Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011738.1 Kokia drynarioides strain JFW-HI SEQ_126732, 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: 180976
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:80 original size:15 final size:17
Alignment explanation
Indices: 60--91 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
50 TTAAATTATT
60 ATAAATA-ATA-ATATA
1 ATAAATATATATATATA
75 ATAAATATATATATATA
1 ATAAATATATATATATA
92 TATATATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAAATATATATATATA
Found at i:872 original size:16 final size:17
Alignment explanation
Indices: 779--862 Score: 105
Period size: 17 Copynumber: 4.9 Consensus size: 17
769 ATTAATTTTT
779 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTCA
* *
796 AATTTAAAGTAAATTTA
1 AATTTAAAATAAATTCA
* * * *
813 AACTCAAAATGAATTTA
1 AATTTAAAATAAATTCA
830 AATTTAAAAATAAATTCA
1 AATTT-AAAATAAATTCA
848 AATTTAAAATAAATT
1 AATTTAAAATAAATT
863 AATATTAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
17 41 0.73
18 15 0.27
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (17 bp):
AATTTAAAATAAATTCA
Found at i:873 original size:17 final size:17
Alignment explanation
Indices: 779--874 Score: 86
Period size: 17 Copynumber: 5.6 Consensus size: 17
769 ATTAATTTTT
*
779 AATTTAAAATAAATTCA
1 AATTAAAAATAAATTCA
* * *
796 AATTTAAAGTAAATTTA
1 AATTAAAAATAAATTCA
* * * *
813 AACTCAAAATGAATTTA
1 AATTAAAAATAAATTCA
830 AATTTAAAAATAAATTCA
1 AA-TTAAAAATAAATTCA
*
848 AATTTAAAATAAATT-A
1 AATTAAAAATAAATTCA
864 ATATTAAAAAT
1 A-ATTAAAAAT
875 TAAAAGTTGG
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
16 2 0.03
17 50 0.77
18 13 0.20
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.35
Consensus pattern (17 bp):
AATTAAAAATAAATTCA
Found at i:11595 original size:69 final size:69
Alignment explanation
Indices: 11480--11619 Score: 199
Period size: 69 Copynumber: 2.0 Consensus size: 69
11470 TATATATTAT
* *
11480 TTATCTTATTTATTCTTAAACATATAATAAAAATATAAACCACAAATTTATGGATATGGTTTTAG
1 TTATCTTATTTATTCATAAACATATAATAAAAATATAAACCACAAATTTATGGACATGGTTTTAG
*
11545 ATAA
66 ACAA
* * * * * *
11549 TTATCTTCTTTATTGATAGACATATCATAAAAATATAAATCTCAAATTTATGGACATGGTTTTAG
1 TTATCTTATTTATTCATAAACATATAATAAAAATATAAACCACAAATTTATGGACATGGTTTTAG
11614 ACAA
66 ACAA
11618 TT
1 TT
11620 TGAGGACTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.41
Consensus pattern (69 bp):
TTATCTTATTTATTCATAAACATATAATAAAAATATAAACCACAAATTTATGGACATGGTTTTAG
ACAA
Found at i:11741 original size:30 final size:29
Alignment explanation
Indices: 11685--11741 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
11675 TCCGGAGTCA
* *
11685 TTTTAATTTTCAATTTACTTTTTTTGTTT
1 TTTTAATTTTAAATTTACTTTATTTGTTT
11714 TTTTAATTTTTAAATTTA-TATTATTTGT
1 TTTTAA-TTTTAAATTTACT-TTATTTGT
11742 CAAACTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.70
Consensus pattern (29 bp):
TTTTAATTTTAAATTTACTTTATTTGTTT
Found at i:11872 original size:16 final size:16
Alignment explanation
Indices: 11851--11881 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11841 ATTAAAAAAA
*
11851 TATTTTTTATATTTTT
1 TATTTTTTAAATTTTT
11867 TATTTTTTAAATTTT
1 TATTTTTTAAATTTT
11882 AATAATTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TATTTTTTAAATTTTT
Found at i:17843 original size:22 final size:21
Alignment explanation
Indices: 17800--17855 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
17790 GCAATTTGAC
17800 AAATAAAAATAAAACAACAAA
1 AAATAAAAATAAAACAACAAA
**
17821 AAATAAAAATAAAAGTACAAA
1 AAATAAAAATAAAACAACAAA
17842 AAATTAAAAATAAA
1 AAA-TAAAAATAAA
17856 TAAAGCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 22 0.69
22 10 0.31
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (21 bp):
AAATAAAAATAAAACAACAAA
Found at i:21030 original size:121 final size:119
Alignment explanation
Indices: 20891--21132 Score: 432
Period size: 121 Copynumber: 2.0 Consensus size: 119
20881 GTGGAGAGAT
20891 AGAGGTTACCTGCTTTCAAGTTGACGCCTCAAGCATTTTATACCT-CTCCTCTTGAGGTGTCACG
1 AGAGGTTACCTGCTTTCAAGTTGACGCCTCAAGCATTTTATACCTCCT-CTCTTGAGGTGTCACG
*
20955 TGTTGAGTCATTATGACGAGTTAGAAGCAAGTGACTTACTATCATAAGGTTAGGTAG
65 TGTTGAGTCATTATGACGAGTTAGAAGCAAGTGACTTAATAT--TAAGGTTAGGTAG
21012 AGAGGTTACCTGCTTTCAAGTTGACGCCTCAAGCATTTTATACCTCCTCTCTTGAGGTGTCACGT
1 AGAGGTTACCTGCTTTCAAGTTGACGCCTCAAGCATTTTATACCTCCTCTCTTGAGGTGTCACGT
*
21077 GTTGAGTCATTATGGCGAGTTAGAAGCAAGTGACTTAATATTAAGGTTAGGTAG
66 GTTGAGTCATTATGACGAGTTAGAAGCAAGTGACTTAATATTAAGGTTAGGTAG
21131 AG
1 AG
21133 TAGCGTTATG
Statistics
Matches: 118, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
119 15 0.13
121 101 0.86
122 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (119 bp):
AGAGGTTACCTGCTTTCAAGTTGACGCCTCAAGCATTTTATACCTCCTCTCTTGAGGTGTCACGT
GTTGAGTCATTATGACGAGTTAGAAGCAAGTGACTTAATATTAAGGTTAGGTAG
Found at i:26070 original size:32 final size:32
Alignment explanation
Indices: 25977--26094 Score: 106
Period size: 32 Copynumber: 3.9 Consensus size: 32
25967 TTAATAGAAC
** * *
25977 ATTTGGTACTTTAACTTGACA-CTTTTTACTA
1 ATTTGGTACTCAAACTTGACATTTTTTTCCTA
**
26008 ATTTGGTAC-CTAAACTT----TTTTGGTCC-A
1 ATTTGGTACTC-AAACTTGACATTTTTTTCCTA
26035 ATTTGGTACTCAAACTTGACATTTTTTTCCTA
1 ATTTGGTACTCAAACTTGACATTTTTTTCCTA
* *
26067 ATTTGTTACTTAAACTTGACATTTTTTT
1 ATTTGGTACTCAAACTTGACATTTTTTT
26095 TTAAAGTTGG
Statistics
Matches: 69, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
27 16 0.23
28 5 0.07
31 21 0.30
32 27 0.39
ACGTcount: A:0.25, C:0.16, G:0.10, T:0.49
Consensus pattern (32 bp):
ATTTGGTACTCAAACTTGACATTTTTTTCCTA
Found at i:26109 original size:32 final size:32
Alignment explanation
Indices: 25979--26115 Score: 99
Period size: 32 Copynumber: 4.5 Consensus size: 32
25969 AATAGAACAT
* * * *
25979 TTGGTACTTTAACTTGACA-CTTTTTACTAAT
1 TTGGTACTTAAACTTGACATTTTTTTCCTAAG
* ** *
26010 TTGGTACCTAAACTT----TTTTGGTCC-AAT
1 TTGGTACTTAAACTTGACATTTTTTTCCTAAG
* *
26037 TTGGTACTCAAACTTGACATTTTTTTCCTAAT
1 TTGGTACTTAAACTTGACATTTTTTTCCTAAG
* *
26069 TTGTTACTTAAACTTGACATTTTTTT-TTAAAG
1 TTGGTACTTAAACTTGACATTTTTTTCCT-AAG
*
26101 TTGGTACTTCAACTT
1 TTGGTACTTAAACTT
26116 TTTGAGGTCC
Statistics
Matches: 83, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
27 16 0.19
28 4 0.05
31 21 0.25
32 42 0.51
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (32 bp):
TTGGTACTTAAACTTGACATTTTTTTCCTAAG
Found at i:26158 original size:91 final size:90
Alignment explanation
Indices: 25977--26166 Score: 238
Period size: 91 Copynumber: 2.1 Consensus size: 90
25967 TTAATAGAAC
* * * *
25977 ATTTGGTACTTTAACTTGACACTTTTTACTAATTTGGTACCTAAACTTTTTTGGTCCAATTTGGT
1 ATTTGGTACTTAAACTTGACACTTTTTACTAAGTTGGTACCTAAACTTTTTAGGTCCAATTTGGA
*
26042 ACTCAAACTTGACATTTTTTTCCTA
66 ACTCAAACTTGACATCTTTTTCCTA
* * ** * *
26067 ATTTGTTACTTAAACTTGACATTTTTTTTTAAAGTTGGTACTTCAACTTTTTGAGGTCCAATTTG
1 ATTTGGTACTTAAACTTGACACTTTTTACT-AAGTTGGTACCTAAACTTTTT-AGGTCCAATTTG
* *
26132 GAACTTAAATTTGAC-TCTTTTTCCTA
64 GAACTCAAACTTGACATCTTTTTCCTA
26158 ATTTGGTAC
1 ATTTGGTAC
26167 CTAATCTTTT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
90 25 0.30
91 36 0.43
92 23 0.27
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (90 bp):
ATTTGGTACTTAAACTTGACACTTTTTACTAAGTTGGTACCTAAACTTTTTAGGTCCAATTTGGA
ACTCAAACTTGACATCTTTTTCCTA
Found at i:26386 original size:31 final size:31
Alignment explanation
Indices: 26348--26509 Score: 122
Period size: 31 Copynumber: 5.4 Consensus size: 31
26338 AAAAATGCTT
*
26348 AGGTACCAAATTAGGAAAAAATGCCAAGTTC
1 AGGTACCAAATTAGGAAAAAATGTCAAGTTC
* * *
26379 AGGTACCAAATTGGGTTCAAAAA----AA-TTT
1 AGGTACCAAATTAGG--AAAAAATGTCAAGTTC
* * * *
26407 AGATACAAAATTAAGAAAAAGTGTCAAGTTC
1 AGGTACCAAATTAGGAAAAAATGTCAAGTTC
* * ** *
26438 AAGTATCAAATTAGGTAAAAAA--AAAAGTTT
1 AGGTACCAAATTAGG-AAAAAATGTCAAGTTC
*
26468 AGGTACCAAATTAGGAAAAAGTGTCAAGTTC
1 AGGTACCAAATTAGGAAAAAATGTCAAGTTC
26499 AGGTACCAAAT
1 AGGTACCAAAT
26510 CTTATATTTA
Statistics
Matches: 96, Mismatches: 25, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
26 4 0.04
28 13 0.14
29 7 0.07
30 20 0.21
31 42 0.44
32 5 0.05
33 5 0.05
ACGTcount: A:0.48, C:0.11, G:0.18, T:0.23
Consensus pattern (31 bp):
AGGTACCAAATTAGGAAAAAATGTCAAGTTC
Found at i:26435 original size:59 final size:58
Alignment explanation
Indices: 26319--26509 Score: 220
Period size: 61 Copynumber: 3.2 Consensus size: 58
26309 TAATAAATTT
** * * *
26319 AGGTACCAAATTGAATCTAAAAAATGCTTAGGTACCAAATTAGGAAAAAATGCCAAGTTC
1 AGGTACCAAATTGGTTCAAAAAAAT--TTAGGTACCAAATTAGGAAAAAGTGTCAAGTTC
* * *
26379 AGGTACCAAATTGGGTTCAAAAAAATTTAGATACAAAATTAAGAAAAAGTGTCAAGTTC
1 AGGTACCAAATT-GGTTCAAAAAAATTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTC
* * **
26438 AAGTATCAAATTAGGTAAAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTC
1 AGGTACCAAATT-GGT-TCAAAAAAA-TTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTC
26499 AGGTACCAAAT
1 AGGTACCAAAT
26510 CTTATATTTA
Statistics
Matches: 110, Mismatches: 18, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
59 41 0.37
60 19 0.17
61 50 0.45
ACGTcount: A:0.47, C:0.12, G:0.17, T:0.24
Consensus pattern (58 bp):
AGGTACCAAATTGGTTCAAAAAAATTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTC
Found at i:26486 original size:61 final size:60
Alignment explanation
Indices: 26337--26509 Score: 222
Period size: 59 Copynumber: 2.9 Consensus size: 60
26327 AATTGAATCT
* * * * * **
26337 AAAAAATGCTTAGGTACCAAATTAGGAAAAAATGCCAAGTTCAGGTACCAAATTGGGTTC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTAGGTAA
* * * * *
26397 AAAAAAA-TTTAGATACAAAATTAAGAAAAAGTGTCAAGTTCAAGTATCAAATTAGGTAAA
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTAGGT-AA
26457 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAAT
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAAT
26510 CTTATATTTA
Statistics
Matches: 94, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 41 0.44
60 13 0.14
61 40 0.43
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (60 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAGGTACCAAATTAGGTAA
Found at i:28110 original size:7 final size:7
Alignment explanation
Indices: 28098--28123 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
28088 GTCCTCGTTC
28098 TTTGTTG
1 TTTGTTG
28105 TTTGTTG
1 TTTGTTG
28112 TTTGTTG
1 TTTGTTG
28119 TTTGT
1 TTTGT
28124 CAAAAGATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.27, T:0.73
Consensus pattern (7 bp):
TTTGTTG
Found at i:29782 original size:19 final size:20
Alignment explanation
Indices: 29741--29783 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
29731 AGAAATATAA
*
29741 ATTTTGAAATTTTTATAAAT
1 ATTTTGAAATTTTGATAAAT
29761 ATTTTG-AATTTTGA-AAATT
1 ATTTTGAAATTTTGATAAA-T
29780 ATTT
1 ATTT
29784 AATTTTTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 12 0.57
20 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
ATTTTGAAATTTTGATAAAT
Found at i:40775 original size:20 final size:20
Alignment explanation
Indices: 40750--40818 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
40740 GAACATGATT
40750 ATAATTTTAAAATATTTTTA
1 ATAATTTTAAAATATTTTTA
*
40770 ATAATTTT---ATATTTTAAAA
1 ATAATTTTAAAATATTTT--TA
*
40789 ATTAATTTTAAAATAATTTTA
1 A-TAATTTTAAAATATTTTTA
40810 ATAATTTTA
1 ATAATTTTA
40819 GAATCATTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
17 7 0.17
19 2 0.05
20 23 0.57
21 2 0.05
23 6 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATAATTTTAAAATATTTTTA
Found at i:40807 original size:11 final size:11
Alignment explanation
Indices: 40750--40818 Score: 55
Period size: 9 Copynumber: 6.8 Consensus size: 11
40740 GAACATGATT
40750 ATAATTTTAAA
1 ATAATTTTAAA
*
40761 AT-ATTTT-TA
1 ATAATTTTAAA
40770 ATAATTTT---
1 ATAATTTTAAA
40778 AT-ATTTTAAAA
1 ATAATTTT-AAA
40789 ATTAATTTTAAA
1 A-TAATTTTAAA
40801 ATAATTTT--A
1 ATAATTTTAAA
40810 ATAATTTTA
1 ATAATTTTA
40819 GAATCATTTG
Statistics
Matches: 49, Mismatches: 1, Indels: 17
0.73 0.01 0.25
Matches are distributed among these distances:
7 5 0.10
8 2 0.04
9 12 0.24
10 10 0.20
11 10 0.20
12 5 0.10
13 5 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:42929 original size:250 final size:250
Alignment explanation
Indices: 42634--43135 Score: 896
Period size: 250 Copynumber: 2.0 Consensus size: 250
42624 TATACTCTTT
*
42634 ATATATATATATTGACAACCAACATTACAAGCATATACATGTAACCTTTACAACACTTAGTACAT
1 ATATATATATATTGACAACCAACATTACAAGCATATACATGTAACCTATACAACACTTAGTACAT
*
42699 GTCAATTTTACCAAAAGGGGAGAATTACGTCACCGAATTTATACTGAGGTCGGGATCGATCTAGA
66 GTCAATTTTACCAAAAGGGGAGAATTACATCACCGAATTTATACTGAGGTCGGGATCGATCTAGA
*
42764 TGCTGAACCAGGACCTTAACTTCTACTAACCTGCGCACAGAAACAACCGTACGCTGAGTATTTCA
131 TGCTGAACCAGGAACTTAACTTCTACTAACCTGCGCACAGAAACAACCGTACGCTGAGTATTTCA
42829 TACTCAGTAGTATTACTATAATTCAAATTATAAATAACCAAATAAATTTCACATA
196 TACTCAGTAGTATTACTATAATTCAAATTATAAATAACCAAATAAATTTCACATA
*
42884 ATATATATATATTGACAACCAACATTACAAGCATATACTTGTAACCTATACAACACTTAGTACAT
1 ATATATATATATTGACAACCAACATTACAAGCATATACATGTAACCTATACAACACTTAGTACAT
* * *
42949 GTCACTTTTACCAAAAGGGGAGAATTACATTACCGAATTTATACTGAGGTCGGGATCGATCTGGA
66 GTCAATTTTACCAAAAGGGGAGAATTACATCACCGAATTTATACTGAGGTCGGGATCGATCTAGA
* * * *
43014 TGTTGAACCAGGAACTTAACTTCTACTAACCTGTGCACGGAAATAACCGTACGCTGAGTATTTCA
131 TGCTGAACCAGGAACTTAACTTCTACTAACCTGCGCACAGAAACAACCGTACGCTGAGTATTTCA
*
43079 TACTCAGTGGTATTACTATAATTCAAATTATAAATAACCAAATAAATTTCACATA
196 TACTCAGTAGTATTACTATAATTCAAATTATAAATAACCAAATAAATTTCACATA
43134 AT
1 AT
43136 CAATCGTATA
Statistics
Matches: 240, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
250 240 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.29
Consensus pattern (250 bp):
ATATATATATATTGACAACCAACATTACAAGCATATACATGTAACCTATACAACACTTAGTACAT
GTCAATTTTACCAAAAGGGGAGAATTACATCACCGAATTTATACTGAGGTCGGGATCGATCTAGA
TGCTGAACCAGGAACTTAACTTCTACTAACCTGCGCACAGAAACAACCGTACGCTGAGTATTTCA
TACTCAGTAGTATTACTATAATTCAAATTATAAATAACCAAATAAATTTCACATA
Found at i:43693 original size:12 final size:12
Alignment explanation
Indices: 43671--43704 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
43661 ATTCATATCG
43671 CTTTCAATTTCA
1 CTTTCAATTTCA
* *
43683 ATTTCACTTTCA
1 CTTTCAATTTCA
43695 CTTTCAATTT
1 CTTTCAATTT
43705 TGATCACAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (12 bp):
CTTTCAATTTCA
Found at i:44242 original size:22 final size:22
Alignment explanation
Indices: 44200--44243 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
44190 TACATTTGGC
* *
44200 TTTAATATATATATTTCATTAA
1 TTTAATAAATATATATCATTAA
44222 TTTAATAAATA-ATATCAATTAA
1 TTTAATAAATATATATC-ATTAA
44244 ATAATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTAATAAATATATATCATTAA
Found at i:50792 original size:30 final size:31
Alignment explanation
Indices: 50735--50792 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
50725 AATTTAATCC
*
50735 TCAACATTTTAAAAGGAATCAAATTTGTCCA
1 TCAACATTTTAAAAAGAATCAAATTTGTCCA
* *
50766 TCAACCTTTTAAAAATAATC-AATTTGT
1 TCAACATTTTAAAAAGAATCAAATTTGT
50793 TGTTTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 7 0.29
31 17 0.71
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.36
Consensus pattern (31 bp):
TCAACATTTTAAAAAGAATCAAATTTGTCCA
Found at i:50909 original size:17 final size:19
Alignment explanation
Indices: 50889--50928 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
50879 ATTTTTGAAA
*
50889 TTTTATG-ATTTTT-TTAT
1 TTTTATGAATTTTTATAAT
50906 TTTT-TGAATTTTTATAAT
1 TTTTATGAATTTTTATAAT
50924 TTTTA
1 TTTTA
50929 AATTATCCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 2 0.11
17 10 0.53
18 7 0.37
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (19 bp):
TTTTATGAATTTTTATAAT
Found at i:54820 original size:21 final size:21
Alignment explanation
Indices: 54796--54853 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 21
54786 ATTTTACTTC
*
54796 TTAAATTTTTAAAAATAAAAA
1 TTAAATATTTAAAAATAAAAA
*
54817 TTAAAAAACTTTAAAAATAAAAA
1 TT-AAATA-TTTAAAAATAAAAA
*
54840 TAAAATATTTAAAA
1 TTAAATATTTAAAA
54854 GTTCTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 9 0.29
22 7 0.23
23 15 0.48
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAAATATTTAAAAATAAAAA
Found at i:54830 original size:23 final size:21
Alignment explanation
Indices: 54803--54853 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 21
54793 TTCTTAAATT
54803 TTTAAAAATAAAAATTAAAAAA
1 TTTAAAAATAAAAA-TAAAAAA
*
54825 CTTTAAAAATAAAAATAAAATA
1 -TTTAAAAATAAAAATAAAAAA
54847 TTTAAAA
1 TTTAAAA
54854 GTTCTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 7 0.26
22 6 0.22
23 14 0.52
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
TTTAAAAATAAAAATAAAAAA
Found at i:55487 original size:19 final size:20
Alignment explanation
Indices: 55463--55506 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
55453 CTTTAAATTG
* *
55463 TTTTATTTGTAATATT-TTA
1 TTTTATTTATAAAATTATTA
55482 TTTTATTTATAAAATTATTA
1 TTTTATTTATAAAATTATTA
55502 TTTTA
1 TTTTA
55507 ATAAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTATTTATAAAATTATTA
Found at i:55611 original size:10 final size:10
Alignment explanation
Indices: 55540--55611 Score: 54
Period size: 10 Copynumber: 7.2 Consensus size: 10
55530 ATGAGAAAAA
*
55540 ATATATATTT
1 ATATATTTTT
* *
55550 ATTTATTTAT
1 ATATATTTTT
*
55560 AAATATTTTT
1 ATATATTTTT
* *
55570 AAAAATTTTT
1 ATATATTTTT
*
55580 ATGTATTTTT
1 ATATATTTTT
* * *
55590 ATAAAATCTT
1 ATATATTTTT
55600 ATATATTTTT
1 ATATATTTTT
55610 AT
1 AT
55612 TGAAAAATGA
Statistics
Matches: 45, Mismatches: 17, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
10 45 1.00
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (10 bp):
ATATATTTTT
Found at i:55746 original size:29 final size:30
Alignment explanation
Indices: 55667--55746 Score: 74
Period size: 29 Copynumber: 2.7 Consensus size: 30
55657 TTTTTAAAAA
* *
55667 TTAAGACTAAATTGATAAAATGTGTAAGGT
1 TTAAGACTAAATTGATAGAATGTGTAAGAT
* * * * *
55697 TGAGAGA-TAAATTAATTGAAT-TTTTAGAT
1 TTA-AGACTAAATTGATAGAATGTGTAAGAT
55726 TTAAGACTAAATTGATAGAAT
1 TTAAGACTAAATTGATAGAAT
55747 CTATAAAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
28 3 0.08
29 19 0.50
30 13 0.34
31 3 0.08
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.36
Consensus pattern (30 bp):
TTAAGACTAAATTGATAGAATGTGTAAGAT
Found at i:59312 original size:79 final size:80
Alignment explanation
Indices: 59032--59407 Score: 445
Period size: 80 Copynumber: 4.7 Consensus size: 80
59022 TATGGCACGC
* * * ** * *
59032 AGTGCCTAGCGGA-ATAACTGCGAAA-GTGAGCCTAGCTCTAGTTGGATT-AACCAACAAATATT
1 AGTGCTTAGCGGATA-AACCGC-AAATGTGAGCCCAGCTCTAGTCAG-TTAAACCGACAAATATC
* ** *
59094 CGTCAAATCCTATTACCC
63 CGTCAAATCTTAGCACCT
* * *
59112 AGTGCTTAGCGGATAAACCGCAAATGTGAGCCCATCTCTAGTCAGTTAAATCGGCAAATATCCGT
1 AGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCGACAAATATCCGT
*
59177 CAAATCTTAGCACCC
66 CAAATCTTAGCACCT
* * *
59192 AGTGCTTAGTGGATAAACCGCAAATGTGAGCCCAACTCTAGTCATTTAAACCGACAAATATCCGT
1 AGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCGACAAATATCCGT
*
59257 TAAATCTTAGCA-CT
66 CAAATCTTAGCACCT
* * * * *
59271 AGTGCTTAGTGGATAAATCGCAAATGTGAGCTCAGCTCTAGTCGGTTAAACTGACAAATATCCGT
1 AGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCGACAAATATCCGT
*
59336 CAAATCTTGGCACCT
66 CAAATCTTAGCACCT
* * *
59351 AGTGCCTAGCGGATAAACCGCAATTGTGAGCCCAGCTCTAGTCAGTTAAACTGACAA
1 AGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCGACAA
59408 CATGTATTCA
Statistics
Matches: 258, Mismatches: 34, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
79 75 0.29
80 182 0.71
81 1 0.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (80 bp):
AGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAACCGACAAATATCCGT
CAAATCTTAGCACCT
Found at i:59401 original size:159 final size:159
Alignment explanation
Indices: 59112--59407 Score: 450
Period size: 159 Copynumber: 1.9 Consensus size: 159
59102 CCTATTACCC
* *
59112 AGTGCTTAGCGGATAAACCGCAAATGTGAGCCCATCTCTAGTCAGTTAAATCGGCAAATATCCGT
1 AGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAATCGACAAATATCCGT
* * *
59177 CAAATCTTAGCACCCAGTGCTTAGTGGATAAACCGCAAATGTGAGCCCAACTCTAGTCATTTAAA
66 CAAATCTTAGCACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAACTCTAGTCAGTTAAA
59242 CCGACAAATATCCGTTAAATCTTAGCACT
131 CCGACAAATATCCGTTAAATCTTAGCACT
* * * *
59271 AGTGCTTAGTGGATAAATCGCAAATGTGAGCTCAGCTCTAGTCGGTTAAA-CTGACAAATATCCG
1 AGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAATC-GACAAATATCCG
* * * *
59335 TCAAATCTTGGCACCTAGTGCCTAGCGGATAAACCGCAATTGTGAGCCCAGCTCTAGTCAGTTAA
65 TCAAATCTTAGCACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAACTCTAGTCAGTTAA
*
59400 ACTGACAA
130 ACCGACAA
59408 CATGTATTCA
Statistics
Matches: 122, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
158 1 0.01
159 121 0.99
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.25
Consensus pattern (159 bp):
AGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTCAGTTAAATCGACAAATATCCGT
CAAATCTTAGCACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAACTCTAGTCAGTTAAA
CCGACAAATATCCGTTAAATCTTAGCACT
Found at i:61965 original size:40 final size:39
Alignment explanation
Indices: 61921--62066 Score: 132
Period size: 40 Copynumber: 3.7 Consensus size: 39
61911 GTGTTATCAC
* **
61921 TGAACTGGCAGTGACACTGTAATTACTGCAATATTATTA
1 TGAACTGGCAGTGAAACTGTAAACACTGCAATATTATTA
* *
61960 TTGAACTGGCAGT-AAGATTATAAACACTGCAATATTATTA
1 -TGAACTGGCAGTGAA-ACTGTAAACACTGCAATATTATTA
* * * **
62000 TAAACTGGCAGTGAAACTGTAAACGCTGTAACGTTATTA
1 TGAACTGGCAGTGAAACTGTAAACACTGCAATATTATTA
* * * *
62039 CTGTACTAGCTGTGACACTGTAAACACT
1 -TGAACTGGCAGTGAAACTGTAAACACT
62067 TCTAGACAAT
Statistics
Matches: 85, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
39 30 0.35
40 55 0.65
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (39 bp):
TGAACTGGCAGTGAAACTGTAAACACTGCAATATTATTA
Found at i:61999 original size:20 final size:20
Alignment explanation
Indices: 61945--62004 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
61935 CACTGTAATT
**
61945 ACTGCAATATTATTATTGA-
1 ACTGCAATATTATTATAAAC
* **
61964 ACTGGCAGTAAGATTATAAAC
1 ACT-GCAATATTATTATAAAC
61985 ACTGCAATATTATTATAAAC
1 ACTGCAATATTATTATAAAC
62005 TGGCAGTGAA
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
19 3 0.10
20 25 0.81
21 3 0.10
ACGTcount: A:0.42, C:0.13, G:0.12, T:0.33
Consensus pattern (20 bp):
ACTGCAATATTATTATAAAC
Found at i:63045 original size:27 final size:28
Alignment explanation
Indices: 62994--63046 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
62984 AGAAAACAAA
62994 AATAAGTTTATATTTTAAAAAATAATAT
1 AATAAGTTTATATTTTAAAAAATAATAT
* *
63022 AATAATTTTATA-TTTAAAGAATAAT
1 AATAAGTTTATATTTTAAAAAATAAT
63047 TTTAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (28 bp):
AATAAGTTTATATTTTAAAAAATAATAT
Found at i:68927 original size:21 final size:22
Alignment explanation
Indices: 68903--68951 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
68893 GTCTGTGGTT
* *
68903 ATTTTGCTATTG-TTTGTTGCC
1 ATTTTGATATTGCTTTGCTGCC
*
68924 ATTTTGATGTTGCTTTGCTGCC
1 ATTTTGATATTGCTTTGCTGCC
68946 ATTTTG
1 ATTTTG
68952 TTACTATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.10, C:0.14, G:0.20, T:0.55
Consensus pattern (22 bp):
ATTTTGATATTGCTTTGCTGCC
Found at i:69085 original size:17 final size:18
Alignment explanation
Indices: 69063--69096 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
69053 TAATTATTTT
69063 AATATTATTTAA-GTATA
1 AATATTATTTAATGTATA
*
69080 AATATTTTTTAATGTAT
1 AATATTATTTAATGTAT
69097 TTTTAGTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
AATATTATTTAATGTATA
Found at i:76249 original size:16 final size:16
Alignment explanation
Indices: 76228--76261 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
76218 CAAAGCTTAG
76228 CTTTTTCTATTTATTA
1 CTTTTTCTATTTATTA
76244 CTTTTTCTATTTATTA
1 CTTTTTCTATTTATTA
76260 CT
1 CT
76262 CTTTGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.68
Consensus pattern (16 bp):
CTTTTTCTATTTATTA
Found at i:76805 original size:2 final size:2
Alignment explanation
Indices: 76798--76825 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
76788 TATCTTTTGT
76798 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
76826 AGCTACTCAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:76954 original size:23 final size:24
Alignment explanation
Indices: 76926--76970 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
76916 AGAAAAGATC
76926 TTTCTTTCCA-GTGTTTGTTCCCT
1 TTTCTTTCCAGGTGTTTGTTCCCT
* *
76949 TTTCTTTGCAGGTTTTTGTTCC
1 TTTCTTTCCAGGTGTTTGTTCC
76971 TTGATTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.04, C:0.22, G:0.16, T:0.58
Consensus pattern (24 bp):
TTTCTTTCCAGGTGTTTGTTCCCT
Found at i:84966 original size:38 final size:37
Alignment explanation
Indices: 84920--84991 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
84910 GCCCGAACTC
*
84920 AAAATAAACT-AATACCCAAATCTCAAGTTAAAAAAAA
1 AAAATAAACTCAATACCCAAA-CACAAGTTAAAAAAAA
* *
84957 AAAATTAAACTCAATACCTAAACACAATTTAAAAA
1 AAAA-TAAACTCAATACCCAAACACAAGTTAAAAA
84992 GTTAAAAGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
37 4 0.13
38 17 0.57
39 9 0.30
ACGTcount: A:0.61, C:0.17, G:0.01, T:0.21
Consensus pattern (37 bp):
AAAATAAACTCAATACCCAAACACAAGTTAAAAAAAA
Found at i:85606 original size:2 final size:2
Alignment explanation
Indices: 85571--85631 Score: 63
Period size: 2 Copynumber: 30.5 Consensus size: 2
85561 TATATAATGC
* * *
85571 TA TA TCA TA TCA TA TA -A TA TA T- TA AA AA TT TA TA TA TA TA TA
1 TA TA T-A TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
85613 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
85632 GCACCCATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
1 2 0.04
2 45 0.88
3 4 0.08
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:90741 original size:30 final size:30
Alignment explanation
Indices: 90707--90778 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
90697 TGAAAATGAA
*
90707 ATTTTAGAAAAGCTCGAGGGTCAAAATATG
1 ATTTTGGAAAAGCTCGAGGGTCAAAATATG
** * * *
90737 ATTTTGGAAAATTTTGAGGGTTAAAATGTG
1 ATTTTGGAAAAGCTCGAGGGTCAAAATATG
90767 ATTTTGGAAAAG
1 ATTTTGGAAAAG
90779 TTTAGGGGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.38, C:0.04, G:0.25, T:0.33
Consensus pattern (30 bp):
ATTTTGGAAAAGCTCGAGGGTCAAAATATG
Found at i:90771 original size:60 final size:60
Alignment explanation
Indices: 90699--90839 Score: 169
Period size: 60 Copynumber: 2.4 Consensus size: 60
90689 AATCGGGATG
* * * *
90699 AAAATGAAATTTTAGAAAAGCTCGA-GGGTCAAAATATGATTTTGGAAAA-TTTTGAGGGTT
1 AAAATGTAATTTTGGAAAAG-TCGAGGGGTCAAAATATAATTTTGGAAAAGTTTAG-GGGTT
* ** * *
90759 AAAATGTGATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGTT
1 AAAATGTAATTTTGGAAAAGTCGAGGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGTT
90819 AAAATGTAATTTTGGAAAAGT
1 AAAATGTAATTTTGGAAAAGT
90840 TTAGGGACCT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 2 0.03
60 63 0.91
61 4 0.06
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (60 bp):
AAAATGTAATTTTGGAAAAGTCGAGGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGTT
Found at i:90788 original size:30 final size:30
Alignment explanation
Indices: 90737--90845 Score: 184
Period size: 30 Copynumber: 3.6 Consensus size: 30
90727 TCAAAATATG
* *
90737 ATTTTGGAAAA-TTTTGAGGGTTAAAATGTG
1 ATTTTGGAAAAGTTTAG-GGGTTAAAATGTA
90767 ATTTTGGAAAAGTTTAGGGGTTAAAATGTA
1 ATTTTGGAAAAGTTTAGGGGTTAAAATGTA
90797 ATTTTGGAAAAGTTTAGGGGTTAAAATGTA
1 ATTTTGGAAAAGTTTAGGGGTTAAAATGTA
90827 ATTTTGGAAAAGTTTAGGG
1 ATTTTGGAAAAGTTTAGGG
90846 ACCTCTTGAG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
30 72 0.95
31 4 0.05
ACGTcount: A:0.35, C:0.00, G:0.28, T:0.38
Consensus pattern (30 bp):
ATTTTGGAAAAGTTTAGGGGTTAAAATGTA
Found at i:91321 original size:1 final size:1
Alignment explanation
Indices: 91317--91355 Score: 78
Period size: 1 Copynumber: 39.0 Consensus size: 1
91307 NNNNNNNNNN
91317 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
91356 CAGTTTCACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:91935 original size:13 final size:13
Alignment explanation
Indices: 91919--91943 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
91909 TTTGTATTGA
91919 TTTTGTATTTTTT
1 TTTTGTATTTTTT
91932 TTTTGTATTTTT
1 TTTTGTATTTTT
91944 CGTGGGTAAA
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:0.08, C:0.00, G:0.08, T:0.84
Consensus pattern (13 bp):
TTTTGTATTTTTT
Found at i:94628 original size:23 final size:23
Alignment explanation
Indices: 94602--94647 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
94592 ATTGTTTAGG
**
94602 TTTAGATATTTTTTTTTATTAAT
1 TTTAGATATTTTTAATTATTAAT
*
94625 TTTATATATTTTTAATTATTAAT
1 TTTAGATATTTTTAATTATTAAT
94648 AAAGTATCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTAGATATTTTTAATTATTAAT
Found at i:98342 original size:2 final size:2
Alignment explanation
Indices: 98335--98360 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
98325 AACGGTCGGC
98335 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
98361 TATTCATATT
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:98669 original size:13 final size:14
Alignment explanation
Indices: 98651--98684 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
98641 CTCCTGCTTC
98651 AGAAAACTA-AAAG
1 AGAAAACTAGAAAG
98664 AGAAAACTAGAAAG
1 AGAAAACTAGAAAG
*
98678 AAAAAAC
1 AGAAAAC
98685 GATGGCAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.71, C:0.09, G:0.15, T:0.06
Consensus pattern (14 bp):
AGAAAACTAGAAAG
Found at i:109610 original size:39 final size:40
Alignment explanation
Indices: 109567--109663 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 40
109557 TAGCGAGTGA
* *
109567 GATTTTTCTTCAGTGTACTCTTTTGGTGCCACCAACTG-G
1 GATTTTTCTTCAGTGTACTCTTTCGATGCCACCAACTGAG
* * * *
109606 GATTTTTCTTCAATGTACTCTTTCGATGTCATCAGCTGAG
1 GATTTTTCTTCAGTGTACTCTTTCGATGCCACCAACTGAG
*
109646 G-TTTCTCTTCAGTGTACT
1 GATTTTTCTTCAGTGTACT
109664 GAACAGTGGA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 47 0.96
40 2 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (40 bp):
GATTTTTCTTCAGTGTACTCTTTCGATGCCACCAACTGAG
Found at i:121545 original size:21 final size:21
Alignment explanation
Indices: 121493--121545 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
121483 AAGTCTTGAC
* * * *
121493 ACTTGGCCCATAAGTCTCAAT
1 ACTTAGCCTATAACTCTCAAG
*
121514 ACTTAGGCTATAACTCTCAAG
1 ACTTAGCCTATAACTCTCAAG
*
121535 ACTTCGCCTAT
1 ACTTAGCCTAT
121546 TTATTGTAGT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (21 bp):
ACTTAGCCTATAACTCTCAAG
Found at i:123255 original size:161 final size:161
Alignment explanation
Indices: 123064--123395 Score: 526
Period size: 161 Copynumber: 2.1 Consensus size: 161
123054 TATTACTTAT
* *
123064 TTTCATTTACCCATTAGTTGACCATGTCACTATACT-ACATATTTTAACAGATCATTTATTCACT
1 TTTCATTTACCCATTAGTTGAACATGTCACTATA-TGACATATTTTAACAGACCATTTATTCACT
* * *
123128 AATCTGTCGTAATTCGGTGTAGCAGATTAAACTAGTTTTCTCATTTGAGGAGCTAG-AGTACAAG
65 AATATGTCGTAATTCGGTGTAACAGATTAAACTAGTTTTCGCATTTGAGGAGCTAGTA-TACAAG
* *
123192 TACTTTTATTATGTTTTAGTCGAGTTTTTATAA
129 CACTTTTATTATGTTTTAGTCGAGCTTTTATAA
123225 TTTCATTTACCCATTACG-TGAACATGTCACTATATGACATATTTTAACAGACCATTTATTCACT
1 TTTCATTTACCCATTA-GTTGAACATGTCACTATATGACATATTTTAACAGACCATTTATTCACT
* *
123289 GATATGTCGTAATTCGGTGTAACAGATTAAACTAGTTTTCGCATTTGAGGAGCTTGTATACAAGC
65 AATATGTCGTAATTCGGTGTAACAGATTAAACTAGTTTTCGCATTTGAGGAGCTAGTATACAAGC
*
123354 ACTTTTGTTATGTTTTAGTCGAGCTTTTATAA
130 ACTTTTATTATGTTTTAGTCGAGCTTTTATAA
123386 TTTCATTTAC
1 TTTCATTTAC
123396 ATTCAATAAA
Statistics
Matches: 158, Mismatches: 10, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
160 1 0.01
161 155 0.98
162 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.41
Consensus pattern (161 bp):
TTTCATTTACCCATTAGTTGAACATGTCACTATATGACATATTTTAACAGACCATTTATTCACTA
ATATGTCGTAATTCGGTGTAACAGATTAAACTAGTTTTCGCATTTGAGGAGCTAGTATACAAGCA
CTTTTATTATGTTTTAGTCGAGCTTTTATAA
Found at i:123511 original size:22 final size:22
Alignment explanation
Indices: 123486--123529 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
123476 GAGTGTGCAG
*
123486 GAAATCATTAGAGGGAGTACAA
1 GAAATCATTAGAGGAAGTACAA
123508 GAAATCATTAGAGGAAGTACAA
1 GAAATCATTAGAGGAAGTACAA
123530 ACTCAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.18
Consensus pattern (22 bp):
GAAATCATTAGAGGAAGTACAA
Found at i:125593 original size:94 final size:94
Alignment explanation
Indices: 125432--125645 Score: 356
Period size: 94 Copynumber: 2.3 Consensus size: 94
125422 TATGCATACT
* ** *
125432 CTCGACAGCTCGTGTGAACAACATCGTTAGGGAACAGTTTATAGTACAGGTAGGCATTGTACCGA
1 CTCGACAGCTCGTGTGAGCAACATCGTTAGGGAACAGTTTATAGTACAGACAGGCACTGTACCGA
*
125497 TGGCTGGGGTACCACATACGTTGCGAGTC
66 TGGCTGGGGTACCACATACGTTGCGAGCC
125526 CTCGACAGCTCGTGTGAGCAACATCGTTAGGGAACAGTTTATAGTACAGACAGGCACTGTACCGA
1 CTCGACAGCTCGTGTGAGCAACATCGTTAGGGAACAGTTTATAGTACAGACAGGCACTGTACCGA
*
125591 TGGCTGGGGTACCGCATACGTTGCGAGCC
66 TGGCTGGGGTACCACATACGTTGCGAGCC
* *
125620 CTCGACAGATCGTGTGAGCAGCATCG
1 CTCGACAGCTCGTGTGAGCAACATCG
125646 AGTACTGGTA
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 112 1.00
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.22
Consensus pattern (94 bp):
CTCGACAGCTCGTGTGAGCAACATCGTTAGGGAACAGTTTATAGTACAGACAGGCACTGTACCGA
TGGCTGGGGTACCACATACGTTGCGAGCC
Found at i:127381 original size:9 final size:9
Alignment explanation
Indices: 127367--127413 Score: 53
Period size: 9 Copynumber: 5.1 Consensus size: 9
127357 GCAAATGATT
127367 TTAAAATTA
1 TTAAAATTA
127376 TTAAAATTA
1 TTAAAATTA
127385 TTTTTAAAA-TA
1 ---TTAAAATTA
127396 -TAAAATTA
1 TTAAAATTA
127404 TTAAAATTA
1 TTAAAATTA
127413 T
1 T
127414 ATCGTCATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
7 5 0.15
8 2 0.06
9 18 0.55
11 2 0.06
12 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAAAATTA
Found at i:127401 original size:19 final size:21
Alignment explanation
Indices: 127365--127405 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
127355 TAGCAAATGA
127365 TTTTAAAATTATTAAAATTAT
1 TTTTAAAATTATTAAAATTAT
127386 TTTTAAAA-TA-TAAAATTAT
1 TTTTAAAATTATTAAAATTAT
127405 T
1 T
127406 AAAATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 2 0.10
21 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAAAATTATTAAAATTAT
Found at i:127415 original size:19 final size:20
Alignment explanation
Indices: 127366--127415 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
127356 AGCAAATGAT
127366 TTTAAAATTAT-TAAAATTA
1 TTTAAAATTATATAAAATTA
*
127385 TTTTTAAA--ATATAAAATTA
1 -TTTAAAATTATATAAAATTA
127404 -TTAAAATTATAT
1 TTTAAAATTATAT
127416 CGTCATCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
17 5 0.20
18 2 0.08
19 12 0.48
20 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTAAAATTATATAAAATTA
Found at i:128335 original size:11 final size:11
Alignment explanation
Indices: 128319--128396 Score: 62
Period size: 11 Copynumber: 7.6 Consensus size: 11
128309 GATGATGATT
128319 ATAATTTTAAA
1 ATAATTTTAAA
128330 ATAATTTT--A
1 ATAATTTTAAA
128339 ATAATTTT---
1 ATAATTTTAAA
*
128347 ATATTTTTAAAA
1 ATAATTTT-AAA
128359 ATAATTTTAAA
1 ATAATTTTAAA
*
128370 TTAATTTT--A
1 ATAATTTTAAA
*
128379 ATAGTTTTAAA
1 ATAATTTTAAA
*
128390 ATCATTT
1 ATAATTT
128397 GCTAAAGTGG
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
8 7 0.13
9 16 0.30
11 24 0.44
12 7 0.13
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:128344 original size:20 final size:20
Alignment explanation
Indices: 128319--128396 Score: 72
Period size: 20 Copynumber: 3.9 Consensus size: 20
128309 GATGATGATT
128319 ATAATTTTAAAATAATTTTA
1 ATAATTTTAAAATAATTTTA
*
128339 ATAATTTT---ATATTTTTAAAA
1 ATAATTTTAAAATAATTTT---A
*
128359 ATAATTTTAAATTAATTTTA
1 ATAATTTTAAAATAATTTTA
* *
128379 ATAGTTTTAAAATCATTT
1 ATAATTTTAAAATAATTT
128397 GCTAAAGTGG
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
17 7 0.15
20 33 0.72
23 6 0.13
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (20 bp):
ATAATTTTAAAATAATTTTA
Found at i:131418 original size:17 final size:18
Alignment explanation
Indices: 131386--131419 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
131376 TTAAAAATTA
*
131386 TAAAAGTATATTAATATT
1 TAAAAGTATATAAATATT
131404 TAAAA-TATATAAATAT
1 TAAAAGTATATAAATAT
131420 AATTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TAAAAGTATATAAATATT
Found at i:132255 original size:81 final size:81
Alignment explanation
Indices: 132130--132295 Score: 323
Period size: 81 Copynumber: 2.0 Consensus size: 81
132120 TCAACGCAGG
132130 ATTCGGTGTTAAAAAAGAGATTTGATGATGTAGGGTAATGATAGTATACAAAGCTATACATGATT
1 ATTCGGTGTTAAAAAAGAGATTTGATGATGTAGGGTAATGATAGTATACAAAGCTATACATGATT
132195 AGCTCATCAACTAGGA
66 AGCTCATCAACTAGGA
*
132211 ATTCGGTGTTAAAAAGGAGATTTGATGATGTAGGGTAATGATAGTATACAAAGCTATACATGATT
1 ATTCGGTGTTAAAAAAGAGATTTGATGATGTAGGGTAATGATAGTATACAAAGCTATACATGATT
132276 AGCTCATCAACTAGGA
66 AGCTCATCAACTAGGA
132292 ATTC
1 ATTC
132296 ATATTAATGC
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 84 1.00
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.30
Consensus pattern (81 bp):
ATTCGGTGTTAAAAAAGAGATTTGATGATGTAGGGTAATGATAGTATACAAAGCTATACATGATT
AGCTCATCAACTAGGA
Found at i:146444 original size:6 final size:6
Alignment explanation
Indices: 146433--146467 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
146423 TAACTAGACT
* *
146433 ATTATA ATTATA ATTGTA ATTATA ATTACA ATTAT
1 ATTATA ATTATA ATTATA ATTATA ATTATA ATTAT
146468 TATTTGAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (6 bp):
ATTATA
Found at i:147461 original size:2 final size:2
Alignment explanation
Indices: 147454--147479 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
147444 CCAATGTGGG
147454 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
147480 GAAATCCCAC
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:149989 original size:19 final size:19
Alignment explanation
Indices: 149965--150001 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
149955 CCAAAAACTT
* *
149965 TTGATTTTTGTTTATCTAA
1 TTGATTTATATTTATCTAA
149984 TTGATTTATATTTATCTA
1 TTGATTTATATTTATCTA
150002 GATTTATTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (19 bp):
TTGATTTATATTTATCTAA
Found at i:151334 original size:22 final size:22
Alignment explanation
Indices: 151309--151357 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
151299 TTACCTAATT
*
151309 AAAAAGTTACCACACATTTCTC
1 AAAAAGTTACCACACATTTCCC
** * *
151331 AAAATTTTACTACACTTTTCCC
1 AAAAAGTTACCACACATTTCCC
151353 AAAAA
1 AAAAA
151358 TCCAAGATGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAAAGTTACCACACATTTCCC
Found at i:151500 original size:16 final size:17
Alignment explanation
Indices: 151479--151519 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
151469 TAATCACCCT
151479 TTTCTAAAACCAT-AAA
1 TTTCTAAAACCATAAAA
*
151495 TTTCTAAACCCATAAAA
1 TTTCTAAAACCATAAAA
151512 TTTC-AAAA
1 TTTCTAAAA
151520 GTGTTATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32
Consensus pattern (17 bp):
TTTCTAAAACCATAAAA
Found at i:159928 original size:58 final size:58
Alignment explanation
Indices: 159838--159954 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
159828 TAATTTGGTT
159838 TATGGTTTATTACCATAAATACCAAAAAACTCAGTTTTTGGAAAATTTTGAACTTTTA
1 TATGGTTTATTACCATAAATACCAAAAAACTCAGTTTTTGGAAAATTTTGAACTTTTA
159896 TATGGTTTATTACCATAAATACCAAAAAACTCAGTTTTTGGAAAATTTTGAACTTTTA
1 TATGGTTTATTACCATAAATACCAAAAAACTCAGTTTTTGGAAAATTTTGAACTTTTA
159954 T
1 T
159955 GGTGCCTTAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (58 bp):
TATGGTTTATTACCATAAATACCAAAAAACTCAGTTTTTGGAAAATTTTGAACTTTTA
Found at i:168916 original size:13 final size:12
Alignment explanation
Indices: 168893--168919 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
168883 TTTTTATCAG
168893 CATAATTTTTTT
1 CATAATTTTTTT
168905 CATAATTTTTTT
1 CATAATTTTTTT
168917 CAT
1 CAT
168920 TTATTATTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (12 bp):
CATAATTTTTTT
Found at i:169910 original size:80 final size:80
Alignment explanation
Indices: 169777--169937 Score: 313
Period size: 80 Copynumber: 2.0 Consensus size: 80
169767 ATAGTTTGAG
169777 TAAGTCTTGAATGAGCCCCTCGAAAGCTTGATGCAAATAAACTAATTTTTGTTCGACGTCTACGA
1 TAAGTCTTGAATGAGCCCCTCGAAAGCTTGATGCAAATAAACTAATTTTTGTTCGACGTCTACGA
169842 GCTATATATCCCCGT
66 GCTATATATCCCCGT
169857 TAAGTCTTGAATGAGCCCCTCGAAAGCTTGATGCAAATAAACTAATTTTTGTTCGACGTCTACGA
1 TAAGTCTTGAATGAGCCCCTCGAAAGCTTGATGCAAATAAACTAATTTTTGTTCGACGTCTACGA
*
169922 GCTATATATTCCCGT
66 GCTATATATCCCCGT
169937 T
1 T
169938 TAATTATGGT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (80 bp):
TAAGTCTTGAATGAGCCCCTCGAAAGCTTGATGCAAATAAACTAATTTTTGTTCGACGTCTACGA
GCTATATATCCCCGT
Found at i:170942 original size:14 final size:14
Alignment explanation
Indices: 170899--170943 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
170889 TTTTGTTAAA
*
170899 AATATTTTAAATTA
1 AATATTTTAAATTC
*
170913 AATAATTTAAAGTTC
1 AATATTTTAAA-TTC
*
170928 AGTATTTTAAATTC
1 AATATTTTAAATTC
170942 AA
1 AA
170944 GTTATTCATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (14 bp):
AATATTTTAAATTC
Found at i:174039 original size:12 final size:12
Alignment explanation
Indices: 173987--174040 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
173977 TATTAATGAA
*
173987 ATAATATATTTT
1 ATAATATATTAT
173999 ATAATATA-TA-
1 ATAATATATTAT
174009 AT-ATA-ATTAT
1 ATAATATATTAT
174019 -T-AT-TATTAT
1 ATAATATATTAT
174028 ATAATATATTAT
1 ATAATATATTAT
174040 A
1 A
174041 ATAAAAGATA
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
8 1 0.03
9 13 0.37
10 3 0.09
11 3 0.09
12 15 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATAATATATTAT
Found at i:176992 original size:24 final size:25
Alignment explanation
Indices: 176947--176994 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
176937 AAATAAATCA
**
176947 ATTTTTTATATTGAATAAATATAATT
1 ATTTTTTATATACAAT-AATATAATT
176973 ATTTTTTATATACAAT-ATATAA
1 ATTTTTTATATACAATAATATAA
176995 ATGTAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
26 14 0.70
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (25 bp):
ATTTTTTATATACAATAATATAATT
Found at i:180889 original size:4 final size:4
Alignment explanation
Indices: 180880--180941 Score: 72
Period size: 4 Copynumber: 15.2 Consensus size: 4
180870 AAATAAACGG
* *
180880 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GAAG GAGAG GAAA GAAA G-AA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA
*
180929 GAAG GAAA GAAA G
1 GAAA GAAA GAAA G
180942 GTAATGTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
3 3 0.06
4 40 0.78
5 8 0.16
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:180902 original size:17 final size:16
Alignment explanation
Indices: 180880--180941 Score: 72
Period size: 17 Copynumber: 3.8 Consensus size: 16
180870 AAATAAACGG
180880 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAA-GAAA
*
180897 GAAAGAAAGAAAGAAG
1 GAAAGAAAGAAAGAAA
*
180913 GAGAGGAAAGAAAG-AA
1 GA-AAGAAAGAAAGAAA
*
180929 GAAGGAAAGAAAG
1 GAAAGAAAGAAAG
180942 GTAATGTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
15 11 0.27
16 8 0.20
17 22 0.54
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (16 bp):
GAAAGAAAGAAAGAAA
Found at i:180909 original size:25 final size:24
Alignment explanation
Indices: 180880--180942 Score: 90
Period size: 25 Copynumber: 2.6 Consensus size: 24
180870 AAATAAACGG
180880 GAAAGAAAGAAAGGAAAGAAAGAAA
1 GAAAGAAAGAAAGGAAAGAAAG-AA
* *
180905 GAAAGAAGGAGAGGAAAGAAAGAA
1 GAAAGAAAGAAAGGAAAGAAAGAA
*
180929 GAAGGAAAGAAAGG
1 GAAAGAAAGAAAGG
180943 TAATGTGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 13 0.39
25 20 0.61
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (24 bp):
GAAAGAAAGAAAGGAAAGAAAGAA
Done.