Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005291.1 Hibiscus syriacus cultivar Beakdansim tig00011967_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: 110690
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:5020 original size:20 final size:23
Alignment explanation
Indices: 4973--5016 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
4963 TTTTTATTAT
4973 TATTATTATAATTAAATAAAATA
1 TATTATTATAATTAAATAAAATA
*
4996 TATTATTATTATTAAATAAAA
1 TATTATTATAATTAAATAAAA
5017 ATTACAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATTATAATTAAATAAAATA
Found at i:6455 original size:24 final size:24
Alignment explanation
Indices: 6403--6477 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 24
6393 TATTACCTTT
*
6403 TTTATTTAT-TTTAGTCATTGTT-TA
1 TTTATTTATATTTA-T-ATTATTATA
6427 TTTATTTATATTTATATT-TTATA
1 TTTATTTATATTTATATTATTATA
*
6450 TGTTA--TATATTTA-ATTATTATT
1 T-TTATTTATATTTATATTATTATA
6472 TTTATT
1 TTTATT
6478 ATTATTATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
21 6 0.14
22 15 0.34
23 6 0.14
24 13 0.30
25 4 0.09
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (24 bp):
TTTATTTATATTTATATTATTATA
Found at i:6835 original size:134 final size:134
Alignment explanation
Indices: 6593--6954 Score: 565
Period size: 133 Copynumber: 2.7 Consensus size: 134
6583 TAATCATATT
6593 TTAA-ATTTATTTATTTTTTTAATATTAAGAAAT-GAGCTGTCTTAAAGCACCTAGAAGTCCTTT
1 TTAATATTTATTTA--TTTTTAATATTAAGAAATAG-GCTGTCTTAAAGCACCTAGAAGTCCTTT
6656 TCCGATA-TCTTAAATAAATAAATATCCTATTTTTATAATTTATATATAATTATTTT-ATAGAAA
63 TCCGATATTCTTAAATAAATAAATATCCTATTTTTATAATTTATATATAATTATTTTAATAGAAA
6719 TGTTTTA
128 TGTTTTA
6726 TTAATATTTATTTATTTATTAATATTAAGAAATAGGCTGTCTTAAAGCACCTAGAAGTCCTTTTC
1 TTAATATTTATTTATTT-TTAATATTAAGAAATAGGCTGTCTTAAAGCACCTAGAAGTCCTTTTC
6791 CGATATTCTTAAATAAATAAATATCCTATTTTTATAATTTATATATAATTATTTTAATAGAAATG
65 CGATATTCTTAAATAAATAAATATCCTATTTTTATAATTTATATATAATTATTTTAATAGAAATG
6856 TTTTA
130 TTTTA
* * * **
6861 TTAATATTTATTTATTTTTAATA-TAAGAAATAGACTGTCTTAAAGCACCTAAAAGTCATTTTTT
1 TTAATATTTATTTATTTTTAATATTAAGAAATAGGCTGTCTTAAAGCACCTAGAAGTCCTTTTCC
* * *
6925 GATATT-TCTAAGTAAATAAATGTCTTATTT
66 GATATTCT-TAAATAAATAAATATCCTATTT
6955 ATAAAAATAA
Statistics
Matches: 215, Mismatches: 8, Indels: 12
0.91 0.03 0.05
Matches are distributed among these distances:
132 4 0.02
133 115 0.53
134 65 0.30
135 31 0.14
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (134 bp):
TTAATATTTATTTATTTTTAATATTAAGAAATAGGCTGTCTTAAAGCACCTAGAAGTCCTTTTCC
GATATTCTTAAATAAATAAATATCCTATTTTTATAATTTATATATAATTATTTTAATAGAAATGT
TTTA
Found at i:8878 original size:17 final size:16
Alignment explanation
Indices: 8850--8884 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
8840 ATAAATAAAT
*
8850 ATAAAATTAAAATTTA
1 ATAAAATTAAAATGTA
8866 ATAAAATTAAAAATGTA
1 ATAAAATT-AAAATGTA
8883 AT
1 AT
8885 GATATAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
ATAAAATTAAAATGTA
Found at i:11297 original size:31 final size:31
Alignment explanation
Indices: 11259--11330 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
11249 ACTTTTAAAA
* * *
11259 TTTGTAATATAATCTCTCAATATTTAGTCTG
1 TTTGTAATATAATCTCTCAACATTTAATCCG
**
11290 TTTGTAATATGGTCTCTCAACATTTAATCCG
1 TTTGTAATATAATCTCTCAACATTTAATCCG
*
11321 TTTGCAATAT
1 TTTGTAATAT
11331 GGTCTCTGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (31 bp):
TTTGTAATATAATCTCTCAACATTTAATCCG
Found at i:11331 original size:31 final size:31
Alignment explanation
Indices: 11271--11337 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
11261 TGTAATATAA
* * * *
11271 TCTCTCAATATTTAGTCTGTTTGTAATATGG
1 TCTCTCAACATTTAATCCGTTTGCAATATGG
11302 TCTCTCAACATTTAATCCGTTTGCAATATGG
1 TCTCTCAACATTTAATCCGTTTGCAATATGG
11333 TCTCT
1 TCTCT
11338 GACGTAACTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.45
Consensus pattern (31 bp):
TCTCTCAACATTTAATCCGTTTGCAATATGG
Found at i:13780 original size:2 final size:2
Alignment explanation
Indices: 13773--13800 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13763 GCATGCATAA
13773 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
13801 TCTCAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14785 original size:21 final size:21
Alignment explanation
Indices: 14760--14803 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
14750 AAAATGTTAA
* *
14760 AAAAACATTGATGTTTTAAAT
1 AAAAACAATAATGTTTTAAAT
* *
14781 AAAAATAATAATTTTTTAAAT
1 AAAAACAATAATGTTTTAAAT
14802 AA
1 AA
14804 TTTTTTATCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (21 bp):
AAAAACAATAATGTTTTAAAT
Found at i:15532 original size:20 final size:19
Alignment explanation
Indices: 15503--15597 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 19
15493 CTATTCTCTT
* *
15503 GTAATCTTACATTTACATTG
1 GTAATTTTACATTT-CACTG
*
15523 GTAATTTTACATTTCTATTG
1 GTAATTTTACATTTC-ACTG
* *
15543 GTAATCTTACATTTATACTG
1 GTAATTTTACATTT-CACTG
*
15563 ATAATCTTATA-ATTTCACTG
1 GTAAT-TT-TACATTTCACTG
*
15583 ATAATTTTACATTTC
1 GTAATTTTACATTTC
15598 GTAAACCAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
18 2 0.03
19 8 0.13
20 46 0.73
21 5 0.08
22 2 0.03
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (19 bp):
GTAATTTTACATTTCACTG
Found at i:17666 original size:89 final size:91
Alignment explanation
Indices: 17557--17761 Score: 308
Period size: 91 Copynumber: 2.3 Consensus size: 91
17547 AAGGAAAAAT
* * **
17557 AATTTATTTGAAAATTATTAATCGAACGAAATTAACCG-A-TTTTTTTAACATTAATCGAACTGA
1 AATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTTAACATTAATCGAACCAA
17620 AATTATTTAACCGTTAATT-GAACCGA
66 AATTATTTAACCGTT-ATTCGAACCGA
*
17646 AATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTTAACATTAATCGAGCCAA
1 AATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTTAACATTAATCGAACCAA
* *
17711 AATTATTTGACCGTTATTCGAACTGA
66 AATTATTTAACCGTTATTCGAACCGA
*
17737 AATTTATTTGAAAATCATTAACCGA
1 AATTTATTTGAAAATTATTAACCGA
17762 TTTTTTTCTT
Statistics
Matches: 105, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
89 36 0.34
90 4 0.04
91 65 0.62
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.37
Consensus pattern (91 bp):
AATTTATTTGAAAATTATTAACCGAACCAAATTAACCGAATTTTTTTTAACATTAATCGAACCAA
AATTATTTAACCGTTATTCGAACCGA
Found at i:17824 original size:80 final size:77
Alignment explanation
Indices: 17676--17824 Score: 199
Period size: 80 Copynumber: 1.9 Consensus size: 77
17666 ACCGAACCAA
* * ** *
17676 ATTAACCGAATTTTTTTTAACATTAATCGAGCCAAAATTATTTGACCGTTATTCGAACTGAAATT
1 ATTAACCGAATTTTTTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCCAAAAT
17741 TATTTGAAAATC
66 TATTTGAAAATC
* * *
17753 ATTAACCGATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACTGTTAATCGCACCCAA
1 ATTAACCGA-ATTTTT-TTTAA-CATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCCAA
17818 AATTATT
63 AATTATT
17825 AACCGAATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
77 9 0.15
78 5 0.08
79 5 0.08
80 42 0.69
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.39
Consensus pattern (77 bp):
ATTAACCGAATTTTTTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCCAAAAT
TATTTGAAAATC
Found at i:17894 original size:66 final size:66
Alignment explanation
Indices: 17816--17949 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 66
17806 AATCGCACCC
* * *
17816 AAAATTATTAACCGAATAAAAT-AA-ATTATTTTTTCTTTAACCGTTAATCGAACCGAAATTTAT
1 AAAATTATTAACCGAACAAAATCAACAAT-TTTTTTCTTTAACCATTAATCGAACCGAAA-TTAT
17879 TTG
64 TTG
*
17882 AAAATTATTAACCGAACCAAATCAACCAATTTTTTTCTTTAACCATTAATCGAACCGAAATTATT
1 AAAATTATTAACCGAACAAAATCAA-CAATTTTTTTCTTTAACCATTAATCGAACCGAAATTATT
17947 TG
65 TG
17949 A
1 A
17950 CCGTTAATAG
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
66 20 0.33
67 10 0.16
68 29 0.48
69 2 0.03
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.37
Consensus pattern (66 bp):
AAAATTATTAACCGAACAAAATCAACAATTTTTTTCTTTAACCATTAATCGAACCGAAATTATTT
G
Found at i:17930 original size:149 final size:151
Alignment explanation
Indices: 17756--18095 Score: 452
Period size: 159 Copynumber: 2.2 Consensus size: 151
17746 GAAAATCATT
* *
17756 AACCGATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACTGTTAATCG-C-A-CCCAA
1 AACCGATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATAGACAATCCCAA
*
17818 AATTATTAACCGAATAAAATAAATTATTTTTTCTTTAACCGTTAATCGAACCGAAATTTATTTGA
66 AATTATTAACCGAATAAAATAAATTATTTTTTC-TTAACCGTTAATCGAACCAAAATTTATTTGA
17883 AAATTATTAACCGAACCAAATC
130 AAATTATTAACCGAACCAAATC
* *
17905 AACCAATTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACCGTTAATAGAATCAAAATT
1 AACCGATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATAG-A-C---A--
*** * *
17970 TATTTTAAAATTATTAACCTAATAAAATATATTATTTTTTCTTAACCGTTAATCGAACCAAAATT
59 -ATCCCAAAATTATTAACCGAATAAAATAAATTATTTTTTCTTAACCGTTAATCGAACCAAAATT
* * *
18035 TATTTGAAAATTATTAACCGAATCGAATT
123 TATTTGAAAATTATTAACCGAACCAAATC
*
18064 AACCGATTTTTTTCTGTAACCATTAATCGAAC
1 AACCGATTTTTTTCTTTAACCATTAATCGAAC
18096 TGAAATTTAT
Statistics
Matches: 165, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
149 51 0.31
152 1 0.01
159 80 0.48
160 33 0.20
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.38
Consensus pattern (151 bp):
AACCGATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATAGACAATCCCAA
AATTATTAACCGAATAAAATAAATTATTTTTTCTTAACCGTTAATCGAACCAAAATTTATTTGAA
AATTATTAACCGAACCAAATC
Found at i:17982 original size:160 final size:160
Alignment explanation
Indices: 17816--18107 Score: 487
Period size: 159 Copynumber: 1.8 Consensus size: 160
17806 AATCGCACCC
*
17816 AAAATTATTAACCGAATAAAATAAATTATTTTTTCTTTAACCGTTAATCGAACCGAAATTTATTT
1 AAAATTATTAACCGAATAAAATAAATTATTTTTTC-TTAACCGTTAATCGAACCAAAATTTATTT
*
17881 GAAAATTATTAACCGAACCAAATCAACCAATTTTTTTCTTTAACCATTAATCGAACCGAAA-TTA
65 GAAAATTATTAACCGAACCAAATCAACCAATTTTTTTCTGTAACCATTAATCGAACCGAAATTTA
17945 TTTGACCGTTAATAGAATCAAAATTTATTTT
130 TTTGACCGTTAATAGAATCAAAATTTATTTT
* *
17976 AAAATTATTAACCTAATAAAATATATTATTTTTTCTTAACCGTTAATCGAACCAAAATTTATTTG
1 AAAATTATTAACCGAATAAAATAAATTATTTTTTCTTAACCGTTAATCGAACCAAAATTTATTTG
* * * * *
18041 AAAATTATTAACCGAATCGAATTAACCGATTTTTTTCTGTAACCATTAATCGAACTGAAATTTAT
66 AAAATTATTAACCGAACCAAATCAACCAATTTTTTTCTGTAACCATTAATCGAACCGAAATTTAT
18106 TT
131 TT
18108 AACCAAATAA
Statistics
Matches: 122, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
159 83 0.68
160 39 0.32
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (160 bp):
AAAATTATTAACCGAATAAAATAAATTATTTTTTCTTAACCGTTAATCGAACCAAAATTTATTTG
AAAATTATTAACCGAACCAAATCAACCAATTTTTTTCTGTAACCATTAATCGAACCGAAATTTAT
TTGACCGTTAATAGAATCAAAATTTATTTT
Found at i:18074 original size:65 final size:66
Alignment explanation
Indices: 17949--18107 Score: 178
Period size: 65 Copynumber: 2.4 Consensus size: 66
17939 AAATTATTTG
* * * * **
17949 ACCGTTAATAGAATCAAAATTTATTTTAAAATTATTAACCTAATAAAATATATTATTTTTTCT-T
1 ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAATAAAATATACGATTTTTTCTGT
18013 A
66 A
**
18014 ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAATCGAAT-TAACCGATTTTTTTC
1 ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAATAAAATAT-A-CGA-TTTTTTC
18078 TGTA
63 TGTA
* **
18082 ACCATTAATCGAACTGAAATTTATTT
1 ACCGTTAATCGAACCAAAATTTATTT
18108 AACCAAATAA
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 1 0.01
65 44 0.56
66 1 0.01
67 8 0.10
68 25 0.32
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (66 bp):
ACCGTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAATAAAATATACGATTTTTTCTGT
A
Found at i:19522 original size:73 final size:74
Alignment explanation
Indices: 19403--19539 Score: 215
Period size: 73 Copynumber: 1.9 Consensus size: 74
19393 ATGCTATCAT
*
19403 CAGTGGGCAGGGTTCAAGCCCTGTGCAACCCATCCCCTTCCCCCAAATTCGTAGTGAC-AAAAAT
1 CAGTGGCCAGGGTTCAAGCCCTGTGCAACCCATCCCCTTCCCCCAAATTCGTAGTGACGAAAAAT
19467 ACCTACCAC
66 ACCTACCAC
* * *
19476 CAGTGGCCAGGTTTCAAGGCCC-GTGCAACCCATCCCCTTCCCCCAAATTTGTATTGACGAAAAA
1 CAGTGGCCAGGGTTCAA-GCCCTGTGCAACCCATCCCCTTCCCCCAAATTCGTAGTGACGAAAAA
19540 ATGTAATGTC
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
73 49 0.84
74 9 0.16
ACGTcount: A:0.27, C:0.34, G:0.18, T:0.20
Consensus pattern (74 bp):
CAGTGGCCAGGGTTCAAGCCCTGTGCAACCCATCCCCTTCCCCCAAATTCGTAGTGACGAAAAAT
ACCTACCAC
Found at i:26967 original size:22 final size:22
Alignment explanation
Indices: 26942--26996 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
26932 TCAGGAGTTA
* *
26942 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
26964 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
26986 CAGGAGTTATA
1 CAGGAGTTATA
26997 ACAACTGAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:32241 original size:5 final size:5
Alignment explanation
Indices: 32232--32265 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
32222 CTCGTCTTGT
* *
32232 CTCGG CTCGG CTAGG CACGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
32266 TGGTCGTGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.06, C:0.38, G:0.38, T:0.18
Consensus pattern (5 bp):
CTCGG
Found at i:32589 original size:22 final size:22
Alignment explanation
Indices: 32564--32613 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
32554 TCATGAGGTA
** *
32564 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTACATGATATAATTC
* *
32586 CAGGGGTTACATGATATAATTT
1 CAGGAGTTACATGATATAATTC
32608 CAGGAG
1 CAGGAG
32614 AAATAATAGC
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.10, G:0.24, T:0.36
Consensus pattern (22 bp):
CAGGAGTTACATGATATAATTC
Found at i:40132 original size:18 final size:19
Alignment explanation
Indices: 40109--40147 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
40099 TTATTTTTTA
40109 TATTTTTA-TTTAAAAATT
1 TATTTTTACTTTAAAAATT
40127 TATTTTTATCTTTAAAAATT
1 TATTTTTA-CTTTAAAAATT
40147 T
1 T
40148 TACAAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
20 11 0.58
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTTACTTTAAAAATT
Found at i:41671 original size:16 final size:16
Alignment explanation
Indices: 41650--41693 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
41640 ATGAAACTAC
*
41650 GTATGTGTGCATGTGT
1 GTATGTGTGCATGTAT
*
41666 GTATGTGTGTATGTAT
1 GTATGTGTGCATGTAT
*
41682 GTATGTATGCAT
1 GTATGTGTGCAT
41694 ATGATTGCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.18, C:0.05, G:0.32, T:0.45
Consensus pattern (16 bp):
GTATGTGTGCATGTAT
Found at i:41690 original size:8 final size:8
Alignment explanation
Indices: 41650--41687 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
41640 ATGAAACTAC
41650 GTATGTGT
1 GTATGTGT
*
41658 GCATGTGT
1 GTATGTGT
41666 GTATGTGT
1 GTATGTGT
*
41674 GTATGTAT
1 GTATGTGT
41682 GTATGT
1 GTATGT
41688 ATGCATATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.16, C:0.03, G:0.34, T:0.47
Consensus pattern (8 bp):
GTATGTGT
Found at i:44456 original size:2 final size:2
Alignment explanation
Indices: 44449--44476 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44439 TAAACAAATG
44449 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
44477 TTGGGGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47024 original size:43 final size:43
Alignment explanation
Indices: 46971--47316 Score: 424
Period size: 43 Copynumber: 8.1 Consensus size: 43
46961 TCGAGACATA
* * * *
46971 TAGCGGCGTTTTTCTTTACAAATGCCGCTATTGATTGTGTAAT
1 TAGCGGCGTTTTTCTTTACAAACGCTGCTATTGACTGTGTATT
* * * *
47014 TAGCGTCGTTTGTCTTTACAAACGTTGCTATTGACTGTATATT
1 TAGCGGCGTTTTTCTTTACAAACGCTGCTATTGACTGTGTATT
* *
47057 TAGCGGCATTTTTCTTTACAAACGCCGCTATTGACTGTGTATT
1 TAGCGGCGTTTTTCTTTACAAACGCTGCTATTGACTGTGTATT
* * * * *
47100 TAGCTGCATTTATCTTTACTAACGCTGCTATTAACTGTGTATT
1 TAGCGGCGTTTTTCTTTACAAACGCTGCTATTGACTGTGTATT
* * * * *
47143 TAACGGC-ATTGTCTTTACAAATGCCGCTATTGACTGTGTATT
1 TAGCGGCGTTTTTCTTTACAAACGCTGCTATTGACTGTGTATT
*
47185 TAGCGGCGTTTTTCTTTACAAATGCTGCTATTGACTGTGTATT
1 TAGCGGCGTTTTTCTTTACAAACGCTGCTATTGACTGTGTATT
* * * * *
47228 TAGTGGCGTTTGTCTTTATAAACACTACTATTGACTGTGTATT
1 TAGCGGCGTTTTTCTTTACAAACGCTGCTATTGACTGTGTATT
* **
47271 TAGCGGTGTTTTTCTTTACAAACATTGCTATTGACTGTGTATT
1 TAGCGGCGTTTTTCTTTACAAACGCTGCTATTGACTGTGTATT
47314 TAG
1 TAG
47317 TGACATTTTT
Statistics
Matches: 259, Mismatches: 43, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
42 35 0.14
43 224 0.86
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (43 bp):
TAGCGGCGTTTTTCTTTACAAACGCTGCTATTGACTGTGTATT
Found at i:47174 original size:128 final size:129
Alignment explanation
Indices: 47023--47326 Score: 398
Period size: 128 Copynumber: 2.4 Consensus size: 129
47013 TTAGCGTCGT
*
47023 TTGTCTTTACAAACGTTGCTATTGACTGTATATTTAGCGGCATTTTTCTTTACAAACGCCGCTAT
1 TTGTCTTTACAAACGTTGCTATTGACTGTGTATTTAGCGGCATTTTTCTTTACAAACGCCGCTAT
* *
47088 TGACTGTGTATTTAGCT-GCATTTATCTTTACT-AACGCTGCTATTAACTGTGTATTTAACGG-C
66 TGACTGTGTATTTAG-TGGCATTTATCTTTA-TAAACACTACTATTAACTGTGTATTTAACGGTC
47150 A
129 A
* ** * * *
47151 TTGTCTTTACAAATGCCGCTATTGACTGTGTATTTAGCGGCGTTTTTCTTTACAAATGCTGCTAT
1 TTGTCTTTACAAACGTTGCTATTGACTGTGTATTTAGCGGCATTTTTCTTTACAAACGCCGCTAT
* * * * **
47216 TGACTGTGTATTTAGTGGCGTTTGTCTTTATAAACACTACTATTGACTGTGTATTTAGCGGTGT
66 TGACTGTGTATTTAGTGGCATTTATCTTTATAAACACTACTATTAACTGTGTATTTAACGGTCA
* * * *
47280 TTTTCTTTACAAACATTGCTATTGACTGTGTATTTAGTGACATTTTT
1 TTGTCTTTACAAACGTTGCTATTGACTGTGTATTTAGCGGCATTTTT
47327 AATTAAAAAT
Statistics
Matches: 150, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
127 2 0.01
128 109 0.73
129 39 0.26
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (129 bp):
TTGTCTTTACAAACGTTGCTATTGACTGTGTATTTAGCGGCATTTTTCTTTACAAACGCCGCTAT
TGACTGTGTATTTAGTGGCATTTATCTTTATAAACACTACTATTAACTGTGTATTTAACGGTCA
Found at i:47268 original size:171 final size:171
Alignment explanation
Indices: 46983--47315 Score: 468
Period size: 171 Copynumber: 1.9 Consensus size: 171
46973 GCGGCGTTTT
* * *
46983 TCTTTACAAATGCCGCTATTGATTGTGTAATTAGCGTCGTTTGTCTTTACAAACGTTGCTATTGA
1 TCTTTACAAATGCCGCTATTGACTGTGTAATTAGCGGCGTTTGTCTTTACAAACGCTGCTATTGA
* * * *
47048 CTGTATATTTAGCGGCATTTTTCTTTACAAACGCCGCTATTGACTGTGTATTTAGCTGCATTTAT
66 CTGTATATTTAGCGGCATTTGTCTTTACAAACACCACTATTGACTGTGTATTTAGCGGCATTTAT
* *
47113 CTTTACTAACGCTGCTATTAACTGTGTATTTAACGGCATTG
131 CTTTACAAACACTGCTATTAACTGTGTATTTAACGGCATTG
* * *
47154 TCTTTACAAATGCCGCTATTGACTGTGTATTTAGCGGCGTTTTTCTTTACAAATGCTGCTATTGA
1 TCTTTACAAATGCCGCTATTGACTGTGTAATTAGCGGCGTTTGTCTTTACAAACGCTGCTATTGA
* * * * * ** *
47219 CTGTGTATTTAGTGGCGTTTGTCTTTATAAACACTACTATTGACTGTGTATTTAGCGGTGTTTTT
66 CTGTATATTTAGCGGCATTTGTCTTTACAAACACCACTATTGACTGTGTATTTAGCGGCATTTAT
* *
47284 CTTTACAAACATTGCTATTGACTGTGTATTTA
131 CTTTACAAACACTGCTATTAACTGTGTATTTA
47316 GTGACATTTT
Statistics
Matches: 140, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
171 140 1.00
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (171 bp):
TCTTTACAAATGCCGCTATTGACTGTGTAATTAGCGGCGTTTGTCTTTACAAACGCTGCTATTGA
CTGTATATTTAGCGGCATTTGTCTTTACAAACACCACTATTGACTGTGTATTTAGCGGCATTTAT
CTTTACAAACACTGCTATTAACTGTGTATTTAACGGCATTG
Found at i:50979 original size:26 final size:27
Alignment explanation
Indices: 50943--51005 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 27
50933 CTTCTGTTGG
50943 GAATGAAAAAATACGTGAAAT-GGAAA
1 GAATGAAAAAATACGTGAAATGGGAAA
*
50969 GAATGAAAAAATACGTGAAATGGGGAA
1 GAATGAAAAAATACGTGAAATGGGAAA
50996 GAATGAAAAA
1 GAATGAAAAA
51006 GGGTTAAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 21 0.60
27 14 0.40
ACGTcount: A:0.57, C:0.03, G:0.25, T:0.14
Consensus pattern (27 bp):
GAATGAAAAAATACGTGAAATGGGAAA
Found at i:51101 original size:41 final size:40
Alignment explanation
Indices: 51044--51265 Score: 189
Period size: 41 Copynumber: 5.5 Consensus size: 40
51034 GGTAAACTTC
* ** *
51044 CACTAAAGTATGAGTCTATAATGGTGTTTGTATAAAAACGA
1 CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAA-GA
* *
51085 CACTAAAGTACGAGTCT-TCAGTGGCGTTTATATAAAAA-A
1 CACTAAAGTACGAGTCTAT-AGCGGCGTTTGTATAAAAAGA
* * *
51124 CCACTAAAGTACGAATATATAGCGGCGTTTGTATAAAAATA
1 -CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAAGA
* * * * * *
51165 CCATTAAAGTATGAGTCTTTAGCGACGTTTATATAAAAACAA
1 -CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAA-GA
* * * *
51207 CACTAAAGTACAAATATATAGCGGCGTTTGTATAAAAAGC
1 CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAAGA
* *
51247 CACT-AAGTATGATTCTATA
1 CACTAAAGTACGAGTCTATA
51266 AAACGTTATT
Statistics
Matches: 146, Mismatches: 30, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
39 12 0.08
40 37 0.25
41 96 0.66
42 1 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (40 bp):
CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAAGA
Found at i:51181 original size:81 final size:82
Alignment explanation
Indices: 51069--51252 Score: 257
Period size: 81 Copynumber: 2.3 Consensus size: 82
51059 CTATAATGGT
* * *
51069 GTTTGTATAAAAACGACACTAAAGTACGAGTCTTCAGTGGCGTTTATATAAAAA-ACCACTAAAG
1 GTTTGTATAAAAACGACACTAAAGTACGAGTCTTCAGCGACGTTTATATAAAAACAACACTAAAG
*
51133 TACGAATATATAGCGGC
66 TACAAATATATAGCGGC
* * * *
51150 GTTTGTATAAAAA-TACCATTAAAGTATGAGTCTTTAGCGACGTTTATATAAAAACAACACTAAA
1 GTTTGTATAAAAACGA-CACTAAAGTACGAGTCTTCAGCGACGTTTATATAAAAACAACACTAAA
51214 GTACAAATATATAGCGGC
65 GTACAAATATATAGCGGC
*
51232 GTTTGTATAAAAA-GCCACTAA
1 GTTTGTATAAAAACGACACTAA
51253 GTATGATTCT
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
80 1 0.01
81 51 0.57
82 38 0.42
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (82 bp):
GTTTGTATAAAAACGACACTAAAGTACGAGTCTTCAGCGACGTTTATATAAAAACAACACTAAAG
TACAAATATATAGCGGC
Found at i:51320 original size:41 final size:41
Alignment explanation
Indices: 51273--51370 Score: 106
Period size: 41 Copynumber: 2.4 Consensus size: 41
51263 ATAAAACGTT
* *
51273 ATTAAAGTACGAGTCTATAATAACGTTTGTATAAAAAAACC
1 ATTAAAGTACGAGTCTATAACAACGTTTATATAAAAAAACC
* * * * **
51314 ATTAAAGTATGAGTCTTTAGCGACGTTTATATAAAAATGCC
1 ATTAAAGTACGAGTCTATAACAACGTTTATATAAAAAAACC
* *
51355 ACTAAAATACGAGTCT
1 ATTAAAGTACGAGTCT
51371 TAGCGGCGTT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (41 bp):
ATTAAAGTACGAGTCTATAACAACGTTTATATAAAAAAACC
Found at i:51374 original size:40 final size:41
Alignment explanation
Indices: 51295--51405 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 41
51285 GTCTATAATA
* ** * * *
51295 ACGTTTGTATAAAAAAACCATTAAAGTATGAGTCTTTAGCG
1 ACGTTTATATAAAAATGCCACTAAAATACGAGTCTTTAGCG
51336 ACGTTTATATAAAAATGCCACTAAAATACGAGTC-TTAGCG
1 ACGTTTATATAAAAATGCCACTAAAATACGAGTCTTTAGCG
* *
51376 GCGTTTATTCTAAAAATGCCACTAAAATAC
1 ACGTTTA-TATAAAAATGCCACTAAAATAC
51406 AAATCTATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 12 0.20
41 49 0.80
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (41 bp):
ACGTTTATATAAAAATGCCACTAAAATACGAGTCTTTAGCG
Found at i:59424 original size:2 final size:2
Alignment explanation
Indices: 59419--59487 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
59409 TGTTTGTGTT
59419 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
59461 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
59488 CGTTAGTTAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:62219 original size:5 final size:5
Alignment explanation
Indices: 62209--62235 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
62199 TAAAGGGATC
62209 TTAAA TTAAA TTAAA TTAAA TTAAA TT
1 TTAAA TTAAA TTAAA TTAAA TTAAA TT
62236 CAAACTTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:65773 original size:19 final size:19
Alignment explanation
Indices: 65735--65776 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
65725 TTTGCATTTG
* **
65735 CATTTTACTTTTCGTTTTA
1 CATTTTACCTTTCGCATTA
65754 CATTTTACCTTTCGCATTA
1 CATTTTACCTTTCGCATTA
65773 CATT
1 CATT
65777 CTATTCATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.05, T:0.55
Consensus pattern (19 bp):
CATTTTACCTTTCGCATTA
Found at i:68650 original size:45 final size:45
Alignment explanation
Indices: 68597--68764 Score: 284
Period size: 45 Copynumber: 3.7 Consensus size: 45
68587 TTTATACTTT
*
68597 CTTTCATGCCTTTTATACACCATGATACATTTCATTTATGGCATC
1 CTTTCATGCCTTTTATACACCATTATACATTTCATTTATGGCATC
68642 CTTTCATGCCTTTTATACACCATTATACATTTCATTTATGGCATC
1 CTTTCATGCCTTTTATACACCATTATACATTTCATTTATGGCATC
*
68687 CTTTCATTG-CTTTTATACACCATTATGCATTTCATTTATGGCATC
1 CTTTCA-TGCCTTTTATACACCATTATACATTTCATTTATGGCATC
* *
68732 CTTTCATGCCTTTTATACATCATTATGCATTTC
1 CTTTCATGCCTTTTATACACCATTATACATTTC
68765 TATCCATCTA
Statistics
Matches: 118, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
44 2 0.02
45 114 0.97
46 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.08, T:0.45
Consensus pattern (45 bp):
CTTTCATGCCTTTTATACACCATTATACATTTCATTTATGGCATC
Found at i:68724 original size:23 final size:22
Alignment explanation
Indices: 68608--68725 Score: 73
Period size: 23 Copynumber: 5.2 Consensus size: 22
68598 TTTCATGCCT
*
68608 TTTATACACCATGATACATTTCA
1 TTTATACACCATTAT-CATTTCA
* ** *
68631 TTTATGGCATCC-TT-TCATGCCT
1 TTTAT-ACA-CCATTATCATTTCA
68653 TTTATACACCATTATACATTTCA
1 TTTATACACCATTAT-CATTTCA
* * *
68676 TTTATGGCATCC-TT-TCATTGCT
1 TTTAT-ACA-CCATTATCATTTCA
68698 TTTATACACCATTATGCATTTCA
1 TTTATACACCATTAT-CATTTCA
68721 TTTAT
1 TTTAT
68726 GGCATCCTTT
Statistics
Matches: 70, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
20 4 0.06
21 8 0.11
22 21 0.30
23 26 0.37
24 7 0.10
25 4 0.06
ACGTcount: A:0.25, C:0.22, G:0.07, T:0.46
Consensus pattern (22 bp):
TTTATACACCATTATCATTTCA
Found at i:69018 original size:54 final size:54
Alignment explanation
Indices: 68947--69314 Score: 337
Period size: 54 Copynumber: 6.8 Consensus size: 54
68937 TATACAATAT
* * * * * *
68947 TTCATCAACTCACGATGAATTCCGTGGGTTGCACACATAGTTCCTCTATGGTTA
1 TTCATCAAATCAGGATGAATTCCGTGGATTGCACACATAGTGCCTGTACGGTTA
* * * * *
69001 TTCATCAAATCATGATGAATTCTGTGGGTTTGCACACATAGCGCCTGTACTGTTA
1 TTCATCAAATCAGGATGAATTCCGT-GGATTGCACACATAGTGCCTGTACGGTTA
* * * ** * *
69056 TTCATCAACTCATGATGTATTTTGTGGATTAGCACACATAGTGCATGTACGATTA
1 TTCATCAAATCAGGATGAATTCCGTGGATT-GCACACATAGTGCCTGTACGGTTA
* * * * *
69111 TTCACCAACTCATGACGAATTCCGTGGATTTGCACTCATAGTGCCTGTACGGTTA
1 TTCATCAAATCAGGATGAATTCCGTGGA-TTGCACACATAGTGCCTGTACGGTTA
* * * *
69166 TTCATCCACAT-AGGATGAATTCCGTGGAATGCACACTTATTGCCTGTACGGTTA
1 TTCAT-CAAATCAGGATGAATTCCGTGGATTGCACACATAGTGCCTGTACGGTTA
* * * * *
69220 TTCATCCATAT-AGGATGAATTCCGTGGAATGCACACTTAGTGCATGTATGGTTA
1 TTCAT-CAAATCAGGATGAATTCCGTGGATTGCACACATAGTGCCTGTACGGTTA
* * * *
69274 TTCATCTACAT-AGGATGAATTCTGTGGAATGCACACTTAGT
1 TTCATC-AAATCAGGATGAATTCCGTGGATTGCACACATAGT
69315 TCCTATTTGG
Statistics
Matches: 269, Mismatches: 40, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
53 1 0.00
54 135 0.50
55 128 0.48
56 5 0.02
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (54 bp):
TTCATCAAATCAGGATGAATTCCGTGGATTGCACACATAGTGCCTGTACGGTTA
Found at i:69059 original size:55 final size:55
Alignment explanation
Indices: 68947--69300 Score: 276
Period size: 55 Copynumber: 6.5 Consensus size: 55
68937 TATACAATAT
* * * *
68947 TTCATCAACTCACGATGAATTCCGTGGG-TTGCACACATAGTTCCTCTA-TGGTTA
1 TTCATCAAATCAGGATGAATTCCGTGGGTTTGCACACATAGTGCCTGTACT-GTTA
* * *
69001 TTCATCAAATCATGATGAATTCTGTGGGTTTGCACACATAGCGCCTGTACTGTTA
1 TTCATCAAATCAGGATGAATTCCGTGGGTTTGCACACATAGTGCCTGTACTGTTA
* * * ** * * *
69056 TTCATCAACTCATGATGTATTTTGTGGATTAGCACACATAGTGCATGTAC-GATTA
1 TTCATCAAATCAGGATGAATTCCGTGGGTTTGCACACATAGTGCCTGTACTG-TTA
* * * * * * *
69111 TTCACCAACTCATGACGAATTCCGTGGATTTGCACTCATAGTGCCTGTACGGTTA
1 TTCATCAAATCAGGATGAATTCCGTGGGTTTGCACACATAGTGCCTGTACTGTTA
* ** * * *
69166 TTCATCCACAT-AGGATGAATTCCGT-GGAATGCACACTTATTGCCTGTACGGTTA
1 TTCAT-CAAATCAGGATGAATTCCGTGGGTTTGCACACATAGTGCCTGTACTGTTA
* ** * *
69220 TTCATCCATAT-AGGATGAATTCCGT-GGAATGCACACTTAGTGCATGTA-TGGTTA
1 TTCAT-CAAATCAGGATGAATTCCGTGGGTTTGCACACATAGTGCCTGTACT-GTTA
* *
69274 TTCATCTACAT-AGGATGAATTCTGTGG
1 TTCATC-AAATCAGGATGAATTCCGTGG
69301 AATGCACACT
Statistics
Matches: 254, Mismatches: 38, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
53 1 0.00
54 119 0.47
55 129 0.51
56 5 0.02
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (55 bp):
TTCATCAAATCAGGATGAATTCCGTGGGTTTGCACACATAGTGCCTGTACTGTTA
Found at i:69131 original size:110 final size:109
Alignment explanation
Indices: 68947--69314 Score: 321
Period size: 110 Copynumber: 3.4 Consensus size: 109
68937 TATACAATAT
* * * * * *
68947 TTCATCAACTCACGATGAATTCCGTGGGTTGCACACATAGTTCCTCTATGGTTATTCATCAAATC
1 TTCATCAACTCACGATGAATTCCGTGGATTGCACACATAGTGCATCTACGATTATTCACCAAATC
* * * *
69012 ATGATGAATTCTGTGGGTTTGCACACATAGCGCCTGTACTGTTA
66 ATGACGAATTCCGTGGATTTGCACACATAGCGCCTGTACGGTTA
* * ** * *
69056 TTCATCAACTCATGATGTATTTTGTGGATTAGCACACATAGTGCATGTACGATTATTCACCAACT
1 TTCATCAACTCACGATGAATTCCGTGGATT-GCACACATAGTGCATCTACGATTATTCACCAAAT
* *
69121 CATGACGAATTCCGTGGATTTGCACTCATAGTGCCTGTACGGTTA
65 CATGACGAATTCCGTGGATTTGCACACATAGCGCCTGTACGGTTA
* * * * * * * * *
69166 TTCATCCACAT-AGGATGAATTCCGTGGAATGCACACTTATTGCCTGTACGGTTATTCATCCATA
1 TTCATCAAC-TCACGATGAATTCCGTGGATTGCACACATAGTGCATCTACGATTATTCA-CCAAA
* * * * * * *
69230 T-AGGATGAATTCCGTGGA-ATGCACACTTAGTGCATGTATGGTTA
64 TCATGACGAATTCCGTGGATTTGCACACATAGCGCCTGTACGGTTA
* * * * *
69274 TTCATCTACAT-AGGATGAATTCTGTGGAATGCACACTTAGT
1 TTCATCAAC-TCACGATGAATTCCGTGGATTGCACACATAGT
69315 TCCTATTTGG
Statistics
Matches: 216, Mismatches: 40, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
108 59 0.27
109 64 0.30
110 92 0.43
111 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (109 bp):
TTCATCAACTCACGATGAATTCCGTGGATTGCACACATAGTGCATCTACGATTATTCACCAAATC
ATGACGAATTCCGTGGATTTGCACACATAGCGCCTGTACGGTTA
Found at i:69338 original size:108 final size:109
Alignment explanation
Indices: 69127--69339 Score: 270
Period size: 108 Copynumber: 2.0 Consensus size: 109
69117 AACTCATGAC
* * *
69127 GAATTCCGTGGATTTGCACTCATAGTGCCTGTACGGTTATTCATCCACATAGGATGAATTCCGTG
1 GAATTCCGTGGATATGCACACATAGTGCATGTACGGTTATTCATCCACATAGGATGAATTCCGTG
* ** *
69192 GAATGCACACTTATTGCCTGTACGGTTATTCATCCATATAGGAT
66 GAATGCACACTTATTGCCTATACGGTTAACCACCCATATAGGAT
* * * *
69236 GAATTCCGTGGA-ATGCACACTTAGTGCATGTATGGTTATTCATCTACATAGGATGAATTCTGTG
1 GAATTCCGTGGATATGCACACATAGTGCATGTACGGTTATTCATCCACATAGGATGAATTCCGTG
**
69300 GAATGCACACTTAGTT-CCTATTTGG-TAACCACCACATATA
66 GAATGCACACTTA-TTGCCTATACGGTTAACCACC-CATATA
69340 TTTTTAATAG
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
107 5 0.06
108 70 0.79
109 14 0.16
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (109 bp):
GAATTCCGTGGATATGCACACATAGTGCATGTACGGTTATTCATCCACATAGGATGAATTCCGTG
GAATGCACACTTATTGCCTATACGGTTAACCACCCATATAGGAT
Found at i:69678 original size:19 final size:19
Alignment explanation
Indices: 69654--69690 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
69644 TCGATACTAC
69654 TATATTATGGTACCGATAA
1 TATATTATGGTACCGATAA
*
69673 TATATTATGGTATCGATA
1 TATATTATGGTACCGATA
69691 CCATTTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (19 bp):
TATATTATGGTACCGATAA
Found at i:72784 original size:30 final size:30
Alignment explanation
Indices: 72750--72854 Score: 167
Period size: 30 Copynumber: 3.5 Consensus size: 30
72740 AATTGGTTTT
72750 CTAGAAAATGAATTATTGGAATTTGAATTA
1 CTAGAAAATGAATTATTGGAATTTGAATTA
72780 CTAGAAAATGAATTATTGGAATTTGAATTA
1 CTAGAAAATGAATTATTGGAATTTGAATTA
* *
72810 CTAGAAAATGAATTACTAGAATTTTGAATT-
1 CTAGAAAATGAATTATTGGAA-TTTGAATTA
*
72840 CTGGAAAATGAATTA
1 CTAGAAAATGAATTA
72855 CATTTATGGA
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
30 63 0.89
31 8 0.11
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (30 bp):
CTAGAAAATGAATTATTGGAATTTGAATTA
Found at i:72821 original size:15 final size:15
Alignment explanation
Indices: 72750--72855 Score: 97
Period size: 15 Copynumber: 7.1 Consensus size: 15
72740 AATTGGTTTT
72750 CTAGAAAATGAATTA
1 CTAGAAAATGAATTA
* * **
72765 TTGGAATTTGAATTA
1 CTAGAAAATGAATTA
72780 CTAGAAAATGAATTA
1 CTAGAAAATGAATTA
* * **
72795 TTGGAATTTGAATTA
1 CTAGAAAATGAATTA
72810 CTAGAAAATGAATTA
1 CTAGAAAATGAATTA
**
72825 CTAGAATTTTGAATT-
1 CTAGAA-AATGAATTA
*
72840 CTGGAAAATGAATTA
1 CTAGAAAATGAATTA
72855 C
1 C
72856 ATTTATGGAA
Statistics
Matches: 68, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
14 6 0.09
15 56 0.82
16 6 0.09
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (15 bp):
CTAGAAAATGAATTA
Found at i:73095 original size:20 final size:20
Alignment explanation
Indices: 73070--73109 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
73060 TATTTTAAAA
73070 TATTAAA-ATAATTTATTTAT
1 TATTAAATATAATTT-TTTAT
*
73090 TATTAAATATTATTTTTTAT
1 TATTAAATATAATTTTTTAT
73110 AATTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTAAATATAATTTTTTAT
Found at i:73222 original size:35 final size:34
Alignment explanation
Indices: 73183--73257 Score: 82
Period size: 35 Copynumber: 2.1 Consensus size: 34
73173 ATTAATTATT
*
73183 TATTAA-AGTAATATTGTTATATTATATTT-TAAAAA
1 TATTAATAGT-ATATT-TTA-AATATATTTATAAAAA
*
73218 TATTAATTAGTATATTTTAAATATATTTATTAAAA
1 TATTAA-TAGTATATTTTAAATATATTTATAAAAA
73253 TATTA
1 TATTA
73258 TTATATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
34 8 0.23
35 19 0.54
36 5 0.14
37 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (34 bp):
TATTAATAGTATATTTTAAATATATTTATAAAAA
Found at i:73234 original size:23 final size:23
Alignment explanation
Indices: 73205--73249 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
73195 ATTGTTATAT
73205 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
73228 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
73250 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:73255 original size:23 final size:23
Alignment explanation
Indices: 73206--73274 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
73196 TTGTTATATT
* * **
73206 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTTATTAAA
73229 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAATATATTTATTAAA
*
73252 ATATTATTATAT-TATTATATTAA
1 ATATT-TTAAATATATT-TATTAA
73275 TATTAAATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.72
24 11 0.28
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (23 bp):
ATATTTTAAATATATTTATTAAA
Found at i:73278 original size:34 final size:34
Alignment explanation
Indices: 73193--73278 Score: 83
Period size: 33 Copynumber: 2.6 Consensus size: 34
73183 TATTAAAGTA
*
73193 ATATTGTTATATT-ATATTTTAAAAATATTAATT
1 ATATTATTATATTAATATTTTAAAAATATTAATT
*
73226 AGTA-TATT-T-TAAATATATTTATTAAAATATT-ATT
1 A-TATTATTATATTAATAT-TTTA--AAAATATTAATT
73260 ATATTATTATATTAATATT
1 ATATTATTATATTAATATT
73279 AAATATACAA
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
31 1 0.02
32 5 0.12
33 10 0.24
34 10 0.24
35 10 0.24
36 6 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (34 bp):
ATATTATTATATTAATATTTTAAAAATATTAATT
Found at i:73285 original size:23 final size:22
Alignment explanation
Indices: 73183--73285 Score: 61
Period size: 23 Copynumber: 4.5 Consensus size: 22
73173 ATTAATTATT
*
73183 TATTAAAGTAATATTGTTATATTATA
1 TATTAAA-T-ATATTATTATA-TA-A
* *
73209 TTTTAAAAATATTAATTAGTAT-A
1 TATTAAATATATT-ATTA-TATAA
*
73232 TTTTAAATATATTTATTA-A-AA
1 TATTAAATATA-TTATTATATAA
*
73253 TATT-ATTATATTATTATATTAA
1 TATTAAATATATTATTATA-TAA
73275 TATTAAATATA
1 TATTAAATATA
73286 CAAATAATAT
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
19 6 0.10
20 6 0.10
21 5 0.08
22 6 0.10
23 20 0.32
24 7 0.11
25 4 0.06
26 8 0.13
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
TATTAAATATATTATTATATAA
Found at i:73296 original size:29 final size:30
Alignment explanation
Indices: 73262--73329 Score: 86
Period size: 28 Copynumber: 2.3 Consensus size: 30
73252 ATATTATTAT
* *
73262 ATTATTATATTAATATTAAATATACAAATA
1 ATTATTATATCAATATTAAATATACAAAAA
* *
73292 A-TATTAT-TCATTATTAAATATATAAAAA
1 ATTATTATATCAATATTAAATATACAAAAA
73320 ATTATTATAT
1 ATTATTATAT
73330 ATTTATTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 18 0.56
29 12 0.38
30 2 0.06
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (30 bp):
ATTATTATATCAATATTAAATATACAAAAA
Found at i:73369 original size:23 final size:23
Alignment explanation
Indices: 73343--73395 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
73333 TATTAAAATA
*
73343 ATAATATAATAT-CTTATATTATT
1 ATAATATAAT-TGATTATATTATT
*
73366 ATAATATAATTGATTATTTTATT
1 ATAATATAATTGATTATATTATT
73389 ATAATAT
1 ATAATAT
73396 TAAAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (23 bp):
ATAATATAATTGATTATATTATT
Found at i:73396 original size:8 final size:8
Alignment explanation
Indices: 73340--73428 Score: 51
Period size: 8 Copynumber: 11.1 Consensus size: 8
73330 ATTTATTAAA
*
73340 ATAATAAT
1 ATAATATT
73348 ATAATATCTT
1 ATAATA--TT
*
73358 ATATTATT
1 ATAATATT
73366 ATAATA-T
1 ATAATATT
*
73373 A-ATTGATT
1 ATAAT-ATT
**
73381 ATTTTATT
1 ATAATATT
73389 ATAATATT
1 ATAATATT
*
73397 A-AA-AAT
1 ATAATATT
73403 ATAATATT
1 ATAATATT
*
73411 ATATTATT
1 ATAATATT
73419 ATAAATATT
1 AT-AATATT
73428 A
1 A
73429 ATAAATATAT
Statistics
Matches: 62, Mismatches: 11, Indels: 15
0.70 0.12 0.17
Matches are distributed among these distances:
6 5 0.08
7 7 0.11
8 36 0.58
9 8 0.13
10 6 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (8 bp):
ATAATATT
Found at i:73413 original size:22 final size:23
Alignment explanation
Indices: 73385--73431 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
73375 TTGATTATTT
73385 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
73407 TATTATATTATTATAAATATTAA
1 TATTATAATATTAAAAATATTAA
73430 TA
1 TA
73432 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:73437 original size:24 final size:22
Alignment explanation
Indices: 73388--73439 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
73378 ATTATTTTAT
* *
73388 TATAATATTAAAAATATAATAT
1 TATATTATTAAAAATATAATAA
*
73410 TATATTATTATAAATATTAATAAA
1 TATATTATTAAAAATA-TAAT-AA
73434 TATATT
1 TATATT
73440 TTAGATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 14 0.56
23 4 0.16
24 7 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATATTATTAAAAATATAATAA
Found at i:75966 original size:115 final size:115
Alignment explanation
Indices: 75764--76170 Score: 600
Period size: 115 Copynumber: 3.5 Consensus size: 115
75754 TTATCTCTGA
* * * * *
75764 AGGGAATATTAAATCTTGGAAGATAGGAATTTGTTCCGCTTCGTCTGAATGGAATATCAGATCTG
1 AGGGAATATCAAATCCTGGAAGATAGGAATCTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTG
*
75829 GAAAGAGATGTGATCCATTGAATTAGGGCAGATTTGTTCCGCTATCACTC
66 GAAAGAGATGTGATCCATTGAATTAGGGCAGATTTGTTCCGCTGTCACTC
* *
75879 AGGGAATATCAAATCCTGGAAGATAGGAATTTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTA
1 AGGGAATATCAAATCCTGGAAGATAGGAATCTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTG
* * * *
75944 GAAAGAGATGTGACCCAATGAATTAGGGTAGATTTATTCCGCTGTCACTC
66 GAAAGAGATGTGATCCATTGAATTAGGGCAGATTTGTTCCGCTGTCACTC
* **
75994 AGGGAATATCAAATCTTGGAAGATAGGAATCTGTTTTGCTTCTTCTGAAGGGAATATCAGATCTG
1 AGGGAATATCAAATCCTGGAAGATAGGAATCTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTG
* * *
76059 GAAAGAGTTGTGATACATTGAATTAGGGCAGATTTGTTTCGCTGTCACTC
66 GAAAGAGATGTGATCCATTGAATTAGGGCAGATTTGTTCCGCTGTCACTC
* * * *
76109 AGGGAATATCAAA-CCTTGAAAAAGAGGAATCTGTTCAGCTTCTTCTGAAGGGAATATCAGAT
1 AGGGAATATCAAATCC-TGGAAGATAGGAATCTGTTCCGCTTCTTCTGAAGGGAATATCAGAT
76171 TTTTCAAAAT
Statistics
Matches: 263, Mismatches: 28, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
114 1 0.00
115 262 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (115 bp):
AGGGAATATCAAATCCTGGAAGATAGGAATCTGTTCCGCTTCTTCTGAAGGGAATATCAGATCTG
GAAAGAGATGTGATCCATTGAATTAGGGCAGATTTGTTCCGCTGTCACTC
Found at i:76605 original size:151 final size:151
Alignment explanation
Indices: 76302--77468 Score: 1801
Period size: 151 Copynumber: 7.7 Consensus size: 151
76292 AAGGCTTACA
* * * ** *
76302 GATGACCCGAAGGATTTATAAATTTTGGAAATAGTTTACTAACTAAGAAACCTTTCTTTCTTTTC
1 GATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
* * * ** *
76367 -AAAATTTC-AATTTTTAGATTTAATATGAGAAACCTTTCTCATATTTCAAAAGACATGTGAAAA
66 AAAAATTTCAAATTTTCAAATTTGA-ATGAGAAACCTTTCTCATATTTTGATAGACATGTGAAAA
***
76430 CATCCTGCTTGAAGGTCTTATG
130 CATCCTGCCCAAAGGTCTTATG
76452 GATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
1 GATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
* * *
76517 AAAAATTTCAAATTTTCAAATTTGAATGGGAAACTTTTCTCATATTTTGATAGGCATGTGAAAAC
66 AAAAATTTCAAATTTTCAAATTTGAATGAGAAACCTTTCTCATATTTTGATAGACATGTGAAAAC
76582 ATCCTGCCCAAAGGTCTTATG
131 ATCCTGCCCAAAGGTCTTATG
76603 GATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
1 GATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
*
76668 AAAAATTTCAAAATTTCAAATTTGAATGAGAAACCTTTCTCATATTTTGATAGACATGTG-AAAC
66 AAAAATTTCAAATTTTCAAATTTGAATGAGAAACCTTTCTCATATTTTGATAGACATGTGAAAAC
*
76732 TATCCTGTCCAAAGGTCTTATG
131 -ATCCTGCCCAAAGGTCTTATG
* * * *
76754 GATGGCCTGAAAGACTTATAAATTTTGGAAATATTTTACTAAGTAAGAAACCTTTTTTACTTTTC
1 GATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
* *
76819 AAAAATTTCAAA-TTTCAAATTTGAATGAGAAACCTTTCTCATTTTTTGATAGGCATGTGAAAAC
66 AAAAATTTCAAATTTTCAAATTTGAATGAGAAACCTTTCTCATATTTTGATAGACATGTGAAAAC
*
76883 ATCCTGCCCAAAGGTCTAATG
131 ATCCTGCCCAAAGGTCTTATG
*
76904 GATGGCCCTTAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTT
1 GATGGCCC-GAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTT
* * * *
76969 CAAAAATTTCAAATTTTCAGATTTAATATGAGAAACCTTTCTCATA-TTTAAAAGACATGTGAAA
65 CAAAAATTTCAAATTTTCAAATTTGA-ATGAGAAACCTTTCTCATATTTTGATAGACATGTGAAA
* *
77033 ACATCCTACCCAAAGGTCTTATA
129 ACATCCTGCCCAAAGGTCTTATG
*
77056 GATGGCCCAAAGGACTTA-AAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
1 GATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
*
77120 AAAAATTTCAAAATTTCAAATTTGAATGAGAAACCTTTCTCATATTTTGATAGACATGTGAAAAC
66 AAAAATTTCAAATTTTCAAATTTGAATGAGAAACCTTTCTCATATTTTGATAGACATGTGAAAAC
*
77185 ATCCTGCCTAAAGGTCTTATG
131 ATCCTGCCCAAAGGTCTTATG
* *
77206 GATGGCCCGAATGA-TATATAAATTTTGGAAATATTTTACTTGGTAAGAAACCTTTCTTACTTTT
1 GATGGCCCGAAGGACT-TATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTT
* *
77270 CAAAAATTTCAAATTTTCAAATATGATTGAGAAACCTTTCTCATATTTTGATAGACATGTGAAAA
65 CAAAAATTTCAAATTTTCAAATTTGAATGAGAAACCTTTCTCATATTTTGATAGACATGTGAAAA
*
77335 CATCCTGCCCAAAGGTCTTATA
130 CATCCTGCCCAAAGGTCTTATG
** *
77357 GATAACCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAAAAACCTTTCTTACTTTTC
1 GATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
* * *
77422 AAAAATTTTAAA-TTTCAAATTTGAATGAGAAACCTTGCTCATTTTTT
66 AAAAATTTCAAATTTTCAAATTTGAATGAGAAACCTTTCTCATATTTT
77469 CACTTATAAA
Statistics
Matches: 934, Mismatches: 72, Indels: 22
0.91 0.07 0.02
Matches are distributed among these distances:
149 20 0.02
150 283 0.30
151 547 0.59
152 66 0.07
153 18 0.02
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (151 bp):
GATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTC
AAAAATTTCAAATTTTCAAATTTGAATGAGAAACCTTTCTCATATTTTGATAGACATGTGAAAAC
ATCCTGCCCAAAGGTCTTATG
Found at i:77465 original size:603 final size:603
Alignment explanation
Indices: 76311--77468 Score: 1955
Period size: 603 Copynumber: 1.9 Consensus size: 603
76301 AGATGACCCG
* *
76311 AAGGATTTATAAATTTTGGAAATAGTTTACTAACTAAGAAACCTTTCTTTCTTTTCAAAATTTCA
1 AAGGACTTATAAATTTTGGAAATAGTTTACTAACTAAGAAACCTTTCTTACTTTTCAAAATTTCA
* * ***
76376 ATTTTTAGATTTAATATGAGAAACCTTTCTCATATTTCAAAAGACATGTGAAAACATCCTGCTTG
66 ATTTTCAGATTTAATATGAGAAACCTTTCTCATATTTCAAAAGACATGTGAAAACATCCTACCCA
* *
76441 AAGGTCTTATGGATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTT
131 AAGGTCTTATAGATGGCCCAAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTT
* * * *
76506 TCTTACTTTTCAAAAATTTCAAATTTTCAAATTTGAATGGGAAACTTTTCTCATATTTTGATAGG
196 TCTTACTTTTCAAAAATTTCAAAATTTCAAATTTGAATGAGAAACCTTTCTCATATTTTGATAGA
76571 CATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATAAATTTTGGAAATA
261 CATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATAAATTTTGGAAATA
*
76636 TTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAAATTTCAAATTTGAATGAGAAA
326 TTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAAATTTCAAATATGAATGAGAAA
* * ** *
76701 CCTTTCTCATATTTTGATAGACATGTGAAACTATCCTGTCCAAAGGTCTTATGGATGGCCTGAAA
391 CCTTTCTCATATTTTGATAGACATGTGAAACTATCCTGCCCAAAGGTCTTATAGATAACCCGAAA
* *
76766 GACTTATAAATTTTGGAAATATTTTACTAAGTAAGAAACCTTTTTTACTTTTCAAAAATTTCAAA
456 GACTTATAAATTTTGGAAATATTTTACTAAGTAAAAAACCTTTCTTACTTTTCAAAAATTTCAAA
*
76831 TTTCAAATTTGAATGAGAAACCTTTCTCATTTTTTGATAGGCATGTGAAAACATCCTGCCCAAAG
521 TTTCAAATTTGAATGAGAAACCTTGCTCATTTTTTGATAGGCATGTGAAAACATCCTGCCCAAAG
76896 GTCTAATGGATGGCCCTT
586 GTCTAATGGATGGCCCTT
* **
76914 AAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTC
1 AAGGACTTATAAATTTTGGAAATAGTTTACTAACTAAGAAACCTTTCTTACTTTTC-AAAATTTC
76979 AAATTTTCAGATTTAATATGAGAAACCTTTCTCATATTT-AAAAGACATGTGAAAACATCCTACC
65 -AATTTTCAGATTTAATATGAGAAACCTTTCTCATATTTCAAAAGACATGTGAAAACATCCTACC
77043 CAAAGGTCTTATAGATGGCCCAAAGGACTTA-AAATTTTGGAAATATTTTACTAGGTAAGAAACC
129 CAAAGGTCTTATAGATGGCCCAAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACC
77107 TTTCTTACTTTTCAAAAATTTCAAAATTTCAAATTTGAATGAGAAACCTTTCTCATATTTTGATA
194 TTTCTTACTTTTCAAAAATTTCAAAATTTCAAATTTGAATGAGAAACCTTTCTCATATTTTGATA
* *
77172 GACATGTGAAAACATCCTGCCTAAAGGTCTTATGGATGGCCCGAATGA-TATATAAATTTTGGAA
259 GACATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACT-TATAAATTTTGGAA
* * *
77236 ATATTTTACTTGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAATTTTCAAATATGATTGAG
323 ATATTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAAATTTCAAATATGAATGAG
77301 AAACCTTTCTCATATTTTGATAGACATGTGAAAAC-ATCCTGCCCAAAGGTCTTATAGATAACCC
388 AAACCTTTCTCATATTTTGATAGACATGTG-AAACTATCCTGCCCAAAGGTCTTATAGATAACCC
* *
77365 GAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAAAAACCTTTCTTACTTTTCAAAAATTT
452 GAAAGACTTATAAATTTTGGAAATATTTTACTAAGTAAAAAACCTTTCTTACTTTTCAAAAATTT
*
77430 TAAATTTCAAATTTGAATGAGAAACCTTGCTCATTTTTT
517 CAAATTTCAAATTTGAATGAGAAACCTTGCTCATTTTTT
77469 CACTTATAAA
Statistics
Matches: 518, Mismatches: 33, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
602 1 0.00
603 418 0.81
604 62 0.12
605 37 0.07
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.36
Consensus pattern (603 bp):
AAGGACTTATAAATTTTGGAAATAGTTTACTAACTAAGAAACCTTTCTTACTTTTCAAAATTTCA
ATTTTCAGATTTAATATGAGAAACCTTTCTCATATTTCAAAAGACATGTGAAAACATCCTACCCA
AAGGTCTTATAGATGGCCCAAAGGACTTATAAATTTTGGAAATATTTTACTAGGTAAGAAACCTT
TCTTACTTTTCAAAAATTTCAAAATTTCAAATTTGAATGAGAAACCTTTCTCATATTTTGATAGA
CATGTGAAAACATCCTGCCCAAAGGTCTTATGGATGGCCCGAAGGACTTATAAATTTTGGAAATA
TTTTACTAGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAAAATTTCAAATATGAATGAGAAA
CCTTTCTCATATTTTGATAGACATGTGAAACTATCCTGCCCAAAGGTCTTATAGATAACCCGAAA
GACTTATAAATTTTGGAAATATTTTACTAAGTAAAAAACCTTTCTTACTTTTCAAAAATTTCAAA
TTTCAAATTTGAATGAGAAACCTTGCTCATTTTTTGATAGGCATGTGAAAACATCCTGCCCAAAG
GTCTAATGGATGGCCCTT
Found at i:78846 original size:115 final size:115
Alignment explanation
Indices: 78644--78874 Score: 356
Period size: 115 Copynumber: 2.0 Consensus size: 115
78634 CTTCACTAGT
* * * *
78644 GCCCCAACATTATCTTATACTGGTACGGGTCTTCAAAATGCCCTAACACCTCAAATTGTAAGGCT
1 GCCCCAACATTATCTTATACTGGTACGAGCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCT
* * *
78709 CATGCTCAATTCCTTCTTGGTCTGAATCTTGTTATCTTAACATGATGTGG
66 CATGCTCAATGCCTTCTTGGTCTGAATCTTGTCATCTCAACATGATGTGG
*
78759 GCCCCAACATTATCTTATACTGGTACGAGCCTTTAAAATGCCCCAACACCTCAAATTATAAGGCT
1 GCCCCAACATTATCTTATACTGGTACGAGCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCT
* *
78824 CATTCTTAATGCC-TCATTGGTCTGAATCTTGTCATCTCAACATGATGTGG
66 CATGCTCAATGCCTTC-TTGGTCTGAATCTTGTCATCTCAACATGATGTGG
78874 G
1 G
78875 TTCAGTCCTA
Statistics
Matches: 105, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
114 2 0.02
115 103 0.98
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.32
Consensus pattern (115 bp):
GCCCCAACATTATCTTATACTGGTACGAGCCTTCAAAATGCCCCAACACCTCAAATTATAAGGCT
CATGCTCAATGCCTTCTTGGTCTGAATCTTGTCATCTCAACATGATGTGG
Found at i:90669 original size:12 final size:12
Alignment explanation
Indices: 90652--90676 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
90642 AAAGGATTGA
90652 TAACTTTTAATT
1 TAACTTTTAATT
90664 TAACTTTTAATT
1 TAACTTTTAATT
90676 T
1 T
90677 TATTTTATTT
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:0.08, G:0.00, T:0.60
Consensus pattern (12 bp):
TAACTTTTAATT
Found at i:92157 original size:26 final size:26
Alignment explanation
Indices: 92128--92190 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
92118 ATGTCCACTC
*
92128 TAAAATTTTATTGTACCCATCCCATT
1 TAAAATTTTATTGTACCCATCCAATT
***
92154 TAAAAATTTTA-TGTTGTCATCCAATT
1 T-AAAATTTTATTGTACCCATCCAATT
92180 TAAAATTTTAT
1 TAAAATTTTAT
92191 GTTATTAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 9 0.29
26 13 0.42
27 9 0.29
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (26 bp):
TAAAATTTTATTGTACCCATCCAATT
Found at i:92190 original size:25 final size:26
Alignment explanation
Indices: 92145--92193 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
92135 TTATTGTACC
*
92145 CATCCCATTTAAAAATTTTATGTTGT
1 CATCCAATTTAAAAATTTTATGTTGT
92171 CATCCAATTT-AAAATTTTATGTT
1 CATCCAATTTAAAAATTTTATGTT
92194 ATTAACATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (26 bp):
CATCCAATTTAAAAATTTTATGTTGT
Found at i:92552 original size:2 final size:2
Alignment explanation
Indices: 92545--92576 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
92535 GTATTAAAAT
92545 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
92577 GTTAATTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:95172 original size:28 final size:28
Alignment explanation
Indices: 95140--95202 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
95130 ATGATAAAAT
95140 ATAAAATTATTTAAGGAGCGTTTGGTTA
1 ATAAAATTATTTAAGGAGCGTTTGGTTA
95168 ATAAAATTATTTAAGGAGCGTTTGGTTA
1 ATAAAATTATTTAAGGAGCGTTTGGTTA
95196 ATAAAAT
1 ATAAAAT
95203 GTAAGATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.40, C:0.03, G:0.19, T:0.38
Consensus pattern (28 bp):
ATAAAATTATTTAAGGAGCGTTTGGTTA
Found at i:95172 original size:35 final size:33
Alignment explanation
Indices: 95133--95212 Score: 89
Period size: 28 Copynumber: 2.5 Consensus size: 33
95123 TGTTTGAATG
95133 ATAAAATATAAAATTATTTAAGGAGCGTTTGGT
1 ATAAAATATAAAATTATTTAAGGAGCGTTTGGT
95166 -T---A-ATAAAATTATTTAAGGAGCGTTTGGTT
1 ATAAAATATAAAATTATTTAAGGAGCGTTTGG-T
* *
95195 AATAAAATGTAAGATTAT
1 -ATAAAATATAAAATTAT
95213 ATTTGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
28 25 0.66
29 2 0.05
31 1 0.03
32 1 0.03
34 1 0.03
35 8 0.21
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (33 bp):
ATAAAATATAAAATTATTTAAGGAGCGTTTGGT
Found at i:98173 original size:13 final size:13
Alignment explanation
Indices: 98155--98184 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
98145 ATTTGTCTTC
98155 TTGAACTCACCAA
1 TTGAACTCACCAA
98168 TTGAACTCACCAA
1 TTGAACTCACCAA
98181 TTGA
1 TTGA
98185 TCCCACCAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.27, G:0.10, T:0.27
Consensus pattern (13 bp):
TTGAACTCACCAA
Found at i:102486 original size:39 final size:39
Alignment explanation
Indices: 102420--102534 Score: 139
Period size: 39 Copynumber: 3.0 Consensus size: 39
102410 ATTTTTATTT
* *
102420 ATAA-TTATCAAATTATTTCA-TTCTAACATTCTAAATTC
1 ATAATTTATTAAATTATTTCACAT-TAACATTCTAAATTC
102458 ATAATTTATTAAATT-TTATCACCA-TAACATTCTAAATTC
1 ATAATTTATTAAATTATT-TCA-CATTAACATTCTAAATTC
* *
102497 TTAATTTCTTAAATTATTTCACATTAACATTCTAAATT
1 ATAATTTATTAAATTATTTCACATTAACATTCTAAATT
102535 ATTTTTAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
38 8 0.12
39 57 0.85
40 2 0.03
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.46
Consensus pattern (39 bp):
ATAATTTATTAAATTATTTCACATTAACATTCTAAATTC
Found at i:105611 original size:22 final size:22
Alignment explanation
Indices: 105581--105622 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
105571 ATGTATCGAT
*
105581 ACTCATAGGGGTATCGATACTTG
1 ACTCATA-GGGTATCAATACTTG
105604 ACTC-TAGGGTATCAATACT
1 ACTCATAGGGTATCAATACT
105623 ACAAGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 2 0.11
23 4 0.22
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (22 bp):
ACTCATAGGGTATCAATACTTG
Done.