Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015150.1 Kokia drynarioides strain JFW-HI SEQ_130194, 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: 411378
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 313 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:14731 original size:14 final size:14
Alignment explanation
Indices: 14712--14741 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
14702 ACATTAGCAC
14712 TAGTGAAGATAACA
1 TAGTGAAGATAACA
14726 TAGTGAAGATAACA
1 TAGTGAAGATAACA
14740 TA
1 TA
14742 TGACAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (14 bp):
TAGTGAAGATAACA
Found at i:15792 original size:25 final size:24
Alignment explanation
Indices: 15758--15856 Score: 81
Period size: 24 Copynumber: 4.1 Consensus size: 24
15748 TGAGTCTTCC
*
15758 AAAAATTTAGCTCATACGAGCCCA
1 AAAAAATTAGCTCATACGAGCCCA
* *
15782 AACAAAATTAGCTCATACAAGCCTA
1 AA-AAAATTAGCTCATACGAGCCCA
* ** *
15807 AATAGGTTAGCTCTTACGAGCCCA
1 AAAAAATTAGCTCATACGAGCCCA
* * * **
15831 TATAAGTTAGCTCATTTGAGCCCA
1 AAAAAATTAGCTCATACGAGCCCA
15855 AA
1 AA
15857 CAGAGTTTAA
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
24 38 0.64
25 21 0.36
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.24
Consensus pattern (24 bp):
AAAAAATTAGCTCATACGAGCCCA
Found at i:15828 original size:24 final size:24
Alignment explanation
Indices: 15756--15845 Score: 83
Period size: 24 Copynumber: 3.8 Consensus size: 24
15746 ACTGAGTCTT
* *
15756 CCAAA-AATTTAGCTCATACGAGC
1 CCAAATAAGTTAGCTCATACAAGC
* *
15779 CCAAACAAAATTAGCTCATACAAGC
1 CCAAA-TAAGTTAGCTCATACAAGC
* * * *
15804 CTAAATAGGTTAGCTCTTACGAGC
1 CCAAATAAGTTAGCTCATACAAGC
*
15828 CCATATAAGTTAGCTCAT
1 CCAAATAAGTTAGCTCAT
15846 TTGAGCCCAA
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
23 5 0.09
24 28 0.53
25 20 0.38
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.24
Consensus pattern (24 bp):
CCAAATAAGTTAGCTCATACAAGC
Found at i:21296 original size:3 final size:3
Alignment explanation
Indices: 21288--21313 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
21278 CGGAAGGAAA
21288 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
21314 ATTCCTTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:24320 original size:2 final size:2
Alignment explanation
Indices: 24315--24343 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
24305 CGTTTTTTCC
24315 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24344 ATACTTACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32625 original size:16 final size:15
Alignment explanation
Indices: 32604--32641 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
32594 AATGGAATGA
32604 AAATAAATATTTAATT
1 AAATAAA-ATTTAATT
32620 AAAT-AAATTTAATT
1 AAATAAAATTTAATT
*
32634 AATTAAAA
1 AAATAAAA
32642 ATTTTAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 11 0.55
15 5 0.25
16 4 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATAAAATTTAATT
Found at i:32865 original size:113 final size:113
Alignment explanation
Indices: 32715--32948 Score: 369
Period size: 113 Copynumber: 2.1 Consensus size: 113
32705 CTTCTTCTTC
* **
32715 TTTCTTTTTTATTCCAACATCTTTAGTTACAAATCTGTCTCAAAACTTGAATCTTTAAAATTCAT
1 TTTC-TTTTGATTCCAACATCTTTAGTTACAAATCTGTCTCAAAACTTGAATCTTTAAAACCCAT
**
32780 TAACCAAAAGATTCAATATATTTGGTTCAAATATCTTCTTCCTGTTAAG
65 TAACCAAAAGATTCAATATATTTGGTTCAAATATCTTCTTCCCATTAAG
* *
32829 TTTCTTTTGATTCCAATATCTTTAGTTACAAATCTGTCTCAAAGCTTGAATCTTTAAAACCCATT
1 TTTCTTTTGATTCCAACATCTTTAGTTACAAATCTGTCTCAAAACTTGAATCTTTAAAACCCATT
* * *
32894 AACCAAAATATTCAATATCTTTGGTTCCAATATCTTCTTCCCATTAAG
66 AACCAAAAGATTCAATATATTTGGTTCAAATATCTTCTTCCCATTAAG
32942 TTTCTTT
1 TTTCTTT
32949 AGGTTAATGA
Statistics
Matches: 110, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
113 106 0.96
114 4 0.04
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.43
Consensus pattern (113 bp):
TTTCTTTTGATTCCAACATCTTTAGTTACAAATCTGTCTCAAAACTTGAATCTTTAAAACCCATT
AACCAAAAGATTCAATATATTTGGTTCAAATATCTTCTTCCCATTAAG
Found at i:33637 original size:14 final size:15
Alignment explanation
Indices: 33615--33652 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
33605 AAATATATGA
*
33615 AACAATTAAA-TTTT
1 AACATTTAAAGTTTT
33629 AACATTTAAAGTTTT
1 AACATTTAAAGTTTT
*
33644 AAGATTTAA
1 AACATTTAA
33653 GGTATTTAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (15 bp):
AACATTTAAAGTTTT
Found at i:39783 original size:25 final size:25
Alignment explanation
Indices: 39754--39802 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
39744 GAAGGCTAAG
39754 CCATTTATAGCTTGGAATGGTATCA
1 CCATTTATAGCTTGGAATGGTATCA
39779 CCATTTATAGCTTGGAATGGTATC
1 CCATTTATAGCTTGGAATGGTATC
39803 TGCACTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (25 bp):
CCATTTATAGCTTGGAATGGTATCA
Found at i:45517 original size:11 final size:11
Alignment explanation
Indices: 45501--45531 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
45491 AGATGGAGCC
45501 TTTTTCTTTCT
1 TTTTTCTTTCT
45512 TTTTTCTTTCT
1 TTTTTCTTTCT
45523 TTTTTCTTT
1 TTTTTCTTT
45532 TGTGTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTCT
Found at i:46944 original size:18 final size:18
Alignment explanation
Indices: 46921--46955 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46911 TTGATTAAAT
46921 TTTATTAGTAAAATTTGA
1 TTTATTAGTAAAATTTGA
* *
46939 TTTATTATTGAAATTTG
1 TTTATTAGTAAAATTTG
46956 TTATTCAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTATTAGTAAAATTTGA
Found at i:60802 original size:152 final size:152
Alignment explanation
Indices: 60526--60832 Score: 499
Period size: 152 Copynumber: 2.0 Consensus size: 152
60516 ATATTTTTTA
* * *
60526 TGGATTGATCATCATTCAAGATAGGTAATATGTAGGCGTGAAGATTCAAACAGATAATTTGAAGG
1 TGGATTGACCATCATTCAAGATAGGAAATATGTAAGCGTGAAGATTCAAACAGATAATTTGAAGG
* * * * *
60591 CGATCAAGGTCACTCAAGATTCTTTCTTGACGGATTCAAGTTCTGTCTTCATTAAACGTATTCAT
66 CGATCAAGGTCACTCAAAATTCTTTCTTGACGAATTCAAGCTCTGCCCTCATTAAACGTATTCAT
60656 CTTCTTCTGAAACGTAAGACTT
131 CTTCTTCTGAAACGTAAGACTT
*
60678 TGGATTGACCATCATTCAAGATAGGAAATATGTAAGCGTGAAGATTTAAACAGATAATTTGAAGG
1 TGGATTGACCATCATTCAAGATAGGAAATATGTAAGCGTGAAGATTCAAACAGATAATTTGAAGG
*
60743 CGATCAAGGTCACTCAAAA-TCTTTTCTTGACGAATTCAAGCTCTGCCCTCATTAGACGTATTCA
66 CGATCAAGGTCACTCAAAATTC-TTTCTTGACGAATTCAAGCTCTGCCCTCATTAAACGTATTCA
*
60807 TTTTCTTCTGAAACGTAAGACTT
130 TCTTCTTCTGAAACGTAAGACTT
60830 TGG
1 TGG
60833 TCCATACAAT
Statistics
Matches: 143, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
151 2 0.01
152 141 0.99
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (152 bp):
TGGATTGACCATCATTCAAGATAGGAAATATGTAAGCGTGAAGATTCAAACAGATAATTTGAAGG
CGATCAAGGTCACTCAAAATTCTTTCTTGACGAATTCAAGCTCTGCCCTCATTAAACGTATTCAT
CTTCTTCTGAAACGTAAGACTT
Found at i:61261 original size:27 final size:27
Alignment explanation
Indices: 61231--61296 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
61221 TAAATAATCA
61231 ATATATAATTTAAAA-AA-TATTATATTG
1 ATAT-TAATTTAAAATAATTA-TATATTG
*
61258 ATATTAATTAAAAATAATTATATATTG
1 ATATTAATTTAAAATAATTATATATTG
61285 ATATTAATTTAA
1 ATATTAATTTAA
61297 TATTTTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 9 0.26
27 24 0.69
28 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (27 bp):
ATATTAATTTAAAATAATTATATATTG
Found at i:61317 original size:16 final size:17
Alignment explanation
Indices: 61296--61328 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
61286 TATTAATTTA
61296 ATATTTTCA-ATTTTTT
1 ATATTTTCATATTTTTT
*
61312 ATATTTTTATATTTTTT
1 ATATTTTCATATTTTTT
61329 GAAATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (17 bp):
ATATTTTCATATTTTTT
Found at i:61335 original size:18 final size:17
Alignment explanation
Indices: 61292--61339 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
61282 TTGATATTAA
*
61292 TTTAATATTTTCA-ATTT
1 TTTAA-ATTTTTATATTT
*
61309 TTTATATTTTTATATTT
1 TTTAAATTTTTATATTT
61326 TTTGAAATTTTTAT
1 TTT-AAATTTTTAT
61340 TACAATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 6 0.23
17 11 0.42
18 9 0.35
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTAAATTTTTATATTT
Found at i:76092 original size:25 final size:27
Alignment explanation
Indices: 76047--76101 Score: 80
Period size: 25 Copynumber: 2.1 Consensus size: 27
76037 GTTACTTCAT
76047 GAAAAAATTTAAATTATAAAA-AAT-A
1 GAAAAAATTTAAATTATAAAAGAATGA
76072 GAAAAAA-TTAAATTATAAAAAGAATGA
1 GAAAAAATTTAAATTAT-AAAAGAATGA
76099 GAA
1 GAA
76102 TAGAAGCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 9 0.33
25 11 0.41
26 3 0.11
27 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (27 bp):
GAAAAAATTTAAATTATAAAAGAATGA
Found at i:79868 original size:27 final size:26
Alignment explanation
Indices: 79831--79883 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
79821 AATCCTAAAT
*
79831 TTTAAATCTTAAA-CATCAAATCTCGAA
1 TTTAAACCTTAAATCAT-AAAT-TCGAA
79858 TTTAAACCTTAAATCATAAATTCGAA
1 TTTAAACCTTAAATCATAAATTCGAA
79884 AACTCAAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 16 0.67
28 3 0.12
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.34
Consensus pattern (26 bp):
TTTAAACCTTAAATCATAAATTCGAA
Found at i:80430 original size:21 final size:20
Alignment explanation
Indices: 80380--80432 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
80370 ATTAAATTAT
*
80380 ATATTTTTATTGTAATAAAA
1 ATATTTTTATTATAATAAAA
80400 ATATAATTTTATTAT-ATAAACTA
1 ATAT--TTTTATTATAATAAA--A
80423 ATATTTTTAT
1 ATATTTTTAT
80433 AATTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 4 0.14
21 11 0.39
22 8 0.29
23 5 0.18
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (20 bp):
ATATTTTTATTATAATAAAA
Found at i:80876 original size:17 final size:17
Alignment explanation
Indices: 80854--80888 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
80844 TATACCATAA
80854 AATATTAAAATATTATT
1 AATATTAAAATATTATT
* *
80871 AATATTAATATTTTATT
1 AATATTAAAATATTATT
80888 A
1 A
80889 TTTAATTGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATATTAAAATATTATT
Found at i:84172 original size:6 final size:6
Alignment explanation
Indices: 84161--84188 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
84151 GTAAAGAGGA
84161 GAAGAG GAAGAG GAAGAG GAAGAG GAAG
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAG
84189 CATCGGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:91228 original size:28 final size:29
Alignment explanation
Indices: 91182--91237 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
91172 AAATTAATAA
91182 TAATAAAATTATACATTAACT-TTTAAAG
1 TAATAAAATTATACATTAACTATTTAAAG
* *
91210 TAATAAAATTTTA-ATTTAATTATTTAAA
1 TAATAAAATTATACA-TTAACTATTTAAA
91238 ATTTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 1 0.04
28 17 0.71
29 6 0.25
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (29 bp):
TAATAAAATTATACATTAACTATTTAAAG
Found at i:91650 original size:18 final size:18
Alignment explanation
Indices: 91627--91661 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
91617 TTTTTATCCA
91627 ATAAAATATT-TATATTTG
1 ATAAAA-ATTATATATTTG
91645 ATAAAAATTATATATTT
1 ATAAAAATTATATATTT
91662 TAGTACTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
ATAAAAATTATATATTTG
Found at i:92691 original size:12 final size:14
Alignment explanation
Indices: 92674--92707 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
92664 TTATATTTTG
92674 AATAAAAT-CA-AT
1 AATAAAATACATAT
92686 AATAAAATACATAT
1 AATAAAATACATAT
92700 AATAAAAT
1 AATAAAAT
92708 TTAAATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 2 0.10
14 10 0.50
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAAAATACATAT
Found at i:97047 original size:21 final size:20
Alignment explanation
Indices: 97022--97069 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
97012 AGCATATAAT
97022 TATATTTTAAAGAGT-AAAATA
1 TATATTTTAAA-A-TCAAAATA
*
97043 TATATCTTAAAATCAAAATA
1 TATATTTTAAAATCAAAATA
97063 T-TATTTT
1 TATATTTT
97070 GTAAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 6 0.25
20 8 0.33
21 10 0.42
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (20 bp):
TATATTTTAAAATCAAAATA
Found at i:98348 original size:17 final size:17
Alignment explanation
Indices: 98284--98338 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
98274 CAGGCCTAAT
*
98284 TTTATTCTAAATTTAAA
1 TTTATTATAAATTTAAA
* *
98301 TTTGGTT-GAAATTTAAA
1 TTT-ATTATAAATTTAAA
98318 TTTATTATAAATTTAAA
1 TTTATTATAAATTTAAA
98335 TTTA
1 TTTA
98339 AAATTTATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 2 0.06
17 28 0.88
18 2 0.06
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (17 bp):
TTTATTATAAATTTAAA
Found at i:99027 original size:12 final size:12
Alignment explanation
Indices: 99010--99039 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
99000 GAGATTTATT
99010 ATTATTAAAAAA
1 ATTATTAAAAAA
*
99022 ATTATTAAAAAT
1 ATTATTAAAAAA
99034 ATTATT
1 ATTATT
99040 TTTAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATTATTAAAAAA
Found at i:99868 original size:12 final size:12
Alignment explanation
Indices: 99851--99875 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
99841 AGGAAAGGGC
99851 GAGAGGATTTTG
1 GAGAGGATTTTG
99863 GAGAGGATTTTG
1 GAGAGGATTTTG
99875 G
1 G
99876 TTTTTTTTTT
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:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (12 bp):
GAGAGGATTTTG
Found at i:100414 original size:29 final size:29
Alignment explanation
Indices: 100372--100741 Score: 298
Period size: 29 Copynumber: 12.6 Consensus size: 29
100362 CACGTGTCCC
*
100372 CGAACCTTCCAAAAATTACCATTTTACCCC
1 CGAA-CTTCCAAAAATTACCATTTTACCCT
* * *
100402 CGAACTTCTAAAAA-TCCCATTTTTAACCT
1 CGAACTTCCAAAAATTACCA-TTTTACCCT
*
100431 CGAACCTTCCAAAAATTACCATTTTGCCCT
1 CGAA-CTTCCAAAAATTACCATTTTACCCT
100461 CGAACTTCCAAAAA-T-CTCATTTTTGA-CCT
1 CGAACTTCCAAAAATTAC-CA-TTTT-ACCCT
* *
100490 CGAACCTTCC-AAAATTACCATTTTGCCCC
1 CGAA-CTTCCAAAAATTACCATTTTACCCT
* * * *
100519 CAAACTTCCAAAAA-TCCCTTTTTAACCT
1 CGAACTTCCAAAAATTACCATTTTACCCT
100547 CGAACCTTCCAAAAATTACCATTTTACCC-
1 CGAA-CTTCCAAAAATTACCATTTTACCCT
* *
100576 CTAAACTTCCAAAAA-TCCCATTTTAGACCCT
1 C-GAACTTCCAAAAATTACCATTTT--ACCCT
100607 CGAACCTTCCAAAAATTACCATTTTACCC-
1 CGAA-CTTCCAAAAATTACCATTTTACCCT
* * *
100636 CTAAACTTCCAAAAA-TCCCATTTTTAACCT
1 C-GAACTTCCAAAAATTACCA-TTTTACCCT
* * *
100666 CGAACCTT-CTAAAATTACAATTTTACCCC
1 CGAA-CTTCCAAAAATTACCATTTTACCCT
*
100695 CGAACTTTCAAAAATT-CCATTTTTGA-CCT
1 CGAACTTCCAAAAATTACCA-TTTT-ACCCT
* *
100724 CGAACATCTAAAAATTAC
1 CGAACTTCCAAAAATTAC
100742 TACTTTACTC
Statistics
Matches: 272, Mismatches: 40, Indels: 56
0.74 0.11 0.15
Matches are distributed among these distances:
27 1 0.00
28 41 0.15
29 141 0.52
30 65 0.24
31 16 0.06
32 8 0.03
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (29 bp):
CGAACTTCCAAAAATTACCATTTTACCCT
Found at i:100749 original size:58 final size:59
Alignment explanation
Indices: 100372--100741 Score: 525
Period size: 58 Copynumber: 6.3 Consensus size: 59
100362 CACGTGTCCC
*
100372 CGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCTAAAAATCCCATTTTTAACCT
1 CGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCT
* * * *
100431 CGAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCTCATTTTTGACCT
1 CGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCT
* *
100490 CGAACCTTCC-AAAATTACCATTTTGCCCCCAAACTTCCAAAAATCCC-TTTTTAACCT
1 CGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCT
**
100547 CGAACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCA-TTTTAGACCCT
1 CGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTA-A-CCT
**
100607 CGAACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCT
1 CGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCT
* * * * *
100666 CGAACCTT-CTAAAATTACAATTTTACCCCCGAACTTTCAAAAATTCCATTTTTGACCT
1 CGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCT
* *
100724 CGAA-CATCTAAAAATTAC
1 CGAACCTTCCAAAAATTAC
100742 TACTTTACTC
Statistics
Matches: 284, Mismatches: 21, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
57 21 0.07
58 129 0.45
59 76 0.27
60 53 0.19
61 5 0.02
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.31
Consensus pattern (59 bp):
CGAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCT
Found at i:100811 original size:176 final size:176
Alignment explanation
Indices: 100372--100754 Score: 479
Period size: 176 Copynumber: 2.2 Consensus size: 176
100362 CACGTGTCCC
* * * *
100372 CGAACCTTCCAAAAATTACCATTTTACCCCCG-AACTTCTAAAAATCCCATTTTTA-A-CCTCGA
1 CGAACCATCCAAAAATTACCACTTTA-CCCCGAAACTTCCAAAAATCCCA-TTTTAGACCCTCAA
* * * * *
100434 ACCTTCCAAAAATTACCATTTT-GCCCTCGAACTTCCAAAAATCTCATTTTTGACCTCGAACCTT
64 AACTTCCAAAAATTACCATTTTACCCCT-AAACTTCCAAAAATCCCATTTTTAACCTCGAACCTT
* * *
100498 CCAAAATTACCATTTTGCCCCCAAACTTCCAAAAATCCCTTTTTAACCT
128 CCAAAATTACAATTTTACCCCCAAACTTCCAAAAATCCATTTTTAACCT
* * * * *
100547 CGAACCTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTAGACCCTCGAAC
1 CGAACCATCCAAAAATTACCACTTTACCCCGAAACTTCCAAAAATCCCATTTTAGACCCTCAAAA
*
100612 CTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTCGAACCTTCTA
66 CTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTCGAACCTTCCA
* * *
100677 AAATTACAATTTTACCCCCGAACTTTCAAAAATTCCATTTTTGACCT
131 AAATTACAATTTTACCCCCAAACTTCCAAAAA-TCCATTTTTAACCT
* *
100724 CGAA-CATCTAAAAATTACTACTTTACTCCCG
1 CGAACCATCCAAAAATTACCACTTTAC-CCCG
100755 GATGTTCGAA
Statistics
Matches: 184, Mismatches: 18, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
174 9 0.05
175 43 0.23
176 109 0.59
177 23 0.12
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (176 bp):
CGAACCATCCAAAAATTACCACTTTACCCCGAAACTTCCAAAAATCCCATTTTAGACCCTCAAAA
CTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTCGAACCTTCCA
AAATTACAATTTTACCCCCAAACTTCCAAAAATCCATTTTTAACCT
Found at i:111290 original size:211 final size:211
Alignment explanation
Indices: 110966--112734 Score: 2565
Period size: 211 Copynumber: 8.4 Consensus size: 211
110956 AGAAGAAGAT
* *
110966 CCAAACGAGG-T-GAAACGATGCAAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGA
1 CCAAACGAGGCTCGAAACGA-GC-A--AAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGA
111029 AGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCT
62 AGCAGGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCT
* * * * *
111094 TCTTGATGAGATACGGAGAAGTGAATTATAACAAACGATACAGTCATCTTCCGGACGAGATACTG
127 TCCTGATGAGATACGGAGAAGCGAATTAAAACAAACGATGCGGTCATCTTCCGGACGAGATACTG
111159 AGAAGAAGACCAAATCAAAC
192 AGAAGAAGACCAAATCAAAC
* * *
111179 CCAAATGAGGCTTGAAACGAGTAAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA
1 CCAAACGAGGCTCGAAACGAGCAAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA
*
111244 GGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACCT-AGAAGTGTACCAAATTCATCTTCC
66 GGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATA-CTGAGAAGTGTACCAAATTCGTCTTCC
* * *
111308 TGATGAGATACGGAGAAGCAAATTAAAACAAACGATGCGGTCATCTTCTGGACAAGATACTGAGA
130 TGATGAGATACGGAGAAGCGAATTAAAACAAACGATGCGGTCATCTTCCGGACGAGATACTGAGA
111373 AGAAGACCAAATCAAAC
195 AGAAGACCAAATCAAAC
* * * *
111390 CCAAACGAGGCTCAAAACAAGCAAAATCTTTGAACCTCGGCTTCCTGATGAGATACTGAGAAGCA
1 CCAAACGAGGCTCGAAACGAGCAAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA
* * *
111455 GGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTTCCAAATTTGTCTTCTT
66 GGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCT
* ** * * *
111520 GATGAGGTATAGAGAAGCGAATTGAAACGAACAAACAATGCGGTCATCTTCCTGACGAGATAATG
131 GATGAGATACGGAGAAGCGAATT--AA--AACAAACGATGCGGTCATCTTCCGGACGAGATACTG
*
111585 AGAAAAAGACCAAATCAAAC
192 AGAAGAAGACCAAATCAAAC
111605 CCAAACGAGGCTCGAAACGAGCAAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA
1 CCAAACGAGGCTCGAAACGAGCAAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA
* *
111670 GGTCAAAGCAATAAAAGATTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCT
66 GGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCT
**
111735 GATGAGATACAAAGAAGCGAATTAAAACAAACGATGCGGTCATCTTCCGGACGAGATACTGAGAA
131 GATGAGATACGGAGAAGCGAATTAAAACAAACGATGCGGTCATCTTCCGGACGAGATACTGAGAA
111800 GAAGACCAAATCAAAC
196 GAAGACCAAATCAAAC
** * * *
111816 CCAAACGATACTCGAAACGAGAAAAATCTTTGAACCCCAGCTTTCTGATGAGATTCTGAGAAGCA
1 CCAAACGAGGCTCGAAACGAGCAAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA
* *
111881 GGTCGAAGCAATAAAAGATTAGCTTCCTGATGAGATACCGAGAAGTGTACCAAATTCGTCTTCCT
66 GGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCT
*
111946 GATGAGATACGGAGAAGCGAATTAAAACAAACGATGCGGTCATCTTCCGCACGAGATACTGAGAA
131 GATGAGATACGGAGAAGCGAATTAAAACAAACGATGCGGTCATCTTCCGGACGAGATACTGAGAA
112011 GAAGACCAAATCAAAC
196 GAAGACCAAATCAAAC
* * * *
112027 CCAAACGAGGCTCGAAACGAGTAAAATCTTTGAACCCCAGCTTGCTAATGAGATACGGAGAAGCA
1 CCAAACGAGGCTCGAAACGAGCAAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA
*
112092 GGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCATCTTCCT
66 GGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCT
* * * *
112157 GATGAGATACGGAGAAGCAAATTGAAACAAATGATACGGTCATCTTCCGGACGAGATACTGAGAA
131 GATGAGATACGGAGAAGCGAATTAAAACAAACGATGCGGTCATCTTCCGGACGAGATACTGAGAA
*
112222 TAAGACCAAATCAAAC
196 GAAGACCAAATCAAAC
* *
112238 CCAAACGAGACTCGAAACGAGTAAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA
1 CCAAACGAGGCTCGAAACGAGCAAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA
* * * *
112303 AGTCAAAGCAATAAAAGGTTAGCTTCTTGATGAGATACCGAGAAGTGTACCAAATTCGTCTTCCT
66 GGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCT
* * * *
112368 GATGAGATACGGAGAAGCGAATTAAAACAAATGATGCGGTCAACTTCTGGATGAGATACTGAGAA
131 GATGAGATACGGAGAAGCGAATTAAAACAAACGATGCGGTCATCTTCCGGACGAGATACTGAGAA
*
112433 GAAGACCAAATAAAAC
196 GAAGACCAAATCAAAC
* * * *
112449 CCAAACGAGGCTCGAAACGAGCAAAATCTTCGAACCCCAACTTCTTGATGAGACACTGAGAAGCA
1 CCAAACGAGGCTCGAAACGAGCAAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA
* * * *
112514 GGTCGAAGCAATAAAGGGTTAGCTTCCTGATGAGATACTTAGAAGTGAACCAAATTTGTCTTCCT
66 GGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCT
* * ** * * * * ** *
112579 AATGAGGTATAGAGAAGCGAATTGAAACGAGCAGCGACGCGATCATCTTCCTAACGAGACACT--
131 GATGAGATACGGAGAAGCGAATTAAAAC-A--AACGATGCGGTCATCTTCCGGACGAGATACTGA
112642 G-AGAAG----AAT---AC
193 GAAGAAGACCAAATCAAAC
* * * * *
112653 CCAAACGAGGCTCGAAACGAGCAAAATCTTCGAACCCCAGCTTCTTGATGAGACACGGGGAAGCA
1 CCAAACGAGGCTCGAAACGAGCAAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA
*
112718 GGTCGAAGTAATAAAAG
66 GGTCGAAGCAATAAAAG
112735 TCATCTTCCC
Statistics
Matches: 1418, Mismatches: 127, Indels: 31
0.90 0.08 0.02
Matches are distributed among these distances:
204 79 0.06
207 3 0.00
210 2 0.00
211 1095 0.77
212 4 0.00
213 14 0.01
214 23 0.02
215 198 0.14
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (211 bp):
CCAAACGAGGCTCGAAACGAGCAAAATCTTTGAACCCCAGCTTCCTGATGAGATACTGAGAAGCA
GGTCGAAGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGTACCAAATTCGTCTTCCT
GATGAGATACGGAGAAGCGAATTAAAACAAACGATGCGGTCATCTTCCGGACGAGATACTGAGAA
GAAGACCAAATCAAAC
Found at i:113338 original size:17 final size:17
Alignment explanation
Indices: 113249--113325 Score: 91
Period size: 17 Copynumber: 4.5 Consensus size: 17
113239 CCCAATCAAC
*
113249 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAT
* *
113266 TTAAGTTTATTCTAAAT
1 TTAAATTTATTTTAAAT
** *
113283 TTAAATTTGGTTGAAAT
1 TTAAATTTATTTTAAAT
*
113300 TTAAATTTATTATAAAT
1 TTAAATTTATTTTAAAT
113317 TTAAATTTA
1 TTAAATTTA
113326 AAATTATTTT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.42, C:0.01, G:0.05, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTTTAAAT
Found at i:115147 original size:29 final size:30
Alignment explanation
Indices: 115106--115309 Score: 185
Period size: 29 Copynumber: 6.9 Consensus size: 30
115096 ATGGTCCCCA
*
115106 AACCTTCCAAAAATTACCATTTT-ACTCTTG
1 AACCTTCCAAAAATTACCATTTTGAC-CCTG
*
115136 AA-CTTTCAAAAA-T-CTCATTTTTGACCCTG
1 AACCTTCCAAAAATTAC-CA-TTTTGACCCTG
* *
115165 AACCTTCCAAAAATTACCATTTTGCCCCCG
1 AACCTTCCAAAAATTACCATTTTGACCCTG
* * **
115195 AA-CTTCCAAAAA-TCCCATTTTTTACCCCA
1 AACCTTCCAAAAATTACCA-TTTTGACCCTG
115224 AACCTTCCAAAAATTACCATTTTG-CCCTCG
1 AACCTTCCAAAAATTACCATTTTGACCCT-G
* **
115254 AA-CTTCCAAAAA-TCCCATTTTTGACCCCA
1 AACCTTCCAAAAATTACCA-TTTTGACCCTG
115283 AACCTTCCAAAAATTACCATTTT-ACCC
1 AACCTTCCAAAAATTACCATTTTGACCC
115310 CCAAACTTCC
Statistics
Matches: 143, Mismatches: 17, Indels: 29
0.76 0.09 0.15
Matches are distributed among these distances:
27 1 0.01
28 11 0.08
29 62 0.43
30 57 0.40
31 11 0.08
32 1 0.01
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (30 bp):
AACCTTCCAAAAATTACCATTTTGACCCTG
Found at i:115310 original size:29 final size:27
Alignment explanation
Indices: 115101--115334 Score: 164
Period size: 29 Copynumber: 8.0 Consensus size: 27
115091 CCCCGATGGT
115101 CCCCAAACCTTCCAAAAATTACCATTTTA
1 CCCCAAA-CTTCCAAAAA-TACCATTTTA
*** *
115130 CTCTTGAACTTTCAAAAAT-CTCATTTTTGA
1 C-CCCAAACTTCCAAAAATAC-CA-TTTT-A
* * *
115160 CCCTGAACCTTCCAAAAATTACCATTTTGC
1 CCC-CAAACTTCCAAAAA-TACCATTTT-A
* *
115190 CCCCGAACTTCCAAAAATCCCATTTTTTA
1 CCCCAAACTTCCAAAAATACCA--TTTTA
*
115219 CCCCAAACCTTCCAAAAATTACCATTTTG
1 CCCCAAA-CTTCCAAAAA-TACCATTTTA
* *
115248 CCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCC-CAAACTTCCAAAAATACCA-TTTT-A
115278 CCCCAAACCTTCCAAAAATTACCATTTTA
1 CCCCAAA-CTTCCAAAAA-TACCATTTTA
* *
115307 CCCCCAAACTTCCAAGAATCCCATTTTA
1 -CCCCAAACTTCCAAAAATACCATTTTA
115335 AACCCCGAAC
Statistics
Matches: 163, Mismatches: 25, Indels: 35
0.73 0.11 0.16
Matches are distributed among these distances:
27 1 0.01
28 20 0.12
29 66 0.40
30 64 0.39
31 11 0.07
32 1 0.01
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.30
Consensus pattern (27 bp):
CCCCAAACTTCCAAAAATACCATTTTA
Found at i:115340 original size:59 final size:59
Alignment explanation
Indices: 115101--115333 Score: 349
Period size: 59 Copynumber: 3.9 Consensus size: 59
115091 CCCCGATGGT
* ** * *
115101 CCCCAAACCTTCCAAAAATTACCATTTTACTCTTGAACTTTCAAAAATCTCATTTTTGA
1 CCCCAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
** * *
115160 CCCTGAACCTTCCAAAAATTACCATTTTGCCCCCGAACTTCCAAAAATCCCATTTTTTA
1 CCCCAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* *
115219 CCCCAAACCTTCCAAAAATTACCATTTTGCCCTCGAACTTCCAAAAATCCCATTTTTGA
1 CCCCAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* *
115278 CCCCAAACCTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAGAATCCCATTTT
1 CCCCAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTT
115334 AAACCCCGAA
Statistics
Matches: 157, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 157 1.00
ACGTcount: A:0.33, C:0.33, G:0.04, T:0.30
Consensus pattern (59 bp):
CCCCAAACCTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:117908 original size:27 final size:27
Alignment explanation
Indices: 117867--117951 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
117857 AACACATTAG
*
117867 GAAATGAAAGCCTTTGCGGTAAATCAT
1 GAAATGAAAGCCTTTGCGGCAAATCAT
* * * *
117894 GAAATTAAAGTCTTTGTGGCGAATCAT
1 GAAATGAAAGCCTTTGCGGCAAATCAT
* * *
117921 GAAA-GAAAAACCTTTGTGGCAAATTAT
1 GAAATG-AAAGCCTTTGCGGCAAATCAT
117948 GAAA
1 GAAA
117952 AGAATAGCAT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (27 bp):
GAAATGAAAGCCTTTGCGGCAAATCAT
Found at i:117964 original size:28 final size:27
Alignment explanation
Indices: 117906--117968 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
117896 AATTAAAGTC
* *
117906 TTTGTGGCGAATCATGAAAGAAAAACC
1 TTTGTGGCAAATCATGAAAGAAAAACA
* * *
117933 TTTGTGGCAAATTATGAAAAGAATAGCA
1 TTTGTGGCAAATCATG-AAAGAAAAACA
117961 TTTGTGGC
1 TTTGTGGC
117969 GTACTCTGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 14 0.47
28 16 0.53
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.29
Consensus pattern (27 bp):
TTTGTGGCAAATCATGAAAGAAAAACA
Found at i:118783 original size:13 final size:13
Alignment explanation
Indices: 118765--118798 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
118755 TATCGTTGTA
118765 ATTGTATTTACTT
1 ATTGTATTTACTT
*
118778 ATTGTATATACTT
1 ATTGTATTTACTT
118791 A-TGTATTT
1 ATTGTATTT
118799 CAATTTGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (13 bp):
ATTGTATTTACTT
Found at i:135088 original size:24 final size:25
Alignment explanation
Indices: 135061--135107 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
135051 TTTAATATGA
*
135061 TTTT-AATAATACCCACTTAGATAC
1 TTTTAAATAAAACCCACTTAGATAC
135085 TTTTAAATAAAACCCACTTAGAT
1 TTTTAAATAAAACCCACTTAGAT
135108 CTCCACATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.36
Consensus pattern (25 bp):
TTTTAAATAAAACCCACTTAGATAC
Found at i:135258 original size:51 final size:50
Alignment explanation
Indices: 135193--135297 Score: 129
Period size: 51 Copynumber: 2.1 Consensus size: 50
135183 TATCTCTACC
* * * *
135193 ATTATTTATTTATGTAAATTTGTTTTTAGGTTATTCAGTTATCTATTTTTA
1 ATTATTTATCTATGTAAATTTGTATTTACGTTACTCAGTTATCTA-TTTTA
** * *
135244 ATTATTTATCTATGTATTTTTGTATTTACTTTACTCATTTATCTATTTTA
1 ATTATTTATCTATGTAAATTTGTATTTACGTTACTCAGTTATCTATTTTA
135294 ATTA
1 ATTA
135298 CAAAATAATG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
50 9 0.20
51 37 0.80
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.61
Consensus pattern (50 bp):
ATTATTTATCTATGTAAATTTGTATTTACGTTACTCAGTTATCTATTTTA
Found at i:141776 original size:25 final size:27
Alignment explanation
Indices: 141747--141796 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
141737 GACCCCAATC
141747 GAATTAATTCGATT-AA-TGATTAACT
1 GAATTAATTCGATTGAATTGATTAACT
*
141772 GAATTAATTCGGTTGAATTGATTAA
1 GAATTAATTCGATTGAATTGATTAA
141797 ATCAACTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.59
26 2 0.09
27 7 0.32
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.40
Consensus pattern (27 bp):
GAATTAATTCGATTGAATTGATTAACT
Found at i:142249 original size:14 final size:14
Alignment explanation
Indices: 142230--142260 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
142220 TAAGTTTAAA
142230 AAATTTAATTAATT
1 AAATTTAATTAATT
*
142244 AAATTTATTTAATT
1 AAATTTAATTAATT
142258 AAA
1 AAA
142261 AATCTATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTTAATTAATT
Found at i:143175 original size:14 final size:14
Alignment explanation
Indices: 143157--143191 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
143147 ATAAAATTTT
*
143157 AAAATTGATAAAAA
1 AAAATTAATAAAAA
*
143171 CAAATTAATAAAAA
1 AAAATTAATAAAAA
143185 AAAATTA
1 AAAATTA
143192 GTTATATAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (14 bp):
AAAATTAATAAAAA
Found at i:152537 original size:18 final size:18
Alignment explanation
Indices: 152514--152550 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
152504 TATAGTTTGA
* *
152514 TATTCGATTTATTTAAAT
1 TATTCGAGTTATTGAAAT
152532 TATTCGAGTTATTGAAAT
1 TATTCGAGTTATTGAAAT
152550 T
1 T
152551 CGAAAACTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TATTCGAGTTATTGAAAT
Found at i:159402 original size:9 final size:9
Alignment explanation
Indices: 159353--159440 Score: 56
Period size: 9 Copynumber: 9.6 Consensus size: 9
159343 TAAATGTTTT
159353 TTTTTACAA
1 TTTTTACAA
*
159362 CTTTTA-ATA
1 TTTTTACA-A
*
159371 TTTTTAGAA
1 TTTTTACAA
*
159380 TATTTTAAATA
1 T-TTTTACA-A
159391 TTTTTTAC-A
1 -TTTTTACAA
*
159400 TTTTATATAA
1 TTTT-TACAA
*
159410 TTTTTATAA
1 TTTTTACAA
159419 TTTTTACAA
1 TTTTTACAA
*
159428 TTCTTA-AA
1 TTTTTACAA
159436 TTTTT
1 TTTTT
159441 TATAATAATG
Statistics
Matches: 64, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
8 11 0.17
9 34 0.53
10 12 0.19
11 6 0.09
12 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.60
Consensus pattern (9 bp):
TTTTTACAA
Found at i:159541 original size:9 final size:8
Alignment explanation
Indices: 159485--159572 Score: 60
Period size: 8 Copynumber: 11.0 Consensus size: 8
159475 TTTTTTGTAA
159485 TTTT-TAT
1 TTTTATAT
159492 TTTTATACT
1 TTTTATA-T
159501 TTTTA-AT
1 TTTTATAT
*
159508 AATTTATAT
1 -TTTTATAT
159517 TTTT-T-T
1 TTTTATAT
* *
159523 TTCTAGAT
1 TTTTATAT
159531 TTTATATAT
1 TTT-TATAT
159540 TTTTGA-AT
1 TTTT-ATAT
159548 TTTTATATT
1 TTTTATA-T
159557 TTTTATAT
1 TTTTATAT
*
159565 TTATATAT
1 TTTTATAT
159573 ATTTGATAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
6 4 0.06
7 7 0.11
8 29 0.45
9 24 0.38
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (8 bp):
TTTTATAT
Found at i:159978 original size:11 final size:12
Alignment explanation
Indices: 159959--160040 Score: 75
Period size: 11 Copynumber: 7.2 Consensus size: 12
159949 TTGGGCCCCC
*
159959 TTTTTAATTT-A
1 TTTTAAATTTAA
159970 TTTTAAATTTAA
1 TTTTAAATTTAA
*
159982 TTTT-ATTTTAA
1 TTTTAAATTTAA
*
159993 ATTTAAA-TTAA
1 TTTTAAATTTAA
*
160004 -TCTAAATTTAA
1 TTTTAAATTTAA
*
160015 ATTT-AATTTAA
1 TTTTAAATTTAA
*
160026 ATTTAAATTTAA
1 TTTTAAATTTAA
160038 TTT
1 TTT
160041 CAAAATTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
10 5 0.08
11 37 0.63
12 17 0.29
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTTAAATTTAA
Found at i:159988 original size:17 final size:16
Alignment explanation
Indices: 159961--160040 Score: 97
Period size: 17 Copynumber: 4.8 Consensus size: 16
159951 GGGCCCCCTT
*
159961 TTTAATTTATTTTAAA
1 TTTAATTTAATTTAAA
*
159977 TTTAATTTTATTTTAAA
1 TTTAA-TTTAATTTAAA
* *
159994 TTTAAATTAATCTAAA
1 TTTAATTTAATTTAAA
160010 TTTAAATTTAATTTAAA
1 TTT-AATTTAATTTAAA
160027 TTTAAATTTAATTT
1 TTT-AATTTAATTT
160041 CAAAATTAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
16 16 0.28
17 41 0.72
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTAATTTAATTTAAA
Found at i:159998 original size:33 final size:33
Alignment explanation
Indices: 159961--160038 Score: 102
Period size: 33 Copynumber: 2.3 Consensus size: 33
159951 GGGCCCCCTT
* * * *
159961 TTTAATTTATTTTAAATTTAATTTTATTTTAAA
1 TTTAATTTAATCTAAATTTAAATTTAATTTAAA
*
159994 TTTAAATTAATCTAAATTTAAATTTAATTTAAA
1 TTTAATTTAATCTAAATTTAAATTTAATTTAAA
160027 TTTAAATTTAAT
1 TTT-AATTTAAT
160039 TTCAAAATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
33 31 0.82
34 7 0.18
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (33 bp):
TTTAATTTAATCTAAATTTAAATTTAATTTAAA
Found at i:160051 original size:6 final size:6
Alignment explanation
Indices: 159971--160050 Score: 80
Period size: 6 Copynumber: 14.0 Consensus size: 6
159961 TTTAATTTAT
* * *
159971 TTTAAA TTT-AA TTTTAT TTTAAA TTTAAA -TT-AA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
160016 TTT-AA TTTAAA TTTAAA TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
160051 AGAAAAGAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
4 2 0.03
5 18 0.29
6 38 0.61
7 4 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:160160 original size:26 final size:25
Alignment explanation
Indices: 160081--160160 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 25
160071 AACAATGTCC
*
160081 AATTACAAATGGCCCAAGTCAGCCA
1 AATTACAAATGGCCCAAGTCAACCA
* * * *
160106 AAATAC--ATGACCCAAATGCCATACTA
1 AATTACAAATGGCCC-AA-GTCA-ACCA
160132 AATTACAAATGGCCCAAGTCAACCCA
1 AATTACAAATGGCCCAAGTCAA-CCA
160158 AAT
1 AAT
160161 ACCCTAAGCC
Statistics
Matches: 40, Mismatches: 9, Indels: 11
0.67 0.15 0.18
Matches are distributed among these distances:
23 6 0.15
24 2 0.05
25 9 0.22
26 15 0.38
27 2 0.05
28 6 0.15
ACGTcount: A:0.44, C:0.28, G:0.11, T:0.17
Consensus pattern (25 bp):
AATTACAAATGGCCCAAGTCAACCA
Found at i:160708 original size:30 final size:30
Alignment explanation
Indices: 160637--160919 Score: 254
Period size: 30 Copynumber: 9.4 Consensus size: 30
160627 CGAACTTCTG
* *
160637 AAAATCCCATTTTTGACCCTAAAACTTCCAA
1 AAAATCCCATTTTTTACCCCAAAACTTCC-A
* ** *
160668 AAAATTCCATTTTTTACCCCCGAACTTCTA
1 AAAATCCCATTTTTTACCCCAAAACTTCCA
* *
160698 AAAATCCCATTTTTGACCCCAAAACTTCTA
1 AAAATCCCATTTTTTACCCCAAAACTTCCA
* **
160728 AAAATTCCA-TTTTTACCCTCGGAACTTCCA
1 AAAATCCCATTTTTTACCC-CAAAACTTCCA
* *
160758 AAAATTCTA-TTTTTACCCCCAAAACTTCCA
1 AAAATCCCATTTTTTA-CCCCAAAACTTCCA
*
160788 AAAATCCCATTTTTGACCCCAAAAACTTCCA
1 AAAATCCCATTTTTTACCCC-AAAACTTCCA
* * *
160819 AAAAT--TATATTTTTACCCTC-AAACTTTCT
1 AAAATCCCAT-TTTTTACCC-CAAAACTTCCA
* *
160848 AAAATCCCATTTTTGACCCCAAAACTTCAA
1 AAAATCCCATTTTTTACCCCAAAACTTCCA
* * * *
160878 AAAATTCTA-TTTTTACCCCTAAATTTCCA
1 AAAATCCCATTTTTTACCCCAAAACTTCCA
*
160907 AAAATGCCATTTT
1 AAAATCCCATTTT
160920 AACCTCGGAA
Statistics
Matches: 204, Mismatches: 38, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
29 46 0.23
30 109 0.53
31 49 0.24
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (30 bp):
AAAATCCCATTTTTTACCCCAAAACTTCCA
Found at i:160722 original size:61 final size:59
Alignment explanation
Indices: 160645--160919 Score: 302
Period size: 60 Copynumber: 4.6 Consensus size: 59
160635 TGAAAATCCC
* * * * * * *
160645 ATTTTTGACCCTAAAACTTCCAAAAAATTCCATTTTTTACCCCCGAACTTCTAAAAATCCC
1 ATTTTT-ACCCCAAAACTTCC-AAAAATCCCATTTTTGACCCCAGAACTTCCAAAAATTCT
* * *
160706 ATTTTTGACCCCAAAACTTCTAAAAATTCCATTTTT-ACCCTCGGAACTTCCAAAAATTCT
1 ATTTTT-ACCCCAAAACTTCCAAAAATCCCATTTTTGACCC-CAGAACTTCCAAAAATTCT
* *
160766 ATTTTTACCCCCAAAACTTCCAAAAATCCCATTTTTGACCCCAAAAACTTCCAAAAATTAT
1 ATTTTTA-CCCCAAAACTTCCAAAAATCCCATTTTTGACCCC-AGAACTTCCAAAAATTCT
* * * *
160827 ATTTTTACCCTC-AAACTTTCTAAAATCCCATTTTTGACCCCAAAACTTCAAAAAATTCT
1 ATTTTTACCC-CAAAACTTCCAAAAATCCCATTTTTGACCCCAGAACTTCCAAAAATTCT
* * *
160886 ATTTTTACCCCTAAATTTCCAAAAATGCCATTTT
1 ATTTTTACCCCAAAACTTCCAAAAATCCCATTTT
160920 AACCTCGGAA
Statistics
Matches: 189, Mismatches: 19, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
58 1 0.01
59 49 0.26
60 93 0.49
61 46 0.24
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (59 bp):
ATTTTTACCCCAAAACTTCCAAAAATCCCATTTTTGACCCCAGAACTTCCAAAAATTCT
Found at i:160793 original size:90 final size:90
Alignment explanation
Indices: 160637--160919 Score: 324
Period size: 90 Copynumber: 3.1 Consensus size: 90
160627 CGAACTTCTG
* * * *
160637 AAAATCCCATTTTTGACCCT-AAAACTTCCAAAAAATTCCATTTTTTACCCCC-GAACTTCTAAA
1 AAAATTCCATTTTT-ACCCTCGAAACTTCC-AAAAATTCCA-TTTTTACCCCCAAAACTTCAAAA
*
160700 AATCCCATTTTTGACCCCAAAACTTCTA
63 AATCCCATTTTTGACCCCAAAACTTCCA
* * *
160728 AAAATTCCATTTTTACCCTCGGAACTTCCAAAAATTCTATTTTTACCCCCAAAACTTCCAAAAAT
1 AAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTTACCCCCAAAACTTCAAAAAAT
160793 CCCATTTTTGACCCCAAAAACTTCCA
66 CCCATTTTTGACCCC-AAAACTTCCA
** * * *
160819 AAAATTATATTTTTACCCTC-AAACTTTCTAAAATCCCATTTTTGA-CCCCAAAACTTCAAAAAA
1 AAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTT-ACCCCCAAAACTTCAAAAAA
* * * *
160882 TTCTATTTTT-ACCCCTAAATTTCCA
65 TCCCATTTTTGACCCCAAAACTTCCA
*
160907 AAAATGCCATTTT
1 AAAATTCCATTTT
160920 AACCTCGGAA
Statistics
Matches: 166, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
88 18 0.11
89 16 0.10
90 84 0.51
91 48 0.29
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.34
Consensus pattern (90 bp):
AAAATTCCATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTTACCCCCAAAACTTCAAAAAAT
CCCATTTTTGACCCCAAAACTTCCA
Found at i:160967 original size:87 final size:87
Alignment explanation
Indices: 160877--161042 Score: 205
Period size: 87 Copynumber: 1.9 Consensus size: 87
160867 CAAAACTTCA
* * *
160877 AAAAATTCTATTTTT-ACCCCTAAA-TTT-CCAAAAATGCCATTTTAACCTCG-GAACTCTCAAA
1 AAAAATTCCATTTTTAACCCC-AAATTTTCCCAAAAATACCATTTCAACCTCGAGAA-T-TCAAA
*
160938 ATTACCCTTTTACCCTCGAATATTG
63 ATTACCATTTTACCCTCGAATATTG
* * * *
160963 AAAAATTCCATTTTTAAGCCCAAATTTTCCCAAAATTACTATTTCACCCTCGAGAATTCAAAATT
1 AAAAATTCCATTTTTAACCCCAAATTTTCCCAAAAATACCATTTCAACCTCGAGAATTCAAAATT
161028 ACCATTTTACCCTCG
66 ACCATTTTACCCTCG
161043 GGTATCCGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
86 17 0.25
87 29 0.43
88 19 0.28
89 3 0.04
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (87 bp):
AAAAATTCCATTTTTAACCCCAAATTTTCCCAAAAATACCATTTCAACCTCGAGAATTCAAAATT
ACCATTTTACCCTCGAATATTG
Found at i:172228 original size:27 final size:27
Alignment explanation
Indices: 172197--172255 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
172187 AATTTTCAAT
*
172197 TAATATTGTCTCCTTTGATCCTCCTTG
1 TAATATTGTCTCCTTCGATCCTCCTTG
* * * *
172224 TAATATTGTTTCGTTCGATCCTCTTTT
1 TAATATTGTCTCCTTCGATCCTCCTTG
172251 TAATA
1 TAATA
172256 GAATTCTTGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.20, G:0.10, T:0.51
Consensus pattern (27 bp):
TAATATTGTCTCCTTCGATCCTCCTTG
Found at i:173265 original size:181 final size:181
Alignment explanation
Indices: 172956--173479 Score: 922
Period size: 181 Copynumber: 2.9 Consensus size: 181
172946 AGATTGAATG
172956 CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGGTATGAGCAAA
1 CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGGTATGAGCAAA
*
173021 GCTTCGAATCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTC
66 GCTTCGAATCCCAGCTTCTTGGTGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTC
*
173086 CTGATGAGATACTGAGAAGTGAACCAAATTCGCGGATTGAAACAAGCGACG
131 CTGATGAGATACTGAGAAGTGAACCAAATTCGCGGATTGAAACAAGCGACA
* * *
173137 TGGTCATCTTCCTGATGAGATACTGAGAAGAATACCAAGTCAAACCCACGCTCGGTGTGAGCAAA
1 CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGGTATGAGCAAA
* *
173202 GCTTCGAATCCCAGCTTCCTGGTGAGACACTGAGAAGCAGGTCGAAGCAATAAACGATTAGCTTC
66 GCTTCGAATCCCAGCTTCTTGGTGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTC
* * *
173267 CTGATGAGATAATGAGAAGTGAACCAAATTCACGGATTGATACAAGCGACA
131 CTGATGAGATACTGAGAAGTGAACCAAATTCGCGGATTGAAACAAGCGACA
*
173318 CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGGTATGAACAAA
1 CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGGTATGAGCAAA
* *
173383 GCTTTGAATCCCAGCTTCTTGGTGAGACACTGAGAAGCAGGTCGAAGCAATAAATGGTTAGCTTC
66 GCTTCGAATCCCAGCTTCTTGGTGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTC
*
173448 CTGATGATATACTGAGAAGTGAACCAAATTCG
131 CTGATGAGATACTGAGAAGTGAACCAAATTCG
173480 TTCTCCTGAT
Statistics
Matches: 322, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
181 322 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (181 bp):
CGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGGTATGAGCAAA
GCTTCGAATCCCAGCTTCTTGGTGAGACACTGAGAAGCAGGTCGAAGCAATAAACGGTTAGCTTC
CTGATGAGATACTGAGAAGTGAACCAAATTCGCGGATTGAAACAAGCGACA
Found at i:174113 original size:17 final size:16
Alignment explanation
Indices: 174084--174173 Score: 99
Period size: 17 Copynumber: 5.4 Consensus size: 16
174074 AGGCCCCTTT
*
174084 TTTAAATTATTTTAAA
1 TTTAAATTAATTTAAA
* *
174100 TTTAGATATATTTTAAA
1 TTTAAAT-TAATTTAAA
*
174117 TTTAAATTAATCTAAA
1 TTTAAATTAATTTAAA
174133 TTTAAATTTAATTTAAA
1 TTTAAA-TTAATTTAAA
174150 TTTAAATTTAATTTCAAA
1 TTTAAA-TTAATTT-AAA
*
174168 ATTAAA
1 TTTAAA
174174 AGAAAAGAGT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
16 19 0.29
17 38 0.58
18 8 0.12
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (16 bp):
TTTAAATTAATTTAAA
Found at i:174121 original size:33 final size:33
Alignment explanation
Indices: 174084--174157 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
174074 AGGCCCCTTT
* * * *
174084 TTTAAATTATTTTAAATTTAGATATATTTTAAA
1 TTTAAATTAATCTAAATTTAAATATAATTTAAA
*
174117 TTTAAATTAATCTAAATTTAAATTTAATTTAAA
1 TTTAAATTAATCTAAATTTAAATATAATTTAAA
174150 TTTAAATT
1 TTTAAATT
174158 TAATTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (33 bp):
TTTAAATTAATCTAAATTTAAATATAATTTAAA
Found at i:174126 original size:11 final size:11
Alignment explanation
Indices: 174112--174173 Score: 63
Period size: 11 Copynumber: 5.5 Consensus size: 11
174102 TAGATATATT
174112 TTAAATTTAAA
1 TTAAATTTAAA
*
174123 TT-AATCTAAA
1 TTAAATTTAAA
*
174133 TTTAAATTTAAT
1 -TTAAATTTAAA
174145 TTAAATTTAAA
1 TTAAATTTAAA
*
174156 TTTAATTTCAAAA
1 TTAAATTT--AAA
174169 TTAAA
1 TTAAA
174174 AGAAAAGAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
10 7 0.17
11 21 0.51
12 6 0.15
13 7 0.17
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:174174 original size:6 final size:6
Alignment explanation
Indices: 174111--174173 Score: 71
Period size: 6 Copynumber: 11.0 Consensus size: 6
174101 TTAGATATAT
*
174111 TTTAAA TTTAAA -TT-AA TCTAAA TTTAAA TTT-AA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
174156 TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTT-AAA TTTAAA
174174 AGAAAAGAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 2 0.04
5 13 0.27
6 30 0.61
7 4 0.08
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:175895 original size:30 final size:30
Alignment explanation
Indices: 175850--176142 Score: 264
Period size: 30 Copynumber: 9.9 Consensus size: 30
175840 CCCTGGAGGT
*
175850 CCCCG-AACTTTCAAAAATCCCATTTTTGA-
1 CCCCGAAACTTCCAAAAATCCCATTTTT-AC
** *
175879 CCTTGAAACTTCCAAAAATTCCATTTTTAC
1 CCCCGAAACTTCCAAAAATCCCATTTTTAC
* *
175909 CCTCG-AACTTCCAAAAATCCCA-TTTTAA
1 CCCCGAAACTTCCAAAAATCCCATTTTTAC
**
175937 CCCCGAAACTTCCAAAAAT-TTAGTTTTTAC
1 CCCCGAAACTTCCAAAAATCCCA-TTTTTAC
* * *
175967 CCACGAAACTTCCAAAAATTCTATTTTTAC
1 CCCCGAAACTTCCAAAAATCCCATTTTTAC
*
175997 CCCCAAAACTTCCAAAAATCCCATTTTTAAC
1 CCCCGAAACTTCCAAAAATCCCATTTTT-AC
* ** **
176028 CACATAAACTTCCAAAAATTTCATTTTTA-
1 CCCCGAAACTTCCAAAAATCCCATTTTTAC
*
176057 CCCCTAAACTTCCAAAAATCCCATTTTTGA-
1 CCCCGAAACTTCCAAAAATCCCATTTTT-AC
* **
176087 CCCCAAAACTT-CAAAAATTTC-TATTTTA-
1 CCCCGAAACTTCCAAAAATCCCAT-TTTTAC
* *
176115 CCCCTAAATTTCCAAAAATCCCATTTTT
1 CCCCGAAACTTCCAAAAATCCCATTTTT
176143 GATCTCGAAA
Statistics
Matches: 220, Mismatches: 33, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
28 21 0.10
29 81 0.37
30 91 0.41
31 27 0.12
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (30 bp):
CCCCGAAACTTCCAAAAATCCCATTTTTAC
Found at i:175917 original size:29 final size:28
Alignment explanation
Indices: 175850--176142 Score: 232
Period size: 29 Copynumber: 10.0 Consensus size: 28
175840 CCCTGGAGGT
* *
175850 CCCCGAACTTTCAAAAATCCCATTTTTGA
1 CCCCGAACTTCCAAAAATTCCATTTTT-A
**
175879 CCTTGAAACTTCCAAAAATTCCATTTTTA
1 CCCCG-AACTTCCAAAAATTCCATTTTTA
* *
175908 CCCTCGAACTTCCAAAAATCCCATTTTAA
1 CCC-CGAACTTCCAAAAATTCCATTTTTA
*
175937 CCCCGAAACTTCCAAAAATT-TAGTTTTTA
1 CCCCG-AACTTCCAAAAATTCCA-TTTTTA
*
175966 CCCACGAAACTTCCAAAAATTCTATTTTTA
1 CCC-CG-AACTTCCAAAAATTCCATTTTTA
* *
175996 CCCCCAAAACTTCCAAAAATCCCATTTTTAA
1 -CCCC-GAACTTCCAAAAATTCCATTTTT-A
** *
176027 CCACATAAACTTCCAAAAATTTCATTTTTA
1 CC-C-CGAACTTCCAAAAATTCCATTTTTA
* *
176057 CCCCTAAACTTCCAAAAATCCCATTTTTGA
1 CCCC-GAACTTCCAAAAATTCCATTTTT-A
* *
176087 CCCCAAAACTT-CAAAAATTTC-TATTTTA
1 CCCC-GAACTTCCAAAAATTCCAT-TTTTA
* * *
176115 CCCCTAAATTTCCAAAAATCCCATTTTT
1 CCCC-GAACTTCCAAAAATTCCATTTTT
176143 GATCTCGAAA
Statistics
Matches: 221, Mismatches: 27, Indels: 32
0.79 0.10 0.11
Matches are distributed among these distances:
28 14 0.06
29 97 0.44
30 82 0.37
31 28 0.13
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (28 bp):
CCCCGAACTTCCAAAAATTCCATTTTTA
Found at i:176144 original size:58 final size:59
Alignment explanation
Indices: 175884--176142 Score: 305
Period size: 58 Copynumber: 4.4 Consensus size: 59
175874 TTTGACCTTG
* * * * * * *
175884 AAACTTCCAAAAATTCCATTTTTACCCTC-GAACTTCCAAAAATCCCATTTTAACCCCG
1 AAACTTCCAAAAATCCCATTTTTACCCACAAAACTTCCAAAAATTCTATTTTTACCCCT
** * *
175942 AAACTTCCAAAAAT-TTAGTTTTTACCCACGAAACTTCCAAAAATTCTATTTTTACCCCCA
1 AAACTTCCAAAAATCCCA-TTTTTACCCACAAAACTTCCAAAAATTCTATTTTTA-CCCCT
*
176002 AAACTTCCAAAAATCCCATTTTTAACCACATAAACTTCCAAAAATT-TCATTTTTACCCCT
1 AAACTTCCAAAAATCCCATTTTTACCCACA-AAACTTCCAAAAATTCT-ATTTTTACCCCT
176062 AAACTTCCAAAAATCCCATTTTTGACCC-CAAAACTT-CAAAAATTTCTA-TTTTACCCCT
1 AAACTTCCAAAAATCCCATTTTT-ACCCACAAAACTTCCAAAAA-TTCTATTTTTACCCCT
*
176120 AAATTTCCAAAAATCCCATTTTT
1 AAACTTCCAAAAATCCCATTTTT
176143 GATCTCGAAA
Statistics
Matches: 177, Mismatches: 15, Indels: 18
0.84 0.07 0.09
Matches are distributed among these distances:
57 1 0.01
58 62 0.35
59 29 0.16
60 59 0.33
61 26 0.15
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATCCCATTTTTACCCACAAAACTTCCAAAAATTCTATTTTTACCCCT
Found at i:176172 original size:58 final size:58
Alignment explanation
Indices: 175888--176210 Score: 230
Period size: 58 Copynumber: 5.5 Consensus size: 58
175878 ACCTTGAAAC
* * * * *
175888 TTCCAAAAATTCCATTTTT-ACCCTC-GAACTTCCAAAAA-TCCCATTTTAACCCCGAAAC
1 TTCCAAAAATCCCATTTTTGACCC-CAAAACTT-CAAAAATTACCATTTT-ACCCCTAAAT
** * * * *
175946 TTCCAAAAAT-TTAGTTTTT-ACCCACGAAACTTCCAAAAATT-CTATTTTTACCCCCAAAAC
1 TTCCAAAAATCCCA-TTTTTGACCC-CAAAACTT-CAAAAATTACCA-TTTTA-CCCCTAAAT
* * * *
176006 TTCCAAAAATCCCATTTTTAACCACATAAACTTCCAAAAATT-TCATTTTTACCCCTAAAC
1 TTCCAAAAATCCCATTTTTGACCCCA-AAACTT-CAAAAATTACCA-TTTTACCCCTAAAT
* *
176066 TTCCAAAAATCCCATTTTTGACCCCAAAACTTCAAAAATTTCTATTTTACCCCTAAAT
1 TTCCAAAAATCCCATTTTTGACCCCAAAACTTCAAAAATTACCATTTTACCCCTAAAT
* * * * * **
176124 TTCCAAAAATCCCATTTTTGATCTCGAAAC-TCTTAAAATTACCCTTTTACCCCCGAAT
1 TTCCAAAAATCCCATTTTTGACCCCAAAACTTC-AAAAATTACCATTTTACCCCTAAAT
* * * *
176182 ATCAAAAAATTCCATTTTTAACCCCAAAA
1 TTCCAAAAATCCCATTTTTGACCCCAAAA
176211 TTACTATTTC
Statistics
Matches: 221, Mismatches: 34, Indels: 20
0.80 0.12 0.07
Matches are distributed among these distances:
57 3 0.01
58 109 0.49
59 22 0.10
60 61 0.28
61 26 0.12
ACGTcount: A:0.37, C:0.28, G:0.02, T:0.33
Consensus pattern (58 bp):
TTCCAAAAATCCCATTTTTGACCCCAAAACTTCAAAAATTACCATTTTACCCCTAAAT
Found at i:181864 original size:29 final size:29
Alignment explanation
Indices: 181832--181917 Score: 136
Period size: 29 Copynumber: 3.0 Consensus size: 29
181822 GAAATAATAC
* * *
181832 AGATACAGTTATAGATATAGTCATGTCAG
1 AGATATAGTTATAGATACAATCATGTCAG
181861 AGATATAGTTATAGATACAATCATGTCAG
1 AGATATAGTTATAGATACAATCATGTCAG
*
181890 AGATATAGTTACAGATACAATCATGTCA
1 AGATATAGTTATAGATACAATCATGTCA
181918 CGCAGTCATG
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (29 bp):
AGATATAGTTATAGATACAATCATGTCAG
Found at i:182716 original size:57 final size:56
Alignment explanation
Indices: 182644--182851 Score: 186
Period size: 57 Copynumber: 3.6 Consensus size: 56
182634 GCTAGTGTGC
182644 CACACACACCCTGACACATACCCGTGTGTCAGCCCATGTGCCTCCAAACAGTATACA
1 CACACACACCCTGACACA-ACCCGTGTGTCAGCCCATGTGCCTCCAAACAGTATACA
* * * * * * *
182701 CATACACACCTTGACACAA-GCTTGTGTGCTAGTCCATTTGCTTCCAAACAGTATACACACA
1 CACACACACCCTGACACAACCCGTGTGT-C-AGCCCATGTGCCTCCAAACAGTAT----ACA
* * *
182762 CACACACACCCTGACACACGCCCGTGTGTTAACCCATGTGCCAT-CAAACAGTATACA
1 CACACACACCCTGACACA-ACCCGTGTGTCAGCCCATGTGCC-TCCAAACAGTATACA
* * * *
182819 CACACAAACCCTAACACACCCTCGTGTGCCAGC
1 CACACACACCCTGACACAACC-CGTGTGTCAGC
182852 TCGTGTACCA
Statistics
Matches: 118, Mismatches: 23, Indels: 20
0.73 0.14 0.12
Matches are distributed among these distances:
55 6 0.05
56 4 0.03
57 64 0.54
61 37 0.31
62 1 0.01
63 6 0.05
ACGTcount: A:0.31, C:0.37, G:0.13, T:0.19
Consensus pattern (56 bp):
CACACACACCCTGACACAACCCGTGTGTCAGCCCATGTGCCTCCAAACAGTATACA
Found at i:182789 original size:61 final size:60
Alignment explanation
Indices: 182644--182824 Score: 185
Period size: 61 Copynumber: 3.0 Consensus size: 60
182634 GCTAGTGTGC
*
182644 CACACACACCCTGACACATA-CCCGTGTGTCAGCCCATGTGCCTCCAAACAGTAT----ACA
1 CACACACACCCTGACACA-AGCCCGTGTGT-AGCCCATGTGCATCCAAACAGTATACACACA
* * ** * * *
182701 CATACACACCTTGACACAAGCTTGTGTGCTAGTCCATTTGCTTCCAAACAGTATACACACA
1 CACACACACCCTGACACAAGCCCGTGTG-TAGCCCATGTGCATCCAAACAGTATACACACA
* *
182762 CACACACACCCTGACACACGCCCGTGTGTTAACCCATGTGCCAT-CAAACAGTATACACACA
1 CACACACACCCTGACACAAGCCCGTGTG-TAGCCCATGTG-CATCCAAACAGTATACACACA
182823 CA
1 CA
182825 AACCCTAACA
Statistics
Matches: 100, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
56 1 0.01
57 43 0.43
58 1 0.01
61 53 0.53
62 2 0.02
ACGTcount: A:0.31, C:0.35, G:0.13, T:0.20
Consensus pattern (60 bp):
CACACACACCCTGACACAAGCCCGTGTGTAGCCCATGTGCATCCAAACAGTATACACACA
Found at i:188839 original size:14 final size:13
Alignment explanation
Indices: 188813--188837 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
188803 TCATGTGTTT
188813 TTTTTAATATTTA
1 TTTTTAATATTTA
188826 TTTTTAATATTT
1 TTTTTAATATTT
188838 TACTATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTAATATTTA
Found at i:195473 original size:2 final size:2
Alignment explanation
Indices: 195466--195495 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
195456 ATTAAAAATA
195466 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
195496 GTAAAAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:195677 original size:20 final size:20
Alignment explanation
Indices: 195638--195678 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
195628 ATATATTTTT
**
195638 AAAATATAAAAAATGGAAAA
1 AAAATATAAAAAATCCAAAA
195658 AAAATATAAAAAATCCAAAA
1 AAAATATAAAAAATCCAAAA
195678 A
1 A
195679 TATAACTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (20 bp):
AAAATATAAAAAATCCAAAA
Found at i:199371 original size:14 final size:14
Alignment explanation
Indices: 199349--199380 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
199339 TGTTTGTTTA
*
199349 TATGTAAAATATTT
1 TATGAAAAATATTT
199363 TATGAAAAATATTT
1 TATGAAAAATATTT
199377 TATG
1 TATG
199381 TATTTTCCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (14 bp):
TATGAAAAATATTT
Found at i:202672 original size:6 final size:6
Alignment explanation
Indices: 202661--202719 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
202651 GGCCCAACAG
* * * * *
202661 AATTTA AATTT- ATTTTA AAATTA AGTTT- ATTTTA AATTTA AATTGAA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATT-TA
202708 AATTTA AATTTA
1 AATTTA AATTTA
202720 TCATAAATTT
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
5 8 0.20
6 28 0.68
7 5 0.12
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:202689 original size:17 final size:17
Alignment explanation
Indices: 202664--202704 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
202654 CCAACAGAAT
202664 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
202681 TTAAGTTTATTTTAAAT
1 TTAAATTTATTTTAAAA
202698 TTAAATT
1 TTAAATT
202705 GAAAATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:202729 original size:17 final size:17
Alignment explanation
Indices: 202661--202750 Score: 62
Period size: 17 Copynumber: 5.5 Consensus size: 17
202651 GGCCCAACAG
*
202661 AATTTAAATTTATTTTA
1 AATTTAAATTTATTATA
* * *
202678 AAATTAAGTTTATTTTA
1 AATTTAAATTTATTATA
*
202695 AATTTAAA--T-TGA-A
1 AATTTAAATTTATTATA
*
202708 AATTTAAATTTATCATA
1 AATTTAAATTTATTATA
* **
202725 AATTTGAATTTAAAATA
1 AATTTAAATTTATTATA
*
202742 TATTTAAAT
1 AATTTAAAT
202751 AATGTCCCAT
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
15 2 0.04
16 2 0.04
17 43 0.75
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:203436 original size:21 final size:19
Alignment explanation
Indices: 203410--203454 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 19
203400 TAATAGTAAT
203410 TAATAAATGTATTAATTATTA
1 TAATAAAT-TATT-ATTATTA
203431 TAAT-AA-TATTATTATTA
1 TAATAAATTATTATTATTA
203448 -AATAAAT
1 TAATAAAT
203455 AAAAAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
16 3 0.14
17 9 0.41
18 4 0.18
20 2 0.09
21 4 0.18
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
TAATAAATTATTATTATTA
Found at i:203455 original size:17 final size:18
Alignment explanation
Indices: 203419--203452 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
203409 TTAATAAATG
203419 TATTAATTATTATAATAA
1 TATTAATTATTATAATAA
203437 TATT-ATTATTA-AATAA
1 TATTAATTATTATAATAA
203453 ATAAAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 7 0.44
18 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTAATTATTATAATAA
Found at i:204433 original size:29 final size:30
Alignment explanation
Indices: 204386--204637 Score: 144
Period size: 29 Copynumber: 8.6 Consensus size: 30
204376 TAATTTTATT
204386 AAATT-CCATCTTTAACCCT-GATTTCACCAA
1 AAATTACCAT-TTT-ACCCTCGATTTCACCAA
*
204416 AAATTATCATTTTACCCTCGAACTTT--CC-A
1 AAATTACCATTTTACCCTCG-A-TTTCACCAA
204445 AAATT-CCATTTTAACCCT-GATTTCACCAA
1 AAATTACCATTTT-ACCCTCGATTTCACCAA
**
204474 AAATTACCATTTTACCCCTAAACTTT--CC-A
1 AAATTACCATTTTA-CCCTCGA-TTTCACCAA
*
204503 AAATT-CCATTTTTAACCTCGATTTCACCAA
1 AAATTACCA-TTTTACCCTCGATTTCACCAA
* * *
204533 AAATTACTATTTTACCCGCGAACTTC-CC-A
1 AAATTACCATTTTACCCTCG-ATTTCACCAA
** *
204562 AAATT-CCATTTTTGACCC-CGATTT-TTCTA
1 AAATTACCA-TTTT-ACCCTCGATTTCACCAA
* * * * *
204591 AAATTATCATTTTACCCTTGA-GT-ATCTA
1 AAATTACCATTTTACCCTCGATTTCACCAA
204619 AAATTACCATTTTACCCTC
1 AAATTACCATTTTACCCTC
204638 CGAGTATCCA
Statistics
Matches: 179, Mismatches: 19, Indels: 50
0.72 0.08 0.20
Matches are distributed among these distances:
26 3 0.02
27 4 0.02
28 48 0.27
29 60 0.34
30 47 0.26
31 11 0.06
32 6 0.03
ACGTcount: A:0.32, C:0.27, G:0.04, T:0.37
Consensus pattern (30 bp):
AAATTACCATTTTACCCTCGATTTCACCAA
Found at i:204477 original size:58 final size:59
Alignment explanation
Indices: 204386--204608 Score: 294
Period size: 58 Copynumber: 3.8 Consensus size: 59
204376 TAATTTTATT
*
204386 AAATTCCATCTTTAACCCTGATTTCACCAAAAATTATCATTTTACCCTCGAACTTTCCA
1 AAATTCCATTTTTAACCCTGATTTCACCAAAAATTATCATTTTACCCTCGAACTTTCCA
* *
204445 AAATTCCA-TTTTAACCCTGATTTCACCAAAAATTACCATTTTACCC-CTAAACTTTCCA
1 AAATTCCATTTTTAACCCTGATTTCACCAAAAATTATCATTTTACCCTC-GAACTTTCCA
* *
204503 AAATTCCATTTTTAA-CCTCGATTTCACCAAAAATTA-CTATTTTACCCGCGAACTTCCCA
1 AAATTCCATTTTTAACCCT-GATTTCACCAAAAATTATC-ATTTTACCCTCGAACTTTCCA
* * ** *
204562 AAATTCCATTTTTGACCCCGATTT-TTCTAAAATTATCATTTTACCCT
1 AAATTCCATTTTTAACCCTGATTTCACCAAAAATTATCATTTTACCCT
204609 TGAGTATCTA
Statistics
Matches: 146, Mismatches: 11, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
57 1 0.01
58 74 0.51
59 68 0.47
60 3 0.02
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.37
Consensus pattern (59 bp):
AAATTCCATTTTTAACCCTGATTTCACCAAAAATTATCATTTTACCCTCGAACTTTCCA
Found at i:204545 original size:59 final size:59
Alignment explanation
Indices: 204386--204585 Score: 275
Period size: 59 Copynumber: 3.4 Consensus size: 59
204376 TAATTTTATT
*
204386 AAATTCCATCTTTAACCCTGATTTCACCAAAAATTA-TCATTTTA-CCCTCGAACTTTCCA
1 AAATTCCATTTTTAACCCTGATTTCACCAAAAATTACT-ATTTTACCCCT-GAACTTTCCA
* *
204445 AAATTCCA-TTTTAACCCTGATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCCA
1 AAATTCCATTTTTAACCCTGATTTCACCAAAAATTACTATTTTACCCCTGAACTTTCCA
*
204503 AAATTCCATTTTTAA-CCTCGATTTCACCAAAAATTACTATTTTACCCGC-GAACTTCCCA
1 AAATTCCATTTTTAACCCT-GATTTCACCAAAAATTACTATTTTACCC-CTGAACTTTCCA
* *
204562 AAATTCCATTTTTGACCCCGATTT
1 AAATTCCATTTTTAACCCTGATTT
204586 TTCTAAAATT
Statistics
Matches: 127, Mismatches: 8, Indels: 12
0.86 0.05 0.08
Matches are distributed among these distances:
58 52 0.41
59 72 0.57
60 3 0.02
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.35
Consensus pattern (59 bp):
AAATTCCATTTTTAACCCTGATTTCACCAAAAATTACTATTTTACCCCTGAACTTTCCA
Found at i:204594 original size:117 final size:117
Alignment explanation
Indices: 204386--204607 Score: 315
Period size: 117 Copynumber: 1.9 Consensus size: 117
204376 TAATTTTATT
* *
204386 AAATTCCATCTTTAACCCTGATTTCACCAAAAATTATCATTTTACCCTCGAACTTTCCAAAATTC
1 AAATTCCATCTTTAACCCTGATTTCACCAAAAATTATCATTTTACCCGCGAACTTCCCAAAATTC
*
204451 CATTTTAACCCTGATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCCA
66 CATTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCCA
*
204503 AAATTCCATTTTTAA-CCTCGATTTCACCAAAAATTA-CTATTTTACCCGCGAACTTCCCAAAAT
1 AAATTCCATCTTTAACCCT-GATTTCACCAAAAATTATC-ATTTTACCCGCGAACTTCCCAAAAT
* ** * *
204566 TCCATTTTTGACCCCGATTT-TTCTAAAATTATCATTTTACCC
64 TCCA-TTTTAACCCCGATTTCACCAAAAATTACCATTTTACCC
204608 TTGAGTATCT
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
116 4 0.04
117 76 0.82
118 13 0.14
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (117 bp):
AAATTCCATCTTTAACCCTGATTTCACCAAAAATTATCATTTTACCCGCGAACTTCCCAAAATTC
CATTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTAAACTTTCCA
Found at i:204619 original size:28 final size:29
Alignment explanation
Indices: 204587--204650 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 29
204577 CCCCGATTTT
* *
204587 TCTAAAATTATCATTTTACCCT-TGAGTA
1 TCTAAAATTACCATTTTACCCTCCGAGTA
204615 TCTAAAATTACCATTTTACCCTCCGAGTA
1 TCTAAAATTACCATTTTACCCTCCGAGTA
*
204644 TCCAAAA
1 TCTAAAA
204651 ATCACATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
28 21 0.66
29 11 0.34
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.36
Consensus pattern (29 bp):
TCTAAAATTACCATTTTACCCTCCGAGTA
Found at i:204658 original size:29 final size:28
Alignment explanation
Indices: 204598--204660 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
204588 CTAAAATTAT
* * *
204598 CATTTTACCCTTGAGTATCTAAAATTAC
1 CATTTTACCCTCGAGTATCAAAAATCAC
204626 CATTTTACCCTCCGAGTATCCAAAAATCA-
1 CATTTTACCCT-CGAGTAT-CAAAAATCAC
204655 CATTTT
1 CATTTT
204661 CAACTTCGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 11 0.37
29 12 0.40
30 7 0.23
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (28 bp):
CATTTTACCCTCGAGTATCAAAAATCAC
Found at i:208111 original size:29 final size:31
Alignment explanation
Indices: 208069--208126 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
208059 ATTCAAGTAT
*
208069 CACATTGAATATTTT-T-AAAGTAGAGGTGC
1 CACATTGAATATTTTATGAAAGTACAGGTGC
*
208098 CACATTGGATATTTTATGAAAGTACAGGT
1 CACATTGAATATTTTATGAAAGTACAGGT
208127 ACCAAAATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.56
30 1 0.04
31 10 0.40
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.34
Consensus pattern (31 bp):
CACATTGAATATTTTATGAAAGTACAGGTGC
Found at i:209092 original size:41 final size:41
Alignment explanation
Indices: 209027--209116 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
209017 GGTCCTTGAG
209027 GAAAGAAT-ATCAAATCGGATTTTGTTTTGATGCTAAACATT
1 GAAA-AATGATCAAATCGGATTTTGTTTTGATGCTAAACATT
209068 GAAAAATGATCAAATCGGATTTTGTTTTGATGCTAAACATT
1 GAAAAATGATCAAATCGGATTTTGTTTTGATGCTAAACATT
209109 GAAAAATG
1 GAAAAATG
209117 TTGTATTTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 3 0.06
41 45 0.94
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (41 bp):
GAAAAATGATCAAATCGGATTTTGTTTTGATGCTAAACATT
Found at i:210024 original size:113 final size:114
Alignment explanation
Indices: 209812--210027 Score: 346
Period size: 113 Copynumber: 1.9 Consensus size: 114
209802 GGTTAATAGG
* * *
209812 GATTATGGAACATGTATTTTGCTTATTGACATGGGATATTGAATGTTAAATGTGAATTGTGAAAT
1 GATTATGGAACATGTATTTTGCTTATTAACATAGGATATTGAATGTTAAAAGTGAATTGTGAAAT
*
209877 TGCATATTATTGTTAAAGCAATAAAAGATCATGCAATTTGATTAATAAC
66 TGCATATTAATGTTAAAGCAATAAAAGATCATGCAATTTGATTAATAAC
** *
209926 GATTATGGGCCATGTATTTTTCTTATTAACATAGGATATTGAATG-TAAAAGTGAATTGTGAAAT
1 GATTATGGAACATGTATTTTGCTTATTAACATAGGATATTGAATGTTAAAAGTGAATTGTGAAAT
209990 TGCATATTAATGTTAAAGCAATGAAAA-ATCATGCAATT
66 TGCATATTAATGTTAAAGCAAT-AAAAGATCATGCAATT
210028 CATTTAATAC
Statistics
Matches: 94, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
113 50 0.53
114 44 0.47
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (114 bp):
GATTATGGAACATGTATTTTGCTTATTAACATAGGATATTGAATGTTAAAAGTGAATTGTGAAAT
TGCATATTAATGTTAAAGCAATAAAAGATCATGCAATTTGATTAATAAC
Found at i:211509 original size:9 final size:9
Alignment explanation
Indices: 211495--211548 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
211485 ACAATCAAAA
*
211495 TGAGAGACT
1 TGAGAGAGT
*
211504 TGAGAGGATT
1 TGAGA-GAGT
*
211514 TGAAAGAGT
1 TGAGAGAGT
*
211523 TGAGAAAGTT
1 TGAGAGAG-T
211533 TGAGAGAGT
1 TGAGAGAGT
211542 TGAGAGA
1 TGAGAGA
211549 TGATGTGAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
9 22 0.59
10 15 0.41
ACGTcount: A:0.37, C:0.02, G:0.37, T:0.24
Consensus pattern (9 bp):
TGAGAGAGT
Found at i:211527 original size:19 final size:20
Alignment explanation
Indices: 211503--211548 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
211493 AATGAGAGAC
*
211503 TTGAGAGGA-TTTGAAAGAG
1 TTGAGAGAAGTTTGAAAGAG
*
211522 TTGAGA-AAGTTTGAGAGAG
1 TTGAGAGAAGTTTGAAAGAG
211541 TTGAGAGA
1 TTGAGAGA
211549 TGATGTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 21 0.91
20 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.26
Consensus pattern (20 bp):
TTGAGAGAAGTTTGAAAGAG
Found at i:212513 original size:22 final size:22
Alignment explanation
Indices: 212485--212529 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
212475 AAAGAAAATG
212485 TAAATTCTTCAATTTACTTTAT
1 TAAATTCTTCAATTTACTTTAT
212507 TAAATTCTTCAATTTACTTTAT
1 TAAATTCTTCAATTTACTTTAT
212529 T
1 T
212530 TTCCCCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.00, T:0.56
Consensus pattern (22 bp):
TAAATTCTTCAATTTACTTTAT
Found at i:217159 original size:19 final size:19
Alignment explanation
Indices: 217135--217182 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
217125 AAATTATTTT
217135 TTTTTATAAAATTTTTAAA
1 TTTTTATAAAATTTTTAAA
* * *
217154 TTTTTATATATTTTTTAGA
1 TTTTTATAAAATTTTTAAA
217173 TTTTT-TAAAA
1 TTTTTATAAAA
217183 AATTATATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TTTTTATAAAATTTTTAAA
Found at i:217212 original size:18 final size:18
Alignment explanation
Indices: 217172--217212 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
217162 TATTTTTTAG
* *
217172 ATTTTTTAAAAAATTATA
1 ATTTTTTAAAAAATAAAA
*
217190 TTTTTTTAAAAAATAAAA
1 ATTTTTTAAAAAATAAAA
217208 ATTTT
1 ATTTT
217213 AGAATTTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTTTAAAAAATAAAA
Found at i:217250 original size:18 final size:19
Alignment explanation
Indices: 217208--217272 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
217198 AAAAATAAAA
*
217208 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAA-TTTTAAAAATT
217228 ATTTTGAA-TTTAAAAATT
1 ATTTTGAATTTTAAAAATT
* *
217246 ATTTTCAATTTTTGAAAATT
1 ATTTTGAA-TTTTAAAAATT
217266 ATTTTGA
1 ATTTTGA
217273 TTATTCTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
17 7 0.18
18 8 0.21
19 3 0.08
20 20 0.53
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:217789 original size:19 final size:19
Alignment explanation
Indices: 217733--217780 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
217723 CCACTGTCAC
*
217733 CTATCGTAATCAAATTTAT
1 CTATCGTAATCAAATTTGT
*
217752 CCATCGTAATCAAATTTGT
1 CTATCGTAATCAAATTTGT
217771 CTATCGTAAT
1 CTATCGTAAT
217781 AAAAATTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.40
Consensus pattern (19 bp):
CTATCGTAATCAAATTTGT
Found at i:218546 original size:169 final size:168
Alignment explanation
Indices: 218239--218553 Score: 388
Period size: 169 Copynumber: 1.9 Consensus size: 168
218229 TGGAGTAAAA
* *
218239 TTTTGAGGGAAAGTAAATAGGGGAGTAAAATTTTGGAAGAAAAATATTCAAAAAAATTGGAAGGA
1 TTTTGAGGGAAAGTAAATAGGGGAGTAAAATTTTAGAAGAAAAATATTAAAAAAAATTGG-AGGA
* * * ** *
218304 GGGATGGGCTTGGGGTAGATGGGGGGTTGGATGGGAGGGGAGTAAAAGTTTTAGGGGGAAAGTGA
65 GGAATGGGCTTGGGATAGATGGGGGGTTGGATGAGAGGACAGTAAAAGTTTTAGGGGGAAAGTAA
*
218369 GAGAGTAAAAGCTTTGAGAAAAATAAAGAGTTTTGAGGG
130 AAGAGTAAAAGCTTTGAGAAAAATAAAGAGTTTTGAGGG
* * *
218408 TTTTGAGGGGAAA-TAAATGGGGGGAGTAAAATTTTAGAGGGAAAATATTAAAGAAAAATTGG-G
1 TTTTGA-GGGAAAGTAAAT-AGGGGAGTAAAATTTTAGAAGAAAAATATTAAA-AAAAATTGGAG
* * *
218471 G-GGAAATGGGTTTGGGATTGATTGGGGG-TGAGATGAGAGGACAGTAAAAGTTTT-GGGGGAAA
63 GAGG-AATGGGCTTGGGATAGATGGGGGGTTG-GATGAGAGGACAGTAAAAGTTTTAGGGGGAAA
*
218533 GTAAAAGGAGTAAAAGTTTTG
126 GTAAAA-GAGTAAAAGCTTTG
218554 GGGGAAAAGT
Statistics
Matches: 124, Mismatches: 16, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
168 16 0.13
169 65 0.52
170 34 0.27
171 9 0.07
ACGTcount: A:0.37, C:0.01, G:0.37, T:0.24
Consensus pattern (168 bp):
TTTTGAGGGAAAGTAAATAGGGGAGTAAAATTTTAGAAGAAAAATATTAAAAAAAATTGGAGGAG
GAATGGGCTTGGGATAGATGGGGGGTTGGATGAGAGGACAGTAAAAGTTTTAGGGGGAAAGTAAA
AGAGTAAAAGCTTTGAGAAAAATAAAGAGTTTTGAGGG
Found at i:218547 original size:28 final size:29
Alignment explanation
Indices: 218513--218567 Score: 103
Period size: 28 Copynumber: 1.9 Consensus size: 29
218503 ATGAGAGGAC
218513 AGTAAAAGTTTTGGGGG-AAAGTAAAAGG
1 AGTAAAAGTTTTGGGGGAAAAGTAAAAGG
218541 AGTAAAAGTTTTGGGGGAAAAGTAAAA
1 AGTAAAAGTTTTGGGGGAAAAGTAAAA
218568 AAGTTTGGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.33, T:0.22
Consensus pattern (29 bp):
AGTAAAAGTTTTGGGGGAAAAGTAAAAGG
Found at i:218583 original size:22 final size:23
Alignment explanation
Indices: 218544--218590 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
218534 TAAAAGGAGT
*
218544 AAAAGTTTTGGGGGAAAA-GTAA
1 AAAAGTTTTGGGGAAAAATGTAA
218566 AAAAG-TTTGGGGTAAAAATGTAA
1 AAAAGTTTTGGGG-AAAAATGTAA
218589 AA
1 AA
218591 TATTATAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 9 0.41
23 6 0.27
ACGTcount: A:0.49, C:0.00, G:0.28, T:0.23
Consensus pattern (23 bp):
AAAAGTTTTGGGGAAAAATGTAA
Found at i:218590 original size:21 final size:22
Alignment explanation
Indices: 218542--218590 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
218532 AGTAAAAGGA
*
218542 GTAAAAGTTTTGGGGGAAAAGT
1 GTAAAAGTTTTGGGGGAAAAAT
** *
218564 AAAAAAG-TTTGGGGTAAAAAT
1 GTAAAAGTTTTGGGGGAAAAAT
218585 GTAAAA
1 GTAAAA
218591 TATTATAGTT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (22 bp):
GTAAAAGTTTTGGGGGAAAAAT
Found at i:219813 original size:16 final size:17
Alignment explanation
Indices: 219788--219824 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
219778 TCTTAAAAAA
*
219788 TAAAATTAAAAAT-TTT
1 TAAAAGTAAAAATATTT
219804 TAAAAGTAAAAATATTT
1 TAAAAGTAAAAATATTT
219821 TAAA
1 TAAA
219825 GTTTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAAAGTAAAAATATTT
Found at i:220740 original size:36 final size:36
Alignment explanation
Indices: 220693--220766 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
220683 ATTACAGATA
220693 AAAAAATATTTATTTTATTTCATACTGAAACAAACC
1 AAAAAATATTTATTTTATTTCATACTGAAACAAACC
220729 AAAAAATATTTATTTTATTTCATACTGAAACAAACC
1 AAAAAATATTTATTTTATTTCATACTGAAACAAACC
220765 AA
1 AA
220767 TATTATTCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.35
Consensus pattern (36 bp):
AAAAAATATTTATTTTATTTCATACTGAAACAAACC
Found at i:223633 original size:19 final size:20
Alignment explanation
Indices: 223609--223656 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
223599 ATTTATTTAT
*
223609 TAAAATAATAATGGTACAAA
1 TAAAATAATAATAGTACAAA
* *
223629 T-AAATAACAATATTACAAA
1 TAAAATAATAATAGTACAAA
223648 TAAAATAAT
1 TAAAATAAT
223657 TTAAGTGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.27
Consensus pattern (20 bp):
TAAAATAATAATAGTACAAA
Found at i:224302 original size:207 final size:207
Alignment explanation
Indices: 223930--224325 Score: 487
Period size: 207 Copynumber: 1.9 Consensus size: 207
223920 TTAATCTTTT
*
223930 CCTTAATCTCTCTTCCTCCTCGTCTAACGTTTTTCTTTCTTCCGCAAAAATATCAATCAGAGCGA
1 CCTTAATCTCTCTTCCTCCTCGTCTAACGCTTTTCTTTCTTCCGCAAAAATATCAATCAGAGCGA
* * ** * * * **
223995 TCAGCTCCTTGTCTAACACTTCACTCTGTTGTTTTTCTTGCTTAATTTGATTTTCAATTGTTTCG
66 TCAGCTCCTTGTCCAACAATTCACTCCATTGTTGTTCTTGCTTAACTTGATATTCAAGCGTTTCG
* * * *
224060 ATTCTCTCTGTTTTGGGCTATAAATCGCTAATCATTTTATTCAATCTTTCCTTCAAGTCCTGATT
131 ATTCTCTCTCTTTTGGGCTATAAATCACCAATCATTTTATTCAATCTTTCCCTCAAGTCCTGATT
224125 CTCTGCTTTTGC
196 CTCTGCTTTTGC
** * * *
224137 CCTTAATCTCTCTTCCTCCTCGTCT-TGGCTTTTCTTTTCTTTCGCAAAAA-ACTTAATCAGGGC
1 CCTTAATCTCTCTTCCTCCTCGTCTAACGCTTTTC-TTTCTTCCGCAAAAATA-TCAATCAGAGC
* * *
224200 -AGTCTGTTCCTTGTCCAACAATTCATTCCATTGTTGTTCTTGCTTAACTTGCA-ATTCAAGCGT
64 GA-TCAGCTCCTTGTCCAACAATTCACTCCATTGTTGTTCTTGCTTAACTTG-ATATTCAAGCGT
* * *
224263 GTT-GCTTCTCTCTCTTTTGGTCTGTAAATCACCAATCATTTTATTCAATCTTTCCCTCAAGTC
127 -TTCGATTCTCTCTCTTTTGGGCTATAAATCACCAATCATTTTATTCAATCTTTCCCTCAAGTC
224326 ATTAAAATCT
Statistics
Matches: 159, Mismatches: 25, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
206 8 0.05
207 148 0.93
208 3 0.02
ACGTcount: A:0.19, C:0.26, G:0.11, T:0.44
Consensus pattern (207 bp):
CCTTAATCTCTCTTCCTCCTCGTCTAACGCTTTTCTTTCTTCCGCAAAAATATCAATCAGAGCGA
TCAGCTCCTTGTCCAACAATTCACTCCATTGTTGTTCTTGCTTAACTTGATATTCAAGCGTTTCG
ATTCTCTCTCTTTTGGGCTATAAATCACCAATCATTTTATTCAATCTTTCCCTCAAGTCCTGATT
CTCTGCTTTTGC
Found at i:228623 original size:26 final size:26
Alignment explanation
Indices: 228589--228649 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
228579 TTATTAAAAT
*
228589 TATTTTTTTGAAATATAAAATTATTA
1 TATTATTTTGAAATATAAAATTATTA
** * *
228615 TATTATTTTTTAATATGAAATTGTTA
1 TATTATTTTGAAATATAAAATTATTA
*
228641 TATAATTTT
1 TATTATTTT
228650 AATTTCCAAT
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:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (26 bp):
TATTATTTTGAAATATAAAATTATTA
Found at i:229732 original size:38 final size:39
Alignment explanation
Indices: 229681--229760 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 39
229671 TAAAATCATA
229681 TAATAATTTTATATTTCAAAAAAAGAA-TATAATAATTT
1 TAATAATTTTATATTTCAAAAAAAGAATTATAATAATTT
* *
229719 TAATAATTTTATATTTCAAAAAAATAATTTTAATAATTT
1 TAATAATTTTATATTTCAAAAAAAGAATTATAATAATTT
229758 TAA
1 TAA
229761 AATCATTTGC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 26 0.67
39 13 0.33
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (39 bp):
TAATAATTTTATATTTCAAAAAAAGAATTATAATAATTT
Found at i:231362 original size:23 final size:23
Alignment explanation
Indices: 231332--231432 Score: 109
Period size: 23 Copynumber: 4.3 Consensus size: 23
231322 TGCTGGGTAA
231332 CAGAGGGCACACAAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
*
231355 CAGAGGGCACACGAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
*
231378 CATAGAGGGCACACACAGTGCTGAA-
1 C--AGAGGGCACACAAAGTGCT-AAT
*
231403 CAGA-GG-ACACGAAACGTGCTAAA
1 CAGAGGGCACAC-AAA-GTGCTAAT
231426 CAGAGGG
1 CAGAGGG
231433 TGCACTAGTG
Statistics
Matches: 67, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
21 4 0.06
22 6 0.09
23 35 0.52
24 2 0.03
25 18 0.27
26 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.30, T:0.11
Consensus pattern (23 bp):
CAGAGGGCACACAAAGTGCTAAT
Found at i:231362 original size:48 final size:48
Alignment explanation
Indices: 231306--231432 Score: 122
Period size: 48 Copynumber: 2.7 Consensus size: 48
231296 GAAGTACTTC
* **
231306 ACAGAGGGCACA-TAAGTGCTGGGTAACAGAGGGCACACAAAGTGCT-A
1 ACAGAGGGCACACGAAGTGCT-AATAACAGAGGGCACACAAAGTGCTGA
* * *
231353 ATCAGAGGGCACACGAAGTGCTAATCATAGAGGGCACACACAGTGCTGA
1 A-CAGAGGGCACACGAAGTGCTAATAACAGAGGGCACACAAAGTGCTGA
231402 ACAGA-GG-ACACGAAACGTGCT-A-AACAGAGGG
1 ACAGAGGGCACACG-AA-GTGCTAATAACAGAGGG
231433 TGCACTAGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
46 12 0.18
47 6 0.09
48 40 0.60
49 9 0.13
ACGTcount: A:0.37, C:0.20, G:0.31, T:0.12
Consensus pattern (48 bp):
ACAGAGGGCACACGAAGTGCTAATAACAGAGGGCACACAAAGTGCTGA
Found at i:234143 original size:53 final size:53
Alignment explanation
Indices: 234080--234182 Score: 188
Period size: 53 Copynumber: 1.9 Consensus size: 53
234070 TTAGTACCTT
*
234080 TCCATTTGAATCTTCCCTTTCCTCATCCTGATTTTCCATCTCGCTCGGTTGCA
1 TCCATTTGAATCTTCCCTTTCCTCATCCTGATTTTCCATCTCACTCGGTTGCA
*
234133 TCCATTTGAATCTTCCCTTTCCTCATCCTGCTTTTCCATCTCACTCGGTT
1 TCCATTTGAATCTTCCCTTTCCTCATCCTGATTTTCCATCTCACTCGGTT
234183 TCGTCTCCTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 48 1.00
ACGTcount: A:0.13, C:0.35, G:0.10, T:0.43
Consensus pattern (53 bp):
TCCATTTGAATCTTCCCTTTCCTCATCCTGATTTTCCATCTCACTCGGTTGCA
Found at i:237781 original size:134 final size:134
Alignment explanation
Indices: 237628--237878 Score: 421
Period size: 134 Copynumber: 1.9 Consensus size: 134
237618 TTTAATAAAA
* ** *
237628 TAATGGGTGAACTATATAAATGGCTACCCAACTGTTAGCATATTTCTATTTTTGTTATTCAAGTT
1 TAATGGGTGAACTATATAAATGGCCACCCAACCATTAGCATATTTCTATTTTGGTTATTCAAGTT
* *
237693 TAAAAATGTCTATTTTAGTCACTAACGTTATTGAAATTTAATATTTTAGTCACTTGTCTATTAAA
66 TAAAAATATATATTTTAGTCACTAACGTTATTGAAATTTAATATTTTAGTCACTTGTCTATTAAA
237758 TCAT
131 TCAT
* *
237762 TAATGGGTGAACTATATAAATGGCCACTCAACCATTAGCATGTTTCTATTTTGGTTATTCAAGTT
1 TAATGGGTGAACTATATAAATGGCCACCCAACCATTAGCATATTTCTATTTTGGTTATTCAAGTT
*
237827 TAAAAATATATATTTTAGTCACTAACGTTATTGAAATTTAATATTTTTGTCA
66 TAAAAATATATATTTTAGTCACTAACGTTATTGAAATTTAATATTTTAGTCA
237879 GTCATCCATT
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
134 108 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (134 bp):
TAATGGGTGAACTATATAAATGGCCACCCAACCATTAGCATATTTCTATTTTGGTTATTCAAGTT
TAAAAATATATATTTTAGTCACTAACGTTATTGAAATTTAATATTTTAGTCACTTGTCTATTAAA
TCAT
Found at i:238359 original size:23 final size:23
Alignment explanation
Indices: 238333--238378 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
238323 AATCATTTCA
238333 TTTAGTTTTATATTTTAT-TTATT
1 TTTAGTTTTAT-TTTTATCTTATT
*
238356 TTTATTTTTATTTTTATCTTATT
1 TTTAGTTTTATTTTTATCTTATT
238379 ATGTACTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (23 bp):
TTTAGTTTTATTTTTATCTTATT
Found at i:238364 original size:16 final size:17
Alignment explanation
Indices: 238327--238368 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
238317 AATCAAAATC
*
238327 ATTTCATTTAGTTTTAT
1 ATTTTATTTAGTTTTAT
*
238344 ATTTTATTTATTTTTAT
1 ATTTTATTTAGTTTTAT
238361 -TTTTATTT
1 ATTTTATTT
238369 TTATCTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (17 bp):
ATTTTATTTAGTTTTAT
Found at i:238431 original size:16 final size:16
Alignment explanation
Indices: 238410--238440 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
238400 TTGTCAGTTT
*
238410 TTTTTATTTTGTTATC
1 TTTTTATTTTCTTATC
238426 TTTTTATTTTCTTAT
1 TTTTTATTTTCTTAT
238441 TTATTTTTGT
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:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTATTTTCTTATC
Found at i:238518 original size:22 final size:22
Alignment explanation
Indices: 238490--238532 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
238480 TGTACTTCAT
238490 TTAGAATCGCTCACGATTCCAA
1 TTAGAATCGCTCACGATTCCAA
*
238512 TTAGAATTGCTCACGATTCCA
1 TTAGAATCGCTCACGATTCCA
238533 GATTTTAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (22 bp):
TTAGAATCGCTCACGATTCCAA
Found at i:239242 original size:22 final size:22
Alignment explanation
Indices: 239198--239243 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
239188 TTAACCCATA
*
239198 TTTATGTGGTAAAATTATCTTT
1 TTTATGTGGTAAAATTATATTT
*
239220 TTTATGTTGTAAAAGTT-TATTT
1 TTTATGTGGTAAAA-TTATATTT
239242 TT
1 TT
239244 GATAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.26, C:0.02, G:0.13, T:0.59
Consensus pattern (22 bp):
TTTATGTGGTAAAATTATATTT
Found at i:243928 original size:17 final size:18
Alignment explanation
Indices: 243906--243940 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
243896 AAAATTGAAA
*
243906 TGAATTTT-TATTTTTAT
1 TGAATTTTAAATTTTTAT
243923 TGAATTTTAAATTTTTAT
1 TGAATTTTAAATTTTTAT
243941 GATATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (18 bp):
TGAATTTTAAATTTTTAT
Found at i:245629 original size:21 final size:20
Alignment explanation
Indices: 245580--245629 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 20
245570 ACCATAGCTC
* *
245580 TTTTCTCCTTTTTCTTTTTCT
1 TTTTC-CCTTTTTATTTTCCT
245601 TTTT--CTTTTTATTCTTCCT
1 TTTTCCCTTTTTATT-TTCCT
245620 TTTTCCCTTT
1 TTTTCCCTTT
245630 ATGACCCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
18 8 0.33
19 8 0.33
21 8 0.33
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTCCCTTTTTATTTTCCT
Found at i:248066 original size:9 final size:9
Alignment explanation
Indices: 248052--248131 Score: 61
Period size: 9 Copynumber: 8.3 Consensus size: 9
248042 ATTATATTTT
248052 AAATTATAA
1 AAATTATAA
248061 AAATTATAA
1 AAATTATAA
* *
248070 AACTAATAA
1 AAATTATAA
*
248079 AACTTATTTAA
1 AAATTA--TAA
**
248090 ATTTTAATAA
1 AAATT-ATAA
*
248100 AAATGATAA
1 AAATTATAA
248109 AAACTTATAA
1 AAA-TTATAA
248119 AAACTTATAA
1 AAA-TTATAA
248129 AAA
1 AAA
248132 AATATTGAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
9 28 0.48
10 23 0.40
11 6 0.10
12 1 0.02
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (9 bp):
AAATTATAA
Found at i:248111 original size:10 final size:10
Alignment explanation
Indices: 248098--248150 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
248088 AAATTTTAAT
*
248098 AAAAATGATA
1 AAAAATTATA
*
248108 AAAACTTATA
1 AAAAATTATA
*
248118 AAAACTTATA
1 AAAAATTATA
*
248128 AAAAAATATTGA
1 AAAAATTA-T-A
248140 AAAAATTATA
1 AAAAATTATA
248150 A
1 A
248151 TAATAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 26 0.72
11 2 0.06
12 8 0.22
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (10 bp):
AAAAATTATA
Found at i:258190 original size:14 final size:14
Alignment explanation
Indices: 258167--258197 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
258157 TTTTATATTA
258167 TTTTAAATTTTAAT
1 TTTTAAATTTTAAT
*
258181 TTTTATATTTTAAT
1 TTTTAAATTTTAAT
258195 TTT
1 TTT
258198 GAGATAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTAAATTTTAAT
Found at i:258579 original size:2 final size:2
Alignment explanation
Indices: 258572--258597 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
258562 ATTAAATTCA
258572 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
258598 TCAAAATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:263016 original size:18 final size:18
Alignment explanation
Indices: 262993--263027 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
262983 TTTTGAATTG
*
262993 GGAGAATAACCTCATTAT
1 GGAGAAGAACCTCATTAT
263011 GGAGAAGAACCTCATTA
1 GGAGAAGAACCTCATTA
263028 GTTATCCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (18 bp):
GGAGAAGAACCTCATTAT
Found at i:270018 original size:20 final size:22
Alignment explanation
Indices: 269993--270032 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
269983 GTGTTGATAA
269993 TTTAAAAGG-AT-ATAATTTCT
1 TTTAAAAGGAATGATAATTTCT
*
270013 TTTAAATGGAATGATAATTT
1 TTTAAAAGGAATGATAATTT
270033 TAAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 2 0.12
22 7 0.41
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (22 bp):
TTTAAAAGGAATGATAATTTCT
Done.