Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008512.1 Hibiscus syriacus cultivar Beakdansim tig00111372_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1759229
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:281236 original size:15 final size:16
Alignment explanation
Indices: 281216--281247 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
281206 GTTTACCTAT
281216 TTGGCCACG-TGCTGA
1 TTGGCCACGTTGCTGA
281231 TTGGCCACGTTGCTGA
1 TTGGCCACGTTGCTGA
281247 T
1 T
281248 GGGTTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.12, C:0.25, G:0.31, T:0.31
Consensus pattern (16 bp):
TTGGCCACGTTGCTGA
Found at i:282968 original size:2 final size:2
Alignment explanation
Indices: 282956--283008 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
282946 AATCTATAAT
282956 TA TA T- TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
282995 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
283009 ATTTATATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:282976 original size:17 final size:17
Alignment explanation
Indices: 282956--283008 Score: 92
Period size: 17 Copynumber: 3.2 Consensus size: 17
282946 AATCTATAAT
282956 TATATTATATATATATA
1 TATATTATATATATATA
282973 TATA-T-TATATATATA
1 TATATTATATATATATA
282988 TATATTATATATATATA
1 TATATTATATATATATA
283005 TATA
1 TATA
283009 ATTTATATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.41
16 2 0.06
17 18 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATATATATATA
Found at i:283015 original size:17 final size:18
Alignment explanation
Indices: 282950--283016 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 18
282940 GATTAAAATC
282950 TATAATTATAT-TATATA
1 TATAATTATATATATATA
282967 TAT-ATATATATTATATATA
1 TATAAT-TATA-TATATATA
282986 TATATATTATATATATATA
1 TATA-ATTATATATATATA
283005 TATAATT-TATAT
1 TATAATTATATAT
283017 TGTTATCGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
16 2 0.04
17 12 0.27
18 4 0.09
19 21 0.47
20 4 0.09
21 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATAATTATATATATATA
Found at i:283016 original size:15 final size:15
Alignment explanation
Indices: 282963--283007 Score: 90
Period size: 15 Copynumber: 3.0 Consensus size: 15
282953 AATTATATTA
282963 TATATATATATATAT
1 TATATATATATATAT
282978 TATATATATATATAT
1 TATATATATATATAT
282993 TATATATATATATAT
1 TATATATATATATAT
283008 AATTTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:294601 original size:14 final size:14
Alignment explanation
Indices: 294582--294611 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
294572 ACCAGGAGCT
294582 GAAAAGGGATGTAG
1 GAAAAGGGATGTAG
294596 GAAAAGGGATGTAG
1 GAAAAGGGATGTAG
294610 GA
1 GA
294612 TCGTTAGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.43, T:0.13
Consensus pattern (14 bp):
GAAAAGGGATGTAG
Found at i:304395 original size:157 final size:157
Alignment explanation
Indices: 304110--304424 Score: 614
Period size: 157 Copynumber: 2.0 Consensus size: 157
304100 CTATAACCTA
304110 AAATTATTCGAGAGGCATTAACTCATCCAAGATGGCGTACGACTATGATTGAGAAATGATGCTCT
1 AAATTATTCGAGAGGCATTAACTCATCCAAGATGGCGTACGACTATGATTGAGAAATGATGCTCT
304175 AAATGTTAATGATATATGAACTTTGGTTACCTTACTTGTTAGTAAACAAGCTATTAGATATAAAT
66 AAATGTTAATGATATATGAACTTTGGTTACCTTACTTGTTAGTAAACAAGCTATTAGATATAAAT
304240 -GGTGTTTACTGTCAAAATTAACCATG
131 GGGTGTTTACTGTCAAAATTAACCATG
304266 AAATTATTCGAGAGGCATTAACTCATCCAAGATGGCGTACGACTATGATTGAGAAATGGATGCTC
1 AAATTATTCGAGAGGCATTAACTCATCCAAGATGGCGTACGACTATGATTGAGAAAT-GATGCTC
304331 TAAATGTTAATGATATATGAACTTTGGTTACCTTACTTGTTAGTAAACAAGCTATTAGATATAAA
65 TAAATGTTAATGATATATGAACTTTGGTTACCTTACTTGTTAGTAAACAAGCTATTAGATATAAA
304396 TGGGTGTTTACTGTCAAAATTAACCATG
130 TGGGTGTTTACTGTCAAAATTAACCATG
304424 A
1 A
304425 TGGTTCCACT
Statistics
Matches: 157, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
156 57 0.36
157 73 0.46
158 27 0.17
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.33
Consensus pattern (157 bp):
AAATTATTCGAGAGGCATTAACTCATCCAAGATGGCGTACGACTATGATTGAGAAATGATGCTCT
AAATGTTAATGATATATGAACTTTGGTTACCTTACTTGTTAGTAAACAAGCTATTAGATATAAAT
GGGTGTTTACTGTCAAAATTAACCATG
Found at i:309915 original size:13 final size:13
Alignment explanation
Indices: 309897--309946 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 13
309887 AGGGTCCTTT
309897 TTTCCTATTTTAA
1 TTTCCTATTTTAA
309910 TTTCC--TTTT--
1 TTTCCTATTTTAA
309919 TTT-CTATTTTAA
1 TTTCCTATTTTAA
309931 TTTCCTAATTTTAA
1 TTTCCT-ATTTTAA
309945 TT
1 TT
309947 GGACAAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
8 1 0.03
9 3 0.10
10 4 0.13
11 4 0.13
12 3 0.10
13 7 0.23
14 9 0.29
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTCCTATTTTAA
Found at i:309922 original size:22 final size:21
Alignment explanation
Indices: 309891--309936 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
309881 TCTCGTAGGG
*
309891 TCCTTTTTTCCTATTTTAATT
1 TCCTTTTTTTCTATTTTAATT
309912 TCCTTTTTTTCTATTTTAATT
1 TCCTTTTTTTCTATTTTAATT
309933 TCCT
1 TCCT
309937 AATTTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.13, C:0.20, G:0.00, T:0.67
Consensus pattern (21 bp):
TCCTTTTTTTCTATTTTAATT
Found at i:309942 original size:21 final size:22
Alignment explanation
Indices: 309896--309942 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
309886 TAGGGTCCTT
*
309896 TTTTCCTATTTTAATTTCCT-T
1 TTTTCCTATTTTAATTTCCTAA
*
309917 TTTTTCTATTTTAATTTCCTAA
1 TTTTCCTATTTTAATTTCCTAA
309939 TTTT
1 TTTT
309943 AATTGGACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTCCTATTTTAATTTCCTAA
Found at i:311128 original size:20 final size:19
Alignment explanation
Indices: 311082--311371 Score: 118
Period size: 20 Copynumber: 14.7 Consensus size: 19
311072 TTGCGATTTT
311082 CCAT-AATCGCAACGCGAA
1 CCATAAATCGCAACGCGAA
**
311100 TGA-AAATCGCAACGCGAA
1 CCATAAATCGCAACGCGAA
*
311118 CACATAAATCGCAACGCGTAT
1 C-CATAAATCGCAACGCG-AA
* * *
311139 CCGTAAATCGCAACGTGTAT
1 CCATAAATCGCAACGCG-AA
* *
311159 CCGTAAATCGCAAACGCGTAT
1 CCATAAATCGC-AACGCG-AA
*** * *
311180 GGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCG-AA
* * *
311200 CCGTATATCGCAACGCGTAT
1 CCATAAATCGCAACGCG-AA
* *
311220 CCGTAAATCGCAACGCGTAT
1 CCATAAATCGCAACGCG-AA
* * *
311240 CCGTAAA-CTGCAACGTGTAT
1 CCATAAATC-GCAACGCG-AA
* *
311260 CCGTAAATCGCAACGCGTA
1 CCATAAATCGCAACGCGAA
* * * *
311279 TCGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCG-AA
* *
311299 CCGTAAATCGCAACGCGTAT
1 CCATAAATCGCAACGCG-AA
* **
311319 CCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGAA
* *
311338 TCCGTAAATCGCAACGCGTAT
1 -CCATAAATCGCAACGCG-AA
*
311359 CCGTAAATCGCAA
1 CCATAAATCGCAA
311372 ACGATAATCC
Statistics
Matches: 230, Mismatches: 32, Indels: 18
0.82 0.11 0.06
Matches are distributed among these distances:
18 15 0.07
19 18 0.08
20 176 0.77
21 21 0.09
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (19 bp):
CCATAAATCGCAACGCGAA
Found at i:311166 original size:40 final size:40
Alignment explanation
Indices: 311086--311452 Score: 419
Period size: 40 Copynumber: 9.2 Consensus size: 40
311076 GATTTTCCAT
* * * *
311086 AATCGCAACGCGAAT--GAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATC-CGTA
*
311124 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
** *
311164 AATCGCAAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGC-AACGCGTATCCGTAAATCGCAACGCGTATCCGTA
*
311205 TATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
*
311245 AA-CTGCAACGTGTATCCGTAAATCGCAACGCGTAT-CGTA
1 AATC-GCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
*
311284 AATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
*
311324 AATCGCAACG-ATAATCCGTAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGT-ATCCGTAAATCGCAACGCGTATCCGTA
* * * *
311364 AATCGCAAACG-ATAATCCGT-AATCGCAACGAGAATCTGTA
1 AATCGC-AACGCGT-ATCCGTAAATCGCAACGCGTATCCGTA
* * * *
311404 AATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTA
1 AATCGCAACGCGT-ATCCGTAAATCGCAACGCGTATCCGTA
*
311444 AATCACAAC
1 AATCGCAAC
311453 ACTTAAATTT
Statistics
Matches: 296, Mismatches: 23, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
38 14 0.05
39 50 0.17
40 182 0.61
41 50 0.17
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
Found at i:311167 original size:60 final size:60
Alignment explanation
Indices: 311086--311452 Score: 419
Period size: 60 Copynumber: 6.2 Consensus size: 60
311076 GATTTTCCAT
* * * *
311086 AATCGCAACGCGAAT--GAAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATC-CGTAAATCGCAACGCGTATCCGTA
* ** *
311144 AATCGCAACGTGTATCCGTAAATCGCAAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGC-AACGCGTATCCGTAAATCGCAACGCGTATCCGTA
* *
311205 TATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAA-CTGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATC-GCAACGCGTATCCGTA
*
311265 AATCGCAACGCGTAT-CGTAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
* *
311324 AATCGCAACG-ATAATCCGTAAATCGCAACGCGTATCCGTAAATCGCAAACG-ATAATCCGT-
1 AATCGCAACGCGT-ATCCGTAAATCGCAACGCGTATCCGTAAATCGC-AACGCGT-ATCCGTA
* * * * * * *
311384 AATCGCAACGAGAATCTGTAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGT-ATCCGTAAATCGCAACGCGTATCCGTA
*
311444 AATCACAAC
1 AATCGCAAC
311453 ACTTAAATTT
Statistics
Matches: 267, Mismatches: 28, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
58 14 0.05
59 63 0.24
60 128 0.48
61 61 0.23
62 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
Found at i:311387 original size:20 final size:20
Alignment explanation
Indices: 311122--311452 Score: 253
Period size: 20 Copynumber: 16.6 Consensus size: 20
311112 CGCGAACACA
*
311122 TAAATCGCAACGCGT-ATCCG
1 TAAATCGCAACG-ATAATCCG
*
311142 TAAATCGCAACG-TGTATCCG
1 TAAATCGCAACGAT-AATCCG
* **
311162 TAAATCGCAAACGCGT-ATGGG
1 TAAATCGC-AACG-ATAATCCG
311183 TAAATCGCAATGCG-T-ATCCG
1 TAAATCGCAA--CGATAATCCG
* *
311203 TATATCGCAACGCGT-ATCCG
1 TAAATCGCAACG-ATAATCCG
*
311223 TAAATCGCAACGCGT-ATCCG
1 TAAATCGCAACG-ATAATCCG
*
311243 TAAA-CTGCAACG-TGTATCCG
1 TAAATC-GCAACGAT-AATCCG
*
311263 TAAATCGCAACGCGT-AT-CG
1 TAAATCGCAACG-ATAATCCG
311282 TAAATCGCAATGCG-T-ATCCG
1 TAAATCGCAA--CGATAATCCG
*
311302 TAAATCGCAACGCGT-ATCCG
1 TAAATCGCAACG-ATAATCCG
311322 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGATAATCCG
*
311342 TAAATCGCAACGCGT-ATCCG
1 TAAATCGCAACG-ATAATCCG
311362 TAAATCGCAAACGATAATCCG
1 TAAATCGC-AACGATAATCCG
* *
311383 T-AATCGCAACGAGAATCTG
1 TAAATCGCAACGATAATCCG
311402 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGATAATCCG
* *
311422 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGATAATCCG
*
311442 TAAATCACAAC
1 TAAATCGCAAC
311453 ACTTAAATTT
Statistics
Matches: 270, Mismatches: 16, Indels: 50
0.80 0.05 0.15
Matches are distributed among these distances:
18 6 0.02
19 28 0.10
20 203 0.75
21 29 0.11
22 3 0.01
23 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGATAATCCG
Found at i:312162 original size:24 final size:23
Alignment explanation
Indices: 312123--312168 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
312113 AAATTTGGTC
312123 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGA-TTTGATA
312147 TTGGTCAATA-CACGGATTTGAT
1 TTGGTCAATATC-CGGATTTGAT
312169 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (23 bp):
TTGGTCAATATCCGGATTTGATA
Found at i:312359 original size:12 final size:12
Alignment explanation
Indices: 312342--312366 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
312332 ATATAATCCT
312342 GAAGAAGAAAAA
1 GAAGAAGAAAAA
312354 GAAGAAGAAAAA
1 GAAGAAGAAAAA
312366 G
1 G
312367 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:315219 original size:25 final size:25
Alignment explanation
Indices: 315186--315259 Score: 132
Period size: 25 Copynumber: 3.0 Consensus size: 25
315176 ATGGCTTATA
315186 GATC-ATTTGCCGTTAATAATGACT
1 GATCTATTTGCCGTTAATAATGACT
315210 GATCTATTTGCCGTTAATAATGACT
1 GATCTATTTGCCGTTAATAATGACT
*
315235 GATCTATTTACCGTTAATAATGACT
1 GATCTATTTGCCGTTAATAATGACT
315260 TGTTTTTCAG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
24 4 0.08
25 44 0.92
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (25 bp):
GATCTATTTGCCGTTAATAATGACT
Found at i:317669 original size:18 final size:18
Alignment explanation
Indices: 317636--317671 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
317626 ATGTGTTATA
*
317636 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTACAGGACAT
*
317654 AGTGGTCCTACGGGACAT
1 AGTGGTCCTACAGGACAT
317672 TCTACATGCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTACAGGACAT
Found at i:319567 original size:13 final size:14
Alignment explanation
Indices: 319549--319577 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
319539 AGTCTGTTCT
319549 TTTATGTTC-GTCG
1 TTTATGTTCTGTCG
319562 TTTATGTTCTGTCG
1 TTTATGTTCTGTCG
319576 TT
1 TT
319578 CATATTCAAC
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:0.07, C:0.14, G:0.21, T:0.59
Consensus pattern (14 bp):
TTTATGTTCTGTCG
Found at i:339107 original size:46 final size:46
Alignment explanation
Indices: 339051--339183 Score: 178
Period size: 46 Copynumber: 2.9 Consensus size: 46
339041 TTTTGAATAA
*
339051 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTTGAGC
1 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTCGAGC
*
339097 ATGTATGCGAACTAGAAATCATGCGGCTAGGTTTATTTTTCTCGAGC
1 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTT-TCGAGC
* * * * * *
339144 AAGCATGCAAATTAGATATCATGCGGTTAGGATT-TTTTTT
1 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTT
339184 GTGAATGACA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
45 1 0.01
46 44 0.57
47 32 0.42
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.38
Consensus pattern (46 bp):
ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTCGAGC
Found at i:343850 original size:125 final size:125
Alignment explanation
Indices: 343688--343915 Score: 305
Period size: 125 Copynumber: 1.8 Consensus size: 125
343678 GAATACCCAC
* ** * * * *
343688 ATTGGGGCATGACTGAACCCCCATCATTTTGAGATGACATGATTCGGACGAAGAAGG-CATTGAG
1 ATTGGGGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAG-AGGACATTGAG
* ** *
343752 AATAAGCCTTACAATTTGAGGTTTTGGGGCATTTTGAAGACCCGTACCAGTAAAAGATAAT
65 AATAAGCCTTACAACTTGAAATGTTGGGGCATTTTGAAGACCCGTACCAGTAAAAGATAAT
*
343813 ATTGGGGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAGGACGTTGAGA
1 ATTGGGGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAGGACATTGAGA
* * *
343878 GTGAGTCTTACAACTTGAAATGTTGGGGCATTTTGAAG
66 ATAAGCCTTACAACTTGAAATGTTGGGGCATTTTGAAG
343916 GCTTATTCTA
Statistics
Matches: 87, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
124 3 0.03
125 84 0.97
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.25
Consensus pattern (125 bp):
ATTGGGGCATGACTGAACCCACATCATGATGAAATGACAAGATTCAGACCAAGAGGACATTGAGA
ATAAGCCTTACAACTTGAAATGTTGGGGCATTTTGAAGACCCGTACCAGTAAAAGATAAT
Found at i:345155 original size:37 final size:37
Alignment explanation
Indices: 345105--345218 Score: 142
Period size: 37 Copynumber: 3.1 Consensus size: 37
345095 AAAGCCAAGT
* *
345105 CTTCACAAAAGAGTAGTGAAGCAAATCCATTTTGAGC
1 CTTCACTAAAGAGTAGTGAAGCAAATCCATTTTAAGC
*
345142 CTTCACTAAAGAGTAGTGAAGCAAA-CCATCTTAAGC
1 CTTCACTAAAGAGTAGTGAAGCAAATCCATTTTAAGC
* * * *
345178 CTTCA-TCGAAGAGTAGTGAAGCATATCCTTTTTAAAC
1 CTTCACT-AAAGAGTAGTGAAGCAAATCCATTTTAAGC
345215 CTTC
1 CTTC
345219 TCGGAAGAGT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
35 1 0.01
36 30 0.45
37 36 0.54
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (37 bp):
CTTCACTAAAGAGTAGTGAAGCAAATCCATTTTAAGC
Found at i:345190 original size:36 final size:37
Alignment explanation
Indices: 345113--345244 Score: 128
Period size: 37 Copynumber: 3.6 Consensus size: 37
345103 GTCTTCACAA
* * **
345113 AAGAGTAGTGAAGCAAATCCATTTTGAGCCTTCA-CTA
1 AAGAGTAGTGAAGCAAA-CCATCTTAAGCCTTCATCGG
345150 AAGAGTAGTGAAGCAAACCATCTTAAGCCTTCATC-G
1 AAGAGTAGTGAAGCAAACCATCTTAAGCCTTCATCGG
* * * *
345186 AAGAGTAGTGAAGCATATCCTTTTTAAACCTTC-TCGG
1 AAGAGTAGTGAAGCA-AACCATCTTAAGCCTTCATCGG
*
345223 AAGAGT-GTTGGAGCAAACCATC
1 AAGAGTAG-TGAAGCAAACCATC
345245 AGACTATCAG
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
36 36 0.45
37 44 0.55
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (37 bp):
AAGAGTAGTGAAGCAAACCATCTTAAGCCTTCATCGG
Found at i:346026 original size:54 final size:54
Alignment explanation
Indices: 345603--346007 Score: 666
Period size: 54 Copynumber: 7.5 Consensus size: 54
345593 GTAGTAAAGC
* *
345603 AGAAGAACATGTTCGAGTTCCATACTCCCTAGATAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * * **
345657 AGAAGAAGATATTCAAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACATGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* * * * * *
345711 AGTAGAATATGTTTGAGTTTCATACTCCCTAGATAAAGAGGGAGCGAACCAGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
345765 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
345819 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
*
345873 AGAAGAAGATGTTCGAGTTCCATACTCTCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
345927 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
1 AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
* *
345981 AGAAGAAGACGTTTGAGTTCCATACTC
1 AGAAGAAGATGTTCGAGTTCCATACTC
346008 TCTGAAGCAA
Statistics
Matches: 324, Mismatches: 27, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 324 1.00
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.20
Consensus pattern (54 bp):
AGAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTA
Found at i:348928 original size:24 final size:24
Alignment explanation
Indices: 348901--348980 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 24
348891 AAATCAAAAT
348901 AGAATTCAGATAAGATATCAGAAC
1 AGAATTCAGATAAGATATCAGAAC
* * *
348925 AGAATCCAGATCAGAAATCAGAAC
1 AGAATTCAGATAAGATATCAGAAC
* *
348949 AAAATTCAGGTAATG-TATCAGAAC
1 AGAATTCAGATAA-GATATCAGAAC
348973 AGAATTCA
1 AGAATTCA
348981 AGTCGGAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
24 45 0.98
25 1 0.02
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.20
Consensus pattern (24 bp):
AGAATTCAGATAAGATATCAGAAC
Found at i:348968 original size:48 final size:48
Alignment explanation
Indices: 348903--348994 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
348893 ATCAAAATAG
348903 AATTCAGATAAGATATCAGAACAGAATCC-AGATCAGAAATCAGAACAA
1 AATTCAGATAAGATATCAGAACAGAATCCAAG-TCAGAAATCAGAACAA
* * *
348951 AATTCAGGTAATG-TATCAGAACAGAATTCAAGTCGGAAATCAGA
1 AATTCAGATAA-GATATCAGAACAGAATCCAAGTCAGAAATCAGA
348995 TAAAATATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
48 36 0.92
49 3 0.08
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.20
Consensus pattern (48 bp):
AATTCAGATAAGATATCAGAACAGAATCCAAGTCAGAAATCAGAACAA
Found at i:348992 original size:24 final size:24
Alignment explanation
Indices: 348891--348994 Score: 70
Period size: 24 Copynumber: 4.3 Consensus size: 24
348881 AAGATATCAT
* * *
348891 AAATCAAAATAGAATTC-AGATAAG
1 AAATCAGAACAGAATTCAAG-TCAG
* *
348915 ATATCAGAACAGAA-TCCAGATCAG
1 AAATCAGAACAGAATTCAAG-TCAG
* * *
348939 AAATCAGAACAAAATTCAGGTAATG
1 AAATCAGAACAGAATTCAAGTCA-G
* *
348964 -TATCAGAACAGAATTCAAGTCGG
1 AAATCAGAACAGAATTCAAGTCAG
348987 AAATCAGA
1 AAATCAGA
348995 TAAAATATTT
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
23 3 0.05
24 54 0.89
25 4 0.07
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.19
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAAGTCAG
Found at i:351488 original size:5 final size:5
Alignment explanation
Indices: 351478--351502 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
351468 GTCGGGTAAA
351478 CGGGT CGGGT CGGGT CGGGT CGGGT
1 CGGGT CGGGT CGGGT CGGGT CGGGT
351503 TATGACCGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.60, T:0.20
Consensus pattern (5 bp):
CGGGT
Found at i:353610 original size:48 final size:49
Alignment explanation
Indices: 353541--353651 Score: 140
Period size: 48 Copynumber: 2.3 Consensus size: 49
353531 GTAAACAGAG
*
353541 ATATCAGAAATCA-AAACAGAATTCAGATCA-GATATCAGAACAGAATCC
1 ATATCAGAAATCAGAAACAGAATTCAGATAATG-TATCAGAACAGAATCC
* * *
353589 ATATAAGAAATCAGAAA-AGAATTCAGGTAATGTATCAGAACAGAATTC
1 ATATCAGAAATCAGAAACAGAATTCAGATAATGTATCAGAACAGAATCC
353637 A-AGTCAGAAATCAGA
1 ATA-TCAGAAATCAGA
353652 TAAAATATTT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
47 1 0.02
48 50 0.91
49 4 0.07
ACGTcount: A:0.50, C:0.14, G:0.15, T:0.20
Consensus pattern (49 bp):
ATATCAGAAATCAGAAACAGAATTCAGATAATGTATCAGAACAGAATCC
Found at i:353649 original size:24 final size:24
Alignment explanation
Indices: 353544--353651 Score: 96
Period size: 24 Copynumber: 4.5 Consensus size: 24
353534 AACAGAGATA
*
353544 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCAGAACAGAATTCAAG
* *
353567 ATCAGATATCAGAACAGAATCCATA-
1 -TCAGAAATCAGAACAGAATTCA-AG
* * *
353592 TAAGAAATCAGAAAAGAATTCAGG
1 TCAGAAATCAGAACAGAATTCAAG
* *
353616 TAATG-TATCAGAACAGAATTCAAG
1 TCA-GAAATCAGAACAGAATTCAAG
353640 TCAGAAATCAGA
1 TCAGAAATCAGA
353652 TAAAATATTT
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
23 1 0.02
24 63 0.95
25 1 0.02
26 1 0.02
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAAG
Found at i:358467 original size:20 final size:21
Alignment explanation
Indices: 358425--358466 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
358415 AACTGAGTGG
358425 AATTTAACTACAAACAATAAA
1 AATTTAACTACAAACAATAAA
358446 AATTTAACTAC-AAC-ATAAA
1 AATTTAACTACAAACAATAAA
358465 AA
1 AA
358467 AAATACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 3 0.14
21 11 0.52
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (21 bp):
AATTTAACTACAAACAATAAA
Found at i:358784 original size:22 final size:23
Alignment explanation
Indices: 358742--358784 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
358732 TTTATAGTAT
*
358742 TAAATTAATTTTTAAAAATATAG
1 TAAATTAATTATTAAAAATATAG
*
358765 TAAATT-ATTATTAAATATAT
1 TAAATTAATTATTAAAAATAT
358785 TATTTTTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TAAATTAATTATTAAAAATATAG
Found at i:359728 original size:24 final size:23
Alignment explanation
Indices: 359701--359768 Score: 75
Period size: 24 Copynumber: 2.9 Consensus size: 23
359691 TTTAATATCG
*
359701 ATATAAAAATATTTAAAAAATCAA
1 ATATAAAAATATTAAAAAAAT-AA
* *
359725 ATATACAAATACTAAAAAAATAA
1 ATATAAAAATATTAAAAAAATAA
359748 ATTACTAAAAA-ATTAAAAAAA
1 A-TA-TAAAAATATTAAAAAAA
359769 CTAAGAACAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 3 0.08
24 29 0.78
25 5 0.14
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (23 bp):
ATATAAAAATATTAAAAAAATAA
Found at i:359755 original size:16 final size:16
Alignment explanation
Indices: 359734--359764 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
359724 AATATACAAA
359734 TACTAAAAAAATAAAT
1 TACTAAAAAAATAAAT
*
359750 TACTAAAAAATTAAA
1 TACTAAAAAAATAAA
359765 AAAACTAAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
TACTAAAAAAATAAAT
Found at i:362235 original size:126 final size:126
Alignment explanation
Indices: 362010--362261 Score: 477
Period size: 126 Copynumber: 2.0 Consensus size: 126
362000 TACATACAAT
362010 TCTACAATACTTTTACCCTTAGATAAAGTATAAACAACACAATGATGGTCTATTATTTATCTAAA
1 TCTACAATACTTTTACCCTTAGATAAAGTATAAACAACACAATGATGGTCTATTATTTATCTAAA
362075 ACTACAGCTAGCAACTACAAAATTGGCTATACTTTTCATATTAACATATAATTATTAATTA
66 ACTACAGCTAGCAACTACAAAATTGGCTATACTTTTCATATTAACATATAATTATTAATTA
* *
362136 TCTACAATACTTTTACCCTTGGATAAAGTATAAACAGCACAATGATGGTCTATTATTTATCTAAA
1 TCTACAATACTTTTACCCTTAGATAAAGTATAAACAACACAATGATGGTCTATTATTTATCTAAA
*
362201 ACTACAGCTAGCAGCTACAAAATTGGCTATACTTTTCATATTAACATATAATTATTAATTA
66 ACTACAGCTAGCAACTACAAAATTGGCTATACTTTTCATATTAACATATAATTATTAATTA
362262 CCAACAAAAA
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
126 123 1.00
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (126 bp):
TCTACAATACTTTTACCCTTAGATAAAGTATAAACAACACAATGATGGTCTATTATTTATCTAAA
ACTACAGCTAGCAACTACAAAATTGGCTATACTTTTCATATTAACATATAATTATTAATTA
Found at i:365678 original size:15 final size:15
Alignment explanation
Indices: 365655--365687 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
365645 CGTAGGACTC
365655 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
365670 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
365685 CTA
1 CTA
365688 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:365816 original size:29 final size:29
Alignment explanation
Indices: 365772--365845 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
365762 TTTCATTTGT
*
365772 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTGGTGA
365800 TCATGTAGCTCATGTCATTTCTCTGGTGA
1 TCATGTAGCTCATGTCATTTCTCTGGTGA
365829 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
365846 CTTCATATCA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.16
29 37 0.84
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.42
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTGGTGA
Found at i:366300 original size:64 final size:64
Alignment explanation
Indices: 366192--366368 Score: 194
Period size: 64 Copynumber: 2.8 Consensus size: 64
366182 TAATGAAGGT
* * ** * * **
366192 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-GTCACTATTAATGGG
* ** * * *
366256 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATATTTCACTATTAATGTG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTGTCACTATTAATGGG
* *
366320 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTACATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT
366369 CTTTATTTTA
Statistics
Matches: 93, Mismatches: 19, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
63 1 0.01
64 92 0.99
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTGTCACTATTAATGGG
Found at i:366389 original size:64 final size:64
Alignment explanation
Indices: 366255--366416 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 64
366245 TTATTGCTGG
* * * *
366255 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATATTTCACTATTAATGT
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATATTTCACTATTAAAGA
** * * *
366319 GATGCATCGATGCACTACTTATGCATCGATGCATGAATTACATTCGATGTCTTTA-TTTTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATAT-TTCACTATTAAAGA
** *
366382 GAGTGCATCGATGCACTACCAATGCATCAATGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
366417 ATTCAAACAA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 2 0.02
64 78 0.94
65 3 0.04
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (64 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATATTTCACTATTAAAGA
Found at i:372706 original size:28 final size:28
Alignment explanation
Indices: 372674--372746 Score: 130
Period size: 28 Copynumber: 2.6 Consensus size: 28
372664 TTTCATATGT
372674 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCA-TTCTCTTGTGA
372702 TCATGTAGCTCATGTCATTCTCTTGTGA
1 TCATGTAGCTCATGTCATTCTCTTGTGA
372730 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
372747 CTTCATATCA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
28 35 0.80
29 9 0.20
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.42
Consensus pattern (28 bp):
TCATGTAGCTCATGTCATTCTCTTGTGA
Found at i:372779 original size:12 final size:12
Alignment explanation
Indices: 372762--372796 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
372752 TATCATGTTC
372762 TCATATCACATA
1 TCATATCACATA
372774 TCATATCACATA
1 TCATATCACATA
372786 TCATATCACAT
1 TCATATCACAT
372797 GAACATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (12 bp):
TCATATCACATA
Found at i:373260 original size:19 final size:19
Alignment explanation
Indices: 373161--373274 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
373151 TATTGTTGGG
*
373161 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTACTT
* *
373180 ATGCATCGATGCACCAATT
1 ATGCATCGATGCACTACTT
*
373199 A--CATTCGATGTTCACTATTAATGT
1 ATGCA-TCGATG--CAC---TACT-T
373223 GATGCATCGATGC-CTACTT
1 -ATGCATCGATGCACTACTT
*
373242 ATGCATCAATGCACTACTT
1 ATGCATCGATGCACTACTT
373261 ATGCATCGATGCAC
1 ATGCATCGATGCAC
373275 GAATTGCATT
Statistics
Matches: 77, Mismatches: 7, Indels: 22
0.73 0.07 0.21
Matches are distributed among these distances:
17 2 0.03
18 17 0.22
19 37 0.48
20 6 0.08
23 4 0.05
24 2 0.03
25 1 0.01
26 6 0.08
27 2 0.03
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (19 bp):
ATGCATCGATGCACTACTT
Found at i:376205 original size:21 final size:21
Alignment explanation
Indices: 376179--376224 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
376169 GCCAGATTCT
376179 TCCCAAAGCAAGGGCTGGTCG
1 TCCCAAAGCAAGGGCTGGTCG
376200 TCCCAAAGCAAGGGCTGGTCG
1 TCCCAAAGCAAGGGCTGGTCG
376221 TCCC
1 TCCC
376225 CCTTTGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.33, G:0.30, T:0.15
Consensus pattern (21 bp):
TCCCAAAGCAAGGGCTGGTCG
Found at i:376995 original size:191 final size:192
Alignment explanation
Indices: 376614--376965 Score: 410
Period size: 191 Copynumber: 1.8 Consensus size: 192
376604 TCCCGTATTG
*
376614 ATTTTCCAGCCTGCACAGTCTTCATCTATCTGAGCATATCTCGAGTTACCAATATCGGATTGAAG
1 ATTTTCCAGCCTGCACAGTCTTCATCTATCTGAGCATATCTCGAGCTACCAATATCGGATTGAAG
* * * * ****
376679 CGATTCAAAGTGCGTTGGAAAGCTAAGAGATAATGGAATAATTGTTAAGAAGACTTAATCGTCCA
66 CGATTAAAAGTGAGTTGGAAAGATAAGAGATAATAGAATAATTGTTAAGAAGACTTAAGAAACCA
* * * * * *
376744 AATATACTTGTAACACGTTCAAAATTGGCGATACATCTGAATCGTGATCTGTCCACTGGACA
131 AAGATACTTGGAACACGTTCAAAATTGACAATACATATGAATCGTGAACTGTCCACTGGACA
* *
376806 ATTTT-CAGCCTGCACTGTCTTCAT-TAAT-TTAGCCATATCTCGAGCT-CCAAATATCGGATTG
1 ATTTTCCAGCCTGCACAGTCTTCATCT-ATCTGAG-CATATCTCGAGCTACC-AATATCGGATTG
* * *
376867 ATA-CGGTTAAAAGTGAGTTGGAAAGATAAGAGATAATAGAATAATTG-TAAGAATACTTCAGAA
63 A-AGCGATTAAAAGTGAGTTGGAAAGATAAGAGATAATAGAATAATTGTTAAGAAGACTTAAGAA
* * * *
376930 ACCGACGATGCTTGGAACATGTTCAAAATTGACAAT
127 ACCAAAGATACTTGGAACACGTTCAAAATTGACAAT
376966 CAATATGGAT
Statistics
Matches: 134, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
190 44 0.33
191 84 0.63
192 6 0.04
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (192 bp):
ATTTTCCAGCCTGCACAGTCTTCATCTATCTGAGCATATCTCGAGCTACCAATATCGGATTGAAG
CGATTAAAAGTGAGTTGGAAAGATAAGAGATAATAGAATAATTGTTAAGAAGACTTAAGAAACCA
AAGATACTTGGAACACGTTCAAAATTGACAATACATATGAATCGTGAACTGTCCACTGGACA
Found at i:377579 original size:53 final size:54
Alignment explanation
Indices: 377516--377845 Score: 375
Period size: 55 Copynumber: 6.1 Consensus size: 54
377506 AATCTTCTGT
* * * * *
377516 AATCGGGTCTGCTCCCTATTTCTTAAGAGAGTATAAGAC-CCACAGTCTTCATC
1 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAAC
*
377569 AATCGCGTCTG-TCCCCTATTTCTTCAGAGAGTATAAGACTCGAAACAATCTTCAAC
1 AATCGTGTCTGCT-CCCTATTTCTTCAGAGAGTATAAGACTC--AACAATCTTCAAC
* * * * *
377625 GATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTTCAAC
1 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAAC
* * *
377680 AATCGTGTATGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAAC
1 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGAC-TCAACAATCTTCAAC
* * *
377735 AATCGTGTCTGCTCCCTATTTCTTC--AGAGTATAAGATTTGAACAATCTT-AAT
1 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGA-CTCAACAATCTTCAAC
* *
377787 AAT-GTGTCTACTCCCTATTTCTTCAGAGAGTATAAGATTCGAACAATCTTCAAC
1 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTC-AACAATCTTCAAC
*
377841 CATCG
1 AATCG
377846 GGTTCGCTCC
Statistics
Matches: 241, Mismatches: 24, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
51 20 0.08
52 8 0.03
53 77 0.32
54 5 0.02
55 83 0.34
56 48 0.20
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (54 bp):
AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCAACAATCTTCAAC
Found at i:377695 original size:164 final size:160
Alignment explanation
Indices: 377480--377857 Score: 415
Period size: 164 Copynumber: 2.3 Consensus size: 160
377470 TCGCTCCCTC
* *** * *
377480 TTCTTCAG-GAAGTAT-AGAACTCAAATAATCTTCTGTAATCGGGTCTGCTCCCTATTTCTTAAG
1 TTCTTCAGAG-AGTATAAG-ACTCGAATAATCTTCAACAATCGGGTATGCTCCCTATTCCTTAAG
* * *
377543 AGAGTATAAGAC-CCACAGTCTTCATCAATCGCGTCTG-TCCCCTATTTCTTCAGAGAGTATAAG
64 AGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCT-CCCTATTTCTTC--AGAGTATAAG
* *
377606 ACTCGAAACAATCTTCAACGATCGCGTATGCCCCCTAT
126 ACTCG-AACAATCTT-AACAAT-GCGTATACCCCCTAT
* *
377644 TTCTTCAGAGAGTATAAGACTCGAATAATCTTCAACAATCGTGTATGCTCCCTATTCCTTCAGAG
1 TTCTTCAGAGAGTATAAGACTCGAATAATCTTCAACAATCGGGTATGCTCCCTATTCCTTAAGAG
* * * *
377709 AGTATAAGACTTGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGTATAAGATTT
66 AGTATAAGAC-TCAACAATCTTCAACAATCGCGTCTGCTCCCTATTTCTTCAGAGTATAAGACTC
* * * *
377774 GAACAATCTTAATAATGTGTCTACTCCCTAT
130 GAACAATCTTAACAATGCGTATACCCCCTAT
* * *
377805 TTCTTCAGAGAGTATAAGATTCGAACAATCTTCAACCATCGGGT-TCGCTCCCT
1 TTCTTCAGAGAGTATAAGACTCGAATAATCTTCAACAATCGGGTAT-GCTCCCT
377858 CTTTTTAGGG
Statistics
Matches: 183, Mismatches: 25, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
160 1 0.01
161 58 0.32
162 4 0.02
163 9 0.05
164 75 0.41
165 3 0.02
166 32 0.17
167 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (160 bp):
TTCTTCAGAGAGTATAAGACTCGAATAATCTTCAACAATCGGGTATGCTCCCTATTCCTTAAGAG
AGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCTCCCTATTTCTTCAGAGTATAAGACTCG
AACAATCTTAACAATGCGTATACCCCCTAT
Found at i:377699 original size:55 final size:55
Alignment explanation
Indices: 377516--377883 Score: 416
Period size: 53 Copynumber: 6.8 Consensus size: 55
377506 AATCTTCTGT
* * * * *
377516 AATCGGGTCTGCTCCCTATTTCTTAAGAGAGTATAAGAC-C-CACAGTCTTCATC
1 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
*
377569 AATCGCGTCTG-TCCCCTATTTCTTCAGAGAGTATAAGACTCGAAACAATCTTCAAC
1 AATCGTGTCTGCT-CCCTATTTCTTCAGAGAGTATAAGACTCG-AACAATCTTCAAC
* * * * *
377625 GATCGCGTATGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAATAATCTTCAAC
1 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* * *
377680 AATCGTGTATGCTCCCTATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAAC
1 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* * *
377735 AATCGTGTCTGCTCCCTATTTCTTC--AGAGTATAAGATTTGAACAATCTT-AAT
1 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* *
377787 AAT-GTGTCTACTCCCTATTTCTTCAGAGAGTATAAGATTCGAACAATCTTCAAC
1 AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
* * * *
377841 CATCGGGT-TCGCTCCCTCTTT-TT-AGGGAGTAT-AGAACTCGAAC
1 AATCGTGTCT-GCTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAAC
377884 TTCTTCTGCA
Statistics
Matches: 276, Mismatches: 28, Indels: 22
0.85 0.09 0.07
Matches are distributed among these distances:
51 20 0.07
52 8 0.03
53 96 0.35
54 8 0.03
55 96 0.35
56 48 0.17
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.32
Consensus pattern (55 bp):
AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAC
Found at i:377907 original size:52 final size:53
Alignment explanation
Indices: 377844--379083 Score: 973
Period size: 54 Copynumber: 23.7 Consensus size: 53
377834 CTTCAACCAT
* *
377844 CGGGTTCGCTCCCTCTTT-TTAGGGAGTATAGAACTCGAACTTCTTCTGCAAA
1 CGGGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACATCTTCTTCAAA
* * * **
377896 CGGGTTTGCT-CCTCTTTATTAGGGAGTATACAACTC-AA-A-AATC-TCAAA
1 CGGGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACATCTTCTTCAAA
* * * *
377944 CGGATTTGTTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCT-TAGGGAGTATAGAACTCGAACATCTTCTTCAAA
* *
377998 C-GGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACA--ATCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACATCTTCTTCAAA
* * **
378049 CGGGTTCGCTCCCTCTCT-TTAGGGAGTATGGAACTCGAACATCTTCTTCTTA
1 CGGGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACATCTTCTTCAAA
* * * * *
378101 TGGGTTCACTCCCACTTTCTCTA-GG-G-ATAGAACTCGGACAT-ATCTTCAAA
1 CGGGTTCGCTCCCTCTTTCT-TAGGGAGTATAGAACTCGAACATCTTCTTCAAA
* * * **
378151 TGGGTTCGCT-CCTCTTTCTTCAGGGAGTATGGAACT-AAACATCTTCTTCTTA
1 CGGGTTCGCTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACATCTTCTTCAAA
* * * *
378203 CGGGTTTGCT-CCTCTTTCTCTAGGGAGTATATAACTCAAACA--ATCTTCAAA
1 CGGGTTCGCTCCCTCTTTCT-TAGGGAGTATAGAACTCGAACATCTTCTTCAAA
* *
378254 CGGGTTCGCT-CCTC--TCTTAGGGAGTATAGAACTCGAACATATTCCTCAAA
1 CGGGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACATCTTCTTCAAA
*
378304 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
1 CGGGTTCGCTCCCTCTTTCT-TAGGGAGTATAGAACTCGAACATCTTCTTCAAA
* * * * *
378358 CAGGTTCGC-CTCCTCTTTCTTCAGGAAGTATAGAACTTGGACATATTCTTCAAAAA
1 CGGGTTCGCTC-CCTCTTTCTT-AGGGAGTATAGAACTCGAACATCTTCTTC--AAA
* *
378414 CGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAACATCTTTTTCAAA
1 CGGGTTCGCTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACATCTTCTTCAAA
** * * *
378468 CAAGTTCGCTCCATCTTTCTTCAGGAAGTATAGAACTCGAACA--ATCTTCAAA
1 CGGGTTCGCTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACATCTTCTTCAAA
378520 CGGGTTCGCT-CCTCTTTCTCTAGGGAGTATAGAACTCGAACA---TCTTC-AA
1 CGGGTTCGCTCCCTCTTTCT-TAGGGAGTATAGAACTCGAACATCTTCTTCAAA
* **
378569 CTGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTC-AAAATCTTCTTCTTA
1 C-GGGTTCGCTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACATCTTCTTCAAA
* * **
378623 CGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAACA---TCTTCAAA
1 CGGGTTCGCTCCCTCTTTC-TTAGGGAGTATAGAACTCGAACATCTTCTTCAAA
* * * * *
378674 CGGGTTCGCTCCTTCTTCCTTTAAGGAGTATGGAACTCGAACATCTT-TTAAAA
1 CGGGTTCGCTCCCTCTTTC-TTAGGGAGTATAGAACTCGAACATCTTCTTCAAA
* * * * * ** *
378727 AGTGTAT-GCTCCCTATTCCTTCAGAGAGTAT-GAGAC-CGAACAATCTTCGACAAT
1 CGGGT-TCGCTCCCTCTTTCTT-AGGGAGTATAGA-ACTCGAAC-ATCTTCTTCAAA
* * * * * ** *
378781 CGTG-TCTACT-CCT-ATTCTTTCAGAGAGTAT-GAGACTCGAATAATC-TCAACAAT
1 CGGGTTC-GCTCCCTCTTTC-TT-AGGGAGTATAGA-ACTCGAA-CATCTTCTTCAAA
* * * * ** *
378834 CGTG-TCTGCTCCCT-ATTCTTTCAGAGAGTATA-AGACTCGAACAAACTTCAACAAT
1 CGGGTTC-GCTCCCTCTTTC-TT-AGGGAGTATAGA-ACTCGAAC-ATCTTCTTCAAA
* * * *
378889 CGGGTTCG-TTCCTCTTTCTCTAGGGATTATGGAACTCGAATC-TCTTCTGCAAA
1 CGGGTTCGCTCCCTCTTTCT-TAGGGAGTATAGAACTCGAA-CATCTTCTTCAAA
* * *
378942 CGAGTTCGCTCTCTCTTTCTCTAGGGAGTATAGAACTCGAACA-ATT-TTCAAA
1 CGGGTTCGCTCCCTCTTTCT-TAGGGAGTATAGAACTCGAACATCTTCTTCAAA
*
378994 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-AGACATC-TCTTCAAA
1 CGGGTTCGCTCCCTCTTTCT-TAGGGAGTATAGAACTCGA-ACATCTTCTTCAAA
* *
379047 CGGGTTCGCTCCCTCTCTCTTAGGGAGTATGGAACTC
1 CGGGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTC
379084 AAATAATCTT
Statistics
Matches: 990, Mismatches: 130, Indels: 136
0.79 0.10 0.11
Matches are distributed among these distances:
48 33 0.03
49 25 0.03
50 87 0.09
51 161 0.16
52 196 0.20
53 195 0.20
54 225 0.23
55 18 0.02
56 49 0.05
57 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (53 bp):
CGGGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACATCTTCTTCAAA
Found at i:377976 original size:102 final size:105
Alignment explanation
Indices: 377825--379095 Score: 1000
Period size: 104 Copynumber: 12.1 Consensus size: 105
377815 AGTATAAGAT
* *
377825 TCGAACAATCTTCAACCATCGGGTTCGCTCCCTCTTT-TTAGGGAGTATAGAACTCGAACTTCTT
1 TCGAAAAATCTTCAA--A-CGGGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACATCTT
* * * *
377889 CTGCAAACGGGTTTGCT-CCTCTTTAT-TAGGGAGTATACAAC
63 CTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAAC
* * * *
377930 TC-AAAAATC-TCAAACGGATTTGTTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCT
1 TCGAAAAATCTTCAAACGGGTTCGCTCCCTCTTTCT-TAGGGAGTATAGAACTCGAACATCTTCT
*
377993 TCAAAC-GGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAAC
65 TCAAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAAC
* * *
378033 TCGAACAATCTTCAAACGGGTTCGCTCCCTCTCT-TTAGGGAGTATGGAACTCGAACATCTTCTT
1 TCGAAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACATCTTCTT
** * * *
378097 CTTATGGGTTCACTCCCACTTTCTCTA-GG-G-ATAGAAC
66 CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAAC
* * * * *
378134 TCGGACATATCTTCAAATGGGTTCGCT-CCTCTTTCTTCAGGGAGTATGGAACT-AAACATCTTC
1 TC-GAAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACATCTTC
** * *
378197 TTCTTACGGGTTTGCT-CCTCTTTCTCTAGGGAGTATATAAC
64 TTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAAC
* *
378238 TC-AAACAATCTTCAAACGGGTTCGCT-CCTC--TCTTAGGGAGTATAGAACTCGAACATATTCC
1 TCGAAA-AATCTTCAAACGGGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACATCTTCT
378299 TCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAAC
65 TCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAAC
*** * * * * *
378340 TCGGACATCTTCTTCAAACAGGTTCGC-CTCCTCTTTCTTCAGGAAGTATAGAACTTGGACATAT
1 TC-GA-AAAATCTTCAAACGGGTTCGCTC-CCTCTTTCTT-AGGGAGTATAGAACTCGAACATCT
*
378404 TCTTCAAAAACGGGTTCGCTCCCTCTTTCT-TCAGGAAGTATAGAAC
62 TCTTC--AAACGGGTTCGCTCCCTCTTTCTCT-AGGGAGTATAGAAC
* ** * * *
378450 TCG-AACATCTTTTTCAAACAAGTTCGCTCCATCTTTCTTCAGGAAGTATAGAACTCGAACA--A
1 TCGAAAAATC---TTCAAACGGGTTCGCTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACATCT
378512 TCTTCAAACGGGTTCGCT-CCTCTTTCTCTAGGGAGTATAGAAC
62 TCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAAC
* *
378555 TCG-AACATCTTC-AACTGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTC-AAAATCTTC
1 TCGAAAAATCTTCAAAC-GGGTTCGCTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACATCTTC
** * * * **
378617 TTCTTACGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAAC
64 TTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAAC
* * * * *
378659 TCG-AACATCTTCAAACGGGTTCGCTCCTTCTTCCTTTAAGGAGTATGGAACTCGAACATCTT-T
1 TCGAAAAATCTTCAAACGGGTTCGCTCCCTCTTTC-TTAGGGAGTATAGAACTCGAACATCTTCT
* * * * * *
378722 TAAAAAGTGTAT-GCTCCCTATTCCT-TCAGAGAGTAT-GAGAC
65 TCAAACGGGT-TCGCTCCCTCTTTCTCT-AGGGAGTATAGA-AC
* * * * * *
378763 -CGAACAATCTTCGACAATCGTG-TCTACT-CCT-ATTCTTTCAGAGAGTAT-GAGACTCGAATA
1 TCGAAAAATCTTC-A-AA-CGGGTTC-GCTCCCTCTTTC-TT-AGGGAGTATAGA-ACTCGAA-C
** * * * * *
378823 ATC-TCAACAATCGTG-TCTGCTCCCT-ATTCTTTCAGAGAGTATA-AGAC
58 ATCTTCTTCAAACGGGTTC-GCTCCCTCTTTCTCT-AGGGAGTATAGA-AC
* * *
378870 TCGAACAAA-CTTCAACAATCGGGTTCG-TTCCTCTTTCTCTAGGGATTATGGAACTCGAATC-T
1 TCGAA-AAATCTTC-A-AA-CGGGTTCGCTCCCTCTTTCT-TAGGGAGTATAGAACTCGAA-CAT
* * *
378932 CTTCTGCAAACGAGTTCGCTCTCTCTTTCTCTAGGGAGTATAGAAC
60 CTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAAC
* * *
378978 TCGAACAATTTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-AGACATC-TC
1 TCGAAAAATCTTCAAACGGGTTCGCTCCCTCTTTCT-TAGGGAGTATAGAACTCGA-ACATCTTC
* *
379041 TTCAAACGGGTTCGCTCCCTCTCTCT-TAGGGAGTATGGAAC
64 TTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAAC
379082 TC-AAATAATCTTCA
1 TCGAAA-AATCTTCA
379096 TTTGCTTCAC
Statistics
Matches: 959, Mismatches: 135, Indels: 145
0.77 0.11 0.12
Matches are distributed among these distances:
100 29 0.03
101 65 0.07
102 151 0.16
103 109 0.11
104 172 0.18
105 114 0.12
106 70 0.07
107 49 0.05
108 98 0.10
109 20 0.02
110 81 0.08
111 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (105 bp):
TCGAAAAATCTTCAAACGGGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACATCTTCTT
CAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAAC
Found at i:378652 original size:53 final size:50
Alignment explanation
Indices: 377844--378720 Score: 416
Period size: 51 Copynumber: 16.9 Consensus size: 50
377834 CTTCAACCAT
* * * *
377844 CGGGTTCGCTCCCTC-TT-TTTAGGGAGTATAGAACTCGAACTTCTTCTGCAAA
1 CGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCAAACATC-T-T-C-AA
* * * * *
377896 CGGGTTTGCTCC-TCTTT-ATTAGGGAGTATACAACTCAAAAATC-TCAAA
1 CGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCAAACATCTTC-AA
* * * * * * * *
377944 CGGATTTGTTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
1 CGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTC--A-AACATCTTC-AA
* * *
377998 C-GGTTCGCTCCCTCTTTC-TTCAGGAAGTATAGAACTCGAACAATCTTCAAA
1 CGGGTTCGCTCCTTCTTTCTTTAAGG-AGTATAGAACTCAAAC-ATCTTC-AA
* * * * *
378049 CGGGTTCGCTCC--CTCTCTTTAGGGAGTATGGAACTCGAACATCTTCTTCTTA
1 CGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTC-AA-A-CATCTTC-AA
* * ** * * *
378101 TGGGTTCACTCCCACTTTCTCT-AGG-G-ATAGAACTCGGACATATCTTCAAA
1 CGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTC--AAACATCTTC-AA
* * * * *
378151 TGGGTTCGCTCC-TCTTTCTTCAGGGAGTATGGAACT-AAACATCTTCTTCTTA
1 CGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCAAACA---TCTTC-AA
* * * *
378203 CGGGTTTGCTCC-TCTTTCTCTAGGGAGTATATAACTCAAACAATCTTCAAA
1 CGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCAAAC-ATCTTC-AA
* * *
378254 CGGGTTCGCTCC-TC--TC-TTAGGGAGTATAGAACTCGAACATATTCCTCAAA
1 CGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTC-AA-ACA-TCTTC-AA
* * * * *
378304 CGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGGACATCTTCTTCAAA
1 CGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTC--A-AACATCTTC-AA
* * * * *
378358 CAGGTTCGCCTCC-TCTTTC-TTCAGGAAGTATAGAACTTGGACATATTCTTCAAAAA
1 CGGGTTCG-CTCCTTCTTTCTTTAAGG-AGTATAGAAC-T-CAAACA-TCTTC---AA
* * *
378414 CGGGTTCGCTCCCTCTTTC-TTCAGGAAGTATAGAACTCGAACATCTTTTTCAAA
1 CGGGTTCGCTCCTTCTTTCTTTAAGG-AGTATAGAACTCAAACATC---TTC-AA
** * * *
378468 CAAGTTCGCTCCATCTTTC-TTCAGGAAGTATAGAACTCGAACAATCTTCAAA
1 CGGGTTCGCTCCTTCTTTCTTTAAGG-AGTATAGAACTCAAAC-ATCTTC-AA
* * *
378520 CGGGTTCGCTCC-TCTTTCTCTAGGGAGTATAGAACTCGAACATCTTCAA
1 CGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCAAACATCTTCAA
* * * * *
378569 CTGGGTTCGCTCCCTCTTTCTTCAGGGAGTATAGAACTCAAAATCTTCTTCTTA
1 C-GGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTC-AAA-CATCTTC-AA
* * *
378623 CGGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTCAAA
1 CGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCAAACATCTTC-AA
* * *
378674 CGGGTTCGCTCCTTCTTCCTTTAAGGAGTATGGAACTCGAACATCTT
1 CGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCAAACATCTT
378721 TTAAAAAGTG
Statistics
Matches: 663, Mismatches: 110, Indels: 105
0.76 0.13 0.12
Matches are distributed among these distances:
48 30 0.05
49 23 0.03
50 89 0.13
51 142 0.21
52 134 0.20
53 81 0.12
54 112 0.17
55 15 0.02
56 37 0.06
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (50 bp):
CGGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCAAACATCTTCAA
Found at i:379353 original size:36 final size:36
Alignment explanation
Indices: 379251--379433 Score: 169
Period size: 36 Copynumber: 5.1 Consensus size: 36
379241 CTGATGGTCG
* *
379251 GATGGTTTG-TTC-CAACTCTTCT-GAGAAGGCTTAA
1 GATGGTTTGCTTCACTACTC-TCTGGTGAAGGCTTAA
* * *
379285 AATGGATCTGCTTCACTACT-T-TGGTGAAGACTTAA
1 GATGG-TTTGCTTCACTACTCTCTGGTGAAGGCTTAA
* *
379320 GATGGTTTGCTTCACTACTCTCTGGTGAAGACTTAT
1 GATGGTTTGCTTCACTACTCTCTGGTGAAGGCTTAA
* * *
379356 GATGGTTTGCTTCACTATTCTCCGGTGAAGGCTTCA
1 GATGGTTTGCTTCACTACTCTCTGGTGAAGGCTTAA
* * * * *
379392 GATTGATTGCTTCAACTATTCTCCGGTGAAGGCTTCA
1 GATGGTTTGCTTC-ACTACTCTCTGGTGAAGGCTTAA
379429 GATGG
1 GATGG
379434 ACTTTTCTCC
Statistics
Matches: 126, Mismatches: 16, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
34 18 0.14
35 19 0.15
36 58 0.46
37 31 0.25
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (36 bp):
GATGGTTTGCTTCACTACTCTCTGGTGAAGGCTTAA
Found at i:386804 original size:21 final size:21
Alignment explanation
Indices: 386778--386823 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
386768 GCCAGATTCT
386778 TCCCAAAGCAAGGGCTGGTCG
1 TCCCAAAGCAAGGGCTGGTCG
386799 TCCCAAAGCAAGGGCTGGTCG
1 TCCCAAAGCAAGGGCTGGTCG
386820 TCCC
1 TCCC
386824 CTCTTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.33, G:0.30, T:0.15
Consensus pattern (21 bp):
TCCCAAAGCAAGGGCTGGTCG
Found at i:387575 original size:192 final size:194
Alignment explanation
Indices: 387231--387579 Score: 449
Period size: 192 Copynumber: 1.8 Consensus size: 194
387221 TTCCGTATTG
*
387231 ATTTTCCAGCCTGCACAGTCTTCATCTATCTGAGCATATCTCGAGTTACCAATATCGGATTGAAG
1 ATTTTCCAGCCTGCACAGTCTTCATCTATCTGAGCATATCTCGAGCTACCAATATCGGATTGAAG
* * * ****
387296 CGATTCAAAGTGCGTTGGAAAGCTAAGAGATAATGGAATAATTGTTAAGAAGACTTAATCGTCCA
66 CGATTCAAAGTGAGTTGGAAAGATAAGAGATAATAGAATAATTGTTAAGAAGACTTAAGAAACCA
* *
387361 AATATACTTGTAACACGTTCAAAATTGGCGATACATCTGAATGTCGTGATCTGTCCACTGGACA
131 AAGATACTTGGAACACGTTCAAAATTGGCGATACATCTGAATGTCGTGATCTGTCCACTGGACA
* *
387425 ATTTT-CAGCCTGCACTGTCTTCAT-TAAT-TTAGCCATATCTCGAGCT-CCAAATATCGGATTG
1 ATTTTCCAGCCTGCACAGTCTTCATCT-ATCTGAG-CATATCTCGAGCTACC-AATATCGGATTG
* * *
387486 ATA-CGGTT-AAAGTGAGTTGGAAAGATAAGAGATAATAGAATAATTGTTAAGAATACTTCAGAA
63 A-AGCGATTCAAAGTGAGTTGGAAAGATAAGAGATAATAGAATAATTGTTAAGAAGACTTAAGAA
* * * *
387549 ACCGACGATGCTTGGAACATGTTCAAAATTG
127 ACCAAAGATACTTGGAACACGTTCAAAATTG
387580 ACAATCAATA
Statistics
Matches: 132, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
192 77 0.58
193 49 0.37
194 6 0.05
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (194 bp):
ATTTTCCAGCCTGCACAGTCTTCATCTATCTGAGCATATCTCGAGCTACCAATATCGGATTGAAG
CGATTCAAAGTGAGTTGGAAAGATAAGAGATAATAGAATAATTGTTAAGAAGACTTAAGAAACCA
AAGATACTTGGAACACGTTCAAAATTGGCGATACATCTGAATGTCGTGATCTGTCCACTGGACA
Found at i:392236 original size:34 final size:34
Alignment explanation
Indices: 392193--392277 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
392183 TATGATTGAT
392193 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
392227 CTCTCGGCGTCTTCAGTTGGATTCTTCGTAGGAA
1 CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
*
392261 ATCTCGGCGTCTTCAGT
1 CTCTCGGCGTCTTCAGT
392278 GCTGTGCATG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (34 bp):
CTCTCGGCGTCTTCAGTTGGATTCTTCATAGGAA
Found at i:392331 original size:22 final size:22
Alignment explanation
Indices: 392299--392352 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
392289 GACTGGACGT
*
392299 GAGAAATCACGGGTTCTGCAAG
1 GAGAAAGCACGGGTTCTGCAAG
*
392321 GAGAGAGCACGGGTTCTGCAAG
1 GAGAAAGCACGGGTTCTGCAAG
392343 GAGAAAGCAC
1 GAGAAAGCAC
392353 AGAAATCACG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.19, G:0.35, T:0.13
Consensus pattern (22 bp):
GAGAAAGCACGGGTTCTGCAAG
Found at i:392405 original size:23 final size:23
Alignment explanation
Indices: 392375--392418 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
392365 TCCTGCAGGG
392375 CTGCACGTCTGCATGTGGGGGTC
1 CTGCACGTCTGCATGTGGGGGTC
392398 CTGCACGTCTGCATGTGGGGG
1 CTGCACGTCTGCATGTGGGGG
392419 GCATGCAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (23 bp):
CTGCACGTCTGCATGTGGGGGTC
Found at i:392425 original size:23 final size:22
Alignment explanation
Indices: 392372--392425 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
392362 GGGTCCTGCA
392372 GGGCTGCACGTCTGCATGTGGG
1 GGGCTGCACGTCTGCATGTGGG
*
392394 GGTCCTGCACGTCTGCATGTGGG
1 GG-GCTGCACGTCTGCATGTGGG
392417 GGGCATGCA
1 GGGC-TGCA
392426 ACTGTTGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 25 0.89
ACGTcount: A:0.11, C:0.24, G:0.43, T:0.22
Consensus pattern (22 bp):
GGGCTGCACGTCTGCATGTGGG
Found at i:393112 original size:172 final size:170
Alignment explanation
Indices: 392873--393223 Score: 526
Period size: 172 Copynumber: 2.1 Consensus size: 170
392863 TTGTAAAGTT
* * * *
392873 TTAGGGACCGTTTGTAAAATTTAAGGAATTTAAGGAATAAGAGTAAATTATTAAAAGTTACTATA
1 TTAGGGATCGTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTACTATA
*
392938 CTATGCTGGAATTTAGTATTAGTATGCTTAATTGGTTAAATTAGAAAGAATTTA-AAATTTA-TG
66 CTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT-
*
393001 GATTAAATTGCTAACTTTGAAAATGTTGAGAACCAAATAGTAA
130 GATT-AATTGCAAACTTTGAAAATGTTGAGAACC-AATAGTAA
* * **
393044 TTAGGGATCGTTTTGCAAAATTTGAGGAATTTAAGAAATTAGAGTAAATTATAAAAAGTTGGTAT
1 TTAGGGATCG-TTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTACTAT
* *
393109 ACTATGCTTGAATTTAGTATTAATATGCTTAATTGGTTAAATTTGAAAGAATTTATAAATTTAGT
65 ACTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGT
* *
393174 GATTAATTGCAAAGTTTGAAAATGTTGAGAAGCAATAGTAA
130 GATTAATTGCAAACTTTGAAAATGTTGAGAACCAATAGTAA
393215 TTAGGGATC
1 TTAGGGATC
393224 ATTTATATTG
Statistics
Matches: 163, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
171 26 0.16
172 125 0.77
173 11 0.07
174 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (170 bp):
TTAGGGATCGTTTGCAAAATTTAAGGAATTTAAGAAATAAGAGTAAATTATAAAAAGTTACTATA
CTATGCTGGAATTTAGTATTAATATGCTTAATTGGTTAAATTAGAAAGAATTTATAAATTTAGTG
ATTAATTGCAAACTTTGAAAATGTTGAGAACCAATAGTAA
Found at i:395471 original size:42 final size:42
Alignment explanation
Indices: 395422--395745 Score: 245
Period size: 47 Copynumber: 7.4 Consensus size: 42
395412 ATATATTTAC
* *
395422 TATTATTATATCAGT-AAATATAAATCATTAAAGTCAAGTAAT
1 TATTATTAAATCATTAAAAT-TAAATCATTAAAGTCAAGTAAT
* *
395464 TATTATTAAATCATTAAAATTAAATCATTAAAATTAAGTAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTAAT
* *
395506 TATTATTAAATTATTAAAATTAAATCATTAAAGT-AATTATTAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTA--AT
* * **
395549 TAAATCATTAAAGTAATTATTATTAAATCATTAAA-TCATTAAAGTAAT
1 T--ATTATTAAA-TCATTAAAATTAAATCATTAAAGTC----AAGTAAT
* *
395597 TATTATTAAAGCATTAAAGTTAAATCATT--A---AAGTAAT
1 TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTAAT
*
395634 TATTATTAAATCATTAAATCATTAAATCATTAAA-TCATTAAAATAAT
1 TATTATTAAATCATTAAA--ATTAAATCATTAAAGTC----AAGTAAT
*
395681 TATTATTAAATCATTAAATCATTAAATCATTAAA-TCATTAAAATAAT
1 TATTATTAAATCATTAAA--ATTAAATCATTAAAGTC----AAGTAAT
*
395728 AATTATTAAATCATTAAA
1 TATTATTAAATCATTAAA
395746 TCATTAAAGT
Statistics
Matches: 239, Mismatches: 22, Indels: 37
0.80 0.07 0.12
Matches are distributed among these distances:
37 24 0.10
39 10 0.04
41 5 0.02
42 65 0.27
43 8 0.03
45 23 0.10
46 27 0.11
47 70 0.29
48 3 0.01
50 4 0.02
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (42 bp):
TATTATTAAATCATTAAAATTAAATCATTAAAGTCAAGTAAT
Found at i:395479 original size:14 final size:14
Alignment explanation
Indices: 395462--395977 Score: 136
Period size: 14 Copynumber: 35.9 Consensus size: 14
395452 AAGTCAAGTA
395462 ATTATTATTAAATC
1 ATTATTATTAAATC
**
395476 ATTAAAATTAAATC
1 ATTATTATTAAATC
** * *
395490 ATTAAAATTAAGTA
1 ATTATTATTAAATC
*
395504 ATTATTATTAAATT
1 ATTATTATTAAATC
**
395518 ATTAAAATTAAATC
1 ATTATTATTAAATC
* * *
395532 ATTA-AAGTAATTATT
1 ATTATTATTAA--ATC
* *
395547 ATTAAATCATTAAAGTA
1 ATT--ATTATTAAA-TC
395564 ATTATTATTAAATC
1 ATTATTATTAAATC
* *
395578 ATTAAATCATTAAAGTA
1 ATT--ATTATTAAA-TC
*
395595 ATTATTATTAAAGC
1 ATTATTATTAAATC
*
395609 ATTA-AAGTTAAATC
1 ATTATTA-TTAAATC
* *
395623 ---ATTA--AAGTA
1 ATTATTATTAAATC
395632 ATTATTATTAAATC
1 ATTATTATTAAATC
*
395646 ATTAAATCATTAAATC
1 ATT--ATTATTAAATC
* *
395662 ATTAAATCATTAAAATA
1 ATT--ATTATT-AAATC
395679 ATTATTATTAAATC
1 ATTATTATTAAATC
*
395693 ATTAAATCATTAAATC
1 ATT--ATTATTAAATC
* *
395709 ATTAAATCATTAAAATA
1 ATT--ATTATT-AAATC
*
395726 ATAATTATTAAATC
1 ATTATTATTAAATC
* *
395740 ATTAAATCATTAAAGTT
1 ATT--ATTATTAAA-TC
* *
395757 A-AATCATTAAATC
1 ATTATTATTAAATC
**
395770 ATTAAAATTAAATC
1 ATTATTATTAAATC
* *
395784 ---ATTA--AAGTA
1 ATTATTATTAAATC
395793 ATTATTATTAAATC
1 ATTATTATTAAATC
**
395807 ATTAAAATTAAATC
1 ATTATTATTAAATC
* * *
395821 ATTA-AAGTAATTATT
1 ATTATTATTAA--ATC
*
395836 ATTAAATCATTAAAGT-
1 ATT--ATTATTAAA-TC
* *
395852 -TAATTCATTAAAGTA
1 ATTATT-ATTAAA-TC
395867 ATTATTATTAAATC
1 ATTATTATTAAATC
* *
395881 ATTA-AAGTTAAATA
1 ATTATTA-TTAAATC
395895 ATTATTATTAAATC
1 ATTATTATTAAATC
* *
395909 ATTA-AAGTTAAATA
1 ATTATTA-TTAAATC
395923 ATTATTATTAAATC
1 ATTATTATTAAATC
* *
395937 ATTA-AAGTTAAATA
1 ATTATTA-TTAAATC
* *
395951 ATTA-AATTTAAATA
1 ATTATTA-TTAAATC
395965 ATTATTATTAAAT
1 ATTATTATTAAAT
395978 ATGTACTCGA
Statistics
Matches: 381, Mismatches: 75, Indels: 92
0.70 0.14 0.17
Matches are distributed among these distances:
9 6 0.02
11 3 0.01
12 9 0.02
13 18 0.05
14 201 0.53
15 46 0.12
16 64 0.17
17 26 0.07
18 8 0.02
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (14 bp):
ATTATTATTAAATC
Found at i:395481 original size:8 final size:8
Alignment explanation
Indices: 395468--395942 Score: 264
Period size: 8 Copynumber: 63.8 Consensus size: 8
395458 AGTAATTATT
395468 ATTAAATC
1 ATTAAATC
395476 ATTAAA--
1 ATTAAATC
395482 ATTAAATC
1 ATTAAATC
395490 ATTAAA--
1 ATTAAATC
* *
395496 ATTAAGTA
1 ATTAAATC
*
395504 ATT--ATT
1 ATTAAATC
*
395510 ATTAAATT
1 ATTAAATC
395518 ATTAAA--
1 ATTAAATC
395524 ATTAAATC
1 ATTAAATC
*
395532 ATTAAAGTA
1 ATTAAA-TC
*
395541 ATT--ATT
1 ATTAAATC
395547 ATTAAATC
1 ATTAAATC
*
395555 ATTAAAGTA
1 ATTAAA-TC
*
395564 ATT--ATT
1 ATTAAATC
395570 ATTAAATC
1 ATTAAATC
395578 ATTAAATC
1 ATTAAATC
*
395586 ATTAAAGTA
1 ATTAAA-TC
*
395595 ATT--ATT
1 ATTAAATC
*
395601 ATTAAAGC
1 ATTAAATC
395609 ATTAAA--
1 ATTAAATC
*
395615 GTTAAATC
1 ATTAAATC
*
395623 ATTAAAGTA
1 ATTAAA-TC
*
395632 ATT--ATT
1 ATTAAATC
395638 ATTAAATC
1 ATTAAATC
395646 ATTAAATC
1 ATTAAATC
395654 ATTAAATC
1 ATTAAATC
395662 ATTAAATC
1 ATTAAATC
*
395670 ATTAAAATA
1 ATT-AAATC
*
395679 ATT--ATT
1 ATTAAATC
395685 ATTAAATC
1 ATTAAATC
395693 ATTAAATC
1 ATTAAATC
395701 ATTAAATC
1 ATTAAATC
395709 ATTAAATC
1 ATTAAATC
395717 ATTAAA--
1 ATTAAATC
* *
395723 ATAATAATT
1 ATTA-AATC
395732 ATTAAATC
1 ATTAAATC
395740 ATTAAATC
1 ATTAAATC
395748 ATTAAA--
1 ATTAAATC
*
395754 GTTAAATC
1 ATTAAATC
395762 ATTAAATC
1 ATTAAATC
395770 ATTAAA--
1 ATTAAATC
395776 ATTAAATC
1 ATTAAATC
*
395784 ATTAAAGTA
1 ATTAAA-TC
*
395793 ATT--ATT
1 ATTAAATC
395799 ATTAAATC
1 ATTAAATC
395807 ATTAAA--
1 ATTAAATC
395813 ATTAAATC
1 ATTAAATC
*
395821 ATTAAAGTA
1 ATTAAA-TC
*
395830 ATT--ATT
1 ATTAAATC
395836 ATTAAATC
1 ATTAAATC
395844 ATTAAA--
1 ATTAAATC
* *
395850 GTTAATTC
1 ATTAAATC
*
395858 ATTAAAGTA
1 ATTAAA-TC
*
395867 ATT--ATT
1 ATTAAATC
395873 ATTAAATC
1 ATTAAATC
395881 ATTAAA--
1 ATTAAATC
* *
395887 GTTAAATA
1 ATTAAATC
*
395895 ATT--ATT
1 ATTAAATC
395901 ATTAAATC
1 ATTAAATC
395909 ATTAAA--
1 ATTAAATC
* *
395915 GTTAAATA
1 ATTAAATC
*
395923 ATT--ATT
1 ATTAAATC
395929 ATTAAATC
1 ATTAAATC
395937 ATTAAA
1 ATTAAA
395943 GTTAAATAAT
Statistics
Matches: 367, Mismatches: 47, Indels: 106
0.71 0.09 0.20
Matches are distributed among these distances:
6 103 0.28
7 9 0.02
8 217 0.59
9 38 0.10
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.41
Consensus pattern (8 bp):
ATTAAATC
Found at i:395550 original size:23 final size:23
Alignment explanation
Indices: 395524--395977 Score: 328
Period size: 23 Copynumber: 19.3 Consensus size: 23
395514 AATTATTAAA
395524 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
395547 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
* *
395570 ATTAAATCATTAAA-TCATTA-A
1 ATTAAATCATTAAAGTAATTATT
* * * *
395591 AGTAATTATTATTAAAG-CATTA-A
1 ATTAA--ATCATTAAAGTAATTATT
395614 AGTTAAATCATTAAAGTAATTATT
1 A-TTAAATCATTAAAGTAATTATT
* *
395638 ATTAAATCATTAAA-TCATTAAATC
1 ATTAAATCATTAAAGTAATT--ATT
*
395662 ATTAAATCATTAAAATAATTATT
1 ATTAAATCATTAAAGTAATTATT
* *
395685 ATTAAATCATTAAA-TCATTAAATC
1 ATTAAATCATTAAAGTAATT--ATT
* *
395709 ATTAAATCATTAAAATAATAATT
1 ATTAAATCATTAAAGTAATTATT
* *
395732 ATTAAATCATTAAA-TCATTA-A
1 ATTAAATCATTAAAGTAATTATT
* **
395753 AGTTAAATCATTAAA-TCATTAAA
1 A-TTAAATCATTAAAGTAATTATT
395776 ATTAAATCATTAAAGTAATTATT
1 ATTAAATCATTAAAGTAATTATT
* *
395799 ATTAAATCATTAAAATTAAATCATT
1 ATTAAATCATT-AAAGT-AATTATT
* * * *
395824 AAAGTAATTATTATTAAA-TCATTA-A
1 --ATTAA--ATCATTAAAGTAATTATT
*
395849 AGTTAATTCATTAAAGTAATTATT
1 A-TTAAATCATTAAAGTAATTATT
395873 ATTAAATCATTAAAGTTAAATAATTATT
1 ATTAAATCATTAAAG-----TAATTATT
395901 ATTAAATCATTAAAGTTAAATAATTATT
1 ATTAAATCATTAAAG-----TAATTATT
*
395929 ATTAAATCATTAAAGTTAA--ATA
1 ATTAAATCATTAAAG-TAATTATT
395951 ATTAAAT--TTAAA-TAATTATT
1 ATTAAATCATTAAAGTAATTATT
395971 ATTAAAT
1 ATTAAAT
395978 ATGTACTCGA
Statistics
Matches: 361, Mismatches: 39, Indels: 65
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.01
20 14 0.04
21 5 0.01
22 74 0.20
23 138 0.38
24 47 0.13
25 13 0.04
26 3 0.01
27 5 0.01
28 54 0.15
29 5 0.01
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (23 bp):
ATTAAATCATTAAAGTAATTATT
Found at i:395887 original size:37 final size:37
Alignment explanation
Indices: 395499--395898 Score: 334
Period size: 37 Copynumber: 11.0 Consensus size: 37
395489 CATTAAAATT
*
395499 AAGTAATTATTATTAAATTATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* *
395536 AAGTAATTATTATTAAATCATT-AAAGTAATTATTATTA
1 AAGTAATTATTATTAAATCATTAAAATTAA--ATCATTA
* * * ** *
395574 AA-TCATTAAATCATTAAAGTAATTATTATTAAAGCATTA
1 AAGTAATT--ATTATTAAA-TCATTAAAATTAAATCATTA
* * **
395613 AAGTTAA--ATCATTAAAGTAATTATTATTAAATCATTA
1 AAG-TAATTATTATTAAA-TCATTAAAATTAAATCATTA
* * *
395650 AA-TCATTAAATCATTAAATCATTAAAA-T-AATTATT-
1 AAGTAATT--ATTATTAAATCATTAAAATTAAATCATTA
* *
395685 -ATTAA--ATCATTAAATCATTAAATCATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAA--ATTAAATCATTA
* *
395721 AAATAATAATTATTAAATC------ATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
*
395752 AAGTTAA--ATCATTAAATCATTAAAATTAAATCATTA
1 AAG-TAATTATTATTAAATCATTAAAATTAAATCATTA
395788 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* *
395825 AAGTAATTATTATTAAATCATTAAAGTTAATTCATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
* *
395862 AAGTAATTATTATTAAATCATTAAAGTTAAATAATTA
1 AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
395899 TTATTAAATC
Statistics
Matches: 304, Mismatches: 29, Indels: 60
0.77 0.07 0.15
Matches are distributed among these distances:
30 10 0.03
31 31 0.10
32 3 0.01
33 1 0.00
34 2 0.01
35 13 0.04
36 27 0.09
37 159 0.52
38 14 0.05
39 34 0.11
40 4 0.01
41 6 0.02
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (37 bp):
AAGTAATTATTATTAAATCATTAAAATTAAATCATTA
Found at i:395962 original size:56 final size:57
Alignment explanation
Indices: 395859--395968 Score: 179
Period size: 56 Copynumber: 1.9 Consensus size: 57
395849 AGTTAATTCA
* *
395859 TTAAAGTAATTATTATTAAATCATTAAAGTTAAATAATTATTATTAAATCATTAAAG
1 TTAAAGTAATTATTATTAAATCATTAAAGTTAAATAATTAATATTAAATAATTAAAG
395916 TTAAA-TAATTATTATTAAATCATTAAAGTTAAATAATTAA-ATTTAAATAATTA
1 TTAAAGTAATTATTATTAAATCATTAAAGTTAAATAATTAATA-TTAAATAATTA
395969 TTATTAAATA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
55 1 0.02
56 44 0.88
57 5 0.10
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.43
Consensus pattern (57 bp):
TTAAAGTAATTATTATTAAATCATTAAAGTTAAATAATTAATATTAAATAATTAAAG
Found at i:397282 original size:18 final size:18
Alignment explanation
Indices: 397259--397305 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
397249 AAATTATTAG
*
397259 TCTCACGTTTCAGACGAA
1 TCTCACGCTTCAGACGAA
397277 TCTCACGCTTCAGACGAA
1 TCTCACGCTTCAGACGAA
397295 TCTCACGCTTC
1 TCTCACGCTTC
397306 GACCACAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.28
Consensus pattern (18 bp):
TCTCACGCTTCAGACGAA
Found at i:397755 original size:32 final size:32
Alignment explanation
Indices: 397714--397779 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
397704 ATCATGGAAA
397714 AATTAACCCTAAAAACGCCGAGATATCCAAAG
1 AATTAACCCTAAAAACGCCGAGATATCCAAAG
397746 AATTAACCCTAAAAACGCCGAGATATCCAAAG
1 AATTAACCCTAAAAACGCCGAGATATCCAAAG
397778 AA
1 AA
397780 CCACTTGAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.15
Consensus pattern (32 bp):
AATTAACCCTAAAAACGCCGAGATATCCAAAG
Found at i:399987 original size:19 final size:19
Alignment explanation
Indices: 399950--399988 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
399940 ATAATATTTG
*
399950 TTTATATATATTTTATATT
1 TTTATATATATTTAATATT
399969 TTTATAT-TATTTAATTATT
1 TTTATATATATTTAA-TATT
399988 T
1 T
399989 CATGTTCGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTATATATATTTAATATT
Found at i:411032 original size:30 final size:30
Alignment explanation
Indices: 410976--411052 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 30
410966 ATGTTAAAAT
* *
410976 TAACAAATTGGTCATTAACATGATCGATTTG
1 TAACAAAAT-GTCACTAACATGATCGATTTG
*
411007 TAACAAAATGTCACTAACGTGATCGATTTG
1 TAACAAAATGTCACTAACATGATCGATTTG
411037 TAACAAAATGATCACT
1 TAACAAAATG-TCACT
411053 CCACCATTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
30 29 0.69
31 13 0.31
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (30 bp):
TAACAAAATGTCACTAACATGATCGATTTG
Found at i:412170 original size:29 final size:29
Alignment explanation
Indices: 412127--412236 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
412117 TTTTATATGT
412127 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
412155 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
412184 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
412213 TCATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
412237 ATATCACATA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.09
29 66 0.85
30 5 0.06
ACGTcount: A:0.17, C:0.20, G:0.16, T:0.46
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:412680 original size:64 final size:63
Alignment explanation
Indices: 412611--412767 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 63
412601 TAATGAAGGT
* **
412611 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGATG-TTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATGTTTTTATT-TTAA-AA
412674 G
63 G
* * *
412675 ATGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAG
*
412738 AGTGCATCGATGCACTACATGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
412768 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 67 0.85
65 9 0.11
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAG
Found at i:419100 original size:29 final size:29
Alignment explanation
Indices: 419057--419166 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
419047 ATTTATATGT
419057 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
419085 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
419114 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
419143 TTATGTAGCTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
419167 ATATCACATA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
28 7 0.09
29 65 0.84
30 5 0.06
ACGTcount: A:0.17, C:0.20, G:0.16, T:0.46
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:419608 original size:64 final size:63
Alignment explanation
Indices: 419539--419695 Score: 176
Period size: 64 Copynumber: 2.5 Consensus size: 63
419529 TAATGAAGGT
* **
419539 ATGCATCGATGCAATACTTGTGCATCGGTGCA-TAAAATGCATTCGATG-TTTTATTATTAATGG
1 ATGCATCGATGCAATACTTGTGCATCGATGCACT-AAATGCATTCGATGTTTTTATT-TTAA-AA
419602 G
63 G
* * *
419603 ATGCATCGATGC-ATGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTATTTTAAAAG
1 ATGCATCGATGCAAT-ACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAG
* *
419666 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCAATACTTGTGCATCGAT
419696 ACACCTTCAA
Statistics
Matches: 78, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
63 4 0.05
64 65 0.83
65 9 0.12
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCAATACTTGTGCATCGATGCACTAAATGCATTCGATGTTTTTATTTTAAAAG
Found at i:421217 original size:46 final size:46
Alignment explanation
Indices: 421164--421254 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
421154 GTATGAAAGC
**
421164 ACAATATTCTTGCAATGGTTTTACATTTTGTAAAAGGAAAAGTTGG
1 ACAATATTAATGCAATGGTTTTACATTTTGTAAAAGGAAAAGTTGG
*
421210 ACAATATTAATGCAATGGTTTTACATTTTGTAAAAGGAAAGGTTG
1 ACAATATTAATGCAATGGTTTTACATTTTGTAAAAGGAAAAGTTG
421255 TATGAAAGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (46 bp):
ACAATATTAATGCAATGGTTTTACATTTTGTAAAAGGAAAAGTTGG
Found at i:433587 original size:2 final size:2
Alignment explanation
Indices: 433580--433625 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
433570 CAATTTGCTT
433580 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
433622 TA TA
1 TA TA
433626 GCTACAACTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:435445 original size:97 final size:97
Alignment explanation
Indices: 435279--435479 Score: 402
Period size: 97 Copynumber: 2.1 Consensus size: 97
435269 ATACACATTA
435279 ATTCAAGAATTAAATGAAATATATATGGAAGAAAGTGGGAAGTGAAGGAATAGGTTGTTGGTTCA
1 ATTCAAGAATTAAATGAAATATATATGGAAGAAAGTGGGAAGTGAAGGAATAGGTTGTTGGTTCA
435344 TTTGTAAAATTAAAGCAAGGAATCCATGCTCT
66 TTTGTAAAATTAAAGCAAGGAATCCATGCTCT
435376 ATTCAAGAATTAAATGAAATATATATGGAAGAAAGTGGGAAGTGAAGGAATAGGTTGTTGGTTCA
1 ATTCAAGAATTAAATGAAATATATATGGAAGAAAGTGGGAAGTGAAGGAATAGGTTGTTGGTTCA
435441 TTTGTAAAATTAAAGCAAGGAATCCATGCTCT
66 TTTGTAAAATTAAAGCAAGGAATCCATGCTCT
435473 ATTCAAG
1 ATTCAAG
435480 TTGTATATTA
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 104 1.00
ACGTcount: A:0.40, C:0.07, G:0.23, T:0.29
Consensus pattern (97 bp):
ATTCAAGAATTAAATGAAATATATATGGAAGAAAGTGGGAAGTGAAGGAATAGGTTGTTGGTTCA
TTTGTAAAATTAAAGCAAGGAATCCATGCTCT
Found at i:438494 original size:13 final size:13
Alignment explanation
Indices: 438476--438500 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
438466 TCCTTGAAAA
438476 TCAAGTGTTGGAT
1 TCAAGTGTTGGAT
438489 TCAAGTGTTGGA
1 TCAAGTGTTGGA
438501 CACATGCACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (13 bp):
TCAAGTGTTGGAT
Found at i:444206 original size:14 final size:14
Alignment explanation
Indices: 444187--444244 Score: 73
Period size: 14 Copynumber: 4.1 Consensus size: 14
444177 GGTCTATTTG
444187 ACTCGTCTC-AGTCA
1 ACTCGTC-CGAGTCA
444201 ACTCGTCCGAGTCA
1 ACTCGTCCGAGTCA
* *
444215 ACTTGTCTGAGTCA
1 ACTCGTCCGAGTCA
*
444229 ACTTGTCCGAGTCA
1 ACTCGTCCGAGTCA
444243 AC
1 AC
444245 CCGTTGACTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
13 1 0.03
14 39 0.98
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (14 bp):
ACTCGTCCGAGTCA
Found at i:444231 original size:28 final size:28
Alignment explanation
Indices: 444191--444244 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
444181 TATTTGACTC
444191 GTCTCAGTCAACTCGTCCGAGTCAACTT
1 GTCTCAGTCAACTCGTCCGAGTCAACTT
* *
444219 GTCTGAGTCAACTTGTCCGAGTCAAC
1 GTCTCAGTCAACTCGTCCGAGTCAAC
444245 CCGTTGACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (28 bp):
GTCTCAGTCAACTCGTCCGAGTCAACTT
Found at i:450081 original size:5 final size:5
Alignment explanation
Indices: 450071--450108 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
450061 AATAAAGCCG
*
450071 GAGAA GAGAA GAGAG GAGAA GAGAA GAGAA GAGAA GAG
1 GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAGAA GAG
450109 TAGTGAGGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (5 bp):
GAGAA
Found at i:455835 original size:31 final size:30
Alignment explanation
Indices: 455770--455835 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
455760 TTTTGACTCT
*
455770 AATTTTAGATGAAATATCATTTGACCATTA
1 AATTTTAGATGAAATATCATTTGACCACTA
* * *
455800 AATTTTAGATTAAATATCAATTTGACCCCTG
1 AATTTTAGATGAAATATC-ATTTGACCACTA
455831 AATTT
1 AATTT
455836 GACCAAAGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (30 bp):
AATTTTAGATGAAATATCATTTGACCACTA
Found at i:468914 original size:14 final size:14
Alignment explanation
Indices: 468895--468934 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
468885 AACGAATATA
468895 AACGAACACAAACG
1 AACGAACACAAACG
* *
468909 AACGAATATAAACG
1 AACGAACACAAACG
468923 AAC-AACACAAAC
1 AACGAACACAAAC
468935 ACAAAAAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.60, C:0.25, G:0.10, T:0.05
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:469210 original size:14 final size:16
Alignment explanation
Indices: 469191--469222 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
469181 GCCCTCTGTT
469191 CGAACATA-AAT-GAA
1 CGAACATATAATCGAA
469205 CGAACATATAATCGAA
1 CGAACATATAATCGAA
469221 CG
1 CG
469223 TTCACGAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (16 bp):
CGAACATATAATCGAA
Found at i:476474 original size:4 final size:4
Alignment explanation
Indices: 476465--476489 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
476455 ATATTATATC
476465 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
476490 ATTATTTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:477040 original size:6 final size:7
Alignment explanation
Indices: 477017--477047 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
477007 CGAATCAGTT
477017 TTTTAAA
1 TTTTAAA
477024 TTTTAAA
1 TTTTAAA
477031 TTTT-AA
1 TTTTAAA
477037 TTTTAAA
1 TTTTAAA
477044 TTTT
1 TTTT
477048 TTTTGCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
TTTTAAA
Found at i:477040 original size:13 final size:14
Alignment explanation
Indices: 477017--477047 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
477007 CGAATCAGTT
477017 TTTTAAATTTTAAA
1 TTTTAAATTTTAAA
477031 TTTT-AATTTTAAA
1 TTTTAAATTTTAAA
477044 TTTT
1 TTTT
477048 TTTTGCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 13 0.76
14 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTAAATTTTAAA
Found at i:484905 original size:20 final size:20
Alignment explanation
Indices: 484880--484927 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
484870 ATAAATAACT
484880 ATAAAACTAATTTTCTGATC
1 ATAAAACTAATTTTCTGATC
484900 ATAAAACTAATTTTCTGATC
1 ATAAAACTAATTTTCTGATC
484920 ATAAAACT
1 ATAAAACT
484928 CAAAAAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (20 bp):
ATAAAACTAATTTTCTGATC
Found at i:485660 original size:36 final size:36
Alignment explanation
Indices: 485603--485703 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 36
485593 TTTCGTCCTA
485603 CTAGGATTCAAACT-CTCAAAAATAGGATAGAATTATG
1 CTAGGATTC-AACTCCT-AAAAATAGGATAGAATTATG
* *
485640 CTAGGATTCAACTCCTAAAAATATGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAAATAGGATAGAATTATG
** * *
485676 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAAAATAGGAT
485704 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
36 25 0.45
37 30 0.55
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (36 bp):
CTAGGATTCAACTCCTAAAAATAGGATAGAATTATG
Found at i:486204 original size:26 final size:24
Alignment explanation
Indices: 486175--486244 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 24
486165 TTTTTTAAAG
486175 TTATCATATATATATATTTATAACTA
1 TTATCATATATATATATTT-T-ACTA
*
486201 TTAT-ATTTAT-TATTATTTTACTA
1 TTATCATATATATA-TATTTTACTA
*
486224 TTAACATATATAATATATTTT
1 TTATCATATAT-ATATATTTT
486245 TCTCTTTTGC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
23 7 0.19
24 8 0.22
25 16 0.43
26 6 0.16
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (24 bp):
TTATCATATATATATATTTTACTA
Found at i:486206 original size:23 final size:21
Alignment explanation
Indices: 486180--486235 Score: 51
Period size: 23 Copynumber: 2.5 Consensus size: 21
486170 TAAAGTTATC
486180 ATATATATATATTTATAACTATT
1 ATATATATATATTT-T-ACTATT
*
486203 ATATTTATTATTATTTTACTATT
1 ATATATA-TA-TATTTTACTATT
*
486226 A-ACATATATA
1 ATATATATATA
486236 ATATATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 2 0.07
21 2 0.07
22 3 0.11
23 13 0.46
24 3 0.11
25 5 0.18
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATATATATATTTTACTATT
Found at i:486245 original size:26 final size:24
Alignment explanation
Indices: 486179--486245 Score: 57
Period size: 24 Copynumber: 2.7 Consensus size: 24
486169 TTAAAGTTAT
*
486179 CATATATATATATTTATAACTATTA
1 CATATATATATATTT-TTACTATTA
* *
486204 TATTTAT-TAT-TATTTTACTATTAA
1 CATATATATATAT-TTTTACTATT-A
486228 CATATATAATATATTTTT
1 CATATAT-ATATATTTTT
486246 CTCTTTTGCT
Statistics
Matches: 32, Mismatches: 5, Indels: 9
0.70 0.11 0.20
Matches are distributed among these distances:
23 8 0.25
24 11 0.34
25 5 0.16
26 7 0.22
27 1 0.03
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (24 bp):
CATATATATATATTTTTACTATTA
Found at i:486309 original size:48 final size:50
Alignment explanation
Indices: 486208--486314 Score: 182
Period size: 48 Copynumber: 2.2 Consensus size: 50
486198 CTATTATATT
* *
486208 TATTATTATTTTACTATTAACATATATAATATATTTTTCTCTTTTGCTAC
1 TATTATTATTTTACTATTAACAGATATAATATATTTTTCTCTTTTACTAC
486258 TATTATTATTTTACTATTAAC-GATATAA-ATATTTTTCTCTTTTACTAC
1 TATTATTATTTTACTATTAACAGATATAATATATTTTTCTCTTTTACTAC
486306 TATTATTAT
1 TATTATTAT
486315 CATTATATGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
48 28 0.51
49 6 0.11
50 21 0.38
ACGTcount: A:0.31, C:0.11, G:0.02, T:0.56
Consensus pattern (50 bp):
TATTATTATTTTACTATTAACAGATATAATATATTTTTCTCTTTTACTAC
Found at i:490250 original size:25 final size:25
Alignment explanation
Indices: 490194--490244 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
490184 ACTTGTACAT
490194 GCTGAAGGGAGAGACTTTGCTAGAA
1 GCTGAAGGGAGAGACTTTGCTAGAA
490219 GCTGAAGGGAGAGACTTTGCTAGAA
1 GCTGAAGGGAGAGACTTTGCTAGAA
490244 G
1 G
490245 TAGAAGCCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.37, T:0.20
Consensus pattern (25 bp):
GCTGAAGGGAGAGACTTTGCTAGAA
Found at i:493733 original size:17 final size:17
Alignment explanation
Indices: 493706--493744 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
493696 AATTTACAAT
493706 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
493722 TAATTATAAATAATATC
1 TAATTATAAATAATATC
493739 TAATTA
1 TAATTA
493745 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:496560 original size:2 final size:2
Alignment explanation
Indices: 496553--496588 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
496543 ATAATTAAAT
496553 TA TA TA TA TA 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 TA TA TA TA TA
496589 CTACTTCTCT
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):
TA
Found at i:497471 original size:30 final size:30
Alignment explanation
Indices: 497435--497506 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
497425 ATGAATCTTC
497435 CTTGCTGAGTTGCTGAGTTGGTGTGATATG
1 CTTGCTGAGTTGCTGAGTTGGTGTGATATG
*
497465 CTTGCTGAGTTGCTGGGTTGGTGTGATATG
1 CTTGCTGAGTTGCTGAGTTGGTGTGATATG
497495 CTTGCTGAGTTG
1 CTTGCTGAGTTG
497507 GAGGATGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.11, C:0.11, G:0.38, T:0.40
Consensus pattern (30 bp):
CTTGCTGAGTTGCTGAGTTGGTGTGATATG
Found at i:502693 original size:29 final size:29
Alignment explanation
Indices: 502661--502751 Score: 76
Period size: 31 Copynumber: 3.0 Consensus size: 29
502651 TTTCTAATAT
502661 ATAATATTATATTTTAATATTATAATAAA
1 ATAATATTATATTTTAATATTATAATAAA
* * * *
502690 ATAATCAATTATATTATAATAATATAA-GAT
1 ATAAT--ATTATATTTTAATATTATAATAAA
* *
502720 ATTATATTTTTATTTTAATAATATATAATAAA
1 ATAATA-TTATATTTTAAT-AT-TATAATAAA
502752 TTATTAATAA
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
28 1 0.02
29 15 0.33
30 6 0.13
31 23 0.50
32 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (29 bp):
ATAATATTATATTTTAATATTATAATAAA
Found at i:502828 original size:19 final size:18
Alignment explanation
Indices: 502804--502872 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
502794 ATATTATTAA
502804 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
502823 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
502841 ATTAATCTAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
502863 ATT-TTAATAA
1 ATTATTAATAA
502873 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:502887 original size:23 final size:23
Alignment explanation
Indices: 502867--502911 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
502857 AATAATATTT
502867 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
502890 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
502912 TATAACACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:503331 original size:25 final size:25
Alignment explanation
Indices: 503297--503348 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
503287 TTTTAGAAAA
503297 TTAGATAAGAAATAAAACCCTAATG
1 TTAGATAAGAAATAAAACCCTAATG
*
503322 TTAGATAAGAATTAAAACCCTAATG
1 TTAGATAAGAAATAAAACCCTAATG
503347 TT
1 TT
503349 CCTTTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.29
Consensus pattern (25 bp):
TTAGATAAGAAATAAAACCCTAATG
Found at i:508521 original size:15 final size:16
Alignment explanation
Indices: 508498--508545 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
508488 TCGTTATAAA
*
508498 TTTTGTTATAATT-TT
1 TTTTATTATAATTATT
508513 TTTTATTATAATTATT
1 TTTTATTATAATTATT
* *
508529 ATTTATTATGATTATT
1 TTTTATTATAATTATT
508545 T
1 T
508546 GAAAAAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (16 bp):
TTTTATTATAATTATT
Found at i:511497 original size:17 final size:18
Alignment explanation
Indices: 511475--511515 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
511465 AAATTATATT
511475 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
511492 AGTAAAATGTTTAAATAA
1 AGTAAAATGATTAAATAA
*
511510 ATTAAA
1 AGTAAA
511516 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:518328 original size:10 final size:10
Alignment explanation
Indices: 518314--518344 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
518304 AAAACCGAAA
518314 AAAAACCGGG
1 AAAAACCGGG
*
518324 GAAAACCGGG
1 AAAAACCGGG
518334 AAAAACCGGG
1 AAAAACCGGG
518344 A
1 A
518345 TTACTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.48, C:0.19, G:0.32, T:0.00
Consensus pattern (10 bp):
AAAAACCGGG
Found at i:518337 original size:21 final size:20
Alignment explanation
Indices: 518303--518343 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
518293 CGGACCGACT
518303 GAAAACCGAAAAAAAACCGGG
1 GAAAACCG-AAAAAAACCGGG
**
518324 GAAAACCGGGAAAAACCGGG
1 GAAAACCGAAAAAAACCGGG
518344 ATTACTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.51, C:0.20, G:0.29, T:0.00
Consensus pattern (20 bp):
GAAAACCGAAAAAAACCGGG
Found at i:522653 original size:14 final size:14
Alignment explanation
Indices: 522634--522660 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
522624 ATATTAAATA
522634 ATAACTATAATTAT
1 ATAACTATAATTAT
522648 ATAACTATAATTA
1 ATAACTATAATTA
522661 AAAAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAACTATAATTAT
Found at i:524114 original size:19 final size:19
Alignment explanation
Indices: 524079--524115 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
524069 ATGACCAACA
* *
524079 AAATCGCAATGCTATCTCT
1 AAATCGCAACGCGATCTCT
524098 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
524116 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:524164 original size:20 final size:20
Alignment explanation
Indices: 524141--524232 Score: 80
Period size: 20 Copynumber: 4.6 Consensus size: 20
524131 GTTTCCAGAT
*
524141 TCGCAACGCGATTTTG-ACTA
1 TCGCAACGCGATTATGTA-TA
* * *
524161 TCGCAATGCGAATACGTATA
1 TCGCAACGCGATTATGTATA
* * *
524181 TCGCAATGCGAATATGTAAA
1 TCGCAACGCGATTATGTATA
*
524201 TCGCAACGCGATTCTG-ACTA
1 TCGCAACGCGATTATGTA-TA
524221 TCGCAACGCGAT
1 TCGCAACGCGAT
524233 AATATAAAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
19 1 0.02
20 58 0.97
21 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATTATGTATA
Found at i:524840 original size:20 final size:19
Alignment explanation
Indices: 524801--524917 Score: 75
Period size: 20 Copynumber: 6.2 Consensus size: 19
524791 AAAATCGCAA
524801 CGATAGTCAAATTT-GCGTTG
1 CGATAGTC--ATTTCGCGTTG
*
524821 CGATAGTCATTTTCGTGTTG
1 CGATAGTCA-TTTCGCGTTG
** *
524841 CGATTTTCATTCCGCGTTG
1 CGATAGTCATTTCGCGTTG
*
524860 CGAT--T-A--TCTCGTTG
1 CGATAGTCATTTCGCGTTG
* *
524874 CAATAGTCAAATTCGCGTTG
1 CGATAGTC-ATTTCGCGTTG
*
524894 CGATAGTCATTTTCGTGTTG
1 CGATAGTCA-TTTCGCGTTG
524914 CGAT
1 CGAT
524918 TTTAAGTTTC
Statistics
Matches: 76, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
14 9 0.12
16 2 0.03
17 1 0.01
18 2 0.03
19 16 0.21
20 46 0.61
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (19 bp):
CGATAGTCATTTCGCGTTG
Found at i:524904 original size:53 final size:54
Alignment explanation
Indices: 524816--524918 Score: 127
Period size: 53 Copynumber: 1.9 Consensus size: 54
524806 GTCAAATTTG
* ** * **
524816 CGTTGCGATAGTCATTTTCGTGTTGCGATTTTCA-TTCCGCGTTGCGATTATCT
1 CGTTGCAATAGTCAAATTCGCGTTGCGATAGTCATTTCCGCGTTGCGATTATCT
* *
524869 CGTTGCAATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATT
1 CGTTGCAATAGTCAAATTCGCGTTGCGATAGTCATTTCCGCGTTGCGATT
524919 TTAAGTTTCA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
53 28 0.68
54 13 0.32
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (54 bp):
CGTTGCAATAGTCAAATTCGCGTTGCGATAGTCATTTCCGCGTTGCGATTATCT
Found at i:524949 original size:73 final size:73
Alignment explanation
Indices: 524803--524939 Score: 177
Period size: 73 Copynumber: 1.9 Consensus size: 73
524793 AATCGCAACG
* * *****
524803 ATAGTCAAATTTGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTCATTCCGCGTTGCGATTATC
1 ATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAATTCCGAAAAACGATTATC
524868 TCGTTGCA
66 TCGTTGCA
* *
524876 ATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAAGTTTC-AAAAACTATTAT
1 ATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAA-TTCCGAAAAACGATTAT
524940 TCTTCTGCAA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
73 51 0.94
74 3 0.06
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.41
Consensus pattern (73 bp):
ATAGTCAAATTCGCGTTGCGATAGTCATTTTCGTGTTGCGATTTTAATTCCGAAAAACGATTATC
TCGTTGCA
Found at i:526851 original size:20 final size:20
Alignment explanation
Indices: 526826--526874 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
526816 CGAAACTTAA
526826 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
526846 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
526866 ATCGCAACG
1 ATCGCAACG
526875 GGATAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:526915 original size:14 final size:14
Alignment explanation
Indices: 526896--526928 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
526886 ATGCGAAATA
*
526896 AAAATCGCAATGTG
1 AAAATCGCAATGCG
526910 AAAATCGCAATGCG
1 AAAATCGCAATGCG
526924 AAAAT
1 AAAAT
526929 GACTATCGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.15, G:0.18, T:0.18
Consensus pattern (14 bp):
AAAATCGCAATGCG
Found at i:526965 original size:19 final size:19
Alignment explanation
Indices: 526941--526981 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
526931 CTATCGCAAC
526941 GCGAATTTAGTTTCACGTT
1 GCGAATTTAGTTTCACGTT
* *
526960 GCGAATTTGGTTTCGCGTT
1 GCGAATTTAGTTTCACGTT
526979 GCG
1 GCG
526982 TTTTTCTCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.17, G:0.29, T:0.39
Consensus pattern (19 bp):
GCGAATTTAGTTTCACGTT
Found at i:527007 original size:33 final size:33
Alignment explanation
Indices: 526951--527030 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 33
526941 GCGAATTTAG
* * * *
526951 TTTCACGTTGCGAATTTGGTTTCGCGTTGCGTT
1 TTTCACGTTGCGATTTTGATTTCGCATTGCGAT
* *
526984 TTTCTCGTTGCGATTTTTATTTCGCATTGCGAT
1 TTTCACGTTGCGATTTTGATTTCGCATTGCGAT
* *
527017 TATCCCGTTGCGAT
1 TTTCACGTTGCGAT
527031 AGTCAAATTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (33 bp):
TTTCACGTTGCGATTTTGATTTCGCATTGCGAT
Found at i:527047 original size:20 final size:20
Alignment explanation
Indices: 527022--527070 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
527012 GCGATTATCC
527022 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
527042 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
527062 TGTTGCGAT
1 CGTTGCGAT
527071 TTAAGTTTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:527081 original size:19 final size:20
Alignment explanation
Indices: 527057--527098 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
527047 CGATAGTCAT
527057 TTTCGTGTTGCGA-TTTAAG
1 TTTCGTGTTGCGATTTTAAG
527076 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
527096 TTT
1 TTT
527099 TAGAAACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.14, C:0.10, G:0.24, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:527675 original size:21 final size:21
Alignment explanation
Indices: 527575--527676 Score: 91
Period size: 21 Copynumber: 4.9 Consensus size: 21
527565 GCCCGACTTA
527575 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGCC
* *
527596 TCT-CCTATCGTTCAAGAGGCC
1 CCTGTC-ATCGTTCAAGAGGCC
* ** *
527617 CCTATCATCCCTCAAGAGTCC
1 CCTGTCATCGTTCAAGAGGCC
**
527638 CCTCCCA-CAGTTCAAGAGGCC
1 CCTGTCATC-GTTCAAGAGGCC
*
527659 CCTGTCATCGTTGAAGAG
1 CCTGTCATCGTTCAAGAG
527677 ATCCCTCCTA
Statistics
Matches: 62, Mismatches: 15, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.03
21 58 0.94
22 2 0.03
ACGTcount: A:0.22, C:0.35, G:0.20, T:0.24
Consensus pattern (21 bp):
CCTGTCATCGTTCAAGAGGCC
Found at i:527676 original size:42 final size:43
Alignment explanation
Indices: 527575--527697 Score: 137
Period size: 42 Copynumber: 2.9 Consensus size: 43
527565 GCCCGACTTA
* * *
527575 CCTGTCATCGTTCAAGAGGCCTCTCCTATC-GTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCTACCAGTTCAAGAGGCC
* ** *
527617 CCTATCATCCCTCAAGAGTCCCCTCCCA-CAGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGTCCCCTCCTACCAGTTCAAGAGGCC
*
527659 CCTGTCATCGTTGAAGAGAT-CCCTCCTACCA-TTCAAGAG
1 CCTGTCATCGTTCAAGAG-TCCCCTCCTACCAGTTCAAGAG
527698 CCCGATTCAT
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.01
42 63 0.94
43 3 0.04
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.24
Consensus pattern (43 bp):
CCTGTCATCGTTCAAGAGTCCCCTCCTACCAGTTCAAGAGGCC
Found at i:529105 original size:14 final size:14
Alignment explanation
Indices: 529086--529122 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
529076 GCTTGTTTAA
*
529086 TTGATTTGTAAAAT
1 TTGATTTGTAAAAG
529100 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
529114 TTGATTTGT
1 TTGATTTGT
529123 TTAATATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:529117 original size:28 final size:29
Alignment explanation
Indices: 529086--529140 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
529076 GCTTGTTTAA
*
529086 TTGATTTGTAAAAT-TTGATTTGTAAAAG
1 TTGATTTGTAAAATATTGATGTGTAAAAG
**
529114 TTGATTTGTTTAATATTGATGTGTAAA
1 TTGATTTGTAAAATATTGATGTGTAAA
529141 TAATTCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (29 bp):
TTGATTTGTAAAATATTGATGTGTAAAAG
Found at i:529269 original size:20 final size:21
Alignment explanation
Indices: 529244--529297 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
529234 AGGTACACTT
529244 TCGCAACGCT-AAA-CTCAAAA
1 TCGCAACGCTGAAAGC-CAAAA
*
529264 TCGCAATG-TGAAAGCCAAAA
1 TCGCAACGCTGAAAGCCAAAA
529284 TCGCAACGC-GAAAG
1 TCGCAACGCTGAAAG
529298 TCAATTCGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.43, C:0.26, G:0.19, T:0.13
Consensus pattern (21 bp):
TCGCAACGCTGAAAGCCAAAA
Done.