Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006831.1 Hibiscus syriacus cultivar Beakdansim tig00017367_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 178850
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:864 original size:16 final size:16
Alignment explanation
Indices: 843--905 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
833 GTTACACGTG
*
843 ATTCGTTGCTTGTTAA
1 ATTCGTTGCTCGTTAA
*
859 ATTCGTTACTCGTTAA
1 ATTCGTTGCTCGTTAA
* * *
875 TTTTGTTGCTCATTAA
1 ATTCGTTGCTCGTTAA
*
891 ATTCGATGCTCGTTA
1 ATTCGTTGCTCGTTA
906 CTTGTTAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.48
Consensus pattern (16 bp):
ATTCGTTGCTCGTTAA
Found at i:2097 original size:24 final size:24
Alignment explanation
Indices: 2056--2103 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2046 AATTATTATA
* *
2056 TTAAATAAATATCATAAATAAATT
1 TTAAATAAAAATCATAAAAAAATT
**
2080 TTAAATAAAAATTTTAAAAAAATT
1 TTAAATAAAAATCATAAAAAAATT
2104 ATTTAGTTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAAATAAAAATCATAAAAAAATT
Found at i:5475 original size:131 final size:133
Alignment explanation
Indices: 5239--5584 Score: 433
Period size: 131 Copynumber: 2.6 Consensus size: 133
5229 TACCCAAGTG
* *
5239 GTGAAAGCGCGTTCCT-GGGG-GCGTGCTTCTATTATTTTGTCAGCGAATATGTTATCATTGCCC
1 GTGAAAGCGCGTTCCTGGGGGCGCGCGCTTCCATTATTTTGTCA--GAATATGTTATCATTGCCC
*
5302 TATTATGTCACTCATGTCTCCCGAGAAATATTCATGTCAGTACCTATTATTT-TTATGG-GACTT
64 TATTATGTCACTCATGTCCCCCGAGAAATATTCATGTCAGTACCTATTATTTCTTA-GGAGACTT
*
5365 GGTAAA
128 GGCAAA
*
5371 GTGAAAGCGCGTTCCTGGGGGCGCGCGCTTCCATTA-TTTATCAGAATATGTTATCATTGCCCTA
1 GTGAAAGCGCGTTCCTGGGGGCGCGCGCTTCCATTATTTTGTCAGAATATGTTATCATTGCCCTA
*
5435 TTATGTCACTCATGTCCCCCGA-ATAACTATT-ATGTTAGTACCTATTATTTCTTAGGAGACTTG
66 TTATGTCACTCATGTCCCCCGAGA-AA-TATTCATGTCAGTACCTATTATTTCTTAGGAGACTTG
5498 GCAAA
129 GCAAA
* * * *
5503 GTGGTAAAAGTGCGTTCCCGGGGGCGC-C-CTTCCATTATTTTGTCAGAGAATATATTATCATTA
1 GT-G--AAAGCGCGTTCCTGGGGGCGCGCGCTTCCATTATTTTGTC--AGAATATGTTATCATTG
*
5566 CCCTA-TATGTTACTCATGT
61 CCCTATTATGTCACTCATGT
5585 GAAATTTGAT
Statistics
Matches: 190, Mismatches: 12, Indels: 21
0.85 0.05 0.09
Matches are distributed among these distances:
130 1 0.01
131 64 0.34
132 35 0.18
133 20 0.11
134 18 0.09
135 32 0.17
136 20 0.11
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (133 bp):
GTGAAAGCGCGTTCCTGGGGGCGCGCGCTTCCATTATTTTGTCAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCCCGAGAAATATTCATGTCAGTACCTATTATTTCTTAGGAGACTTGGC
AAA
Found at i:5654 original size:22 final size:22
Alignment explanation
Indices: 5629--5670 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5619 ATGTGAAGTT
*
5629 TGAATAAATTGGATAAATGTTA
1 TGAATAAATTGAATAAATGTTA
5651 TGAATAAATTGAATAAATGT
1 TGAATAAATTGAATAAATGT
5671 GAAGTCATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.36
Consensus pattern (22 bp):
TGAATAAATTGAATAAATGTTA
Found at i:5704 original size:61 final size:63
Alignment explanation
Indices: 5628--5748 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 63
5618 TATGTGAAGT
* *
5628 TTGAATAAATTGGAT-AAATGTTATGAATAAATT-GAATAAATGTGAAGTCATCAGTTGGTTG
1 TTGAATAAATTGGATAAAATGTTATGAATAAATTGGAAAAAATGTGAAGTCATAAGTTGGTTG
* * *
5689 TTGAATATATTGGATAAAATGTTATGGATAAATTGGAAAAAATGTGAAGTGATAAGTTGG
1 TTGAATAAATTGGATAAAATGTTATGAATAAATTGGAAAAAATGTGAAGTCATAAGTTGG
5749 CTGACATTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
61 14 0.26
62 17 0.32
63 22 0.42
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (63 bp):
TTGAATAAATTGGATAAAATGTTATGAATAAATTGGAAAAAATGTGAAGTCATAAGTTGGTTG
Found at i:5748 original size:24 final size:23
Alignment explanation
Indices: 5697--5748 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
5687 TGTTGAATAT
* * *
5697 ATTGGATAAAATGTTATGGATAA
1 ATTGGAAAAAATGTGAAGGATAA
5720 ATTGGAAAAAATGTGAAGTGATAA
1 ATTGGAAAAAATGTGAAG-GATAA
*
5744 GTTGG
1 ATTGG
5749 CTGACATTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (23 bp):
ATTGGAAAAAATGTGAAGGATAA
Found at i:5979 original size:33 final size:34
Alignment explanation
Indices: 5930--6001 Score: 110
Period size: 33 Copynumber: 2.1 Consensus size: 34
5920 TTAAGTTGAA
5930 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
* *
5964 TTTAAT-TTATATTTCGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCGAATACCATAATTTGTAT
*
5997 ATTAA
1 TTTAA
6002 AAACATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
33 29 0.83
34 6 0.17
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAATACCATAATTTGTAT
Found at i:6538 original size:21 final size:21
Alignment explanation
Indices: 6506--6578 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
6496 GGTGTCATAA
* *
6506 AACCCTGCGGGATAGGCATGT
1 AACCCTGTGGGATAGGAATGT
6527 AA-CCTGGTGGGATAGGAATGT
1 AACCCT-GTGGGATAGGAATGT
* *
6548 AACCCTGAGGGCTAGGAATGT
1 AACCCTGTGGGATAGGAATGT
6569 AACCCTGTGG
1 AACCCTGTGG
6579 AGATGGCATA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
AACCCTGTGGGATAGGAATGT
Found at i:6602 original size:42 final size:42
Alignment explanation
Indices: 6556--6638 Score: 94
Period size: 42 Copynumber: 2.0 Consensus size: 42
6546 GTAACCCTGA
* *
6556 GGGCTAGGAATGTAACCCTGTGGAGATGGCATATAAACTGGT
1 GGGCTAGGAATATAACCCTGAGGAGATGGCATATAAACTGGT
* * * * * *
6598 GGGCTTGGCATATACCCCTGAGGAGATTGCATCTGAACTGG
1 GGGCTAGGAATATAACCCTGAGGAGATGGCATATAAACTGG
6639 AGGGTTGGGT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (42 bp):
GGGCTAGGAATATAACCCTGAGGAGATGGCATATAAACTGGT
Found at i:10367 original size:184 final size:182
Alignment explanation
Indices: 10003--10377 Score: 574
Period size: 184 Copynumber: 2.0 Consensus size: 182
9993 AACCGAAATT
* *
10003 AATTTTAAATATATTATATAACATATGAGTTAAGCCCAAATAATTTAAAACACAATTAATAATTT
1 AATTTTAAATATATTATATAACATATGAGCTAAGCCCAAACAATTTAAAACACAATTAATAATTT
* * *
10068 AATATCCAATAAGTTTAAATATAAATCAATATTAATTAATTAAAAATTTATATAATTTTTTATTT
66 AAGATCCAATAAGTTTAAACATAAATCAATATTAATTAATTAAAAATTTATATAAATTTTTATTT
* *
10133 TATAATTATATATTATTTAAATTAATTGTAAACTATTTTTTTTGAATTAAAA
131 TATAATTATATATTATTTAAATTAAATATAAACTATTTTTTTTGAATTAAAA
* * * **
10185 AATTTTAAATATATTATATATAACGTATGAGCTCAGCCCAAACCATTTAAAATTCAATTAATAAT
1 AATTTTAAATATA-T-TATATAACATATGAGCTAAGCCCAAACAATTTAAAACACAATTAATAAT
*
10250 TTAAGATCCAATAACTTTTAAACATAAATCAATATTAATTAATTAAAAAATTTATATAAATTTTT
64 TTAAGATCCAATAA-GTTTAAACATAAATCAATATTAATTAATT-AAAAATTTATATAAATTTTT
10315 ATTTTATAATTATATATTATTTAAATTAAATATAAACTA-TTTTTTT-AATTAAAA
127 ATTTTATAATTATATATTATTTAAATTAAATATAAACTATTTTTTTTGAATTAAAA
10369 AATATTTAA
1 AAT-TTTAA
10378 TTTTTATATA
Statistics
Matches: 175, Mismatches: 13, Indels: 7
0.90 0.07 0.04
Matches are distributed among these distances:
182 13 0.07
183 1 0.01
184 66 0.38
185 39 0.22
186 56 0.32
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (182 bp):
AATTTTAAATATATTATATAACATATGAGCTAAGCCCAAACAATTTAAAACACAATTAATAATTT
AAGATCCAATAAGTTTAAACATAAATCAATATTAATTAATTAAAAATTTATATAAATTTTTATTT
TATAATTATATATTATTTAAATTAAATATAAACTATTTTTTTTGAATTAAAA
Found at i:11251 original size:43 final size:40
Alignment explanation
Indices: 11151--11264 Score: 151
Period size: 39 Copynumber: 2.8 Consensus size: 40
11141 TTTTAAATGT
*
11151 TATT-TTTAATATTTTATTGATCACATATTTAAATAAATA
1 TATTCTTTAATATTTTATTCATCACATATTTAAATAAATA
* * *
11190 TATTCTCTCA-ATTATATTCATCACATATTTAAATAAATA
1 TATTCTTTAATATTTTATTCATCACATATTTAAATAAATA
11229 TATTCTTATTTAATATTTTATTCATCACATATTTAA
1 TATTC---TTTAATATTTTATTCATCACATATTTAA
11265 TATTTTATAC
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
39 36 0.57
40 3 0.05
42 3 0.05
43 21 0.33
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.50
Consensus pattern (40 bp):
TATTCTTTAATATTTTATTCATCACATATTTAAATAAATA
Found at i:11643 original size:22 final size:21
Alignment explanation
Indices: 11618--11660 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
11608 AGTTTAAATT
*
11618 AATATAATTGATTAAAATAAAA
1 AATATAATTGAAT-AAATAAAA
11640 AATATAATTGAATAAATAAAA
1 AATATAATTGAATAAATAAAA
11661 TAAGAATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
AATATAATTGAATAAATAAAA
Found at i:17634 original size:12 final size:12
Alignment explanation
Indices: 17617--17641 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17607 CTCAAACAGA
17617 GAGAATGAACGT
1 GAGAATGAACGT
17629 GAGAATGAACGT
1 GAGAATGAACGT
17641 G
1 G
17642 TTGCATGGCA
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:0.40, C:0.08, G:0.36, T:0.16
Consensus pattern (12 bp):
GAGAATGAACGT
Found at i:17703 original size:29 final size:28
Alignment explanation
Indices: 17670--17754 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 28
17660 TCCCAACACA
17670 TAGGTCGCCATGCCTTCCGGGCGACCTTG
1 TAGGTCGCCATGCC-TCCGGGCGACCTTG
17699 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATG-CCTCCGGGCGACCTTG
17728 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGC-CTCCGGGCGACCT
17755 ACCCTCGCTC
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
28 1 0.02
29 51 0.94
30 2 0.04
ACGTcount: A:0.12, C:0.36, G:0.31, T:0.21
Consensus pattern (28 bp):
TAGGTCGCCATGCCTCCGGGCGACCTTG
Found at i:17806 original size:23 final size:23
Alignment explanation
Indices: 17772--17831 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
17762 CTCGGCTTCC
17772 CTCGGATT-CCCTCGCATAGCTCG
1 CTCGG-TTGCCCTCGCATAGCTCG
17795 CTCGGTTGCCCTCGCATAGCTCG
1 CTCGGTTGCCCTCGCATAGCTCG
* * *
17818 TTCGGATGGCCTCG
1 CTCGGTTGCCCTCG
17832 GATGGCCTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.10, C:0.37, G:0.27, T:0.27
Consensus pattern (23 bp):
CTCGGTTGCCCTCGCATAGCTCG
Found at i:17834 original size:10 final size:10
Alignment explanation
Indices: 17819--17865 Score: 69
Period size: 10 Copynumber: 4.7 Consensus size: 10
17809 CATAGCTCGT
17819 TCGGATGGCC
1 TCGGATGGCC
17829 TCGGATGGCC
1 TCGGATGGCC
17839 TCGGAT-GCTC
1 TCGGATGGC-C
17849 TCGGATGGCC
1 TCGGATGGCC
*
17859 TAGGATG
1 TCGGATG
17866 CCCAGCGTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
9 2 0.06
10 30 0.88
11 2 0.06
ACGTcount: A:0.13, C:0.26, G:0.38, T:0.23
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:17942 original size:29 final size:29
Alignment explanation
Indices: 17905--17962 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
17895 GCAATCTCTT
**
17905 GTAGCTCGCTGGGAAAACATGGCGACCTA
1 GTAGCTCGCCCGGAAAACATGGCGACCTA
* **
17934 GTAGGTCGCCCGGAAGGCATGGCGACCTA
1 GTAGCTCGCCCGGAAAACATGGCGACCTA
17963 CGGCCAACAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.24, C:0.26, G:0.34, T:0.16
Consensus pattern (29 bp):
GTAGCTCGCCCGGAAAACATGGCGACCTA
Found at i:18781 original size:2 final size:2
Alignment explanation
Indices: 18774--18807 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
18764 TTTATACGTG
18774 TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18808 GTTTGCAAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:18903 original size:38 final size:39
Alignment explanation
Indices: 18835--19227 Score: 433
Period size: 38 Copynumber: 10.2 Consensus size: 39
18825 GAAAATACAA
* ** *
18835 ATATAATATATAGTCTTT-AAAAAAACATTTTTAAAAACAT
1 ATATATTATATAGT-TTTGAAAATTA-ATTTTTAAAAATAT
* * * **
18875 ATACATTATATAGTTTTTAAAA-CAATTTTTTGAAATAT
1 ATATATTATATAGTTTTGAAAATTAATTTTTAAAAATAT
* *
18913 ATATATTATATAGTTTTGAAAATTAGTTTTTTAAAATAT
1 ATATATTATATAGTTTTGAAAATTAATTTTTAAAAATAT
* * *
18952 ATATATTATATAGTTTTAAAAATT-AGTTTTAAAAAAAT
1 ATATATTATATAGTTTTGAAAATTAATTTTTAAAAATAT
* *
18990 ATATATTATATAGTTTTGAAAATT-AGTTTTAAAAAAAT
1 ATATATTATATAGTTTTGAAAATTAATTTTTAAAAATAT
*
19028 ATATATTATATAGTTTTGAAAATTAGTTTTT-AAAATAT
1 ATATATTATATAGTTTTGAAAATTAATTTTTAAAAATAT
* *
19066 ATATATTATATAATTTTGAAAATTAGTTTTT-AAAATAT
1 ATATATTATATAGTTTTGAAAATTAATTTTTAAAAATAT
*
19104 ATATATTATATAGTTTTGAAAATTAGTTTTTAAAAAT-T
1 ATATATTATATAGTTTTGAAAATTAATTTTTAAAAATAT
* * * * *
19142 ATATATTACATAATTTTGAAAATTATTTTTTTCAAAA-CT
1 ATATATTATATAGTTTTGAAAATTA-ATTTTTAAAAATAT
* * *
19181 ATATATTATATGGTTTTGAAAATTATTTTCTTTAAAAACAT
1 ATATATTATATAGTTTTGAAAATTA-ATT-TTTAAAAATAT
19222 ATATAT
1 ATATAT
19228 AGTTTTAAAA
Statistics
Matches: 314, Mismatches: 31, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
38 199 0.63
39 85 0.27
40 23 0.07
41 7 0.02
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (39 bp):
ATATATTATATAGTTTTGAAAATTAATTTTTAAAAATAT
Found at i:19024 original size:13 final size:13
Alignment explanation
Indices: 18962--18986 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18952 ATATATTATA
18962 TAGTTTTAAAAAT
1 TAGTTTTAAAAAT
18975 TAGTTTTAAAAA
1 TAGTTTTAAAAA
18987 AATATATATT
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:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
TAGTTTTAAAAAT
Found at i:19044 original size:76 final size:76
Alignment explanation
Indices: 18862--19227 Score: 480
Period size: 76 Copynumber: 4.7 Consensus size: 76
18852 TAAAAAAACA
* * ** * * * *
18862 TTTTTAAAAACATATACATTATATAGTTTTTAAAACAATTTTTTGAAATATATATATTATATAGT
1 TTTTTAAAAA-ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAAATATATATTATATAAT
18927 TTTGAAAATTAG
65 TTTGAAAATTAG
* * * *
18939 TTTTTTAAAATATATATATTATATAGTTTTAAAAATTAGTTTTAAAAAAATATATATTATATAGT
1 -TTTTTAAAAAATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAAATATATATTATATAAT
19004 TTTGAAAATTAG
65 TTTGAAAATTAG
* *
19016 TTTTAAAAAAATATATATTATATAGTTTTGAAAATTAGTTTTTAAAATATATATATTATATAATT
1 TTTTTAAAAAATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAAATATATATTATATAATT
19081 TTGAAAATTAG
66 TTGAAAATTAG
* * *
19092 TTTTTAAAATATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAATTATATATTACATAATT
1 TTTTTAAAAAATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAAATATATATTATATAATT
*
19157 TTGAAAATTATT
66 TTGAAAATTA-G
* * * *
19169 TTTTTCAAAACTATATATTATATGGTTTTGAAAATTATTTTCTTTAAAAACATATATAT
1 TTTTTAAAAAATATATATTATATAGTTTTGAAAATTA-GTT-TTTAAAAA-ATATATAT
19228 AGTTTTAAAA
Statistics
Matches: 257, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
76 140 0.54
77 91 0.35
78 11 0.04
79 8 0.03
80 7 0.03
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.48
Consensus pattern (76 bp):
TTTTTAAAAAATATATATTATATAGTTTTGAAAATTAGTTTTTAAAAAATATATATTATATAATT
TTGAAAATTAG
Found at i:19044 original size:115 final size:115
Alignment explanation
Indices: 18835--19209 Score: 486
Period size: 114 Copynumber: 3.3 Consensus size: 115
18825 GAAAATACAA
* ** * * * * **
18835 ATATAATATATAGTCTTTAAAAAAACATTTTTAAAAACATATACATTATATAGTTTTTAAAACAA
1 ATATATTATATAGT-TTT-AAAAATTAGTTTTAAAAAAATATATATTATATAGTTTTGAAAATTA
* * *
18900 TTTTTTGAAATATATATATTATATAGTTTTGAAAATTAGTTTTTTAAAATAT
64 GTTTTTAAAAAATATATATTATATAGTTTTGAAAATTAGTTTTTTAAAATAT
18952 ATATATTATATAGTTTTAAAAATTAGTTTTAAAAAAATATATATTATATAGTTTTGAAAATTAGT
1 ATATATTATATAGTTTTAAAAATTAGTTTTAAAAAAATATATATTATATAGTTTTGAAAATTAGT
*
19017 TTTAAAAAAATATATATTATATAGTTTTGAAAATTAG-TTTTTAAAATAT
66 TTTTAAAAAATATATATTATATAGTTTTGAAAATTAGTTTTTTAAAATAT
* * * *
19066 ATATATTATATAATTTTGAAAATTAGTTTTTAAAATATATATATTATATAGTTTTGAAAATTAGT
1 ATATATTATATAGTTTTAAAAATTAGTTTTAAAAAAATATATATTATATAGTTTTGAAAATTAGT
* * * * *
19131 TTTTAAAAATTATATATTACATAATTTTGAAAATTATTTTTTTCAAAA-CT
66 TTTTAAAAAATATATATTATATAGTTTTGAAAATTAGTTTTTT-AAAATAT
* *
19181 ATATATTATATGGTTTTGAAAATTA-TTTT
1 ATATATTATATAGTTTTAAAAATTAGTTTT
19210 CTTTAAAAAC
Statistics
Matches: 231, Mismatches: 25, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
114 109 0.47
115 102 0.44
116 7 0.03
117 13 0.06
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (115 bp):
ATATATTATATAGTTTTAAAAATTAGTTTTAAAAAAATATATATTATATAGTTTTGAAAATTAGT
TTTTAAAAAATATATATTATATAGTTTTGAAAATTAGTTTTTTAAAATAT
Found at i:19264 original size:18 final size:19
Alignment explanation
Indices: 19241--19280 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
19231 TTTAAAAAAA
19241 ATTTTTCTTTATTT-ATTT
1 ATTTTTCTTTATTTCATTT
19259 ATTTTTCTTTATTTCATTT
1 ATTTTTCTTTATTTCATTT
19278 ATT
1 ATT
19281 ATTATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.75
Consensus pattern (19 bp):
ATTTTTCTTTATTTCATTT
Found at i:20340 original size:16 final size:16
Alignment explanation
Indices: 20315--20379 Score: 85
Period size: 16 Copynumber: 4.1 Consensus size: 16
20305 TAATAAATAA
20315 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
20331 ACGAATATAAATGAAC
1 ACGAACATAAACGAAC
* *
20347 ACGAACATAAATGAAT
1 ACGAACATAAACGAAC
*
20363 ATGAACATAAACGAAC
1 ACGAACATAAACGAAC
20379 A
1 A
20380 TAAATGTTAG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.57, C:0.17, G:0.12, T:0.14
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:20373 original size:32 final size:32
Alignment explanation
Indices: 20307--20379 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
20297 CGTTCATTTA
*
20307 ATAAAT-AA-ACGAACATAAACGAACACGAAT
1 ATAAATGAACACGAACATAAACGAACACGAAC
* * *
20337 ATAAATGAACACGAACATAAATGAATATGAAC
1 ATAAATGAACACGAACATAAACGAACACGAAC
*
20369 ATAAACGAACA
1 ATAAATGAACA
20380 TAAATGTTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 6 0.17
31 2 0.06
32 28 0.78
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.15
Consensus pattern (32 bp):
ATAAATGAACACGAACATAAACGAACACGAAC
Found at i:20648 original size:23 final size:23
Alignment explanation
Indices: 20616--20673 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
20606 AGCTCGACTC
*
20616 GAGCTTGATTGAAGCTCAATTTT
1 GAGCTCGATTGAAGCTCAATTTT
*
20639 GAGCTCGATTCAAGCTCAATTTT
1 GAGCTCGATTGAAGCTCAATTTT
20662 GAGCTCGATTGA
1 GAGCTCGATTGA
20674 CCCAGTCCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCAATTTT
Found at i:21926 original size:21 final size:21
Alignment explanation
Indices: 21900--21958 Score: 93
Period size: 21 Copynumber: 2.8 Consensus size: 21
21890 AATCAGATTA
21900 AGGGTTT-AGATTTTAGGGGTT
1 AGGGTTTAAG-TTTTAGGGGTT
21921 AGGGTTTAAGTTTTAGGGGTT
1 AGGGTTTAAGTTTTAGGGGTT
*
21942 AGAGTTTAAGTTTTAGG
1 AGGGTTTAAGTTTTAGG
21959 TTTTATGGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 34 0.94
22 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.36, T:0.42
Consensus pattern (21 bp):
AGGGTTTAAGTTTTAGGGGTT
Found at i:21991 original size:14 final size:14
Alignment explanation
Indices: 21974--22025 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
21964 TGGATTATGA
*
21974 TTTAAGATTTAAGG
1 TTTAAGATTTAGGG
*
21988 TTTAGGATTTAGGG
1 TTTAAGATTTAGGG
22002 TTT-AGAGTTTAGGG
1 TTTAAGA-TTTAGGG
*
22016 TTTAGGATTT
1 TTTAAGATTT
22026 TTAATAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 2 0.06
14 28 0.88
15 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (14 bp):
TTTAAGATTTAGGG
Found at i:21999 original size:7 final size:7
Alignment explanation
Indices: 21953--22025 Score: 53
Period size: 7 Copynumber: 10.4 Consensus size: 7
21943 GAGTTTAAGT
*
21953 TTTAGGT
1 TTTAGGA
21960 TTTATGGA
1 TTTA-GGA
*
21968 -TTATGA
1 TTTAGGA
*
21974 TTTAAGA
1 TTTAGGA
21981 TTTAAGG-
1 TTT-AGGA
21988 TTTAGGA
1 TTTAGGA
*
21995 TTTAGGG
1 TTTAGGA
22002 TTTA-GA
1 TTTAGGA
*
22008 GTTTAGGG
1 -TTTAGGA
22016 TTTAGGA
1 TTTAGGA
22023 TTT
1 TTT
22026 TTAATAATTA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
6 6 0.12
7 41 0.79
8 5 0.10
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (7 bp):
TTTAGGA
Found at i:22055 original size:7 final size:7
Alignment explanation
Indices: 22044--22075 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
22034 TAGATTAAGG
*
22044 GTTTATG
1 GTTTATA
22051 GTTTATA
1 GTTTATA
22058 GTTTATA
1 GTTTATA
22065 GTTTATA
1 GTTTATA
22072 GTTT
1 GTTT
22076 TAGGGTTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.19, T:0.59
Consensus pattern (7 bp):
GTTTATA
Found at i:22244 original size:14 final size:14
Alignment explanation
Indices: 22227--22258 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
22217 AACGAACATA
22227 AACGAACATAACCG
1 AACGAACATAACCG
22241 AACGAACATAACCG
1 AACGAACATAACCG
22255 AACG
1 AACG
22259 TTCACGAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.16, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:22268 original size:24 final size:24
Alignment explanation
Indices: 22206--22257 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
22196 ATAAATGAAT
* *
22206 GAACATAAACAAACGAACATAAAC
1 GAACATAACCGAACGAACATAAAC
*
22230 GAACATAACCGAACGAACATAACC
1 GAACATAACCGAACGAACATAAAC
22254 GAAC
1 GAAC
22258 GTTCACGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.08
Consensus pattern (24 bp):
GAACATAACCGAACGAACATAAAC
Found at i:22314 original size:21 final size:21
Alignment explanation
Indices: 22288--22329 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
22278 GAATGAGACC
22288 TATGTTCAT-GTTCGTTCATTT
1 TATGTTC-TCGTTCGTTCATTT
22309 TATGTTCTCGTTCGTTCATTT
1 TATGTTCTCGTTCGTTCATTT
22330 AATTAAACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.12, C:0.17, G:0.14, T:0.57
Consensus pattern (21 bp):
TATGTTCTCGTTCGTTCATTT
Found at i:22664 original size:13 final size:12
Alignment explanation
Indices: 22640--22680 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
22630 TCCCTTTATC
*
22640 TATTTATTTACT
1 TATTTTTTTACT
22652 TACTTTTTTTACT
1 TA-TTTTTTTACT
22665 T-TTTTTTT-CT
1 TATTTTTTTACT
22675 TATTTT
1 TATTTT
22681 ATTTTCCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 3 0.12
11 11 0.42
12 2 0.08
13 10 0.38
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTTTTACT
Found at i:23427 original size:2 final size:2
Alignment explanation
Indices: 23420--23487 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
23410 TATAAAAATG
23420 AT AT AT AT AT AT 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 AT AT AT AT AT AT
23462 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
23488 TAAAATACTA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23513 original size:20 final size:20
Alignment explanation
Indices: 23490--23531 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
23480 ATATATATTA
23490 AAATACTAAAACTTATAAAT
1 AAATACTAAAACTTATAAAT
* *
23510 AAATATTAAAATTTATAAAT
1 AAATACTAAAACTTATAAAT
23530 AA
1 AA
23532 TTAAAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATACTAAAACTTATAAAT
Found at i:23529 original size:8 final size:9
Alignment explanation
Indices: 23410--23591 Score: 51
Period size: 10 Copynumber: 19.9 Consensus size: 9
23400 GAGGTACACA
*
23410 TATAAAAAT
1 TATAAATAT
* *
23419 GATATATAT
1 TATAAATAT
*
23428 ATATATATAT
1 -TATAAATAT
*
23438 ATATATATAT
1 -TATAAATAT
*
23448 ATATATATAT
1 -TATAAATAT
*
23458 ATATATATAT
1 -TATAAATAT
*
23468 ATATATATAT
1 -TATAAATAT
*
23478 ATATATATAT
1 -TATAAATAT
*
23488 TA-AAATAC
1 TATAAATAT
23496 TA-AAACTTAT
1 TATAAA--TAT
*
23506 AAATAAATAT
1 -TATAAATAT
23516 TA-AAAT-T
1 TATAAATAT
23523 TATAAATAAT
1 TATAAAT-AT
*
23533 TAAAAATAT
1 TATAAATAT
*
23542 TA-AAATTT
1 TATAAATAT
*
23550 TGA-AAATAAA
1 T-ATAAAT-AT
23560 TATAAA-A-
1 TATAAATAT
23567 TATAAAT-T
1 TATAAATAT
23575 TATAAATAAT
1 TATAAAT-AT
23585 TA-AAATA
1 TATAAATA
23592 ATATTTTAAA
Statistics
Matches: 145, Mismatches: 13, Indels: 31
0.77 0.07 0.16
Matches are distributed among these distances:
7 9 0.06
8 32 0.22
9 23 0.16
10 77 0.53
11 1 0.01
12 3 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (9 bp):
TATAAATAT
Found at i:23536 original size:17 final size:17
Alignment explanation
Indices: 23508--23590 Score: 59
Period size: 17 Copynumber: 4.9 Consensus size: 17
23498 AAACTTATAA
23508 ATAAAT-ATTAAAATTT
1 ATAAATAATTAAAATTT
23524 ATAAATAATTAAAAATATT
1 ATAAATAATT-AAAAT-TT
* **
23543 A-AAAT-TTTGAAAATAA
1 ATAAATAATT-AAAATTT
23559 ATATAA-AA-TATAAATTT
1 ATA-AATAATTA-AAATTT
23576 ATAAATAATTAAAAT
1 ATAAATAATTAAAAT
23591 AATATTTTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 17
0.68 0.09 0.23
Matches are distributed among these distances:
16 10 0.20
17 25 0.49
18 13 0.25
19 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (17 bp):
ATAAATAATTAAAATTT
Found at i:23546 original size:26 final size:26
Alignment explanation
Indices: 23510--23589 Score: 103
Period size: 26 Copynumber: 3.1 Consensus size: 26
23500 ACTTATAAAT
23510 AAATATTAAAATTTATAAATAATTAA
1 AAATATTAAAATTTATAAATAATTAA
*
23536 AAATATTAAAATTT-TGAAAATAAATATA
1 AAATATTAAAATTTAT--AAATAATTA-A
23564 AAATA-T-AAATTTATAAATAATTAA
1 AAATATTAAAATTTATAAATAATTAA
23588 AA
1 AA
23590 TAATATTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
24 3 0.06
25 9 0.19
26 20 0.42
27 10 0.21
28 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (26 bp):
AAATATTAAAATTTATAAATAATTAA
Found at i:23592 original size:21 final size:23
Alignment explanation
Indices: 23504--23610 Score: 60
Period size: 26 Copynumber: 4.4 Consensus size: 23
23494 ACTAAAACTT
* *
23504 ATAAATAAATATTAAAATTTATAA
1 ATAATTAAATA-TAATATTTATAA
*
23528 ATAATTAAAAATATTAAAATTT-TGAAA
1 ATAATT--AAATA-TAATATTTAT--AA
23555 ATAAATATAAAATATAA-ATTTATAA
1 AT-AAT-T-AAATATAATATTTATAA
23580 ATAATTAAA-ATAATATTT-TAAA
1 ATAATTAAATATAATATTTAT-AA
*
23602 ATACTTAAA
1 ATAATTAAA
23611 CTTAAAACTT
Statistics
Matches: 72, Mismatches: 2, Indels: 20
0.77 0.02 0.21
Matches are distributed among these distances:
21 5 0.07
22 17 0.24
23 1 0.01
24 8 0.11
25 5 0.07
26 18 0.25
27 8 0.11
28 9 0.12
29 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (23 bp):
ATAATTAAATATAATATTTATAA
Found at i:23603 original size:22 final size:22
Alignment explanation
Indices: 23521--23610 Score: 65
Period size: 23 Copynumber: 3.7 Consensus size: 22
23511 AATATTAAAA
23521 TTTATAAATAATTAAAAATATTAAAAT
1 TTTA-AAATAATT-AAAATA-T--AAT
*
23548 TTTGAAAATAAATATAAAATATAAA
1 TTT-AAAAT-AAT-TAAAATATAAT
23573 TTTATAAATAATTAAAATA-ATAT
1 TTTA-AAATAATTAAAATATA-AT
*
23596 TTTAAAATACTTAAA
1 TTTAAAATAATTAAA
23611 CTTAAAACTT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
22 11 0.20
23 12 0.22
24 4 0.07
25 9 0.16
27 8 0.15
28 10 0.18
29 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (22 bp):
TTTAAAATAATTAAAATATAAT
Found at i:27714 original size:29 final size:29
Alignment explanation
Indices: 27671--27753 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
27661 CTCACCTAAC
27671 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
27701 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
27730 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
27754 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:32484 original size:29 final size:29
Alignment explanation
Indices: 32441--32523 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
32431 CTCACCTAAC
32441 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
32471 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
32500 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
32524 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:34384 original size:2 final size:2
Alignment explanation
Indices: 34377--34401 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34367 GTATGATTTA
34377 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 A
34402 CATTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35439 original size:13 final size:13
Alignment explanation
Indices: 35421--35446 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35411 AATCTCAATA
35421 AAAAAATTATATG
1 AAAAAATTATATG
35434 AAAAAATTATATG
1 AAAAAATTATATG
35447 TATATTGGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
AAAAAATTATATG
Found at i:39052 original size:88 final size:89
Alignment explanation
Indices: 38960--39136 Score: 295
Period size: 88 Copynumber: 2.0 Consensus size: 89
38950 GATATTGACA
* *
38960 TATCACCATTAATTTTTTAACGGTGAGTGACCAAAATGAAACAAAAACATAACATGAGGTATGGT
1 TATCACCATTAATTTTTTAACGGTGAGTGACCAAAATGAAACAAAAACATAACATAAGGTATGAT
39025 TTT-AAAC-AAAAAATTGCTAGGTG
66 TTTGAAACAAAAAAATT-CTAGGTG
* *
39048 TATCACCATTAATTTTTTAACGGTGGGTGACCAAAATGAAACCAAAACATAACATAAGGTATGAT
1 TATCACCATTAATTTTTTAACGGTGAGTGACCAAAATGAAACAAAAACATAACATAAGGTATGAT
39113 TTTGAAACAAAAAAATTCTAGGTG
66 TTTGAAACAAAAAAATTCTAGGTG
39137 ACCAAAGAGG
Statistics
Matches: 83, Mismatches: 4, Indels: 3
0.92 0.04 0.03
Matches are distributed among these distances:
88 64 0.77
89 11 0.13
90 8 0.10
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.28
Consensus pattern (89 bp):
TATCACCATTAATTTTTTAACGGTGAGTGACCAAAATGAAACAAAAACATAACATAAGGTATGAT
TTTGAAACAAAAAAATTCTAGGTG
Found at i:45030 original size:16 final size:16
Alignment explanation
Indices: 45009--45040 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
44999 TGACGAGTAT
45009 CGATGAACACTATTAA
1 CGATGAACACTATTAA
45025 CGATGAACACTATTAA
1 CGATGAACACTATTAA
45041 TTTAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (16 bp):
CGATGAACACTATTAA
Found at i:45173 original size:15 final size:15
Alignment explanation
Indices: 45153--45207 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
45143 AACCGGTTTT
45153 GGTTTTAAAAAAACC
1 GGTTTTAAAAAAACC
* *
45168 GGTTTTTTTAAAAAATC
1 GG--TTTTAAAAAAACC
*
45185 GGTTATAAAAAAACC
1 GGTTTTAAAAAAACC
*
45200 GATTTTAA
1 GGTTTTAA
45208 TATTATTAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
15 18 0.58
17 13 0.42
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.35
Consensus pattern (15 bp):
GGTTTTAAAAAAACC
Found at i:45180 original size:17 final size:17
Alignment explanation
Indices: 45155--45205 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
45145 CCGGTTTTGG
45155 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
* *
45172 TTTTTAAAAAATCGG--
1 TTTTAAAAAAACCGGTT
* *
45187 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
45204 TT
1 TT
45206 AATATTATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
15 11 0.42
17 15 0.58
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:45295 original size:33 final size:33
Alignment explanation
Indices: 45253--45339 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
45243 AGTTTACGAT
* * **
45253 AATTGAAATACTTAAATACTTCCAAATTTGATA
1 AATTCAAATACTTAAAAACTTCCAAATTCAATA
*
45286 AATTCAAATACTTAAAAACTTCCAAGTTCAATA
1 AATTCAAATACTTAAAAACTTCCAAATTCAATA
45319 AATTCAAATACTTAAAAACTT
1 AATTCAAATACTTAAAAACTT
45340 TAAGTTCGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.48, C:0.15, G:0.03, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAATTCAATA
Found at i:45371 original size:21 final size:21
Alignment explanation
Indices: 45347--45387 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
45337 CTTTAAGTTC
45347 GATAATTGAAACAAAGTTTAT
1 GATAATTGAAACAAAGTTTAT
*
45368 GATAATTGAAATAAAGTTTA
1 GATAATTGAAACAAAGTTTA
45388 AAAATAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.15, T:0.34
Consensus pattern (21 bp):
GATAATTGAAACAAAGTTTAT
Found at i:47231 original size:15 final size:15
Alignment explanation
Indices: 47211--47248 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
47201 TGCGGTGTAA
47211 GATTCGATTGACTAG
1 GATTCGATTGACTAG
47226 GATTCGATTGACTAG
1 GATTCGATTGACTAG
*
47241 GATCCGAT
1 GATTCGAT
47249 CTTGAGCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (15 bp):
GATTCGATTGACTAG
Found at i:47689 original size:11 final size:12
Alignment explanation
Indices: 47668--47707 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
47658 TCCGGATAAA
47668 AACCGGTTTTTT
1 AACCGGTTTTTT
47680 AACCGGTTTTTTT
1 AACCGG-TTTTTT
47693 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
47707 A
1 A
47708 TCCGATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 6 0.24
15 6 0.24
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:47698 original size:15 final size:14
Alignment explanation
Indices: 47667--47706 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
47657 TTCCGGATAA
47667 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
47680 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
47693 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
47707 ATCCGATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:48327 original size:14 final size:14
Alignment explanation
Indices: 48308--48359 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
48298 TTTCATTTCG
48308 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
48322 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
48341 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
48355 CGTTG
1 CGTTG
48360 TGATAGTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 16 0.52
16 2 0.06
17 2 0.06
19 11 0.35
ACGTcount: A:0.10, C:0.25, G:0.25, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:48337 original size:33 final size:33
Alignment explanation
Indices: 48300--48384 Score: 152
Period size: 33 Copynumber: 2.5 Consensus size: 33
48290 TTTAGGTTTT
48300 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
*
48333 TCATTTCGCGTTGCGATTCTCTCGTTGTGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
48366 TCATTTCCGCGTTGCGATT
1 TCATTT-CGCGTTGCGATT
48385 TTCATTCTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 38 0.76
34 12 0.24
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.41
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
Found at i:48389 original size:20 final size:21
Alignment explanation
Indices: 48366--48412 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
48356 GTTGTGATAG
48366 TCATTTC-CGCGTTGCGATTT
1 TCATTTCTCGCGTTGCGATTT
*
48386 TCA-TTCTCTCGTTGCGATTT
1 TCATTTCTCGCGTTGCGATTT
48406 TCATTTC
1 TCATTTC
48413 AACCAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 3 0.12
20 18 0.75
21 3 0.12
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.49
Consensus pattern (21 bp):
TCATTTCTCGCGTTGCGATTT
Found at i:50286 original size:94 final size:94
Alignment explanation
Indices: 50099--50403 Score: 494
Period size: 94 Copynumber: 3.3 Consensus size: 94
50089 TAGATTGCTT
* *
50099 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAA-T-TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
50160 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
50189 AGTAAATTTATTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
50254 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
50283 AGTAAATTTGTTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
50348 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
50377 AGTAAATTTGTTCGTTTGCTGCCAATT
1 AGTAAATTTATTCGGTTGCTGCCAATT
50404 GAAACTATTC
Statistics
Matches: 201, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
90 33 0.16
91 1 0.00
92 3 0.01
93 22 0.11
94 142 0.71
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:50872 original size:21 final size:21
Alignment explanation
Indices: 50848--50914 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
50838 TAATTCCTCG
50848 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
50869 AGAGGCCACTGTCATCGTTAA
1 AGAGTCCCCTCCCACCGTTCA
*
50890 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
50911 AGAG
1 AGAG
50915 CCCTATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:51584 original size:14 final size:14
Alignment explanation
Indices: 51565--51600 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
51555 ATTGTTTAAT
51565 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
51579 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
51593 TGATTTGT
1 TGATTTGT
51601 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:51775 original size:19 final size:19
Alignment explanation
Indices: 51707--51768 Score: 88
Period size: 19 Copynumber: 3.3 Consensus size: 19
51697 AAAAATGACT
* * *
51707 ATCGCAATGCGAAATTGAA
1 ATCGCAACGCGAAACTAAA
51726 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
51745 ATCGCAACGCGAAACTAAA
1 ATCGCAACGCGAAACTAAA
*
51764 TTCGC
1 ATCGC
51769 GTTGCGATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAACTAAA
Found at i:51786 original size:19 final size:19
Alignment explanation
Indices: 51764--51914 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
51754 CGAAACTAAA
51764 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
51783 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
51798 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
51816 TTCGCATTGCGA--TTC-T
1 TTCGCGTTGCGATTTTCAT
51832 TT--CGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
51849 TTCGCATTACGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
51864 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
51882 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
51901 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
51915 AGACATTAAG
Statistics
Matches: 98, Mismatches: 18, Indels: 31
0.67 0.12 0.21
Matches are distributed among these distances:
14 23 0.23
16 12 0.12
17 12 0.12
19 41 0.42
20 10 0.10
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:51810 original size:33 final size:33
Alignment explanation
Indices: 51768--51894 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
51758 ACTAAATTCG
* *
51768 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
51801 CGTTGCGATTTTCATTTCGCATTGCGATTCTTT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
51834 CGTTGCGATTTTCATTTCGCATTACGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
51867 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
51895 AGTCATTTCC
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:51841 original size:14 final size:14
Alignment explanation
Indices: 51789--51876 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
51779 TCATTTCGCT
**
51789 TTGCGATTCCCTCG
1 TTGCGATTCTTTCG
51803 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
51820 CATTGCGATTCTTTCG
1 --TTGCGATTCTTTCG
51836 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TTTCG
* *
51853 CATTACGATTCTCTCG
1 --TTGCGATTCTTTCG
51869 TTGCGATT
1 TTGCGATT
51877 TTCATTTCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 19 0.32
16 15 0.25
17 14 0.24
19 11 0.19
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTTTCG
Found at i:51913 original size:20 final size:20
Alignment explanation
Indices: 51867--51960 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
51857 ACGATTCTCT
**
51867 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
51886 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
51906 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
51925 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
51947 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
51961 AATGATTGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:54242 original size:12 final size:12
Alignment explanation
Indices: 54225--54249 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54215 TCTTCGGGGA
54225 CTTTTTCTTCTT
1 CTTTTTCTTCTT
54237 CTTTTTCTTCTT
1 CTTTTTCTTCTT
54249 C
1 C
54250 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:54458 original size:24 final size:24
Alignment explanation
Indices: 54424--54477 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
54414 CTGAAACATC
*
54424 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
54448 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
54472 ATCAAA
1 ATCAAA
54478 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:55243 original size:20 final size:20
Alignment explanation
Indices: 55217--55370 Score: 184
Period size: 20 Copynumber: 7.7 Consensus size: 20
55207 GATTCTGTAT
* *
55217 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
55237 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
55257 AATCGCGTTACGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
55277 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
55297 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
55317 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
55338 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
55358 TATCGCATTGCGA
1 TATCGCGTTGCGA
55371 TTTTCCAAAT
Statistics
Matches: 119, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
19 3 0.03
20 100 0.84
21 14 0.12
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:55343 original size:21 final size:21
Alignment explanation
Indices: 55317--55413 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
55307 CGAAAGTCAG
55317 TATCGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATTTTGTAT
* *
55338 TATCGCGTTGCGA--TAGTCAG
1 TATCGCGTTGCGATTTTGT-AT
* **
55358 TATCGCATTGCGATTTTCCA-
1 TATCGCGTTGCGATTTTGTAT
* *
55378 AATTCGCATTGCGATTTTGTAT
1 TA-TCGCGTTGCGATTTTGTAT
*
55400 TATCGCGTTACGAT
1 TATCGCGTTGCGAT
55414 AGTCAGTATC
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
19 3 0.05
20 14 0.24
21 40 0.68
22 2 0.03
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.40
Consensus pattern (21 bp):
TATCGCGTTGCGATTTTGTAT
Found at i:55371 original size:20 final size:20
Alignment explanation
Indices: 55217--55433 Score: 179
Period size: 20 Copynumber: 10.7 Consensus size: 20
55207 GATTCTGTAT
*
55217 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
55237 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
55257 AATCGCGTTACGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
55277 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
55297 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
55317 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
55338 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* **
55358 TATCGCATTGCGATTTTCCA-
1 TATCGCGTTGCGATAGT-CAG
* * * *
55378 AATTCGCATTGCGATTTTGT-AT
1 TA-TCGCGTTGCGA--TAGTCAG
*
55400 TATCGCGTTACGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
55420 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
55434 TTTCCAAATT
Statistics
Matches: 165, Mismatches: 23, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
19 6 0.04
20 116 0.70
21 37 0.22
22 3 0.02
23 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:55390 original size:41 final size:41
Alignment explanation
Indices: 55197--55392 Score: 137
Period size: 40 Copynumber: 4.8 Consensus size: 41
55187 AACTTTGAAA
* ** * * *
55197 ATCGCATTGCGATTCTGTATTATCTCGTTGCGATAGTCAGA
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
* * *** * * *
55238 ATCTCGTTGCGAAAGTCAGA-ATCGCGTTACGAAAGTCAGT
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
* *** * *
55278 ATCGCGTTGCGAAAGTC-AGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
* ** *
55318 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
*
55359 ATCGCATTGCGATTTTCCAAAT-TCGCATTGCGAT
1 ATCGCATTGCGATTTT-CAAATATCGCGTTGCGAT
55393 TTTGTATTAT
Statistics
Matches: 124, Mismatches: 28, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
40 64 0.52
41 58 0.47
42 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
Found at i:55414 original size:62 final size:62
Alignment explanation
Indices: 55319--55456 Score: 258
Period size: 62 Copynumber: 2.2 Consensus size: 62
55309 AAAGTCAGTA
* *
55319 TCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTGTATTATCGCGTTACGATAGTCAGTATCGCATTGCGATTTTCCAAAT
55381 TCGCATTGCGATTTTGTATTATCGCGTTACGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTGTATTATCGCGTTACGATAGTCAGTATCGCATTGCGATTTTCCAAAT
55443 TCGCATTGCGATTT
1 TCGCATTGCGATTT
55457 ACTTATTCGC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 74 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (62 bp):
TCGCATTGCGATTTTGTATTATCGCGTTACGATAGTCAGTATCGCATTGCGATTTTCCAAAT
Found at i:55446 original size:21 final size:20
Alignment explanation
Indices: 55422--55473 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
55412 ATAGTCAGTA
*
55422 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACAAAT
**
55443 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACAAAT
55463 TCGCATTGCGA
1 TCGCATTGCGA
55474 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:55466 original size:20 final size:21
Alignment explanation
Indices: 55360--55473 Score: 74
Period size: 21 Copynumber: 5.5 Consensus size: 21
55350 ATAGTCAGTA
*
55360 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
** *
55381 TCGCATTGCGATTTT-GTATT
1 TCGCATTGCGATTTTACAAAT
* * ** *
55401 ATCGCGTTACGATAGT-C-AGT
1 -TCGCATTGCGATTTTACAAAT
*
55421 ATCGCATTGCGATTTTCCAAAT
1 -TCGCATTGCGATTTTACAAAT
**
55443 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
55463 TCGCATTGCGA
1 TCGCATTGCGA
55474 ATTGGGAAAA
Statistics
Matches: 73, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
20 33 0.45
21 38 0.52
22 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.18, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:55515 original size:21 final size:22
Alignment explanation
Indices: 55463--55515 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
55453 ATTTACTTAT
55463 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
55484 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
55505 TCGCATTGCGA
1 TCGCATTGCGA
55516 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:63419 original size:31 final size:29
Alignment explanation
Indices: 63375--63448 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
63365 GGATTTAACG
* *
63375 GTTCAATGGTATAATTGAAACGAAAA-TCAAA
1 GTTCAGTGGTATAATTG--AC-AAAATTAAAA
*
63406 GTTCAGTGCTATAATTGACAAAATTAAAA
1 GTTCAGTGGTATAATTGACAAAATTAAAA
63435 GTTCAGTGGTATAA
1 GTTCAGTGGTATAA
63449 ACGATACAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 4 0.11
29 19 0.50
31 15 0.39
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (29 bp):
GTTCAGTGGTATAATTGACAAAATTAAAA
Found at i:65264 original size:4 final size:4
Alignment explanation
Indices: 65255--65281 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
65245 TTTAGCTTAA
65255 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
65282 AATTAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:66758 original size:31 final size:32
Alignment explanation
Indices: 66723--66824 Score: 147
Period size: 31 Copynumber: 3.3 Consensus size: 32
66713 TGAAATCATC
* *
66723 ATTTTGTTATAAATCGATAACGTTGGTGATC-
1 ATTTTGTTATAAATTGATAACGTTAGTGATCG
*
66754 ATTTTGTTATAAATTGATAACGTTAGTGA-CT
1 ATTTTGTTATAAATTGATAACGTTAGTGATCG
*
66785 ATTTTGTTATAAATTGATAACATTAGTGATCG
1 ATTTTGTTATAAATTGATAACGTTAGTGATCG
66817 A-TTTGTTA
1 ATTTTGTTA
66825 CTTTCAAAAC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
30 1 0.02
31 62 0.95
32 2 0.03
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (32 bp):
ATTTTGTTATAAATTGATAACGTTAGTGATCG
Found at i:73042 original size:20 final size:20
Alignment explanation
Indices: 73019--73056 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
73009 AATAGTGCAT
*
73019 ATATTGTGTGAACAGTAACG
1 ATATTGTATGAACAGTAACG
73039 ATATTGTATGAACAGTAA
1 ATATTGTATGAACAGTAA
73057 TGAGCAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (20 bp):
ATATTGTATGAACAGTAACG
Found at i:73854 original size:14 final size:15
Alignment explanation
Indices: 73818--73854 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
73808 AATGTTACTC
*
73818 CAAGTTTTTAAATGT
1 CAAGTTTTCAAATGT
73833 CAAGTTTTCAAATGT
1 CAAGTTTTCAAATGT
73848 CAA-TTTT
1 CAAGTTTT
73855 AAACCTTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (15 bp):
CAAGTTTTCAAATGT
Found at i:74106 original size:19 final size:19
Alignment explanation
Indices: 74082--74151 Score: 122
Period size: 19 Copynumber: 3.7 Consensus size: 19
74072 ATGTAATTAG
74082 TGTACCGATACACCTGGGA
1 TGTACCGATACACCTGGGA
74101 TGTACCGATACACCTGGGA
1 TGTACCGATACACCTGGGA
74120 TGTACCGATACACCTGGGA
1 TGTACCGATACACCTGGGA
* *
74139 TATACCAATACAC
1 TGTACCGATACAC
74152 TAAGTCTGCC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 49 1.00
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (19 bp):
TGTACCGATACACCTGGGA
Found at i:75713 original size:20 final size:22
Alignment explanation
Indices: 75688--75727 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
75678 TGTTGTATAT
75688 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
75708 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
75728 TCTACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:75856 original size:21 final size:21
Alignment explanation
Indices: 75832--75915 Score: 109
Period size: 21 Copynumber: 4.0 Consensus size: 21
75822 CTAGCCGTTG
*
75832 CAGCCTTCG-TGCATGGATGCA
1 CAGCCTT-GATGCATCGATGCA
**
75853 CAG-CAGGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
75873 CAGCCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
*
75894 CAACCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCA
75915 C
1 C
75916 TGATTGCATT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.02
20 15 0.27
21 39 0.71
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.21
Consensus pattern (21 bp):
CAGCCTTGATGCATCGATGCA
Found at i:75877 original size:41 final size:42
Alignment explanation
Indices: 75832--75915 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 42
75822 CTAGCCGTTG
* *
75832 CAGCCTTCG-TGCATGGATGCAC-AGCAGGATGCATCGATGCA
1 CAGCCTT-GATGCATCGATGCACAACCAGGATGCATCGATGCA
**
75873 CAGCCTTGATGCATCGATGCACAACCTTGATGCATCGATGCA
1 CAGCCTTGATGCATCGATGCACAACCAGGATGCATCGATGCA
75915 C
1 C
75916 TGATTGCATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
40 1 0.03
41 19 0.51
42 17 0.46
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.21
Consensus pattern (42 bp):
CAGCCTTGATGCATCGATGCACAACCAGGATGCATCGATGCA
Found at i:75997 original size:13 final size:13
Alignment explanation
Indices: 75979--76003 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
75969 CTAGTGCAAG
75979 TGCAGGGATGCAC
1 TGCAGGGATGCAC
75992 TGCAGGGATGCA
1 TGCAGGGATGCA
76004 TGGATGCACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.40, T:0.16
Consensus pattern (13 bp):
TGCAGGGATGCAC
Found at i:76008 original size:21 final size:21
Alignment explanation
Indices: 75937--76034 Score: 103
Period size: 21 Copynumber: 4.7 Consensus size: 21
75927 GGTGTTTGAG
*
75937 TGCATGGATGCACTGCATGG-
1 TGCATGGATGCACTGCAGGGA
* *
75957 TGCATCGATGCACT--AGTGCAA
1 TGCATGGATGCACTGCAG-G-GA
*
75978 GTGCAGGGATGCACTGCAGGGA
1 -TGCATGGATGCACTGCAGGGA
*
76000 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
76021 TGCATGGATGCACT
1 TGCATGGATGCACT
76035 TTGACACCCT
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.02
19 1 0.02
20 13 0.20
21 33 0.52
22 13 0.20
23 1 0.02
24 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.21
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:76024 original size:42 final size:41
Alignment explanation
Indices: 75935--76034 Score: 114
Period size: 42 Copynumber: 2.4 Consensus size: 41
75925 TCGGTGTTTG
*
75935 AGTGCATGGATGCACTGCATGGTGCATCGATGCACTAGTGCA
1 AGTGCATGGATGCACTGCAGGGTGCATCGATGCACTAGTG-A
* *
75977 AGTGCAGGGATGCACTGCAGGGATGCATGGATGCACTGCAG-G-
1 AGTGCATGGATGCACTGCAGGG-TGCATCGATGCACT--AGTGA
*
76019 GGTGCATGGATGCACT
1 AGTGCATGGATGCACT
76035 TTGACACCCT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
42 34 0.68
43 13 0.26
44 1 0.02
45 2 0.04
ACGTcount: A:0.23, C:0.20, G:0.36, T:0.21
Consensus pattern (41 bp):
AGTGCATGGATGCACTGCAGGGTGCATCGATGCACTAGTGA
Found at i:76135 original size:29 final size:29
Alignment explanation
Indices: 76114--76171 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
76104 AAACTTTGAA
76114 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
76143 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
76172 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:76161 original size:30 final size:30
Alignment explanation
Indices: 76114--76173 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
76104 AAACTTTGAA
76114 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
76143 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
76174 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:79443 original size:20 final size:20
Alignment explanation
Indices: 79418--79485 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
79408 TTCGTACATG
* *
79418 GATGCACATCAGGATGCATC
1 GATGCACACCACGATGCATC
* **
79438 GATGCATAACCTTGATGCATC
1 GATGCA-CACCACGATGCATC
**
79459 GATGCACAGAACGATGCATC
1 GATGCACACCACGATGCATC
79479 GATGCAC
1 GATGCAC
79486 TGATTGCATT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.21
Consensus pattern (20 bp):
GATGCACACCACGATGCATC
Found at i:79553 original size:22 final size:23
Alignment explanation
Indices: 79520--79562 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
79510 ATGGATGCAC
79520 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
79543 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
79563 GCAGGAATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:79575 original size:21 final size:19
Alignment explanation
Indices: 79510--79604 Score: 91
Period size: 21 Copynumber: 4.6 Consensus size: 19
79500 GTTTGAGTGT
79510 ATGGATGCACTGCATGGTGC
1 ATGGATGCACTGCA-GGTGC
*
79530 ATCGATGCACTAGTGCAGGTGC
1 ATGGATGCAC---TGCAGGTGC
79552 ATGGATGCACTGCAGGAATGC
1 ATGGATGCACTGCAGG--TGC
*
79573 ATGGATGTACTGCAGGGGTGC
1 ATGGATGCACTGCA--GGTGC
*
79594 ATGTATGCACT
1 ATGGATGCACT
79605 TTGACACCCT
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
19 6 0.10
20 9 0.14
21 28 0.44
22 14 0.22
23 6 0.10
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (19 bp):
ATGGATGCACTGCAGGTGC
Found at i:79736 original size:30 final size:30
Alignment explanation
Indices: 79685--79744 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
79675 AAACTTTGAA
79685 TAAATTCAATTAAGTCAAAAAA-CATTTTG
1 TAAATTCAATTAAGTCAAAAAACCATTTTG
*
79714 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCAAAAAACCATTTTG
79745 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCAAAAAACCATTTTG
Found at i:79753 original size:34 final size:29
Alignment explanation
Indices: 79685--79744 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 29
79675 AAACTTTGAA
79685 TAAATTCAATTAAGTCAAAAAACATTTTG
1 TAAATTCAATTAAGTCAAAAAACATTTTG
*
79714 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGT-CAAAAAACATTTTG
79745 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 4 0.14
31 13 0.46
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTAAGTCAAAAAACATTTTG
Found at i:81129 original size:11 final size:11
Alignment explanation
Indices: 81113--81163 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
81103 TTTGAGTTAT
81113 TAAAATATTAA
1 TAAAATATTAA
*
81124 TAAAATA-AACA
1 TAAAATATTA-A
* **
81135 TGAGTTATTAA
1 TAAAATATTAA
81146 TAAAATATTAA
1 TAAAATATTAA
81157 TAAAATA
1 TAAAATA
81164 AATTCGAGTT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
10 1 0.03
11 28 0.93
12 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (11 bp):
TAAAATATTAA
Found at i:81139 original size:30 final size:29
Alignment explanation
Indices: 81105--81182 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 29
81095 ATTTAAACTT
81105 TGAGTTATTAAAATATTAATAAAATAAACA
1 TGAGTTATTAAAATATTAATAAAATAAA-A
*
81135 TGAGTTATTAATAAAATATTAATAAAATAAAT
1 TGAGTTA-T--TAAAATATTAATAAAATAAAA
81167 TCGAGTTATTAAAATA
1 T-GAGTTATTAAAATA
81183 AGAGCAATTC
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
30 14 0.33
31 1 0.02
32 2 0.05
33 26 0.60
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (29 bp):
TGAGTTATTAAAATATTAATAAAATAAAA
Found at i:81155 original size:33 final size:33
Alignment explanation
Indices: 81113--81178 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
81103 TTTGAGTTAT
81113 TAAAATATTAATAAAATAAACAT-GAGTTATTAA
1 TAAAATATTAATAAAATAAA-ATCGAGTTATTAA
*
81146 TAAAATATTAATAAAATAAATTCGAGTTATTAA
1 TAAAATATTAATAAAATAAAATCGAGTTATTAA
81179 AATAAGAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 1 0.03
33 30 0.97
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (33 bp):
TAAAATATTAATAAAATAAAATCGAGTTATTAA
Found at i:81978 original size:18 final size:20
Alignment explanation
Indices: 81942--81994 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
81932 TATGAAAATA
*
81942 TTTTAAAATATTTAGTTATT
1 TTTTAAAATATATAGTTATT
*
81962 TTTTAAAATTATATTATTTATT
1 TTTTAAAA-TATA-TAGTTATT
81984 TATTTAAAATA
1 T-TTTAAAATA
81995 ATATTAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 8 0.29
21 3 0.11
22 10 0.36
23 7 0.25
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TTTTAAAATATATAGTTATT
Found at i:81989 original size:23 final size:22
Alignment explanation
Indices: 81942--82000 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
81932 TATGAAAATA
81942 TTTTAAAA-TAT-TTAGTTATT
1 TTTTAAAATTATATTAGTTATT
*
81962 TTTTAAAATTATATTATTTATT
1 TTTTAAAATTATATTAGTTATT
*
81984 TATTTAAAATAATATTA
1 T-TTTAAAATTATATTA
82001 AATTAAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 8 0.24
21 3 0.09
22 9 0.26
23 14 0.41
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTAAAATTATATTAGTTATT
Found at i:86231 original size:21 final size:21
Alignment explanation
Indices: 86179--86233 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
86169 TTAATATCGA
*
86179 TTCGCGTTGCAATAGTCGAAG
1 TTCGCGTTGCGATAGTCGAAG
*
86200 TTCGCGTTGCGATAGTCTAAG
1 TTCGCGTTGCGATAGTCGAAG
86221 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
86234 TTATTTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCGAAG
Found at i:86565 original size:24 final size:23
Alignment explanation
Indices: 86509--86569 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
86499 TAATGTTCAT
*
86509 TTATTTAT-TGTTCACGAATATA
1 TTATTTATATGTTCATGAATATA
*
86531 TTTTTTA-ATGTTCATGAATATA
1 TTATTTATATGTTCATGAATATA
86553 TTCATTTATATGTTCAT
1 TT-ATTTATATGTTCAT
86570 TTAGTATTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 21 0.64
23 4 0.12
24 8 0.24
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.54
Consensus pattern (23 bp):
TTATTTATATGTTCATGAATATA
Found at i:86616 original size:22 final size:22
Alignment explanation
Indices: 86585--86628 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
86575 ATTCACAAAT
86585 GTGTTCGTTTAAT-GTTCATTTA
1 GTGTTCGTTT-ATCGTTCATTTA
*
86607 GTGTTTGTTTATCGTTCATTTA
1 GTGTTCGTTTATCGTTCATTTA
86629 TATGTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.16, C:0.09, G:0.18, T:0.57
Consensus pattern (22 bp):
GTGTTCGTTTATCGTTCATTTA
Found at i:86870 original size:24 final size:24
Alignment explanation
Indices: 86842--86892 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
86832 AATATAAATG
86842 AATGAATC-GATAAACGAGATCTTA
1 AATG-ATCTGATAAACGAGATCTTA
* *
86866 AATGATCTTATAAACGAGCTCTTA
1 AATGATCTGATAAACGAGATCTTA
86890 AAT
1 AAT
86893 AAAGAAAGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (24 bp):
AATGATCTGATAAACGAGATCTTA
Found at i:90452 original size:36 final size:36
Alignment explanation
Indices: 90412--90482 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
90402 AGGATCTCAA
90412 TTTTTAGGAA-CTGGTTG-AACAGGTTCCGGTTCCCAT
1 TTTTTAGGAATC-GG-TGCAACAGGTTCCGGTTCCCAT
90448 TTTTTAGGAATCGGTGCAACAGGTTCCGGTTCCCA
1 TTTTTAGGAATCGGTGCAACAGGTTCCGGTTCCCA
90483 AAAAATAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 2 0.06
36 30 0.91
37 1 0.03
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (36 bp):
TTTTTAGGAATCGGTGCAACAGGTTCCGGTTCCCAT
Found at i:97809 original size:16 final size:16
Alignment explanation
Indices: 97788--97821 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
97778 GCAGATTTAG
97788 AAAAGAAAAGAAAA-GA
1 AAAAGAAAA-AAAACGA
97804 AAAAGAAAAAAAACGA
1 AAAAGAAAAAAAACGA
97820 AA
1 AA
97822 CCAAGCCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAAACGA
Found at i:99158 original size:29 final size:30
Alignment explanation
Indices: 99100--99158 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
99090 TTTTTACCCT
* * *
99100 AAATTAAAATTTTATGAATAATATTTAATA
1 AAATTAAAATTTCATGAATAACATTAAATA
*
99130 AAATTAAAA-TTCATGTATAACATTAAATA
1 AAATTAAAATTTCATGAATAACATTAAATA
99159 TTTGACCAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (30 bp):
AAATTAAAATTTCATGAATAACATTAAATA
Found at i:104862 original size:13 final size:13
Alignment explanation
Indices: 104844--104870 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
104834 AAATATCTTC
104844 CATAGCCAGCTTT
1 CATAGCCAGCTTT
104857 CATAGCCAGCTTT
1 CATAGCCAGCTTT
104870 C
1 C
104871 TCATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.30
Consensus pattern (13 bp):
CATAGCCAGCTTT
Found at i:108031 original size:20 final size:20
Alignment explanation
Indices: 108009--108261 Score: 274
Period size: 20 Copynumber: 12.6 Consensus size: 20
107999 TCAGTTTCCA
* ** *
108009 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCCGT
* *
108029 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATC-CGT
* *
108049 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* *
108069 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
108089 TAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
108109 AAATCGCAACGATAATACAT
1 AAATCGCAACGAGAATCCGT
* *
108129 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGAGAATCCGT
*
108150 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
108170 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
108190 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
108210 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
108230 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
108250 AAATCGCAACGA
1 AAATCGCAACGA
108262 TGATGTTTCA
Statistics
Matches: 199, Mismatches: 31, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
20 183 0.92
21 16 0.08
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:108261 original size:40 final size:40
Alignment explanation
Indices: 108009--108260 Score: 310
Period size: 40 Copynumber: 6.3 Consensus size: 40
107999 TCAGTTTCCA
** * ** *
108009 AAATCGCAACGCGAATATGAAAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGATAATC-CGT
* *
108049 AAATCGCAACGCGTATCCGTAAATCGCAACG-TGTATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGAT-AATCCGT
* * * *
108089 TAATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGATAATCCGT
*
108129 AAAATCGCAACGCGTATCCGTAAATCGCAACGATAATCCGT
1 -AAATCGCAACGCGAATCCGTAAATCGCAACGATAATCCGT
* *
108170 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGATAATCCGT
* *
108210 AAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGTAAATCGCAACGATAATCCGT
108250 AAATCGCAACG
1 AAATCGCAACG
108261 ATGATGTTTC
Statistics
Matches: 191, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
40 152 0.80
41 39 0.20
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (40 bp):
AAATCGCAACGCGAATCCGTAAATCGCAACGATAATCCGT
Found at i:110785 original size:33 final size:34
Alignment explanation
Indices: 110748--110931 Score: 144
Period size: 33 Copynumber: 5.2 Consensus size: 34
110738 GCAACGAGAG
110748 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACAATGAA
* * *
110781 AATCGCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCCCAACAATGAA
*
110815 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C--AATGAA
* * * * *
110853 AATCGCAACGAGAGAATCG-CAAT-GCGA-AATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAATGAA
*
110886 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C--AATGAA
110924 AATCGCAA
1 AATCGCAA
110932 CGAGAGAATC
Statistics
Matches: 123, Mismatches: 12, Indels: 27
0.76 0.07 0.17
Matches are distributed among these distances:
31 1 0.01
32 6 0.05
33 47 0.38
34 29 0.24
35 2 0.02
37 1 0.01
38 30 0.24
39 6 0.05
40 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCCCAACAATGAA
Found at i:110802 original size:34 final size:33
Alignment explanation
Indices: 110734--110837 Score: 147
Period size: 33 Copynumber: 3.1 Consensus size: 33
110724 CGGAAATTAC
* *
110734 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCCCAACGAGAAAATCGCAATGCGAAATGAA
110767 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCCCAACGA-GAAAATCGCAATGC-GAAATGAA
* *
110801 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCCCAACGAGAAAATCGCAATGCGAAATGAA
110834 AATC
1 AATC
110838 GCAATGCGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
32 1 0.02
33 33 0.52
34 29 0.45
35 1 0.02
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCCCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:110839 original size:19 final size:19
Alignment explanation
Indices: 110748--110969 Score: 241
Period size: 19 Copynumber: 12.7 Consensus size: 19
110738 GCAACGAGAG
110748 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
110767 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
110781 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
110801 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
110815 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
110834 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
110853 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
110867 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
110886 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
110905 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
110924 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
110938 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
110957 AATCGCATTGCGA
1 AATCGCAATGCGA
110970 TTCTCCCGTT
Statistics
Matches: 172, Mismatches: 10, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 42 0.24
15 3 0.02
16 7 0.04
17 6 0.03
18 4 0.02
19 97 0.56
20 13 0.08
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:110861 original size:52 final size:52
Alignment explanation
Indices: 110776--110963 Score: 265
Period size: 52 Copynumber: 3.6 Consensus size: 52
110766 AAATCCCAAC
110776 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
110829 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
110881 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
* *
110931 ACGAGAGAATCGCAATGCGAAATTAAAATCGCA
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCA
110964 TTGCGATTCT
Statistics
Matches: 126, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
50 7 0.06
51 7 0.06
52 96 0.76
53 16 0.13
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:110904 original size:71 final size:71
Alignment explanation
Indices: 110815--110969 Score: 292
Period size: 71 Copynumber: 2.2 Consensus size: 71
110805 GCAACGAGAG
110815 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
110880 AATGAA
66 AATGAA
110886 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
*
110951 AATTAA
66 AATGAA
*
110957 AATCGCATTGCGA
1 AATCGCAATGCGA
110970 TTCTCCCGTT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 82 1.00
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
AATGAA
Found at i:110947 original size:33 final size:33
Alignment explanation
Indices: 110834--110963 Score: 197
Period size: 33 Copynumber: 3.8 Consensus size: 33
110824 GCGAAATGAA
110834 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
110867 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
110905 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
110938 AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
110964 TTGCGATTCT
Statistics
Matches: 89, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
33 54 0.61
34 1 0.01
35 2 0.02
36 2 0.02
37 1 0.01
38 29 0.33
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:110969 original size:52 final size:52
Alignment explanation
Indices: 110748--110969 Score: 229
Period size: 52 Copynumber: 4.2 Consensus size: 52
110738 GCAACGAGAG
* * *
110748 AATCGCAATGCGA-AAT-GAAAATCCCAACATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAGAATCG-AAATGCGAA-ACGAAAATCGCAATGC-GAAATGAA
* * * *
110801 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAGAATCGAAATGCGAAACGAAAATCGCAATGCGAAATGAA
* * * *
110853 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAGAATCGAAATGCGAAACGAAAATCGCAATGCGAAATGAA
* *
110905 AATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAGAATCG-AAATGCGAAACGA-A-AATCGCAATGCGAAATGAA
*
110957 AATCGCATTGCGA
1 AATCGCAATGCGA
110970 TTCTCCCGTT
Statistics
Matches: 152, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
50 7 0.05
51 7 0.05
52 101 0.66
53 27 0.18
54 9 0.06
55 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAGAATCGAAATGCGAAACGAAAATCGCAATGCGAAATGAA
Found at i:111018 original size:19 final size:19
Alignment explanation
Indices: 110978--111056 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
110968 GATTCTCCCG
110978 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
110998 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
111017 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
111031 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
111050 TTGCGAT
1 TTGCGAT
111057 AGTCAATTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 6 0.12
16 7 0.13
17 7 0.13
19 17 0.33
20 15 0.29
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:111182 original size:14 final size:14
Alignment explanation
Indices: 111163--111199 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
111153 CATCAATTAC
111163 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
111177 ACAAATCATCTTTT
1 ACAAATCAACTTTT
111191 ACAAATCAA
1 ACAAATCAA
111200 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:113196 original size:14 final size:14
Alignment explanation
Indices: 113177--113233 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
113167 GCGAAATGAA
*
113177 AATCGCAACGACAG
1 AATCGCAACGAAAG
113191 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
113208 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
113224 AATCGCAACG
1 AATCGCAACG
113234 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:113204 original size:33 final size:33
Alignment explanation
Indices: 113158--113250 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
113148 GCGAAACCAA
*
113158 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
113191 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
113224 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
113251 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Done.