Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008650.1 Hibiscus syriacus cultivar Beakdansim tig00111640_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: 1713193
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:14577 original size:21 final size:21
Alignment explanation
Indices: 14551--14594 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
14541 ATTTCTGGGT
* *
14551 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
14572 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
14593 AA
1 AA
14595 ACGACAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:15151 original size:23 final size:24
Alignment explanation
Indices: 15108--15154 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
15098 ATATGGCCTG
*
15108 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
15132 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
15155 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:15370 original size:31 final size:31
Alignment explanation
Indices: 15332--15487 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
15322 AGGGTCGAGG
15332 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
15363 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
15394 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
15425 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
15456 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
15487 G
1 G
15488 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:18510 original size:21 final size:21
Alignment explanation
Indices: 18484--18527 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
18474 ATTTCTGGGT
* *
18484 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
18505 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
18526 AA
1 AA
18528 ACGACAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:19084 original size:23 final size:24
Alignment explanation
Indices: 19041--19087 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
19031 ATATGGCCTG
*
19041 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
19065 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
19088 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:19303 original size:31 final size:31
Alignment explanation
Indices: 19265--19420 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
19255 AGGGTCGAGG
19265 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
19296 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
19327 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
19358 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
* *
19389 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
19420 G
1 G
19421 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:20361 original size:2 final size:2
Alignment explanation
Indices: 20354--20385 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20344 TTCCTGTTCT
20354 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
20386 AAGCAAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39879 original size:2 final size:2
Alignment explanation
Indices: 39872--39899 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39862 GTTTTGAACG
39872 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39900 GGTGGGAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47714 original size:23 final size:23
Alignment explanation
Indices: 47688--47732 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
47678 CACCACAGCT
* *
47688 CGTATAAATGCACTGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
47711 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
47733 ATATAATAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:55096 original size:17 final size:17
Alignment explanation
Indices: 55074--55107 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55064 GTATCTATTT
*
55074 TGAAATTTTATTGATAC
1 TGAAATTTTATTAATAC
55091 TGAAATTTTATTAATAC
1 TGAAATTTTATTAATAC
55108 CTGCTTCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (17 bp):
TGAAATTTTATTAATAC
Found at i:59342 original size:9 final size:10
Alignment explanation
Indices: 59321--59347 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
59311 GGACCGGCTG
59321 AAAACCGGAA
1 AAAACCGGAA
59331 AAAACCGGAA
1 AAAACCGGAA
59341 AAAACCG
1 AAAACCG
59348 AGATTTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.22, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAACCGGAA
Found at i:61565 original size:22 final size:23
Alignment explanation
Indices: 61521--61566 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
61511 CTGTTATCAG
* *
61521 GTTTTTCGTTTGTTTGTTTTTTTA
1 GTTTATCGTTTG-TTGTTATTTTA
61545 GTTTATCGTTTG-TGTTATTTTA
1 GTTTATCGTTTGTTGTTATTTTA
61567 AATAGTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
24 11 0.55
ACGTcount: A:0.09, C:0.04, G:0.17, T:0.70
Consensus pattern (23 bp):
GTTTATCGTTTGTTGTTATTTTA
Found at i:64068 original size:25 final size:25
Alignment explanation
Indices: 64021--64068 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
64011 ACCATAAGCT
* ***
64021 AAAATGGCTTCCAAAGCCTTTAAAA
1 AAAATGGCTTCAAAAGAAATTAAAA
64046 AAAATGGCTTCAAAAGAAATTAA
1 AAAATGGCTTCAAAAGAAATTAA
64069 TTATGAAGCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.50, C:0.15, G:0.12, T:0.23
Consensus pattern (25 bp):
AAAATGGCTTCAAAAGAAATTAAAA
Found at i:65754 original size:27 final size:26
Alignment explanation
Indices: 65715--65775 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
65705 AAAATATGTT
*
65715 TTCTCTCCCTCCCCTAGAATTTTATAAG
1 TTCT-TCCCT-CCCTAGAATTTTAGAAG
* *
65743 TTCTTCCTTCCCTATAATTTTAGAAG
1 TTCTTCCCTCCCTAGAATTTTAGAAG
65769 TT-TTCCC
1 TTCTTCCC
65776 CAAATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.14
26 17 0.59
27 4 0.14
28 4 0.14
ACGTcount: A:0.20, C:0.30, G:0.07, T:0.44
Consensus pattern (26 bp):
TTCTTCCCTCCCTAGAATTTTAGAAG
Found at i:65755 original size:26 final size:25
Alignment explanation
Indices: 65726--65774 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
65716 TCTCTCCCTC
*
65726 CCCTAGAATTTTATAAGTTCTTCCTT
1 CCCTAGAATTTTAGAAGTT-TTCCTT
*
65752 CCCTATAATTTTAGAAGTTTTCC
1 CCCTAGAATTTTAGAAGTTTTCC
65775 CCAAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.45
Consensus pattern (25 bp):
CCCTAGAATTTTAGAAGTTTTCCTT
Found at i:67084 original size:36 final size:36
Alignment explanation
Indices: 67044--67118 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
67034 CCTAATAAGT
*
67044 AGTCTTTATTTTCAAGTCTCTATAATTATGCTATCA
1 AGTCTTTATTTTAAAGTCTCTATAATTATGCTATCA
*
67080 AGTCTTTCTTTTAAAGTCTCTATAATTATGCTATCA
1 AGTCTTTATTTTAAAGTCTCTATAATTATGCTATCA
67116 AGT
1 AGT
67119 TTCCTAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (36 bp):
AGTCTTTATTTTAAAGTCTCTATAATTATGCTATCA
Found at i:68685 original size:21 final size:21
Alignment explanation
Indices: 68659--68698 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
68649 AGACCAAAGC
*
68659 CATCGA-GGACTCTCCTTCCGA
1 CATCGATGGA-TCACCTTCCGA
68680 CATCGATGGATCACCTTCC
1 CATCGATGGATCACCTTCC
68699 TCCGACGGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.20, C:0.38, G:0.17, T:0.25
Consensus pattern (21 bp):
CATCGATGGATCACCTTCCGA
Found at i:74144 original size:17 final size:17
Alignment explanation
Indices: 74122--74155 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
74112 AATGAAAAAT
*
74122 AATTTTTTATTTTTTAG
1 AATTTTTAATTTTTTAG
74139 AATTTTTAATTTTTTAG
1 AATTTTTAATTTTTTAG
74156 CCGCTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
AATTTTTAATTTTTTAG
Found at i:81449 original size:7 final size:7
Alignment explanation
Indices: 81420--81465 Score: 60
Period size: 7 Copynumber: 6.7 Consensus size: 7
81410 ATTGGGTAAA
81420 GGGAGA-
1 GGGAGAG
81426 GGGAG-G
1 GGGAGAG
*
81432 GAGAGGAG
1 GGGA-GAG
81440 GGGAGAG
1 GGGAGAG
81447 GGGAGAG
1 GGGAGAG
81454 GGGAGAG
1 GGGAGAG
81461 GGGAG
1 GGGAG
81466 GGGAGGGGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
6 8 0.23
7 23 0.66
8 4 0.11
ACGTcount: A:0.28, C:0.00, G:0.72, T:0.00
Consensus pattern (7 bp):
GGGAGAG
Found at i:85556 original size:11 final size:11
Alignment explanation
Indices: 85540--85565 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
85530 TAATATCATC
85540 AAAAAATTGAA
1 AAAAAATTGAA
85551 AAAAAATTGAA
1 AAAAAATTGAA
85562 AAAA
1 AAAA
85566 TGAATTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAAATTGAA
Found at i:89465 original size:15 final size:15
Alignment explanation
Indices: 89445--89487 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
89435 CCTAAGGAGT
89445 AGTATCGATACCAGG
1 AGTATCGATACCAGG
89460 AGTATCGATACCAGG
1 AGTATCGATACCAGG
89475 AGTATCGATACCA
1 AGTATCGATACCA
89488 ATGTACAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (15 bp):
AGTATCGATACCAGG
Found at i:91066 original size:24 final size:27
Alignment explanation
Indices: 91021--91074 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
91011 CATGTTATAG
**
91021 TATATATATTATATGAGTTGTG-TAAA
1 TATATATATTATATGAAATGTGATAAA
91047 TATATATA-TATAT-AAATGTGATAAA
1 TATATATATTATATGAAATGTGATAAA
91072 TAT
1 TAT
91075 GTGAAATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 12 0.48
26 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (27 bp):
TATATATATTATATGAAATGTGATAAA
Found at i:91170 original size:16 final size:17
Alignment explanation
Indices: 91149--91186 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
91139 ATAAGAAAGA
*
91149 ATATGAAATATTAAA-C
1 ATATGAAATATGAAATC
91165 ATATG-AATATGAAATC
1 ATATGAAATATGAAATC
91181 ATATGA
1 ATATGA
91187 GAGGTGACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.53, C:0.05, G:0.11, T:0.32
Consensus pattern (17 bp):
ATATGAAATATGAAATC
Found at i:91384 original size:30 final size:28
Alignment explanation
Indices: 91350--91405 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
91340 GATTAGATGA
91350 GAAATGAACATGAGATATATGAATATGAAT
1 GAAATG-ACATG-GATATATGAATATGAAT
* *
91380 GAAATGATATGGTTATATGAATATGA
1 GAAATGACATGGATATATGAATATGA
91406 GAAAAGGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.58
29 4 0.17
30 6 0.25
ACGTcount: A:0.46, C:0.02, G:0.21, T:0.30
Consensus pattern (28 bp):
GAAATGACATGGATATATGAATATGAAT
Found at i:91417 original size:28 final size:27
Alignment explanation
Indices: 91365--91418 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 27
91355 GAACATGAGA
*
91365 TATATGAATATGAATGAAATGATATGGT
1 TATATGAATATGAA-GAAAGGATATGGT
91393 TATATGAATATG-AGAAAAGGTATATG
1 TATATGAATATGAAG-AAAGG-ATATG
91419 TGATAAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.04
27 5 0.22
28 17 0.74
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (27 bp):
TATATGAATATGAAGAAAGGATATGGT
Found at i:93287 original size:6 final size:6
Alignment explanation
Indices: 93278--93351 Score: 67
Period size: 6 Copynumber: 12.2 Consensus size: 6
93268 ATGAACACTG
* * * **
93278 AATGAT AATGAT AATGAT GATGAA AACAGAT GTTGAT AATGAT AATGAT
1 AATGAT AATGAT AATGAT AATGAT AA-TGAT AATGAT AATGAT AATGAT
* * *
93327 AGTGAT AATGAT GATGAT GATGAT A
1 AATGAT AATGAT AATGAT AATGAT A
93352 TATTTATATG
Statistics
Matches: 53, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
6 51 0.96
7 2 0.04
ACGTcount: A:0.45, C:0.01, G:0.23, T:0.31
Consensus pattern (6 bp):
AATGAT
Found at i:109321 original size:22 final size:22
Alignment explanation
Indices: 109296--109338 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
109286 TAGAAGAAAT
*
109296 AATGATGCCATTTGCTATAAAG
1 AATGATGACATTTGCTATAAAG
* *
109318 AATGATTACATTTGTTATAAA
1 AATGATGACATTTGCTATAAA
109339 CAGATTCGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (22 bp):
AATGATGACATTTGCTATAAAG
Found at i:112276 original size:26 final size:26
Alignment explanation
Indices: 112230--112281 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
112220 ATTTGTATCA
*
112230 TTAGCTCACTAGGAACGATCCGGCCC
1 TTAGCTCACTAGGAACGATCCAGCCC
* **
112256 TTAGCTCACTATGAATTATCCAGCCC
1 TTAGCTCACTAGGAACGATCCAGCCC
112282 AATTTGAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (26 bp):
TTAGCTCACTAGGAACGATCCAGCCC
Found at i:113208 original size:31 final size:31
Alignment explanation
Indices: 113139--113210 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
113129 TATTTAATAT
* * * *
113139 AAATTTAAGTGTAAAGTTAGTATTTTATTTG
1 AAATTTAAGGGTAAAGTTAGTAATTTATCTA
* * *
113170 AAGTTTAAGGGTTAAGTTATTAATTTATCTA
1 AAATTTAAGGGTAAAGTTAGTAATTTATCTA
113201 AAATTTAAGG
1 AAATTTAAGG
113211 TTCAAATTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.38, C:0.01, G:0.17, T:0.44
Consensus pattern (31 bp):
AAATTTAAGGGTAAAGTTAGTAATTTATCTA
Found at i:113909 original size:17 final size:17
Alignment explanation
Indices: 113883--113927 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
113873 TGCATCATCT
*
113883 TCTCTCCTCCCTTTTTC
1 TCTCTTCTCCCTTTTTC
113900 TCTCTTCTCCCCTTTTTC
1 TCTCTTCT-CCCTTTTTC
*
113918 TCCCTTCTCC
1 TCTCTTCTCC
113928 TACAACAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (17 bp):
TCTCTTCTCCCTTTTTC
Found at i:113914 original size:18 final size:18
Alignment explanation
Indices: 113891--113927 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
113881 CTTCTCTCCT
*
113891 CCCTTTTTCTCTCTTCTC
1 CCCTTTTTCTCCCTTCTC
113909 CCCTTTTTCTCCCTTCTC
1 CCCTTTTTCTCCCTTCTC
113927 C
1 C
113928 TACAACAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (18 bp):
CCCTTTTTCTCCCTTCTC
Found at i:119828 original size:62 final size:62
Alignment explanation
Indices: 119700--119828 Score: 161
Period size: 62 Copynumber: 2.1 Consensus size: 62
119690 TCATCCAAGT
** ** *** *
119700 TAAAAGTTTCACATGCTATTAAAAGTGGTTGGTTTAAGAAAGATTGGTTTAAGTTATTTAAT
1 TAAAAGTTTCACATGCTATTAAAAGTGGTTGGTTTAAGAAAGATTAATTTAAGACAACCAAC
*
119762 TAAAAGTTTCACATGCTATTAAAAGTGGTTGGTTTAAGAAAGATTAATTTAA-ACACACCCAC
1 TAAAAGTTTCACATGCTATTAAAAGTGGTTGGTTTAAGAAAGATTAATTTAAGACA-ACCAAC
119824 TAAAA
1 TAAAA
119829 CTAAATATAC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
61 1 0.02
62 56 0.98
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (62 bp):
TAAAAGTTTCACATGCTATTAAAAGTGGTTGGTTTAAGAAAGATTAATTTAAGACAACCAAC
Found at i:126762 original size:25 final size:23
Alignment explanation
Indices: 126689--126764 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 23
126679 TTTTACCTCA
*
126689 TAAA-ATTACAAATAATTAATATAT
1 TAAATATTA-AAAT-ATTAATATTT
*
126713 TAAATATTAAAATATGAAATAATTT
1 TAAATATTAAAATAT-TAAT-ATTT
*
126738 TAAATATTCAAATTTATTAATATTT
1 TAAATATT-AAA-ATATTAATATTT
126763 TA
1 TA
126765 TTAAATTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
23 2 0.05
24 11 0.26
25 21 0.49
26 6 0.14
27 3 0.07
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (23 bp):
TAAATATTAAAATATTAATATTT
Found at i:127590 original size:23 final size:22
Alignment explanation
Indices: 127567--127618 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
127557 TAAATTATTA
127567 AAAATAATATTAATATAATTTT
1 AAAATAATATTAATATAATTTT
* * * *
127589 AAAATTATGTTAATATTACTTTG
1 AAAATAATATTAATA-TAATTTT
127612 AAAATAA
1 AAAATAA
127619 ATATCACCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (22 bp):
AAAATAATATTAATATAATTTT
Found at i:129655 original size:21 final size:21
Alignment explanation
Indices: 129631--129673 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
129621 AGCTCTGTCC
* *
129631 GAGTAATATTTATAATTATTG
1 GAGTAATATTTAGAATAATTG
*
129652 GAGTAATTTTTAGAATAATTG
1 GAGTAATATTTAGAATAATTG
129673 G
1 G
129674 CTCCTTTTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (21 bp):
GAGTAATATTTAGAATAATTG
Found at i:132439 original size:42 final size:42
Alignment explanation
Indices: 132380--132503 Score: 203
Period size: 42 Copynumber: 3.0 Consensus size: 42
132370 GAAAGGTGAA
*
132380 TAAAGTAGAACGAAGGGAAGCATCTCACTTTCGATTCTCGTC
1 TAAAGTAGAACGAAGGGAAGCATCGCACTTTCGATTCTCGTC
* *
132422 TAAAGTAGAACGAAGGGAAGCATCGCATTTTCGATACTCGTC
1 TAAAGTAGAACGAAGGGAAGCATCGCACTTTCGATTCTCGTC
* *
132464 TAAAGTAGAACGAAGGGAATCATAGCACTTTCGATTCTCG
1 TAAAGTAGAACGAAGGGAAGCATCGCACTTTCGATTCTCG
132504 ATGAATCACC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (42 bp):
TAAAGTAGAACGAAGGGAAGCATCGCACTTTCGATTCTCGTC
Found at i:138868 original size:31 final size:31
Alignment explanation
Indices: 138833--138895 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
138823 CAGAACTAAA
138833 ACATAAATAGTTAGAACTTACATTTTTTACT
1 ACATAAATAGTTAGAACTTACATTTTTTACT
138864 ACATAAATAGTTAGAACTTACATTTTTTACT
1 ACATAAATAGTTAGAACTTACATTTTTTACT
138895 A
1 A
138896 GATATCGACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.41
Consensus pattern (31 bp):
ACATAAATAGTTAGAACTTACATTTTTTACT
Found at i:140881 original size:2 final size:2
Alignment explanation
Indices: 140874--140923 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
140864 ATTCATAGAC
140874 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
140916 AG AG AG AG
1 AG AG AG AG
140924 GAACATACGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:160662 original size:25 final size:24
Alignment explanation
Indices: 160634--160681 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
160624 CGTGTAATGC
160634 ACAAA-GTTTAATACCAAATAATAAT
1 ACAAAGGTTTAATA-CAAA-AATAAT
160659 ACAAAGGTTTAATACAAAAATAA
1 ACAAAGGTTTAATACAAAAATAA
160682 ATGTATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.23
25 9 0.41
26 8 0.36
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.25
Consensus pattern (24 bp):
ACAAAGGTTTAATACAAAAATAAT
Found at i:171354 original size:12 final size:12
Alignment explanation
Indices: 171337--171362 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
171327 CGTGTATAAA
171337 ATTTTAAAAAAT
1 ATTTTAAAAAAT
171349 ATTTTAAAAAAT
1 ATTTTAAAAAAT
171361 AT
1 AT
171363 ATAATAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTTTAAAAAAT
Found at i:175610 original size:3 final size:3
Alignment explanation
Indices: 175602--175691 Score: 162
Period size: 3 Copynumber: 30.0 Consensus size: 3
175592 TATTTTACCT
*
175602 ATA ATA ATA ATA ATA ATA ATT ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
175650 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
175692 GCACTTAATT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 83 1.00
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:177360 original size:38 final size:38
Alignment explanation
Indices: 177309--177429 Score: 206
Period size: 38 Copynumber: 3.2 Consensus size: 38
177299 TCTATGGTTA
*
177309 AATATCATCAGTTGAATATGCAATTGATTTTGGTTTAG
1 AATATAATCAGTTGAATATGCAATTGATTTTGGTTTAG
* *
177347 AATATAATTAGTTGAATACGCAATTGATTTTGGTTTAG
1 AATATAATCAGTTGAATATGCAATTGATTTTGGTTTAG
*
177385 AATATAATCAGTTGAATATGCAATTGGTTTTGGTTTAG
1 AATATAATCAGTTGAATATGCAATTGATTTTGGTTTAG
177423 AATATAA
1 AATATAA
177430 GTAATTGACT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 77 1.00
ACGTcount: A:0.35, C:0.06, G:0.18, T:0.41
Consensus pattern (38 bp):
AATATAATCAGTTGAATATGCAATTGATTTTGGTTTAG
Found at i:181290 original size:15 final size:15
Alignment explanation
Indices: 181270--181301 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
181260 ATCTGTGTCA
181270 TCAGACATAATCAAT
1 TCAGACATAATCAAT
181285 TCAGACATAATCAAT
1 TCAGACATAATCAAT
181300 TC
1 TC
181302 CTCGAGAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (15 bp):
TCAGACATAATCAAT
Found at i:188220 original size:36 final size:36
Alignment explanation
Indices: 188180--188389 Score: 357
Period size: 36 Copynumber: 5.8 Consensus size: 36
188170 TTGCATCATT
*
188180 GGCACTTCCGATTCAAGTCGAACGGAAGGAAGAATC
1 GGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATC
188216 GGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATC
1 GGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATC
*
188252 TGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATC
1 GGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATC
*
188288 GGCACTTCCGATTCAAGTCGAACGGAAGGAAGTATC
1 GGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATC
* * *
188324 GACACTTCCGATTCAAGTCGAACGAAAGGAAGTATC
1 GGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATC
*
188360 GACACTTCCGATTCAAGTCGAACGGAAGGA
1 GGCACTTCCGATTCAAGTCGAACGGAAGGA
188390 TGTATGTCTT
Statistics
Matches: 167, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 167 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.18
Consensus pattern (36 bp):
GGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATC
Found at i:191518 original size:391 final size:391
Alignment explanation
Indices: 190797--192326 Score: 2783
Period size: 391 Copynumber: 3.9 Consensus size: 391
190787 ATTAAACCAT
* *
190797 AAAACTTAGTTTTGGAGGAAGATTGCAGTTAGTCAAATATGTTCTATTCAGCATCTTTAATTTTT
1 AAAACTTAGTTTTGGAGGAAGATTGCAGTTAGTCAAATCTGTTCTATTCAACATCTTTAATTTTT
* * *
190862 GGTGTAGGCAGCTTATCATTCTTAAAGGGATTATTAAGGAAGTGGATAGATTTTGCATGCGTTTT
66 GGTGTAGGCAGCTTATCATTCCTAAAGGGATTATTAAGGAAGTGGAGAGACTTTGCATGCGTTTT
*
190927 TTCTGGAAAGGGTGTGACACTCCGGCTAGAGGAGCCCGAGTAGGCTGGAGTCACATATGCTCCTT
131 TTCTGGAAAGGGTGTGACACTCCGGCTAGAGGAGCCCGAGTAGGCTGGAGTCAAATATGCTCCTT
190992 GAAGTCTGAGGGTGGGCTGGGACTCAGGGACCTTGCTCTATGGAGTAAATCGTGTTGCCTGATGC
196 GAAGTCTGAGGGTGGGCTGGGACTCAGGGACCTTGCTCTATGGAGTAAATCGTGTTGCCTGATGC
191057 TAATTAGGAATATCCTAGCTAATGCTGGTTCATTGTGGATAGCTTGGATAAAGGCTTACTGTCTT
261 TAATTAGGAATATCCTAGCTAATGCTGGTTCATTGTGGATAGCTTGGATAAAGGCTTACTGTCTT
*
191122 AAATCAGAAAGTTACTGGGAGGTTGTTAGTAAGAATTAAGGACAAATTGAGGCAATGGTCCAGCA
326 AAATCAAAAAGTTACTGGGAGGTTGTTAGTAAGAATTAAGGACAAATTGAGGCAATGGTCCAGCA
191187 A
391 A
* * *
191188 AAAACTTAGTTTTGGAGGAAGGTTGCAGTTAGTCAAATCTGTTATATTCAGCATCTTTAATTTTT
1 AAAACTTAGTTTTGGAGGAAGATTGCAGTTAGTCAAATCTGTTCTATTCAACATCTTTAATTTTT
191253 GGTGTAGGCAGCTTATCATTCCTAAAGGGATTATTAAGGAAGTGGAGAGACTTTGCATGCGTTTT
66 GGTGTAGGCAGCTTATCATTCCTAAAGGGATTATTAAGGAAGTGGAGAGACTTTGCATGCGTTTT
*
191318 TTCTGGAAAGGGTGTGACACTCCGGCTAGAGGAGCCCGAGTAGGCTGGAGTCATATATGCTCCTT
131 TTCTGGAAAGGGTGTGACACTCCGGCTAGAGGAGCCCGAGTAGGCTGGAGTCAAATATGCTCCTT
*
191383 GAAGTCTGAGGGTGGGCTGGGACTCAGGGACCTTGCTGTATGGAGTAAATCGTGTTGCCTGATGC
196 GAAGTCTGAGGGTGGGCTGGGACTCAGGGACCTTGCTCTATGGAGTAAATCGTGTTGCCTGATGC
*
191448 TAATTAGGAATATCTTAGCTAATGCTGGTTCATTGTGGATAGCTTGGATAAAGGCTTACTGTCTT
261 TAATTAGGAATATCCTAGCTAATGCTGGTTCATTGTGGATAGCTTGGATAAAGGCTTACTGTCTT
191513 AAATCAAAAAGTTACTGGGAGGTTGTTAGTAAGAATTAAGGACAAATTGAGGCAATGGTCCAGCA
326 AAATCAAAAAGTTACTGGGAGGTTGTTAGTAAGAATTAAGGACAAATTGAGGCAATGGTCCAGCA
191578 A
391 A
*
191579 AAAACTTAGTTTTGGAGGAAGATTGCAGTTAGTCAAATTTGTTCTATTCAACATCTTTAATTTTT
1 AAAACTTAGTTTTGGAGGAAGATTGCAGTTAGTCAAATCTGTTCTATTCAACATCTTTAATTTTT
191644 GGTGTAGGCAGCTTATCATTCCTAAAGGGATTATTAAGGAAGTGGAGAGACTTTGCATGCGTTTT
66 GGTGTAGGCAGCTTATCATTCCTAAAGGGATTATTAAGGAAGTGGAGAGACTTTGCATGCGTTTT
*
191709 TTCTGGAAAGGGTGTGACACTCCGGCTAGAGGAGCCCGAGTAGGCTGAAGTCAAATATGCTCCTT
131 TTCTGGAAAGGGTGTGACACTCCGGCTAGAGGAGCCCGAGTAGGCTGGAGTCAAATATGCTCCTT
* *
191774 GAAGTCTGAGGGTGGGCTGGGACTCAAGGACCTTGCTCTATGGAGTAAATCGTGTCGCCTGATGC
196 GAAGTCTGAGGGTGGGCTGGGACTCAGGGACCTTGCTCTATGGAGTAAATCGTGTTGCCTGATGC
*
191839 TAATTAGGAATATCCTAGCTAATGCTGGTTCATTGTGGATAGCTTAGATAAAGGCTTACTGTCTT
261 TAATTAGGAATATCCTAGCTAATGCTGGTTCATTGTGGATAGCTTGGATAAAGGCTTACTGTCTT
191904 AAATCAAAAAGTTACTGGGAGGTTGTTAGTAAGAATTAAGGACAAATTGAGGCAATGGTCCAGC-
326 AAATCAAAAAGTTACTGGGAGGTTGTTAGTAAGAATTAAGGACAAATTGAGGCAATGGTCCAGCA
191968 A
391 A
* * *
191969 AAAACTTAGTTTTGGAGGAGGATTGAAGTTAGTCAAATCTGTTTTATTCAACATCTTTAATTTTT
1 AAAACTTAGTTTTGGAGGAAGATTGCAGTTAGTCAAATCTGTTCTATTCAACATCTTTAATTTTT
*
192034 GGTGTAGGCAGCTTATCATTCCTAAAGGGATTATTAAGGAAGTGGAGAGACTTTGCATGCATTTT
66 GGTGTAGGCAGCTTATCATTCCTAAAGGGATTATTAAGGAAGTGGAGAGACTTTGCATGCGTTTT
* *
192099 TTCTGGAAAGGGTGTGACACTCCGGCTAGAGGAGCCCGAGTAGGCTGGAGTCAGATCTGCTCCTT
131 TTCTGGAAAGGGTGTGACACTCCGGCTAGAGGAGCCCGAGTAGGCTGGAGTCAAATATGCTCCTT
* * * *
192164 GAAGTCTAAGGGTGGGCTGGGACTCAGGGACCTTGGTCTATGGAGTAAATCGTGCTACCTGATGC
196 GAAGTCTGAGGGTGGGCTGGGACTCAGGGACCTTGCTCTATGGAGTAAATCGTGTTGCCTGATGC
192229 TAATTAGGAATATCCTAGCTAATGCTGGTTCATTGTGGATAGCTTGGATAAAGGCTTACTGTCTT
261 TAATTAGGAATATCCTAGCTAATGCTGGTTCATTGTGGATAGCTTGGATAAAGGCTTACTGTCTT
* *
192294 AAATCAGAAAGTTACTGGGAGGCTGTTAGTAAG
326 AAATCAAAAAGTTACTGGGAGGTTGTTAGTAAG
192327 CCTCATTACA
Statistics
Matches: 1101, Mismatches: 38, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
390 342 0.31
391 759 0.69
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (391 bp):
AAAACTTAGTTTTGGAGGAAGATTGCAGTTAGTCAAATCTGTTCTATTCAACATCTTTAATTTTT
GGTGTAGGCAGCTTATCATTCCTAAAGGGATTATTAAGGAAGTGGAGAGACTTTGCATGCGTTTT
TTCTGGAAAGGGTGTGACACTCCGGCTAGAGGAGCCCGAGTAGGCTGGAGTCAAATATGCTCCTT
GAAGTCTGAGGGTGGGCTGGGACTCAGGGACCTTGCTCTATGGAGTAAATCGTGTTGCCTGATGC
TAATTAGGAATATCCTAGCTAATGCTGGTTCATTGTGGATAGCTTGGATAAAGGCTTACTGTCTT
AAATCAAAAAGTTACTGGGAGGTTGTTAGTAAGAATTAAGGACAAATTGAGGCAATGGTCCAGCA
A
Found at i:203086 original size:39 final size:39
Alignment explanation
Indices: 203041--203119 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
203031 ATTCTTCGAA
*
203041 AAGCATTAATATATGCTGACATATAAAATTATCTTTTTG
1 AAGCATTAATATATGCTGACAAATAAAATTATCTTTTTG
*
203080 AAGCATTAATATATGTTGACAAATAAAATTATCTTTTTG
1 AAGCATTAATATATGCTGACAAATAAAATTATCTTTTTG
203119 A
1 A
203120 CCATAAAAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.41
Consensus pattern (39 bp):
AAGCATTAATATATGCTGACAAATAAAATTATCTTTTTG
Found at i:206336 original size:19 final size:19
Alignment explanation
Indices: 206312--206359 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
206302 AACTAAATCA
206312 CAATGCGATCGATAATTCG
1 CAATGCGATCGATAATTCG
206331 CAATGCGATCGATAATTCG
1 CAATGCGATCGATAATTCG
*
206350 CAACGCGATC
1 CAATGCGATC
206360 TCCGGTATCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (19 bp):
CAATGCGATCGATAATTCG
Found at i:206437 original size:21 final size:21
Alignment explanation
Indices: 206413--206478 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
206403 GACTATCGCA
206413 TTGCGATTTATTCCAAGTTCG
1 TTGCGATTTATTCCAAGTTCG
* *
206434 TTGCGA--TAGTCGAAGTTTGCG
1 TTGCGATTTATTCCAAG-TT-CG
*
206455 TTGCGATTTATTCCAAATTCG
1 TTGCGATTTATTCCAAGTTCG
206476 TTG
1 TTG
206479 TGATATTCCA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
19 7 0.19
20 2 0.06
21 19 0.53
22 2 0.06
23 6 0.17
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.41
Consensus pattern (21 bp):
TTGCGATTTATTCCAAGTTCG
Found at i:206645 original size:23 final size:22
Alignment explanation
Indices: 206615--206683 Score: 67
Period size: 23 Copynumber: 3.3 Consensus size: 22
206605 GAGACGAACT
206615 ATCGCAACGCAAATTTGGAATAA
1 ATCGCAACGC-AATTTGGAATAA
* *
206638 ATCGCAACGCGAACTTGGACT--
1 ATCGCAACGC-AATTTGGAATAA
206659 ATCGCAACG-AATTTGG-A-AA
1 ATCGCAACGCAATTTGGAATAA
206678 ATCGCA
1 ATCGCA
206684 TTGCGATAGT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 12 0.31
21 9 0.23
23 18 0.46
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (22 bp):
ATCGCAACGCAATTTGGAATAA
Found at i:206681 original size:19 final size:19
Alignment explanation
Indices: 206615--206683 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 19
206605 GAGACGAACT
206615 ATCGCAACGCAAATTTGGAATAA
1 ATCGCAACG--AATTTGG-A-AA
* **
206638 ATCGCAACGCGAACTTGGACT
1 ATCGCAA--CGAATTTGGAAA
206659 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
206678 ATCGCA
1 ATCGCA
206684 TTGCGATAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 15 0.39
21 7 0.18
22 1 0.03
23 13 0.34
25 2 0.05
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:206708 original size:21 final size:21
Alignment explanation
Indices: 206679--206731 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
206669 ATTTGGAAAA
*
206679 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
206700 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
206721 TCGCGTTGCGA
1 TCGCGTTGCGA
206732 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:207248 original size:15 final size:15
Alignment explanation
Indices: 207228--207259 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
207218 TAAAGTATAT
207228 TAATGGGTTATGAAC
1 TAATGGGTTATGAAC
*
207243 TAATGGGTTGTGAAC
1 TAATGGGTTATGAAC
207258 TA
1 TA
207260 TGTTCATCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.28, T:0.34
Consensus pattern (15 bp):
TAATGGGTTATGAAC
Found at i:208218 original size:33 final size:34
Alignment explanation
Indices: 208181--208253 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
208171 GGTAAGAAAT
* * *
208181 TTATTTTTATGTTAGTAT-TTT-TTTAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
208214 TTATTTTTATATTAATATATTTATGTAAATATTA
1 TTATTTTTATATTAATATATTTATGTAAATATTA
208248 TT-TTTT
1 TTATTTT
208254 ATTAAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 20 0.57
34 8 0.23
35 7 0.20
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:208279 original size:32 final size:30
Alignment explanation
Indices: 208202--208287 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 30
208192 TTAGTATTTT
* * *
208202 TTTAAATAGTTATTATTTTTATATTAATATA
1 TTTATATAATTATTATTTTT-TATTAAAATA
* *
208233 TTTATGTAAATATTATTTTTTATTAAAATAA
1 TTTATATAATTATTATTTTTTATTAAAAT-A
208264 TATTATATAATTATTATTTATTTA
1 T-TTATATAATTATTATTT-TTTA
208288 GAATTATTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
30 8 0.18
31 18 0.40
32 15 0.33
33 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTATATAATTATTATTTTTTATTAAAATA
Found at i:208449 original size:17 final size:17
Alignment explanation
Indices: 208427--208480 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
208417 AATGTTAATA
208427 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
208444 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
208461 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
208478 TTT
1 TTT
208481 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:211621 original size:19 final size:19
Alignment explanation
Indices: 211582--211659 Score: 66
Period size: 19 Copynumber: 3.8 Consensus size: 19
211572 TTTAAATAAT
*
211582 TTTAATATTTAATATTAAGAA
1 TTTAATA-TT-ATACTAAGAA
211603 TTTAATATTATACTAAGAAA
1 TTTAATATTATACTAAG-AA
** * *
211623 CAATATATATAATATTAAGAA
1 -TTTA-ATATTATACTAAGAA
211644 TTTAATATTATACTAA
1 TTTAATATTATACTAA
211660 TAAACAATAT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
19 17 0.38
20 6 0.13
21 11 0.24
22 11 0.24
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (19 bp):
TTTAATATTATACTAAGAA
Found at i:211636 original size:41 final size:41
Alignment explanation
Indices: 211586--211679 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
211576 AATAATTTTA
*
211586 ATATTTAATATTAAGAATTTAATATTATACTAAGAAACAAT
1 ATATATAATATTAAGAATTTAATATTATACTAAGAAACAAT
*
211627 ATATATAATATTAAGAATTTAATATTATACTAATAAACAAT
1 ATATATAATATTAAGAATTTAATATTATACTAAGAAACAAT
211668 ATATATATATAT
1 ATATATA-ATAT
211680 ATATATATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 46 0.92
42 4 0.08
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.40
Consensus pattern (41 bp):
ATATATAATATTAAGAATTTAATATTATACTAAGAAACAAT
Found at i:211673 original size:2 final size:2
Alignment explanation
Indices: 211666--211709 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
211656 CTAATAAACA
211666 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
211708 AT
1 AT
211710 TATGTTGTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:211673 original size:22 final size:22
Alignment explanation
Indices: 211607--211678 Score: 62
Period size: 23 Copynumber: 3.4 Consensus size: 22
211597 TAAGAATTTA
*
211607 ATATTATACTAAGAAACAATAT
1 ATATTATACTAATAAACAATAT
* * *
211629 ATA-TA-A-T-ATTAAGAATTT
1 ATATTATACTAATAAACAATAT
211647 AATATTATACTAATAAACAATAT
1 -ATATTATACTAATAAACAATAT
211670 ATATATATA
1 ATAT-TATA
211679 TATATATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 11
0.67 0.13 0.20
Matches are distributed among these distances:
18 7 0.19
19 4 0.11
20 3 0.08
21 3 0.08
22 8 0.22
23 12 0.32
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.38
Consensus pattern (22 bp):
ATATTATACTAATAAACAATAT
Found at i:215961 original size:21 final size:22
Alignment explanation
Indices: 215919--215961 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
215909 ATATTTACTA
* *
215919 TTAAAAATTTATTTTCATCTCT
1 TTAAAAATTTAATTTCACCTCT
*
215941 TTAAAATTTTAATTT-ACCTCT
1 TTAAAAATTTAATTTCACCTCT
215962 AATATAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAAAATTTAATTTCACCTCT
Found at i:217058 original size:30 final size:31
Alignment explanation
Indices: 216975--217067 Score: 161
Period size: 31 Copynumber: 3.0 Consensus size: 31
216965 CGAATCGAGT
216975 TTATAAAATTATAACTTGAAATTAATTTGAG
1 TTATAAAATTATAACTTGAAATTAATTTGAG
*
217006 TTATAAAATTATAACTTGAAATTGATTTGAG
1 TTATAAAATTATAACTTGAAATTAATTTGAG
*
217037 TTGTAAAATTATAAC-TGAAATTAATTTGAG
1 TTATAAAATTATAACTTGAAATTAATTTGAG
217067 T
1 T
217068 CGGGTCAAGT
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
30 15 0.25
31 44 0.75
ACGTcount: A:0.43, C:0.03, G:0.12, T:0.42
Consensus pattern (31 bp):
TTATAAAATTATAACTTGAAATTAATTTGAG
Found at i:233119 original size:51 final size:52
Alignment explanation
Indices: 233044--233498 Score: 541
Period size: 51 Copynumber: 8.9 Consensus size: 52
233034 ACCAACTCCG
** * * *
233044 CAAGGTGGAAACACAGAG-TGCCAAACATATAATCAGCTACCACAACAGCTA
1 CAAGGTGGAAACATTGAGATCCCAAACATATACTCAGCTACCACAACAGCAA
* * ** *
233095 CAAAGTGGAAAGACCGAG-TCCCAAACATATAATCAGCTACCACAACAGCAA
1 CAAGGTGGAAACATTGAGATCCCAAACATATACTCAGCTACCACAACAGCAA
* ** * * **
233146 CAAGTTGGAAACACAGAG-TCCCAAACATATAATCAGCTACCACAACAACTG
1 CAAGGTGGAAACATTGAGATCCCAAACATATACTCAGCTACCACAACAGCAA
* * * *
233197 CAAGCTGGAAACA-TCAGATCCCAAACATATAATCAGCTACCACAACAGCAG
1 CAAGGTGGAAACATTGAGATCCCAAACATATACTCAGCTACCACAACAGCAA
* *
233248 CAAGGCGGAAACATTG-GATCCCAAACATATACTCAGCTAACACAACAGCAA
1 CAAGGTGGAAACATTGAGATCCCAAACATATACTCAGCTACCACAACAGCAA
* *
233299 CAAGGCGGAAACATTG-GATCCCAAACATATACTCAGCTAACACAACAGCAA
1 CAAGGTGGAAACATTGAGATCCCAAACATATACTCAGCTACCACAACAGCAA
* * *
233350 CAAGGCGGAAACATTG-GATCCCAAACATATACTCAGCTGCCACAACAGCAG
1 CAAGGTGGAAACATTGAGATCCCAAACATATACTCAGCTACCACAACAGCAA
* * *
233401 CAAGGTGGAAACATTGA-TTCCCAAACATTTACTCAACTACCACAACAGCAA
1 CAAGGTGGAAACATTGAGATCCCAAACATATACTCAGCTACCACAACAGCAA
* * *
233452 CAAGGTGGAAACATTG-GTTCCGAAACATATACTCAGCGACCACAACA
1 CAAGGTGGAAACATTGAGATCCCAAACATATACTCAGCTACCACAACA
233499 TCTCTTAATG
Statistics
Matches: 364, Mismatches: 36, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
50 2 0.01
51 361 0.99
52 1 0.00
ACGTcount: A:0.42, C:0.27, G:0.16, T:0.15
Consensus pattern (52 bp):
CAAGGTGGAAACATTGAGATCCCAAACATATACTCAGCTACCACAACAGCAA
Found at i:238554 original size:3 final size:3
Alignment explanation
Indices: 238543--238606 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
238533 TTTTTTTCCG
*
238543 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA -TA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
238588 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
238607 CAATTTTTGC
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:238749 original size:25 final size:25
Alignment explanation
Indices: 238721--238859 Score: 253
Period size: 25 Copynumber: 5.6 Consensus size: 25
238711 GCCCAATCCC
238721 GGTTTCAAACCCTAAATCAATTTAG
1 GGTTTCAAACCCTAAATCAATTTAG
*
238746 GGTTTCAAACCCTAAATCAGTTTAG
1 GGTTTCAAACCCTAAATCAATTTAG
*
238771 GGTTTCAAACCCTAAATCAGTTTAG
1 GGTTTCAAACCCTAAATCAATTTAG
238796 GGTTTCAAACCCTAAATCAATTTAG
1 GGTTTCAAACCCTAAATCAATTTAG
238821 GGTTTCAAACCCTAAATCAATTTAG
1 GGTTTCAAACCCTAAATCAATTTAG
238846 GGTTTC-AACCCTAA
1 GGTTTCAAACCCTAA
238860 TCCCCTTCCA
Statistics
Matches: 112, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
24 8 0.07
25 104 0.93
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.32
Consensus pattern (25 bp):
GGTTTCAAACCCTAAATCAATTTAG
Found at i:240472 original size:15 final size:16
Alignment explanation
Indices: 240449--240482 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
240439 TAGAAATTAT
*
240449 TTTTATTGTTATTTTA
1 TTTTATTGTTAATTTA
240465 TTTT-TTGTTAATTTA
1 TTTTATTGTTAATTTA
240480 TTT
1 TTT
240483 GATGTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTATTGTTAATTTA
Found at i:252166 original size:1 final size:1
Alignment explanation
Indices: 252121--252149 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
252111 TATTACACTT
252121 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
252150 GAGAAGGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:253281 original size:41 final size:41
Alignment explanation
Indices: 253222--253453 Score: 189
Period size: 41 Copynumber: 5.4 Consensus size: 41
253212 CCAGATCTCT
* *
253222 TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGCCGTCC
1 TCATCACGTAAGAACCGTGTCAACCTGATAACCAGTCGTCC
* * ** *
253263 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATC-TCT
1 TCATCACGTAAGAACCGTGTCA--ACC--T-GATAACCAG-TCGTCC
* *
253309 TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGCCGTCC
1 TCATCACGTAAGAACCGTGTCAACCTGATAACCAGTCGTCC
* * ** *
253350 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATC-TCT
1 TCATCACGTAAGAACCGTGTCA--ACC--T-GATAACCAG-TCGTCC
*
253396 TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGTCGTCC
1 TCATCACGTAAGAACCGTGTCAACCTGATAACCAGTCGTCC
* *
253437 TCATTACGTAGGAACCG
1 TCATCACGTAAGAACCG
253454 AGTTATCATC
Statistics
Matches: 147, Mismatches: 30, Indels: 28
0.72 0.15 0.14
Matches are distributed among these distances:
40 3 0.02
41 70 0.48
42 2 0.01
43 6 0.04
44 6 0.04
45 2 0.01
46 56 0.38
47 2 0.01
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.25
Consensus pattern (41 bp):
TCATCACGTAAGAACCGTGTCAACCTGATAACCAGTCGTCC
Found at i:253324 original size:87 final size:87
Alignment explanation
Indices: 253127--253506 Score: 526
Period size: 87 Copynumber: 4.3 Consensus size: 87
253117 CCAGACTTCC
* * * *
253127 TCATCACGTAGGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTTATCACGTAGAAACCGAGTT
1 TCATCACGTAAGAGCCGTGTCAAC-CT--GATAACCAGCCGTCCTCATCACGTAGGAACCGAG-T
253192 ATCACCTCACCTTTAGATGGCCAGATCTCT
62 -T-A--TCACCTTTAGATGGCCAGATCTCT
*
253222 TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
1 TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATC
253287 ACCTTTAGATGGCCAGATCTCT
66 ACCTTTAGATGGCCAGATCTCT
*
253309 TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATC
1 TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATC
253374 ACCTTTAGATGGCCAGATCTCT
66 ACCTTTAGATGGCCAGATCTCT
* *
253396 TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGTCGTCCTCATTACGTAGGAACCGAGTTATC
1 TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATC
** * * * *
253461 ATCCCTAAAAATGACCAGATTTCC
66 A--CCTTTAGATGGCCAGATCTCT
* *
253485 TCATCACGTAGGAGCCATGTCA
1 TCATCACGTAAGAGCCGTGTCA
253507 CCCTTAGACG
Statistics
Matches: 267, Mismatches: 16, Indels: 10
0.91 0.05 0.03
Matches are distributed among these distances:
87 174 0.65
89 36 0.13
90 1 0.00
91 1 0.00
92 31 0.12
94 1 0.00
95 23 0.09
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (87 bp):
TCATCACGTAAGAGCCGTGTCAACCTGATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATC
ACCTTTAGATGGCCAGATCTCT
Found at i:253720 original size:3 final size:3
Alignment explanation
Indices: 253709--253778 Score: 101
Period size: 3 Copynumber: 24.0 Consensus size: 3
253699 TTTTTTTCCG
*
253709 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
253755 TTA TT- TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA
253779 CAATTTTTGC
Statistics
Matches: 61, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
2 6 0.10
3 52 0.85
4 3 0.05
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:253921 original size:25 final size:25
Alignment explanation
Indices: 253893--254056 Score: 294
Period size: 25 Copynumber: 6.6 Consensus size: 25
253883 GCCCAATCCC
253893 GGTTTCAAACCCTAAATCAATTTAG
1 GGTTTCAAACCCTAAATCAATTTAG
*
253918 GGTTTCAAACCCTAAATCAGTTTAG
1 GGTTTCAAACCCTAAATCAATTTAG
*
253943 GGTTTCAAACCCTAAATCAGTTTAG
1 GGTTTCAAACCCTAAATCAATTTAG
*
253968 GGTTTCAAACCCTAAATCAGTTTAG
1 GGTTTCAAACCCTAAATCAATTTAG
253993 GGTTTCAAACCCTAAATCAATTTAG
1 GGTTTCAAACCCTAAATCAATTTAG
254018 GGTTTCAAACCCTAAATCAATTTAG
1 GGTTTCAAACCCTAAATCAATTTAG
254043 GGTTTC-AACCCTAA
1 GGTTTCAAACCCTAA
254057 TCCCCTTCCA
Statistics
Matches: 137, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
24 8 0.06
25 129 0.94
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.32
Consensus pattern (25 bp):
GGTTTCAAACCCTAAATCAATTTAG
Found at i:255669 original size:15 final size:16
Alignment explanation
Indices: 255646--255679 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
255636 TAGAAATTAT
*
255646 TTTTATTGTTATTTTA
1 TTTTATTGTTAATTTA
255662 TTTT-TTGTTAATTTA
1 TTTTATTGTTAATTTA
255677 TTT
1 TTT
255680 GATGTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTATTGTTAATTTA
Found at i:256839 original size:11 final size:11
Alignment explanation
Indices: 256819--256848 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
256809 ATATCGTATC
256819 TTTA-TTTTTT
1 TTTATTTTTTT
256829 TTTATTTTTTT
1 TTTATTTTTTT
256840 TTTATTTTT
1 TTTATTTTT
256849 GATAAGTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTATTTTTTT
Found at i:257601 original size:15 final size:15
Alignment explanation
Indices: 257581--257666 Score: 111
Period size: 15 Copynumber: 5.8 Consensus size: 15
257571 ACCCTTAATT
**
257581 AAAATGAATTACCAG
1 AAAATGAATTACTGG
257596 AAAATGAATTACTGG
1 AAAATGAATTACTGG
**
257611 AATTTGAATTACTGG
1 AAAATGAATTACTGG
257626 AAAATGAATTACTGG
1 AAAATGAATTACTGG
**
257641 AATTTGAATT-CTGG
1 AAAATGAATTACTGG
257655 AAAATGAATTAC
1 AAAATGAATTAC
257667 ATTTATGTAA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.30
Consensus pattern (15 bp):
AAAATGAATTACTGG
Found at i:257664 original size:29 final size:30
Alignment explanation
Indices: 257585--257666 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
257575 TTAATTAAAA
**
257585 TGAATTACCAGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
257615 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
257645 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
257667 ATTTATGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:257711 original size:20 final size:20
Alignment explanation
Indices: 257649--257711 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
257639 GGAATTTGAA
257649 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
* *
257669 TTATGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
257689 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
257709 TTC
1 TTC
257712 CAGAAAACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:257717 original size:20 final size:19
Alignment explanation
Indices: 257654--257718 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 19
257644 TTGAATTCTG
257654 GAAAATGAATTACATTT-A
1 GAAAATGAATTACATTTCA
*
257672 TGTAAAATGAATTACATTTCTG
1 -G-AAAATGAATTACATTTC-A
257694 GAAAATGAATTACATTTCCA
1 GAAAATGAATTACATTT-CA
257714 GAAAA
1 GAAAA
257719 CATCTGGAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.03
20 37 0.93
21 2 0.05
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.32
Consensus pattern (19 bp):
GAAAATGAATTACATTTCA
Found at i:257942 original size:30 final size:29
Alignment explanation
Indices: 257886--257940 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
257876 TTACTAAAAT
*
257886 ATTATTGAAATATATAAATAATATTATTC
1 ATTATTGAAATATATAAAAAATATTATTC
257915 ATTATT-AAATATATAAAAAA-ATTATT
1 ATTATTGAAATATATAAAAAATATTATT
257941 ATATATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.24
28 13 0.52
29 6 0.24
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
ATTATTGAAATATATAAAAAATATTATTC
Found at i:258027 original size:22 final size:23
Alignment explanation
Indices: 258002--258045 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
257992 GATTATTTTA
258002 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
258024 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
258046 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:258050 original size:22 final size:22
Alignment explanation
Indices: 258006--258062 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
257996 ATTTTATATA
* *
258006 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
258027 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
258049 ATATTTTAAATATT
1 ATATTATAAATATT
258063 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:258310 original size:42 final size:42
Alignment explanation
Indices: 258251--258370 Score: 195
Period size: 42 Copynumber: 2.9 Consensus size: 42
258241 ATGAATTACA
*
258251 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
258293 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
258335 TTCCGGAAAACAAATTACGTGAAACAAATACGGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
258371 TTCGGGGAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.46, C:0.17, G:0.19, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:258483 original size:22 final size:23
Alignment explanation
Indices: 258440--258483 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
258430 TTCTACCTTT
**
258440 TACTGTTGATTATCTTTAAAAAA
1 TACTGTTGATTATAATTAAAAAA
258463 TACTGTTGATTA-AATTAAAAA
1 TACTGTTGATTATAATTAAAAA
258484 GATTAGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (23 bp):
TACTGTTGATTATAATTAAAAAA
Found at i:260465 original size:24 final size:24
Alignment explanation
Indices: 260437--260487 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
260427 ACATCCTGCT
260437 CCACAGAATGAGTTGAGGTCACCA
1 CCACAGAATGAGTTGAGGTCACCA
260461 CCACAGAATGAGTTGAGGTCACCA
1 CCACAGAATGAGTTGAGGTCACCA
260485 CCA
1 CCA
260488 ACTTGTCCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (24 bp):
CCACAGAATGAGTTGAGGTCACCA
Found at i:263167 original size:15 final size:16
Alignment explanation
Indices: 263133--263169 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
263123 AATTATTATG
*
263133 TTAATTTATTGAATTA
1 TTAATTTATAGAATTA
263149 TTAATTTATAGAA-TA
1 TTAATTTATAGAATTA
263164 TTAATT
1 TTAATT
263170 CATAAAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (16 bp):
TTAATTTATAGAATTA
Found at i:263386 original size:37 final size:40
Alignment explanation
Indices: 263336--263430 Score: 103
Period size: 37 Copynumber: 2.5 Consensus size: 40
263326 TAAAAAAATA
*
263336 GTTTAAAATTTAAATATTTAATATTAT-TATTAAAA-TAT-T
1 GTTT-AAA-TTAAATATTTAATATTATACATTAAAATTATAT
* *
263375 TTTTAAATTAAATA-ATAATATTATACATTAAAATTATAT
1 GTTTAAATTAAATATTTAATATTATACATTAAAATTATAT
263414 GTTTAAA-T-AATATTTAA
1 GTTTAAATTAAATATTTAA
263431 GTTCTCTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
36 9 0.19
37 18 0.38
38 10 0.21
39 10 0.21
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (40 bp):
GTTTAAATTAAATATTTAATATTATACATTAAAATTATAT
Found at i:280401 original size:23 final size:23
Alignment explanation
Indices: 280347--280401 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
280337 CGAGCCATTA
280347 AAAAATAATTTTTTAAAAAAATTT
1 AAAAA-AATTTTTTAAAAAAATTT
* * * *
280371 -AAATAATTTTTTTATAAATTTT
1 AAAAAAATTTTTTAAAAAAATTT
280393 AAAAAAATT
1 AAAAAAATT
280402 AGGTGTAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAAAAATTTTTTAAAAAAATTT
Found at i:282633 original size:7 final size:7
Alignment explanation
Indices: 282623--282671 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
282613 TATAAAAAAA
282623 CCTAAAC
1 CCTAAAC
*
282630 CCTAAAT
1 CCTAAAC
*
282637 CATAAAAC
1 CCT-AAAC
282645 CCTAAAC
1 CCTAAAC
*
282652 CTTAAAC
1 CCTAAAC
*
282659 CCTAACC
1 CCTAAAC
282666 CCTAAA
1 CCTAAA
282672 TTATATATGC
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
7 28 0.85
8 5 0.15
ACGTcount: A:0.45, C:0.37, G:0.00, T:0.18
Consensus pattern (7 bp):
CCTAAAC
Found at i:282801 original size:21 final size:21
Alignment explanation
Indices: 282775--282823 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
282765 TTTATAAAAC
*
282775 CCCTAAAATTTAAATAATAAA
1 CCCTAAAATTTAAACAATAAA
* **
282796 CCCTAAACTTTAAACCCTAAA
1 CCCTAAAATTTAAACAATAAA
282817 CCCTAAA
1 CCCTAAA
282824 CCCTAACCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (21 bp):
CCCTAAAATTTAAACAATAAA
Found at i:282802 original size:7 final size:7
Alignment explanation
Indices: 282792--282843 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
282782 ATTTAAATAA
282792 TAAACCC
1 TAAACCC
**
282799 TAAACTT
1 TAAACCC
282806 TAAACCC
1 TAAACCC
282813 TAAACCC
1 TAAACCC
282820 TAAACCC
1 TAAACCC
*
282827 T-AACCTT
1 TAAACC-C
282834 TAAACCC
1 TAAACCC
282841 TAA
1 TAA
282844 TATAAATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
6 4 0.11
7 29 0.78
8 4 0.11
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:282816 original size:28 final size:28
Alignment explanation
Indices: 282785--282854 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 28
282775 CCCTAAAATT
282785 TAAATAATAAACCCTAAACTTTAAACCC
1 TAAATAATAAACCCTAAACTTTAAACCC
*** *
282813 TAAACCCTAAACCCTAACCTTTAAACCC
1 TAAATAATAAACCCTAAACTTTAAACCC
282841 TAATATAAATAAAC
1 TAA-AT-AATAAAC
282855 TAGCACTAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
28 27 0.82
29 1 0.03
30 5 0.15
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (28 bp):
TAAATAATAAACCCTAAACTTTAAACCC
Found at i:283185 original size:13 final size:13
Alignment explanation
Indices: 283153--283179 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
283143 TAATTTACAT
283153 TTAAATAATTTTA
1 TTAAATAATTTTA
283166 TTAAATAATTTTA
1 TTAAATAATTTTA
283179 T
1 T
283180 ATAATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:283741 original size:14 final size:14
Alignment explanation
Indices: 283722--283768 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
283712 ATTTTTTCTT
283722 TATATAAATTAAAC
1 TATATAAATTAAAC
283736 TATAT-AATT----
1 TATATAAATTAAAC
283745 TATATAAATTAAAC
1 TATATAAATTAAAC
*
283759 TATATTAATT
1 TATATAAATT
283769 TTCATTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:283747 original size:23 final size:24
Alignment explanation
Indices: 283720--283769 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
283710 TTATTTTTTC
283720 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
283743 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
283767 TTT
1 TTT
283770 TCATTTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:284058 original size:16 final size:16
Alignment explanation
Indices: 284037--284075 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
284027 CGGATCATTT
*
284037 ACAGGTTAGGTTAAAA
1 ACAGGTCAGGTTAAAA
*
284053 ACAGGTCAGTTTAAAA
1 ACAGGTCAGGTTAAAA
284069 ACAGGTC
1 ACAGGTC
284076 GGGTAATACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:287907 original size:41 final size:41
Alignment explanation
Indices: 287871--288418 Score: 476
Period size: 41 Copynumber: 13.2 Consensus size: 41
287861 TTTTTTCAAT
* * *
287871 AAACGTCGCAAAAGAGTAGTACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTAAAGAATAGTACTTTAGTGGCGTTTTTATAC
* * * *
287912 AAACGCCGCTAAAGACTCGTAATTTAGTGGCATTTTTATAC
1 AAACGCCGCTAAAGAATAGTACTTTAGTGGCGTTTTTATAC
* *
287953 AAACGCCGCTATAGAATTGTACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTAAAGAATAGTACTTTAGTGGCGTTTTTATAC
* * * * * *
287994 AAACGTCGTTATACACAT-GTACTGTAGTGGCGTTTGTGTTTAC
1 AAACGCCGCTAAAGA-ATAGTACTTTAGTGGCGTTT-T-TATAC
* *
288037 AAACGCCGCTAAAGACTCA-TAATTTAGTGGCGTTTTTATAC
1 AAACGCCGCTAAAGAAT-AGTACTTTAGTGGCGTTTTTATAC
*
288078 AAACGCCGCTAAAGACTCA-TACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTAAAGAAT-AGTACTTTAGTGGCGTTTTTATAC
* *
288119 AAACGCCGTTAAAGACTCA-TACTTTAGTGGCGTTTTTATAC
1 AAACGCCGCTAAAGAAT-AGTACTTTAGTGGCGTTTTTATAC
* *** * *
288160 AAACTCCGCTAAAGACGCGTACTTTAGTGGCATTTTTATTC
1 AAACGCCGCTAAAGAATAGTACTTTAGTGGCGTTTTTATAC
* * * * * * * *
288201 AAACGTCGTTATACACTTGTACTATAGTGGCGTTTGTGTTTAC
1 AAACGCCGCTAAAGAATAGTACTTTAGTGGCGTTT-T-TATAC
* * * * *
288244 AAACGTCGCTAAAGACTCGTAATTTAGTGGCATTTTTATAC
1 AAACGCCGCTAAAGAATAGTACTTTAGTGGCGTTTTTATAC
* * ** *
288285 AAACGCCGCTAAAGACTCA-TACTTTATTAACATTTTTATAC
1 AAACGCCGCTAAAGAAT-AGTACTTTAGTGGCGTTTTTATAC
* * *
288326 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATTC
1 AAACGCCGCTAAAGAATAGTACTTTAGTGGCGTTTTTATAC
* * * * * * *
288367 AAACGCTGCTATACACTTGTACTATAGTGGCGTTTGTGTTTAC
1 AAACGCCGCTAAAGAATAGTACTTTAGTGGCGTTT-T-TATAC
288410 AAACGCCGC
1 AAACGCCGC
288419 AAGTTTACAA
Statistics
Matches: 424, Mismatches: 71, Indels: 22
0.82 0.14 0.04
Matches are distributed among these distances:
41 345 0.81
42 8 0.02
43 71 0.17
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (41 bp):
AAACGCCGCTAAAGAATAGTACTTTAGTGGCGTTTTTATAC
Found at i:288076 original size:166 final size:164
Alignment explanation
Indices: 287893--288418 Score: 588
Period size: 166 Copynumber: 3.2 Consensus size: 164
287883 AGAGTAGTAC
287893 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAACG
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAACG
* ** * * *
287958 CCGCTATAGAATTGTACTTTAGTGGCGTTTTTATACAAACGT-CGTTATACACATGTACTGTAGT
66 CCGCTAAAGAATCATACTTTAGTGGCGTTTTTATACAAAC-TCCGCTAAACACACGTACTGTAGT
* *
288022 GGCGTTTGTGT-TTACAAACGCCGCTAAAGACTCATAA
130 GGCATTT-T-TATT-CAAACGCCGCTAAACACTCATAA
* * *
288059 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACG
1 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAACG
* * * * *
288124 CCGTTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACTCCGCTAAAGACGCGTACTTTAGTG
66 CCGCTAAAGAATCATACTTTAGTGGCGTTTTTATACAAACTCCGCTAAACACACGTACTGTAGTG
* * * ** *
288189 GCATTTTTATTCAAACGTCGTTATACACTTGTAC
131 GCATTTTTATTCAAACGCCGCTAAACACTCATAA
* * *
288223 TATAGTGGCGTTTGTGTTTACAAACGTCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAA
1 TTTAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAA
* * ** * * * * *
288288 CGCCGCTAAAGACTCATACTTTATTAACATTTTTATACAAACGCCGCTAAAGACTCGTACTTTAG
64 CGCCGCTAAAGAATCATACTTTAGTGGCGTTTTTATACAAACTCCGCTAAACACACGTACTGTAG
* * * ** *
288353 TGGCGTTTTTATTCAAACGCTGCTATACACTTGTAC
129 TGGCATTTTTATTCAAACGCCGCTAAACACTCATAA
* *
288389 TATAGTGGCGTTTGTGTTTACAAACGCCGC
1 TTTAGTGGCGTTT-T-TATACAAACGCCGC
288419 AAGTTTACAA
Statistics
Matches: 316, Mismatches: 40, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
164 29 0.09
165 5 0.02
166 282 0.89
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (164 bp):
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAACG
CCGCTAAAGAATCATACTTTAGTGGCGTTTTTATACAAACTCCGCTAAACACACGTACTGTAGTG
GCATTTTTATTCAAACGCCGCTAAACACTCATAA
Found at i:288185 original size:207 final size:207
Alignment explanation
Indices: 287890--288377 Score: 778
Period size: 207 Copynumber: 2.4 Consensus size: 207
287880 AAAAGAGTAG
* *
287890 TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAA
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAA
* ** * *
287955 ACGCCGCTATAGAATTGTACTTTAGTGGCGTTTTTATACAAACGTCGTTATACACATGTACTGTA
66 ACGCCGCTAAAGAAGCGTACTTTAGTGGCATTTTTATACAAACGTCGTTATACACATGTACTATA
*
288020 GTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATAATTTAGTGGCGTTTTTATACAAACGCC
131 GTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATAATTTAGTGGCATTTTTATACAAACGCC
288085 GCTAAAGACTCA
196 GCTAAAGACTCA
* *
288097 TACTTTAGTGGCGTTTTTATACAAACGCCGTTAAAGACTCATACTTTAGTGGCGTTTTTATACAA
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAA
* * * *
288162 ACTCCGCTAAAGACGCGTACTTTAGTGGCATTTTTATTCAAACGTCGTTATACACTTGTACTATA
66 ACGCCGCTAAAGAAGCGTACTTTAGTGGCATTTTTATACAAACGTCGTTATACACATGTACTATA
* *
288227 GTGGCGTTTGTGTTTACAAACGTCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAACGCC
131 GTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATAATTTAGTGGCATTTTTATACAAACGCC
288292 GCTAAAGACTCA
196 GCTAAAGACTCA
* ** * *
288304 TACTTTATTAACATTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATTCAA
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAA
*
288369 ACGCTGCTA
66 ACGCCGCTA
288378 TACACTTGTA
Statistics
Matches: 256, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
207 256 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (207 bp):
TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAA
ACGCCGCTAAAGAAGCGTACTTTAGTGGCATTTTTATACAAACGTCGTTATACACATGTACTATA
GTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATAATTTAGTGGCATTTTTATACAAACGCC
GCTAAAGACTCA
Found at i:289087 original size:32 final size:32
Alignment explanation
Indices: 289050--289116 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
289040 CCACATAGGT
* * *
289050 TTTGATACTAAGAAAATGGTTTTTTGAATTTG
1 TTTGATACTAAGAAAATGGCTTTTGGAACTTG
* * *
289082 TTTGATGCTTAGAAACTGGCTTTTGGAACTTG
1 TTTGATACTAAGAAAATGGCTTTTGGAACTTG
289114 TTT
1 TTT
289117 AATATGTGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.46
Consensus pattern (32 bp):
TTTGATACTAAGAAAATGGCTTTTGGAACTTG
Found at i:291553 original size:43 final size:41
Alignment explanation
Indices: 291224--291574 Score: 274
Period size: 43 Copynumber: 8.2 Consensus size: 41
291214 AAGGTAATTA
* * * * *
291224 GCGGCGTTTGTATCCAAAAACACCGCTATAGGTCTAACTTTTT
1 GCGGCGTTTGT-TCTAAAAACGCCG-TATAGATCTGACCTTTT
* * *
291267 GCGGCGTTTGTGT-TCAAAAACGCCATTATAGGTCTGACATTTT
1 GCGGCGTTTGT-TCT-AAAAACGCC-GTATAGATCTGACCTTTT
* *
291310 GCGGCGTTTGTGTCTAAAAACGCCACTATAGGTCTGACCTTTT
1 GCGGCGTTTGT-TCTAAAAACGCC-GTATAGATCTGACCTTTT
* * * * *
291353 ACGTCGTTTGTTCTAAAAACGCCAGTATAGGTCTTATCTTTT
1 GCGGCGTTTGTTCTAAAAACGCC-GTATAGATCTGACCTTTT
* *
291395 GCGGCGTTTGTATC-CAAAACGCCGCTATAGATCTTACCTTTT
1 GCGGCGTTTGT-TCTAAAAACGCCG-TATAGATCTGACCTTTT
* * * * *
291437 GCGGCGTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTT
1 GCGGCGTTTGTTCTAAAAACGCCG-TATAGATC-TGACCTTTT
* * * *
291480 GCGGCGTTTATTCCAAAAACGCTGCTATAGATATCGACCTTTT
1 GCGGCGTTTGTTCTAAAAACGCCG-TATAGATCT-GACCTTTT
* * * *
291523 GCGGCGTTTGTTCAAAAAACGCCGTAATAGATATTAACCTATT
1 GCGGCGTTTGTTCTAAAAACGCCGT-ATAGAT-CTGACCTTTT
291566 GCGGCGTTT
1 GCGGCGTTT
291575 TTTGTTCTCA
Statistics
Matches: 260, Mismatches: 38, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
41 3 0.01
42 88 0.34
43 167 0.64
44 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (41 bp):
GCGGCGTTTGTTCTAAAAACGCCGTATAGATCTGACCTTTT
Found at i:293072 original size:15 final size:16
Alignment explanation
Indices: 293047--293079 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
293037 CACCACAAAT
293047 ATAATTATAAATACAA
1 ATAATTATAAATACAA
*
293063 ATAA-TATAAATATAA
1 ATAATTATAAATACAA
293078 AT
1 AT
293080 CATCATCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATTATAAATACAA
Found at i:303444 original size:15 final size:15
Alignment explanation
Indices: 303419--303490 Score: 101
Period size: 15 Copynumber: 4.9 Consensus size: 15
303409 TGGTTTTCCA
303419 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
303434 GAATTTGAATTACTG
1 GAAAATGAATTACTG
303449 GAAAATGAATTACTG
1 GAAAATGAATTACTG
**
303464 GAATTTGAATTA-TG
1 GAAAATGAATTACTG
303478 GAAAATGAATTAC
1 GAAAATGAATTAC
303491 ATTTCTGTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
14 12 0.25
15 36 0.75
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (15 bp):
GAAAATGAATTACTG
Found at i:303489 original size:29 final size:30
Alignment explanation
Indices: 303419--303490 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
303409 TGGTTTTCCA
303419 GAAAATGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATTACTG
303449 GAAAATGAATTACTGGAATTTGAATTA-TG
1 GAAAATGAATTACTGGAATTTGAATTACTG
303478 GAAAATGAATTAC
1 GAAAATGAATTAC
303491 ATTTCTGTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 15 0.36
30 27 0.64
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.32
Consensus pattern (30 bp):
GAAAATGAATTACTGGAATTTGAATTACTG
Found at i:303502 original size:20 final size:20
Alignment explanation
Indices: 303476--303542 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
303466 ATTTGAATTA
303476 TGGAAAATGAATTACATTTC
1 TGGAAAATGAATTACATTTC
*
303496 TGTAAAATGAATTACATTTC
1 TGGAAAATGAATTACATTTC
303516 TGGAAAATGAATTACATTTC
1 TGGAAAATGAATTACATTTC
303536 TGGAAAA
1 TGGAAAA
303543 CATCTGGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (20 bp):
TGGAAAATGAATTACATTTC
Found at i:303764 original size:28 final size:27
Alignment explanation
Indices: 303709--303773 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
303699 TTTACTAAAA
*
303709 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAATATTAT
303737 TCATTATTAAATATATAAAAAA-ATTTAT
1 T-ATTATTAAATATATAAAAAATA-TTAT
303765 TATATATTA
1 TAT-TATTA
303774 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 3 0.09
28 24 0.73
29 6 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAATATTAT
Found at i:303799 original size:31 final size:32
Alignment explanation
Indices: 303709--303806 Score: 84
Period size: 31 Copynumber: 3.2 Consensus size: 32
303699 TTTACTAAAA
*
303709 TATTATTGAAATATAT--AAATA-ATATTAT-T
1 TATTATT-AAATATATAAAAAAATATATTATAT
* *
303738 CATTATTAAATATATAAAAAAATTTATTATA-
1 TATTATTAAATATATAAAAAAATATATTATAT
*
303769 TATTATTAAA-ATA-AAAATATAATATCTTATAT
1 TATTATTAAATATATAAAA-A-AATATATTATAT
303801 TATTAT
1 TATTAT
303807 AATATAATTG
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
28 8 0.14
29 10 0.18
30 8 0.14
31 24 0.43
32 6 0.11
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (32 bp):
TATTATTAAATATATAAAAAAATATATTATAT
Found at i:303851 original size:22 final size:23
Alignment explanation
Indices: 303826--303869 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
303816 GATTATTTTA
303826 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
303848 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
303870 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:303874 original size:22 final size:22
Alignment explanation
Indices: 303830--303886 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
303820 ATTTTATATA
* *
303830 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
303851 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
303873 ATATTTTAAATATT
1 ATATTATAAATATT
303887 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:303885 original size:52 final size:51
Alignment explanation
Indices: 303766--303886 Score: 133
Period size: 54 Copynumber: 2.3 Consensus size: 51
303756 AAAATTTATT
**
303766 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTATAATATAATTG
1 ATATATT-TTAAATATTAAAAATATAATA-CTTATATTATTATAATATAATAA
303817 AT-TATTTTATATAATATTAAAAATATAATA-TTATATTATTATAAATATTAATAA
1 ATATA-TTT-TA-AATATTAAAAATATAATACTTATATTATTAT-AATA-TAATAA
303871 ATATATTTTAAATATT
1 ATATATTTTAAATATT
303887 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 15
0.78 0.03 0.19
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 20 0.33
53 7 0.12
54 22 0.37
55 2 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (51 bp):
ATATATTTTAAATATTAAAAATATAATACTTATATTATTATAATATAATAA
Found at i:304132 original size:41 final size:42
Alignment explanation
Indices: 304075--304189 Score: 187
Period size: 42 Copynumber: 2.8 Consensus size: 42
304065 ATGAATTACA
* * *
304075 TTCCGGTAAATGAATTACGTGAAACAAACACGGG-AAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
304116 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
*
304158 TTTCGGAAAACGAATTACGTGAAACAAACACG
1 TTCCGGAAAACGAATTACGTGAAACAAACACG
304190 AGAATTCGGG
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
41 32 0.46
42 37 0.54
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:305013 original size:103 final size:103
Alignment explanation
Indices: 304846--305059 Score: 419
Period size: 103 Copynumber: 2.1 Consensus size: 103
304836 GTCCATAAGA
304846 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
*
304911 TCACACATGTTCCAAAGAATACATATATGTCCCGAATG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
304949 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
305014 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
305052 ACCACATA
1 ACCACATA
305060 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
TCACACATGTTCCAAAGAATACATATATGTCCCGAAGG
Found at i:306087 original size:2 final size:2
Alignment explanation
Indices: 306080--306106 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
306070 ATATTTCATT
306080 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
306107 CAAAGATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:308151 original size:14 final size:14
Alignment explanation
Indices: 308132--308158 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
308122 TAAATTCATT
308132 TATGTTCGTTTGTA
1 TATGTTCGTTTGTA
308146 TATGTTCGTTTGT
1 TATGTTCGTTTGT
308159 GTTCATTTGT
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:0.11, C:0.07, G:0.22, T:0.59
Consensus pattern (14 bp):
TATGTTCGTTTGTA
Found at i:311620 original size:76 final size:77
Alignment explanation
Indices: 311483--311632 Score: 230
Period size: 76 Copynumber: 2.0 Consensus size: 77
311473 TGTCGACCTC
* * * * *
311483 TTTTTGTATGTATCTTCATTGTCCAACATTTTTTTTAATAATCATCACCACCAGACACAACATTC
1 TTTTCGTATGTATCTTCATTGCCCAACATTTATTCTAATAATCATCACCACCAAACACAACATTC
311548 GTTATACTCGAG
66 GTTATACTCGAG
* *
311560 TTTTCGTATGTATCTTCATTGCCCAACA-TTATTCTAATAATCATCACCACTAAACACAACATTT
1 TTTTCGTATGTATCTTCATTGCCCAACATTTATTCTAATAATCATCACCACCAAACACAACATTC
311624 GTTATACTC
66 GTTATACTC
311633 AAGAGCTTCA
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
76 40 0.61
77 26 0.39
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.39
Consensus pattern (77 bp):
TTTTCGTATGTATCTTCATTGCCCAACATTTATTCTAATAATCATCACCACCAAACACAACATTC
GTTATACTCGAG
Found at i:314423 original size:54 final size:54
Alignment explanation
Indices: 314341--314451 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
314331 TTTTTTTTAA
314341 ATATGAATTCCACTCTTTAGTTAAATATTTTTTTACTACACTGAAGAAGGAGAT
1 ATATGAATTCCACTCTTTAGTTAAATATTTTTTTACTACACTGAAGAAGGAGAT
*
314395 ATATGAATTCCACTCTTTAGTTAAATATTTTTTTATTACACTGAAGAAGGAGAT
1 ATATGAATTCCACTCTTTAGTTAAATATTTTTTTACTACACTGAAGAAGGAGAT
314449 ATA
1 ATA
314452 AATACTAATA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.40
Consensus pattern (54 bp):
ATATGAATTCCACTCTTTAGTTAAATATTTTTTTACTACACTGAAGAAGGAGAT
Found at i:316687 original size:24 final size:24
Alignment explanation
Indices: 316635--316687 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
316625 AAAATTTGAA
*
316635 GTAAATATTACATATCTCTCTTTT
1 GTAAATATTACATATCTCTCTCTT
*
316659 TTAAATATTACATATCTCGTC-CTT
1 GTAAATATTACATATCTC-TCTCTT
316683 GTAAA
1 GTAAA
316688 ATGTGGACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (24 bp):
GTAAATATTACATATCTCTCTCTT
Found at i:317587 original size:198 final size:198
Alignment explanation
Indices: 317238--317636 Score: 674
Period size: 198 Copynumber: 2.0 Consensus size: 198
317228 TATTCAATTA
* * *
317238 GATCACTTACCGTTAATAGAAGTATTGACATGACAATTAATAAAATCGATATAATTACACATTTG
1 GATCACTTACCATTAACAGAAGTACTGACATGACAATTAATAAAATCGATATAATTACACATTTG
*
317303 ATCCTCAATATTTATATATCCTATCAATTTAGTCATAATTTTAATTTAATTTAATAAATTTAATT
66 ATCCTCAATATTTATACATCCTATCAATTTAGTCATAATTTTAATTTAATTTAATAAATTTAATT
* *
317368 TCCAATTAGATGGTTACATGTGTCATTTTTAAATTGTTTTATTTTTCATCTAATCATGTGGTGAT
131 TCCAATTAGATGATGACATGTGTCATTTTTAAATTGTTTTATTTTTCATCTAATCATGTGGTGAT
317433 ACG
196 ACG
* * * *
317436 GATCACTTATCATTAACAGAAGTACTGACATGGA-GATTAATAAATTCGATATAATTATACATTT
1 GATCACTTACCATTAACAGAAGTACTGACAT-GACAATTAATAAAATCGATATAATTACACATTT
317500 GATCCTCAATATTTATACATCCTATCAATTTAGTCATAATTTTAATTTAATTTAATAAATTTAAT
65 GATCCTCAATATTTATACATCCTATCAATTTAGTCATAATTTTAATTTAATTTAATAAATTTAAT
* *
317565 TTCCAATTATATTATGACATGTGTCATTTTTAAATTGTTTTATTTTTCATCTAATCATGTGGTGA
130 TTCCAATTAGATGATGACATGTGTCATTTTTAAATTGTTTTATTTTTCATCTAATCATGTGGTGA
317630 TACG
195 TACG
317634 GAT
1 GAT
317637 TTCCACCTTA
Statistics
Matches: 188, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
198 186 0.99
199 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (198 bp):
GATCACTTACCATTAACAGAAGTACTGACATGACAATTAATAAAATCGATATAATTACACATTTG
ATCCTCAATATTTATACATCCTATCAATTTAGTCATAATTTTAATTTAATTTAATAAATTTAATT
TCCAATTAGATGATGACATGTGTCATTTTTAAATTGTTTTATTTTTCATCTAATCATGTGGTGAT
ACG
Found at i:317900 original size:58 final size:58
Alignment explanation
Indices: 317833--317965 Score: 239
Period size: 58 Copynumber: 2.3 Consensus size: 58
317823 AAAAACTTTC
* *
317833 TAATTTATCATTATCTGTTTTATTATATTAAATCAATCAATAAAAATAATTAATTTAT
1 TAATTTATCATTAACTGTTTTATTATATTAAATCAATCAATAAAAATAATAAATTTAT
317891 TAATTTATCATTAACTGTTTTATTATATTAAATCAATCAATAAAAATAATAAATTTAT
1 TAATTTATCATTAACTGTTTTATTATATTAAATCAATCAATAAAAATAATAAATTTAT
*
317949 TAATTTATCACTAACTG
1 TAATTTATCATTAACTG
317966 ATTTGTCTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 72 1.00
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (58 bp):
TAATTTATCATTAACTGTTTTATTATATTAAATCAATCAATAAAAATAATAAATTTAT
Found at i:328093 original size:30 final size:30
Alignment explanation
Indices: 328059--328120 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
328049 TCTATATTGG
328059 TGTGAAAATAGATTTTCAATAGAAAATATA
1 TGTGAAAATAGATTTTCAATAGAAAATATA
328089 TGTGAAAATAGATTTTCAATAGAAAATATA
1 TGTGAAAATAGATTTTCAATAGAAAATATA
328119 TG
1 TG
328121 GATAAAATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.34
Consensus pattern (30 bp):
TGTGAAAATAGATTTTCAATAGAAAATATA
Found at i:331005 original size:8 final size:8
Alignment explanation
Indices: 330986--331020 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
330976 TCAAAATGTA
330986 TTTAAA-T
1 TTTAAATT
330993 TTTAAATT
1 TTTAAATT
331001 TTTAAATT
1 TTTAAATT
331009 TTTAAATT
1 TTTAAATT
331017 TTTA
1 TTTA
331021 TTTATTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTAAATT
Found at i:331915 original size:15 final size:14
Alignment explanation
Indices: 331895--331924 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
331885 GATGATTATC
331895 TTTTTTATTTGTTTT
1 TTTTTTATTT-TTTT
331910 TTTTTTATTTTTTT
1 TTTTTTATTTTTTT
331924 T
1 T
331925 CATAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.07, C:0.00, G:0.03, T:0.90
Consensus pattern (14 bp):
TTTTTTATTTTTTT
Found at i:337716 original size:2 final size:2
Alignment explanation
Indices: 337709--337742 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
337699 CATGACCTAT
337709 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
337743 CCCACCGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.