAAAGTGTGGTGTGCGTTTACAAAAATTACACAAAAGCATAATCATGAAAATGA
**
35474461 AAATTCTTGTAGATGAAATAAGCCAACCATGTGTATTGAAGAAGAAATTTGATGTTTGGCAAGAG
66 AAATTCTTGTAGATGAAATAAGCCAACCATGTGTATTGAAGAAGAAAAATGATGTTTGGCAAGAG
35474526 AGAAAATTAGGAAAAAATGGTAGCGAAAAAAAACAAT
131 AGAAAATTAGGAAAAAATGGTAGCGAAAAAAAACAAT
* *
35474563 GATTTTAAGTTGAAAGTGTGGTGTGGGTTTAC-AAAATTACACAAAAGCATGACTACAATCATGA
1 GATTTTAAATTGAAAGTGTGGTGTGCGTTTACAAAAATTACACAAAAGC---A-T--AATCATGA
* * * *
35474627 AAATGAAAATTCTTGTTGATGAAATGAGCCAACCATGTGTTTTGAAGAAGAAAAATGGTGTTTGG
60 AAATGAAAATTCTTGTAGATGAAATAAGCCAACCATGTGTATTGAAGAAGAAAAATGATGTTTGG
35474692 CAAGAGAGAAAAT
125 CAAGAGAGAAAAT
35474705 GAAAGAAATT
Statistics
Matches: 126, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
166 16 0.13
167 30 0.24
169 1 0.01
170 1 0.01
172 78 0.62
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (167 bp):
GATTTTAAATTGAAAGTGTGGTGTGCGTTTACAAAAATTACACAAAAGCATAATCATGAAAATGA
AAATTCTTGTAGATGAAATAAGCCAACCATGTGTATTGAAGAAGAAAAATGATGTTTGGCAAGAG
AGAAAATTAGGAAAAAATGGTAGCGAAAAAAAACAAT
Found at i:35487806 original size:21 final size:21
Alignment explanation
Indices: 35487782--35487821 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
35487772 ACCCTGTACG
* *
35487782 TCTACCGATACATGTATGAGT
1 TCTACCGAAACAAGTATGAGT
35487803 TCTACCGAAACAAGTATGA
1 TCTACCGAAACAAGTATGA
35487822 AGTTTTTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
TCTACCGAAACAAGTATGAGT
Found at i:35489909 original size:26 final size:21
Alignment explanation
Indices: 35489845--35489896 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
35489835 TCATTTTCTA
35489845 AAACCACTTAACTTTTAAACC
1 AAACCACTTAACTTTTAAACC
*
35489866 AAACCACTTGACTTTTAAACC
1 AAACCACTTAACTTTTAAACC
35489887 AAACCACTTA
1 AAACCACTTA
35489897 TATAAACTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.42, C:0.29, G:0.02, T:0.27
Consensus pattern (21 bp):
AAACCACTTAACTTTTAAACC
Found at i:35492015 original size:3 final size:3
Alignment explanation
Indices: 35492007--35492039 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
35491997 AAGTACGTAG
35492007 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35492040 AGAATGGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:35492163 original size:14 final size:14
Alignment explanation
Indices: 35492138--35492174 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
35492128 AGCTAAAGTA
35492138 GGGGAGAAAAAAAT
1 GGGGAGAAAAAAAT
35492152 -GGGAGAAAAAAAT
1 GGGGAGAAAAAAAT
35492165 GGGGAGAAAA
1 GGGGAGAAAA
35492175 CCTAAGGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.38, T:0.05
Consensus pattern (14 bp):
GGGGAGAAAAAAAT
Found at i:35493082 original size:16 final size:16
Alignment explanation
Indices: 35493061--35493093 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
35493051 AATATGAAGT
35493061 AAGTTGCTAACTATAA
1 AAGTTGCTAACTATAA
35493077 AAGTTGCTAACTATAA
1 AAGTTGCTAACTATAA
35493093 A
1 A
35493094 CTTATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (16 bp):
AAGTTGCTAACTATAA
Found at i:35493270 original size:24 final size:24
Alignment explanation
Indices: 35493206--35493400 Score: 185
Period size: 24 Copynumber: 7.9 Consensus size: 24
35493196 TATCTGATAA
* *
35493206 GCTGACGAGCGTAAATGTATATATAT
1 GCTGACGAGCGTAAACGTAT-T-CAT
* *
35493232 GCTGATGAGCATAAACGTATTCAT
1 GCTGACGAGCGTAAACGTATTCAT
* *
35493256 GCTGACAAGCGTAAACATATTCAT
1 GCTGACGAGCGTAAACGTATTCAT
* * *
35493280 GCTGATGAGCATAAAAGTATTCAT
1 GCTGACGAGCGTAAACGTATTCAT
* * *
35493304 GCTGACAAACGTAAATGTATAT-AT
1 GCTGACGAGCGTAAACGTAT-TCAT
* *
35493328 GCTGTCGAGCGTAAACGTATATATATAT
1 GCTGACGAGCGTAAACG--TAT-T-CAT
*
35493356 GCTGATGAGCGTAAACGTATTCAT
1 GCTGACGAGCGTAAACGTATTCAT
35493380 GCTGACGAGCGTAAACGTATT
1 GCTGACGAGCGTAAACGTATT
35493401 TATATGAACG
Statistics
Matches: 138, Mismatches: 26, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
24 93 0.67
25 3 0.02
26 25 0.18
28 17 0.12
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (24 bp):
GCTGACGAGCGTAAACGTATTCAT
Found at i:35493355 original size:28 final size:28
Alignment explanation
Indices: 35493321--35493405 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 28
35493311 AACGTAAATG
35493321 TATATATGCTGTCGAGCGTAAACGTATA
1 TATATATGCTGTCGAGCGTAAACGTATA
35493349 TATATATGCTGAT-GAGCGTAAACG--TA
1 TATATATGCTG-TCGAGCGTAAACGTATA
* * *
35493375 T-T-CATGCTGACGAGCGTAAACGTATT
1 TATATATGCTGTCGAGCGTAAACGTATA
35493401 TATAT
1 TATAT
35493406 GAACGATCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
24 17 0.36
25 1 0.02
26 5 0.11
27 1 0.02
28 22 0.47
29 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (28 bp):
TATATATGCTGTCGAGCGTAAACGTATA
Found at i:35493411 original size:24 final size:23
Alignment explanation
Indices: 35493333--35493421 Score: 70
Period size: 24 Copynumber: 3.6 Consensus size: 23
35493323 TATATGCTGT
35493333 CGAGCGTAAACGTATATATATATGCTGA
1 CGAGCGTAAACGTAT-T-TATA---TGA
* * *
35493361 TGAGCGTAAACGTATTCATGCTGA
1 CGAGCGTAAACGTATTTAT-ATGA
35493385 CGAGCGTAAACGTATTTATATGAA
1 CGAGCGTAAACGTATTTATATG-A
* *
35493409 CGATCATAAACGT
1 CGAGCGTAAACGT
35493422 TCATTAGCCG
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
23 2 0.04
24 32 0.63
26 2 0.04
27 1 0.02
28 14 0.27
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (23 bp):
CGAGCGTAAACGTATTTATATGA
Found at i:35493419 original size:76 final size:76
Alignment explanation
Indices: 35493278--35493421 Score: 182
Period size: 76 Copynumber: 1.9 Consensus size: 76
35493268 AAACATATTC
* * * *
35493278 ATGCTGATGAGCATAAAAGTATTCATGCTGACAAACGTAAATGTATATATGCTGTCGAGCGTAAA
1 ATGCTGATGAGCATAAAAGTATTCATGCTGACAAACGTAAACGTATATATGATGACGAGCATAAA
35493343 CGTATATATAT
66 CGTATATATAT
* * * * * *
35493354 ATGCTGATGAGCGTAAACGTATTCATGCTGACGAGCGTAAACGTATTTAT-ATGAACGATCATAA
1 ATGCTGATGAGCATAAAAGTATTCATGCTGACAAACGTAAACGTATATATGATG-ACGAGCATAA
35493418 ACGT
65 ACGT
35493422 TCATTAGCCG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
75 2 0.04
76 55 0.96
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (76 bp):
ATGCTGATGAGCATAAAAGTATTCATGCTGACAAACGTAAACGTATATATGATGACGAGCATAAA
CGTATATATAT
Found at i:35496348 original size:24 final size:24
Alignment explanation
Indices: 35496316--35496446 Score: 208
Period size: 24 Copynumber: 5.5 Consensus size: 24
35496306 TTCAGCCAAC
*
35496316 ACGAGCCCACAATGATTAGCTCTT
1 ACGAGCCCAAAATGATTAGCTCTT
35496340 ACGAGCCCAAAATGATTAGCTCTT
1 ACGAGCCCAAAATGATTAGCTCTT
35496364 ACGAGCCCAAAATGATTAGCTCTT
1 ACGAGCCCAAAATGATTAGCTCTT
* *
35496388 ACGAGCCCAGAATGATTAACTCTT
1 ACGAGCCCAAAATGATTAGCTCTT
* * *
35496412 ATGAGACCAGAATGATTAGCTCTT
1 ACGAGCCCAAAATGATTAGCTCTT
35496436 ACGAGCCCAAA
1 ACGAGCCCAAA
35496447 CAGAGTTTAA
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 98 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (24 bp):
ACGAGCCCAAAATGATTAGCTCTT
Found at i:35498077 original size:14 final size:13
Alignment explanation
Indices: 35498056--35498089 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
35498046 TTAATTTAAT
35498056 AATTAAAATTCAA
1 AATTAAAATTCAA
*
35498069 AATTCAAAATTCCA
1 AATT-AAAATTCAA
35498083 AATTAAA
1 AATTAAA
35498090 TTATTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATTAAAATTCAA
Found at i:35500111 original size:21 final size:20
Alignment explanation
Indices: 35500066--35500118 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
35500056 CTGTACTAGT
*
35500066 TCTACCGATACAAGTGACATT
1 TCTACCGATACAAGT-ACATA
35500087 TCTACCGATACAAGT-CATGCA
1 TCTACCGATACAAGTACAT--A
35500108 TCTACCGATAC
1 TCTACCGATAC
35500119 TAAAAACTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 3 0.10
21 26 0.90
ACGTcount: A:0.32, C:0.28, G:0.13, T:0.26
Consensus pattern (20 bp):
TCTACCGATACAAGTACATA
Found at i:35500834 original size:24 final size:24
Alignment explanation
Indices: 35500807--35500859 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
35500797 CAACCAACAA
*
35500807 GAGCCCAGAATGATTAGCTATTAC
1 GAGCCCAAAATGATTAGCTATTAC
*
35500831 GAGCCCAAAATGATTAGCTCTTAC
1 GAGCCCAAAATGATTAGCTATTAC
35500855 GAGCC
1 GAGCC
35500860 TAGACAGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (24 bp):
GAGCCCAAAATGATTAGCTATTAC
Found at i:35504006 original size:26 final size:26
Alignment explanation
Indices: 35503974--35504037 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
35503964 TTTTACCCTA
*
35503974 GTAAAATTTTGATGA-TTTTACATATG
1 GTAAAATTTTGACGATTTTTACAT-TG
* *
35504000 GTAAAATTTTGACGATTTTTTCCTTG
1 GTAAAATTTTGACGATTTTTACATTG
35504026 GTAAAATTTTGA
1 GTAAAATTTTGA
35504038 GAAAATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 28 0.82
27 6 0.18
ACGTcount: A:0.31, C:0.06, G:0.16, T:0.47
Consensus pattern (26 bp):
GTAAAATTTTGACGATTTTTACATTG
Found at i:35506206 original size:22 final size:22
Alignment explanation
Indices: 35506181--35506228 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
35506171 TTCTGCTACA
*
35506181 TTTTACTGTTATTATGTTGTTG
1 TTTTACTGCTATTATGTTGTTG
** *
35506203 TTTTGTTGCTATTATGTTGTTT
1 TTTTACTGCTATTATGTTGTTG
35506225 TTTT
1 TTTT
35506229 GCTACAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.10, C:0.04, G:0.17, T:0.69
Consensus pattern (22 bp):
TTTTACTGCTATTATGTTGTTG
Found at i:35509615 original size:23 final size:24
Alignment explanation
Indices: 35509589--35509636 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
35509579 TTATGTTTAT
35509589 GTTTTT-TTGGTTTA-GGATTTAAG
1 GTTTTTATT-GTTTAGGGATTTAAG
*
35509612 GTTTTTATTGTTTAGGGTTTTAAG
1 GTTTTTATTGTTTAGGGATTTAAG
35509636 G
1 G
35509637 GTAAAATAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.56
Consensus pattern (24 bp):
GTTTTTATTGTTTAGGGATTTAAG
Found at i:35518567 original size:30 final size:30
Alignment explanation
Indices: 35518527--35518596 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
35518517 AAAAAAAACA
* * *
35518527 TATTCAAATTTCGAGTTAATCGAGTCGATT
1 TATTCGAATTTCAAGTTAATCGAATCGATT
*
35518557 TATTCGAATTTCAAGTTAATCGAATTGATT
1 TATTCGAATTTCAAGTTAATCGAATCGATT
35518587 TATTCGAATT
1 TATTCGAATT
35518597 ATTCCACTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.43
Consensus pattern (30 bp):
TATTCGAATTTCAAGTTAATCGAATCGATT
Found at i:35528741 original size:19 final size:20
Alignment explanation
Indices: 35528696--35528743 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
35528686 GTTAGTTGCA
35528696 TGCATTTATTTTAATTGTCAT
1 TGCATTT-TTTTAATTGTCAT
*
35528717 TACATTTTTTT-ATTGTC-T
1 TGCATTTTTTTAATTGTCAT
35528735 CTGCATTTT
1 -TGCATTTT
35528744 ATTTGTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 1 0.04
19 13 0.54
20 4 0.17
21 6 0.25
ACGTcount: A:0.19, C:0.12, G:0.08, T:0.60
Consensus pattern (20 bp):
TGCATTTTTTTAATTGTCAT
Found at i:35529860 original size:42 final size:43
Alignment explanation
Indices: 35529714--35529912 Score: 224
Period size: 42 Copynumber: 4.7 Consensus size: 43
35529704 TTATGAGGAG
* * *
35529714 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGCTTATCTCAC
1 AAACGCTGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
* * * *
35529757 AAACGCTGCTAAAGAACATGGTCTTTAACAGCG-TTTTTTGAC
1 AAACGCTGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
* * *
35529799 AAATGCTGCTATAGATCATGGTCTTTAGCGGCGCTTTTCTCAC
1 AAACGCTGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
* * * * *
35529842 AAACGCCGCGAAAG-TCATGTTCTTTAGCGGTGCTTTTCTCAC
1 AAACGCTGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
* *
35529884 AAACGTTGCTAAAG-ACATGTTCTTTAGCG
1 AAACGCTGCTAAAGAACATGGTCTTTAGCG
35529913 ACACGTTTCC
Statistics
Matches: 131, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
42 85 0.65
43 46 0.35
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (43 bp):
AAACGCTGCTAAAGAACATGGTCTTTAGCGGCGCTTTTCTCAC
Found at i:35529886 original size:85 final size:84
Alignment explanation
Indices: 35529714--35529912 Score: 220
Period size: 85 Copynumber: 2.3 Consensus size: 84
35529704 TTATGAGGAG
* * * *
35529714 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGCTTATCTCACAAACGCTGCTAAAGAACATGGT
1 AAACGCTGCTAAAG-ACATGGTCTTTAGCGGCGCTTATCTCACAAACGCCGCGAAAGAACATGGT
* *
35529779 CTTTAACAGCGTTTTTTGAC
65 CTTTAACAGCGTTTTCTCAC
* * * * *
35529799 AAATGCTGCTATAGATCATGGTCTTTAGCGGCGCTTTTCTCACAAACGCCGCGAAAG-TCATGTT
1 AAACGCTGCTAAAGA-CATGGTCTTTAGCGGCGCTTATCTCACAAACGCCGCGAAAGAACATGGT
* * *
35529863 CTTTAGCGGTGCTTTTCTCAC
65 CTTTAACAGCG-TTTTCTCAC
* *
35529884 AAACGTTGCTAAAGACATGTTCTTTAGCG
1 AAACGCTGCTAAAGACATGGTCTTTAGCG
35529913 ACACGTTTCC
Statistics
Matches: 94, Mismatches: 18, Indels: 5
0.80 0.15 0.04
Matches are distributed among these distances:
84 27 0.29
85 67 0.71
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (84 bp):
AAACGCTGCTAAAGACATGGTCTTTAGCGGCGCTTATCTCACAAACGCCGCGAAAGAACATGGTC
TTTAACAGCGTTTTCTCAC
Found at i:35533041 original size:19 final size:21
Alignment explanation
Indices: 35533012--35533061 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
35533002 AAAGGGTAAT
* *
35533012 AGAACAAAGGA-AATCTGAAG
1 AGAACAAAGGAGAAACTAAAG
35533032 AGAA-AAAGGAGAAACTAAAG
1 AGAACAAAGGAGAAACTAAAG
*
35533052 AGAACCAAGG
1 AGAACAAAGG
35533062 GTTAGGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 6 0.24
20 15 0.60
21 4 0.16
ACGTcount: A:0.58, C:0.10, G:0.26, T:0.06
Consensus pattern (21 bp):
AGAACAAAGGAGAAACTAAAG
Found at i:35533968 original size:40 final size:41
Alignment explanation
Indices: 35533868--35534199 Score: 469
Period size: 40 Copynumber: 8.2 Consensus size: 41
35533858 TATTATTGAG
*
35533868 CTTTAGCGGCGC-TTCTTCATAAGCGCCGCTATTGCCCTGAC
1 CTTTAGCGGCGCTTTC-CCATAAGCGCCGCTATTGCCCTGAC
* *
35533909 CTTTAGCGGCGCTTCCCCATAAGCGCCACTATTGCCCT-AC
1 CTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCCCTGAC
* * * * *
35533949 CTTTTGCGGCACTTACCCATAAGCGCCGCTATTTCTCTGAC
1 CTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCCCTGAC
35533990 CTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCCCT-AC
1 CTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCCCTGAC
* *
35534030 CTTTTGCGGCGCTTTCCCATAAACGCCGCTATTGCCCT-AC
1 CTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCCCTGAC
* *
35534070 CTTTTGCGGCGCTTTCCCATAAGCGCCGCTATTTCCCTGAC
1 CTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCCCTGAC
* *
35534111 CTTTAGCGGCGCTTT-CCATAAGCGCTGCTATTGCCTTGAC
1 CTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCCCTGAC
*
35534151 CTTTAGCGACGCTTTCCCATAAGCGCCGCTATTGCCCT-AC
1 CTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCCCTGAC
*
35534191 CTTTTGCGG
1 CTTTAGCGG
35534200 TGTTTTCTGT
Statistics
Matches: 260, Mismatches: 27, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
40 155 0.60
41 103 0.40
42 2 0.01
ACGTcount: A:0.15, C:0.36, G:0.20, T:0.30
Consensus pattern (41 bp):
CTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCCCTGAC
Found at i:35534009 original size:81 final size:80
Alignment explanation
Indices: 35533868--35534199 Score: 486
Period size: 81 Copynumber: 4.1 Consensus size: 80
35533858 TATTATTGAG
* * *
35533868 CTTTAGCGGCGCTTCTTCATAAGCGCCGCTATTGCCCTGACCTTTAGCGGCGCTTCCCCATAAGC
1 CTTTTGCGGCGCTTC-CCATAAGCGCCGCTATTGCCCTGACCTTTAGCGGCGCTTTCCCATAAGC
*
35533933 GCCACTATTGCCCTAC
65 GCCGCTATTGCCCTAC
* * *
35533949 CTTTTGCGGCACTTACCCATAAGCGCCGCTATTTCTCTGACCTTTAGCGGCGCTTTCCCATAAGC
1 CTTTTGCGGCGCTT-CCCATAAGCGCCGCTATTGCCCTGACCTTTAGCGGCGCTTTCCCATAAGC
35534014 GCCGCTATTGCCCTAC
65 GCCGCTATTGCCCTAC
* *
35534030 CTTTTGCGGCGCTTTCCCATAAACGCCGCTATTGCCCT-ACCTTTTGCGGCGCTTTCCCATAAGC
1 CTTTTGCGGCGC-TTCCCATAAGCGCCGCTATTGCCCTGACCTTTAGCGGCGCTTTCCCATAAGC
*
35534094 GCCGCTATTTCCCTGAC
65 GCCGCTATTGCCCT-AC
* * * * *
35534111 CTTTAGCGGCGCTTTCCATAAGCGCTGCTATTGCCTTGACCTTTAGCGACGCTTTCCCATAAGCG
1 CTTTTGCGGCGCTTCCCATAAGCGCCGCTATTGCCCTGACCTTTAGCGGCGCTTTCCCATAAGCG
35534176 CCGCTATTGCCCTAC
66 CCGCTATTGCCCTAC
35534191 CTTTTGCGG
1 CTTTTGCGG
35534200 TGTTTTCTGT
Statistics
Matches: 225, Mismatches: 22, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
80 69 0.31
81 153 0.68
82 3 0.01
ACGTcount: A:0.15, C:0.36, G:0.20, T:0.30
Consensus pattern (80 bp):
CTTTTGCGGCGCTTCCCATAAGCGCCGCTATTGCCCTGACCTTTAGCGGCGCTTTCCCATAAGCG
CCGCTATTGCCCTAC
Found at i:35534089 original size:121 final size:122
Alignment explanation
Indices: 35533868--35534199 Score: 535
Period size: 121 Copynumber: 2.7 Consensus size: 122
35533858 TATTATTGAG
* *
35533868 CTTTAGCGGCGC-TTCTTCATAAGCGCCGCTATTGCCCTGACCTTTAGCGGCGCTTCCCCATAAG
1 CTTTAGCGGCGCTTTC-CCATAAGCGCCGCTATTGCCCTGACCTTTAGCGGCGCTTTCCCATAAG
* *
35533932 CGCCACTATTGCCCTACCTTTTGCGGCACTTACCCATAAGCGCCGCTATTTCTCTGAC
65 CGCCGCTATTGCCCTACCTTTTGCGGCACTTACCCATAAGCGCCGCTATTTCCCTGAC
* *
35533990 CTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCCCT-ACCTTTTGCGGCGCTTTCCCATAAAC
1 CTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCCCTGACCTTTAGCGGCGCTTTCCCATAAGC
* *
35534054 GCCGCTATTGCCCTACCTTTTGCGGCGCTTTCCCATAAGCGCCGCTATTTCCCTGAC
66 GCCGCTATTGCCCTACCTTTTGCGGCACTTACCCATAAGCGCCGCTATTTCCCTGAC
* * *
35534111 CTTTAGCGGCGCTTT-CCATAAGCGCTGCTATTGCCTTGACCTTTAGCGACGCTTTCCCATAAGC
1 CTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCCCTGACCTTTAGCGGCGCTTTCCCATAAGC
35534175 GCCGCTATTGCCCTACCTTTTGCGG
66 GCCGCTATTGCCCTACCTTTTGCGG
35534200 TGTTTTCTGT
Statistics
Matches: 195, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
120 20 0.10
121 139 0.71
122 33 0.17
123 3 0.02
ACGTcount: A:0.15, C:0.36, G:0.20, T:0.30
Consensus pattern (122 bp):
CTTTAGCGGCGCTTTCCCATAAGCGCCGCTATTGCCCTGACCTTTAGCGGCGCTTTCCCATAAGC
GCCGCTATTGCCCTACCTTTTGCGGCACTTACCCATAAGCGCCGCTATTTCCCTGAC
Found at i:35536733 original size:26 final size:26
Alignment explanation
Indices: 35536703--35536756 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
35536693 AGTACACTCA
35536703 TTTTAGTCTCTCAACTTTAGTAATTT
1 TTTTAGTCTCTCAACTTTAGTAATTT
*
35536729 TTTTAGTCTCTCCACTTTAGTAATTT
1 TTTTAGTCTCTCAACTTTAGTAATTT
35536755 TT
1 TT
35536757 CAATTTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.56
Consensus pattern (26 bp):
TTTTAGTCTCTCAACTTTAGTAATTT
Found at i:35537155 original size:157 final size:161
Alignment explanation
Indices: 35536804--35537159 Score: 533
Period size: 163 Copynumber: 2.2 Consensus size: 161
35536794 TTGTTTAATC
* *
35536804 GACTAATGACACTGTTATTGTACACTCATTTTAGTCACTCGACTCGATTGAACACTCACCCTTAA
1 GACTAATGACACTGTTATTGTACACTCATTTTAGTCACTCGACTCGATCGAACACTCACCCCTAA
* *
35536869 TTTCAACTATAGAACCATCGTTAGATAGTTTTTTTTTATTTTTGGTCACTCGTCATTAGATATAT
66 TTTCAACTATAGAACCATCGTTAGATA--TTATTTTTAGTTTTGGTCACTCGTCATTAGATATAT
35536934 ATATTTTTCATTTTAGTCACTCATCGTTAATGT
129 ATATTTTTCATTTTAGTCACTCATCGTTAATGT
* * * * *
35536967 GGCTAATGACACTGTTATTGTACACTTATTTTAGTCACTTGATTCGATCGAACGCTCACCCCTAA
1 GACTAATGACACTGTTATTGTACACTCATTTTAGTCACTCGACTCGATCGAACACTCACCCCTAA
* *
35537032 TTTCAACTATAGAACCA-CTGTTAGATA-TATTTTTAGTTTTGGTCACTTGTCGTTAGAT-T-T-
66 TTTCAACTATAGAACCATC-GTTAGATATTATTTTTAGTTTTGGTCACTCGTCATTAGATATATA
*
35537092 TTTTTTTCATTTTAGTCACTCATCGTTAATGT
130 TATTTTTCATTTTAGTCACTCATCGTTAATGT
*
35537124 GACTAATGGCACTGTTATTGTACACTCATTTTAGTC
1 GACTAATGACACTGTTATTGTACACTCATTTTAGTC
35537160 TCTCAACTTT
Statistics
Matches: 177, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
157 64 0.36
158 1 0.01
159 1 0.01
160 27 0.15
162 1 0.01
163 83 0.47
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (161 bp):
GACTAATGACACTGTTATTGTACACTCATTTTAGTCACTCGACTCGATCGAACACTCACCCCTAA
TTTCAACTATAGAACCATCGTTAGATATTATTTTTAGTTTTGGTCACTCGTCATTAGATATATAT
ATTTTTCATTTTAGTCACTCATCGTTAATGT
Found at i:35541880 original size:21 final size:21
Alignment explanation
Indices: 35541833--35541891 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
35541823 AATAATGCAG
*
35541833 ACTTCTACTAATACAAGTGAT
1 ACTTCTACCAATACAAGTGAT
* *
35541854 AGTTCTACCGATACAAGTGACT
1 ACTTCTACCAATACAAGTGA-T
*
35541876 -CTTCTACCAAAACAAG
1 ACTTCTACCAATACAAG
35541892 CTTTACTTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (21 bp):
ACTTCTACCAATACAAGTGAT
Found at i:35553916 original size:33 final size:36
Alignment explanation
Indices: 35553874--35553939 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 36
35553864 TGTTTATGTG
* *
35553874 AAATTGAAGAGAAA-GAGAAGAG-AG-GCAAGGATC
1 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGGATC
35553907 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGG
1 AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGG
35553940 GGTAAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 13 0.46
34 7 0.25
35 2 0.07
36 6 0.21
ACGTcount: A:0.53, C:0.06, G:0.32, T:0.09
Consensus pattern (36 bp):
AAATTGAAGACAAAGGAAAAGAGTAGAGCAAGGATC
Found at i:35554991 original size:23 final size:23
Alignment explanation
Indices: 35554964--35555107 Score: 184
Period size: 23 Copynumber: 6.2 Consensus size: 23
35554954 ACACTAGCGC
35554964 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
35554987 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
35555010 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
* *
35555035 GCTCTCCGATTAGCACT-TCATGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
35555058 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
35555081 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
35555104 GCTC
1 GCTC
35555108 AGTACTTTGT
Statistics
Matches: 107, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
22 4 0.04
23 83 0.78
24 1 0.01
25 16 0.15
26 3 0.03
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:35555097 original size:46 final size:45
Alignment explanation
Indices: 35554964--35555102 Score: 199
Period size: 48 Copynumber: 3.0 Consensus size: 45
35554954 ACACTAGCGC
* *
35554964 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCT-GT
*
35555010 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCATGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTC-TGT
*
35555058 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTT-TGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCTGT
35555102 G
1 G
35555103 TGCTCAGTAC
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
44 4 0.05
46 39 0.46
48 41 0.48
49 1 0.01
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.40
Consensus pattern (45 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTCTGT
Found at i:35555105 original size:46 final size:46
Alignment explanation
Indices: 35554964--35555150 Score: 192
Period size: 46 Copynumber: 4.2 Consensus size: 46
35554954 ACACTAGCGC
* * *
35554964 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCT-CGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCAC-TTTGTGT
* **
35555010 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCATGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGT
*
35555058 GCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGT
* * * *
35555104 G--CTC-----AGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGT
35555143 GCTCTCTG
1 GCTCTCTG
35555151 TTCAGTACTT
Statistics
Matches: 122, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
39 33 0.27
41 3 0.02
44 3 0.02
46 43 0.35
47 1 0.01
48 39 0.32
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.42
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGT
Found at i:35555126 original size:39 final size:39
Alignment explanation
Indices: 35555072--35555146 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
35555062 TCTGATTAGC
*
35555072 ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTTGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
*
35555111 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTTGTGTACTCTCTGATTAGCACTTTGTGTGCTC
35555147 TCTGTTCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (39 bp):
ACTTTGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:35555141 original size:23 final size:23
Alignment explanation
Indices: 35555111--35555175 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
35555101 TGTGCTCAGT
35555111 ACTTTGTGTACTCTCTGTTTAGC
1 ACTTTGTGTACTCTCTGTTTAGC
* * *
35555134 ACTTTGTGTGCTCTCTGTTCAGT
1 ACTTTGTGTACTCTCTGTTTAGC
*
35555157 ACTTCG-GTACTCTCTGTTT
1 ACTTTGTGTACTCTCTGTTT
35555176 GTTCCGTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 11 0.31
23 25 0.69
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (23 bp):
ACTTTGTGTACTCTCTGTTTAGC
Found at i:35560123 original size:15 final size:16
Alignment explanation
Indices: 35560094--35560123 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35560084 AACAACACGA
35560094 TGAAAAGTGAAATAAC
1 TGAAAAGTGAAATAAC
35560110 TGAAAAGT-AAATAA
1 TGAAAAGTGAAATAA
35560124 AAAAATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.03, G:0.17, T:0.20
Consensus pattern (16 bp):
TGAAAAGTGAAATAAC
Found at i:35572744 original size:14 final size:14
Alignment explanation
Indices: 35572725--35572766 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
35572715 CCAAAAATCA
35572725 GGTTAGTAGAATTG
1 GGTTAGTAGAATTG
35572739 GGTTAGTA-AATTTAG
1 GGTTAGTAGAA-TT-G
35572754 GGTTAGT-GAATTG
1 GGTTAGTAGAATTG
35572767 AAAATCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
13 3 0.12
14 12 0.48
15 10 0.40
ACGTcount: A:0.29, C:0.00, G:0.33, T:0.38
Consensus pattern (14 bp):
GGTTAGTAGAATTG
Found at i:35578017 original size:22 final size:22
Alignment explanation
Indices: 35577992--35578034 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
35577982 TAAATATTTC
*
35577992 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
35578014 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
35578035 TTATTCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:35588941 original size:22 final size:22
Alignment explanation
Indices: 35588916--35588958 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
35588906 AAAATATTTC
*
35588916 ATTA-ATAATTTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
35588938 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
35588959 TTATTCTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:35591874 original size:20 final size:21
Alignment explanation
Indices: 35591849--35591889 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
35591839 CTTATATGCC
*
35591849 AAAGTG-AAAAATTGATTTTT
1 AAAGTGAAAAAAGTGATTTTT
35591869 AAAGTGAAAAAAGTGATTTTT
1 AAAGTGAAAAAAGTGATTTTT
35591890 GTGGTCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (21 bp):
AAAGTGAAAAAAGTGATTTTT
Found at i:35601314 original size:11 final size:11
Alignment explanation
Indices: 35601290--35601324 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
35601280 AATAGAGGTC
*
35601290 TTTATTTTTAT
1 TTTATTTTTCT
*
35601301 TTTCTTTTTCT
1 TTTATTTTTCT
35601312 TTTATTTTTCT
1 TTTATTTTTCT
35601323 TT
1 TT
35601325 CCTTATTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTTCT
Found at i:35601381 original size:3 final size:3
Alignment explanation
Indices: 35601375--35601430 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
35601365 TCATCATCAA
* * * * *
35601375 TAT TAT TAT TGT TGT TGT TGT TGT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35601423 TAT TAT TA
1 TAT TAT TA
35601431 GGGTTTCATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:35601935 original size:148 final size:142
Alignment explanation
Indices: 35601837--35602345 Score: 461
Period size: 148 Copynumber: 3.4 Consensus size: 142
35601827 AATTTTGGTT
* *
35601837 TTTTTTTAAAAACAATTTCGAACTAAAAAGTTTGGATTTTTAAGTAACATAGTGATTTTCTTTA-
1 TTTTTTT--AAACAATTTCGAAAT-AAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTTTAC
* *
35601901 AAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTAGTCATTTTAAAGAAAAATTTA
63 AAAAAGAGAAAGTTTACATTTTTAAAAATAAAAATATG--TTT--T--TTTTAAAGAAAAATTTA
*
35601966 AATTTTTAAATAAAGTTTTGA
122 AATTTTGAAATAAAGTTTTGA
* **
35601987 TTTTTTTAAACTATTTCGAAATAAAAGTTTTTATTTTTAAGTAAAATAGTGATTTTCTTTACAAA
1 TTTTTTTAAACAATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTTTACAAA
* *
35602052 AAGATAAAGTTTACATTTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAAGAAAATTTTAAA
66 AAGAGAAAGTTTACATTTTTAAAAATAAAAATATG---TTT--T--TTTTAAAGAAAAATTTAAA
*
35602117 TTTTTAACA-AAA-TTTTGA
124 TTTTGAA-ATAAAGTTTTGA
* * * * *
35602135 TTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTTTAAGTAAAGTAGTGATTTTCATTA-A
1 TTTTTTTAAACAATTTCGAAATAAAAGTTTGGA--TTTTTAAGTAAAATAGTGATTTTCTTTACA
* * *
35602199 AAATACAGAAAGTTTAGATTTTTTAAAAAATAAAAATCTATGTTGAAATGATTTTAAAGAAAAAT
64 AAA-AGAGAAAGTTTACA-TTTTT-AAAAATAAAAA--TATGTT----T-TTTTTAAAGAAAAA-
* * *
35602264 TTTAAATTTTTTAAACAAAATTTTGAA
118 TTTAAA-TTTTGAAATAAAGTTTTG-A
* * * *
35602291 TTTTTTT-AGCTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAGTAGTGATTTT
1 TTTTTTTAAACAATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTT
35602346 GTTTTATCCA
Statistics
Matches: 319, Mismatches: 21, Indels: 35
0.85 0.06 0.09
Matches are distributed among these distances:
147 36 0.11
148 84 0.26
149 42 0.13
150 45 0.14
151 7 0.02
152 23 0.07
153 30 0.09
154 15 0.05
155 29 0.09
156 8 0.03
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (142 bp):
TTTTTTTAAACAATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTTCTTTACAAA
AAGAGAAAGTTTACATTTTTAAAAATAAAAATATGTTTTTTTTAAAGAAAAATTTAAATTTTGAA
ATAAAGTTTTGA
Found at i:35602298 original size:22 final size:22
Alignment explanation
Indices: 35602250--35602296 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
35602240 GTTGAAATGA
35602250 TTTTAAAGAAAAATTTTAAATT
1 TTTTAAAGAAAAATTTTAAATT
* *
35602272 TTTTAAA-CAAAATTTTGAATT
1 TTTTAAAGAAAAATTTTAAATT
35602293 TTTT
1 TTTT
35602297 TAGCTATTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (22 bp):
TTTTAAAGAAAAATTTTAAATT
Found at i:35603096 original size:10 final size:11
Alignment explanation
Indices: 35603061--35603122 Score: 54
Period size: 11 Copynumber: 5.3 Consensus size: 11
35603051 TAAAAAAAAT
35603061 AATTATTTTTTA
1 AATTA-TTTTTA
35603073 AACTATATTTTTTA
1 AA-T-TA-TTTTTA
35603087 AA-TATTTTTA
1 AATTATTTTTA
* *
35603097 AATTAATTTAA
1 AATTATTTTTA
35603108 AATTATTTTTTA
1 AATTA-TTTTTA
35603120 AAT
1 AAT
35603123 ATAAAATTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.19
11 13 0.31
12 9 0.21
13 1 0.02
14 11 0.26
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (11 bp):
AATTATTTTTA
Found at i:35604002 original size:6 final size:6
Alignment explanation
Indices: 35603991--35604023 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
35603981 AAATAAGAAA
35603991 GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGG
1 GGGAAG GGGAAG GGGAAG GGGAAG GGGAAG GGG
35604024 GGAAGGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.70, T:0.00
Consensus pattern (6 bp):
GGGAAG
Found at i:35604140 original size:23 final size:23
Alignment explanation
Indices: 35604096--35604140 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
35604086 AAATAATTTT
*
35604096 AAATTAATTTTAAAATATTAAAA
1 AAATTAATTTTAAAATAATAAAA
35604119 AAATTATATTTTAAAA-AATAAA
1 AAATTA-ATTTTAAAATAATAAA
35604141 TAATTTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTAATTTTAAAATAATAAAA
Found at i:35604532 original size:21 final size:20
Alignment explanation
Indices: 35604508--35604555 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
35604498 TTATATAATT
* * *
35604508 TATTTATTTATTTTTATTTC
1 TATTTATTCATTTTCATGTC
35604528 ATATTTATTCATTTTCATGTC
1 -TATTTATTCATTTTCATGTC
35604549 TATTTAT
1 TATTTAT
35604556 ATTTATGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (20 bp):
TATTTATTCATTTTCATGTC
Found at i:35608507 original size:16 final size:16
Alignment explanation
Indices: 35608469--35608513 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
35608459 CCCAATGTAG
* *
35608469 TTCATTCATTCATCTA
1 TTCATTTATTCATCAA
35608485 TTCATTTATTCATCAA
1 TTCATTTATTCATCAA
*
35608501 TTCATTTACTCAT
1 TTCATTTATTCAT
35608514 TCGCTCATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (16 bp):
TTCATTTATTCATCAA
Found at i:35617080 original size:200 final size:200
Alignment explanation
Indices: 35616719--35617300 Score: 950
Period size: 200 Copynumber: 2.9 Consensus size: 200
35616709 CTTAGCCTAT
* * *
35616719 TTACTCTTAAATTTGTCTTGTTTTGGTACTGATGTCGCTACATAAGTAATTTCAGACTGCGTCCA
1 TTACCCTTAATTTTGTCATGTTTTGGTACTGATGTCGCTACATAAGTAATTTCAGACTGCGTCCA
*
35616784 GGATTGTCGTTGCATCTAACAGCTGTCCGGATAAGAACAGAAATGTGTGAGCTATCCAATCTGGT
66 GGATTGTCGTCGCATCTAACAGCTGTCCGGATAAGAACAGAAATGTGTGAGCTATCCAATCTGGT
35616849 ATAACTAACTTGTACAACCAGTGACAGCTTGATTCTGATGAAAGGACACCTGCATAATGACAACT
131 ATAACTAACTTGTACAACCAGTGACAGCTTGATTCTGATGAAAGGACACCTGCATAATGACAACT
35616914 TGTAC
196 TGTAC
35616919 TTACCCTTAATTTTGTCATGTTTTGGTACTGATGTCGCTACATAAGTAATTTCAGACTGCGTCCA
1 TTACCCTTAATTTTGTCATGTTTTGGTACTGATGTCGCTACATAAGTAATTTCAGACTGCGTCCA
35616984 GGATTGTCGTCGCATCTAACAGCTGTCCGGATAAGAACAGAAATGTGTGAGCTATCCAATCTGGT
66 GGATTGTCGTCGCATCTAACAGCTGTCCGGATAAGAACAGAAATGTGTGAGCTATCCAATCTGGT
35617049 ATAACTAACTTGTACAACCAGTGACAGCTTGATTCTGATGAAAGGACACCTGCATAATGACAACT
131 ATAACTAACTTGTACAACCAGTGACAGCTTGATTCTGATGAAAGGACACCTGCATAATGACAACT
35617114 TGTAC
196 TGTAC
* * *
35617119 TTACCCTTAATTTTGTCATGTTTTGGTACTAATGTCGCTGCATAAGTAATTTCAGATTGCGTCCA
1 TTACCCTTAATTTTGTCATGTTTTGGTACTGATGTCGCTACATAAGTAATTTCAGACTGCGTCCA
* * * * * * * * * *
35617184 GAATTATCGTCGCATCTGACAGTTGTTCAGATAAGAACGGAAATGTGTGAGCTGTCCAGTCTAGT
66 GGATTGTCGTCGCATCTAACAGCTGTCCGGATAAGAACAGAAATGTGTGAGCTATCCAATCTGGT
* * * * *
35617249 ATAACCAACTTGTACGACCAGAGACAACTTGATTCTG-TAGAAAAGACACCTG
131 ATAACTAACTTGTACAACCAGTGACAGCTTGATTCTGAT-GAAAGGACACCTG
35617301 TACAGTTTGG
Statistics
Matches: 359, Mismatches: 22, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
199 1 0.00
200 358 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (200 bp):
TTACCCTTAATTTTGTCATGTTTTGGTACTGATGTCGCTACATAAGTAATTTCAGACTGCGTCCA
GGATTGTCGTCGCATCTAACAGCTGTCCGGATAAGAACAGAAATGTGTGAGCTATCCAATCTGGT
ATAACTAACTTGTACAACCAGTGACAGCTTGATTCTGATGAAAGGACACCTGCATAATGACAACT
TGTAC
Found at i:35620022 original size:17 final size:17
Alignment explanation
Indices: 35619997--35620030 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35619987 TGTTAGTAAA
*
35619997 CATTGTCATTGCATTTT
1 CATTATCATTGCATTTT
35620014 CATTATCATTGCATTTT
1 CATTATCATTGCATTTT
35620031 GGGGAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.53
Consensus pattern (17 bp):
CATTATCATTGCATTTT
Found at i:35621650 original size:38 final size:38
Alignment explanation
Indices: 35621599--35621679 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
35621589 TAAGTCTATT
* *
35621599 CAGAATTATGCCCAGAATTGTCACTACATGACAATGTC
1 CAGAATTACGCCCAAAATTGTCACTACATGACAATGTC
* *
35621637 CAGAATTGCGCCCAAAATTGTCACTACATGACGATGTC
1 CAGAATTACGCCCAAAATTGTCACTACATGACAATGTC
35621675 CAGAA
1 CAGAA
35621680 ATGTCGCTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (38 bp):
CAGAATTACGCCCAAAATTGTCACTACATGACAATGTC
Found at i:35635442 original size:21 final size:20
Alignment explanation
Indices: 35635403--35635442 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
35635393 TGCATTTTTA
* *
35635403 GCATTTTATATTTAGTAATT
1 GCATTTTATAGTCAGTAATT
35635423 GCATTTTATAAGTCAGTAAT
1 GCATTTTAT-AGTCAGTAAT
35635443 GTTTGGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (20 bp):
GCATTTTATAGTCAGTAATT
Found at i:35635756 original size:37 final size:37
Alignment explanation
Indices: 35635672--35635757 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 37
35635662 ATTTTCGGAA
*
35635672 TGCACCCA-ATACTGTCGCTGCATAAATATTTTTCAAAT
1 TGCACCCAGA-ACTATCGCTGCATAAATATTTTT-AAAT
* *
35635710 TGCATCCAGAACTATCGCTGCATAAGTATTCTTT-AAT
1 TGCACCCAGAACTATCGCTGCATAAATATT-TTTAAAT
35635747 TGCACCCAGAA
1 TGCACCCAGAA
35635758 ATGTTGCTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
37 13 0.31
38 25 0.60
39 4 0.10
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (37 bp):
TGCACCCAGAACTATCGCTGCATAAATATTTTTAAAT
Found at i:35635767 original size:37 final size:37
Alignment explanation
Indices: 35635686--35635769 Score: 98
Period size: 37 Copynumber: 2.2 Consensus size: 37
35635676 CCCAATACTG
* *
35635686 TCGCTGCATAAATATTTTTCAAATTGCATCCAGAACTA
1 TCGCTGCATAAATATTTTT-AAATTGCACCCAGAAATA
* *
35635724 TCGCTGCATAAGTATTCTTT-AATTGCACCCAGAAATG
1 TCGCTGCATAAATATT-TTTAAATTGCACCCAGAAATA
*
35635761 TTGCTGCAT
1 TCGCTGCAT
35635770 GAACATGTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
37 22 0.55
38 15 0.38
39 3 0.08
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (37 bp):
TCGCTGCATAAATATTTTTAAATTGCACCCAGAAATA
Found at i:35635808 original size:26 final size:26
Alignment explanation
Indices: 35635752--35635812 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
35635742 TTAATTGCAC
* * *
35635752 CCAGAAATGTTGCTGCATGAACATGT
1 CCAGAATTGTCGCTGCATGAACATAT
* *
35635778 ACAGAATTGTCGCTGCATGAACGTAT
1 CCAGAATTGTCGCTGCATGAACATAT
35635804 CCAGAATTG
1 CCAGAATTG
35635813 CGTCCAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (26 bp):
CCAGAATTGTCGCTGCATGAACATAT
Found at i:35640424 original size:12 final size:12
Alignment explanation
Indices: 35640407--35640431 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35640397 TGCATGAACG
35640407 TGTCCAGAATTA
1 TGTCCAGAATTA
35640419 TGTCCAGAATTA
1 TGTCCAGAATTA
35640431 T
1 T
35640432 CGCCTCATCT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TGTCCAGAATTA
Found at i:35645728 original size:20 final size:20
Alignment explanation
Indices: 35645705--35645753 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
35645695 TTAGTTGTTC
35645705 CGGTAGAAGTATACTTGTAT
1 CGGTAGAAGTATACTTGTAT
* * *
35645725 CGGTAGAACTGTAGTTGTAT
1 CGGTAGAAGTATACTTGTAT
*
35645745 CAGTAGAAG
1 CGGTAGAAG
35645754 AGGAGTTCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.31
Consensus pattern (20 bp):
CGGTAGAAGTATACTTGTAT
Found at i:35645988 original size:20 final size:20
Alignment explanation
Indices: 35645960--35646013 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
35645950 ACTCTTCAAG
*
35645960 GTATTGGTAGAAGTGGAGTT
1 GTATCGGTAGAAGTGGAGTT
* *
35645980 GTATCGGTAAAAGTGTAGTT
1 GTATCGGTAGAAGTGGAGTT
* *
35646000 CTACCGGTAGAAGT
1 GTATCGGTAGAAGT
35646014 CTCACTAGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.28, C:0.07, G:0.33, T:0.31
Consensus pattern (20 bp):
GTATCGGTAGAAGTGGAGTT
Found at i:35646504 original size:17 final size:17
Alignment explanation
Indices: 35646482--35646515 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35646472 TGTTAGTAAC
35646482 CATTGTCATTGCATTTT
1 CATTGTCATTGCATTTT
*
35646499 CATTGTCATTGTATTTT
1 CATTGTCATTGCATTTT
35646516 GGTGTTAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.15, G:0.12, T:0.56
Consensus pattern (17 bp):
CATTGTCATTGCATTTT
Found at i:35647602 original size:26 final size:26
Alignment explanation
Indices: 35647563--35647653 Score: 96
Period size: 26 Copynumber: 3.5 Consensus size: 26
35647553 TTGCGCCCAG
*
35647563 AATTGTCACAGCATGACGATGTCCAA
1 AATTGTCACTGCATGACGATGTCCAA
*
35647589 AATTGTCACTGCATGACGATATCCAGA
1 AATTGTCACTGCATGACGATGTCCA-A
* * *
35647616 AA-TGTCGCTGCATGA-GCATGCCCAG
1 AATTGTCACTGCATGACG-ATGTCCAA
*
35647641 AATTGTCGCTGCA
1 AATTGTCACTGCA
35647654 GGAACTCATT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
25 3 0.05
26 50 0.89
27 3 0.05
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (26 bp):
AATTGTCACTGCATGACGATGTCCAA
Found at i:35647747 original size:38 final size:38
Alignment explanation
Indices: 35647696--35647769 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
35647686 ATGTCTAGAG
*
35647696 TTGTCGCTGTATAAGCATGTCTAGAATTGCACCCAGAA
1 TTGTCGCTGTATAAGCATGTCTAGAATTGAACCCAGAA
35647734 TTGTCGCTGTATAAGCATGTCTAGAATTGAACCCAG
1 TTGTCGCTGTATAAGCATGTCTAGAATTGAACCCAG
35647770 TAAGGGAGCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (38 bp):
TTGTCGCTGTATAAGCATGTCTAGAATTGAACCCAGAA
Found at i:35651542 original size:101 final size:101
Alignment explanation
Indices: 35651265--35651855 Score: 676
Period size: 101 Copynumber: 5.9 Consensus size: 101
35651255 AATGAAACAT
* * * * * *
35651265 CAAATCATATAACCTTAAAGTTGCAAGGATCGGATTAAAACTAACATTAACAAATCTTTATCTCC
1 CAAATCCTATATCCCTAAAGTTGCAGGGATCGGATTAAAACTAACAGTAGCAAATCTTTATCTCC
* *
35651330 TTAAAGTTGCAGTGGAGCAAGATGAAGC-AGC-A--C
66 CTGAAGTTGCAGTGGAGCAAGATGAAGCTA-CAACCC
* * * * * * *
35651363 CAAATCCTATCTTCCTGAAGTTGCAGTGAAGCGAATTAAAA-T-A-A-TAGCGAATCTTTATCTC
1 CAAATCCTATATCCCTAAAGTTGCAG-GGATCGGATTAAAACTAACAGTAGCAAATCTTTATCTC
* *
35651424 CCTGAAGTTGCAGTGGAGAAACATGAAGCTACAACCC
65 CCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACCC
* * *
35651461 CAAATCCTATATCCCTAAAGTTGTAGGGATCGGATTAAAACTAATAGTAGCAAATGTTTATCTCC
1 CAAATCCTATATCCCTAAAGTTGCAGGGATCGGATTAAAACTAACAGTAGCAAATCTTTATCTCC
* * * *
35651526 TTGAAGTTGCAATGGAGCAGGATGAAGCTACAACAC
66 CTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACCC
* * * * * * *
35651562 CAAAACCTATATCTCTGAAGTTGCAAGGATCGGATTAAAACTAACATTGGAAAATCTTTATCTCC
1 CAAATCCTATATCCCTAAAGTTGCAGGGATCGGATTAAAACTAACAGTAGCAAATCTTTATCTCC
* *
35651627 CTGAAGTTACAGTGGAGCAAGATAAAGCTACAACCC
66 CTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACCC
** * *
35651663 CAAATCCTATATCTTTAAAGTTGTAGGGATCGAATTAAAACTAACAGTAGCAAATCTTTATCTCC
1 CAAATCCTATATCCCTAAAGTTGCAGGGATCGGATTAAAACTAACAGTAGCAAATCTTTATCTCC
* * *
35651728 CTGAAGTTGTAGTAGAGCAAGATAAAGCTACAACCC
66 CTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACCC
* * * * * * *
35651764 CAAATCCTATATCCCTGAAGTTGTAGGGATCGGATTAAAACCAATAGTGGCAAACCTTTATCTTC
1 CAAATCCTATATCCCTAAAGTTGCAGGGATCGGATTAAAACTAACAGTAGCAAATCTTTATCTCC
*
35651829 CTAAAGTTGCAGTGGAGCAAGATGAAG
66 CTGAAGTTGCAGTGGAGCAAGATGAAG
35651856 TCACGTCACT
Statistics
Matches: 412, Mismatches: 72, Indels: 15
0.83 0.14 0.03
Matches are distributed among these distances:
95 41 0.10
96 3 0.01
97 12 0.03
98 44 0.11
99 12 0.03
100 1 0.00
101 299 0.73
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (101 bp):
CAAATCCTATATCCCTAAAGTTGCAGGGATCGGATTAAAACTAACAGTAGCAAATCTTTATCTCC
CTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACCC
Found at i:35651826 original size:303 final size:296
Alignment explanation
Indices: 35651282--35651855 Score: 789
Period size: 303 Copynumber: 1.9 Consensus size: 296
35651272 TATAACCTTA
* *
35651282 AAGTTGCAAGGATCGGATTAAAACTAACATTAACAAATCTTTATCTCCTTAAAGTTGCAGTGGAG
1 AAGTTGCAAGGATCGGATTAAAACTAACATTAACAAATCTTTATCTCCCTAAAGTTACAGTGGAG
* * *
35651347 CAAGATGAAGCAGCACCAAATCCTATCTTCCTGAAGTTGCAGTGAAGCGAATTAAAATAATAGCG
66 CAAGATAAAGCAGCACCAAATCCTATCTT-CTAAAGTTGCAGTGAAGCGAATTAAAATAATAGCA
* *
35651412 AATCTTTATCTCCCTGAAGTTGCAGTGGAGAAACATGAAGCTACAACCCCAAATCCTATATCCCT
130 AATCTTTATCTCCCTGAAGTTGCAGTAGAGAAACATAAAGCTACAACCCCAAATCCTATATCCCT
* ** *
35651477 AAAGTTGTAGGGATCGGATTAAAACTAATAGTAGCAAATGTTTATC-TCCTTGAAGTTGCAATGG
195 AAAGTTGTAGGGATCGGATTAAAACCAATAGTAGCAAACCTTTATCTTCC-TAAAGTTGCAATGG
*
35651541 AGCAGGATGAAGCTACAACACCAAAACCTATATCTCTG
259 AGCAAGATGAAGCTACAACACCAAAACCTATATCTCTG
* *
35651579 AAGTTGCAAGGATCGGATTAAAACTAACATTGGA-AAATCTTTATCTCCCTGAAGTTACAGTGGA
1 AAGTTGCAAGGATCGGATTAAAACTAACATT-AACAAATCTTTATCTCCCTAAAGTTACAGTGGA
* * *
35651643 GCAAGATAAAGCTA-CAACCCCAAATCCTATATCTT-TAAAGTTGTAG-GGATCGAATTAAAACT
65 GCAAGATAAAGC-AGC-A--CCAAATCC--TATCTTCTAAAGTTGCAGTGAAGCGAATTAAAA-T
* * *
35651705 AACAGTAGCAAATCTTTATCTCCCTGAAGTTGTAGTAGAGCAAGATAAAGCTACAACCCCAAATC
123 -A-A-TAGCAAATCTTTATCTCCCTGAAGTTGCAGTAGAGAAACATAAAGCTACAACCCCAAATC
* *
35651770 CTATATCCCTGAAGTTGTAGGGATCGGATTAAAACCAATAGTGGCAAACCTTTATCTTCCTAAAG
185 CTATATCCCTAAAGTTGTAGGGATCGGATTAAAACCAATAGTAGCAAACCTTTATCTTCCTAAAG
*
35651835 TTGCAGTGGAGCAAGATGAAG
250 TTGCAATGGAGCAAGATGAAG
35651856 TCACGTCACT
Statistics
Matches: 242, Mismatches: 23, Indels: 18
0.86 0.08 0.06
Matches are distributed among these distances:
297 70 0.29
298 3 0.01
299 12 0.05
300 18 0.07
301 1 0.00
302 7 0.03
303 128 0.53
304 3 0.01
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (296 bp):
AAGTTGCAAGGATCGGATTAAAACTAACATTAACAAATCTTTATCTCCCTAAAGTTACAGTGGAG
CAAGATAAAGCAGCACCAAATCCTATCTTCTAAAGTTGCAGTGAAGCGAATTAAAATAATAGCAA
ATCTTTATCTCCCTGAAGTTGCAGTAGAGAAACATAAAGCTACAACCCCAAATCCTATATCCCTA
AAGTTGTAGGGATCGGATTAAAACCAATAGTAGCAAACCTTTATCTTCCTAAAGTTGCAATGGAG
CAAGATGAAGCTACAACACCAAAACCTATATCTCTG
Found at i:35662516 original size:51 final size:51
Alignment explanation
Indices: 35662414--35662517 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
35662404 AAATTTAGGA
* * *
35662414 TTGAAATCATCTATTTAAAGTTACTTTTGGCTGAATGAAAGTGGAGGGCTT
1 TTGAAATCATCTATTTAAAGTTACTTTTGGCTGAATGAAAGCGAAGAGCTT
35662465 TTGAAATCATCTATTTAAAGTTACTTTTGGCTGAATGAAAGCGAAGAGCTT
1 TTGAAATCATCTATTTAAAGTTACTTTTGGCTGAATGAAAGCGAAGAGCTT
35662516 TT
1 TT
35662518 CACTTTTGTT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.38
Consensus pattern (51 bp):
TTGAAATCATCTATTTAAAGTTACTTTTGGCTGAATGAAAGCGAAGAGCTT
Found at i:35678265 original size:45 final size:45
Alignment explanation
Indices: 35678201--35678309 Score: 175
Period size: 45 Copynumber: 2.4 Consensus size: 45
35678191 AGTGAAACGT
* *
35678201 ATATCATGGATATTGTATAGCATAATCAATCAAATAATATTGACC
1 ATATCATGAATATCGTATAGCATAATCAATCAAATAATATTGACC
*
35678246 ATATCATGAATATCGTATAGCATAATCAATCAAATAATATTTACC
1 ATATCATGAATATCGTATAGCATAATCAATCAAATAATATTGACC
35678291 ATATCAT-ACATATCGTATA
1 ATATCATGA-ATATCGTATA
35678310 ATGATAGCAT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
44 1 0.02
45 59 0.98
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (45 bp):
ATATCATGAATATCGTATAGCATAATCAATCAAATAATATTGACC
Found at i:35687916 original size:17 final size:17
Alignment explanation
Indices: 35687890--35687938 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
35687880 ATAGCTTGCA
*
35687890 TGCATCTTTATTGTCAT
1 TGCATTTTTATTGTCAT
35687907 TGCATTTTTATTTTGTCAT
1 TGCATTTTTA--TTGTCAT
35687926 TGCATTTTT-TTGT
1 TGCATTTTTATTGT
35687939 TAATTTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.14
17 9 0.31
19 16 0.55
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.61
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Found at i:35690451 original size:45 final size:44
Alignment explanation
Indices: 35690321--35690472 Score: 223
Period size: 45 Copynumber: 3.4 Consensus size: 44
35690311 GACGCGATCA
* * *
35690321 TATAACATAATTAATCAAATAATATTTACCATATTATGCATATTG
1 TATAGCATAATTAATCAAATAATA-TTACCATATCATGCATATCG
* *
35690366 TATAGCACAATTAATCAAGTAATATTACCATATCATGCATATCG
1 TATAGCATAATTAATCAAATAATATTACCATATCATGCATATCG
* *
35690410 TATAGCATAATCAGTCAAATAATATCTACCATATCATGCATATCG
1 TATAGCATAATTAATCAAATAATAT-TACCATATCATGCATATCG
35690455 TATAGCATAATTAATCAA
1 TATAGCATAATTAATCAA
35690473 TTAGTATTTA
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
44 39 0.41
45 56 0.59
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (44 bp):
TATAGCATAATTAATCAAATAATATTACCATATCATGCATATCG
Found at i:35691494 original size:30 final size:30
Alignment explanation
Indices: 35691458--35691563 Score: 117
Period size: 30 Copynumber: 3.6 Consensus size: 30
35691448 TTTATTGCAA
* *
35691458 TTTACTAAAGTTGAGGGCATTTTTCATAAT
1 TTTACTAAAGTTAAGGGCATTTATCATAAT
* ** *
35691488 TTTACTAAAATTAAGGGTGTTTATCGTAAT
1 TTTACTAAAGTTAAGGGCATTTATCATAAT
*
35691518 TTTACTAAATTTAAGGGCA-TTA-CTATAAT
1 TTTACTAAAGTTAAGGGCATTTATC-ATAAT
*
35691547 TTTACTAAAGTTGAGGG
1 TTTACTAAAGTTAAGGG
35691564 TGTTACTACA
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
28 1 0.02
29 22 0.35
30 40 0.63
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (30 bp):
TTTACTAAAGTTAAGGGCATTTATCATAAT
Found at i:35691511 original size:59 final size:59
Alignment explanation
Indices: 35691448--35691567 Score: 152
Period size: 59 Copynumber: 2.0 Consensus size: 59
35691438 GTATGAGGGC
* * **
35691448 TTTATTGCAA-TTTACTAAAGTTGAGGGCATTTTTCATAATTTTACTAAAATTAAGGGTG
1 TTTATCGCAATTTTACTAAAGTTAAGGGCATTACT-ATAATTTTACTAAAATTAAGGGTG
* * * *
35691507 TTTATCGTAATTTTACTAAATTTAAGGGCATTACTATAATTTTACTAAAGTTGAGGGTG
1 TTTATCGCAATTTTACTAAAGTTAAGGGCATTACTATAATTTTACTAAAATTAAGGGTG
35691566 TT
1 TT
35691568 ACTACAATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
59 32 0.62
60 20 0.38
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (59 bp):
TTTATCGCAATTTTACTAAAGTTAAGGGCATTACTATAATTTTACTAAAATTAAGGGTG
Found at i:35691569 original size:29 final size:29
Alignment explanation
Indices: 35691483--35691614 Score: 108
Period size: 29 Copynumber: 4.6 Consensus size: 29
35691473 GGCATTTTTC
*
35691483 ATAATTTTACTAAAATTAAGGGTGTTTA-T
1 ATAATTTTACTAAAGTTAAGGGTG-TTACT
* * **
35691512 CGTAATTTTACTAAATTTAAGGGCATTACT
1 -ATAATTTTACTAAAGTTAAGGGTGTTACT
*
35691542 ATAATTTTACTAAAGTTGAGGGTGTTACT
1 ATAATTTTACTAAAGTTAAGGGTGTTACT
* * * * * *
35691571 ACAATTTT-CCAAATTTAGGGGTGTGATT
1 ATAATTTTACTAAAGTTAAGGGTGTTACT
*
35691599 GTAATTTTAC-AAAGTT
1 ATAATTTTACTAAAGTT
35691615 TGGGGGCATG
Statistics
Matches: 81, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
28 25 0.31
29 35 0.43
30 21 0.26
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (29 bp):
ATAATTTTACTAAAGTTAAGGGTGTTACT
Found at i:35691604 original size:28 final size:30
Alignment explanation
Indices: 35691573--35691644 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 30
35691563 GTGTTACTAC
**
35691573 AATTTTCCAAA-TTTAGGGGTGTGATTGT-
1 AATTTTCCAAAGTTTAGGGGCATGATTGTA
* * *
35691601 AATTTTACAAAGTTTGGGGGCATGTTTGTA
1 AATTTTCCAAAGTTTAGGGGCATGATTGTA
35691631 AATTTTCCAAAGTT
1 AATTTTCCAAAGTT
35691645 GGCAAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 10 0.28
29 13 0.36
30 13 0.36
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (30 bp):
AATTTTCCAAAGTTTAGGGGCATGATTGTA
Found at i:35693645 original size:25 final size:25
Alignment explanation
Indices: 35693607--35693724 Score: 67
Period size: 25 Copynumber: 4.6 Consensus size: 25
35693597 TACCTTGGAT
**
35693607 TCTGGCTCAAAAGAGCGATATTATG
1 TCTGGCTCGTAAGAGCGATATTATG
*
35693632 TCTGGCTCGTAAGAGTGATACTCTGGAT-
1 TCTGGCTCGTAAGAGCGATA-T-T--ATG
* * * * *
35693660 TTTGGCTAGTAAGAGCGTTATTCTA
1 TCTGGCTCGTAAGAGCGATATTATG
** * *
35693685 TCTGGCTTATAAGAGCGATAATCTG
1 TCTGGCTCGTAAGAGCGATATTATG
*
35693710 TATGGGCTCGTAAGA
1 TCT-GGCTCGTAAGA
35693725 ACTAAACTCT
Statistics
Matches: 70, Mismatches: 17, Indels: 11
0.71 0.17 0.11
Matches are distributed among these distances:
24 1 0.01
25 38 0.54
26 11 0.16
27 2 0.03
28 16 0.23
29 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (25 bp):
TCTGGCTCGTAAGAGCGATATTATG
Found at i:35710034 original size:37 final size:38
Alignment explanation
Indices: 35709992--35710065 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 38
35709982 AATGTCGCTG
*
35709992 CATGAGCACTTCTAGATTACGCCC-AAAACTGTCGCCA
1 CATGAGCACTTCTAGATTACACCCAAAAACTGTCGCCA
* *
35710029 CATGAGCACTTGTAGATTGCACCCAAAAACTGTCGCC
1 CATGAGCACTTCTAGATTACACCCAAAAACTGTCGCC
35710066 GCAGGAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 21 0.64
38 12 0.36
ACGTcount: A:0.30, C:0.31, G:0.18, T:0.22
Consensus pattern (38 bp):
CATGAGCACTTCTAGATTACACCCAAAAACTGTCGCCA
Found at i:35710177 original size:37 final size:38
Alignment explanation
Indices: 35710096--35710181 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 38
35710086 CACCCAAGAC
* * *
35710096 TATCGCTGTATAAATATTCTTCAAATTACATCCAGAAC
1 TATCGCTGCATAAATATTCTTCAAATTACACCCAGAAA
* *
35710134 TATCGCTGCATAAGTATTCTTC-AATTGCACCCAGAAA
1 TATCGCTGCATAAATATTCTTCAAATTACACCCAGAAA
*
35710171 TGTCGCTGCAT
1 TATCGCTGCAT
35710182 GAACATGTAC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
37 22 0.52
38 20 0.48
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (38 bp):
TATCGCTGCATAAATATTCTTCAAATTACACCCAGAAA
Found at i:35710201 original size:26 final size:26
Alignment explanation
Indices: 35710165--35710224 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
35710155 CAATTGCACC
*
35710165 CAGAAATGTCGCTGCATGAACATGTA
1 CAGAATTGTCGCTGCATGAACATGTA
* *
35710191 CAGAATTGTCGCTGCATGAACGTGTC
1 CAGAATTGTCGCTGCATGAACATGTA
35710217 CAGAATTG
1 CAGAATTG
35710225 CACCCAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (26 bp):
CAGAATTGTCGCTGCATGAACATGTA
Found at i:35711045 original size:16 final size:16
Alignment explanation
Indices: 35711024--35711054 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35711014 TTGTGGATCC
35711024 CATTTTACCTTTATTA
1 CATTTTACCTTTATTA
*
35711040 CATTTTATCTTTATT
1 CATTTTACCTTTATT
35711055 TTCACATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
CATTTTACCTTTATTA
Found at i:35711426 original size:21 final size:21
Alignment explanation
Indices: 35711376--35711427 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
35711366 GGAGTTTTTA
*
35711376 GTATCGGTAGAAGCATGACAT
1 GTATCGGTAGAAGCATCACAT
* * *
35711397 GTTTTGGTAGAAGTC-TCACTT
1 GTATCGGTAGAAG-CATCACAT
35711418 GTATCGGTAG
1 GTATCGGTAG
35711428 TACTACCTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGCATCACAT
Found at i:35715869 original size:491 final size:491
Alignment explanation
Indices: 35714947--35716419 Score: 2919
Period size: 491 Copynumber: 3.0 Consensus size: 491
35714937 AATTAAACCA
35714947 CAAGGAATGTAGGTGGATGGTTAAGGGTATGATATATGTTAAATTTGTTTAATTTTAAGTAAGGA
1 CAAGGAATGTAGGTGGATGGTTAAGGGTATGATATATGTTAAATTTGTTTAATTTTAAGTAAGGA
35715012 TAAATACGTAAATTGATAATTTAATGATAATAATGGAAAATGACATGAATTAAGTCATCTTTTTC
66 TAAATACGTAAATTGATAATTTAATGATAATAATGGAAAATGACATGAATTAAGTCATCTTTTTC
35715077 ATCTCTTAAACAAAAAGAAAGAAAGGAAACCCTAAAAGAGGAGCTTTAAGTTTCGACCAAGCTAG
131 ATCTCTTAAACAAAAAGAAAGAAAGGAAACCCTAAAAGAGGAGCTTTAAGTTTCGACCAAGCTAG
35715142 GTTTAACCTTTGGTATGTGATTTTTCGTCCGTTTTTAGTAATTTCTATGTTTCTGAGTCAATATT
196 GTTTAACCTTTGGTATGTGATTTTTCGTCCGTTTTTAGTAATTTCTATGTTTCTGAGTCAATATT
35715207 AGTTTAATCTAGCTAACCCAAGGACTAATTTGTGAATTTGTAAAATATTATAAATTGTGCCATTA
261 AGTTTAATCTAGCTAACCCAAGGACTAATTTGTGAATTTGTAAAATATTATAAATTGTGCCATTA
*
35715272 TTCAATATGATTTTTCTTGAAAGTTTAAAGTGTATTTGTATGCTTGATGGTTGGGTTTAATGTTT
326 TTCAATATGCTTTTTCTTGAAAGTTTAAAGTGTATTTGTATGCTTGATGGTTGGGTTTAATGTTT
35715337 TTATAAAGTGATTTTTGATGAAATTAGGGTTTAAGGACTAAAGTGTTAAAATGATGAAATCGTGT
391 TTATAAAGTGATTTTTGATGAAATTAGGGTTTAAGGACTAAAGTGTTAAAATGATGAAATCGTGT
35715402 GTATTTAGTGTGAAATAATTGAATTGTAGGGACTTG
456 GTATTTAGTGTGAAATAATTGAATTGTAGGGACTTG
35715438 CAAGGAATGTAGGTGGATGGTTAAGGGTATGATATATGTTAAATTTGTTTAATTTTAAGTAAGGA
1 CAAGGAATGTAGGTGGATGGTTAAGGGTATGATATATGTTAAATTTGTTTAATTTTAAGTAAGGA
35715503 TAAATACGTAAATTGATAATTTAATGATAATAATGGAAAATGACATGAATTAAGTCATCTTTTTC
66 TAAATACGTAAATTGATAATTTAATGATAATAATGGAAAATGACATGAATTAAGTCATCTTTTTC
35715568 ATCTCTTAAACAAAAAGAAAGAAAGGAAACCCTAAAAGAGGAGCTTTAAGTTTCGACCAAGCTAG
131 ATCTCTTAAACAAAAAGAAAGAAAGGAAACCCTAAAAGAGGAGCTTTAAGTTTCGACCAAGCTAG
35715633 GTTTAACCTTTGGTATGTGATTTTTCGTCCGTTTTTAGTAATTTCTATGTTTCTGAGTCAATATT
196 GTTTAACCTTTGGTATGTGATTTTTCGTCCGTTTTTAGTAATTTCTATGTTTCTGAGTCAATATT
35715698 AGTTTAATCTAGCTAACCCAAGGACTAATTTGTGAATTTGTAAAATATTATAAATTGTGCCATTA
261 AGTTTAATCTAGCTAACCCAAGGACTAATTTGTGAATTTGTAAAATATTATAAATTGTGCCATTA
35715763 TTCAATATGCTTTTTCTTGAAAGTTTAAAGTGTATTTGTATGCTTGATGGTTGGGTTTAATGTTT
326 TTCAATATGCTTTTTCTTGAAAGTTTAAAGTGTATTTGTATGCTTGATGGTTGGGTTTAATGTTT
35715828 TTATAAAGTGATTTTTGATGAAATTAGGGTTTAAGGACTAAAGTGTTAAAATGATGAAATCGTGT
391 TTATAAAGTGATTTTTGATGAAATTAGGGTTTAAGGACTAAAGTGTTAAAATGATGAAATCGTGT
35715893 GTATTTAGTGTGAAATAATTGAATTGTAGGGACTTG
456 GTATTTAGTGTGAAATAATTGAATTGTAGGGACTTG
35715929 CAAGGAATGTAGGTGGATGGTTAAGGGTATGATATATGTTAAATTTGTTTAATTTTAAGTAAGGA
1 CAAGGAATGTAGGTGGATGGTTAAGGGTATGATATATGTTAAATTTGTTTAATTTTAAGTAAGGA
35715994 TAAATACGTAAATTGATAATTTAATGATAATAATGGAAAATGACATGAATTAAGTCATCTTTTTC
66 TAAATACGTAAATTGATAATTTAATGATAATAATGGAAAATGACATGAATTAAGTCATCTTTTTC
35716059 ATCTCTTAAACAAAAAGAAAGAAAGGAAACCCTAAAAGAGGAGCTTTAAGTTTCGACCAAGCTAG
131 ATCTCTTAAACAAAAAGAAAGAAAGGAAACCCTAAAAGAGGAGCTTTAAGTTTCGACCAAGCTAG
**
35716124 GTTTAACCTTTGGTATGTGATTTTTCGTCCGTTTTTAGTAATTTCTATGTTTCCAAGTCAATATT
196 GTTTAACCTTTGGTATGTGATTTTTCGTCCGTTTTTAGTAATTTCTATGTTTCTGAGTCAATATT
35716189 AGTTTAATCTAGCTAACCCAAGGACTAATTTGTGAATTTGTAAAATATTATAAATTGTGCCATTA
261 AGTTTAATCTAGCTAACCCAAGGACTAATTTGTGAATTTGTAAAATATTATAAATTGTGCCATTA
35716254 TTCAATATGCTTTTTCTTGAAAGTTTAAAGTGTATTTGTATGCTTGATGGTTGGGTTTAATGTTT
326 TTCAATATGCTTTTTCTTGAAAGTTTAAAGTGTATTTGTATGCTTGATGGTTGGGTTTAATGTTT
35716319 TTATAAAGTGATTTTTGATGAAATTAGGGTTTAAGGACTAAAGTGTTAAAATGATGAAATCGTGT
391 TTATAAAGTGATTTTTGATGAAATTAGGGTTTAAGGACTAAAGTGTTAAAATGATGAAATCGTGT
35716384 GTATTTAGTGTGAAATAATTGAATTGTAGGGACTTG
456 GTATTTAGTGTGAAATAATTGAATTGTAGGGACTTG
35716420 TTGAGGGCCA
Statistics
Matches: 979, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
491 979 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (491 bp):
CAAGGAATGTAGGTGGATGGTTAAGGGTATGATATATGTTAAATTTGTTTAATTTTAAGTAAGGA
TAAATACGTAAATTGATAATTTAATGATAATAATGGAAAATGACATGAATTAAGTCATCTTTTTC
ATCTCTTAAACAAAAAGAAAGAAAGGAAACCCTAAAAGAGGAGCTTTAAGTTTCGACCAAGCTAG
GTTTAACCTTTGGTATGTGATTTTTCGTCCGTTTTTAGTAATTTCTATGTTTCTGAGTCAATATT
AGTTTAATCTAGCTAACCCAAGGACTAATTTGTGAATTTGTAAAATATTATAAATTGTGCCATTA
TTCAATATGCTTTTTCTTGAAAGTTTAAAGTGTATTTGTATGCTTGATGGTTGGGTTTAATGTTT
TTATAAAGTGATTTTTGATGAAATTAGGGTTTAAGGACTAAAGTGTTAAAATGATGAAATCGTGT
GTATTTAGTGTGAAATAATTGAATTGTAGGGACTTG
Found at i:35716829 original size:25 final size:25
Alignment explanation
Indices: 35716800--35716932 Score: 110
Period size: 25 Copynumber: 5.2 Consensus size: 25
35716790 CCTTGGATTT
35716800 TGGCTCGAAAGAGCGATATTCTATC
1 TGGCTCGAAAGAGCGATATTCTATC
* * *
35716825 TGGCTCGAAAGAGCGATATTTTGTT
1 TGGCTCGAAAGAGCGATATTCTATC
* * *
35716850 TGGCTCGTAAGAGAGATATTCTATG
1 TGGCTCGAAAGAGCGATATTCTATC
* *
35716875 TGGCTC-ATAAGAGTGATACTCTAGATTC
1 TGGCTCGA-AAGAGCGATATTCT--A-TC
*
35716903 TGGCTTC-TAAGAGC-ATTATTCTATC
1 TGGC-TCGAAAGAGCGA-TATTCTATC
35716928 TGGCT
1 TGGCT
35716933 TGTAAGAGTG
Statistics
Matches: 87, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
24 1 0.01
25 66 0.76
26 1 0.01
27 2 0.02
28 15 0.17
29 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.34
Consensus pattern (25 bp):
TGGCTCGAAAGAGCGATATTCTATC
Found at i:35716862 original size:50 final size:50
Alignment explanation
Indices: 35716798--35716967 Score: 157
Period size: 50 Copynumber: 3.3 Consensus size: 50
35716788 TACCTTGGAT
* *
35716798 TTTGGCTCGAAAGAGCGATATTCTATCTGGCTCGAAAGAGCGATATTTTG
1 TTTGGCTCGTAAGAGCGATATTCTATCTGGCTCGAAAGAGTGATATTTTG
* * * *
35716848 TTTGGCTCGTAAGAGAGATATTCTATGTGGCTC-ATAAGAGTGATACTCTAG
1 TTTGGCTCGTAAGAGCGATATTCTATCTGGCTCGA-AAGAGTGATA-TTTTG
* * *
35716899 ATTCTGGCTTC-TAAGAGC-ATTATTCTATCTGGCTTGTAAGAGTGATAATTTG
1 -TT-TGGC-TCGTAAGAGCGA-TATTCTATCTGGCTCGAAAGAGTGATATTTTG
* *
35716951 TCTGGGCTCATAAGAGC
1 T-TTGGCTCGTAAGAGC
35716968 TAAACTCTGT
Statistics
Matches: 97, Mismatches: 14, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
49 1 0.01
50 41 0.42
51 14 0.14
52 6 0.06
53 33 0.34
54 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (50 bp):
TTTGGCTCGTAAGAGCGATATTCTATCTGGCTCGAAAGAGTGATATTTTG
Found at i:35718291 original size:34 final size:35
Alignment explanation
Indices: 35718224--35718295 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 35
35718214 TTTTTACCGT
* * *
35718224 TCAAGAATTTCAATTCATTCATATATTATAAACAA
1 TCAAGAATTTCAATTCATTCATAAATCAAAAACAA
*
35718259 TCAAGAATTT-AATTTATTCATAAATCAAAAACAA
1 TCAAGAATTTCAATTCATTCATAAATCAAAAACAA
35718293 TCA
1 TCA
35718296 CAAATTCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
34 23 0.70
35 10 0.30
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (35 bp):
TCAAGAATTTCAATTCATTCATAAATCAAAAACAA
Found at i:35719882 original size:45 final size:45
Alignment explanation
Indices: 35719831--35720237 Score: 591
Period size: 45 Copynumber: 9.1 Consensus size: 45
35719821 GGCAAAACGT
*
35719831 ATATCATGCATATTGTATAGCATAATCAATCAAATAATATTTACC
1 ATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACC
*
35719876 ATATCATGCATATCGTATAGCATAATCAATCGAATAATATTTACC
1 ATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACC
*
35719921 ATATCATGCATATCGTATAGCATAATTAATCAAATAATATTTACC
1 ATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACC
* * *
35719966 ATATCGTGCATATCGTATAGCACAATCAATCAAGTAATA-TTACC
1 ATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACC
* * *
35720010 ATATCATGCATATCGTATAACACAATCAATCAAATAATATCTACC
1 ATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACC
* * * **
35720055 ATATCATGCATATAGTATATCATAATTAATCAAATAATATTTGTC
1 ATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACC
35720100 ATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACC
1 ATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACC
* * *
35720145 ATATCATGCATATCGTACAACATAATCAATTAAATAATATTTACC
1 ATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACC
* * * * * * *
35720190 ATATCATGTATATTGTATATCATAATTAATCAATTAGTATTTAGC
1 ATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACC
35720235 ATA
1 ATA
35720238 ATCAAAAAAA
Statistics
Matches: 325, Mismatches: 36, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
44 41 0.13
45 284 0.87
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (45 bp):
ATATCATGCATATCGTATAGCATAATCAATCAAATAATATTTACC
Found at i:35720133 original size:179 final size:180
Alignment explanation
Indices: 35719831--35720222 Score: 597
Period size: 179 Copynumber: 2.2 Consensus size: 180
35719821 GGCAAAACGT
* * *
35719831 ATATCATGCATATTGTATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAG
1 ATATCATGCATATTGTATAACATAATCAATCAAATAATATCTACCATATCATGCATATAGTATAG
* *
35719896 CATAATCAATCGAATAATATTTACCATATCATGCATATCGTATAGCATAATTAATCAAATAATAT
66 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAATAATAT
* * * *
35719961 TTACCATATCGTGCATATCGTATAGCACAATCAATCAAGTAATA-TTACC
131 TTACCATATCATGCATATCGTACAACACAATCAATCAAATAATATTTACC
* * *
35720010 ATATCATGCATATCGTATAACACAATCAATCAAATAATATCTACCATATCATGCATATAGTATAT
1 ATATCATGCATATTGTATAACATAATCAATCAAATAATATCTACCATATCATGCATATAGTATAG
* **
35720075 CATAATTAATCAAATAATATTTGTCATATCATGCATATCGTATAGCATAATCAATCAAATAATAT
66 CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAATAATAT
* *
35720140 TTACCATATCATGCATATCGTACAACATAATCAATTAAATAATATTTACC
131 TTACCATATCATGCATATCGTACAACACAATCAATCAAATAATATTTACC
* * *
35720190 ATATCATGTATATTGTATATCATAATTAATCAA
1 ATATCATGCATATTGTATAACATAATCAATCAA
35720223 TTAGTATTTA
Statistics
Matches: 190, Mismatches: 22, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
179 157 0.83
180 33 0.17
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (180 bp):
ATATCATGCATATTGTATAACATAATCAATCAAATAATATCTACCATATCATGCATATAGTATAG
CATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAGCATAATCAATCAAATAATAT
TTACCATATCATGCATATCGTACAACACAATCAATCAAATAATATTTACC
Found at i:35730046 original size:17 final size:17
Alignment explanation
Indices: 35730026--35730078 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
35730016 GCTGTCATCA
35730026 CATTTCATTTGTCATTG
1 CATTTCATTTGTCATTG
* *
35730043 CATTT-TTCTTGTCACTG
1 CATTTCAT-TTGTCATTG
35730060 C--TTCA-TTGTCATTG
1 CATTTCATTTGTCATTG
35730074 CATTT
1 CATTT
35730079 TCATATATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
14 9 0.32
15 2 0.07
16 3 0.11
17 14 0.50
ACGTcount: A:0.15, C:0.21, G:0.11, T:0.53
Consensus pattern (17 bp):
CATTTCATTTGTCATTG
Found at i:35732889 original size:29 final size:30
Alignment explanation
Indices: 35732856--35732955 Score: 116
Period size: 29 Copynumber: 3.4 Consensus size: 30
35732846 TAGTTTTTCC
*
35732856 AAAGTATGAGGGC-TTTATTGCAA-TTTACT
1 AAAGT-TGAGGGCATTTATCGCAATTTTACT
*
35732885 AAAGTTGAGGGCATTTATCGTAATTTTACT
1 AAAGTTGAGGGCATTTATCGCAATTTTACT
* **
35732915 AAAGTTGAGGGTATTTA-CATAATTTTACT
1 AAAGTTGAGGGCATTTATCGCAATTTTACT
*
35732944 AAATTTGAGGGC
1 AAAGTTGAGGGC
35732956 GTTACTATAA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
28 7 0.11
29 34 0.54
30 22 0.35
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (30 bp):
AAAGTTGAGGGCATTTATCGCAATTTTACT
Found at i:35732915 original size:30 final size:28
Alignment explanation
Indices: 35732879--35732980 Score: 123
Period size: 29 Copynumber: 3.5 Consensus size: 28
35732869 TTTATTGCAA
*
35732879 TTTACTAAAGTTGAGGGCATTTATCGTAAT
1 TTTACTAAAGTTGAGGGC-TTTA-CATAAT
*
35732909 TTTACTAAAGTTGAGGGTATTTACATAAT
1 TTTACTAAAGTTGAGGG-CTTTACATAAT
* *
35732938 TTTACTAAATTTGAGGGCGTTACTATAAT
1 TTTACTAAAGTTGAGGGCTTTAC-ATAAT
*
35732967 TTTACTAAAATTGA
1 TTTACTAAAGTTGA
35732981 AGGTGTTACT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
28 4 0.06
29 39 0.61
30 21 0.33
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (28 bp):
TTTACTAAAGTTGAGGGCTTTACATAAT
Found at i:35732965 original size:29 final size:29
Alignment explanation
Indices: 35732879--35732998 Score: 118
Period size: 29 Copynumber: 4.1 Consensus size: 29
35732869 TTTATTGCAA
* *
35732879 TTTACTAAAGTTGAGGGCATTTA-TCGTAAT
1 TTTACTAAAGTTGAGGGC-GTTACT-ATAAT
**
35732909 TTTACTAAAGTTGAGGGTATTTAC-ATAAT
1 TTTACTAAAGTTGAGGG-CGTTACTATAAT
*
35732938 TTTACTAAATTTGAGGGCGTTACTATAAT
1 TTTACTAAAGTTGAGGGCGTTACTATAAT
* * * *
35732967 TTTACTAAAATTGAAGGTGTTACTACAAT
1 TTTACTAAAGTTGAGGGCGTTACTATAAT
35732996 TTT
1 TTT
35732999 TCAAAATTGG
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.05
29 53 0.68
30 21 0.27
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.42
Consensus pattern (29 bp):
TTTACTAAAGTTGAGGGCGTTACTATAAT
Found at i:35732997 original size:58 final size:59
Alignment explanation
Indices: 35732879--35732998 Score: 138
Period size: 58 Copynumber: 2.1 Consensus size: 59
35732869 TTTATTGCAA
* * * * * *
35732879 TTTACTAAAGTTGAGGGCATTTATCGTAATTTTACTAAAGTTGAGGGTATTTACATAAT
1 TTTACTAAAGTTGAGGGCAGTTATCATAATTTTACTAAAATTGAAGGTAGTTACACAAT
*
35732938 TTTACTAAATTTGAGGGC-GTTA-CTATAATTTTACTAAAATTGAAGGT-GTTACTACAAT
1 TTTACTAAAGTTGAGGGCAGTTATC-ATAATTTTACTAAAATTGAAGGTAGTTAC-ACAAT
35732996 TTT
1 TTT
35732999 TCAAAATTGG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
57 5 0.10
58 30 0.58
59 17 0.33
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.42
Consensus pattern (59 bp):
TTTACTAAAGTTGAGGGCAGTTATCATAATTTTACTAAAATTGAAGGTAGTTACACAAT
Found at i:35733941 original size:26 final size:26
Alignment explanation
Indices: 35733905--35733958 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
35733895 CAAACTCATA
35733905 AAAAATATTCTAAAGCAGCTTTGACC
1 AAAAATATTCTAAAGCAGCTTTGACC
* *
35733931 AAAAATATTCTGAAGTAGCTTTGACC
1 AAAAATATTCTAAAGCAGCTTTGACC
35733957 AA
1 AA
35733959 TTACATGAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.28
Consensus pattern (26 bp):
AAAAATATTCTAAAGCAGCTTTGACC
Found at i:35734156 original size:18 final size:20
Alignment explanation
Indices: 35734083--35734163 Score: 66
Period size: 19 Copynumber: 4.2 Consensus size: 20
35734073 TTAAGGTTAA
35734083 AAAAATCA-TAAAAACTTAT
1 AAAAATCATTAAAAACTTAT
** *
35734102 AAGTATTATTAAAAACTTA-
1 AAAAATCATTAAAAACTTAT
*
35734121 AGAAA-CATTAATAAA-TTAT
1 AAAAATCATTAA-AAACTTAT
35734140 AAAAATCA-TAAAAA-TTAT
1 AAAAATCATTAAAAACTTAT
35734158 ATAAAA
1 A-AAAA
35734164 AAAGTCATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
18 16 0.33
19 21 0.43
20 12 0.24
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAATCATTAAAAACTTAT
Found at i:35735766 original size:24 final size:25
Alignment explanation
Indices: 35735705--35735768 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
35735695 GTGGGTGTTG
*
35735705 AAGATGAAGAAG-AGAAAAGAGAAA
1 AAGAAGAAGAAGAAGAAAAGAGAAA
35735729 AAGAAGGAAG-AGAAGAAAAG-GAAA
1 AAGAA-GAAGAAGAAGAAAAGAGAAA
35735753 AAGAA-AATGAAGAAGA
1 AAGAAGAA-GAAGAAGA
35735769 TTTTGTACCG
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.06
23 1 0.03
24 21 0.60
25 11 0.31
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (25 bp):
AAGAAGAAGAAGAAGAAAAGAGAAA
Found at i:35738520 original size:20 final size:19
Alignment explanation
Indices: 35738493--35738574 Score: 89
Period size: 20 Copynumber: 4.4 Consensus size: 19
35738483 ATTATATTGT
*
35738493 TGTTTTGGTGCTATTTTTAC
1 TGTTTTGGTG-TGTTTTTAC
* *
35738513 TATTTTGGT-TGTTTTTGC
1 TGTTTTGGTGTGTTTTTAC
35738531 TGTTTTGGTGTTGTTTTTAC
1 TGTTTTGGTG-TGTTTTTAC
*
35738551 TGTTTTAGT-T-TTTTTAC
1 TGTTTTGGTGTGTTTTTAC
35738568 TGTTTTG
1 TGTTTTG
35738575 TTTGCTGGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
17 13 0.25
18 16 0.30
20 24 0.45
ACGTcount: A:0.07, C:0.06, G:0.21, T:0.66
Consensus pattern (19 bp):
TGTTTTGGTGTGTTTTTAC
Found at i:35738537 original size:38 final size:37
Alignment explanation
Indices: 35738493--35738574 Score: 110
Period size: 38 Copynumber: 2.2 Consensus size: 37
35738483 ATTATATTGT
* *
35738493 TGTTTTGGTGCTATTTTTACTATTTTGGTTGTTTTTGC
1 TGTTTTGGTGCTATTTTTACTATTTTAGTT-TTTTTAC
* * *
35738531 TGTTTTGGTGTTGTTTTTACTGTTTTAGTTTTTTTAC
1 TGTTTTGGTGCTATTTTTACTATTTTAGTTTTTTTAC
35738568 TGTTTTG
1 TGTTTTG
35738575 TTTGCTGGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
37 13 0.33
38 26 0.67
ACGTcount: A:0.07, C:0.06, G:0.21, T:0.66
Consensus pattern (37 bp):
TGTTTTGGTGCTATTTTTACTATTTTAGTTTTTTTAC
Found at i:35738721 original size:44 final size:44
Alignment explanation
Indices: 35738673--35738768 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
35738663 ATTTTTGTTA
* * *
35738673 TTATTTTTGTTGCTATTTTTATTGTT-TTTGTTGTTGTTTTGCTG
1 TTATTTTTGTTGCTATTTTGATTGTTATTT-TGGTTGTTTTGATG
* *
35738717 TTATTTTTGTTGCTGTTTTGGTTGTTATTTTGGTTGTTTTGATG
1 TTATTTTTGTTGCTATTTTGATTGTTATTTTGGTTGTTTTGATG
35738761 TTATTTTT
1 TTATTTTT
35738769 ATGCGTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 43 0.93
45 3 0.07
ACGTcount: A:0.07, C:0.03, G:0.20, T:0.70
Consensus pattern (44 bp):
TTATTTTTGTTGCTATTTTGATTGTTATTTTGGTTGTTTTGATG
Found at i:35738722 original size:32 final size:35
Alignment explanation
Indices: 35738677--35738748 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 35
35738667 TTGTTATTAT
* *
35738677 TTTTGTTGCTATTTTTATTG-T-TTTT-GTTGTTG
1 TTTTGCTGCTATTTTTATTGCTGTTTTGGTTGTTA
* *
35738709 TTTTGCTGTTATTTTTGTTGCTGTTTTGGTTGTTA
1 TTTTGCTGCTATTTTTATTGCTGTTTTGGTTGTTA
35738744 TTTTG
1 TTTTG
35738749 GTTGTTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 17 0.52
33 1 0.03
34 4 0.12
35 11 0.33
ACGTcount: A:0.06, C:0.04, G:0.21, T:0.69
Consensus pattern (35 bp):
TTTTGCTGCTATTTTTATTGCTGTTTTGGTTGTTA
Found at i:35738764 original size:20 final size:21
Alignment explanation
Indices: 35738698--35738767 Score: 70
Period size: 23 Copynumber: 3.2 Consensus size: 21
35738688 TTTTTATTGT
*
35738698 TTTTGTTGTTGTTTTGCTGTTA
1 TTTTG-TGTTGTTTTGATGTTA
* *
35738720 TTTTTGTTGCTGTTTTGGTTGTTA
1 -TTTTG-TGTTGTTTT-GATGTTA
35738744 TTTTG-GTTGTTTTGATGTTA
1 TTTTGTGTTGTTTTGATGTTA
35738764 TTTT
1 TTTT
35738768 TATGCGTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 10 0.24
21 7 0.17
23 19 0.45
24 6 0.14
ACGTcount: A:0.06, C:0.03, G:0.23, T:0.69
Consensus pattern (21 bp):
TTTTGTGTTGTTTTGATGTTA
Found at i:35738768 original size:12 final size:12
Alignment explanation
Indices: 35738644--35738754 Score: 95
Period size: 12 Copynumber: 9.6 Consensus size: 12
35738634 TTTCTGTTTC
*
35738644 TGTTGCTATTTT
1 TGTTGTTATTTT
*
35738656 TGCTGTTATTTT
1 TGTTGTTATTTT
*
35738668 TGTTATTATTTT
1 TGTTGTTATTTT
*
35738680 TGTTGCTATTTT
1 TGTTGTTATTTT
*
35738692 TATTG---TTTT
1 TGTTGTTATTTT
*
35738701 TGTTGTT-GTTT
1 TGTTGTTATTTT
*
35738712 TGCTGTTATTTT
1 TGTTGTTATTTT
* *
35738724 TGTTGCTGTTTT
1 TGTTGTTATTTT
*
35738736 GGTTGTTATTTT
1 TGTTGTTATTTT
*
35738748 GGTTGTT
1 TGTTGTT
35738755 TTGATGTTAT
Statistics
Matches: 79, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
9 8 0.10
11 9 0.11
12 62 0.78
ACGTcount: A:0.07, C:0.05, G:0.20, T:0.68
Consensus pattern (12 bp):
TGTTGTTATTTT
Found at i:35738776 original size:21 final size:21
Alignment explanation
Indices: 35738708--35738777 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 21
35738698 TTTTGTTGTT
* *
35738708 GTTTTGCTGTTATTTTTGTTGC
1 GTTTTGATGTTATTTTT-ATGC
* ** *
35738730 TGTTTTGGTTGTTATTTTGGT-T
1 -GTTTT-GATGTTATTTTTATGC
35738752 GTTTTGATGTTATTTTTATGC
1 GTTTTGATGTTATTTTTATGC
35738773 GTTTT
1 GTTTT
35738778 TACTATTGTT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
20 11 0.30
21 10 0.27
23 6 0.16
24 10 0.27
ACGTcount: A:0.07, C:0.04, G:0.23, T:0.66
Consensus pattern (21 bp):
GTTTTGATGTTATTTTTATGC
Found at i:35738965 original size:26 final size:27
Alignment explanation
Indices: 35738894--35738971 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 27
35738884 TTTTAATGTA
* *
35738894 TTTTAAATTTGTT-TATGTTTTAATAT
1 TTTTAAATTTGTTGTATATTATAATAT
*
35738920 TTTTAAGTGTAT-TTGATATATTAT-ATAT
1 TTTTAAAT-T-TGTTG-TATATTATAATAT
*
35738948 TTTTAAATTTGTTGTATATAATAA
1 TTTTAAATTTGTTGTATATTATAA
35738972 AATAATTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
26 15 0.37
27 8 0.20
28 12 0.29
29 6 0.15
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (27 bp):
TTTTAAATTTGTTGTATATTATAATAT
Found at i:35738966 original size:28 final size:27
Alignment explanation
Indices: 35738894--35738967 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
35738884 TTTTAATGTA
* *
35738894 TTTTAAATTTGTT-TATGTTTTAATAT
1 TTTTAAATTTGTTGTATATATTAATAT
*
35738920 TTTTAAGTGTAT-TTG-ATATATTATATAT
1 TTTTAAAT-T-TGTTGTATATATTA-ATAT
35738948 TTTTAAATTTGTTGTATATA
1 TTTTAAATTTGTTGTATATA
35738968 ATAAAATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
26 8 0.21
27 13 0.34
28 17 0.45
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (27 bp):
TTTTAAATTTGTTGTATATATTAATAT
Found at i:35740556 original size:28 final size:28
Alignment explanation
Indices: 35740491--35740559 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 28
35740481 CAAAAATTAT
35740491 AATTTTCTATAATTTATTATATTTTTAAG
1 AATTTT-TATAATTTATTATATTTTTAAG
* *
35740520 AATTGTTATAAGTTTTTTAT-TTTTTAA-
1 AATTTTTATAA-TTTATTATATTTTTAAG
35740547 ATATTTTTATAAT
1 A-ATTTTTATAAT
35740560 ATTCTTGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
27 2 0.06
28 21 0.60
29 12 0.34
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (28 bp):
AATTTTTATAATTTATTATATTTTTAAG
Found at i:35740556 original size:49 final size:49
Alignment explanation
Indices: 35740503--35740613 Score: 118
Period size: 49 Copynumber: 2.3 Consensus size: 49
35740493 TTTTCTATAA
* * *
35740503 TTTATTATATTTTTAAGAATTGTTATAAG-TT-TTTTATTTTTTAAATATT
1 TTTATTATATTTTT--GAATTGTTATAAGCTTATATAAATTTTTAAATATT
* * *
35740552 TTTATAATATTCTTGAATTTTTATAAGCTTATATAAATTTTTAAATATT
1 TTTATTATATTTTTGAATTGTTATAAGCTTATATAAATTTTTAAATATT
* *
35740601 TTTAATATGTTTT
1 TTTATTATATTTT
35740614 ATTATTTTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
47 12 0.24
48 2 0.04
49 36 0.72
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.60
Consensus pattern (49 bp):
TTTATTATATTTTTGAATTGTTATAAGCTTATATAAATTTTTAAATATT
Found at i:35740607 original size:9 final size:9
Alignment explanation
Indices: 35740588--35740641 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
35740578 GCTTATATAA
35740588 ATTTTTAAAT
1 ATTTTT-AAT
35740598 ATTTTTAAT
1 ATTTTTAAT
*
35740607 ATGTTTTATT
1 AT-TTTTAAT
35740617 ATTTTT-AT
1 ATTTTTAAT
*
35740625 AGTTTATAAT
1 A-TTTTTAAT
35740635 ATTTTTA
1 ATTTTTA
35740642 TAGGCTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
8 2 0.05
9 18 0.49
10 17 0.46
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:35740637 original size:18 final size:18
Alignment explanation
Indices: 35740591--35740644 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
35740581 TATATAAATT
35740591 TTTA-AATATTTTTAATATG
1 TTTATAATATTTTT-ATA-G
*
35740610 TTT-TATTATTTTTATAG
1 TTTATAATATTTTTATAG
35740627 TTTATAATATTTTTATAG
1 TTTATAATATTTTTATAG
35740645 GCTTTATGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 4 0.13
18 16 0.52
19 11 0.35
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
TTTATAATATTTTTATAG
Found at i:35740670 original size:20 final size:18
Alignment explanation
Indices: 35740647--35740698 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 18
35740637 TTTTATAGGC
35740647 TTTATGATTATTTTAGTATT
1 TTTATGATT-TTTTAGT-TT
* *
35740667 TTTATAAGTTTTTAAGTTT
1 TTTATGA-TTTTTTAGTTT
*
35740686 TTTGTGATTTTTT
1 TTTATGATTTTTT
35740699 TAGCACGTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 5 0.19
19 7 0.27
20 12 0.46
21 2 0.08
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.67
Consensus pattern (18 bp):
TTTATGATTTTTTAGTTT
Found at i:35740743 original size:16 final size:16
Alignment explanation
Indices: 35740724--35740759 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
35740714 ACTGGAATTG
35740724 AATAGGACTGTAATGA
1 AATAGGACTGTAATGA
* *
35740740 AATAGGATTGTAATGG
1 AATAGGACTGTAATGA
35740756 AATA
1 AATA
35740760 AAGCTGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (16 bp):
AATAGGACTGTAATGA
Found at i:35741051 original size:15 final size:16
Alignment explanation
Indices: 35741031--35741063 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
35741021 ATTTAATAAC
35741031 ATTATT-AATATAATT
1 ATTATTAAATATAATT
35741046 ATTATTAAAATATAATT
1 ATTATT-AAATATAATT
35741063 A
1 A
35741064 ATAAAAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTATTAAATATAATT
Done.