Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015294.1 Kokia drynarioides strain JFW-HI SEQ_130339, 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: 417562
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 148 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:2275 original size:23 final size:23
Alignment explanation
Indices: 2245--2291 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2235 AGCTTAATGG
2245 CAGCTTCTCTATGTTGCAAACTT
1 CAGCTTCTCTATGTTGCAAACTT
2268 CAGCTTCTCTATGTTGCAAACTT
1 CAGCTTCTCTATGTTGCAAACTT
2291 C
1 C
2292 TGTCAACCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.28, G:0.13, T:0.38
Consensus pattern (23 bp):
CAGCTTCTCTATGTTGCAAACTT
Found at i:6767 original size:13 final size:12
Alignment explanation
Indices: 6751--6789 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
6741 TTTTTCTATC
6751 TTTTCTTTCATTT
1 TTTTCTTTC-TTT
6764 TTTTC-TTCTTT
1 TTTTCTTTCTTT
6775 ATTTTCTTTCTTT
1 -TTTTCTTTCTTT
6788 TT
1 TT
6790 CCCCTTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.12
12 10 0.42
13 11 0.46
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:6774 original size:16 final size:17
Alignment explanation
Indices: 6753--6790 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
6743 TTTCTATCTT
6753 TTCTTTCATTTT-TTTC
1 TTCTTTCATTTTCTTTC
6769 TTCTTT-ATTTTCTTTC
1 TTCTTTCATTTTCTTTC
6785 TT-TTTC
1 TTCTTTC
6791 CCCTTTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.05, C:0.18, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCTTTCATTTTCTTTC
Found at i:6780 original size:21 final size:23
Alignment explanation
Indices: 6741--6790 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
6731 AACACCTAGA
6741 TTTTTCTATCTTTTCTTTCATT-
1 TTTTTCTATCTTTTCTTTCATTC
*
6763 TTTTTCT-TCTTTAT-TTTCTTTC
1 TTTTTCTATCTTT-TCTTTCATTC
6785 TTTTTC
1 TTTTTC
6791 CCCTTTCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTTCTATCTTTTCTTTCATTC
Found at i:7314 original size:2 final size:2
Alignment explanation
Indices: 7307--7336 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
7297 TTTAGATATT
7307 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
7337 GNGAAGTCGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8348 original size:31 final size:31
Alignment explanation
Indices: 8235--8405 Score: 82
Period size: 31 Copynumber: 5.8 Consensus size: 31
8225 AATTAATATT
*
8235 TACCAAATTAGGAAAAA-TAATCAAGTTCAGG
1 TACCAAATTAGGAAAAAGT-ATCAAGTTTAGG
** *
8266 TACCAAATT-GGACCCCAA--A--AAGTTTAAG
1 TACCAAATTAGGA--AAAAGTATCAAGTTTAGG
* * *
8294 TACCAACTTTA--AAAAAATGTCAAGTTTAGG
1 TACCAA-ATTAGGAAAAAGTATCAAGTTTAGG
8324 TACCAAATTAGGAAAAAGTATCAAGTTT-GAG
1 TACCAAATTAGGAAAAAGTATCAAGTTTAG-G
* *
8355 AACCAAATT-GGACAAAAG-A--AA-TTTAAG
1 TACCAAATTAGGA-AAAAGTATCAAGTTTAGG
** *
8382 TACCAAATTAAAAAAAAGTGTCAA
1 TACCAAATTAGGAAAAAGTATCAA
8406 ATTCAAATAC
Statistics
Matches: 105, Mismatches: 18, Indels: 35
0.66 0.11 0.22
Matches are distributed among these distances:
26 2 0.02
27 17 0.16
28 17 0.16
29 5 0.05
30 25 0.24
31 37 0.35
32 2 0.02
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (31 bp):
TACCAAATTAGGAAAAAGTATCAAGTTTAGG
Found at i:8397 original size:89 final size:88
Alignment explanation
Indices: 8235--8405 Score: 222
Period size: 89 Copynumber: 1.9 Consensus size: 88
8225 AATTAATATT
* * *
8235 TACCAAATTAGGAAAAATAATCAAGTTCAGGTACCAAATTGGACCCCAAAAAGTTTAAGTACCAA
1 TACCAAATTAGGAAAAATAATCAAGTTCAGGAACCAAATTGGA-CCAAAAAAATTTAAGTACCAA
* *
8300 CTTTAAAAAAATGTCAAGTTTAGG
65 ATTAAAAAAAATGTCAAGTTTAGG
*
8324 TACCAAATTAGGAAAAAGT-ATCAAGTT-TGAGAACCAAATTGGA-CAAAAGAAATTTAAGTACC
1 TACCAAATTAGGAAAAA-TAATCAAGTTCAG-GAACCAAATTGGACCAAAA-AAATTTAAGTACC
8386 AAATTAAAAAAAAGTGTCAA
63 AAATTAAAAAAAA-TGTCAA
8406 ATTCAAATAC
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
87 4 0.06
88 24 0.33
89 43 0.60
90 1 0.01
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.23
Consensus pattern (88 bp):
TACCAAATTAGGAAAAATAATCAAGTTCAGGAACCAAATTGGACCAAAAAAATTTAAGTACCAAA
TTAAAAAAAATGTCAAGTTTAGG
Found at i:12719 original size:20 final size:18
Alignment explanation
Indices: 12702--12738 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
12692 GCTGGTTTAA
12702 TGTTTGTTTTTCTAGTTT
1 TGTTTGTTTTTCTAGTTT
* *
12720 TTTTTTTTTTTCTAGTTT
1 TGTTTGTTTTTCTAGTTT
12738 T
1 T
12739 TTTAATTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.05, C:0.05, G:0.11, T:0.78
Consensus pattern (18 bp):
TGTTTGTTTTTCTAGTTT
Found at i:12738 original size:27 final size:27
Alignment explanation
Indices: 12707--12768 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
12697 TTTAATGTTT
* *
12707 GTTTTTCTAGTTT-TTTTTTTTTTTCTA
1 GTTTTTCTAATTTCTTTTTGTTTTT-TA
*
12734 GTTTTTTTAATTTCTTTTTGTTTTTTA
1 GTTTTTCTAATTTCTTTTTGTTTTTTA
12761 -TTTTTCTA
1 GTTTTTCTA
12769 TTACATTTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 7 0.23
27 13 0.43
28 10 0.33
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.77
Consensus pattern (27 bp):
GTTTTTCTAATTTCTTTTTGTTTTTTA
Found at i:17729 original size:18 final size:19
Alignment explanation
Indices: 17708--17743 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17698 CTTTTAATAG
*
17708 TTTTGAGACTT-TAATTTA
1 TTTTAAGACTTGTAATTTA
17726 TTTTAAGACTTGTAATTT
1 TTTTAAGACTTGTAATTT
17744 TGGGGATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.56
Consensus pattern (19 bp):
TTTTAAGACTTGTAATTTA
Found at i:22657 original size:24 final size:24
Alignment explanation
Indices: 22630--22693 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
22620 ACTCTGTTTG
*
22630 GGCTCGAATGAGCTAACTTATCTA
1 GGCTCGAATGAGCTAACCTATCTA
*
22654 GGCTCGTAA-GAGCTAACCTATCTG
1 GGCTCG-AATGAGCTAACCTATCTA
*
22678 GGCTCGTATGAGCTAA
1 GGCTCGAATGAGCTAA
22694 TTTTGTTTAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.03
24 32 0.91
25 2 0.06
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.27
Consensus pattern (24 bp):
GGCTCGAATGAGCTAACCTATCTA
Found at i:26258 original size:31 final size:31
Alignment explanation
Indices: 26220--26282 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
26210 CGAAATATAC
26220 TCTGAACGGGAGTACATTCAGAGGTGATCAG
1 TCTGAACGGGAGTACATTCAGAGGTGATCAG
26251 TCTGAACGGGAGTACATTCAGAGGTGATCAG
1 TCTGAACGGGAGTACATTCAGAGGTGATCAG
26282 T
1 T
26283 GATTCAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.32, T:0.24
Consensus pattern (31 bp):
TCTGAACGGGAGTACATTCAGAGGTGATCAG
Found at i:30254 original size:25 final size:25
Alignment explanation
Indices: 30206--30254 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
30196 CAAATAAATA
* *
30206 AAATTTAACTAAAAAATTATATATC
1 AAATTTAACTAAAAAATGAAATATC
*
30231 AAATTTAACTAAAATATGAAATAT
1 AAATTTAACTAAAAAATGAAATAT
30255 ACTCAACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (25 bp):
AAATTTAACTAAAAAATGAAATATC
Found at i:43040 original size:3 final size:3
Alignment explanation
Indices: 43032--43091 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
43022 ATCTTAATTT
* *
43032 TTC TTC TTC GTT- TTC TTC TT- TGTT TTC TTC TTT TTC TTC TTC TTC
1 TTC TTC TTC -TTC TTC TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC
43077 TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC
43092 ATACGGCCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
2 3 0.06
3 44 0.88
4 3 0.06
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:43881 original size:41 final size:41
Alignment explanation
Indices: 43832--43954 Score: 156
Period size: 41 Copynumber: 3.0 Consensus size: 41
43822 AATTTATATA
* *
43832 AAAGGAAGACTCGTGACTCGAAATGAGCATGAGAAAATGTT
1 AAAGGAAGACTCATGACTCGAAATGAGCATGAGAATATGTT
* ** * *
43873 AAAGGAAGACTCATGTCTCGAGGTGAGAATGAGAATGTGTT
1 AAAGGAAGACTCATGACTCGAAATGAGCATGAGAATATGTT
** *
43914 AAAGGAAGACTCATGACTTAAAATGAGCGTGAGAATATGTT
1 AAAGGAAGACTCATGACTCGAAATGAGCATGAGAATATGTT
43955 TAAAAAGGAA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.39, C:0.11, G:0.28, T:0.23
Consensus pattern (41 bp):
AAAGGAAGACTCATGACTCGAAATGAGCATGAGAATATGTT
Found at i:43947 original size:82 final size:85
Alignment explanation
Indices: 43786--43954 Score: 229
Period size: 82 Copynumber: 2.0 Consensus size: 85
43776 TTCTTGATGT
* * *
43786 TTAAATGGAAGACTCATGTCTCGGGTTGAGAATGATAATTTATATAAAAGGAAGACTCGTGACTC
1 TTAAATGGAAGACTCATGTCTCGGGTTGAGAATGAGAATGTATATAAAAGGAAGACTCATGACTC
*
43851 GAAATGAGCATGAGAAAATG
66 AAAATGAGCATGAGAAAATG
*
43871 TTAAA-GGAAGACTCATGTCTCGAGG-TGAGAATGAGAATGTGT-T-AAAGGAAGACTCATGACT
1 TTAAATGGAAGACTCATGTCTCG-GGTTGAGAATGAGAATGTATATAAAAGGAAGACTCATGACT
* * *
43932 TAAAATGAGCGTGAGAATATG
65 CAAAATGAGCATGAGAAAATG
43953 TT
1 TT
43955 TAAAAAGGAA
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
82 36 0.48
83 1 0.01
84 31 0.41
85 7 0.09
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (85 bp):
TTAAATGGAAGACTCATGTCTCGGGTTGAGAATGAGAATGTATATAAAAGGAAGACTCATGACTC
AAAATGAGCATGAGAAAATG
Found at i:46414 original size:21 final size:21
Alignment explanation
Indices: 46385--46430 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
46375 GGAGTTTTTA
* *
46385 GTATTGGTAGAACTGTCACTT
1 GTATCGGTAGAACTATCACTT
46406 GTATCGGTAGAACTATCACTT
1 GTATCGGTAGAACTATCACTT
46427 GTAT
1 GTAT
46431 AAATAGAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (21 bp):
GTATCGGTAGAACTATCACTT
Found at i:46437 original size:21 final size:21
Alignment explanation
Indices: 46392--46438 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
46382 TTAGTATTGG
* ***
46392 TAGAACTGTCACTTGTATCGG
1 TAGAACTATCACTTGTATAAA
46413 TAGAACTATCACTTGTATAAA
1 TAGAACTATCACTTGTATAAA
46434 TAGAA
1 TAGAA
46439 ATCTGCACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (21 bp):
TAGAACTATCACTTGTATAAA
Found at i:54655 original size:119 final size:117
Alignment explanation
Indices: 54400--54859 Score: 513
Period size: 119 Copynumber: 3.9 Consensus size: 117
54390 GCACACATGT
* * * *
54400 CTGTGTACTATGACAAATTCCATTTATTGTCACTTTAAGATGTAAATATTTGAATTTTTTTATTT
1 CTGTGTACTATGACAAATTCCATTTATTGTTACTTTAAAATGTAAATATTTGAATTTTATCATTT
* *
54465 TG--A-AAGGTGCCAATATTTGATC--TCTCTGAGACCAAGACATATGTGTGTA
66 TGACATAAGGTACCAATGTTTGATCTGTCTCTGAGACCAAGACATAT-T-TGTA
* ** *
54514 -TGTGTACTATGACTAATTCCATTTATTGTTACTTTAAAATGTAAATATTTGAATTTCCTGATTT
1 CTGTGTACTATGACAAATTCCATTTATTGTTACTTTAAAATGTAAATATTTGAATTTTATCA-TT
* *
54578 TTGACATAAGGTACCAAGGTTTGATCTGTCTCTGAGACCAAGACAGATTTGCTA
65 TTGACATAAGGTACCAATGTTTGATCTGTCTCTGAGACCAAGACATATTTG-TA
* * *
54632 CTGTGTTCTATGGCAAATTCCATTTATTGTTGCTTTAAAATGTAAATATTTGAATTTTATCATTT
1 CTGTGTACTATGACAAATTCCATTTATTGTTACTTTAAAATGTAAATATTTGAATTTTATCATTT
* *
54697 TGACATAAGGTACCAATGTTTGGTCTGTGTCTCTGAGACCAAAGACTATATGTGT-
66 TGACATAAGGTACCAATGTTTGATC--TGTCTCTGAGACC-AAGAC-ATATTTGTA
* * * * *** *
54752 CTGTGTACAATGACAAATTCCTTTTATTGTTGCATTAAAATGTAAAGGCTTGAAATTTAT-ATTT
1 CTGTGTACTATGACAAATTCCATTTATTGTTACTTTAAAATGTAAATATTTGAATTTTATCATTT
* * * *
54816 TGAGATAAGGTAGCATTGTTTGAGATGTGTCTCTGAGACCAAGA
66 TGACATAAGGTACCAATGTTT--GATCTGTCTCTGAGACCAAGA
54860 ATTATGTAAT
Statistics
Matches: 297, Mismatches: 35, Indels: 24
0.83 0.10 0.07
Matches are distributed among these distances:
113 55 0.19
114 5 0.02
116 1 0.00
117 18 0.06
118 33 0.11
119 108 0.36
120 64 0.22
121 8 0.03
122 5 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (117 bp):
CTGTGTACTATGACAAATTCCATTTATTGTTACTTTAAAATGTAAATATTTGAATTTTATCATTT
TGACATAAGGTACCAATGTTTGATCTGTCTCTGAGACCAAGACATATTTGTA
Found at i:54849 original size:239 final size:232
Alignment explanation
Indices: 54400--54859 Score: 559
Period size: 239 Copynumber: 2.0 Consensus size: 232
54390 GCACACATGT
* * *
54400 CTGTGTACTATGACAAATTCCATTTATTGTCACTTTAAGATGTAAATATTTGAATTTTTTTATTT
1 CTGTGTACTATGACAAATTCCATTTATTGTCACTTTAAAATGTAAATATTTGAATTTTATCATTT
* * * *
54465 TGAAAGGTGCCAATATTTGATCTCTCTGAGACCAAGACATATGTGTGTATGTGTACTATGACTAA
66 TGAAAGGTACCAATATTTGATCTCTCTGAGACCAAGACATATATGTGTATGTGTACAATGACAAA
* * * *
54530 TTCCATTTATTGTTACTTTAAAATGTAAATATTTGAATTTCCTGATTTTTGACATAAGGTACCAA
131 TTCCATTTATTGTTACATTAAAATGTAAAGACTTGAATTTCATGATTTTTGACATAAGGTACCAA
54595 GGTTTGATCTGTCTCTGAGACCAAGACAGATTTGCTA
196 GGTTTGATCTGTCTCTGAGACCAAGACAGATTTGCTA
* * **
54632 CTGTGTTCTATGGCAAATTCCATTTATTGTTGCTTTAAAATGTAAATATTTGAATTTTATCATTT
1 CTGTGTACTATGACAAATTCCATTTATTGTCACTTTAAAATGTAAATATTTGAATTTTATCATTT
* * *
54697 TGACATAAGGTACCAATGTTTGGTCTGTGTCTCTGAGACCAAAGAC-TATATGTGTCTGTGTACA
66 TG--A-AAGGTACCAATATTTGATC----TCTCTGAGACC-AAGACATATATGTGTATGTGTACA
* * * *
54761 ATGACAAATTCCTTTTATTGTTGCATTAAAATGTAAAGGCTTGAAATTT-AT-A-TTTTGAGATA
123 ATGACAAATTCCATTTATTGTTACATTAAAATGTAAAGACTTG-AATTTCATGATTTTTGACATA
* ** *
54823 AGGTAGCATTGTTTGAGATGTGTCTCTGAGACCAAGA
187 AGGTACCAAGGTTT--GATCTGTCTCTGAGACCAAGA
54860 ATTATGTAAT
Statistics
Matches: 191, Mismatches: 26, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
232 60 0.31
234 1 0.01
235 16 0.08
237 20 0.10
238 1 0.01
239 83 0.43
240 10 0.05
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (232 bp):
CTGTGTACTATGACAAATTCCATTTATTGTCACTTTAAAATGTAAATATTTGAATTTTATCATTT
TGAAAGGTACCAATATTTGATCTCTCTGAGACCAAGACATATATGTGTATGTGTACAATGACAAA
TTCCATTTATTGTTACATTAAAATGTAAAGACTTGAATTTCATGATTTTTGACATAAGGTACCAA
GGTTTGATCTGTCTCTGAGACCAAGACAGATTTGCTA
Found at i:67820 original size:62 final size:62
Alignment explanation
Indices: 67720--67912 Score: 291
Period size: 62 Copynumber: 3.1 Consensus size: 62
67710 TGAAAAGGGT
*
67720 TCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATAAATCCTATTACGGATTAAAGGTC
1 TCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTAAA-GTC
* * *
67783 T-GATGTCTTTGTGATATTGTGAGTATTACATGGGAAATGAATCCTATTACGGATTAAAGTT
1 TCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTAAAGTC
** *
67844 TCGATGTCTTCATGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTTAATGTC
1 TCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGA-TTAAAGTC
67907 -CGATGT
1 TCGATGT
67913 TGGAAATCTT
Statistics
Matches: 118, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
61 3 0.03
62 108 0.92
63 7 0.06
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (62 bp):
TCGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTAAAGTC
Found at i:69745 original size:52 final size:52
Alignment explanation
Indices: 69641--69827 Score: 232
Period size: 52 Copynumber: 3.6 Consensus size: 52
69631 TTCCCATTTA
* * * * *
69641 ACTCACGATGACTCAAAGTCATTCGGACCTTA-AATCCGTAAAAGGATCCATAT
1 ACTCATGATGACACATAGTCA-TCGAACCTTATAATCCGT-AAAGGATTCATAT
* *
69694 GCTCATGATGAAACATAGTCATCGAACCTTATAATCCGTAAAGGATTCATAT
1 ACTCATGATGACACATAGTCATCGAACCTTATAATCCGTAAAGGATTCATAT
* * * *
69746 ACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCGTTT
1 ACTCATGATGACACATAGTCATCGAACCTTATAATCCGTAAAGGATTCATAT
* *
69798 ACTCACGATGACACATAGTTATCGAACCTT
1 ACTCATGATGACACATAGTCATCGAACCTT
69828 TTTGCATTTA
Statistics
Matches: 116, Mismatches: 17, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
52 93 0.80
53 23 0.20
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (52 bp):
ACTCATGATGACACATAGTCATCGAACCTTATAATCCGTAAAGGATTCATAT
Found at i:73979 original size:35 final size:36
Alignment explanation
Indices: 73939--74006 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
73929 AAAAATTATA
73939 TTTAATACAATAAAA-AATTATTATATTTATGTGTT
1 TTTAATACAATAAAACAATTATTATATTTATGTGTT
* *
73974 TTTAATATAATAAAACATTTATTATATTTATGT
1 TTTAATACAATAAAACAATTATTATATTTATGT
74007 TAGGGGGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 14 0.47
36 16 0.53
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (36 bp):
TTTAATACAATAAAACAATTATTATATTTATGTGTT
Found at i:75843 original size:15 final size:17
Alignment explanation
Indices: 75824--75864 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
75814 TAAATCTTTA
75824 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
75840 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
75856 AAAATTATA
1 AAAATTATA
75865 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:82632 original size:23 final size:23
Alignment explanation
Indices: 82598--82642 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
82588 CCAAACCTAC
82598 ATTCCTCATGACTTATGCCAAAG
1 ATTCCTCATGACTTATGCCAAAG
*
82621 ATTCCTCGTGACTTATGCCAAA
1 ATTCCTCATGACTTATGCCAAA
82643 CTTTCTTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (23 bp):
ATTCCTCATGACTTATGCCAAAG
Found at i:83309 original size:40 final size:40
Alignment explanation
Indices: 83222--83417 Score: 212
Period size: 40 Copynumber: 4.9 Consensus size: 40
83212 ATAGCATCGA
* * * ** * *
83222 CACGAAACCTACTAGGCTCAAAGCCTAATAGTATATACCGG
1 CACGAAGCCTGCTAGGCACAAAGCCCGATA-AATACACCGG
* * *
83263 CACGAAGCCTACTAGGCACAAATCTCGATAAATACACCGG
1 CACGAAGCCTGCTAGGCACAAAGCCCGATAAATACACCGG
* * * *
83303 CACGAAGCTTGCTGGGCACTAAGCCCAATAAATACACCGG
1 CACGAAGCCTGCTAGGCACAAAGCCCGATAAATACACCGG
* *
83343 CACGAAGTCTGCTAGGCACTAAGCCCGATAAATACACCGG
1 CACGAAGCCTGCTAGGCACAAAGCCCGATAAATACACCGG
* * *
83383 CACGAAGCTTGCTAGGCACTAAGTCCGATAAATAC
1 CACGAAGCCTGCTAGGCACAAAGCCCGATAAATAC
83418 CGGGGAATTT
Statistics
Matches: 133, Mismatches: 22, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 109 0.82
41 24 0.18
ACGTcount: A:0.35, C:0.29, G:0.20, T:0.17
Consensus pattern (40 bp):
CACGAAGCCTGCTAGGCACAAAGCCCGATAAATACACCGG
Found at i:83358 original size:80 final size:80
Alignment explanation
Indices: 83258--83417 Score: 248
Period size: 80 Copynumber: 2.0 Consensus size: 80
83248 AATAGTATAT
* * *
83258 ACCGGCACGAAGCCTACTAGGCACAAATCTCGATAAATACACCGGCACGAAGCTTGCTGGGCACT
1 ACCGGCACGAAGCCTACTAGGCACAAAGCCCGATAAATACACCGGCACGAAGCTTGCTAGGCACT
83323 AAGCCCAATAAATAC
66 AAGCCCAATAAATAC
* * *
83338 ACCGGCACGAAGTCTGCTAGGCACTAAGCCCGATAAATACACCGGCACGAAGCTTGCTAGGCACT
1 ACCGGCACGAAGCCTACTAGGCACAAAGCCCGATAAATACACCGGCACGAAGCTTGCTAGGCACT
* *
83403 AAGTCCGATAAATAC
66 AAGCCCAATAAATAC
83418 CGGGGAATTT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 72 1.00
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (80 bp):
ACCGGCACGAAGCCTACTAGGCACAAAGCCCGATAAATACACCGGCACGAAGCTTGCTAGGCACT
AAGCCCAATAAATAC
Found at i:89647 original size:13 final size:13
Alignment explanation
Indices: 89640--89693 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
89630 CCACCTAGGA
89640 ATCTCACCTCACG
1 ATCTCACCTCACG
*
89653 ATCTCACCTCGC-
1 ATCTCACCTCACG
* *
89665 AACACCACCTCACG
1 ATC-TCACCTCACG
*
89679 ATCTCACCTCGCG
1 ATCTCACCTCACG
89692 AT
1 AT
89694 ACCACTTAGT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
12 2 0.06
13 28 0.88
14 2 0.06
ACGTcount: A:0.24, C:0.46, G:0.09, T:0.20
Consensus pattern (13 bp):
ATCTCACCTCACG
Found at i:90394 original size:26 final size:26
Alignment explanation
Indices: 90342--90394 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
90332 TTGAAAGTAC
* * *
90342 TTTTTAAAAACACTTTTTCACATCAA
1 TTTTTAAAAACACTATTTCAAAGCAA
90368 TTTTTAAAAACAC-ATTTCAAAAGCAA
1 TTTTTAAAAACACTATTTC-AAAGCAA
90394 T
1 T
90395 GCTAAGCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.43, C:0.17, G:0.02, T:0.38
Consensus pattern (26 bp):
TTTTTAAAAACACTATTTCAAAGCAA
Found at i:95227 original size:11 final size:11
Alignment explanation
Indices: 95213--95283 Score: 52
Period size: 11 Copynumber: 6.2 Consensus size: 11
95203 ATATTCAAAC
95213 AATAATAACAA
1 AATAATAACAA
* *
95224 AATAGTAGCAA
1 AATAATAACAA
* *
95235 TATAACAACAA
1 AATAATAACAA
*
95246 AATAACAACAA
1 AATAATAACAA
* *
95257 AATGATAGGAAAA
1 AATAATA--ACAA
95270 CAATAATAACAA
1 -AATAATAACAA
95282 AA
1 AA
95284 AAAAACTAGG
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
11 33 0.73
12 3 0.07
13 3 0.07
14 6 0.13
ACGTcount: A:0.66, C:0.11, G:0.07, T:0.15
Consensus pattern (11 bp):
AATAATAACAA
Found at i:95293 original size:28 final size:27
Alignment explanation
Indices: 95241--95293 Score: 63
Period size: 28 Copynumber: 1.9 Consensus size: 27
95231 GCAATATAAC
**
95241 AACAAAATAACAACAAAATGATAGGAA
1 AACAAAATAACAACAAAAAAATAGGAA
95268 AACAATAATAACAA-AAAAAAACTAGG
1 AACAA-AATAACAACAAAAAAA-TAGG
95294 CAAATTCCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.68, C:0.11, G:0.09, T:0.11
Consensus pattern (27 bp):
AACAAAATAACAACAAAAAAATAGGAA
Found at i:95841 original size:22 final size:22
Alignment explanation
Indices: 95816--95859 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
95806 TAAATATTTT
*
95816 TTTAAAAATATATAATAATAAA
1 TTTAAAAATATATAAAAATAAA
95838 TTTAAAAATATATAAAAATAAA
1 TTTAAAAATATATAAAAATAAA
95860 AAATTATTGT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
TTTAAAAATATATAAAAATAAA
Found at i:96242 original size:1 final size:1
Alignment explanation
Indices: 96236--96269 Score: 50
Period size: 1 Copynumber: 34.0 Consensus size: 1
96226 AACCATGCTC
* *
96236 TTTTTTTTTCTTTTTTTTTTTTTTTTTTTNTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
96270 GTATTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:105122 original size:15 final size:16
Alignment explanation
Indices: 105096--105125 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
105086 TCATATTTGG
105096 AAAATATATTTATTTA
1 AAAATATATTTATTTA
105112 AAAATAT-TTTATTT
1 AAAATATATTTATTT
105126 TATAAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATATATTTATTTA
Found at i:105127 original size:16 final size:17
Alignment explanation
Indices: 105096--105132 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
105086 TCATATTTGG
105096 AAAATATATTTATTTA-
1 AAAATATATTTATTTAT
105112 AAAATAT-TTTATTTTAT
1 AAAATATATTTA-TTTAT
105129 AAAA
1 AAAA
105133 CATAACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.21
16 11 0.58
17 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAAATATATTTATTTAT
Found at i:105745 original size:12 final size:13
Alignment explanation
Indices: 105715--105743 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
105705 ACAAGAGAGG
105715 AAAAAT-AAAAAT
1 AAAAATAAAAAAT
105727 AAAAATAAAAAAT
1 AAAAATAAAAAAT
105740 AAAA
1 AAAA
105744 TACGATGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:109253 original size:15 final size:15
Alignment explanation
Indices: 109216--109256 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
109206 TTTTCTTTGA
109216 TTTCACAATTTGAAGC
1 TTTCACAATTT-AAGC
109232 --T-ACAATTTAAGC
1 TTTCACAATTTAAGC
109244 TTTCACAATTTAA
1 TTTCACAATTTAA
109257 AGCCACAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.18
13 7 0.32
14 2 0.09
15 9 0.41
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (15 bp):
TTTCACAATTTAAGC
Found at i:112263 original size:9 final size:9
Alignment explanation
Indices: 112249--112275 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
112239 AAAATAAATT
112249 AAAAAACTA
1 AAAAAACTA
112258 AAAAAACTA
1 AAAAAACTA
112267 AAAAAACTA
1 AAAAAACTA
112276 GAGAACGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.78, C:0.11, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAACTA
Found at i:124911 original size:29 final size:28
Alignment explanation
Indices: 124845--124911 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
124835 TATTAATTAT
* *
124845 ATTTTAA--TGTGTAATTATATATATGA
1 ATTTTAATTTGTGTAATTATATACATAA
* *
124871 ATTTTGATTTTGTGTAATTTTATACATAAA
1 ATTTT-AATTTGTGTAATTATATACAT-AA
124901 ATTTTAATTTG
1 ATTTTAATTTG
124912 ATCCAATTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
26 5 0.16
27 1 0.03
29 20 0.62
30 6 0.19
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (28 bp):
ATTTTAATTTGTGTAATTATATACATAA
Found at i:125141 original size:29 final size:30
Alignment explanation
Indices: 125089--125167 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
125079 TTTGAACCAC
* * *
125089 AATTAGAGTTTCATGTGTATAATT-ACATCA
1 AATTAAAG-TTCATGTATACAATTCACATCA
*
125119 AATTAAAGTTCATGTATACAATTGCACATTA
1 AATTAAAGTTCATGTATACAATT-CACATCA
* *
125150 AATCAAAATTCATGTATA
1 AATTAAAGTTCATGTATA
125168 ATTTTGAGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.32
30 7 0.17
31 21 0.51
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (30 bp):
AATTAAAGTTCATGTATACAATTCACATCA
Found at i:127767 original size:100 final size:100
Alignment explanation
Indices: 127602--127796 Score: 309
Period size: 100 Copynumber: 1.9 Consensus size: 100
127592 CATGAGTTGA
* * * *
127602 GTTACCCGTCTAGGCTTGAAGGCTCTTTCGAAATTTGAAAAGAATTGGGAAAAAATATTAGGCCC
1 GTTACCCATCCAGGCCTGAAGACTCTTTCGAAATTTGAAAAGAATTGGGAAAAAATATTAGGCCC
127667 GTTAAAAATATTGATCGAGCTTGGGCTTGAGTCAG
66 GTTAAAAATATTGATCGAGCTTGGGCTTGAGTCAG
* * * *
127702 GTTACCCATCCAGGCCTGAAGACTCTTTCGAAATTTGGAAGGATTTGGGCAAAAATATTAGGCCC
1 GTTACCCATCCAGGCCTGAAGACTCTTTCGAAATTTGAAAAGAATTGGGAAAAAATATTAGGCCC
*
127767 GTTAAAAATATTGATCGGGCTTGGGCTTGA
66 GTTAAAAATATTGATCGAGCTTGGGCTTGA
127797 AAATTCAAGG
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 86 1.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (100 bp):
GTTACCCATCCAGGCCTGAAGACTCTTTCGAAATTTGAAAAGAATTGGGAAAAAATATTAGGCCC
GTTAAAAATATTGATCGAGCTTGGGCTTGAGTCAG
Found at i:134159 original size:19 final size:18
Alignment explanation
Indices: 134090--134165 Score: 57
Period size: 20 Copynumber: 4.0 Consensus size: 18
134080 TATCATTCCA
134090 AAATATAATTAAAATATATT
1 AAATATAATTAAAA-AT-TT
*
134110 -AAT-TTATTAAAAATTT
1 AAATATAATTAAAAATTT
* *
134126 AAATATAACGATAAAATTTT
1 AAATATAA--TTAAAAATTT
134146 AAATCATAATTAAAACATTT
1 AAAT-ATAATTAAAA-ATTT
134166 TTATTATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
16 2 0.05
17 5 0.11
18 10 0.23
19 8 0.18
20 15 0.34
21 4 0.09
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (18 bp):
AAATATAATTAAAAATTT
Found at i:134931 original size:39 final size:40
Alignment explanation
Indices: 134888--134972 Score: 93
Period size: 40 Copynumber: 2.1 Consensus size: 40
134878 CTTTGCTATT
*
134888 TTGTGGCTGATA-ATTTC-AAAGAGTTGAATCTCCATCATA
1 TTGTGGCTGATATATTTCAAAAGA-TTAAATCTCCATCATA
** * * *
134927 TTGTGATTTATATTTTTTAAAAGATTAAATCTCCATCATA
1 TTGTGGCTGATATATTTCAAAAGATTAAATCTCCATCATA
134967 TTGTGG
1 TTGTGG
134973 TTACGGAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
39 9 0.24
40 23 0.62
41 5 0.14
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (40 bp):
TTGTGGCTGATATATTTCAAAAGATTAAATCTCCATCATA
Found at i:137393 original size:30 final size:30
Alignment explanation
Indices: 137346--137411 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
137336 AATTTGTAAA
*
137346 AATAAAATTTTACTTTAACCCTTTAAAAAT
1 AATAAAATTTTACTTTAAACCTTTAAAAAT
**
137376 AATAAAATTTTGA-TTTAAATTTTTAAAAAT
1 AATAAAATTTT-ACTTTAAACCTTTAAAAAT
*
137406 TATAAA
1 AATAAA
137412 GATATACACT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 30 0.97
31 1 0.03
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (30 bp):
AATAAAATTTTACTTTAAACCTTTAAAAAT
Found at i:142602 original size:2 final size:2
Alignment explanation
Indices: 142595--142629 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
142585 AGATTTATTA
142595 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
142630 AACTCTCGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:144801 original size:29 final size:29
Alignment explanation
Indices: 144648--144818 Score: 139
Period size: 30 Copynumber: 5.7 Consensus size: 29
144638 TTGCCTCAGA
*
144648 AACCCCCAAACTTTCCAAAAATTTAGATTT
1 AACCCTCAAAC-TTCCAAAAATTTAGATTT
* * * *
144678 GACACTCAAAATTTTCAAAAATTTAGATTT
1 AACCCTC-AAACTTCCAAAAATTTAGATTT
* * *
144708 GA-CCTCAGAACTTCCAAAAAATTAAAATTT
1 AACCCTCA-AACTTCC-AAAAATTTAGATTT
** *
144738 AACCCTTGAACTTCCCAAAAATTTGGATTT
1 AACCCTCAAACTT-CCAAAAATTTAGATTT
* *
144768 GACCCTCAAACTTCCAAAAATTTGGATTT
1 AACCCTCAAACTTCCAAAAATTTAGATTT
*
144797 AACCC-CTAAACTTTCCCAAAAT
1 AACCCTC-AAAC-TTCCAAAAAT
144819 CACATTTAGA
Statistics
Matches: 113, Mismatches: 21, Indels: 14
0.76 0.14 0.09
Matches are distributed among these distances:
28 2 0.02
29 32 0.28
30 71 0.63
31 8 0.07
ACGTcount: A:0.40, C:0.23, G:0.06, T:0.30
Consensus pattern (29 bp):
AACCCTCAAACTTCCAAAAATTTAGATTT
Found at i:144813 original size:60 final size:60
Alignment explanation
Indices: 144649--144817 Score: 175
Period size: 60 Copynumber: 2.8 Consensus size: 60
144639 TGCCTCAGAA
* * * * *
144649 ACCCCCAAACTTTCCAAAAATTTAGATTTGA-CACTCAAAATTT-TCAAAAATTTAGATTTG
1 ACCCTCAAAC-TTCCAAAAATTTAGATTTAACCCCT-AAACTTTCCCAAAAATTTAGATTTG
* * * * *
144709 A-CCTCAGAACTTCCAAAAAATTAAAATTTAACCCTTGAAC-TTCCCAAAAATTTGGATTTG
1 ACCCTCA-AACTTCC-AAAAATTTAGATTTAACCCCTAAACTTTCCCAAAAATTTAGATTTG
*
144769 ACCCTCAAACTTCCAAAAATTTGGATTTAACCCCTAAACTTTCCCAAAA
1 ACCCTCAAACTTCCAAAAATTTAGATTTAACCCCTAAACTTTCCCAAAA
144818 TCACATTTAG
Statistics
Matches: 88, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
59 30 0.34
60 51 0.58
61 7 0.08
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.30
Consensus pattern (60 bp):
ACCCTCAAACTTCCAAAAATTTAGATTTAACCCCTAAACTTTCCCAAAAATTTAGATTTG
Found at i:144825 original size:29 final size:30
Alignment explanation
Indices: 144794--145008 Score: 198
Period size: 29 Copynumber: 7.4 Consensus size: 30
144784 AAAATTTGGA
*
144794 TTTAACCCCTAAACTTTCCCAAAATCACA-
1 TTTAACCCCTAAACTTTCCCAAAATTACAT
* * *
144823 TTTAGACCCTTAAACTTTACCAAAATCACAT
1 TTTA-ACCCCTAAACTTTCCCAAAATTACAT
* * *
144854 TTTAA-CCC--AATTTTCCCAAAATAAAAT
1 TTTAACCCCTAAACTTTCCCAAAATTACAT
* * **
144881 TTTGACCCTTAAACTTTCTAAAAATTACAT
1 TTTAACCCCTAAACTTTCCCAAAATTACAT
* *
144911 TTTGA-CCCTAAACTTTCCTAAAATTACAT
1 TTTAACCCCTAAACTTTCCCAAAATTACAT
*
144940 TTTAA-CCCTAAACTTT-TCAAAATTACA-
1 TTTAACCCCTAAACTTTCCCAAAATTACAT
* *
144967 TTTAACCCCTAAATCTAT-ACAAAATTACAT
1 TTTAACCCCTAAA-CTTTCCCAAAATTACAT
144997 TTTAA-CCCTAAA
1 TTTAACCCCTAAA
145009 TTCTCTGAAA
Statistics
Matches: 156, Mismatches: 22, Indels: 16
0.80 0.11 0.08
Matches are distributed among these distances:
27 24 0.15
28 18 0.12
29 62 0.40
30 48 0.31
31 4 0.03
ACGTcount: A:0.40, C:0.25, G:0.01, T:0.34
Consensus pattern (30 bp):
TTTAACCCCTAAACTTTCCCAAAATTACAT
Found at i:144888 original size:57 final size:57
Alignment explanation
Indices: 144794--144974 Score: 197
Period size: 57 Copynumber: 3.1 Consensus size: 57
144784 AAAATTTGGA
* * *
144794 TTTAACCCCTAAACTTTCCCAAAATCACATTTAGACCCTTAAACTTTACCAAAATCACAT
1 TTTAA-CCC-AAACTTTCCCAAAATAACATTTTGACCCTTAAACTTT-CCAAAATTACAT
* * *
144854 TTTAACCC-AATTTTCCCAAAATAAAATTTTGACCCTTAAACTTTCTAAAAATTACAT
1 TTTAACCCAAACTTTCCCAAAATAACATTTTGACCCTTAAACTTTC-CAAAATTACAT
* * * * *
144911 TTTGACCCTAAACTTTCCTAAAATTACATTTTAACCC-TAAACTTTTCAAAATTACA-
1 TTTAACCC-AAACTTTCCCAAAATAACATTTTGACCCTTAAACTTTCCAAAATTACAT
144967 TTTAACCC
1 TTTAACCC
144975 CTAAATCTAT
Statistics
Matches: 103, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
56 8 0.08
57 57 0.55
58 8 0.08
59 25 0.24
60 5 0.05
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (57 bp):
TTTAACCCAAACTTTCCCAAAATAACATTTTGACCCTTAAACTTTCCAAAATTACAT
Found at i:144991 original size:57 final size:57
Alignment explanation
Indices: 144870--145008 Score: 165
Period size: 57 Copynumber: 2.4 Consensus size: 57
144860 CCAATTTTCC
* * * * * *
144870 CAAAATAAAATTTTGACCCTTAAACTTTCTAAAAATTACATTTTGACCCTAAACTTTC
1 CAAAATTACATTTTAACCC-TAAACTTTCTAAAAATTACATTTTAACCCTAAACTATA
*
144928 CTAAAATTACATTTTAACCCTAAACTTT-TCAAAATTACA-TTTAACCCCTAAATCTATA
1 C-AAAATTACATTTTAACCCTAAACTTTCTAAAAATTACATTTTAA-CCCTAAA-CTATA
144986 CAAAATTACATTTTAACCCTAAA
1 CAAAATTACATTTTAACCCTAAA
145009 TTCTCTGAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
56 4 0.06
57 39 0.55
58 13 0.18
59 15 0.21
ACGTcount: A:0.42, C:0.22, G:0.01, T:0.35
Consensus pattern (57 bp):
CAAAATTACATTTTAACCCTAAACTTTCTAAAAATTACATTTTAACCCTAAACTATA
Found at i:146281 original size:16 final size:16
Alignment explanation
Indices: 146262--146321 Score: 65
Period size: 14 Copynumber: 4.0 Consensus size: 16
146252 CACAAAGCAC
*
146262 GAATAATTATACGAAT
1 GAATAAATATACGAAT
146278 GAATAAATATACGAA-
1 GAATAAATATACGAAT
*
146293 -AATAAATATAAGAA-
1 GAATAAATATACGAAT
*
146307 AAATAAA-ATACGAAT
1 GAATAAATATACGAAT
146322 CATGAATCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
14 19 0.49
15 6 0.15
16 14 0.36
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.23
Consensus pattern (16 bp):
GAATAAATATACGAAT
Found at i:146531 original size:29 final size:29
Alignment explanation
Indices: 146498--147101 Score: 461
Period size: 29 Copynumber: 20.9 Consensus size: 29
146488 AATTTTGGGA
* *
146498 AAGTTCGGGATAAAAATGTGATTTTTGAG
1 AAGTTCGGGGTAAAAATGTAATTTTTGAG
*
146527 AAGTTCGAGGTAAAAATGTAATTTTTGA-
1 AAGTTCGGGGTAAAAATGTAATTTTTGAG
* * *
146555 AAGTTCGGGGGT-AAAATATAATATTTAAG
1 AAGTTC-GGGGTAAAAATGTAATTTTTGAG
* *
146584 AAGTTTGAGGGTAAAAATGTGATTTTTG-G
1 AAGTTCG-GGGTAAAAATGTAATTTTTGAG
* * *
146613 AAGTT-TGGGCAAAAATATAATTTTTG-G
1 AAGTTCGGGGTAAAAATGTAATTTTTGAG
* * *
146640 AAGTTTGAGGG-AAAAATATAATTTTTAAG
1 AAGTTCG-GGGTAAAAATGTAATTTTTGAG
*
146669 AAGTTCGAGGGTAAAAATGTGATTTTTG-G
1 AAGTTCG-GGGTAAAAATGTAATTTTTGAG
146698 AAGTTCGAGGGTAAAAATGTAATTTTTGAG
1 AAGTTCG-GGGTAAAAATGTAATTTTTGAG
* *
146728 AAATTTGGGGTAAAAAATG--ATTTTTG-G
1 AAGTTCGGGGT-AAAAATGTAATTTTTGAG
* *
146755 AAGTTCGGGG-GAAATTGTAATTTTTG-G
1 AAGTTCGGGGTAAAAATGTAATTTTTGAG
* * *
146782 AAGTTCGAGGGCAAAAATTTAAGTTTTGA-
1 AAGTTCG-GGGTAAAAATGTAATTTTTGAG
146811 AAGTTCGGGGTAAAAATGTAATTTTTGAG
1 AAGTTCGGGGTAAAAATGTAATTTTTGAG
* * * *
146840 AAGTTTAGGAGT-AAAATGTGATATTTG-G
1 AAG-TTCGGGGTAAAAATGTAATTTTTGAG
* *
146868 AAGTTCGGGGGCAAAAATGTAAGTTTTGA-
1 AAGTTC-GGGGTAAAAATGTAATTTTTGAG
* * *
146897 AAGTTCGATGGCAAAGATGTAATTTTTGAG
1 AAGTTCG-GGGTAAAAATGTAATTTTTGAG
* **
146927 AAGTTCGGGAGCAAAAATGTAATTTTT-TT
1 AAGTTCGGG-GTAAAAATGTAATTTTTGAG
*
146956 AAGTTCGGGGTAAAAATGTGATTTTTGAG
1 AAGTTCGGGGTAAAAATGTAATTTTTGAG
* * * *
146985 AAGTTTAGGGGTCAAAATATAATTTTAGA-
1 AAG-TTCGGGGTAAAAATGTAATTTTTGAG
* * * * *
147014 AAGGTTTGAGGGTTTAAAATGAAATTTTGGAA
1 AA-GTTCG-GGG-TAAAAATGTAATTTTTGAG
*** * * *
147046 AAGTTTAAAGATTAAAATGTAATTTTTGAA
1 AAG-TTCGGGGTAAAAATGTAATTTTTGAG
* *
147076 AAGTTTGGGGGTTAAAATGTAATTTT
1 AAG-TTCGGGGTAAAAATGTAATTTT
147102 GGAAAGATTT
Statistics
Matches: 468, Mismatches: 77, Indels: 59
0.77 0.13 0.10
Matches are distributed among these distances:
25 5 0.01
27 49 0.10
28 86 0.18
29 179 0.38
30 129 0.28
31 16 0.03
32 4 0.01
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (29 bp):
AAGTTCGGGGTAAAAATGTAATTTTTGAG
Found at i:147050 original size:61 final size:59
Alignment explanation
Indices: 146962--147134 Score: 154
Period size: 61 Copynumber: 2.9 Consensus size: 59
146952 TTTTAAGTTC
* ** * * *
146962 GGGGTAAAAATGTGATTTTTGAGAAGTTTAGGGGTCAAAATATAATTTTAGAAAGGTTTG
1 GGGGTTAAAATGAAATTTTGGAAAAGTTTA-GGGTCAAAATATAATTTTAGAAAAGTTTG
* * * * * *
147022 AGGGTTTAAAATGAAATTTTGGAAAAGTTTAAAGATTAAAATGTAATTTTTGAAAAGTTTG
1 -GGGGTTAAAATGAAATTTTGGAAAAGTTT-AGGGTCAAAATATAATTTTAGAAAAGTTTG
* * *
147083 GGGGTTAAAATGTAATTTTGG-AAAGATTT-GGGTCAAAATGTGATTTT-GAAAA
1 GGGGTTAAAATGAAATTTTGGAAAAG-TTTAGGGTCAAAATATAATTTTAGAAAA
147135 AATTTGAGCG
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
57 5 0.05
58 14 0.15
59 4 0.04
60 22 0.24
61 46 0.50
62 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.36
Consensus pattern (59 bp):
GGGGTTAAAATGAAATTTTGGAAAAGTTTAGGGTCAAAATATAATTTTAGAAAAGTTTG
Found at i:147113 original size:30 final size:30
Alignment explanation
Indices: 146962--147140 Score: 116
Period size: 30 Copynumber: 6.0 Consensus size: 30
146952 TTTTAAGTTC
* * * *
146962 GGGGTAAAAATGTGATTTTTGAGAAG-TTTA
1 GGGGTTAAAATGTAATTTTGGA-AAGATTTG
* * * *
146992 GGGGTCAAAATATAATTTTAGAAAGGTTTG
1 GGGGTTAAAATGTAATTTTGGAAAGATTTG
* * *
147022 AGGGTTTAAAATGAAATTTTGGAAA-AGTTTA
1 -GGGGTTAAAATGTAATTTTGGAAAGA-TTTG
** * *
147053 AAGATTAAAATGTAATTTTTGAAA-AGTTTG
1 GGGGTTAAAATGTAATTTTGGAAAGA-TTTG
147083 GGGGTTAAAATGTAATTTTGGAAAGATTT-
1 GGGGTTAAAATGTAATTTTGGAAAGATTTG
* * * *
147112 -GGGTCAAAATGTGATTTTGAAAAAATTTG
1 GGGGTTAAAATGTAATTTTGGAAAGATTTG
147141 AGCGAAAAAT
Statistics
Matches: 118, Mismatches: 26, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
28 24 0.20
29 3 0.03
30 68 0.58
31 23 0.19
ACGTcount: A:0.38, C:0.01, G:0.25, T:0.36
Consensus pattern (30 bp):
GGGGTTAAAATGTAATTTTGGAAAGATTTG
Found at i:147139 original size:28 final size:28
Alignment explanation
Indices: 147084--147158 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
147074 AAAAGTTTGG
* * * *
147084 GGGTTAAAATGTAATTTTGGAAAGATTT
1 GGGTAAAAATGTGATTTTGAAAAAATTT
*
147112 GGGTCAAAATGTGATTTTGAAAAAATTT
1 GGGTAAAAATGTGATTTTGAAAAAATTT
147140 GAGCG-AAAAATGTGATTTT
1 G-G-GTAAAAATGTGATTTT
147159 AAATAAAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 25 0.62
29 14 0.35
30 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (28 bp):
GGGTAAAAATGTGATTTTGAAAAAATTT
Found at i:153108 original size:2 final size:2
Alignment explanation
Indices: 153092--153131 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
153082 ATCAAATTTA
*
153092 AT AT AT A- AT AT -T AT AT AT AT AT AT AT AT AT AT TT 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
153132 TTTGTATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:159038 original size:21 final size:21
Alignment explanation
Indices: 159014--159061 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
159004 TCCATATTAG
159014 ATATTAACATAACATAA-AAAA
1 ATATTAACATAACA-AATAAAA
* * *
159035 ATATAAACCTAACAAATTAAA
1 ATATTAACATAACAAATAAAA
159056 ATATTA
1 ATATTA
159062 CATGCATTTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.27
Consensus pattern (21 bp):
ATATTAACATAACAAATAAAA
Found at i:159896 original size:33 final size:34
Alignment explanation
Indices: 159800--159898 Score: 128
Period size: 34 Copynumber: 2.9 Consensus size: 34
159790 AACTCATTTT
* * *
159800 GTAAGTTTTCAAGCTCAAGAAATCAATATGTATC
1 GTAAGTTTTCAAACTCAAGAAATTAGTATGTATC
*
159834 GTAAGTTTTCAAACTCAAGAAATTAGTATGTATT
1 GTAAGTTTTCAAACTCAAGAAATTAGTATGTATC
* * *
159868 TTAAGTTTTCAAATTGAAG-AATTAGTATGTA
1 GTAAGTTTTCAAACTCAAGAAATTAGTATGTA
159899 AAAATGACAT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 12 0.21
34 46 0.79
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (34 bp):
GTAAGTTTTCAAACTCAAGAAATTAGTATGTATC
Found at i:163360 original size:16 final size:16
Alignment explanation
Indices: 163339--163370 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
163329 CTATCCACCC
163339 AAACCCAATCCAATAT
1 AAACCCAATCCAATAT
163355 AAACCCAATCCAATAT
1 AAACCCAATCCAATAT
163371 GTATAAACTC
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:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (16 bp):
AAACCCAATCCAATAT
Found at i:172354 original size:42 final size:42
Alignment explanation
Indices: 172308--172421 Score: 120
Period size: 42 Copynumber: 2.7 Consensus size: 42
172298 GACTAAACTG
* **
172308 AAGCAAATATATTGGCACGTAAGTGCATCACCGGATGAAACA
1 AAGCAAATATACTGGCACGTAAGTGCATCACCAAATGAAACA
* * * * * *
172350 AAGCAAATATACTGACGCATAAGTACATCATCAAATGAACCA
1 AAGCAAATATACTGGCACGTAAGTGCATCACCAAATGAAACA
* * *
172392 AAGCAAATAGACTAGCATGTAAGTGCATCA
1 AAGCAAATATACTGGCACGTAAGTGCATCA
172422 TCAGCTAAAC
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.44, C:0.19, G:0.18, T:0.19
Consensus pattern (42 bp):
AAGCAAATATACTGGCACGTAAGTGCATCACCAAATGAAACA
Found at i:172433 original size:42 final size:41
Alignment explanation
Indices: 172308--172436 Score: 118
Period size: 42 Copynumber: 3.1 Consensus size: 41
172298 GACTAAACTG
* * * *
172308 AAGCAAATATATTGGCACGTAAGTGCATCACCGGATGAAA-CA
1 AAGCAAATATACTAGCA-GTAAGTGCATCATCAGAT-AAACCA
* * *
172350 AAGCAAATATACTGACGCA-TAAGTACATCATCAAATGAACCA
1 AAGCAAATATACT-A-GCAGTAAGTGCATCATCAGATAAACCA
* *
172392 AAGCAAATAGACTAGCATGTAAGTGCATCATCAGCTAAACCA
1 AAGCAAATATACTAGCA-GTAAGTGCATCATCAGATAAACCA
172434 AAG
1 AAG
172437 TATAGACTCG
Statistics
Matches: 70, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
40 3 0.04
41 3 0.04
42 61 0.87
44 3 0.04
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.19
Consensus pattern (41 bp):
AAGCAAATATACTAGCAGTAAGTGCATCATCAGATAAACCA
Found at i:172480 original size:7 final size:7
Alignment explanation
Indices: 172468--172496 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
172458 GGGTATTTGA
172468 CCAATTT
1 CCAATTT
172475 CCAATTT
1 CCAATTT
172482 CCAATTT
1 CCAATTT
172489 CCAATTT
1 CCAATTT
172496 C
1 C
172497 ATTACATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (7 bp):
CCAATTT
Found at i:172616 original size:88 final size:89
Alignment explanation
Indices: 172490--172692 Score: 255
Period size: 88 Copynumber: 2.3 Consensus size: 89
172480 TTCCAATTTC
* * * **
172490 CAATTTCATTACATATTTCAATTCACATTCCATCATTCTCAGTTAATTGTTAATTCACCATTCCA
1 CAATTTCA-TACATATTTCAATACACATTCAATCATTCTCAATTAATCATTAATTCACCATTCCA
* *
172555 ATACACCATATTATATGTTTTAACT
65 ATACACCATATAACATGTTTTAACT
* * * * *
172580 CAATTTCATA-ATATTTCAATACGCATTTAATTATTCTCAATTCATCATTAATTCACCATTTCAA
1 CAATTTCATACATATTTCAATACACATTCAATCATTCTCAATTAATCATTAATTCACCATTCCAA
*
172644 TACACCATGTAACATGTTTTAACT
66 TACACCATATAACATGTTTTAACT
* *
172668 CAATTTCATACATATTCCAACACAC
1 CAATTTCATACATATTTCAATACAC
172693 CATATAACAT
Statistics
Matches: 96, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
88 75 0.78
89 13 0.14
90 8 0.08
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (89 bp):
CAATTTCATACATATTTCAATACACATTCAATCATTCTCAATTAATCATTAATTCACCATTCCAA
TACACCATATAACATGTTTTAACT
Found at i:177067 original size:33 final size:33
Alignment explanation
Indices: 177030--177106 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 33
177020 TTAGTCAAAC
* * * *
177030 TTGTTTATTTTATTAATTTTGTTTTGATTAAAT
1 TTGTTTATTTTACTAATTTTATTTTGACTAAAA
*
177063 TTG-TTATTTTCCTAATTTTATTTTGACTAAAA
1 TTGTTTATTTTACTAATTTTATTTTGACTAAAA
*
177095 TTATTTATTTTA
1 TTGTTTATTTTA
177107 AGTAAATAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 26 0.72
33 10 0.28
ACGTcount: A:0.26, C:0.04, G:0.06, T:0.64
Consensus pattern (33 bp):
TTGTTTATTTTACTAATTTTATTTTGACTAAAA
Found at i:180448 original size:9 final size:9
Alignment explanation
Indices: 180422--180459 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
180412 TGAATTTCAC
180422 AATTCGAAT
1 AATTCGAAT
180431 AACTT-GAAT
1 AA-TTCGAAT
*
180440 AGTTCGAAT
1 AATTCGAAT
180449 AATTCGAAT
1 AATTCGAAT
180458 AA
1 AA
180460 AAGATTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 2 0.08
9 21 0.84
10 2 0.08
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:180543 original size:13 final size:13
Alignment explanation
Indices: 180525--180549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
180515 GTCTCTCATA
180525 CAAAAAAAAATTG
1 CAAAAAAAAATTG
180538 CAAAAAAAAATT
1 CAAAAAAAAATT
180550 AAGATTCAAA
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:0.72, C:0.08, G:0.04, T:0.16
Consensus pattern (13 bp):
CAAAAAAAAATTG
Found at i:183551 original size:29 final size:27
Alignment explanation
Indices: 183498--183551 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
183488 GAAGAAAATG
*
183498 ATTTTTTCTTTTTATAATTATTTTTTT
1 ATTTTTTCTTTTTATAATTAATTTTTT
*
183525 ATTTTCTTCTTCTTTTTAATTAATTTT
1 ATTTT-TTCTT-TTTATAATTAATTTT
183552 GTTTTCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 5 0.22
29 13 0.57
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (27 bp):
ATTTTTTCTTTTTATAATTAATTTTTT
Found at i:195352 original size:39 final size:38
Alignment explanation
Indices: 195299--196325 Score: 285
Period size: 39 Copynumber: 26.3 Consensus size: 38
195289 CAGTTGGCCA
* *
195299 ATCTCTTACCCCGATCATGAGGCAGATTACAATCATCTG
1 ATCTTTTACCCCGATCATG-GGCAGATTACAATCATCCG
* * * *
195338 ATCTTTTACTCCGATCATGGGGTAGATCACAATCAAT-CA
1 ATCTTTTACCCCGATCAT-GGGCAGATTACAATC-ATCCG
** * * *
195377 ATCACTTACCCCGATCATGGGATAGATTGCAACCATCCG
1 ATCTTTTACCCCGATCATGGG-CAGATTACAATCATCCG
* * * ** * *
195416 ATCTTTTACCCCAATCATGGGACAAATCACCGTCAGCCA
1 ATCTTTTACCCCGATCATGGG-CAGATTACAATCATCCG
* *
195455 ATCTTTTACCCTGATCATGGGGCAGATTACAACCATCCG
1 ATCTTTTACCCCGATCAT-GGGCAGATTACAATCATCCG
* * * * * * *
195494 ATCTTTTACCCCGATCGTGAGACAAATCACCATCAACCA
1 ATCTTTTACCCCGATCATG-GGCAGATTACAATCATCCG
* * ** *
195533 ATCTCTTACCCCTCGA-CAAGGGCAGATTGTAACCATCCG
1 ATCTTTTA-CCC-CGATCATGGGCAGATTACAATCATCCG
* * ** *
195572 ATCTTTTACCCCGATCGTGGGACAGATCACCGTCAGT-CA
1 ATCTTTTACCCCGATCATGGG-CAGATTACAATCA-TCCG
* * ** *
195611 ATCTCTTACCCCTCGA-CAAGGGCAGATT-GTACCATCCG
1 ATCTTTTA-CCC-CGATCATGGGCAGATTACAATCATCCG
* ** *
195649 ATCTTTTACCCCGATCATGGGGCAGATCACCGTCATCCA
1 ATCTTTTACCCCGATCAT-GGGCAGATTACAATCATCCG
* * * *
195688 ATCTTTTACCCCCGCGAT-AGGGGTAGATT-CAAACCATTCG
1 ATCTTTTA--CCC-CGATCATGGGCAGATTAC-AATCATCCG
** * ** * *
195728 ATCTTTTA-CCCGATCATGAGATAGATCACCGTCAGCCA
1 ATCTTTTACCCCGATCATG-GGCAGATTACAATCATCCG
* * *
195766 ATCTCTTACCCCG--CGATAGAGGCAGATTGCAACCATCCG
1 ATCTTTTACCCCGATC-AT-G-GGCAGATTACAATCATCCG
* * * * *
195805 ATCTTTTACCCTGATCATGGGGCAAATTATC-GTCAGCCA
1 ATCTTTTACCCCGATCAT-GGGCAGATTA-CAATCATCCG
* ** * *
195844 ATCTTTTACCTCGCGA-CAAGGGCAGATTGTAACCATTCG
1 ATCTTTTACC-C-CGATCATGGGCAGATTACAATCATCCG
* * * ** * *
195883 ATCTTTTATCCCGATCATGAGGTAGATCACCGTCAGCCA
1 ATCTTTTACCCCGATCATG-GGCAGATTACAATCATCCG
* * * * * *
195922 ATCTTTTACCCCGCGA-CAAGAGTAAATTGCAAACATCCG
1 ATCTTTTA-CCC-CGATCATGGGCAGATTACAATCATCCG
* ** *
195961 ATCTTTTACCCCGATCATGAGGCAGATCACCGTCAGCC-
1 ATCTTTTACCCCGATCATG-GGCAGATTACAATCATCCG
* * * * * *
195999 AACTCTTACCCCACGA-CA-GGGATAGATTGCAACCATCCA
1 ATCTTTTA-CCC-CGATCATGGG-CAGATTACAATCATCCG
* * ** * **
196038 ATCTTTTACCCTGATCATGGGGCAGATCACTGTCAGCAA
1 ATCTTTTACCCCGATCAT-GGGCAGATTACAATCATCCG
* * * ** *
196077 ATCTCTTACCCCCACGAT-AGGGGTAGATTGTAACCATCCG
1 ATCTTTTA--CCC-CGATCATGGGCAGATTACAATCATCCG
* ** * ** * *
196117 ATCTTTTATCTTGATCATGGGGCAGATCACCGTCAACCA
1 ATCTTTTACCCCGATCAT-GGGCAGATTACAATCATCCG
* * ** *
196156 ATCTCTTACCCCGTGAT-AGGGGCAGATTGTAACCATCCG
1 ATCTTTTACCCC--GATCATGGGCAGATTACAATCATCCG
* * * ** * *
196195 ATCTTTTACCTCGATCATAGG-ATATATCACCGTCAGCCA
1 ATCTTTTACCCCGATCATGGGCAGAT-T-ACAATCATCCG
* * *
196234 ATCTCTTACCTCGCGA-CAAGGGCAGATTGCAATCATCCG
1 ATCTTTTACC-C-CGATCATGGGCAGATTACAATCATCCG
* * * *
196273 ATCTTTTACCTCGATCATGGGGCAAATTAAAGATATCATCCA
1 ATCTTTTACCCCGATCAT-GGGCAGATT--ACA-ATCATCCG
196315 ATCTTTTACCC
1 ATCTTTTACCC
196326 TAATTAGAGG
Statistics
Matches: 673, Mismatches: 251, Indels: 125
0.64 0.24 0.12
Matches are distributed among these distances:
36 7 0.01
37 36 0.05
38 88 0.13
39 409 0.61
40 79 0.12
41 30 0.04
42 24 0.04
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.26
Consensus pattern (38 bp):
ATCTTTTACCCCGATCATGGGCAGATTACAATCATCCG
Found at i:195433 original size:78 final size:76
Alignment explanation
Indices: 195295--196296 Score: 965
Period size: 78 Copynumber: 12.9 Consensus size: 76
195285 ATTACAGTTG
* * * *
195295 GCCAATCTCTTACCCCGATCATGAGGCAGATTACAATCATCTGATCTTTTACTCCGATCATGGGG
1 GCCAATCTCTTACCCCGA-CATG-GGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGGGG
* **
195360 TAGATCACAATCA
64 CAGATCACCGTCA
** * * * *
195373 ATCAATCACTTACCCCGATCATGGGATAGATTGCAACCATCCGATCTTTTACCCCAATCATGGGA
1 GCCAATCTCTTACCCCGA-CATGGG-CAGATTGCAACCATCCGATCTTTTACCCCGATCATGGGG
*
195438 CAAATCACCGTCA
64 CAGATCACCGTCA
* * * * * *
195451 GCCAATCTTTTACCCTGATCATGGGGCAGATTACAACCATCCGATCTTTTACCCCGATCGTGAGA
1 GCCAATCTCTTACCCCGA-CAT-GGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGGGG
* *
195516 CAAATCACCATCA
64 CAGATCACCGTCA
* * * * *
195529 ACCAATCTCTTACCCCTCGACAAGGGCAGATTGTAACCATCCGATCTTTTACCCCGATCGTGGGA
1 GCCAATCTCTTA-CCC-CGACATGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGGGG
195594 CAGATCACCGTCA
64 CAGATCACCGTCA
* * *
195607 GTCAATCTCTTACCCCTCGACAAGGGCAGATTG-TACCATCCGATCTTTTACCCCGATCATGGGG
1 GCCAATCTCTTA-CCC-CGACATGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGGGG
195671 CAGATCACCGTCA
64 CAGATCACCGTCA
* * * *
195684 TCCAATCTTTTACCCCCG-CGATAGGGGTAGATT-CAAACCATTCGATCTTTTA-CCCGATCATG
1 GCCAATCTCTTA-CCCCGAC-AT--GGGCAGATTGC-AACCATCCGATCTTTTACCCCGATCATG
* **
195746 AGATAGATCACCGTCA
61 GGGCAGATCACCGTCA
*
195762 GCCAATCTCTTACCCCG-CGATAGAGGCAGATTGCAACCATCCGATCTTTTACCCTGATCATGGG
1 GCCAATCTCTTACCCCGAC-AT-G-GGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGGG
* * *
195826 GCAAATTATCGTCA
63 GCAGATCACCGTCA
* * * * * *
195840 GCCAATCTTTTACCTCGCGACAAGGGCAGATTGTAACCATTCGATCTTTTATCCCGATCATGAGG
1 GCCAATCTCTTACC-C-CGACATGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGGGG
*
195905 TAGATCACCGTCA
64 CAGATCACCGTCA
* * * * * * *
195918 GCCAATCTTTTACCCCGCGACAAGAGTAAATTGCAAACATCCGATCTTTTACCCCGATCATGAGG
1 GCCAATCTCTTA-CCC-CGACATGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGGGG
195983 CAGATCACCGTCA
64 CAGATCACCGTCA
* * *
195996 GCCAA-CTCTTACCCCACGACA-GGGATAGATTGCAACCATCCAATCTTTTACCCTGATCATGGG
1 GCCAATCTCTTA-CCC-CGACATGGG-CAGATTGCAACCATCCGATCTTTTACCCCGATCATGGG
*
196059 GCAGATCACTGTCA
63 GCAGATCACCGTCA
* * * * * **
196073 GCAAATCTCTTACCCCCACGATAGGGGTAGATTGTAACCATCCGATCTTTTATCTTGATCATGGG
1 GCCAATCTCTTACCCCGAC-AT--GGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGGG
196138 GCAGATCACCGTCA
63 GCAGATCACCGTCA
* * * * * * *
196152 ACCAATCTCTTACCCCGTGATAGGGGCAGATTGTAACCATCCGATCTTTTACCTCGATCATAGGA
1 GCCAATCTCTTACCCC--GACATGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGGGG
* *
196217 TATATCACCGTCA
64 CAGATCACCGTCA
* * *
196230 GCCAATCTCTTACCTCGCGACAAGGGCAGATTGCAATCATCCGATCTTTTACCTCGATCATGGGG
1 GCCAATCTCTTACC-C-CGACATGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGGGG
196295 CA
64 CA
196297 AATTAAAGAT
Statistics
Matches: 782, Mismatches: 116, Indels: 52
0.82 0.12 0.05
Matches are distributed among these distances:
75 1 0.00
76 9 0.01
77 156 0.20
78 515 0.66
79 89 0.11
80 10 0.01
81 2 0.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.26
Consensus pattern (76 bp):
GCCAATCTCTTACCCCGACATGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGGGGCA
GATCACCGTCA
Found at i:196324 original size:42 final size:42
Alignment explanation
Indices: 196265--196488 Score: 182
Period size: 42 Copynumber: 5.5 Consensus size: 42
196255 GCAGATTGCA
* * * *
196265 ATCATCCGATCTTTTACCTCGATCATGGGGCAAATTAAAGAT
1 ATCATCCAATCTTTTACCTCGATCATGGGGCAGATTGAAGAC
* *
196307 ATCATCCAATCTTTTACC-CTAATTA-GAGGGCAGATTGAAG--
1 ATCATCCAATCTTTTACCTC-GATCATG-GGGCAGATTGAAGAC
* *
196347 A-CA-CCAAT-TTATTACCCCGATCATGGGGGAGATTGAAGAC
1 ATCATCCAATCTT-TTACCTCGATCATGGGGCAGATTGAAGAC
* * *
196387 ATCATCTAATCTTTTACC-CTAATCA-GAGGGCATATTGAAGAC
1 ATCATCCAATCTTTTACCTC-GATCATG-GGGCAGATTGAAGAC
* * * *
196429 A-CA-CCAATCTCTTACCTCGATCATGTGGCAGATTAAAAAC
1 ATCATCCAATCTTTTACCTCGATCATGGGGCAGATTGAAGAC
*
196469 ATCATCCAATCTTCTACCTC
1 ATCATCCAATCTTTTACCTC
196489 TAAATCAAGA
Statistics
Matches: 145, Mismatches: 21, Indels: 32
0.73 0.11 0.16
Matches are distributed among these distances:
37 2 0.01
38 25 0.17
39 4 0.03
40 29 0.20
41 12 0.08
42 71 0.49
43 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (42 bp):
ATCATCCAATCTTTTACCTCGATCATGGGGCAGATTGAAGAC
Found at i:196363 original size:38 final size:38
Alignment explanation
Indices: 196312--196444 Score: 126
Period size: 38 Copynumber: 3.3 Consensus size: 38
196302 AAGATATCAT
*
196312 CCAATCTTTTACCCTAATTAGAGGGCAGATTGAAGACA
1 CCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACA
** *
196350 CCAAT-TTATTACCCCGATCATG-GGGGAGATTGAAGACA
1 CCAATCTT-TTACCCTAATCA-GAGGGCAGATTGAAGACA
*
196388 TCATCTAATCTTTTACCCTAATCAGAGGGCATATTGAAGACACA
1 -C--C-AATCTTTTACCCTAATCAGAGGGCAGATTGAAG--ACA
*
196432 CCAATCTCTTACC
1 CCAATCTTTTACC
196445 TCGATCATGT
Statistics
Matches: 76, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
37 2 0.03
38 29 0.38
39 2 0.03
40 10 0.13
41 3 0.04
42 24 0.32
43 3 0.04
44 3 0.04
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (38 bp):
CCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACA
Found at i:196398 original size:80 final size:81
Alignment explanation
Indices: 196273--196512 Score: 293
Period size: 80 Copynumber: 2.9 Consensus size: 81
196263 CAATCATCCG
* * * *
196273 ATCTTTTACCTCGATCATGGGGCAAATTAAAGATATCATCCAATCTTTTACCCTAATTAGAGGGC
1 ATCTATTACCTCGATCATGGGGCAGATTAAAGACATCATCCAATCTTTTACCCTAATCAGAGGGC
196338 AGATTGAAG-ACACCA
66 AGATTGAAGAACACCA
* * * * *
196353 ATTTATTACCCCGATCATGGGGGAGATTGAAGACATCATCTAATCTTTTACCCTAATCAGAGGGC
1 ATCTATTACCTCGATCATGGGGCAGATTAAAGACATCATCCAATCTTTTACCCTAATCAGAGGGC
*
196418 ATATTGAAGACACACCA
66 AGATTGAAGA-ACACCA
* * * *
196435 ATCTCTTACCTCGATCATGTGGCAGATTAAAAACATCATCCAATCTTCTACCTCTAAATCAAGAG
1 ATCTATTACCTCGATCATGGGGCAGATTAAAGACATCATCCAATCTTTTACC-CT-AATC-AGA-
*
196500 GGGCAAATTGAAG
62 GGGCAGATTGAAG
196513 CTATCATCTT
Statistics
Matches: 134, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
80 64 0.48
82 49 0.37
83 2 0.01
84 4 0.03
85 3 0.02
86 12 0.09
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (81 bp):
ATCTATTACCTCGATCATGGGGCAGATTAAAGACATCATCCAATCTTTTACCCTAATCAGAGGGC
AGATTGAAGAACACCA
Found at i:198229 original size:29 final size:29
Alignment explanation
Indices: 198192--198524 Score: 290
Period size: 30 Copynumber: 11.3 Consensus size: 29
198182 AAAACTATAT
* * * *
198192 TTTTGACCCTTAACTTTTCTAAATTTTCA
1 TTTTAACCCTAAACTTTTCTAAAATTACA
* * *
198221 TTTTAACCCTAAACTTTCCAAAAATCACA
1 TTTTAACCCTAAACTTTTCTAAAATTACA
*
198250 TTTTAACCCTAAAACTTTTCCAAAATTACA
1 TTTTAACCCT-AAACTTTTCTAAAATTACA
* * * *
198280 TTTTGATCCTAAACTTTTATAAAATTGCA
1 TTTTAACCCTAAACTTTTCTAAAATTACA
* * *
198309 TTTTAACCTTTAAACTTTTCCAAAATTGCA
1 TTTTAACC-CTAAACTTTTCTAAAATTACA
* * * *
198339 TTTTGACCTCTAAACTTCTCCAAAATCACA
1 TTTTAACC-CTAAACTTTTCTAAAATTACA
* *
198369 TTTTAACCATTAAACTCTTCTAAAATTACA
1 TTTTAACC-CTAAACTTTTCTAAAATTACA
* *
198399 GTTTAACCCTAAACTTTCCTAAAATTACA
1 TTTTAACCCTAAACTTTTCTAAAATTACA
* * * * *
198428 TGTTAACCCCAAATTTTTCCAAAATCACA
1 TTTTAACCCTAAACTTTTCTAAAATTACA
* * *
198457 TATTAAACCC-AAACTTTACCAAAATTACA
1 T-TTTAACCCTAAACTTTTCTAAAATTACA
* * * *
198486 TTTTTACCCCAAACTTTTTCTAAAAATATA
1 TTTTAACCCTAAAC-TTTTCTAAAATTACA
198516 TTTTAACCC
1 TTTTAACCC
198525 CGTATTCTCT
Statistics
Matches: 244, Mismatches: 55, Indels: 9
0.79 0.18 0.03
Matches are distributed among these distances:
28 6 0.02
29 116 0.48
30 122 0.50
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (29 bp):
TTTTAACCCTAAACTTTTCTAAAATTACA
Found at i:198244 original size:59 final size:59
Alignment explanation
Indices: 198181--198524 Score: 272
Period size: 59 Copynumber: 5.8 Consensus size: 59
198171 TACTTTCTTT
* * * * *
198181 AAAAACTATATTTTTGACCCTT-AACTTTTCTAAATTTTCATTTTAACCCTAAACTTTCC
1 AAAAACTACA-TTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCTAAACTTTCC
* * * *
198240 AAAAA-TCACATTTTAACCCTAAAACTTTTCCAAAATTACATTTTGATCCTAAACTTT-T
1 AAAAACT-ACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCTAAACTTTCC
* * * * *
198298 ATAAAATTGCATTTTAACCTTTAAACTTTTCCAAAATTGCATTTTGACCTCTAAACTTCTCC
1 A-AAAACTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACC-CTAAACTT-TCC
* * * * *
198360 AAAATC-ACATTTTAACCATTAAACTCTTCTAAAATTACAGTTTAACCCTAAACTTTCC
1 AAAAACTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCTAAACTTTCC
* * * * * * *
198418 TAAAATTACATGTTAACCC-CAAATTTTTCCAAAATCACATATTAAACCC-AAACTTTACC
1 AAAAACTACATTTTAACCCTTAAACTTTTCCAAAATTACAT-TTTAACCCTAAACTTT-CC
* * * * * *
198477 -AAAATTACATTTTTACCC-CAAACTTTTTCTAAAAATATATTTTAACCC
1 AAAAACTACATTTTAACCCTTAAAC-TTTTCCAAAATTACATTTTAACCC
198525 CGTATTCTCT
Statistics
Matches: 230, Mismatches: 44, Indels: 23
0.77 0.15 0.08
Matches are distributed among these distances:
58 66 0.29
59 116 0.50
60 43 0.19
61 4 0.02
62 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.38
Consensus pattern (59 bp):
AAAAACTACATTTTAACCCTTAAACTTTTCCAAAATTACATTTTAACCCTAAACTTTCC
Found at i:198267 original size:30 final size:28
Alignment explanation
Indices: 198192--198502 Score: 255
Period size: 29 Copynumber: 10.6 Consensus size: 28
198182 AAAACTATAT
* * * * *
198192 TTTTGACCCTTAACTTTTCTAAATTTTCA
1 TTTTAACCCTAAAC-TTTCCAAAATTACA
*
198221 TTTTAACCCTAAACTTTCCAAAAATCACA
1 TTTTAACCCTAAACTTTCC-AAAATTACA
198250 TTTTAACCCTAAAACTTTTCCAAAATTACA
1 TTTTAACCCT-AAAC-TTTCCAAAATTACA
* * ** *
198280 TTTTGATCCTAAACTTTTATAAAATTGCA
1 TTTTAACCCTAAAC-TTTCCAAAATTACA
* *
198309 TTTTAACCTTTAAACTTTTCCAAAATTGCA
1 TTTTAACC-CTAAAC-TTTCCAAAATTACA
* *
198339 TTTTGACCTCTAAACTTCTCCAAAATCACA
1 TTTTAACC-CTAAACTT-TCCAAAATTACA
* *
198369 TTTTAACCATTAAACTCTTCTAAAATTACA
1 TTTTAACC-CTAAACT-TTCCAAAATTACA
*
198399 GTTTAACCCTAAACTTTCCTAAAATTACA
1 TTTTAACCCTAAACTTTCC-AAAATTACA
* * * *
198428 TGTTAACCCCAAATTTTTCCAAAATCACA
1 TTTTAACCCTAAA-CTTTCCAAAATTACA
*
198457 TATTAAACCC-AAACTTTACCAAAATTACA
1 T-TTTAACCCTAAACTTT-CCAAAATTACA
* *
198486 TTTTTACCCCAAACTTT
1 TTTTAACCCTAAACTTT
198503 TTCTAAAAAT
Statistics
Matches: 231, Mismatches: 40, Indels: 22
0.79 0.14 0.08
Matches are distributed among these distances:
28 16 0.07
29 107 0.46
30 102 0.44
31 6 0.03
ACGTcount: A:0.36, C:0.23, G:0.02, T:0.38
Consensus pattern (28 bp):
TTTTAACCCTAAACTTTCCAAAATTACA
Found at i:198762 original size:19 final size:19
Alignment explanation
Indices: 198738--198776 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
198728 ATTTTCCATT
*
198738 ATTTGCACATTCATATTTA
1 ATTTGCACACTCATATTTA
* *
198757 ATTTGCGCACTCATCTTTA
1 ATTTGCACACTCATATTTA
198776 A
1 A
198777 ATTAAACTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.44
Consensus pattern (19 bp):
ATTTGCACACTCATATTTA
Found at i:200341 original size:19 final size:18
Alignment explanation
Indices: 200297--200342 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
200287 GAGTTAAACG
* * *
200297 AATCGAGTTATTCGAGTT
1 AATCGAATTATTCAAGTC
200315 AATCGAATTATTCAAGTC
1 AATCGAATTATTCAAGTC
200333 AACTCGAATT
1 AA-TCGAATT
200343 TTTTTTTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (18 bp):
AATCGAATTATTCAAGTC
Found at i:200488 original size:29 final size:30
Alignment explanation
Indices: 200446--200503 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
200436 TTACCCCAAA
200446 CCTTTTCCACTT-CCCCCAAAACATTTACT
1 CCTTTTCCACTTCCCCCCAAAACATTTACT
*
200475 CCTTTT-CACTTTCCCCCCAAAACTTTTAC
1 CCTTTTCCAC-TTCCCCCCAAAACATTTAC
200504 ACCCCTCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 3 0.12
29 8 0.31
30 15 0.58
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.36
Consensus pattern (30 bp):
CCTTTTCCACTTCCCCCCAAAACATTTACT
Found at i:223025 original size:21 final size:22
Alignment explanation
Indices: 223001--223044 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
222991 AAAAAATTTA
223001 AAATTGAAAACTTA-AAAGAAT
1 AAATTGAAAACTTACAAAGAAT
** *
223022 AAATTTTAAATTTACAAAGAAT
1 AAATTGAAAACTTACAAAGAAT
223044 A
1 A
223045 TAAAAATTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.30
Consensus pattern (22 bp):
AAATTGAAAACTTACAAAGAAT
Found at i:230293 original size:30 final size:31
Alignment explanation
Indices: 230257--230320 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
230247 CTTAACTAAA
* *
230257 AAAAATTATAATTTGA-TCATTGAACTATTC
1 AAAAATTATAATTTAAGTCACTGAACTATTC
* * *
230287 AAAAATTTTCATTTAAGTCACTGAATTATTC
1 AAAAATTATAATTTAAGTCACTGAACTATTC
230318 AAA
1 AAA
230321 TGTTTTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (31 bp):
AAAAATTATAATTTAAGTCACTGAACTATTC
Found at i:230317 original size:31 final size:31
Alignment explanation
Indices: 230277--230335 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
230267 ATTTGATCAT
230277 TGAACTATTCAAAAATTTTCATTTAAGTCAC
1 TGAACTATTCAAAAATTTTCATTTAAGTCAC
* ** *
230308 TGAATTATTCAAATGTTTTTATTTAAGT
1 TGAACTATTCAAAAATTTTCATTTAAGT
230336 AAGTAGGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (31 bp):
TGAACTATTCAAAAATTTTCATTTAAGTCAC
Found at i:231809 original size:80 final size:80
Alignment explanation
Indices: 231676--231834 Score: 309
Period size: 80 Copynumber: 2.0 Consensus size: 80
231666 GCTTGATCAC
231676 TTAGAAAAAGAACACAACTTACAAGTGAACATAAAAGAGAGTAACAGTTATAAAAGCCGACCATG
1 TTAGAAAAAGAACACAACTTACAAGTGAACATAAAAGAGAGTAACAGTTATAAAAGCCGACCATG
231741 GAATGGTAAAAAGGT
66 GAATGGTAAAAAGGT
*
231756 TTAGAAAAAGAACACAAGTTACAAGTGAACATAAAAGAGAGTAACAGTTATAAAAGCCGACCATG
1 TTAGAAAAAGAACACAACTTACAAGTGAACATAAAAGAGAGTAACAGTTATAAAAGCCGACCATG
231821 GAATGGTAAAAAGG
66 GAATGGTAAAAAGG
231835 CAAATAATGA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.17
Consensus pattern (80 bp):
TTAGAAAAAGAACACAACTTACAAGTGAACATAAAAGAGAGTAACAGTTATAAAAGCCGACCATG
GAATGGTAAAAAGGT
Found at i:239828 original size:31 final size:31
Alignment explanation
Indices: 239793--239859 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
239783 TAAATAATCC
* * *
239793 AGTGACTTGAGTAAAAACTTTCGAATAGTTT
1 AGTGACTTGAATAAAAACTTTAGAATAATTT
* *
239824 AGTGATTTGAATGAAAACTTTAGAATAATTT
1 AGTGACTTGAATAAAAACTTTAGAATAATTT
239855 AGTGA
1 AGTGA
239860 TCATTTTGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (31 bp):
AGTGACTTGAATAAAAACTTTAGAATAATTT
Found at i:244289 original size:6 final size:7
Alignment explanation
Indices: 244263--244288 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
244253 TATATTTTCA
244263 TAAAAAT
1 TAAAAAT
244270 TAAAAAT
1 TAAAAAT
244277 TAAAAAT
1 TAAAAAT
244284 TAAAA
1 TAAAA
244289 TAAAGGGAAA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAAAT
Found at i:249807 original size:17 final size:17
Alignment explanation
Indices: 249752--249808 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
249742 TAATAAAGAT
249752 GGAAGGTTAAAAGTCAA
1 GGAAGGTTAAAAGTCAA
* *
249769 GGAGAGATTAAGGAAG--AT
1 GGA-AGGTTAA--AAGTCAA
249787 GGAAGGTTAAAAGTCAA
1 GGAAGGTTAAAAGTCAA
249804 GGAAG
1 GGAAG
249809 ATGGAAGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
15 3 0.10
17 15 0.48
18 10 0.32
20 3 0.10
ACGTcount: A:0.46, C:0.04, G:0.35, T:0.16
Consensus pattern (17 bp):
GGAAGGTTAAAAGTCAA
Found at i:251740 original size:10 final size:10
Alignment explanation
Indices: 251725--251749 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
251715 TAGTACTATT
251725 TAAGTTACTG
1 TAAGTTACTG
251735 TAAGTTACTG
1 TAAGTTACTG
251745 TAAGT
1 TAAGT
251750 CACGTCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (10 bp):
TAAGTTACTG
Found at i:253619 original size:36 final size:36
Alignment explanation
Indices: 253567--253639 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
253557 AATATGAATA
* *
253567 AGTAGTTAACAGTGAATATTAAACGCAACATTAAAT
1 AGTAGTTAACAATGAATATTAAACGCAACATGAAAT
*
253603 AGTAGTTAACAATGAATATTAGACGCAACATGAAAT
1 AGTAGTTAACAATGAATATTAAACGCAACATGAAAT
253639 A
1 A
253640 AATAGGAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (36 bp):
AGTAGTTAACAATGAATATTAAACGCAACATGAAAT
Found at i:253796 original size:30 final size:30
Alignment explanation
Indices: 253762--253987 Score: 179
Period size: 30 Copynumber: 7.6 Consensus size: 30
253752 GCATGGGGGC
* *
253762 AAAATGGTAGTTTTGGAAGGTTTGGAGTCA
1 AAAATGGTATTTTTGGAAGGTTTGGGGTCA
*
253792 AAAATGAG-ATTTTTGGAA-GTTCGAGGGT--
1 AAAATG-GTATTTTTGGAAGGTTTG-GGGTCA
* * *
253820 AAAATGGTAATTTTCGAAAGGTTCGGGGTCA
1 AAAATGGT-ATTTTTGGAAGGTTTGGGGTCA
*
253851 AAAATGAG-ATTTTTGGAA-GTTCAGGGGT--
1 AAAATG-GTATTTTTGGAAGGTT-TGGGGTCA
* *
253879 AAAATGGTAATTTTTGAAAGGTTTAGGGTCA
1 AAAATGGT-ATTTTTGGAAGGTTTGGGGTCA
253910 AAAATAGG-ATTTTTGGAA-GTTTAGGGGT--
1 AAAAT-GGTATTTTTGGAAGGTTT-GGGGTCA
**
253938 AAAATGGTAATTTTTGGAAGGTTCAGGGTCA
1 AAAATGGT-ATTTTTGGAAGGTTTGGGGTCA
*
253969 AAAATGGGATTTTTGGAAG
1 AAAATGGTATTTTTGGAAG
253988 TTCGAGGAAC
Statistics
Matches: 159, Mismatches: 16, Indels: 42
0.73 0.07 0.19
Matches are distributed among these distances:
27 4 0.03
28 17 0.11
29 50 0.31
30 66 0.42
31 19 0.12
32 3 0.02
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.33
Consensus pattern (30 bp):
AAAATGGTATTTTTGGAAGGTTTGGGGTCA
Found at i:253853 original size:59 final size:60
Alignment explanation
Indices: 253757--253994 Score: 326
Period size: 59 Copynumber: 4.0 Consensus size: 60
253747 CGGATGCATG
* * * *
253757 GGGGCAAAATGGT-AGTTTTGGAAGGTT-TGGAGTCAAAAATGAGATTTTTGGAAGTTCGA
1 GGGGTAAAATGGTAATTTTTGAAAGGTTCAGG-GTCAAAAATGAGATTTTTGGAAGTTCGA
* *
253816 -GGGTAAAATGGTAATTTTCGAAAGGTTCGGGGTCAAAAATGAGATTTTTGGAAGTTC-A
1 GGGGTAAAATGGTAATTTTTGAAAGGTTCAGGGTCAAAAATGAGATTTTTGGAAGTTCGA
* *
253874 GGGGTAAAATGGTAATTTTTGAAAGGTTTAGGGTCAAAAAT-AGGATTTTTGGAAGTT-TA
1 GGGGTAAAATGGTAATTTTTGAAAGGTTCAGGGTCAAAAATGA-GATTTTTGGAAGTTCGA
* *
253933 GGGGTAAAATGGTAATTTTTGGAAGGTTCAGGGTCAAAAATGGGATTTTTGGAAGTTCGA
1 GGGGTAAAATGGTAATTTTTGAAAGGTTCAGGGTCAAAAATGAGATTTTTGGAAGTTCGA
253993 GG
1 GG
253995 AACTTCGAGG
Statistics
Matches: 160, Mismatches: 12, Indels: 13
0.86 0.06 0.07
Matches are distributed among these distances:
58 13 0.08
59 142 0.89
60 5 0.03
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (60 bp):
GGGGTAAAATGGTAATTTTTGAAAGGTTCAGGGTCAAAAATGAGATTTTTGGAAGTTCGA
Found at i:255887 original size:17 final size:18
Alignment explanation
Indices: 255865--255907 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
255855 TTTGAACTTT
*
255865 ATTTTAAATTT-ATAATA
1 ATTTTAAATTTGAAAATA
255882 ATTTTAAATTTGAAAATA
1 ATTTTAAATTTGAAAATA
*
255900 AATTTAAA
1 ATTTTAAA
255908 CTTAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTTAAATTTGAAAATA
Found at i:255924 original size:23 final size:24
Alignment explanation
Indices: 255885--255930 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 24
255875 TATAATAATT
255885 TTAAATTTGAAAATAAATTTAAAC
1 TTAAATTTGAAAATAAATTTAAAC
255909 TTAAATTT-AAAATAAATTTAAA
1 TTAAATTTGAAAATAAATTTAAA
255931 TTTTTAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
TTAAATTTGAAAATAAATTTAAAC
Found at i:255926 original size:11 final size:11
Alignment explanation
Indices: 255886--255930 Score: 63
Period size: 12 Copynumber: 3.9 Consensus size: 11
255876 ATAATAATTT
255886 TAAATTTGAAAA
1 TAAATTT-AAAA
*
255898 TAAATTTAAACT
1 TAAATTTAAA-A
255910 TAAATTTAAAA
1 TAAATTTAAAA
255921 TAAATTTAAA
1 TAAATTTAAA
255931 TTTTTAACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
11 13 0.43
12 17 0.57
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:255929 original size:17 final size:17
Alignment explanation
Indices: 255867--255964 Score: 79
Period size: 17 Copynumber: 5.4 Consensus size: 17
255857 TGAACTTTAT
* *
255867 TTTAAATTTATAATAAT
1 TTTAAATTTAAAATAAA
255884 TTTAAATTTGAAAATAAA
1 TTTAAATTT-AAAATAAA
255902 TTTAAACTTAAATTTAAAATAAA
1 --T----TTAAATTTAAAATAAA
** *
255925 TTTAAATTTTTAACAAA
1 TTTAAATTTAAAATAAA
*
255942 TTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAA
255959 TTTAAA
1 TTTAAA
255965 GGGGAATTTG
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
17 40 0.62
18 6 0.09
20 1 0.02
21 1 0.02
23 8 0.12
24 8 0.12
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:255964 original size:6 final size:6
Alignment explanation
Indices: 255867--255933 Score: 52
Period size: 6 Copynumber: 11.5 Consensus size: 6
255857 TGAACTTTAT
* * *
255867 TTTAAA TTTATAA --TAAT TTTAAA TTTGAAA -ATAAA TTTAAA CTTAAA
1 TTTAAA TTTA-AA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
*
255914 TTTAAA -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTT
255934 TTAACAAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
4 1 0.02
5 9 0.19
6 32 0.68
7 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:263192 original size:29 final size:32
Alignment explanation
Indices: 263142--263215 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 32
263132 ACAAGCCTTC
* * *
263142 CTATTTTGGTCAC-TCATTTTAAA-AATTTGT
1 CTATTTTAGTCACTTCATATTAAATAAGTTGT
263172 -TATTTTAGTCACTTC-TATTAAATAAGTTGT
1 CTATTTTAGTCACTTCATATTAAATAAGTTGT
*
263202 CAATTTTAGTCACT
1 CTATTTTAGTCACT
263216 CTTGTTAGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 17 0.46
30 8 0.22
31 12 0.32
ACGTcount: A:0.28, C:0.14, G:0.09, T:0.49
Consensus pattern (32 bp):
CTATTTTAGTCACTTCATATTAAATAAGTTGT
Found at i:263463 original size:24 final size:25
Alignment explanation
Indices: 263426--263472 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
263416 TCCAAATTCT
*
263426 AAAACTCGACAAATTTATAATTTTA
1 AAAACTCGACAAATATATAATTTTA
* *
263451 AAAACTTGA-AAATATATTATTT
1 AAAACTCGACAAATATATAATTT
263473 ATTATAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (25 bp):
AAAACTCGACAAATATATAATTTTA
Found at i:279013 original size:22 final size:21
Alignment explanation
Indices: 278977--279019 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
278967 CGATTTGAGG
*
278977 AAAAATAAAATAAACAAAATT
1 AAAAATAAAAAAAACAAAATT
*
278998 AAAAATAAAAGAAAACAGAATT
1 AAAAATAAAA-AAAACAAAATT
279020 GAAAGAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.74, C:0.05, G:0.05, T:0.16
Consensus pattern (21 bp):
AAAAATAAAAAAAACAAAATT
Found at i:283301 original size:18 final size:18
Alignment explanation
Indices: 283280--283324 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
283270 ATAAATAATT
* *
283280 ATAATTATATATATAAAA
1 ATAATTATAAAAATAAAA
**
283298 ATAAAAATAAAAATAAAA
1 ATAATTATAAAAATAAAA
283316 ATAATTATA
1 ATAATTATA
283325 CTTATAAGTA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAATTATAAAAATAAAA
Found at i:283309 original size:5 final size:6
Alignment explanation
Indices: 283292--283319 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
283282 AATTATATAT
283292 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAA
283320 TTATACTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:296747 original size:29 final size:31
Alignment explanation
Indices: 296715--296784 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 31
296705 TTTAATTATT
296715 TTTTTATAAATAATTTTA-ATGA-TTTTT-AA
1 TTTTTATAAATAATTTTATAT-ATTTTTTAAA
* *
296744 TTTTTAAAAATAGTTTTATATATTTTTTAAA
1 TTTTTATAAATAATTTTATATATTTTTTAAA
296775 TTTTT-TAAAT
1 TTTTTATAAAT
296785 TTAATTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 17 0.49
30 11 0.31
31 7 0.20
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (31 bp):
TTTTTATAAATAATTTTATATATTTTTTAAA
Found at i:298201 original size:139 final size:141
Alignment explanation
Indices: 298038--298329 Score: 353
Period size: 141 Copynumber: 2.1 Consensus size: 141
298028 GTAGTAAAAT
* *
298038 AATCAAACTTGAGACCCAAGGATGTAA-T-T-ACATCTATCTAACCATCTAACGAAA-AATCTAA
1 AATCAAACTTGAGACCCAAGGATGTAATTGTAAC-TATATCTAACCATCTAACCAAATAA-CTAA
* * * *
298099 TGTGTTAAAAAACATTAATT-AAAA-TTTAAAAGTCTTGAAGCAACATGAAATAAAAAACATAAA
64 TATATT-AAAAACATTAATTAAAAATTTTAAAAAT-TAGAAGCAACATGAAATAAAAAACATAAA
298162 TATAAGTAGGAGAGG
127 TATAAGTAGGAGAGG
* * *
298177 AATCAATCTTGAGACTCAATGATGTAATTGTAACTATATCTAACCATCTAACCAAATAACTAATA
1 AATCAAACTTGAGACCCAAGGATGTAATTGTAACTATATCTAACCATCTAACCAAATAACTAATA
* *
298242 TATTAAAAATATTAATTAAAAATTTTAAAAATTAGAAGCAACATGAAATAAAAAAAATATATAAA
66 TATTAAAAACATTAATTAAAAATTTTAAAAATTAGAAGCAACATGAAAT---AAAAA-ACATAAA
* *
298307 TGTGAGTAGGAGAGG
127 TATAAGTAGGAGAGG
298322 AATCAAAC
1 AATCAAAC
298330 CTGAAACTTA
Statistics
Matches: 129, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
139 24 0.19
140 13 0.10
141 49 0.38
142 12 0.09
144 5 0.04
145 26 0.20
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.27
Consensus pattern (141 bp):
AATCAAACTTGAGACCCAAGGATGTAATTGTAACTATATCTAACCATCTAACCAAATAACTAATA
TATTAAAAACATTAATTAAAAATTTTAAAAATTAGAAGCAACATGAAATAAAAAACATAAATATA
AGTAGGAGAGG
Found at i:299046 original size:32 final size:32
Alignment explanation
Indices: 298978--299047 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
298968 GAACTTGTTT
* **
298978 AAAAATATTTAATTGGTACTTAAACTTCTCTT
1 AAAAATACTTAATTGGTACTTAAACTTCTCCA
* * * *
299010 AAAAATACTTATTTTGTACTTAAATTTGTCCA
1 AAAAATACTTAATTGGTACTTAAACTTCTCCA
299042 AAAAAT
1 AAAAAT
299048 TATACTTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.41
Consensus pattern (32 bp):
AAAAATACTTAATTGGTACTTAAACTTCTCCA
Found at i:306046 original size:17 final size:17
Alignment explanation
Indices: 306024--306109 Score: 92
Period size: 17 Copynumber: 5.2 Consensus size: 17
306014 AATATGAAAA
*
306024 GTTAAGGAAGATGGGAG
1 GTTAAGGAAGATGGAAG
306041 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
306058 GTTAAAGGTCAA-A-GGAA-
1 GTT-AAGG--AAGATGGAAG
306075 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
*
306092 GTTAA--AAGATGAAAG
1 GTTAAGGAAGATGGAAG
306107 GTT
1 GTT
306110 GAACATCCAT
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
14 2 0.03
15 13 0.21
16 8 0.13
17 27 0.44
18 8 0.13
19 1 0.02
20 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.37, T:0.20
Consensus pattern (17 bp):
GTTAAGGAAGATGGAAG
Found at i:311157 original size:34 final size:34
Alignment explanation
Indices: 311104--311196 Score: 109
Period size: 34 Copynumber: 2.7 Consensus size: 34
311094 AGAATATGAA
* * *
311104 AAGTTAAGGTAGATGGAAGGTTAAA-GAT-TAAGG
1 AAGTTAAGGAAGATGGAAGGTTAAATG-TCAAAAG
* *
311137 GAGCTTAAGGAAGATAGAAGGTTAAATGTCAAAAG
1 AAG-TTAAGGAAGATGGAAGGTTAAATGTCAAAAG
311172 AAGTTAAGGAAGATGGAAGGTTAAA
1 AAGTTAAGGAAGATGGAAGGTTAAA
311197 AGATGAAAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
33 2 0.04
34 42 0.84
35 6 0.12
ACGTcount: A:0.45, C:0.02, G:0.31, T:0.22
Consensus pattern (34 bp):
AAGTTAAGGAAGATGGAAGGTTAAATGTCAAAAG
Found at i:311201 original size:15 final size:15
Alignment explanation
Indices: 311181--311223 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
311171 GAAGTTAAGG
*
311181 AAGATGGAAGGTTAA
1 AAGATGAAAGGTTAA
311196 AAGATGAAAGGTTAA
1 AAGATGAAAGGTTAA
311211 AAGATGAAAGGTT
1 AAGATGAAAGGTT
311224 GAACATCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.30, T:0.21
Consensus pattern (15 bp):
AAGATGAAAGGTTAA
Found at i:312358 original size:30 final size:29
Alignment explanation
Indices: 312325--312584 Score: 135
Period size: 30 Copynumber: 8.8 Consensus size: 29
312315 ATTCGAGGGT
312325 AAAATGGTAATTTTTGGAAAGTTTGAGGTTA
1 AAAAT-GTAATTTTTGGAAAGTTTGAGG-TA
** * * **
312356 AAAATAAAATTTTTAGACA-TCCGAGGCT-
1 AAAATGTAATTTTTGGAAAGTTTGAGG-TA
*
312384 -AAATGGTAA-TTTTGGAAGGATTTGAGGTCA
1 AAAAT-GTAATTTTTGGAAAG-TTTGAGGT-A
* *
312414 AAAATG-AAATTTTGGAAAGTTTAGGGGTA
1 AAAATGTAATTTTTGGAAAGTTT-GAGGTA
* *
312443 AAAATGTAATTTTTGAAAAATTT-AGGGTCA
1 AAAATGTAATTTTTGGAAAGTTTGA-GGT-A
*
312473 AAAATG--ATATTTTGGAAAGTTCGAGGCTA
1 AAAATGTAAT-TTTTGGAAAGTTTGAGG-TA
* * *
312502 AAAATGTAGTTTTTGGAAA-ATTCAGGGTCA
1 AAAATGTAATTTTTGGAAAGTTTGA-GGT-A
* * * * *
312532 AAAATG-AAATTTAGGAATGTTCGGGGGTA
1 AAAATGTAATTTTTGGAAAGTT-TGAGGTA
*
312561 AAAATGTAATTTTTGGAAAATTTG
1 AAAATGTAATTTTTGGAAAGTTTG
312585 TATGCCAAAA
Statistics
Matches: 168, Mismatches: 40, Indels: 44
0.67 0.16 0.17
Matches are distributed among these distances:
27 10 0.06
28 5 0.03
29 64 0.38
30 79 0.47
31 10 0.06
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.33
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAAGTTTGAGGTA
Found at i:312455 original size:29 final size:30
Alignment explanation
Indices: 312384--312579 Score: 138
Period size: 30 Copynumber: 6.6 Consensus size: 30
312374 ATCCGAGGCT
* *
312384 AAATGGTAATTTTGGAAGGATTT-GAGGTCAA
1 AAAT-GTAATTTTGGAAAG-TTTAGGGGTCAA
*
312415 AAATGAAATTTTGGAAAGTTTAGGGGT-AA
1 AAATGTAATTTTGGAAAGTTTAGGGGTCAA
* *
312444 AAATGTAATTTTTGAAAAATTTA-GGGTCAA
1 AAATGTAA-TTTTGGAAAGTTTAGGGGTCAA
* *
312474 AAATG-ATATTTTGGAAAG-TTCGAGG-CTAA
1 AAATGTA-ATTTTGGAAAGTTTAGGGGTC-AA
* * *
312503 AAATGTAGTTTTTGGAAAATTCA-GGGTCAA
1 AAATGTA-ATTTTGGAAAGTTTAGGGGTCAA
* * * **
312533 AAATGAAATTTAGGAATGTTCGGGGGT-AA
1 AAATGTAATTTTGGAAAGTTTAGGGGTCAA
312562 AAATGTAATTTTTGGAAA
1 AAATGTAA-TTTTGGAAA
312580 ATTTGTATGC
Statistics
Matches: 129, Mismatches: 25, Indels: 23
0.73 0.14 0.13
Matches are distributed among these distances:
28 3 0.02
29 53 0.41
30 67 0.52
31 6 0.05
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (30 bp):
AAATGTAATTTTGGAAAGTTTAGGGGTCAA
Found at i:312595 original size:59 final size:58
Alignment explanation
Indices: 312266--312584 Score: 265
Period size: 59 Copynumber: 5.4 Consensus size: 58
312256 TCGGGGGGGC
* * * * *
312266 AAAATGGTAATTTTGGGAAAGTTCGGGATCAAAAATGAAATTGTT--AAACATTCGAGGGT-
1 AAAAT-GTAATTTTTGGAAAATTTGGG-TCAAAAATGAAATT-TTGGAAA-GTTCGGGGGTA
* * * * * * * *
312325 AAAATGGTAATTTTTGGAAAGTTTGAGGTTAAAAATAAAATTTTTAGACA-TCCGAGGCT-
1 AAAAT-GTAATTTTTGGAAAATTTG-GGTCAAAAATGAAA-TTTTGGAAAGTTCGGGGGTA
* **
312384 -AAATGGTAA-TTTTGGAAGGATTTGAGGTCAAAAATGAAATTTTGGAAAGTTTAGGGGTA
1 AAAAT-GTAATTTTTGGAA-AATTTG-GGTCAAAAATGAAATTTTGGAAAGTTCGGGGGTA
* * * *
312443 AAAATGTAATTTTTGAAAAATTTAGGGTCAAAAATGATATTTTGGAAAGTTCGAGGCTA
1 AAAATGTAATTTTTGGAAAATTT-GGGTCAAAAATGAAATTTTGGAAAGTTCGGGGGTA
* * * *
312502 AAAATGTAGTTTTTGGAAAATTCAGGGTCAAAAATGAAATTTAGGAATGTTCGGGGGTA
1 AAAATGTAATTTTTGGAAAATT-TGGGTCAAAAATGAAATTTTGGAAAGTTCGGGGGTA
312561 AAAATGTAATTTTTGGAAAATTTG
1 AAAATGTAATTTTTGGAAAATTTG
312585 TATGCCAAAA
Statistics
Matches: 214, Mismatches: 35, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
57 15 0.07
58 31 0.14
59 150 0.70
60 16 0.07
61 2 0.01
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.33
Consensus pattern (58 bp):
AAAATGTAATTTTTGGAAAATTTGGGTCAAAAATGAAATTTTGGAAAGTTCGGGGGTA
Found at i:313098 original size:20 final size:20
Alignment explanation
Indices: 313073--313112 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
313063 TTCTTCGGGA
313073 AAAGAAGTTCACGACCCGTG
1 AAAGAAGTTCACGACCCGTG
313093 AAAGAAGTTCACGACCCGTG
1 AAAGAAGTTCACGACCCGTG
313113 GGCCTTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.15
Consensus pattern (20 bp):
AAAGAAGTTCACGACCCGTG
Found at i:313821 original size:49 final size:49
Alignment explanation
Indices: 313746--313893 Score: 176
Period size: 49 Copynumber: 3.0 Consensus size: 49
313736 TTCCCTTTTG
*
313746 TGTCTTCGTGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCA
1 TGTCTTCGAGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCA
* * *
313795 TGTC-TCTGAGGTA-TAAGG-TTCGCCATTGCGTCTTAAACCTTTCCCTTCG
1 TGTCTTC-GAGGTACT--GGATTCGCCATTGCGGCTTAAATCTTTCCCTTCA
* * * *
313844 TGTCTTCGTGGTACTGGATTCGCCGTTGCAGCTTAAATATTTCCCTTCA
1 TGTCTTCGAGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCA
313893 T
1 T
313894 ATTTCGCGAT
Statistics
Matches: 82, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
48 5 0.06
49 72 0.88
50 5 0.06
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.39
Consensus pattern (49 bp):
TGTCTTCGAGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCA
Found at i:313847 original size:98 final size:97
Alignment explanation
Indices: 313657--313893 Score: 307
Period size: 98 Copynumber: 2.4 Consensus size: 97
313647 TCACTCCGCA
** ** *
313657 TGGTACTAAATTCGCCGTTGCAGCTTAAATTTTCTTTTCATGCTTCTGAGGTATAAGTTTGCCAC
1 TGGTACTGGATTCGCCGTTGCAGCTTAAATTTTCCCTTCATGCTTCTGAGGTATAAGTTCGCCAC
* * *
313722 GGTGACTTAATCCTTTCCCTTTTGTGTCTTCG
66 GGCGACTTAAACCTTTCCCTTTCGTGTCTTCG
* *
313754 TGGTACTGGATTCGCCATTGCGGCTTAAATCTTTCCCTTCATG-TCTCTGAGGTATAAGGTTCGC
1 TGGTACTGGATTCGCCGTTGCAGCTTAAAT-TTTCCCTTCATGCT-TCTGAGGTATAA-GTTCGC
** *
313818 CATTGCGTCTTAAACCTTTCCC-TTCGTGTCTTCG
63 CACGGCGACTTAAACCTTTCCCTTTCGTGTCTTCG
313852 TGGTACTGGATTCGCCGTTGCAGCTTAAATATTTCCCTTCAT
1 TGGTACTGGATTCGCCGTTGCAGCTTAAAT-TTTCCCTTCAT
313894 ATTTCGCGAT
Statistics
Matches: 121, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
97 27 0.22
98 72 0.60
99 22 0.18
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (97 bp):
TGGTACTGGATTCGCCGTTGCAGCTTAAATTTTCCCTTCATGCTTCTGAGGTATAAGTTCGCCAC
GGCGACTTAAACCTTTCCCTTTCGTGTCTTCG
Found at i:314344 original size:18 final size:18
Alignment explanation
Indices: 314318--314352 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
314308 AAAATTACCG
* *
314318 AATATTTACAAGGAACAA
1 AATAATTACAAAGAACAA
314336 AATAATTACAAAGAACA
1 AATAATTACAAAGAACA
314353 GTGTTAGATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.20
Consensus pattern (18 bp):
AATAATTACAAAGAACAA
Found at i:318359 original size:286 final size:289
Alignment explanation
Indices: 317832--318413 Score: 990
Period size: 286 Copynumber: 2.0 Consensus size: 289
317822 CATGTGCAAA
317832 GCCTTTGTCGACCCAATTCCCCCAGACGGGATCTCGTCGTCATTGAAGAAAATAAAGTAGTTAGC
1 GCCTTTGTCGACCCAATTCCCCCAGACGGGATCTCGTCGTCATTGAAGAAAATAAAGTAGTTAGC
*
317897 ACTGACGTTATTAATTAGGCGATCCAGTTTGCACTCAGATATGTCATTAGCCACATATGTTTCGT
66 ACTGACGTTATTAATTAGGCGATCCAGTTTGCACACAGATATGTCATTAGCCACATATGTTTCGT
*
317962 TGAGCACCCTCATCAGTGCATTGGTGGGCTTCTGAACTTAGCAGCAGGGCTAAGATTTATATGCG
131 TGAGCACCCTCATCAGTGCATTGGTGGGCTTCTGAACTTAGCAGCAGGGCAAAGATTTATATGCG
* *
318027 TGCCAGTTGTTTGTGTAATTGCTCGATCACACTGTACTCAC-TA-T-ATTTCAAGAATTCTTTCG
196 TGCCAGTTGTTTGTGTAATTGCTCGACCACACTATACTCACATATTAATTTCAAGAATTCTTTCG
*
318089 TTTCTTTTTCTGCTACTGGCTCATTTACC
261 CTTCTTTTTCTGCTACTGGCTCATTTACC
* *
318118 GCCTTTGTTGACCCCATTCCCCCAGACGGGATCTCGTCGTCATTGAAGAAAATAAAGTAGTTAGC
1 GCCTTTGTCGACCCAATTCCCCCAGACGGGATCTCGTCGTCATTGAAGAAAATAAAGTAGTTAGC
318183 ACTGACGTTATTAATTAGGCGATCCAGTTTGCACACAGATATGTCATTAGCCACATATGTTTCGT
66 ACTGACGTTATTAATTAGGCGATCCAGTTTGCACACAGATATGTCATTAGCCACATATGTTTCGT
*
318248 TGAGCACCCTCATCAGTGCATTGGTGGGCTTTTGAACTTAGCAGCAGGGCAAAGATTTATATGCG
131 TGAGCACCCTCATCAGTGCATTGGTGGGCTTCTGAACTTAGCAGCAGGGCAAAGATTTATATGCG
* * *
318313 TGTCGGTTGTTTGTGTAATTGCTCGACCACACTATACTCGCTATATTTCAAGAATTTCAAGAATT
196 TGCCAGTTGTTTGTGTAATTGCTCGACCACACTATACTCAC-ATA-TT----AATTTCAAGAATT
318378 CTTTCGCTTCTTTTTCTGCTACTGGCTCATTTACC
255 CTTTCGCTTCTTTTTCTGCTACTGGCTCATTTACC
318413 G
1 G
318414 GCTCAGGCTT
Statistics
Matches: 276, Mismatches: 11, Indels: 9
0.93 0.04 0.03
Matches are distributed among these distances:
286 226 0.82
288 2 0.01
290 1 0.00
295 47 0.17
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.34
Consensus pattern (289 bp):
GCCTTTGTCGACCCAATTCCCCCAGACGGGATCTCGTCGTCATTGAAGAAAATAAAGTAGTTAGC
ACTGACGTTATTAATTAGGCGATCCAGTTTGCACACAGATATGTCATTAGCCACATATGTTTCGT
TGAGCACCCTCATCAGTGCATTGGTGGGCTTCTGAACTTAGCAGCAGGGCAAAGATTTATATGCG
TGCCAGTTGTTTGTGTAATTGCTCGACCACACTATACTCACATATTAATTTCAAGAATTCTTTCG
CTTCTTTTTCTGCTACTGGCTCATTTACC
Found at i:322444 original size:28 final size:29
Alignment explanation
Indices: 322407--322482 Score: 102
Period size: 28 Copynumber: 2.7 Consensus size: 29
322397 CAGATACCCG
**
322407 AGGGGTAAAATGGTAATTTT-GAATTTTT
1 AGGGGTAAAATGGTAATTTTGGAAAGTTT
*
322435 AGGGGCAAAATGGTAATTTTGGAAAGTTT
1 AGGGGTAAAATGGTAATTTTGGAAAGTTT
*
322464 AGGGTTAAAAT-GTAATTTT
1 AGGGGTAAAATGGTAATTTT
322483 TAGACATTCG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 27 0.64
29 15 0.36
ACGTcount: A:0.34, C:0.01, G:0.26, T:0.38
Consensus pattern (29 bp):
AGGGGTAAAATGGTAATTTTGGAAAGTTT
Found at i:322570 original size:29 final size:28
Alignment explanation
Indices: 322527--322803 Score: 172
Period size: 29 Copynumber: 9.5 Consensus size: 28
322517 TTTTAAGGTC
*
322527 AAAAATGGAGA-TTTTGGAGGTTCGGGGGT
1 AAAAAT-GAGATTTTTGGAAGTTC-GGGGT
* *
322556 AAAAATGAGATTTTTGTAAGTTTCGAGGT
1 AAAAATGAGATTTTTGGAAG-TTCGGGGT
*
322585 CAAAAATG-GAATTTTTTGG-AGTTTGAGGGT
1 -AAAAATGAG-A-TTTTTGGAAGTTCG-GGGT
*
322615 AAAAAT-AGAATTTTTAGAAGTTCGGGGT
1 AAAAATGAG-ATTTTTGGAAGTTCGGGGT
* * **
322643 CAAAAA-GGGAATTTTTGGAAGTTTTGAAGT
1 -AAAAATGAG-ATTTTTGGAAG-TTCGGGGT
* * *
322673 AAAAAATGAAATTTTGGGAAGTTTCGAGGT
1 -AAAAATGAGATTTTTGGAAG-TTCGGGGT
* *
322703 CAAAAATGTGATTTTTGAAAGTTCAGGGGT
1 -AAAAATGAGATTTTTGGAAGTTC-GGGGT
* *
322733 AAAAATG-GAATTTTAGGAAGTTTTGGGGT
1 AAAAATGAG-ATTTTTGGAAG-TTCGGGGT
* *
322762 AAAAATTCA-ATTTTTGGAAGTTTAGGGGT
1 AAAAA-TGAGATTTTTGGAAG-TTCGGGGT
322791 AAAAATGAGATTT
1 AAAAATGAGATTT
322804 GGGGACAGTT
Statistics
Matches: 198, Mismatches: 32, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
28 17 0.09
29 108 0.55
30 66 0.33
31 7 0.04
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (28 bp):
AAAAATGAGATTTTTGGAAGTTCGGGGT
Found at i:322589 original size:59 final size:59
Alignment explanation
Indices: 322522--322803 Score: 274
Period size: 59 Copynumber: 4.8 Consensus size: 59
322512 GAGCGTTTTA
* ** *
322522 AGGTCAAAAATGGAGA-TTTTGGAGGTTCGGGGGTAAAAATGAGATTTTTGTAAGTTTCG
1 AGGTCAAAAATGGA-ATTTTTGGAAGTTTAGGGGTAAAAATGAGATTTTTGGAAGTTTCG
*
322581 AGGTCAAAAATGGAATTTTTTGG-AGTTT-GAGGGTAAAAAT-AGAATTTTTAGAAG-TTCG
1 AGGTCAAAAATGGAA-TTTTTGGAAGTTTAG-GGGTAAAAATGAG-ATTTTTGGAAGTTTCG
* * * ** * *
322639 GGGTCAAAAAGGGAATTTTTGGAAGTTTTGAAGTAAAAAATGAAATTTTGGGAAGTTTCG
1 AGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGT-AAAAATGAGATTTTTGGAAGTTTCG
* * * *
322699 AGGTCAAAAATGTG-ATTTTTGAAAGTTCAGGGGTAAAAATG-GAATTTTAGGAAGTTTTG
1 AGGTCAAAAATG-GAATTTTTGGAAGTTTAGGGGTAAAAATGAG-ATTTTTGGAAGTTTCG
* **
322758 GGGT-AAAAATTCAATTTTTGGAAGTTTAGGGGTAAAAATGAGATTT
1 AGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGAGATTT
322804 GGGGACAGTT
Statistics
Matches: 184, Mismatches: 26, Indels: 27
0.78 0.11 0.11
Matches are distributed among these distances:
57 7 0.04
58 63 0.34
59 77 0.42
60 36 0.20
61 1 0.01
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (59 bp):
AGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATGAGATTTTTGGAAGTTTCG
Found at i:322793 original size:118 final size:117
Alignment explanation
Indices: 322551--322814 Score: 304
Period size: 118 Copynumber: 2.2 Consensus size: 117
322541 TGGAGGTTCG
* * * *
322551 GGGGTAAAAATGAGATTTTTGTAAGTTTCGAGGTCAAAAATGGAATTTTTTGGAGTTTGAGGGTA
1 GGGGTAAAAATGAGATTTTGGGAAGTTTCGAGGTCAAAAATGGAATTTTTTGAAGTTAGAGGGTA
* *
322616 AAAATAGAATTTTTAGAAGTTCGGGGTCAAAAAGGGAATTTTTGGAAGTTTT
66 AAAATAGAATTTTTAGAAGTTCGGGGTCAAAAAGGCAATTTTTGGAAGTTTA
** *
322668 GAAGTAAAAAATGAAATTTTGGGAAGTTTCGAGGTCAAAAATGTG-A-TTTTTGAAAGTTCAG-G
1 GGGGT-AAAAATGAGATTTTGGGAAGTTTCGAGGTCAAAAATG-GAATTTTTTG-AAGTT-AGAG
* * **
322730 GGTAAAAATGGAA-TTTTAGGAAGTTTTGGGGT-AAAAATTCAATTTTTGGAAGTTTA
62 GGTAAAAATAGAATTTTTA-GAAG-TTCGGGGTCAAAAAGGCAATTTTTGGAAGTTTA
*
322786 GGGGTAAAAATGAGATTTGGGGACAGTTT
1 GGGGTAAAAATGAGATTTTGGGA-AGTTT
322815 AGGGACCTCC
Statistics
Matches: 123, Mismatches: 17, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
117 30 0.24
118 84 0.68
119 9 0.07
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (117 bp):
GGGGTAAAAATGAGATTTTGGGAAGTTTCGAGGTCAAAAATGGAATTTTTTGAAGTTAGAGGGTA
AAAATAGAATTTTTAGAAGTTCGGGGTCAAAAAGGCAATTTTTGGAAGTTTA
Found at i:324477 original size:6 final size:6
Alignment explanation
Indices: 324466--324542 Score: 56
Period size: 6 Copynumber: 13.5 Consensus size: 6
324456 TTTGGACATT
* * *
324466 AATTTA AATTTA AATTT- AACTCA AATTTA TAA--TA AATTTA AATTTT
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA
* * *
324512 AA-GTA AATTTA AACTTA AA-ATA AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AAT
324543 AATGTTGGGC
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
4 2 0.04
5 12 0.22
6 38 0.70
7 2 0.04
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:324504 original size:34 final size:34
Alignment explanation
Indices: 324466--324542 Score: 91
Period size: 34 Copynumber: 2.3 Consensus size: 34
324456 TTTGGACATT
* * * *
324466 AATTTAAATTTAAATTTAACTCAAATTTATAATA
1 AATTTAAATTTAAAGTAAACTCAAACTTAAAATA
* * *
324500 AATTTAAATTTTAAGTAAATTTAAACTTAAAATA
1 AATTTAAATTTAAAGTAAACTCAAACTTAAAATA
324534 AATTTAAAT
1 AATTTAAAT
324543 AATGTTGGGC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (34 bp):
AATTTAAATTTAAAGTAAACTCAAACTTAAAATA
Found at i:324508 original size:17 final size:18
Alignment explanation
Indices: 324466--324542 Score: 72
Period size: 17 Copynumber: 4.5 Consensus size: 18
324456 TTTGGACATT
* *
324466 AATTTAAATTTA-AATTT
1 AATTTAAATTTATAAGTA
* *
324483 AACTCAAATTTATAA-TA
1 AATTTAAATTTATAAGTA
324500 AATTTAAATTT-TAAGTA
1 AATTTAAATTTATAAGTA
* *
324517 AATTTAAACTTA-AAATA
1 AATTTAAATTTATAAGTA
324534 AATTTAAAT
1 AATTTAAAT
324543 AATGTTGGGC
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
16 3 0.06
17 44 0.90
18 2 0.04
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (18 bp):
AATTTAAATTTATAAGTA
Done.