Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013075.1 Kokia drynarioides strain JFW-HI SEQ_128093, 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: 540471
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 504 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:270 original size:20 final size:17
Alignment explanation
Indices: 234--278 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 17
224 GGATCAAATT
234 GAAGAGAAAGGAAAAGA
1 GAAGAGAAAGGAAAAGA
251 GAAGAGCAAAGAGTAAAAGA
1 GAAGAG-AAAG-G-AAAAGA
271 GAAG-GAAA
1 GAAGAGAAA
279 TCAGCCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 2 0.08
20 10 0.40
ACGTcount: A:0.62, C:0.02, G:0.33, T:0.02
Consensus pattern (17 bp):
GAAGAGAAAGGAAAAGA
Found at i:1173 original size:25 final size:23
Alignment explanation
Indices: 1136--1240 Score: 86
Period size: 23 Copynumber: 4.5 Consensus size: 23
1126 ACACTAGCGC
1136 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTCT-GT
* *
1159 GCTCTCTGTTATTAGCGCTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTCTGT
* * * *
1184 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
* * * *
1207 ACTCTCTATTTAGTACTGTGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
1230 GCTCTCTGTTT
1 GCTCTCTGTTT
1241 GTTCCGTATA
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
23 47 0.70
24 1 0.01
25 16 0.24
26 3 0.04
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTCTGT
Found at i:1195 original size:23 final size:23
Alignment explanation
Indices: 1157--1237 Score: 92
Period size: 23 Copynumber: 3.4 Consensus size: 23
1147 AGCACGTCTC
**
1157 GTGCTCTCTGTTATTAGCGCTGTGT
1 GTGCTCTCTG--ATTAGTACTGTGT
*
1182 GTGCTCTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGTACTGTGT
*
1205 GTACTCTCT-ATTTAGTACTGTGT
1 GTGCTCTCTGA-TTAGTACTGTGT
1228 GTGCTCTCTG
1 GTGCTCTCTG
1238 TTTGTTCCGT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
22 1 0.02
23 37 0.77
25 10 0.21
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (23 bp):
GTGCTCTCTGATTAGTACTGTGT
Found at i:8161 original size:12 final size:12
Alignment explanation
Indices: 8144--8168 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8134 GCCGCCAATT
8144 GTCAACGCCAAC
1 GTCAACGCCAAC
8156 GTCAACGCCAAC
1 GTCAACGCCAAC
8168 G
1 G
8169 CTGCTTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.40, G:0.20, T:0.08
Consensus pattern (12 bp):
GTCAACGCCAAC
Found at i:10065 original size:93 final size:92
Alignment explanation
Indices: 9900--10092 Score: 350
Period size: 93 Copynumber: 2.1 Consensus size: 92
9890 AATGCTATAT
9900 GAATTTTAGAACGCTTTGTTAAAGGATATGATTTTTATCGAAAATTACTAAATAGAGGTGCTAAG
1 GAATTTTAGAACGCTTTGTTAAAGGATATGATTTTTATCGAAAATTACTAAATAGAGGTGCTAAG
9965 GGTATATACTTTAACTAACATTCTGTA
66 GGTATATACTTTAACTAACATTCTGTA
*
9992 GAATTTATAGAATGCTTTGTTAAAGGATATGATTTTTATCGAAAATTACTAAATAGAGGTGCTAA
1 GAATTT-TAGAACGCTTTGTTAAAGGATATGATTTTTATCGAAAATTACTAAATAGAGGTGCTAA
*
10057 GGGTATATACTTTAACTAACGTTCTGTA
65 GGGTATATACTTTAACTAACATTCTGTA
*
10085 GGATTTTA
1 GAATTTTA
10093 TACATGTAAA
Statistics
Matches: 97, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
92 8 0.08
93 89 0.92
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (92 bp):
GAATTTTAGAACGCTTTGTTAAAGGATATGATTTTTATCGAAAATTACTAAATAGAGGTGCTAAG
GGTATATACTTTAACTAACATTCTGTA
Found at i:15764 original size:22 final size:23
Alignment explanation
Indices: 15720--15765 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
15710 AAGCCCGCCC
15720 ATATTATTATTTTTTAAATATTT
1 ATATTATTATTTTTTAAATATTT
15743 ATATTA-TATTATTTTAAA-ATTT
1 ATATTATTATT-TTTTAAATATTT
15765 A
1 A
15766 ATAATCTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATATTATTATTTTTTAAATATTT
Found at i:22820 original size:40 final size:40
Alignment explanation
Indices: 22765--22845 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
22755 CACTAAATTA
22765 TTCATATCTTGAGCTAAAGACTTTGAAATTAAGATCCGCT
1 TTCATATCTTGAGCTAAAGACTTTGAAATTAAGATCCGCT
22805 TTCATATCTTGAGCTAAAGACTTTGAAATTAAGATCCGCT
1 TTCATATCTTGAGCTAAAGACTTTGAAATTAAGATCCGCT
22845 T
1 T
22846 GATGTTTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (40 bp):
TTCATATCTTGAGCTAAAGACTTTGAAATTAAGATCCGCT
Found at i:24002 original size:13 final size:11
Alignment explanation
Indices: 23970--24012 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
23960 CCATTTTCTA
*
23970 AATAAAATAAT
1 AATAAAATATT
23981 AAT-AAATATTT
1 AATAAAATA-TT
23992 AAGTAAAATATT
1 AA-TAAAATATT
24004 AATAAAATA
1 AATAAAATA
24013 ATATTTAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 5 0.18
13 5 0.18
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AATAAAATATT
Found at i:31936 original size:22 final size:21
Alignment explanation
Indices: 31909--31966 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
31899 ACCTTAAATA
31909 AAAAATAAAATTATAATGTTTT
1 AAAAATAAAATTAT-ATGTTTT
* * *
31931 AAAAATAAAAATATCTTTTTT
1 AAAAATAAAATTATATGTTTT
*
31952 AAAATTAAAAATTAT
1 AAAAAT-AAAATTAT
31967 GGAAAAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAAATAAAATTATATGTTTT
Found at i:31951 original size:21 final size:22
Alignment explanation
Indices: 31909--31963 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
31899 ACCTTAAATA
*
31909 AAAAATAAAATTATAATGTTTT
1 AAAAATAAAAATATAATGTTTT
* *
31931 AAAAATAAAAATAT-CTTTTTT
1 AAAAATAAAAATATAATGTTTT
*
31952 AAAATTAAAAAT
1 AAAAATAAAAAT
31964 TATGGAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAAATAAAAATATAATGTTTT
Found at i:32041 original size:29 final size:29
Alignment explanation
Indices: 32007--32063 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
31997 TTTTAAAAAT
32007 ATAGCAAAATT-TTACCGATCAACTACGAA
1 ATAGC-AAATTGTTACCGATCAACTACGAA
** *
32036 ATAGCAGTTTGTTGCCGATCAACTACGA
1 ATAGCAAATTGTTACCGATCAACTACGA
32064 GTCATGGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (29 bp):
ATAGCAAATTGTTACCGATCAACTACGAA
Found at i:33295 original size:15 final size:17
Alignment explanation
Indices: 33265--33296 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
33255 AATGAATAGA
33265 ATGATATGTATAATTAT
1 ATGATATGTATAATTAT
33282 ATGA-ATGT-TAATTAT
1 ATGATATGTATAATTAT
33297 GTGTGATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
ATGATATGTATAATTAT
Found at i:34068 original size:23 final size:23
Alignment explanation
Indices: 34039--34176 Score: 213
Period size: 23 Copynumber: 6.0 Consensus size: 23
34029 GCTCTTTGTT
** *
34039 ATTAGCACAGTGTGTGGTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
34062 ATTAGCACTTTGTGTGCTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
34085 ATTAGCACTTTGTGTGCTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
34108 ATTAGCACTTTGTGTGCTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
* *
34131 ATTAGTACTTTGTGTACTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
* *
34154 TTTAGCACTATGTGTGCTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
34177 TTGCCTAGCA
Statistics
Matches: 106, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 106 1.00
ACGTcount: A:0.14, C:0.20, G:0.22, T:0.43
Consensus pattern (23 bp):
ATTAGCACTTTGTGTGCTCTCTG
Found at i:34177 original size:23 final size:23
Alignment explanation
Indices: 34006--34225 Score: 205
Period size: 23 Copynumber: 9.5 Consensus size: 23
33996 ACACTAGCGC
* *
34006 GCTCTCTGTTTAGCACGTCT-CGT
1 GCTCTCTGTTTAGCAC-TTTGTGT
* **
34029 GCTCTTTGTTATTAGCACAGTGTGT
1 GCTCTCTG-T-TTAGCACTTTGTGT
* *
34054 GGTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
34077 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
34100 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
34123 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
* *
34146 ACTCTCTGTTTAGCACTATGTGT
1 GCTCTCTGTTTAGCACTTTGTGT
*
34169 GCTCTCTGTTGCCTAGCAC-TTATGT
1 GCTCTCTGTT---TAGCACTTTGTGT
* *
34194 GCTCTCTG-TTAGTATTTTG-GT
1 GCTCTCTGTTTAGCACTTTGTGT
*
34215 ACTCTCTGTTT
1 GCTCTCTGTTT
34226 GTTCCATATA
Statistics
Matches: 167, Mismatches: 22, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
21 13 0.08
22 4 0.02
23 114 0.68
24 3 0.02
25 27 0.16
26 6 0.04
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTTTGTGT
Found at i:34223 original size:69 final size:69
Alignment explanation
Indices: 34007--34225 Score: 230
Period size: 69 Copynumber: 3.1 Consensus size: 69
33997 CACTAGCGCG
* * * ** * * *
34007 CTCTCTGTTTAGCACGTCT-CGTGCTCTTTGTTATTAGCACAGTGTGTGGTCTCTGATTAGCACT
1 CTCTCTGTTTAGCAC-TATGTGTGCTCTCTG--ATTAGCACTTTATGTGCTCTCTGATTAGTACT
*
34071 TTGTGTG
63 TTGTGTA
* * *
34078 CTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTG
1 CTCTCTGTTTAGCACTATGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTTTG
34143 TGTA
66 TGTA
* *
34147 CTCTCTGTTTAGCACTATGTGTGCTCTCTGTTGCCTAGCAC-TTATGTGCTCTCTG-TTAGTATT
1 CTCTCTGTTTAGCACTATGTGTGCTCTCTGAT---TAGCACTTTATGTGCTCTCTGATTAGTACT
34210 TTG-GTA
63 TTGTGTA
34216 CTCTCTGTTT
1 CTCTCTGTTT
34226 GTTCCATATA
Statistics
Matches: 130, Mismatches: 14, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
69 76 0.58
70 12 0.09
71 36 0.28
72 6 0.05
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (69 bp):
CTCTCTGTTTAGCACTATGTGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTTTG
TGTA
Found at i:35697 original size:21 final size:21
Alignment explanation
Indices: 35671--35717 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
35661 CTACAACTTA
* *
35671 AAGCGGAGGCAACAGCGAGGG
1 AAGCGGAGGCAACAACGAGAG
*
35692 AAGCGGAGGCAGCAACGAGAG
1 AAGCGGAGGCAACAACGAGAG
35713 AAGCG
1 AAGCG
35718 AAAGAAGCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.19, G:0.45, T:0.00
Consensus pattern (21 bp):
AAGCGGAGGCAACAACGAGAG
Found at i:36118 original size:43 final size:42
Alignment explanation
Indices: 36030--36287 Score: 284
Period size: 43 Copynumber: 6.0 Consensus size: 42
36020 ATCTATTAAT
*
36030 TTTAGCGGCGTTTGTGGGTGAAGCG-CGCTAAAGACCATGCTC
1 TTTAGCGGCGTTTGTGGG-GAAGCGCCGCTAAAGACCATGTTC
* **
36072 TTTAGCGGCGTTTGTGAGGGAAGCGCCTCTAAAGACCATGCCC
1 TTTAGCGGCGTTTGTG-GGGAAGCGCCGCTAAAGACCATGTTC
* * *
36115 TTTAGCGGCGTTTATGAGGGAAGCACCGCTAAAGACCATGTTA
1 TTTAGCGGCGTTTGTG-GGGAAGCGCCGCTAAAGACCATGTTC
* * *
36158 TTTAGCGGTGTTTGCGGATGAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGG-GGAAGCGCCGCTAAAGACCATGTTC
** **
36201 TTTAGCGATGTTTGTGGCAAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGG-GGAAGCGCCGCTAAAGACCATGTTC
* * * * *
36244 TGTAGCGGGGTTTGTGTGGAAAGCACCGCTAAAGACAATGTTC
1 TTTAGCGGCGTTTGTG-GGGAAGCGCCGCTAAAGACCATGTTC
36287 T
1 T
36288 ATAATAGCGT
Statistics
Matches: 187, Mismatches: 25, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
42 23 0.12
43 163 0.87
44 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGGGGAAGCGCCGCTAAAGACCATGTTC
Found at i:36268 original size:129 final size:128
Alignment explanation
Indices: 36030--36285 Score: 334
Period size: 129 Copynumber: 2.0 Consensus size: 128
36020 ATCTATTAAT
* * * **
36030 TTTAGCGGCGTTTGTGGGTGAAGCGCGCTAAAGACCATGCTCTTTAGCGGCGTTTGTGAGGGAAG
1 TTTAGCGGCGTTTGCGGATGAAGCGCGCTAAAGACCATGCTCTTTAGCGACGTTTGTGAGAAAAG
* * * *
36095 CGCCTCTAAAGACCATGCCCTTTAGCGGCGTTTATGAGGGAAGCACCGCTAAAGACCATGTTA
66 CGCCGCTAAAGACCATGCCCTGTAGCGGCGTTTATGAGGAAAGCACCGCTAAAGACAATGTTA
* * *
36158 TTTAGCGGTGTTTGCGGATGAAGCGCCGCTAAAGACCATGTTCTTTAGCGATGTTTGTG-GCAAA
1 TTTAGCGGCGTTTGCGGATGAAGCG-CGCTAAAGACCATGCTCTTTAGCGACGTTTGTGAG-AAA
** * * *
36222 AGCGCCGCTAAAGACCATGTTCTGTAGCGGGGTTTGTGTGGAAAGCACCGCTAAAGACAATGTT
64 AGCGCCGCTAAAGACCATGCCCTGTAGCGGCGTTTATGAGGAAAGCACCGCTAAAGACAATGTT
36286 CTATAATAGC
Statistics
Matches: 109, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
128 23 0.21
129 86 0.79
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.26
Consensus pattern (128 bp):
TTTAGCGGCGTTTGCGGATGAAGCGCGCTAAAGACCATGCTCTTTAGCGACGTTTGTGAGAAAAG
CGCCGCTAAAGACCATGCCCTGTAGCGGCGTTTATGAGGAAAGCACCGCTAAAGACAATGTTA
Found at i:40219 original size:3 final size:3
Alignment explanation
Indices: 40211--40245 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
40201 AGCTAGGAAG
*
40211 GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
40246 GATTGCCGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:47499 original size:18 final size:18
Alignment explanation
Indices: 47476--47510 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
47466 GAGTTAAACG
47476 AATCGAGTTATTCAAGTT
1 AATCGAGTTATTCAAGTT
47494 AATCGAGTTATTCAAGT
1 AATCGAGTTATTCAAGT
47511 CAATTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (18 bp):
AATCGAGTTATTCAAGTT
Found at i:51441 original size:6 final size:6
Alignment explanation
Indices: 51430--51457 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
51420 CTGGTGCCAA
51430 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
51458 TTATAATTAA
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:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:55979 original size:73 final size:70
Alignment explanation
Indices: 55894--56038 Score: 170
Period size: 73 Copynumber: 2.0 Consensus size: 70
55884 TTAAAATATA
* * *
55894 ATTTATCCTTTAATTAT-TTCTTCTT-TCAATTAAATTTTATTTTTTAAAATTTAAATTT-TTTT
1 ATTTATCCTTTAAATATGTT-TTCTTCT-AATTAAATTCTATTTTTT--AATTTAAATTTATTCT
55956 GCTTTAAATTG
62 --TTTAAATTG
* *
55967 ATTTATTCTTTAAATATGTTTTCTTCTAATTGAATTCTATTTTTTAATTTAAATTTATTCTTTTA
1 ATTTATCCTTTAAATATGTTTTCTTCTAATTAAATTCTATTTTTTAATTTAAATTTATTCTTTTA
56032 AATTG
66 AATTG
56037 AT
1 AT
56039 ATTTTAATAA
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
70 11 0.17
71 11 0.17
72 3 0.05
73 36 0.56
74 3 0.05
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (70 bp):
ATTTATCCTTTAAATATGTTTTCTTCTAATTAAATTCTATTTTTTAATTTAAATTTATTCTTTTA
AATTG
Found at i:79277 original size:2 final size:2
Alignment explanation
Indices: 79270--79304 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
79260 TGGGTACAAT
79270 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
79305 GAATCATTGA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:83972 original size:20 final size:19
Alignment explanation
Indices: 83925--83973 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
83915 TTTTTTTTTT
83925 TAATTA-AAAAATATAAAA
1 TAATTATAAAAATATAAAA
* * *
83943 TATTTTTAAAAATCTAAAAA
1 TAATTATAAAAATAT-AAAA
83963 TAATTATAAAA
1 TAATTATAAAA
83974 TCAGTATTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 4 0.17
19 7 0.29
20 13 0.54
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
TAATTATAAAAATATAAAA
Found at i:105005 original size:24 final size:24
Alignment explanation
Indices: 104973--105018 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
104963 TCATTTAACT
104973 TAATCGAACATGTTCACGAACATA
1 TAATCGAACATGTTCACGAACATA
*
104997 TAATTGAACATGTTCACGAACA
1 TAATCGAACATGTTCACGAACA
105019 AAGTTAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (24 bp):
TAATCGAACATGTTCACGAACATA
Found at i:108326 original size:20 final size:20
Alignment explanation
Indices: 108285--108326 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
108275 CTCAAAATAA
* *
108285 ATAAATAAATAAATTATTTC
1 ATAAATAAATAAATAATATC
108305 ATAAATTAAAT-AATAATATC
1 ATAAA-TAAATAAATAATATC
108325 AT
1 AT
108327 CCTATAGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAATAAATAAATAATATC
Found at i:121889 original size:30 final size:29
Alignment explanation
Indices: 121828--121890 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
121818 ATTTTATTAT
* *
121828 TTTTATTATTTTTAAAAAATTAAATTAAA
1 TTTTAATATTTTTAAAAAATTAAATGAAA
* *
121857 TTTTAATATTTTTATAAAATTAAAATGCAA
1 TTTTAATATTTTTAAAAAATT-AAATGAAA
121887 TTTT
1 TTTT
121891 TCATTATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (29 bp):
TTTTAATATTTTTAAAAAATTAAATGAAA
Found at i:122560 original size:16 final size:15
Alignment explanation
Indices: 122519--122563 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
122509 AAAAATATAA
*
122519 TTTTATTATTTTAAT
1 TTTTATTTTTTTAAT
* *
122534 GTTTATATTTTGTAAT
1 TTTTAT-TTTTTTAAT
122550 TTTTATTTTTTTAA
1 TTTTATTTTTTTAA
122564 AAATTAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (15 bp):
TTTTATTTTTTTAAT
Found at i:123056 original size:3 final size:3
Alignment explanation
Indices: 123048--123085 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
123038 GCTTTAACAT
123048 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
123086 TGTTACCAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:128191 original size:14 final size:14
Alignment explanation
Indices: 128172--128205 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
128162 TTGTTTGATT
128172 GAAAATGATTTTC-G
1 GAAAATGA-TTTCAG
128186 GAAAATGATTTCAG
1 GAAAATGATTTCAG
128200 GAAAAT
1 GAAAAT
128206 TGTTTACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (14 bp):
GAAAATGATTTCAG
Found at i:129842 original size:52 final size:52
Alignment explanation
Indices: 129761--129865 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
129751 TTTCTGAGAA
129761 ATGTTCCTCGAGTGCTATTATCCTAAGCTGCTAATGAATAATGGAGGAAGAG
1 ATGTTCCTCGAGTGCTATTATCCTAAGCTGCTAATGAATAATGGAGGAAGAG
* *
129813 ATGTTCCTCGAGTGCTATTATCTTGAGCTGCTAATGAATAATGGAGGAAGAG
1 ATGTTCCTCGAGTGCTATTATCCTAAGCTGCTAATGAATAATGGAGGAAGAG
129865 A
1 A
129866 ATATAAGGGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (52 bp):
ATGTTCCTCGAGTGCTATTATCCTAAGCTGCTAATGAATAATGGAGGAAGAG
Found at i:131119 original size:16 final size:16
Alignment explanation
Indices: 131100--131156 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
131090 TTTTTAAGAA
131100 TTAAATTTTATTGGGT
1 TTAAATTTTATTGGGT
** *
131116 TTAAAAATAATTGGGT
1 TTAAATTTTATTGGGT
* *
131132 TTAATTTATTAATGGGTT
1 TTAAATT-TTATTGGG-T
131150 TTAAATT
1 TTAAATT
131157 GGGTAAGATA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 17 0.57
17 6 0.20
18 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (16 bp):
TTAAATTTTATTGGGT
Found at i:131638 original size:7 final size:7
Alignment explanation
Indices: 131619--131648 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
131609 GCACCAACGA
131619 ATATTAT
1 ATATTAT
131626 -TATTAT
1 ATATTAT
131632 ATATTAT
1 ATATTAT
131639 ATATTAT
1 ATATTAT
131646 ATA
1 ATA
131649 AATGGAAGCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATTAT
Found at i:132791 original size:22 final size:22
Alignment explanation
Indices: 132766--132814 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
132756 ATAAGATTCT
*
132766 TTTTAAATG-GTTTTTTAGAGTA
1 TTTTAAATGAATTTTTTA-AGTA
*
132788 TTTTAAATGAATTTTTTAAGTC
1 TTTTAAATGAATTTTTTAAGTA
132810 TTTTA
1 TTTTA
132815 GATTAAAGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 17 0.71
23 7 0.29
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (22 bp):
TTTTAAATGAATTTTTTAAGTA
Found at i:136530 original size:2 final size:2
Alignment explanation
Indices: 136523--136563 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
136513 AAAGAAATAA
136523 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
136564 TGAGCTTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:139535 original size:25 final size:25
Alignment explanation
Indices: 139501--139553 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
139491 AGGGACAGCA
139501 AACCACTACCCTTAAAGAGCTTACG
1 AACCACTACCCTTAAAGAGCTTACG
* *
139526 AACCATTACCCTTAAAGAGCTTATG
1 AACCACTACCCTTAAAGAGCTTACG
139551 AAC
1 AAC
139554 TTTTATAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.38, C:0.28, G:0.11, T:0.23
Consensus pattern (25 bp):
AACCACTACCCTTAAAGAGCTTACG
Found at i:139619 original size:32 final size:31
Alignment explanation
Indices: 139567--139642 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 31
139557 TATAGAACTG
139567 CTACCAATAG--A-TTTTTTTTTTGAACAAAT
1 CTACCAATAGATATTTTTTTTTTTGAA-AAAT
*
139596 CTACCAATAGATATTTTTTTTTTTTGAATAAT
1 CTACCAATAGATA-TTTTTTTTTTTGAAAAAT
139628 CTACCAATAGATATT
1 CTACCAATAGATATT
139643 AATTTATCTG
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
29 10 0.24
31 3 0.07
32 16 0.38
33 13 0.31
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46
Consensus pattern (31 bp):
CTACCAATAGATATTTTTTTTTTTGAAAAAT
Found at i:148355 original size:10 final size:10
Alignment explanation
Indices: 148340--148382 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
148330 AAATTATTAT
148340 GAAAAAAATA
1 GAAAAAAATA
*
148350 GAAAAAAGTA
1 GAAAAAAATA
* *
148360 AAAAAAAAAA
1 GAAAAAAATA
*
148370 AAAAAAAATA
1 GAAAAAAATA
148380 GAA
1 GAA
148383 GCTACCATTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (10 bp):
GAAAAAAATA
Found at i:155277 original size:4 final size:4
Alignment explanation
Indices: 155268--155299 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
155258 CCCCAATGTT
*
155268 TTTA TTTA TTTA TTTA TTTA TTTA TATA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
155300 GGTTTAGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:157209 original size:27 final size:27
Alignment explanation
Indices: 157150--157209 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
157140 TGATCCTATA
*
157150 AATTTTATATTAATAAATGATGAAATT
1 AATTTTATATTAATAAATGATAAAATT
* *
157177 ATATTTTATTTTTA-AAATGATAAAATTT
1 A-ATTTTATATTAATAAATGATAAAA-TT
157205 AATTT
1 AATTT
157210 AATTGTACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 15 0.54
28 13 0.46
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (27 bp):
AATTTTATATTAATAAATGATAAAATT
Found at i:162872 original size:10 final size:10
Alignment explanation
Indices: 162857--162886 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
162847 TCTTTTAGTT
162857 CTTGTTTTCC
1 CTTGTTTTCC
162867 CTTGTTTTCC
1 CTTGTTTTCC
162877 CTTGTTTTCC
1 CTTGTTTTCC
162887 TCGGTTTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.00, C:0.30, G:0.10, T:0.60
Consensus pattern (10 bp):
CTTGTTTTCC
Found at i:169365 original size:10 final size:10
Alignment explanation
Indices: 169314--169389 Score: 52
Period size: 10 Copynumber: 7.8 Consensus size: 10
169304 TAAAACTCTG
169314 AAAAT-TTAA
1 AAAATATTAA
*
169323 AAAATTATAAA
1 AAAA-TATTAA
**
169334 AAAATATTTT
1 AAAATATTAA
*
169344 TAAATATT-A
1 AAAATATTAA
169353 AAAATATTAA
1 AAAATATTAA
169363 AAAAT-TCT-A
1 AAAATAT-TAA
**
169372 AAAATACAAA
1 AAAATATTAA
169382 AAAATATT
1 AAAATATT
169390 TATAATACTT
Statistics
Matches: 50, Mismatches: 11, Indels: 11
0.69 0.15 0.15
Matches are distributed among these distances:
9 18 0.36
10 25 0.50
11 7 0.14
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAATATTAA
Found at i:169367 original size:19 final size:20
Alignment explanation
Indices: 169314--169388 Score: 57
Period size: 19 Copynumber: 3.9 Consensus size: 20
169304 TAAAACTCTG
*
169314 AAAAT-TTAAAAAATTATAAA
1 AAAATATTAAAAAA-TATATA
***
169334 AAAATATTTTTAAATAT-TA
1 AAAATATTAAAAAATATATA
*
169353 AAAATATTAAAAAAT-TCTA
1 AAAATATTAAAAAATATATA
**
169372 AAAATACAAAAAAATAT
1 AAAATATTAAAAAATAT
169389 TTATAATACT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
18 1 0.02
19 28 0.65
20 9 0.21
21 5 0.12
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAATATTAAAAAATATATA
Found at i:174720 original size:8 final size:8
Alignment explanation
Indices: 174707--174738 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
174697 ATTGAAGAGA
174707 AAGGAAAG
1 AAGGAAAG
174715 AAGGAAAG
1 AAGGAAAG
174723 AAGGAAAG
1 AAGGAAAG
174731 AAGGAAAG
1 AAGGAAAG
174739 GGACCAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (8 bp):
AAGGAAAG
Found at i:175203 original size:11 final size:11
Alignment explanation
Indices: 175187--175217 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
175177 TTCTGATTTT
175187 GAAAAATTATA
1 GAAAAATTATA
175198 GAAAAA-TATA
1 GAAAAATTATA
175208 GAAAAATTAT
1 GAAAAATTAT
175218 TAGAGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (11 bp):
GAAAAATTATA
Found at i:175846 original size:23 final size:22
Alignment explanation
Indices: 175820--175986 Score: 112
Period size: 23 Copynumber: 7.5 Consensus size: 22
175810 ACTAGCGCGT
175820 TCTCTGTTTAGCATTGTGTGTGC
1 TCTCTGTTTAGCATT-TGTGTGC
** *
175843 TCTCTGACTAGCACTGTGTGTGC
1 TCTCTGTTTAGCA-TTTGTGTGC
* ** *
175866 TCTCTGTTTACCACGTCTCGTGC
1 TCTCTGTTTAGCATTTGT-GTGC
*
175889 TCTCTGTTATTAGCACTTCGTGTGC
1 TCTCTG-T-TTAGCA-TTTGTGTGC
*
175914 TCTCTGATTAGCACTTTGTGTG-
1 TCTCTGTTTAGCA-TTTGTGTGC
** *
175936 -CTC-AATT--C-TTTGTGTAC
1 TCTCTGTTTAGCATTTGTGTGC
175953 TCTCTGTTTAGCACTTTGTGTGC
1 TCTCTGTTTAGCA-TTTGTGTGC
175976 TCTCTGTTTAG
1 TCTCTGTTTAG
175987 TACTTCGATA
Statistics
Matches: 112, Mismatches: 20, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
16 7 0.06
18 4 0.04
19 2 0.02
20 3 0.03
21 4 0.04
22 3 0.03
23 71 0.63
24 2 0.02
25 15 0.13
26 1 0.01
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (22 bp):
TCTCTGTTTAGCATTTGTGTGC
Found at i:175937 original size:48 final size:46
Alignment explanation
Indices: 175820--175981 Score: 128
Period size: 48 Copynumber: 3.6 Consensus size: 46
175810 ACTAGCGCGT
175820 TCTCTGTTTAGCA-TTGTGTGTGCTCTCTGACTAGCACTGTGTGTGC
1 TCTCTGTTTAGCACTT-TGTGTGCTCTCTGACTAGCACTGTGTGTGC
* * * *
175866 TCTCTGTTTACCACGTCT-CGTGCTCTCTGTTATTAGCACT-TCGTGTGC
1 TCTCTGTTTAGCAC-TTTGTGTGCTCTCTG--ACTAGCACTGT-GTGTGC
* ** * *
175914 TCTCTGATTAGCACTTTGTGTG--CTC--A--A-TTCTTTGTGTAC
1 TCTCTGTTTAGCACTTTGTGTGCTCTCTGACTAGCACTGTGTGTGC
175953 TCTCTGTTTAGCACTTTGTGTGCTCTCTG
1 TCTCTGTTTAGCACTTTGTGTGCTCTCTG
175982 TTTAGTACTT
Statistics
Matches: 93, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
39 28 0.30
40 2 0.02
41 3 0.03
42 1 0.01
46 25 0.27
47 4 0.04
48 30 0.32
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (46 bp):
TCTCTGTTTAGCACTTTGTGTGCTCTCTGACTAGCACTGTGTGTGC
Found at i:175991 original size:23 final size:23
Alignment explanation
Indices: 175943--175991 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
175933 GTGCTCAATT
175943 CTTTGTGTACTCTCTGTTTAGCA
1 CTTTGTGTACTCTCTGTTTAGCA
* *
175966 CTTTGTGTGCTCTCTGTTTAGTA
1 CTTTGTGTACTCTCTGTTTAGCA
175989 CTT
1 CTT
175992 CGATACTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.10, C:0.20, G:0.18, T:0.51
Consensus pattern (23 bp):
CTTTGTGTACTCTCTGTTTAGCA
Found at i:178067 original size:2 final size:2
Alignment explanation
Indices: 178060--178092 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
178050 ATTATTGAAC
178060 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 A
178093 AAACCTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:193345 original size:88 final size:85
Alignment explanation
Indices: 193205--193392 Score: 211
Period size: 88 Copynumber: 2.2 Consensus size: 85
193195 AAATTTAAAA
* * *
193205 AAAAAACAATTAAG-TCTTTTTTTTATGCACTTAATTGAATACTTAAATTTTCAAAATGCATAAA
1 AAAAAACAATTAAGCTCTTTTTTTTATCCACTCAATTGAATACTTAAACTTTCAAAATGCATAAA
* *
193269 AAA-AGCTCTCAAACTTCTTC
66 AAAGA-CACTCAAAATTCTTC
* * * *
193289 AGGAAAAACAATTAAGCTTTTGTTTTTTTTCCCACTCAATTG-GTACTTGAACTTTCAAAATGCA
1 A--AAAAACAATTAAGCTCTT-TTTTTTAT-CCACTCAATTGAATACTTAAACTTTCAAAATGCA
*
193353 TAAAAAAGACACTCAAAATTTTTC
62 TAAAAAAGACACTCAAAATTCTTC
193377 AAAAAAGCAATTAAGC
1 AAAAAA-CAATTAAGC
193393 CCTTGCTCTT
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
84 1 0.01
86 18 0.21
87 12 0.14
88 46 0.53
89 10 0.11
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (85 bp):
AAAAAACAATTAAGCTCTTTTTTTTATCCACTCAATTGAATACTTAAACTTTCAAAATGCATAAA
AAAGACACTCAAAATTCTTC
Found at i:193855 original size:58 final size:56
Alignment explanation
Indices: 193781--193903 Score: 149
Period size: 56 Copynumber: 2.2 Consensus size: 56
193771 TTTTACGAAA
* * * *
193781 TTTATATTTCTCTATATTTTGTATAATTTTCTTATGA-CTTTATAAAATTTTATAATTT
1 TTTATATTTCTATATA-TTT-TATAATTTT-TTACGATCTTTATAAAAATTTACAATTT
** *
193839 TTTATATTTCTATATATTTTATCGTTTTTTACGATTTTTATAAAAATTTACAATTT
1 TTTATATTTCTATATATTTTATAATTTTTTACGATCTTTATAAAAATTTACAATTT
193895 TTTATATTT
1 TTTATATTT
193904 TTTTATTAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
55 5 0.09
56 34 0.60
57 3 0.05
58 15 0.26
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (56 bp):
TTTATATTTCTATATATTTTATAATTTTTTACGATCTTTATAAAAATTTACAATTT
Found at i:193929 original size:30 final size:30
Alignment explanation
Indices: 193873--193930 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
193863 TTTTTTACGA
* *
193873 TTTTTATAAAAATTTACAATTTTTTATATT
1 TTTTTATAAAAATTTACAAATATTTATATT
*
193903 TTTTTATTAAAATTTA-ATAATATTTATA
1 TTTTTATAAAAATTTACA-AATATTTATA
193931 ACCTTTATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTTTATAAAAATTTACAAATATTTATATT
Found at i:206645 original size:7 final size:7
Alignment explanation
Indices: 206633--206662 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
206623 AGCAAAGCTA
206633 CAGTTTC
1 CAGTTTC
206640 CAGTTTC
1 CAGTTTC
206647 CAGTTTC
1 CAGTTTC
206654 CAGTTTC
1 CAGTTTC
206661 CA
1 CA
206663 TCTATTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.30, G:0.13, T:0.40
Consensus pattern (7 bp):
CAGTTTC
Found at i:226441 original size:2 final size:2
Alignment explanation
Indices: 226434--226459 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
226424 GATCTCAACC
226434 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
226460 TATATATTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:243010 original size:2 final size:2
Alignment explanation
Indices: 243003--243033 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
242993 CTTCTATTTA
243003 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 A
243034 AAACTTATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:243338 original size:90 final size:89
Alignment explanation
Indices: 243185--243365 Score: 299
Period size: 90 Copynumber: 2.0 Consensus size: 89
243175 CATTATGACC
* *
243185 AATATTCGACCATGTATGTAACCTCACACTCCTCCTCCCAACGTAAAGTGCAAGAAAAGTTCTGA
1 AATATTCGACCATGAATGTAACCTCACACCCCTCCTCCCAACGTAAAGTGCAAGAAAAGTTCTGA
*
243250 TTGTATTAGAAAAATAAAAACAAGA
66 TTGTACTAGAAAAATAAAAAC-AGA
* * *
243275 AATATTCGACCTTGAATGTAACCTCACACCCCTCCTCCCAGCTTAAAGTGCAAGAAAAGTTCTGA
1 AATATTCGACCATGAATGTAACCTCACACCCCTCCTCCCAACGTAAAGTGCAAGAAAAGTTCTGA
243340 TTGTACTAGAAAAATAAAAACAGA
66 TTGTACTAGAAAAATAAAAACAGA
243364 AA
1 AA
243366 CCTCGGATAT
Statistics
Matches: 85, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 5 0.06
90 80 0.94
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (89 bp):
AATATTCGACCATGAATGTAACCTCACACCCCTCCTCCCAACGTAAAGTGCAAGAAAAGTTCTGA
TTGTACTAGAAAAATAAAAACAGA
Found at i:255707 original size:2 final size:2
Alignment explanation
Indices: 255700--255725 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
255690 GGAATAATAT
255700 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
255726 AAAAAACCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:265429 original size:2 final size:2
Alignment explanation
Indices: 265422--265457 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
265412 GGACCAAATG
265422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
265458 TACTTTTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:275049 original size:26 final size:27
Alignment explanation
Indices: 275011--275073 Score: 65
Period size: 29 Copynumber: 2.3 Consensus size: 27
275001 GGTACCTAAA
*
275011 CTAAACTACTTTT-CCCAAATTGGTAC
1 CTAAACTACTTTTACCAAAATTGGTAC
** *
275037 CTAAACTTTTTTTTAGTCAAAATTGGTAC
1 CTAAAC-TACTTTTA-CCAAAATTGGTAC
275066 CTAAACTA
1 CTAAACTA
275074 TTAAATTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
26 6 0.21
27 5 0.17
28 1 0.03
29 17 0.59
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (27 bp):
CTAAACTACTTTTACCAAAATTGGTAC
Found at i:276805 original size:5 final size:5
Alignment explanation
Indices: 276795--276820 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
276785 GCATATAAAT
276795 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
276821 CATGGGCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:291422 original size:54 final size:56
Alignment explanation
Indices: 291338--291467 Score: 140
Period size: 54 Copynumber: 2.4 Consensus size: 56
291328 AAAATTTAAG
* * * *
291338 ATAAAAAAATATTTTTTTGATATTTCCCAAGCCATGA-TCATCACCC-TTTT-TCAA
1 ATAAAAAAATATTTTTTGGGTACTTCCCAAGCCATGACT-AGCACCCTTTTTATCAA
* * * * *
291392 ATAAAAAAATATTTGTTGGGTACTTGCCAAGTCATTACTAGCACCCTTTTTATCAG
1 ATAAAAAAATATTTTTTGGGTACTTCCCAAGCCATGACTAGCACCCTTTTTATCAA
*
291448 ATAAAAAAATTTTTTTTGGG
1 ATAAAAAAATATTTTTTGGG
291468 GGATTTCAGA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
54 36 0.58
55 5 0.08
56 21 0.34
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (56 bp):
ATAAAAAAATATTTTTTGGGTACTTCCCAAGCCATGACTAGCACCCTTTTTATCAA
Found at i:300663 original size:2 final size:2
Alignment explanation
Indices: 300656--300682 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
300646 TGGGGAGGCC
300656 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
300683 CGACCAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:308739 original size:2 final size:2
Alignment explanation
Indices: 308732--308761 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
308722 ATTAGGTACA
308732 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
308762 CTATCTCTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:309830 original size:58 final size:56
Alignment explanation
Indices: 309678--309853 Score: 210
Period size: 58 Copynumber: 3.1 Consensus size: 56
309668 AATACGAATA
* * * *
309678 AAAAATATTCTTTTGAGTGTTTGCCACCAATGGCCTACACTGCATTTTTCAGATTT
1 AAAAATATTTTTTTGAGTGTTTGCCACCAATGGCTTACACTACATTTTTTAGATTT
* * * *
309734 AAAAATA-TTTTTTGGGTGTTTGTCACCCAATGGCTTACACTACGTTTTTTAAATTT
1 AAAAATATTTTTTTGAGTGTTTGCCA-CCAATGGCTTACACTACATTTTTTAGATTT
* * * *
309790 AAAAATATTTTTTTTGAGTGTTTACCACTCAATGACTTACATTACCTTTTTTAGATTT
1 AAAAATA-TTTTTTTGAGTGTTTGCCAC-CAATGGCTTACACTACATTTTTTAGATTT
309848 AAAAAT
1 AAAAAT
309854 TTTAAATTAT
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
55 15 0.15
56 39 0.39
57 1 0.01
58 46 0.46
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (56 bp):
AAAAATATTTTTTTGAGTGTTTGCCACCAATGGCTTACACTACATTTTTTAGATTT
Found at i:309964 original size:37 final size:40
Alignment explanation
Indices: 309923--310006 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 40
309913 TAAATTGTAA
*
309923 TATTTTAATTTAA-A-AAATTATTTAAATTGT-TTTTAAT
1 TATTTTAATTTAATATAAATTATTTAAATTATGTTTTAAT
*
309960 TATTTTAATTTAATTATAAATTTTTTAAATTATGTTTTAAT
1 TATTTTAATTTAA-TATAAATTATTTAAATTATGTTTTAAT
310001 TATTTT
1 TATTTT
310007 TTAAATTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
37 13 0.32
39 1 0.02
40 14 0.34
41 13 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (40 bp):
TATTTTAATTTAATATAAATTATTTAAATTATGTTTTAAT
Found at i:310001 original size:20 final size:20
Alignment explanation
Indices: 309938--310006 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
309928 TAATTTAAAA
*
309938 AATTA-TTTAAATTGTTTTT
1 AATTATTTTAAATTATTTTT
* * *
309957 AATTATTTTAATTTAATTATA
1 AATTATTTTAAATT-ATTTTT
309978 AATT-TTTTAAATTATGTTTT
1 AATTATTTTAAATTAT-TTTT
309998 AATTATTTT
1 AATTATTTT
310007 TTAAATTTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
19 7 0.18
20 21 0.54
21 11 0.28
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
AATTATTTTAAATTATTTTT
Found at i:310158 original size:55 final size:56
Alignment explanation
Indices: 310083--310235 Score: 195
Period size: 56 Copynumber: 2.7 Consensus size: 56
310073 GAAAAAGTAG
* * *
310083 TGTAAGTCATTTGGTAGCAAACAC-CAAAAAAATATTTTTAAATTTCAGAAAAG-TGA
1 TGTAGGTCA-TTGGTGGCAAACACTCAAAAAAATATTTTTAAATCTCAG-AAAGTTGA
* *
310139 T-TGAGGTCATTGGTGGCAAATACTCAAAAAAATATTTTTAAATCTGAGAAAGTTGA
1 TGT-AGGTCATTGGTGGCAAACACTCAAAAAAATATTTTTAAATCTCAGAAAGTTGA
* *
310195 TGTAGGCCATGGGTGGCAAACACTCAAAAAAATATTTTTAA
1 TGTAGGTCATTGGTGGCAAACACTCAAAAAAATATTTTTAA
310236 TTCGTATTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
55 17 0.20
56 67 0.79
57 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (56 bp):
TGTAGGTCATTGGTGGCAAACACTCAAAAAAATATTTTTAAATCTCAGAAAGTTGA
Found at i:316102 original size:18 final size:17
Alignment explanation
Indices: 316079--316114 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
316069 TTCATGCATT
*
316079 TTTTTTTTGTGGTAGTTA
1 TTTTTTTGGTGGTA-TTA
316097 TTTTTTTGGTGGTATTA
1 TTTTTTTGGTGGTATTA
316114 T
1 T
316115 GCATAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.11, C:0.00, G:0.22, T:0.67
Consensus pattern (17 bp):
TTTTTTTGGTGGTATTA
Found at i:317384 original size:7 final size:7
Alignment explanation
Indices: 317372--317402 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
317362 CAAAGAATGT
317372 CAGTGGG
1 CAGTGGG
317379 CAGTGGG
1 CAGTGGG
317386 CAGTGGG
1 CAGTGGG
*
317393 CAGTGAG
1 CAGTGGG
317400 CAG
1 CAG
317403 AACATCTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.16, G:0.52, T:0.13
Consensus pattern (7 bp):
CAGTGGG
Found at i:325649 original size:17 final size:18
Alignment explanation
Indices: 325617--325650 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
325607 TATTGAAACT
*
325617 AAAAATAATATTAACATG
1 AAAAATAATATAAACATG
325635 AAAAATAA-ATAAACAT
1 AAAAATAATATAAACAT
325651 TTTTTATTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (18 bp):
AAAAATAATATAAACATG
Found at i:328321 original size:30 final size:31
Alignment explanation
Indices: 328252--328321 Score: 74
Period size: 30 Copynumber: 2.3 Consensus size: 31
328242 TAAAAATAAT
* *
328252 AAATAAAAAATTATATAAAATTGTTAATATT
1 AAATAAAAAATAATATAAAATTGTTAATATA
**
328283 AAAT-AAAAATAATATAAATATT-TTTTTA-A
1 AAATAAAAAATAATATAAA-ATTGTTAATATA
328312 AAATAAAAAA
1 AAATAAAAAA
328322 ATAAAAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
29 4 0.12
30 22 0.67
31 7 0.21
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (31 bp):
AAATAAAAAATAATATAAAATTGTTAATATA
Found at i:328327 original size:7 final size:8
Alignment explanation
Indices: 328310--328340 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
328300 ATATTTTTTT
328310 AAAAATAA
1 AAAAATAA
328318 AAAAATAA
1 AAAAATAA
328326 AAAAATAA
1 AAAAATAA
328334 AAAAATA
1 AAAAATA
328341 CGAACCTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAATAA
Found at i:329664 original size:18 final size:21
Alignment explanation
Indices: 329620--329664 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 21
329610 AGTTTCCTAT
329620 TATATTAATTTTTTAATTAAA
1 TATATTAATTTTTTAATTAAA
*
329641 TTTATTAA-TTTTT-A-TAAA
1 TATATTAATTTTTTAATTAAA
329659 TATATT
1 TATATT
329665 TATTACATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 9 0.41
19 1 0.05
20 5 0.23
21 7 0.32
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATATTAATTTTTTAATTAAA
Found at i:329665 original size:22 final size:21
Alignment explanation
Indices: 329617--329669 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
329607 GTTAGTTTCC
*
329617 TATTATATTAATTTTTTAATTA
1 TATT-TATTAATTTTTTAAATA
*
329639 AATTTATTAATTTTTATAAATA
1 TATTTATTAATTTTT-TAAATA
329661 TATTTATTA
1 TATTTATTA
329670 CATAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTATTAATTTTTTAAATA
Found at i:331233 original size:24 final size:24
Alignment explanation
Indices: 331184--331235 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
331174 NCCATCTCCT
* *
331184 CCTCCTCCACCCTCACCGCCACCA
1 CCTCCACCACCCTCACCGCCAACA
*
331208 CCTCCACCTCCCTCA-CGACCAACA
1 CCTCCACCACCCTCACCG-CCAACA
331232 CCTC
1 CCTC
331236 TATTGTAAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.19, C:0.63, G:0.04, T:0.13
Consensus pattern (24 bp):
CCTCCACCACCCTCACCGCCAACA
Found at i:332674 original size:2 final size:2
Alignment explanation
Indices: 332662--332696 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
332652 TGAAAACGAT
*
332662 GA GA G- GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
332697 CATGATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:335050 original size:51 final size:51
Alignment explanation
Indices: 334933--335163 Score: 230
Period size: 51 Copynumber: 4.5 Consensus size: 51
334923 TCATTTAATA
* ** ** ***
334933 CTCACGATGACA-TATAGTCATCGGATCTCTTGTTCCATGTAGGAATTCATACA
1 CTCACGATGACACT-TAGTCATCGGA-CTTTTAATCCATAAAGG-ATTCATTTG
* * *
334986 CTCACGATGACACTAAGTCATCGGACTTTTAATCCATCATGGATTCATTTG
1 CTCACGATGACACTTAGTCATCGGACTTTTAATCCATAAAGGATTCATTTG
* * * * *
335037 CTCACGATGACACTTAGTCATCGAACCTTTAATTCGTAAAGGATTCATTTA
1 CTCACGATGACACTTAGTCATCGGACTTTTAATCCATAAAGGATTCATTTG
* *
335088 CTCACGATGACACTTAGTCATCAGACCCTTGTAATCCATAAAGGATTCATTTG
1 CTCACGATGACACTTAGTCATCGGA--CTTTTAATCCATAAAGGATTCATTTG
* *
335141 CTCACAATGACAGTTAGTCATCG
1 CTCACGATGACACTTAGTCATCG
335164 AATCCCTTTC
Statistics
Matches: 147, Mismatches: 28, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
51 72 0.49
52 11 0.07
53 63 0.43
54 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (51 bp):
CTCACGATGACACTTAGTCATCGGACTTTTAATCCATAAAGGATTCATTTG
Found at i:335151 original size:53 final size:50
Alignment explanation
Indices: 334986--335164 Score: 232
Period size: 51 Copynumber: 3.5 Consensus size: 50
334976 AATTCATACA
* * * *
334986 CTCACGATGACACTAAGTCATCGGACTTTTAATCCATCATGGATTCATTTG
1 CTCACGATGACACTTAGTCATC-GACCTTTAATCCATAAAGGATTCATTTG
* * *
335037 CTCACGATGACACTTAGTCATCGAACCTTTAATTCGTAAAGGATTCATTTA
1 CTCACGATGACACTTAGTCATCG-ACCTTTAATCCATAAAGGATTCATTTG
335088 CTCACGATGACACTTAGTCATCAGACCCTTGTAATCCATAAAGGATTCATTTG
1 CTCACGATGACACTTAGTCATC-GA-CCTT-TAATCCATAAAGGATTCATTTG
* *
335141 CTCACAATGACAGTTAGTCATCGA
1 CTCACGATGACACTTAGTCATCGA
335165 ATCCCTTTCA
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
50 1 0.01
51 65 0.58
52 7 0.06
53 39 0.35
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.31
Consensus pattern (50 bp):
CTCACGATGACACTTAGTCATCGACCTTTAATCCATAAAGGATTCATTTG
Found at i:341969 original size:3 final size:3
Alignment explanation
Indices: 341961--342011 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
341951 TTACTCACAT
341961 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TCTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC
342010 TT
1 TT
342012 TCTCTTCCCA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:342015 original size:6 final size:7
Alignment explanation
Indices: 341961--342018 Score: 60
Period size: 6 Copynumber: 9.4 Consensus size: 7
341951 TTACTCACAT
341961 TTCT-TC
1 TTCTCTC
341967 TTCT-TC
1 TTCTCTC
341973 TTCT-TC
1 TTCTCTC
341979 TTCT-TC
1 TTCTCTC
341985 TTCT-TC
1 TTCTCTC
341991 TTCT-TC
1 TTCTCTC
341997 TTCT-TC
1 TTCTCTC
342003 TTCTCTC
1 TTCTCTC
342010 TT-TCTC
1 TTCTCTC
342016 TTC
1 TTC
342019 CCAAAATTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
6 46 0.92
7 4 0.08
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (7 bp):
TTCTCTC
Found at i:351636 original size:2 final size:2
Alignment explanation
Indices: 351586--351617 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
351576 TACTCAATTA
351586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
351618 TAAGGTAGCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:352502 original size:23 final size:23
Alignment explanation
Indices: 352491--352571 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
352481 TTCATTTAAT
352491 TTAATCGAACATATTCATGAACA
1 TTAATCGAACATATTCATGAACA
*
352514 TTAATCGAACATATTCACGAACA
1 TTAATCGAACATATTCATGAACA
* * * **
352537 ATAAACAAACATGGTCATGAACA
1 TTAATCGAACATATTCATGAACA
*
352560 TATAATTGAACA
1 T-TAATCGAACA
352572 CGTTCACGAA
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 39 0.85
24 7 0.15
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.26
Consensus pattern (23 bp):
TTAATCGAACATATTCATGAACA
Found at i:352707 original size:12 final size:12
Alignment explanation
Indices: 352669--352727 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
352659 TATCATACAA
352669 ATAAACGAGC-T
1 ATAAACGAGCTT
352680 ATAAACGAG-TT
1 ATAAACGAGCTT
*
352691 AATAAATGAGCTT
1 -ATAAACGAGCTT
*
352704 ATAAACAAGCTT
1 ATAAACGAGCTT
*
352716 TTAAACGAGCTT
1 ATAAACGAGCTT
352728 GTTCGTGAAC
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 10 0.25
12 28 0.70
13 2 0.05
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:360796 original size:16 final size:15
Alignment explanation
Indices: 360775--360808 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
360765 GATAGTCTAA
*
360775 ATGCAAGCTAAAGTTG
1 ATGCAAGCCAAAG-TG
360791 ATGCAAGCCAAAGTG
1 ATGCAAGCCAAAGTG
360806 ATG
1 ATG
360809 GATAATCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (15 bp):
ATGCAAGCCAAAGTG
Found at i:369032 original size:16 final size:17
Alignment explanation
Indices: 369011--369045 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
369001 ACACTTTCTT
369011 TATTTTCAATAA-AAAA
1 TATTTTCAATAAGAAAA
*
369027 TATTTTCCATAAGAAAA
1 TATTTTCAATAAGAAAA
369044 TA
1 TA
369046 CAAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (17 bp):
TATTTTCAATAAGAAAA
Found at i:369385 original size:16 final size:16
Alignment explanation
Indices: 369335--369387 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
369325 GTTAGTTAAG
*
369335 TAATTATTTGTTAATA
1 TAATTATTTGTTAAAA
* *
369351 TAAATT-TCTGTCAAAA
1 T-AATTATTTGTTAAAA
*
369367 TAATTATTTGTTAACA
1 TAATTATTTGTTAAAA
369383 TAATT
1 TAATT
369388 TTGAATGTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 4 0.14
16 21 0.72
17 4 0.14
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.49
Consensus pattern (16 bp):
TAATTATTTGTTAAAA
Found at i:370821 original size:2 final size:2
Alignment explanation
Indices: 370814--370840 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
370804 TTAATAGATT
370814 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
370841 TCTTATAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:371494 original size:45 final size:45
Alignment explanation
Indices: 371430--371515 Score: 172
Period size: 45 Copynumber: 1.9 Consensus size: 45
371420 TTGTACGACA
371430 AATATTCTTCTTAGCTACAAAGATGAGAGCATTTTTTTTGTCACT
1 AATATTCTTCTTAGCTACAAAGATGAGAGCATTTTTTTTGTCACT
371475 AATATTCTTCTTAGCTACAAAGATGAGAGCATTTTTTTTGT
1 AATATTCTTCTTAGCTACAAAGATGAGAGCATTTTTTTTGT
371516 GGGCAGTGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (45 bp):
AATATTCTTCTTAGCTACAAAGATGAGAGCATTTTTTTTGTCACT
Found at i:380976 original size:129 final size:129
Alignment explanation
Indices: 380769--381257 Score: 725
Period size: 129 Copynumber: 3.8 Consensus size: 129
380759 AATCGCTCAT
* * * * * *
380769 GATGCAACCAACTCTAAGTTCGAGGCATGCCTGA-CAACTTCCTCTACAGTAATGGATGATTTGG
1 GATGCAGCCGACTTTAAGTTCGAGGCATGCC-AACCAACTTCCTCTTCATTAATGGATGATTTGG
* * * * * *
380833 AGCAACCTCAGATTGACTATAGTATATCAGACATAAAAGAGGGTGAAGAGAATCCGATTACCTAT
65 AGCAACCTCAGATTGACAACAGTACATCTGACATAAAAGAGGGTGAAGAGAATCTGATTACCTAC
* * *
380898 GATGCAGCAGACTTTAAGTTCAAGGCATGCCAACCAACTTCCTCTTCATTAATGGATGATTTGGT
1 GATGCAGCCGACTTTAAGTTCGAGGCATGCCAACCAACTTCCTCTTCATTAATGGATGATTTGGA
*
380963 GGAACCTCAGATTGACAACAGTACATCTGACATAAAAGAGGGTGAAGAGAATCTGATTACCTAC
66 GCAACCTCAGATTGACAACAGTACATCTGACATAAAAGAGGGTGAAGAGAATCTGATTACCTAC
* * *
381027 GATGCAGCCGACTTTAAGTTTGAGGCATGTCAGCCAACTTCCTCTTCATTAATGGATGATTTGGA
1 GATGCAGCCGACTTTAAGTTCGAGGCATGCCAACCAACTTCCTCTTCATTAATGGATGATTTGGA
*
381092 GGAACCTCAGATTGACAACAGTACATCTGACATAAAAGAGGGTGAAGAGAATCTGATTACCTAC
66 GCAACCTCAGATTGACAACAGTACATCTGACATAAAAGAGGGTGAAGAGAATCTGATTACCTAC
* *
381156 GATGCAACCGACTTTAAGTTCGAGGCATGCCAGCCAACTTCCTCTTCATTAATGGATGATTTGGA
1 GATGCAGCCGACTTTAAGTTCGAGGCATGCCAACCAACTTCCTCTTCATTAATGGATGATTTGGA
* *
381221 GCAACCTCAGATTG---ACAGTGCATCTGACCTAAAAGAG
66 GCAACCTCAGATTGACAACAGTACATCTGACATAAAAGAG
381258 ACCTCTCAGG
Statistics
Matches: 331, Mismatches: 28, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
126 21 0.06
128 1 0.00
129 309 0.93
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (129 bp):
GATGCAGCCGACTTTAAGTTCGAGGCATGCCAACCAACTTCCTCTTCATTAATGGATGATTTGGA
GCAACCTCAGATTGACAACAGTACATCTGACATAAAAGAGGGTGAAGAGAATCTGATTACCTAC
Found at i:401025 original size:3 final size:3
Alignment explanation
Indices: 401017--401045 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
401007 CACCTTCCCC
401017 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
401046 AAGAGAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:402721 original size:4 final size:4
Alignment explanation
Indices: 402712--402749 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
402702 GCCTTGTCAT
402712 CTCA CTCA CTCA CTCA CTCA CTCA CTCA CTCA CTCA CT
1 CTCA CTCA CTCA CTCA CTCA CTCA CTCA CTCA CTCA CT
402750 ACTTTACGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.24, C:0.50, G:0.00, T:0.26
Consensus pattern (4 bp):
CTCA
Found at i:408938 original size:20 final size:20
Alignment explanation
Indices: 408893--408946 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 20
408883 TTTTAAAAAA
408893 TAAAAAATATATAAATATTT
1 TAAAAAATATATAAATATTT
408913 TCAAAAAATATATAAATATTT
1 T-AAAAAATATATAAATATTT
408934 TAAAAAATATATA
1 TAAAAAATATATA
408947 TTGGGGGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 13 0.39
21 20 0.61
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAAATATATAAATATTT
Found at i:409031 original size:3 final size:3
Alignment explanation
Indices: 409025--409052 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
409015 TAATAATAAT
409025 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
409053 GGAGGCTAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:416188 original size:8 final size:8
Alignment explanation
Indices: 416175--416204 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
416165 TGACACATAC
416175 AAAACACA
1 AAAACACA
416183 AAAACACA
1 AAAACACA
416191 AAAACACA
1 AAAACACA
416199 AAAACA
1 AAAACA
416205 TTACTTTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAACACA
Found at i:422502 original size:2 final size:2
Alignment explanation
Indices: 422495--422521 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
422485 AAGATAAGTG
422495 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
422522 GCTTGTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:423738 original size:21 final size:21
Alignment explanation
Indices: 423712--423753 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
423702 TTCCTTCTAA
*
423712 AATTTTTA-ATTTAAAAATATT
1 AATTTTTATAATT-AAAATATT
423733 AATTTTTATAATTAAAATATT
1 AATTTTTATAATTAAAATATT
423754 TGAAACAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTTTATAATTAAAATATT
Found at i:431672 original size:58 final size:58
Alignment explanation
Indices: 431577--431689 Score: 199
Period size: 58 Copynumber: 1.9 Consensus size: 58
431567 GATGTGTAGA
* * *
431577 AATCTGTAAATCTCATTAAAGGTATTATCTATATAGTAATTACATGTGTACAAACTAT
1 AATCCGTAAATCTCATTAAAAGTATTATCTATATAGTAATTACATGTGGACAAACTAT
431635 AATCCGTAAATCTCATTAAAAGTATTATCTATATAGTAATTACATGTGGACAAAC
1 AATCCGTAAATCTCATTAAAAGTATTATCTATATAGTAATTACATGTGGACAAAC
431690 AAGTCAAAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.35
Consensus pattern (58 bp):
AATCCGTAAATCTCATTAAAAGTATTATCTATATAGTAATTACATGTGGACAAACTAT
Found at i:432379 original size:159 final size:159
Alignment explanation
Indices: 432090--432408 Score: 638
Period size: 159 Copynumber: 2.0 Consensus size: 159
432080 GAGGCCATAT
432090 TTCTATCTGCATTCATCAGAAAAATAAAGGGGACGAAAGAGTTTGATTTTCTTAATATATGAACA
1 TTCTATCTGCATTCATCAGAAAAATAAAGGGGACGAAAGAGTTTGATTTTCTTAATATATGAACA
432155 TTTATGGACTTTGGTAATGGTGGTCTTTAAGCTAGCCAGCTAGGCTAGCAGATGGAACTACCAAA
66 TTTATGGACTTTGGTAATGGTGGTCTTTAAGCTAGCCAGCTAGGCTAGCAGATGGAACTACCAAA
432220 TGTGAACATGGTCATAATCAGATCATAAA
131 TGTGAACATGGTCATAATCAGATCATAAA
432249 TTCTATCTGCATTCATCAGAAAAATAAAGGGGACGAAAGAGTTTGATTTTCTTAATATATGAACA
1 TTCTATCTGCATTCATCAGAAAAATAAAGGGGACGAAAGAGTTTGATTTTCTTAATATATGAACA
432314 TTTATGGACTTTGGTAATGGTGGTCTTTAAGCTAGCCAGCTAGGCTAGCAGATGGAACTACCAAA
66 TTTATGGACTTTGGTAATGGTGGTCTTTAAGCTAGCCAGCTAGGCTAGCAGATGGAACTACCAAA
432379 TGTGAACATGGTCATAATCAGATCATAAA
131 TGTGAACATGGTCATAATCAGATCATAAA
432408 T
1 T
432409 GACAACGACT
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 160 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.30
Consensus pattern (159 bp):
TTCTATCTGCATTCATCAGAAAAATAAAGGGGACGAAAGAGTTTGATTTTCTTAATATATGAACA
TTTATGGACTTTGGTAATGGTGGTCTTTAAGCTAGCCAGCTAGGCTAGCAGATGGAACTACCAAA
TGTGAACATGGTCATAATCAGATCATAAA
Found at i:442695 original size:30 final size:29
Alignment explanation
Indices: 442619--442801 Score: 174
Period size: 30 Copynumber: 6.2 Consensus size: 29
442609 TAATTTTGAG
*
442619 AGTTTCGAGGTCGAAAATGGAGTTTTTGGA
1 AGTTTCGAGGTC-AAAATGGAATTTTTGGA
* *
442649 CA--TTCGGGGGCAAAATGGTAATTTTTGGA
1 -AGTTTCGAGGTCAAAATGG-AATTTTTGGA
*
442678 AGTTTCGAGGTCAAAATGGGATTTTTGGA
1 AGTTTCGAGGTCAAAATGGAATTTTTGGA
* *
442707 AG-TTCAGGGGGTAAAAATGGAATTTTTGGA
1 AGTTTC--GAGGTCAAAATGGAATTTTTGGA
* *
442737 AGTTTCAAGGTCAAAAATGGAGTTTTTGGA
1 AGTTTCGAGGTC-AAAATGGAATTTTTGGA
* * * *
442767 AGTTTGGGGGTGAAAAAGGAATTTTTGGA
1 AGTTTCGAGGTCAAAATGGAATTTTTGGA
442796 TAGTTT
1 -AGTTT
442802 AGGGACCTTT
Statistics
Matches: 125, Mismatches: 19, Indels: 17
0.78 0.12 0.11
Matches are distributed among these distances:
28 11 0.09
29 45 0.36
30 65 0.52
31 4 0.03
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (29 bp):
AGTTTCGAGGTCAAAATGGAATTTTTGGA
Found at i:442717 original size:59 final size:60
Alignment explanation
Indices: 442612--442801 Score: 234
Period size: 59 Copynumber: 3.2 Consensus size: 60
442602 AAAAGGGTAA
* *
442612 TTTT-GAGAGTTTCGAGGTCGAAAATGGAGTTTTTGGACA-TTCGGGGG-CAAAATGGTAAT
1 TTTTGGAGAGTTTCGAGGTCAAAAATGGAGTTTTTGGA-AGTTCGGGGGTAAAAATGG-AAT
442671 TTTTGGA-AGTTTCGAGGTC-AAAATGG-GATTTTTGGAAGTTCAGGGGGTAAAAATGGAAT
1 TTTTGGAGAGTTTCGAGGTCAAAAATGGAG-TTTTTGGAAGTTC-GGGGGTAAAAATGGAAT
* *
442730 TTTTGGA-AGTTTCAAGGTCAAAAATGGAGTTTTTGGAAGTTTGGGGGTGAAAAA-GGAAT
1 TTTTGGAGAGTTTCGAGGTCAAAAATGGAGTTTTTGGAAGTTCGGGGGT-AAAAATGGAAT
*
442789 TTTTGGATAGTTT
1 TTTTGGAGAGTTT
442802 AGGGACCTTT
Statistics
Matches: 119, Mismatches: 3, Indels: 17
0.86 0.02 0.12
Matches are distributed among these distances:
57 2 0.02
58 18 0.15
59 60 0.50
60 38 0.32
61 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.32, T:0.34
Consensus pattern (60 bp):
TTTTGGAGAGTTTCGAGGTCAAAAATGGAGTTTTTGGAAGTTCGGGGGTAAAAATGGAAT
Found at i:442824 original size:7 final size:7
Alignment explanation
Indices: 442809--442842 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
442799 TTTAGGGACC
442809 TTTAGGG
1 TTTAGGG
*
442816 TTTATGG
1 TTTAGGG
*
442823 TTTAGTG
1 TTTAGGG
442830 TTTAGGG
1 TTTAGGG
442837 TTTAGG
1 TTTAGG
442843 AATTTTTGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (7 bp):
TTTAGGG
Found at i:443710 original size:12 final size:10
Alignment explanation
Indices: 443694--443740 Score: 58
Period size: 12 Copynumber: 4.3 Consensus size: 10
443684 CCCTTTTTTT
443694 TTATTATTAA
1 TTATTATTAA
443704 TGCTATTATTAA
1 T--TATTATTAA
443716 TTATTATTATTA
1 TTATTATTA--A
443728 TTATTATTAA
1 TTATTATTAA
443738 TTA
1 TTA
443741 ATGACTTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 13 0.39
12 20 0.61
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (10 bp):
TTATTATTAA
Found at i:443713 original size:3 final size:3
Alignment explanation
Indices: 443707--443736 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
443697 TTATTAATGC
443707 TAT TAT TAAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TA
443737 ATTAATGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:443722 original size:22 final size:22
Alignment explanation
Indices: 443694--443740 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
443684 CCCTTTTTTT
*
443694 TTATTATTAATGCTATTATTAA
1 TTATTATTAATACTATTATTAA
* *
443716 TTATTATTATTATTATTATTAA
1 TTATTATTAATACTATTATTAA
443738 TTA
1 TTA
443741 ATGACTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATTATTAATACTATTATTAA
Found at i:444505 original size:17 final size:17
Alignment explanation
Indices: 444480--444533 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
444470 GGATTTTTAA
* **
444480 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
444497 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
444514 TTAAATTTAAAAATAAAT
1 TTAAATTT-TAAATAAAT
444532 TT
1 TT
444534 GAATCAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 21 0.70
18 9 0.30
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:451378 original size:22 final size:22
Alignment explanation
Indices: 451352--451396 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
451342 ATGAGCTATC
451352 TGTTAGGTTGATTGCATTCCCT
1 TGTTAGGTTGATTGCATTCCCT
451374 TGTTAGGTTGATTGCATTCCCT
1 TGTTAGGTTGATTGCATTCCCT
451396 T
1 T
451397 CATGACACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (22 bp):
TGTTAGGTTGATTGCATTCCCT
Found at i:459435 original size:2 final size:2
Alignment explanation
Indices: 459430--459454 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
459420 AAAAAAAAAA
459430 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
459455 AAGTCTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:459754 original size:6 final size:6
Alignment explanation
Indices: 459745--459772 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
459735 GATATAGTTT
459745 ATGTGC ATGTGC ATGTGC ATGTGC ATGT
1 ATGTGC ATGTGC ATGTGC ATGTGC ATGT
459773 ATATGTAATT
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:0.18, C:0.14, G:0.32, T:0.36
Consensus pattern (6 bp):
ATGTGC
Found at i:460937 original size:6 final size:6
Alignment explanation
Indices: 460921--460950 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
460911 TACTCACTGT
*
460921 CCTCTC TCTCTC CCTCTC CCTCTC CCTCTC
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC
460951 TCACATACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
CCTCTC
Found at i:469647 original size:12 final size:13
Alignment explanation
Indices: 469620--469652 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
469610 TTGGCATCAA
469620 TCTTTCTTTTCTCT
1 TCTTT-TTTTCTCT
469634 TCTTTTTTTC-CT
1 TCTTTTTTTCTCT
469646 TCTTTTT
1 TCTTTTT
469653 CATGCTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 9 0.47
13 5 0.26
14 5 0.26
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TCTTTTTTTCTCT
Found at i:495541 original size:2 final size:2
Alignment explanation
Indices: 495534--495559 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
495524 ACTTTAGCTT
495534 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
495560 GGACGTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:498009 original size:13 final size:14
Alignment explanation
Indices: 497991--498019 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
497981 AAACTCTAAC
497991 CCTCAAACC-CGAA
1 CCTCAAACCTCGAA
498004 CCTCAAACCTCGAA
1 CCTCAAACCTCGAA
498018 CC
1 CC
498020 AAAATCTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.48, G:0.07, T:0.10
Consensus pattern (14 bp):
CCTCAAACCTCGAA
Found at i:498429 original size:21 final size:22
Alignment explanation
Indices: 498405--498445 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
498395 AACTCTTTTA
*
498405 TTTA-AAAAAAAATCAAAAACT
1 TTTATAAAAAAAATAAAAAACT
498426 TTTATAAAAAAAATAAAAAA
1 TTTATAAAAAAAATAAAAAA
498446 GTATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (22 bp):
TTTATAAAAAAAATAAAAAACT
Found at i:498454 original size:22 final size:22
Alignment explanation
Indices: 498409--498454 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
498399 CTTTTATTTA
* * *
498409 AAAAAAAATCAAAAACTTTTAT
1 AAAAAAAATAAAAAACTATAAT
*
498431 AAAAAAAATAAAAAAGTATAAT
1 AAAAAAAATAAAAAACTATAAT
498453 AA
1 AA
498455 TAAATTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAAAAAATAAAAAACTATAAT
Found at i:502935 original size:20 final size:20
Alignment explanation
Indices: 502912--502953 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
502902 CTTAAATTCT
502912 TCCCATAAAAATAAAATGTA
1 TCCCATAAAAATAAAATGTA
*
502932 TCCCATAAAAATGAAATGTA
1 TCCCATAAAAATAAAATGTA
502952 TC
1 TC
502954 TTACCATAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (20 bp):
TCCCATAAAAATAAAATGTA
Found at i:504968 original size:27 final size:29
Alignment explanation
Indices: 504925--504978 Score: 69
Period size: 27 Copynumber: 1.9 Consensus size: 29
504915 GATTTCATAC
504925 GTTTTTGGGATGATTAAT-AA-TTGGTGT
1 GTTTTTGGGATGATTAATGAACTTGGTGT
*
504952 GTTTTT-GGATTGTTTAATGAACTTGGT
1 GTTTTTGGGA-TGATTAATGAACTTGGT
504979 TATTTCTGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 3 0.13
27 13 0.57
28 2 0.09
29 5 0.22
ACGTcount: A:0.20, C:0.02, G:0.28, T:0.50
Consensus pattern (29 bp):
GTTTTTGGGATGATTAATGAACTTGGTGT
Found at i:510503 original size:14 final size:15
Alignment explanation
Indices: 510484--510517 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
510474 TTCAGTTTTC
510484 ATTAAAGTATGA-AA
1 ATTAAAGTATGATAA
*
510498 ATTAAATTATGATAA
1 ATTAAAGTATGATAA
510513 ATTAA
1 ATTAA
510518 CATTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (15 bp):
ATTAAAGTATGATAA
Found at i:513338 original size:23 final size:23
Alignment explanation
Indices: 513312--513358 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
513302 TGATGAAAGT
513312 TAAATTGAATTAAACATGGTATA
1 TAAATTGAATTAAACATGGTATA
513335 TAAATTGAATTAAACATGGTATA
1 TAAATTGAATTAAACATGGTATA
513358 T
1 T
513359 GACACATATG
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:0.47, C:0.04, G:0.13, T:0.36
Consensus pattern (23 bp):
TAAATTGAATTAAACATGGTATA
Found at i:513713 original size:52 final size:52
Alignment explanation
Indices: 513635--513826 Score: 269
Period size: 52 Copynumber: 3.7 Consensus size: 52
513625 AAAGAAAAAG
* * *
513635 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* *
513687 GGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* **
513739 GGTCTGATGGTTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * *
513791 GGTTCGGT-AGCTATGTGTCATCGTGAGCATATGAAT
1 GGTCCGATGA-CTATGTGTCATCGTGAGTATATGAAT
513827 GAAATGAAAT
Statistics
Matches: 123, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
52 123 1.00
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
Found at i:513823 original size:104 final size:104
Alignment explanation
Indices: 513635--513826 Score: 296
Period size: 104 Copynumber: 1.8 Consensus size: 104
513625 AAAGAAAAAG
513635 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAAGGTCCGATGACTA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAAGGTCCGATGACTA
*
513700 AGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGA
66 AGTGTCATCGTGAGCATATGAATCCTTTATGGATTATGA
* * * * * *
513739 GGTCTGATGGTTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTTCGGT-AGCT
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAAGGTCCGATGA-CT
*
513803 ATGTGTCATCGTGAGCATATGAAT
65 AAGTGTCATCGTGAGCATATGAAT
513827 GAAATGAAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
103 1 0.01
104 78 0.99
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (104 bp):
GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATAAGGTCCGATGACTA
AGTGTCATCGTGAGCATATGAATCCTTTATGGATTATGA
Done.