Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008798.1 Hibiscus syriacus cultivar Beakdansim tig00111947_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: 1825372
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 9
Found at i:254196 original size:19 final size:19
Alignment explanation
Indices: 254155--254204 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
254145 TATATATATA
* * *
254155 TTATTATTATTATCATTAT
1 TTATTATTATTTTCATCAC
*
254174 TTATTATTATTTTTATCAC
1 TTATTATTATTTTCATCAC
254193 TTATT-TTATTTT
1 TTATTATTATTTT
254205 ATTTTTTCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (19 bp):
TTATTATTATTTTCATCAC
Found at i:258677 original size:12 final size:12
Alignment explanation
Indices: 258662--258707 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
258652 CGGTTTTTTT
*
258662 ACCGGATAAAAA
1 ACCGGTTAAAAA
258674 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
258689 ACCGGTTAAAAA
1 ACCGGTTAAAAA
258701 ACCGGTT
1 ACCGGTT
258708 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:258689 original size:15 final size:13
Alignment explanation
Indices: 258668--258708 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
258658 TTTTACCGGA
258668 TAAAAAACCGGTT
1 TAAAAAACCGGTT
258681 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
258695 TAAAAAACCGGTT
1 TAAAAAACCGGTT
258708 T
1 T
258709 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:261020 original size:21 final size:21
Alignment explanation
Indices: 260996--261035 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
260986 TTTATTTTAT
260996 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
261017 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
261036 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:261083 original size:33 final size:33
Alignment explanation
Indices: 261030--261128 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
261020 TTTGTTTCAA
261030 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
261062 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
261095 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
261128 T
1 T
261129 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:261157 original size:13 final size:13
Alignment explanation
Indices: 261114--261168 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
261104 TTGGAAGTAT
261114 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
261127 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
261141 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
261154 TTAAGTATTTGAA
1 TTAAGTATTTCAA
261167 TT
1 TT
261169 TATTGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:261593 original size:14 final size:14
Alignment explanation
Indices: 261563--261617 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
261553 ATCTGGAATA
*
261563 TTAAAATCGGTTTTT
1 TTAAAACCGG-TTTT
*
261578 TTATAACCGGTTTT
1 TTAAAACCGGTTTT
261592 TTAAAAAAACCGGTTTT
1 TT---AAAACCGGTTTT
261609 TTAAAACCG
1 TTAAAACCG
261618 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 13 0.38
15 8 0.24
17 13 0.38
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (14 bp):
TTAAAACCGGTTTT
Found at i:261614 original size:15 final size:15
Alignment explanation
Indices: 261565--261614 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
261555 CTGGAATATT
* *
261565 AAAATCGGTTTTTTT
1 AAAACCGGTTTTTTA
*
261580 ATAACCGGTTTTTTAAA
1 AAAACCGGTTTTTT--A
261597 AAAACCGGTTTTTTA
1 AAAACCGGTTTTTTA
261612 AAA
1 AAA
261615 CCGAAACCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 16 0.55
17 13 0.45
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (15 bp):
AAAACCGGTTTTTTA
Found at i:261626 original size:20 final size:17
Alignment explanation
Indices: 261582--261614 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
261572 GTTTTTTTAT
261582 AACCGGTTTTTTAAAAA
1 AACCGGTTTTTTAAAAA
261599 AACCGGTTTTTTAAAA
1 AACCGGTTTTTTAAAA
261615 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (17 bp):
AACCGGTTTTTTAAAAA
Found at i:261734 original size:15 final size:17
Alignment explanation
Indices: 261708--261739 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
261698 TTCTATGGGA
261708 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
261724 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
261740 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:265959 original size:74 final size:74
Alignment explanation
Indices: 265838--265986 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
265828 TTTTAATAGA
265838 TAGAGGATTTATTTTGATCCACTGACAACACATCATTGATTATCAGTCATAAGAAATTAATACCT
1 TAGAGGATTTATTTTGATCCACTGACAACACATCATTGATTATCAGTCATAAGAAATTAATACCT
265903 CCTAAGCTG
66 CCTAAGCTG
265912 TAGAGGATTTATTTTGATCCACTGACAACACATCATTGATTATCAGTCATAAGAAATTAATACCT
1 TAGAGGATTTATTTTGATCCACTGACAACACATCATTGATTATCAGTCATAAGAAATTAATACCT
265977 CCTAAGCTG
66 CCTAAGCTG
265986 T
1 T
265987 TGATGTATGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (74 bp):
TAGAGGATTTATTTTGATCCACTGACAACACATCATTGATTATCAGTCATAAGAAATTAATACCT
CCTAAGCTG
Found at i:267076 original size:87 final size:87
Alignment explanation
Indices: 266908--267077 Score: 252
Period size: 88 Copynumber: 1.9 Consensus size: 87
266898 TACTACTTTA
* * * *
266908 TTAAGTCTCTCGACTATTAAAAATTACAAAATAGTCCTCTACTATTCATTATGTTCTAAACTAGT
1 TTAAGTCCCTCAACTATTAAAAATTACAAAATAGCCCTCCACTATTCATTATGTTCTAAACTAGT
*
266973 ATTTTTCTATTAAAAAATAGCT
66 ATTTTTCCATTAAAAAATAGCT
*
266995 TTAAGTCCCTCAACTATTAAAAGA-TACAAAATAGCCCTCCACCTATTCATTATGTTTTAAACTA
1 TTAAGTCCCTCAACTATTAAAA-ATTACAAAATAGCCCTCCA-CTATTCATTATGTTCTAAACTA
*
267059 GTCTTTTTCCATTAAAAAA
64 GTATTTTTCCATTAAAAAA
267078 ATTAGTGATT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
87 35 0.47
88 39 0.53
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.38
Consensus pattern (87 bp):
TTAAGTCCCTCAACTATTAAAAATTACAAAATAGCCCTCCACTATTCATTATGTTCTAAACTAGT
ATTTTTCCATTAAAAAATAGCT
Found at i:272467 original size:18 final size:18
Alignment explanation
Indices: 272446--272480 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
272436 ATTGCTCGGA
272446 GGGTACCGATTCCCCCAG
1 GGGTACCGATTCCCCCAG
272464 GGGTACCGATTCCCCCA
1 GGGTACCGATTCCCCCA
272481 TCTCATAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.40, G:0.26, T:0.17
Consensus pattern (18 bp):
GGGTACCGATTCCCCCAG
Found at i:275595 original size:16 final size:16
Alignment explanation
Indices: 275574--275610 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
275564 TGTGTAACAC
*
275574 CTTTAATTTTAATTTA
1 CTTTAATTTGAATTTA
275590 CTTTAATTTGAATTTA
1 CTTTAATTTGAATTTA
275606 -TTTAA
1 CTTTAA
275611 GTATTTTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (16 bp):
CTTTAATTTGAATTTA
Found at i:288646 original size:22 final size:22
Alignment explanation
Indices: 288620--288722 Score: 129
Period size: 22 Copynumber: 4.7 Consensus size: 22
288610 ATAGGGCAGA
288620 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
288642 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCCTTGAAG
* * *
288664 GGGAACCAATTCCCCCTTTGAAG
1 GGGAATCGATACCCCC-TTGAAG
* * *
288687 GGGAACCGATTCCCCCAT--AG
1 GGGAATCGATACCCCCTTGAAG
288707 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
288723 CTGGGTTTTT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 16 0.22
22 36 0.49
23 21 0.29
ACGTcount: A:0.26, C:0.31, G:0.25, T:0.17
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTGAAG
Found at i:288679 original size:23 final size:23
Alignment explanation
Indices: 288631--288702 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
288621 GGAATCGATA
* *
288631 CCCCCTTGAAGGGGAATCGA-TA
1 CCCCCTTGAAGGGGAACCGATTC
*
288653 CCCCCTTGAAGGGGAACCAATTC
1 CCCCCTTGAAGGGGAACCGATTC
*
288676 CCCCTTTGAAGGGGAACCGATTC
1 CCCCCTTGAAGGGGAACCGATTC
288699 CCCC
1 CCCC
288703 ATAGGGGAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 18 0.41
23 26 0.59
ACGTcount: A:0.24, C:0.35, G:0.24, T:0.18
Consensus pattern (23 bp):
CCCCCTTGAAGGGGAACCGATTC
Found at i:295107 original size:13 final size:13
Alignment explanation
Indices: 295089--295116 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
295079 GTTGAATAAT
295089 AAAAAATAAAAAC
1 AAAAAATAAAAAC
295102 AAAAAATAAAAAC
1 AAAAAATAAAAAC
295115 AA
1 AA
295117 TAATGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAAAATAAAAAC
Found at i:299650 original size:239 final size:239
Alignment explanation
Indices: 299228--299664 Score: 730
Period size: 239 Copynumber: 1.8 Consensus size: 239
299218 CGGCAAGGTC
* * *
299228 AGCCGAGGGCTCTAGCTAACAAGCAACAGGACGCACTCGGGGTCGGGGTCAATTCACATCGGGTG
1 AGCCGAGGGCTCTAGCCAACAAGCAACAGGACGCACTCGGGGTCGGGGTCAACTCACACCGGGTG
* * *
299293 TGCACCTAGAACCGAGATGAGTGCACAAAGGGGGCCACTTGGGGGTGAGGGCAGCACACATCGGG
66 TGCACCTAGAAACGAGATGAGTGCACAAAGGGGGCCACCTGGGGGCGAGGGCAGCACACATCGGG
* * ** * *
299358 GGCACACAGGGTGGAAGCCTATGCACATTGAGGGTGCATTGAGGGCCGAGGCCAGCACCGACTTA
131 AGAACACAGGGTCAAAGCCTATGCACACTGAGGGTGCACTGAGGGCCGAGGCCAGCACCGACTTA
299423 GGGTCGCCTAGGATCGTGATCACCGCACACCAAGGTGCACCTAG
196 GGGTCGCCTAGGATCGTGATCACCGCACACCAAGGTGCACCTAG
299467 AGCCGAGGGCTCTAGCCAACAAGCAACAGGACGCACTCGGGGTCGGGGTCAACTCACACCGGGTG
1 AGCCGAGGGCTCTAGCCAACAAGCAACAGGACGCACTCGGGGTCGGGGTCAACTCACACCGGGTG
*
299532 TGCACCTAGAAACGAGATGAGTGCACAAAGGGGGCCACCTGGTGGCGAGGGCAGCACACATCGGG
66 TGCACCTAGAAACGAGATGAGTGCACAAAGGGGGCCACCTGGGGGCGAGGGCAGCACACATCGGG
* * *
299597 AGAACACAGGGTCAAAGCGTATGCATACTGAGGGTGCACTGAGGGCTGAGGCCAGCACCGACTTA
131 AGAACACAGGGTCAAAGCCTATGCACACTGAGGGTGCACTGAGGGCCGAGGCCAGCACCGACTTA
299662 GGG
196 GGG
299665 CCTGTCCACC
Statistics
Matches: 182, Mismatches: 16, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
239 182 1.00
ACGTcount: A:0.26, C:0.26, G:0.35, T:0.14
Consensus pattern (239 bp):
AGCCGAGGGCTCTAGCCAACAAGCAACAGGACGCACTCGGGGTCGGGGTCAACTCACACCGGGTG
TGCACCTAGAAACGAGATGAGTGCACAAAGGGGGCCACCTGGGGGCGAGGGCAGCACACATCGGG
AGAACACAGGGTCAAAGCCTATGCACACTGAGGGTGCACTGAGGGCCGAGGCCAGCACCGACTTA
GGGTCGCCTAGGATCGTGATCACCGCACACCAAGGTGCACCTAG
Found at i:304090 original size:19 final size:18
Alignment explanation
Indices: 304046--304101 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
304036 TGAAGAATGT
304046 GTAGAAAACAAACTGTAG
1 GTAGAAAACAAACTGTAG
** *
304064 AAAGAAAACAGACTGTATG
1 GTAGAAAACAAACTGTA-G
304083 GTAGAAAACAAACTGTAG
1 GTAGAAAACAAACTGTAG
304101 G
1 G
304102 AAACAAACAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
18 16 0.52
19 15 0.48
ACGTcount: A:0.50, C:0.11, G:0.23, T:0.16
Consensus pattern (18 bp):
GTAGAAAACAAACTGTAG
Found at i:304111 original size:18 final size:17
Alignment explanation
Indices: 304050--304111 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 17
304040 GAATGTGTAG
*
304050 AAAACAAACTGTAGAAA
1 AAAACAAACTGTAGGAA
* *
304067 GAAAACAGACTGTATGGTAG
1 -AAAACAAACTGTA-GG-AA
304087 AAAACAAACTGTAGGAA
1 AAAACAAACTGTAGGAA
304104 ACAAACAA
1 A-AAACAA
304112 GTCTGTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
17 2 0.06
18 20 0.56
19 13 0.36
20 1 0.03
ACGTcount: A:0.56, C:0.13, G:0.18, T:0.13
Consensus pattern (17 bp):
AAAACAAACTGTAGGAA
Found at i:305766 original size:12 final size:12
Alignment explanation
Indices: 305749--305776 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
305739 CTGGAAAATC
305749 TGTCAAACTCCA
1 TGTCAAACTCCA
305761 TGTCAAACTCCA
1 TGTCAAACTCCA
305773 TGTC
1 TGTC
305777 TTATTCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.32, G:0.11, T:0.29
Consensus pattern (12 bp):
TGTCAAACTCCA
Found at i:306084 original size:36 final size:36
Alignment explanation
Indices: 306036--306107 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
306026 TTACCTTCTG
*
306036 TTTCAGATGCAACAGGATCCGAATCTGGTTCTTGGC
1 TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
306072 TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
1 TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
306108 GAATGCTAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (36 bp):
TTTCAGAGGCAACAGGATCCGAATCTGGTTCTTGGC
Found at i:312251 original size:11 final size:11
Alignment explanation
Indices: 312235--312262 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
312225 GAAAATGGCT
312235 AAGAAAGGATA
1 AAGAAAGGATA
312246 AAGAAAGGATA
1 AAGAAAGGATA
312257 AAGAAA
1 AAGAAA
312263 AGAAGGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.25, T:0.07
Consensus pattern (11 bp):
AAGAAAGGATA
Found at i:313189 original size:70 final size:68
Alignment explanation
Indices: 313049--313192 Score: 216
Period size: 70 Copynumber: 2.1 Consensus size: 68
313039 TGCCATGTTC
* * *
313049 TTTGAGAGTTGTATATGTCTCCCAAATGCTCCAAGTTGTTCCAACGTGTGTCATGCTCCAATGTA
1 TTTGTGAGTTGTATATGTCTCCCAAATGCTCCAAGCTGTTACAACGTGTGTCATGCTCCAATGTA
313114 CTG
66 CTG
* *
313117 TTTGTGAGTTGTATATGTCTTCCAAATGCTCCACTAGCTGTTACAACGTGTGTCATGTTCCAATG
1 TTTGTGAGTTGTATATGTCTCCCAAATGCTCCA--AGCTGTTACAACGTGTGTCATGCTCCAATG
*
313182 TATTG
64 TACTG
313187 TTTGTG
1 TTTGTG
313193 CAAGAAAAAC
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
68 31 0.46
70 37 0.54
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (68 bp):
TTTGTGAGTTGTATATGTCTCCCAAATGCTCCAAGCTGTTACAACGTGTGTCATGCTCCAATGTA
CTG
Found at i:314539 original size:15 final size:15
Alignment explanation
Indices: 314519--314548 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
314509 CCGTGTGGTA
314519 GAACCTTCGATTTTG
1 GAACCTTCGATTTTG
314534 GAACCTTCGATTTTG
1 GAACCTTCGATTTTG
314549 CTTTCTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (15 bp):
GAACCTTCGATTTTG
Found at i:318138 original size:30 final size:30
Alignment explanation
Indices: 318103--318172 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
318093 ATTTTAATTC
*
318103 AAACTCCAAAATATTGAAAGATGATATTAT
1 AAACTCCAAAATATTGAAAAATGATATTAT
*
318133 AAACTCCAAAATATTGAAAAATGGTATTAT
1 AAACTCCAAAATATTGAAAAATGATATTAT
*
318163 AAACTTCAAA
1 AAACTCCAAA
318173 GTTAATTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (30 bp):
AAACTCCAAAATATTGAAAAATGATATTAT
Found at i:318931 original size:21 final size:22
Alignment explanation
Indices: 318885--318932 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
318875 ATTAAACTAC
318885 TTTTGGTATTAATTGAAATTTG
1 TTTTGGTATTAATTGAAATTTG
*
318907 TTTTGGTATTAATTG-AATTTT
1 TTTTGGTATTAATTGAAATTTG
318928 TTTTG
1 TTTTG
318933 ATATATAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.23, C:0.00, G:0.17, T:0.60
Consensus pattern (22 bp):
TTTTGGTATTAATTGAAATTTG
Found at i:322807 original size:21 final size:21
Alignment explanation
Indices: 322783--322827 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
322773 TTTTAAAAAG
*
322783 AAAAATAAAAATTTAATTACT
1 AAAAATAAAAATTTAAATACT
* **
322804 AAAATTAATGATTTAAATACT
1 AAAAATAAAAATTTAAATACT
322825 AAA
1 AAA
322828 CGTATAGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAAATAAAAATTTAAATACT
Found at i:325573 original size:29 final size:29
Alignment explanation
Indices: 325531--325619 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
325521 GTACCGGGGT
*
325531 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
***
325560 AGGTCGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
325589 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
325618 AG
1 AG
325620 CCAACGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:325887 original size:29 final size:29
Alignment explanation
Indices: 325826--325909 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
325816 ATGAATCCTT
** * **
325826 GGTCGCCCCGAGTGCATGGCGACCTCCTT
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
* *
325855 GGTCGCCGGGCGTGCATGGCGACCTAGGA
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
*
325884 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCGCCGGGAGTGCATGGCGACCTA
325910 TGGTTGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.18
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCATGGCGACCTACGA
Found at i:327250 original size:34 final size:30
Alignment explanation
Indices: 327212--327280 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
327202 TTGATATAAC
*
327212 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTATTTGGACTT-AATTG
327246 AATTT-ACAAAATGTATTTGGACTTAATTG
1 AATTTAACAAAATGTATTTGGACTTAATTG
327275 AATTTA
1 AATTTA
327281 TTCAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTATTTGGACTTAATTG
Found at i:327288 original size:31 final size:31
Alignment explanation
Indices: 327221--327280 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
327211 CAATTTAAGG
*
327221 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
327252 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
327281 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:327379 original size:19 final size:20
Alignment explanation
Indices: 327357--327409 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
327347 GAATAGTAAT
327357 TTACTATTTGAACAAT-AAA
1 TTACTATTTGAACAATAAAA
*
327376 TTACTATTTGAACAGTAAAA
1 TTACTATTTGAACAATAAAA
* *
327396 TCACTGTTTGAACA
1 TTACTATTTGAACA
327410 GTACCCCGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (20 bp):
TTACTATTTGAACAATAAAA
Found at i:327396 original size:20 final size:20
Alignment explanation
Indices: 327357--327412 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
327347 GAATAGTAAT
*
327357 TTACTATTTGAACAAT-AAA
1 TTACTATTTGAACAGTAAAA
327376 TTACTATTTGAACAGTAAAA
1 TTACTATTTGAACAGTAAAA
* *
327396 TCACTGTTTGAACAGTA
1 TTACTATTTGAACAGTA
327413 CCCCGAGGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (20 bp):
TTACTATTTGAACAGTAAAA
Found at i:327545 original size:21 final size:21
Alignment explanation
Indices: 327519--327560 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
327509 ATTTGAATAT
*
327519 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
327540 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
327561 CCCATTCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:327622 original size:21 final size:21
Alignment explanation
Indices: 327589--327628 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
327579 TTTTTGCAGA
*
327589 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
327611 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
327629 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:331117 original size:6 final size:6
Alignment explanation
Indices: 331108--331136 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
331098 TCACACTCAC
331108 AATATA AATATA AATATA AATATA AATAT
1 AATATA AATATA AATATA AATATA AATAT
331137 TATTTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:335970 original size:44 final size:44
Alignment explanation
Indices: 335879--335970 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 44
335869 AATGATGCAA
*
335879 TGTTTATAAATCCTAGGTTTTACTTTCTCCTGATTAGGTTATAT
1 TGTTTATAAATCCTAGGTTTTACTTTCCCCTGATTAGGTTATAT
*
335923 TGTTTATGTAATCCTAGGTTTTACTTTCCCCTGATTAGGTTAT-T
1 TGTTTAT-AAATCCTAGGTTTTACTTTCCCCTGATTAGGTTATAT
335967 TGTT
1 TGTT
335971 ATTTTTAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 12 0.27
45 33 0.73
ACGTcount: A:0.20, C:0.14, G:0.15, T:0.51
Consensus pattern (44 bp):
TGTTTATAAATCCTAGGTTTTACTTTCCCCTGATTAGGTTATAT
Found at i:344299 original size:38 final size:39
Alignment explanation
Indices: 344248--344333 Score: 131
Period size: 39 Copynumber: 2.3 Consensus size: 39
344238 ACACATACAC
*
344248 TTTCAATTTTTCAAAA-CATACCTAAAGTTAAATTTTTG
1 TTTCAATTTTTCAAAATCATACCTAAAGTTAAATGTTTG
* *
344286 TTTCAATTTTTCAAAATCATACCTAAAGTTTAGTGTTTG
1 TTTCAATTTTTCAAAATCATACCTAAAGTTAAATGTTTG
344325 TTTC-ATTTT
1 TTTCAATTTT
344334 AGTACTTCGT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 21 0.48
39 23 0.52
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (39 bp):
TTTCAATTTTTCAAAATCATACCTAAAGTTAAATGTTTG
Found at i:351145 original size:23 final size:23
Alignment explanation
Indices: 351098--351150 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
351088 TGTATAAATG
* *
351098 CGAAGTGCCACATAGAATTGTAC
1 CGAAGTGCCACATAGAAATGCAC
* * *
351121 CGTAGTGCCGCGTAGAAATGCAC
1 CGAAGTGCCACATAGAAATGCAC
351144 CGAAGTG
1 CGAAGTG
351151 ATATAAGGTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (23 bp):
CGAAGTGCCACATAGAAATGCAC
Found at i:356152 original size:24 final size:24
Alignment explanation
Indices: 356118--356163 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
356108 TTAGATAGAA
*
356118 TTGCCAGCAATAACTATCAATTTC
1 TTGCCAACAATAACTATCAATTTC
356142 TTGCCAACAATAACTATCAATT
1 TTGCCAACAATAACTATCAATT
356164 CCTTCCTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.33
Consensus pattern (24 bp):
TTGCCAACAATAACTATCAATTTC
Found at i:359037 original size:63 final size:63
Alignment explanation
Indices: 358911--359039 Score: 163
Period size: 63 Copynumber: 2.0 Consensus size: 63
358901 ATTGAATTTT
* * * *
358911 GAATGCATTTAGGCACGATGCACAAGCCATGCATCGATGCACCCCTGAATATTTTGAAACATC
1 GAATGCATTCAGGCACGATGCACAAGACATGCATCGATGCAACCATGAATATTTTGAAACATC
* **
358974 GAATGCATTCAGTGCACCGATGCACAAGACATGCATCGATG-AACTATGGTTA-TTTGAAACATC
1 GAATGCATTCAG-GCA-CGATGCACAAGACATGCATCGATGCAACCATGAATATTTTGAAACATC
359037 GAA
1 GAA
359040 GCTGATTGTG
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 25 0.44
64 9 0.16
65 23 0.40
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (63 bp):
GAATGCATTCAGGCACGATGCACAAGACATGCATCGATGCAACCATGAATATTTTGAAACATC
Found at i:360967 original size:21 final size:21
Alignment explanation
Indices: 360942--360981 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
360932 AAGACTTTAT
360942 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
360963 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
360982 AATATCTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:365834 original size:64 final size:65
Alignment explanation
Indices: 365683--365835 Score: 170
Period size: 65 Copynumber: 2.4 Consensus size: 65
365673 TTGAATTTCG
* * * * * *
365683 AATGCATTTAGTGAACTGATGCACAAGCCATGCATCGATGCACCCCTGAATATTTGTAAACATCG
1 AATGCATTCAGTGCACCGATGCACAAGACATGCATCGATGCACCCATGAATATTTGTAAACATCA
**
365748 AATGCATTCAGTGCACCGATGCACAAGACATGCATCGATGCA-CCATGGTTATTT-TGAAACATC
1 AATGCATTCAGTGCACCGATGCACAAGACATGCATCGATGCACCCATGAATATTTGT-AAACATC
365811 A
65 A
*
365812 AAGTTG-ATT-TGTGCACCGATGCAC
1 AA--TGCATTCAGTGCACCGATGCAC
365836 TTGGACAACC
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
63 1 0.01
64 32 0.42
65 41 0.54
66 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (65 bp):
AATGCATTCAGTGCACCGATGCACAAGACATGCATCGATGCACCCATGAATATTTGTAAACATCA
Found at i:366441 original size:14 final size:14
Alignment explanation
Indices: 366422--366450 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
366412 GAACCACTCT
366422 AAATCGCTGTGCAA
1 AAATCGCTGTGCAA
366436 AAATCGCTGTGCAA
1 AAATCGCTGTGCAA
366450 A
1 A
366451 TATTTTCTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (14 bp):
AAATCGCTGTGCAA
Found at i:369182 original size:3 final size:3
Alignment explanation
Indices: 369174--369230 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
369164 TTCATTTTAA
** * *
369174 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT AGT AAT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
369220 ATT ATTT ATT A
1 ATT A-TT ATT A
369231 AATATTACAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
3 39 0.87
4 6 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:369200 original size:21 final size:21
Alignment explanation
Indices: 369174--369237 Score: 76
Period size: 21 Copynumber: 2.9 Consensus size: 21
369164 TTCATTTTAA
369174 ATTATTATTATTAAAATTATT
1 ATTATTATTATTAAAATTATT
*
369195 ATTATTATTATTAGTAA-TATT
1 ATTATTATTATTA-AAATTATT
369216 ATTTATTATTTATTAAATATTA
1 A-TTATTA-TTATTAAA-ATTA
369238 CAAAGCCCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 18 0.50
22 9 0.25
23 7 0.19
24 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTATTATTATTAAAATTATT
Found at i:371007 original size:111 final size:111
Alignment explanation
Indices: 370793--371007 Score: 272
Period size: 111 Copynumber: 1.9 Consensus size: 111
370783 ATATCGAATT
* *
370793 AAAGAGCTGTCTTAAGGCACCTAGAAGCCATTTTCTGATATTTTTGAATAAATAAATATCTTACT
1 AAAGAGCTGTCTTAAGGCACCTAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTACT
* * * *
370858 ATATTAAAATAAAATGTTTTTGATATTTATTTTTAAATATCAAAGA
66 ATATTAAAATAAAATATTTTTGAAAATTATTTTGAAATATCAAAGA
* * *
370904 AAAGAGCTGTCTTAAGGTACCTAGAAGCCCTTTTCTGATATTTCTAAATAAGTAAATATCTTA-T
1 AAAGAGCTGTCTTAAGGCACCTAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTACT
* * * * *
370968 TTATGTATATTAATATATTTTCTTAAAATTA-TTTGAAATA
66 ATAT-TAAAATAAAATATTTT-TGAAAATTATTTTGAAATA
371008 GTAGAATTAT
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
110 4 0.05
111 78 0.89
112 6 0.07
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (111 bp):
AAAGAGCTGTCTTAAGGCACCTAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTACT
ATATTAAAATAAAATATTTTTGAAAATTATTTTGAAATATCAAAGA
Found at i:373613 original size:22 final size:22
Alignment explanation
Indices: 373582--373624 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
373572 TTGAATTGCA
373582 CATTTTGCATTCTT-ATTTTTC
1 CATTTTGCATTCTTCATTTTTC
*
373603 CATTTATGCATTTTTCATTTTT
1 CATTT-TGCATTCTTCATTTTT
373625 TTATTTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.16, C:0.16, G:0.05, T:0.63
Consensus pattern (22 bp):
CATTTTGCATTCTTCATTTTTC
Found at i:376150 original size:14 final size:14
Alignment explanation
Indices: 376131--376164 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
376121 AGAAAGAAGG
*
376131 AAAAAAACAAAACA
1 AAAAAAAAAAAACA
*
376145 AAAAAAAAAAAAGA
1 AAAAAAAAAAAACA
376159 AAAAAA
1 AAAAAA
376165 TTGAATCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.91, C:0.06, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAACA
Found at i:378616 original size:114 final size:114
Alignment explanation
Indices: 378412--378634 Score: 347
Period size: 114 Copynumber: 2.0 Consensus size: 114
378402 TGCCATGTGA
*
378412 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* * * *
378477 TTTGGTATAAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGC
66 TTCGGTAGAAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTGC
* *
378526 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* * * *
378591 TTCGGTAGGAATCCCATAACTAATCATTGAAATTGAAAGATGAA
66 TTCGGTAGAAACCCCAAAACCAATCATTGAAATTGAAAGATGAA
378635 CTGCATGATC
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 98 1.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
TTCGGTAGAAACCCCAAAACCAATCATTGAAATTGAAAGATGAATTTGC
Found at i:381071 original size:20 final size:21
Alignment explanation
Indices: 381021--381104 Score: 89
Period size: 22 Copynumber: 4.0 Consensus size: 21
381011 ATCTACACTC
* *
381021 TTCAAAGATGATAGATTCTCTC
1 TTCAAAGATGATAGATT-TATT
381043 TTCAAAGATGATAGATTT-TT
1 TTCAAAGATGATAGATTTATT
* *
381063 TTAAAAGATGACAGATTTTATT
1 TTCAAAGATGATAGA-TTTATT
* *
381085 TTCAAAGATGAAAGCTTTAT
1 TTCAAAGATGATAGATTTAT
381105 CGGATTTCTG
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
20 14 0.26
21 9 0.17
22 31 0.57
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (21 bp):
TTCAAAGATGATAGATTTATT
Found at i:381864 original size:76 final size:76
Alignment explanation
Indices: 381784--381971 Score: 340
Period size: 76 Copynumber: 2.5 Consensus size: 76
381774 CTATTTCCCA
*
381784 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAA
381849 AACCTTCGGGT
66 AACCTTCGGGT
* *
381860 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAA
*
381925 AGCCTTCGGGT
66 AACCTTCGGGT
381936 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA
381972 CCTGCGGGTC
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 107 1.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTCGGGT
Found at i:381962 original size:45 final size:45
Alignment explanation
Indices: 381913--382026 Score: 174
Period size: 45 Copynumber: 2.5 Consensus size: 45
381903 GGGAGCTTTT
381913 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
381958 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGCCTTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
382003 TGATGTTTCCAAAAAGCCTTCGGG
1 TGATGTTTTC--AAAGCCTTCGGG
382027 AGCTTTTTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 51 0.84
47 10 0.16
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:382038 original size:76 final size:76
Alignment explanation
Indices: 381958--382167 Score: 359
Period size: 76 Copynumber: 2.8 Consensus size: 76
381948 CTTCAGTGCA
* *
381958 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGCCTTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTCAGTGCATGATGTTTCCAAAAAGCCTT
382023 CGGGAGCTTTT
66 CGGGAGCTTTT
382034 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTT-AGTGCATGATGTTTCCAAAAAGCCT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAG-CCTTTCAGTGCATGATGTTTCCAAAAAGCCT
382098 TCGGGAGCTTTT
65 TCGGGAGCTTTT
* * *
382110 TGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTCAGTGCATGATGTTTCCAAA
382168 CCTGCGGTCA
Statistics
Matches: 127, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
75 4 0.03
76 118 0.93
77 5 0.04
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (76 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCTTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:382051 original size:121 final size:121
Alignment explanation
Indices: 381837--382092 Score: 476
Period size: 121 Copynumber: 2.1 Consensus size: 121
381827 GGGAGCTTTT
*
381837 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
381902 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
381958 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGCCTTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
382023 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTTAGTGCA
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
382079 TGATGTTTCCAAAA
1 TGATGTTTTCAAAA
382093 AGCCTTCGGG
Statistics
Matches: 131, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 131 1.00
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTGCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:382181 original size:43 final size:45
Alignment explanation
Indices: 382110--382210 Score: 161
Period size: 43 Copynumber: 2.3 Consensus size: 45
382100 GGGAGCTTTT
* *
382110 TGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTGCGGGTCATCTGTAAGCCCTTCAGTGCA
382155 TGATGTTTTCAAA-CCTGC-GGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTGCGGGTCATCTGTAAGCCCTTCAGTGCA
*
382198 TGATGTTTCCAAA
1 TGATGTTTTCAAA
382211 AAGCCTTCGG
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
43 37 0.70
44 4 0.08
45 12 0.23
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.35
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTGCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:382205 original size:119 final size:121
Alignment explanation
Indices: 382034--382286 Score: 447
Period size: 119 Copynumber: 2.1 Consensus size: 121
382024 GGGAGCTTTT
* *
382034 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTGCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
382099 CGGGAGCTTTTTGATGTTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
382155 TGATGTTTTCAAA-CCTGC-GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTGCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
382218 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
66 CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
382274 TGATGTTTCCAAA
1 TGATGTTTTCAAA
382287 AAGCCTTCGG
Statistics
Matches: 127, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
119 110 0.87
120 4 0.03
121 13 0.10
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (121 bp):
TGATGTTTTCAAAGCCTGCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:382261 original size:76 final size:76
Alignment explanation
Indices: 382155--382558 Score: 697
Period size: 76 Copynumber: 5.3 Consensus size: 76
382145 CTTCAGTGCA
*
382155 TGATGTTTTCAAA-CC-T-GCGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCT
1 TGATGTTTTCAAAGCCTTAG-GGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCT
382217 TCGGGAGCTTTT
65 TCGGGAGCTTTT
*
382229 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
382294 CGGGAGCTTTT
66 CGGGAGCTTTT
382305 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
382370 CGGGATCTTTT
66 CGGGAGCTTTT
382381 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
382446 TGGGAGCTTTT
66 CGGGAGCTTTT
* * *
382457 TGATGTTTTCAAAGCCTTAGGTTCATCTGTAAGTCCTGCAATGCATGATGTTTCCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
382522 CGGGAGCTTTT
66 CGGGAGCTTTT
* *
382533 TGATGTTTTCAAACCCTCAGGGTCAT
1 TGATGTTTTCAAAGCCTTAGGGTCAT
382559 TCATAAGACC
Statistics
Matches: 315, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
74 13 0.04
75 2 0.01
76 299 0.95
77 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (76 bp):
TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
CGGGAGCTTTT
Found at i:382274 original size:195 final size:196
Alignment explanation
Indices: 381784--382362 Score: 1043
Period size: 195 Copynumber: 3.0 Consensus size: 196
381774 CTATTTCCCA
* * *
381784 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
381849 AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
381914 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTGCGG
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAACCTGCGG
381979 GT
195 GT
*
381981 CATCTGTAAGCCTTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
382046 AGCCTTCGGGTCATCTGTAAGCCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
382111 GATGTTTTTAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAACCTGC-GG
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAACCTGCGGG
382175 T
196 T
382176 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
382241 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* * *
382306 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
131 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
382363 AAGCCTTCGG
Statistics
Matches: 368, Mismatches: 14, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
195 183 0.50
196 8 0.02
197 177 0.48
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (196 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAACCTGCGGG
T
Found at i:382723 original size:3 final size:3
Alignment explanation
Indices: 382715--382780 Score: 78
Period size: 3 Copynumber: 21.3 Consensus size: 3
382705 TTCATTTTAA
** * *
382715 ATT ATT ATT ATT AAA ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
382763 ATT ATTT ATT ATTT ATT A
1 ATT A-TT ATT A-TT ATT A
382781 AATATTACAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
3 48 0.89
4 6 0.11
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:382784 original size:21 final size:20
Alignment explanation
Indices: 382741--382787 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 20
382731 TTATTATTAT
382741 TATTATTATTATTATTAGTAA
1 TATTATTATTATTATTAG-AA
382762 TATTATTTATTATTTATTA-AA
1 TATTA-TTATTA-TTATTAGAA
382783 TATTA
1 TATTA
382788 CAAAGCCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.50
22 6 0.25
23 6 0.25
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TATTATTATTATTATTAGAA
Found at i:384571 original size:111 final size:111
Alignment explanation
Indices: 384357--384571 Score: 263
Period size: 111 Copynumber: 1.9 Consensus size: 111
384347 ATATCGAATT
* * *
384357 AAAGAGCTGTCTTAAGGCACCTAGAAGCCATTTTCTGATATTTTTGAATAAATAAATATCTTACT
1 AAAGAGCTATCTTAAGGCACCTAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTACT
* * * *
384422 ATATTAAAATAAAATGTTTTTGATATTTATTTTTAAATATCAAAGA
66 ATATTAAAATAAAATATTTTTGAAAATTATTTTGAAATATCAAAGA
* * *
384468 AAAGAGCTATCTTAAGGTACCTAGAAGCCCTTTTCTGATATTTCTAAATAAGTAAATATCTTA-T
1 AAAGAGCTATCTTAAGGCACCTAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTACT
* * * * *
384532 TTATGTATATTAATATATTTTCTTAAAATTA-TTTGAAATA
66 ATAT-TAAAATAAAATATTTT-TGAAAATTATTTTGAAATA
384572 GTAGAATTAT
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
110 4 0.05
111 77 0.89
112 6 0.07
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (111 bp):
AAAGAGCTATCTTAAGGCACCTAGAAGCCATTTTCTGATATTTCTAAATAAATAAATATCTTACT
ATATTAAAATAAAATATTTTTGAAAATTATTTTGAAATATCAAAGA
Found at i:390906 original size:11 final size:12
Alignment explanation
Indices: 390880--390943 Score: 55
Period size: 11 Copynumber: 5.6 Consensus size: 12
390870 ATATAAAAAA
390880 ATAAATATTATT
1 ATAAATATTATT
*
390892 ATAAAT-TTTTT
1 ATAAATATTATT
*
390903 ATAAA-ATTAAT
1 ATAAATATTATT
*
390914 -TAAATAATATAT
1 ATAAATATTAT-T
*
390926 ATTAATATTATT
1 ATAAATATTATT
390938 A-AAATA
1 ATAAATA
390944 ATAATAATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
10 4 0.10
11 19 0.47
12 9 0.22
13 8 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATAAATATTATT
Found at i:390908 original size:147 final size:150
Alignment explanation
Indices: 390641--390933 Score: 357
Period size: 147 Copynumber: 2.0 Consensus size: 150
390631 TAAATTTATT
* * * * * *
390641 AATTTATATAAATAAGATTTTTATTTATTTAGAAATATCAGAAAATAGCTTCTAGGTGTTTTAAG
1 AATTTATATAAATAAAATATTTATTTATTTAAAAATATCAGAAAACAGCATCTAGGTGCTTTAAG
* * *
390706 ACAGCTCTTTCCTTTGATATTAAAAAATAAATAAATATTAAAACATTTATCTAAAAATAA-TAAA
66 ACAGCCCTTTCCTTTGATATAAAAAAATAAATAAATATTAAAACATTTATATAAAAATAATTAAA
390770 -AA-ATAGATTAATATATAC
131 TAATATAGATTAATATATAC
*
390788 AATTTATA-AAAGTAAAATATTTATTTATTTAAAAATATCAGAAAACAGACATCTAGTTGCTTTA
1 AATTTATATAAA-TAAAATATTTATTTATTTAAAAATATCAGAAAACAG-CATCTAGGTGCTTTA
* * * * *
390852 AGACTGCCCCTTT-CTTTGATATAAAAAAATAAAT-ATTATTATAAA-TTTTTTATAAAATTAAT
64 AGACAG-CCCTTTCCTTTGATATAAAAAAATAAATAAATATTA-AAACATTTATATAAAAATAAT
*
390914 TAAATAATATATATTAATAT
127 TAAATAATATAGATTAATAT
390934 TATTAAAATA
Statistics
Matches: 123, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
146 3 0.02
147 58 0.47
148 44 0.36
149 7 0.06
150 11 0.09
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (150 bp):
AATTTATATAAATAAAATATTTATTTATTTAAAAATATCAGAAAACAGCATCTAGGTGCTTTAAG
ACAGCCCTTTCCTTTGATATAAAAAAATAAATAAATATTAAAACATTTATATAAAAATAATTAAA
TAATATAGATTAATATATAC
Found at i:390938 original size:27 final size:28
Alignment explanation
Indices: 390908--390982 Score: 83
Period size: 24 Copynumber: 2.9 Consensus size: 28
390898 TTTTTATAAA
*
390908 ATTAATTAAATAATATATATTAAT-ATT
1 ATTAATTAAATAATATATAATAATAATT
390935 ATT-A--AAATAATA-ATAATAATAATT
1 ATTAATTAAATAATATATAATAATAATT
*
390959 ATTAATT-TA-AATATATAATAATAA
1 ATTAATTAAATAATATATAATAATAA
390983 AATAAAATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
23 7 0.17
24 14 0.34
25 5 0.12
26 12 0.29
27 3 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTAATTAAATAATATATAATAATAATT
Found at i:390971 original size:147 final size:144
Alignment explanation
Indices: 390661--390974 Score: 309
Period size: 148 Copynumber: 2.1 Consensus size: 144
390651 AATAAGATTT
* * * * *
390661 TTATTTATTTAGAAATATCAGAAAATAGCTTCTAGGTGTTTTAAGACAGCTCTTTCCTTTGATAT
1 TTATTAATTTA-AAATATCAGAAAACAGCATCTAGGTGCTTTAAGACAGCCCTTTCCTTTGATAT
*
390726 TAAAAAATAAATAAATATTAAAACATTTATCTAAAAATAATAAAAAATAGATTAATATATACAAT
65 AAAAAAATAAATAAATATTAAAACATTTATCTAAAAATAATAAAAAATAGATTAATATATACAA-
*
390791 TTATAAAAGTAAAATAT
129 -TATAAAAGTAAAATAA
* * *
390808 TTATTTATTTAAAAATATCAGAAAACAGACATCTAGTTGCTTTAAGACTGCCCCTTT-CTTTGAT
1 TTATTAATTT-AAAATATCAGAAAACAG-CATCTAGGTGCTTTAAGACAG-CCCTTTCCTTTGAT
* * * *
390872 ATAAAAAAATAAAT-ATTATTATAA-ATTT-TTTATAAAATTAATTAAATAATATATATTAATAT
63 ATAAAAAAATAAATAAATATTAAAACATTTATCTA-AAAA-TAA-TAAA-AA-ATAGATTAATA-
390934 TATTA-AA-ATAATAA-TAATAATAA
122 TA-TACAATATAA-AAGTAA-AATAA
390957 TTATTAATTTAAATATAT
1 TTATTAATTTAAA-ATAT
390975 AATAATAAAA
Statistics
Matches: 141, Mismatches: 13, Indels: 24
0.79 0.07 0.13
Matches are distributed among these distances:
145 3 0.02
146 8 0.06
147 36 0.26
148 52 0.37
149 26 0.18
150 10 0.07
151 4 0.03
152 2 0.01
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (144 bp):
TTATTAATTTAAAATATCAGAAAACAGCATCTAGGTGCTTTAAGACAGCCCTTTCCTTTGATATA
AAAAAATAAATAAATATTAAAACATTTATCTAAAAATAATAAAAAATAGATTAATATATACAATA
TAAAAGTAAAATAA
Found at i:390976 original size:29 final size:26
Alignment explanation
Indices: 390916--390986 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 26
390906 AAATTAATTA
*
390916 AATAATATATATTAATATTATTAAAAT
1 AATAATA-ATAATAATATTATTAAAAT
*
390943 AATAATAATAATAATTATTAATTTAAAT
1 AATAATAATAATAA-TATT-ATTAAAAT
390971 ATATAATAATAA-AATA
1 A-ATAATAATAATAATA
390987 AAATTGCAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
26 6 0.15
27 13 0.33
28 10 0.26
29 10 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
AATAATAATAATAATATTATTAAAAT
Found at i:391836 original size:22 final size:23
Alignment explanation
Indices: 391808--391857 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
391798 CTCTTCTCCG
*
391808 TTTTTCT-GCTCTCTGTC-CTTCT
1 TTTTTCTAG-TCTCTGTCTCCTCT
391830 TTTTTCTAGTCTCTGTCTCCTCT
1 TTTTTCTAGTCTCTGTCTCCTCT
391853 TTTTT
1 TTTTT
391858 TTTCTTTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.02, C:0.28, G:0.08, T:0.62
Consensus pattern (23 bp):
TTTTTCTAGTCTCTGTCTCCTCT
Found at i:392234 original size:3 final size:3
Alignment explanation
Indices: 392228--392281 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
392218 ATTTTTTTAG
* * *
392228 TAA TAA TAA TAA TAA TTA TTA TAA T-A TTA TAA TAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
392274 -AA TAA TAA
1 TAA TAA TAA
392282 AATTGGGATA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
2 6 0.13
3 39 0.87
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:392269 original size:8 final size:8
Alignment explanation
Indices: 392258--392284 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
392248 ATAATATTAT
392258 AATAATAA
1 AATAATAA
392266 AATAATAA
1 AATAATAA
392274 AATAATAA
1 AATAATAA
392282 AAT
1 AAT
392285 TGGGATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AATAATAA
Found at i:392270 original size:11 final size:12
Alignment explanation
Indices: 392228--392281 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 12
392218 ATTTTTTTAG
392228 TAATAATAATAA
1 TAATAATAATAA
* *
392240 TAATTATTATAA
1 TAATAATAATAA
*
392252 T-ATTATAATAA
1 TAATAATAATAA
392263 TAA-AATAATAA
1 TAATAATAATAA
392274 -AATAATAA
1 TAATAATAA
392282 AATTGGGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 2 0.06
11 22 0.61
12 12 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TAATAATAATAA
Found at i:392812 original size:124 final size:123
Alignment explanation
Indices: 392486--392917 Score: 557
Period size: 122 Copynumber: 3.6 Consensus size: 123
392476 TAATCTAGCA
* *
392486 AAAAGTTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCGTCTTCAGATGAGTTCTTCTCATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* * * *
392551 ATGAACTTTCTTTGGAAATGTTGATGTTGATCTATCTCCTTTTGTGATAGAGTCATGC
66 ATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCATGC
* *
392609 -AAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTTATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
*
392673 ATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCATTCTGTGATAGAGTTATGC
66 ATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCATGC
* *
392731 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGTTCTTCTCAT
** * **
392796 TATGAACTTTCTCTGG-AAA----A-GTTG----ATC-CATTGAGTGAT-GAATTCAAAC
65 TATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCATTCTGTGATAG-AGTCATGC
* * * *
392844 AAAAAGTTGGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAGGTT-GAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCA
392909 TTATGAACT
64 TTATGAACT
392918 CTTATGAATT
Statistics
Matches: 279, Mismatches: 25, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
112 1 0.00
113 20 0.07
114 62 0.22
118 4 0.01
119 1 0.00
122 113 0.41
123 41 0.15
124 37 0.13
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.41
Consensus pattern (123 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCATGC
Found at i:392944 original size:50 final size:50
Alignment explanation
Indices: 392869--392969 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
392859 ATTCTTCTCA
392869 TTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 TTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
392919 TTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 TTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
392969 T
1 T
392970 ACCTGGAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (50 bp):
TTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
Found at i:392951 original size:164 final size:164
Alignment explanation
Indices: 392755--393083 Score: 518
Period size: 164 Copynumber: 2.0 Consensus size: 164
392745 GCTCTTCTCA
* * * *
392755 TTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAA-AGT
1 TTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAATA-C
** *
392818 TGATCCATTGAGTGATGAATTCAAACAAAAAGTTGGAACAAATTCTTCTCATTATGAATTTCTTA
64 TGATCCATCAAGTGATGAATTCAAACAAAAAGTTGGAACAAATTCTTCTCATTATGAATTTATTA
392883 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
129 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
*
392919 TTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATACTG
1 TTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATACTG
* * * *
392984 ATCCATCAAGTGATGAATTCGAGCAAAAGGTTGGAACAAATTCTTCTCATTATGAATTTATTCTT
66 ATCCATCAAGTGATGAATTCAAACAAAAAGTTGGAACAAATTCTTCTCATTATGAATTTATTATT
393049 CCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
131 CCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
393083 T
1 T
393084 ACCTGGCAAT
Statistics
Matches: 151, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
164 148 0.98
165 3 0.02
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (164 bp):
TTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATACTG
ATCCATCAAGTGATGAATTCAAACAAAAAGTTGGAACAAATTCTTCTCATTATGAATTTATTATT
CCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
Found at i:393119 original size:114 final size:114
Alignment explanation
Indices: 392919--393226 Score: 562
Period size: 114 Copynumber: 2.7 Consensus size: 114
392909 TTATGAACTC
* * *
392919 TTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATACTG
1 TTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTG
392984 ATCCATCAAGTGATGAATTCGAGCAAAAGGTTGGAACAAATTCTTCTCA
66 ATCCATCAAGTGATGAATTCGAGCAAAAGGTTGGAACAAATTCTTCTCA
*
393033 TTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTG
1 TTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTG
393098 ATCCATCAAGTGATGAATTCGAGCAAAAGGTTGGAACAAATTCTTCTCA
66 ATCCATCAAGTGATGAATTCGAGCAAAAGGTTGGAACAAATTCTTCTCA
*
393147 TTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTG
1 TTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTG
*
393212 ATCCATCAGGTGATG
66 ATCCATCAAGTGATG
393227 GAAATTTCTG
Statistics
Matches: 187, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 187 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (114 bp):
TTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGCTG
ATCCATCAAGTGATGAATTCGAGCAAAAGGTTGGAACAAATTCTTCTCA
Found at i:393292 original size:36 final size:36
Alignment explanation
Indices: 393252--393378 Score: 128
Period size: 36 Copynumber: 3.5 Consensus size: 36
393242 AGTGAGACTG
393252 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
* * * ** ** **
393288 TCTCAAGTGAGATAAAGTTCTGTTTCGAGTGAAACTG
1 TCTCAAGCGAGACAAA-TTTTGTTTTAAGAAAAACAA
* *
393325 TCTCGAGCGAGACAAATTTTGTTTTAAGAAAAATAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
* *
393361 TCTCAAGTGAGATAAATT
1 TCTCAAGCGAGACAAATT
393379 GCTATTTGAA
Statistics
Matches: 67, Mismatches: 23, Indels: 2
0.73 0.25 0.02
Matches are distributed among these distances:
36 41 0.61
37 26 0.39
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (36 bp):
TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
Found at i:393351 original size:73 final size:73
Alignment explanation
Indices: 393232--393376 Score: 263
Period size: 73 Copynumber: 2.0 Consensus size: 73
393222 TGATGGAAAT
*
393232 TTCTGTTTCGAGTGAGACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTG
1 TTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTG
393297 AGATAAAG
66 AGATAAAG
* *
393305 TTCTGTTTCGAGTGAAACTGTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAATAATCTCAAGTG
1 TTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTG
393370 AGATAAA
66 AGATAAA
393377 TTGCTATTTG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (73 bp):
TTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTG
AGATAAAG
Found at i:394111 original size:22 final size:22
Alignment explanation
Indices: 394086--394161 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
394076 AATAAAGCTT
* *
394086 TCATATTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATATA
* *
394108 TCATCTTT-AAAGAGAGAGTTTA
1 TCATCTTTGAAA-AGAGAATATA
* * *
394130 TCAGCTTTGAAGAGAGGATATA
1 TCATCTTTGAAAAGAGAATATA
394152 TCATCTTTGA
1 TCATCTTTGA
394162 GAAGTGTAGA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
21 3 0.07
22 38 0.88
23 2 0.05
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATATA
Found at i:396779 original size:114 final size:114
Alignment explanation
Indices: 396591--396911 Score: 543
Period size: 114 Copynumber: 2.8 Consensus size: 114
396581 ATCTTCCTAT
* * * *
396591 TCCAATGATTGGTTCTGGGGTTCCTACCAAACCAGATCAGATAACTCAAAGAATATTTCCAGAAG
1 TCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
396656 ATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAAATCATCTTTCAAA
66 ATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAAATCATCTTTCAAA
* *
396705 TCCATTGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAAATCAAAGAACACTTCCAGAAG
1 TCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
396770 ATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAATTCATCTTTCAAA
66 ATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAAATCATCTTTCAAA
*
396819 TCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAT
1 TCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* * *
396884 ATGTTATTGGGGCTCCTTATTTCTACTA
66 ATGCTATTGGGTCTTCTTATTTCTACTA
396912 CGAGAACATG
Statistics
Matches: 194, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 194 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (114 bp):
TCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
ATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAAATCATCTTTCAAA
Found at i:404291 original size:22 final size:23
Alignment explanation
Indices: 404263--404312 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
404253 CTCTTCTCCA
*
404263 TTTTTCT-GCTCTCTGTC-CTTCT
1 TTTTTCTAG-TCTCTGTCTCCTCT
404285 TTTTTCTAGTCTCTGTCTCCTCT
1 TTTTTCTAGTCTCTGTCTCCTCT
404308 TTTTT
1 TTTTT
404313 TTTCTTTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 15 0.60
23 10 0.40
ACGTcount: A:0.02, C:0.28, G:0.08, T:0.62
Consensus pattern (23 bp):
TTTTTCTAGTCTCTGTCTCCTCT
Found at i:404687 original size:3 final size:3
Alignment explanation
Indices: 404681--404734 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
404671 ATTTTTTTAG
* * *
404681 TAA TAA TAA TAA TAA TTA TTA TAA T-A TTA TAA TAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
404727 -AA TAA TAA
1 TAA TAA TAA
404735 AATTGGGATA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
2 6 0.13
3 39 0.87
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:404722 original size:8 final size:8
Alignment explanation
Indices: 404711--404737 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
404701 ATAATATTAT
404711 AATAATAA
1 AATAATAA
404719 AATAATAA
1 AATAATAA
404727 AATAATAA
1 AATAATAA
404735 AAT
1 AAT
404738 TGGGATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
AATAATAA
Found at i:404723 original size:11 final size:12
Alignment explanation
Indices: 404681--404734 Score: 60
Period size: 11 Copynumber: 4.8 Consensus size: 12
404671 ATTTTTTTAG
404681 TAATAATAATAA
1 TAATAATAATAA
* *
404693 TAATTATTATAA
1 TAATAATAATAA
*
404705 T-ATTATAATAA
1 TAATAATAATAA
404716 TAA-AATAATAA
1 TAATAATAATAA
404727 -AATAATAA
1 TAATAATAA
404735 AATTGGGATA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 2 0.06
11 22 0.61
12 12 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TAATAATAATAA
Found at i:405265 original size:124 final size:123
Alignment explanation
Indices: 404939--405370 Score: 557
Period size: 122 Copynumber: 3.6 Consensus size: 123
404929 TAATCTAGCA
* *
404939 AAAAGTTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCGTCTTCAGATGAGTTCTTCTCATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
* * * *
405004 ATGAACTTTCTTTGGAAATGTTGATGTTGATCTATCTCCTTTTGTGATAGAGTCATGC
66 ATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCATGC
* *
405062 -AAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTTATT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
*
405126 ATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCATTCTGTGATAGAGTTATGC
66 ATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCATGC
* *
405184 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGTTCTTCTCAT
* * * **
405249 TATGAACTTTCTCTGG-AAA----A-GTTGATCCATC-GA----GTGAT-GAATTCAAAC
65 TATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCATTCTGTGATAG-AGTCATGC
* * * *
405297 AAAAAGTTGGAACAAATTCTTCTCATTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAGGTT-GAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCA
405362 TTATGAACT
64 TTATGAACT
405371 CTTATGAATT
Statistics
Matches: 279, Mismatches: 25, Indels: 19
0.86 0.08 0.06
Matches are distributed among these distances:
112 1 0.00
113 16 0.06
114 59 0.21
117 1 0.00
118 10 0.04
119 1 0.00
122 113 0.41
123 41 0.15
124 37 0.13
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (123 bp):
AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCATGC
Found at i:405397 original size:50 final size:50
Alignment explanation
Indices: 405322--405422 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
405312 ATTCTTCTCA
405322 TTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 TTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
405372 TTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 TTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
405422 T
1 T
405423 ACCTGGAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (50 bp):
TTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
Found at i:405404 original size:164 final size:164
Alignment explanation
Indices: 405208--405536 Score: 518
Period size: 164 Copynumber: 2.0 Consensus size: 164
405198 GCTCTTCTCA
* * * *
405208 TTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAA-AGT
1 TTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC-CTGGAAATA-C
* * *
405271 TGATCCATCGAGTGATGAATTCAAACAAAAAGTTGGAACAAATTCTTCTCATTATGAATTTCTTA
64 TGATCCATCAAGTGATGAATTCAAACAAAAAGTTGGAAAAAATTCTTCTCATTATGAATTTATTA
405336 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
129 TTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
*
405372 TTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATACTG
1 TTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATACTG
* * * *
405437 ATCCATCAAGTGATGAATTCGAGCAAAAGGTTGGAAAAAATTCTTCTCATTATGAATTTATTCTT
66 ATCCATCAAGTGATGAATTCAAACAAAAAGTTGGAAAAAATTCTTCTCATTATGAATTTATTATT
405502 CCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
131 CCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
405536 T
1 T
405537 ACCTGGCAAT
Statistics
Matches: 151, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
164 148 0.98
165 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (164 bp):
TTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATACTG
ATCCATCAAGTGATGAATTCAAACAAAAAGTTGGAAAAAATTCTTCTCATTATGAATTTATTATT
CCTTCTTCAGATGAGTTCTTCTCATTATGAACTC
Found at i:405572 original size:114 final size:114
Alignment explanation
Indices: 405372--405679 Score: 544
Period size: 114 Copynumber: 2.7 Consensus size: 114
405362 TTATGAACTC
* *
405372 TTATGAATTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGAAATACTG
1 TTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATACTG
405437 ATCCATCAAGTGATGAATTCGAGCAAAAGGTTGGAAAAAATTCTTCTCA
66 ATCCATCAAGTGATGAATTCGAGCAAAAGGTTGGAAAAAATTCTTCTCA
*
405486 TTATGAATTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATACTG
1 TTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATACTG
*
405551 ATCCATCAAGTGATGAATTCGAGCAAAAGGTTGGAACAAATTCTTCTCA
66 ATCCATCAAGTGATGAATTCGAGCAAAAGGTTGGAAAAAATTCTTCTCA
* **
405600 TTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTG
1 TTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATACTG
*
405665 ATCCATCAGGTGATG
66 ATCCATCAAGTGATG
405680 GAAATTTCTG
Statistics
Matches: 185, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 185 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (114 bp):
TTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTGGCAATACTG
ATCCATCAAGTGATGAATTCGAGCAAAAGGTTGGAAAAAATTCTTCTCA
Found at i:405745 original size:36 final size:36
Alignment explanation
Indices: 405705--405831 Score: 137
Period size: 36 Copynumber: 3.5 Consensus size: 36
405695 AGTGAGACTG
405705 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
* * * ** ** **
405741 TCTCAAGTGAGATAAAGTTCTGTTTCGAGTGAAACTT
1 TCTCAAGCGAGACAAA-TTTTGTTTTAAGAAAAACAA
*
405778 TCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
* *
405814 TCTCAAGTGAGATAAATT
1 TCTCAAGCGAGACAAATT
405832 GCTATTTGAA
Statistics
Matches: 68, Mismatches: 22, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
36 42 0.62
37 26 0.38
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (36 bp):
TCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAA
Found at i:405804 original size:73 final size:73
Alignment explanation
Indices: 405685--405829 Score: 263
Period size: 73 Copynumber: 2.0 Consensus size: 73
405675 TGATGGAAAT
*
405685 TTCTGTTTCGAGTGAGACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTG
1 TTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTG
405750 AGATAAAG
66 AGATAAAG
* *
405758 TTCTGTTTCGAGTGAAACTTTCTCGAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTG
1 TTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTG
405823 AGATAAA
66 AGATAAA
405830 TTGCTATTTG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (73 bp):
TTCTGTTTCGAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTG
AGATAAAG
Found at i:406160 original size:163 final size:165
Alignment explanation
Indices: 405867--406195 Score: 554
Period size: 163 Copynumber: 2.0 Consensus size: 165
405857 AGGTCTTATG
* * *
405867 GATGTGGGAAATAATTTACTAAGTAAGATACTATGGAAATCGTTTTCTTACTTTTCAACAATTTC
1 GATGTGGGAAATAATTTACTAAGTAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTC
* * *
405932 ATTTTCAGTAAAGATTGAATGAGAAACTATGGAAATCGTTTTCTCATTATTTTTCAAAATAACAT
66 ATTTTCAGAAAAGATTAAATGAGAAACTATGGAAATCGCTTTCTCATTATTTTTCAAAATAACAT
405997 GTTGATTGGGTAAAATGCCCCAATCTCAAGATAAT
131 GTTGATTGGGTAAAATGCCCCAATCTCAAGATAAT
* * *
406032 GATGTTGGAAATAGTTTACTAAGTAAAAAACTAAGGAAATTGTTTTCTTACTTTTCAACAATTTC
1 GATGTGGGAAATAATTTACTAAGTAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTC
406097 ATTTT-AGAAAAGA-TAAATGAGAAACTATGGAAATCGCTTTCTCATTATTTTTCAAAATAACAT
66 ATTTTCAGAAAAGATTAAATGAGAAACTATGGAAATCGCTTTCTCATTATTTTTCAAAATAACAT
*
406160 GTTGATTGGGTAACATGCCCCAATCTCAAGATAAT
131 GTTGATTGGGTAAAATGCCCCAATCTCAAGATAAT
406195 G
1 G
406196 CTCATTCTTG
Statistics
Matches: 154, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
163 83 0.54
164 7 0.05
165 64 0.42
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (165 bp):
GATGTGGGAAATAATTTACTAAGTAAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTC
ATTTTCAGAAAAGATTAAATGAGAAACTATGGAAATCGCTTTCTCATTATTTTTCAAAATAACAT
GTTGATTGGGTAAAATGCCCCAATCTCAAGATAAT
Found at i:406727 original size:22 final size:22
Alignment explanation
Indices: 406702--406777 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
406692 AATAAAGCTT
406702 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
406724 TCATCTTT-AAAGAGAGAGTTTA
1 TCATCTTTGAAA-AGAGAATCTA
* *
406746 TCAGCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
406768 TCATCTTTGA
1 TCATCTTTGA
406778 GAAGTGTAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
21 3 0.07
22 40 0.89
23 2 0.04
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:409397 original size:114 final size:114
Alignment explanation
Indices: 409209--409529 Score: 534
Period size: 114 Copynumber: 2.8 Consensus size: 114
409199 ATCTTCCTAT
* * * *
409209 TCCAATGATTGGTTCTGGGGTTCCTACCAAACCAGATCAGATAACTCAAAGAATATTTCCAGAAG
1 TCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
409274 ATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAAATCATCTTTCAAA
66 ATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAAATCATCTTTCAAA
* *
409323 TCCATTGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAAATCAAAGAACACTTCCAGAAG
1 TCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
409388 ATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAATTCATCTTTCAAA
66 ATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAAATCATCTTTCAAA
* *
409437 TCCAATGATTGGTTTTGGGGTTCATATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAT
1 TCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* * *
409502 ATGTTATTGGGGCTCCTTATTTCTACTA
66 ATGCTATTGGGTCTTCTTATTTCTACTA
409530 CGAGAACATG
Statistics
Matches: 193, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 193 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (114 bp):
TCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
ATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAAATCATCTTTCAAA
Found at i:415646 original size:24 final size:25
Alignment explanation
Indices: 415590--415646 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
415580 TCAAAGATAT
*
415590 ATTTAATTTTTAATTTAAATTTATTA
1 ATTTAA-TTTTAATGTAAATTTATTA
* *
415616 CTATAATTTTAA-GTAAATTTATTA
1 ATTTAATTTTAATGTAAATTTATTA
415640 ATTTAAT
1 ATTTAAT
415647 AAATAAGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 16 0.62
25 6 0.23
26 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (25 bp):
ATTTAATTTTAATGTAAATTTATTA
Found at i:415923 original size:147 final size:144
Alignment explanation
Indices: 415657--415926 Score: 339
Period size: 147 Copynumber: 1.8 Consensus size: 144
415647 AAATAAGATT
* * * *
415657 TTATTTATTTTAAATATCAGAAAAGAGCTTCTAGGTGCTTTAAGACAGTTCTTTCCTTTGATATT
1 TTATTTATTTAAAATATCAGAAAACAGCATCTAGGTGCTTTAAGACA-TCCTTTCCTTTGATA-T
* *
415722 AAAAAATAAATAAATATTAAAACATTTATCTAAAAATAATAAAAAAATAGATTAATATATACAAT
64 AAAAAATAAATAAATATTAAAAAATTTATATAAAAATAATAAAAAAATAGATTAATATATACAAT
415787 TTATAAAAGTAAAATA
129 TTATAAAAGTAAAATA
*
415803 TTATTTATTTAAAAATATCAGAAAACAGACATCTAGTTGCTTTAAGAC-TCCCTTT-CTTTGATA
1 TTATTTATTT-AAAATATCAGAAAACAG-CATCTAGGTGCTTTAAGACAT-CCTTTCCTTTGATA
* * * * *
415866 -AAAAAATAAATAAATATTATTATAAAATTTTTATAAAATTAATCAAATAATATATTAATAT
63 TAAAAAATAAATAAATATTA--A-AAAATTTATATAAAAATAATAAAAAAATAGATTAATAT
415927 GATTAAAATA
Statistics
Matches: 106, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
144 19 0.18
146 20 0.19
147 50 0.47
148 17 0.16
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (144 bp):
TTATTTATTTAAAATATCAGAAAACAGCATCTAGGTGCTTTAAGACATCCTTTCCTTTGATATAA
AAAATAAATAAATATTAAAAAATTTATATAAAAATAATAAAAAAATAGATTAATATATACAATTT
ATAAAAGTAAAATA
Found at i:416791 original size:21 final size:21
Alignment explanation
Indices: 416760--416811 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
416750 TCCGTCTCCT
* *
416760 CTCCATTTTTCTGCTCTCTGTC
1 CTCC-TTTTTCTACTCTCTCTC
*
416782 CTTCTTTTTCTACTCTCTCTC
1 CTCCTTTTTCTACTCTCTCTC
416803 CTCCTTTTT
1 CTCCTTTTT
416812 TTTTTTGCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.04, C:0.37, G:0.04, T:0.56
Consensus pattern (21 bp):
CTCCTTTTTCTACTCTCTCTC
Found at i:417621 original size:23 final size:23
Alignment explanation
Indices: 417591--417650 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
417581 TTTCGCACCT
*
417591 CTGAATGATTCAGCA-AAACAATG
1 CTGAATGATTCAGCACAAA-AATA
* *
417614 CTGAATGATTTAGCACAGAAATA
1 CTGAATGATTCAGCACAAAAATA
417637 CTGAATGATTCAGC
1 CTGAATGATTCAGC
417651 CATTATCAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 30 0.94
24 2 0.06
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (23 bp):
CTGAATGATTCAGCACAAAAATA
Found at i:418586 original size:3 final size:3
Alignment explanation
Indices: 418578--418657 Score: 105
Period size: 3 Copynumber: 27.0 Consensus size: 3
418568 GTTTCTGTTG
418578 ATT ATT ATT A-T ATT ATT -TT ATTT ATT ATT A-T ATT ATT ATT A-T
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
418620 ATT ATT ATT ATT ATT ATT ATT ATT ATTT ATTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT A-TT ATT ATT
418658 TGAAAGATTT
Statistics
Matches: 71, Mismatches: 0, Indels: 12
0.86 0.00 0.14
Matches are distributed among these distances:
2 8 0.11
3 53 0.75
4 10 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:418604 original size:20 final size:21
Alignment explanation
Indices: 418579--418657 Score: 110
Period size: 20 Copynumber: 3.8 Consensus size: 21
418569 TTTCTGTTGA
418579 TTATTATTATATTATT-TTAT
1 TTATTATTATATTATTATTAT
418599 TTATTATTATATTATTATTAT
1 TTATTATTATATTATTATTAT
418620 ATTATTATTATTATTATTATTA-
1 -TTATTATTA-TATTATTATTAT
418642 TTATTTATT-TATTATT
1 TTA-TTATTATATTATT
418658 TGAAAGATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
20 23 0.42
21 7 0.13
22 14 0.25
23 11 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTATTATATTATTATTAT
Found at i:418608 original size:23 final size:24
Alignment explanation
Indices: 418578--418657 Score: 112
Period size: 23 Copynumber: 3.4 Consensus size: 24
418568 GTTTCTGTTG
418578 ATTATTATTA-TATTATTTTATTT
1 ATTATTATTATTATTATTTTATTT
*
418601 ATTATTA-TATTATTATTATA-TT
1 ATTATTATTATTATTATTTTATTT
418623 ATTATTATTATTATTATTATTATTT
1 ATTATTATTATTATTATT-TTATTT
418648 ATTTATTATT
1 A-TTATTATT
418658 TGAAAGATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
22 11 0.22
23 26 0.52
24 2 0.04
25 3 0.06
26 8 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTATTATTATTATTATTTTATTT
Found at i:420533 original size:13 final size:14
Alignment explanation
Indices: 420515--420547 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
420505 CCAATTCTCT
*
420515 AAAAATAT-TTTTA
1 AAAAATATGCTTTA
420528 AAAAATATGCTTTA
1 AAAAATATGCTTTA
420542 AAAAAT
1 AAAAAT
420548 TGAAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (14 bp):
AAAAATATGCTTTA
Found at i:420815 original size:19 final size:19
Alignment explanation
Indices: 420793--420838 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
420783 AATTATGATT
420793 ATATATTTTTTATATGTTA
1 ATATATTTTTTATATGTTA
420812 ATATATTTTTTATATGTTA
1 ATATATTTTTTATATGTTA
420831 ATATATTT
1 ATATATTT
420839 AAATAATTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (19 bp):
ATATATTTTTTATATGTTA
Found at i:426235 original size:22 final size:21
Alignment explanation
Indices: 426204--426244 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
426194 ATAACCCTTC
*
426204 TAACACAACTTATTTTATTTA
1 TAACACAACTTATTCTATTTA
426225 TAACATCAACTTATTCTATT
1 TAACA-CAACTTATTCTATT
426245 CACATTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (21 bp):
TAACACAACTTATTCTATTTA
Found at i:426259 original size:19 final size:18
Alignment explanation
Indices: 426237--426276 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
426227 ACATCAACTT
*
426237 ATTCTATTCACATTATCAA
1 ATTCTATTCACAATA-CAA
426256 ATTCTATTCACAATACAA
1 ATTCTATTCACAATACAA
426274 ATT
1 ATT
426277 AAATTATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (18 bp):
ATTCTATTCACAATACAA
Found at i:426713 original size:3 final size:3
Alignment explanation
Indices: 426705--426749 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
426695 TTTGAAAACA
*
426705 ATT ATT ATT ATT ATT ATT ATT ATT ATTT AAT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT AT
426750 ATATATCTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:429111 original size:18 final size:18
Alignment explanation
Indices: 429088--429123 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
429078 GAGATCAAAG
429088 ATTACTGTACAACAAAAT
1 ATTACTGTACAACAAAAT
429106 ATTACTGTACAACAAAAT
1 ATTACTGTACAACAAAAT
429124 CAACCTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (18 bp):
ATTACTGTACAACAAAAT
Found at i:437730 original size:14 final size:15
Alignment explanation
Indices: 437713--437741 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
437703 TGCATGATAT
437713 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
437727 GCATAAAACATAAGA
1 GCATAAAACATAAGA
437742 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:438081 original size:15 final size:15
Alignment explanation
Indices: 438017--438072 Score: 103
Period size: 15 Copynumber: 3.7 Consensus size: 15
438007 CGAGGGTATT
438017 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
438032 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
*
438047 ATAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
438062 GTAGTCCTTCG
1 GTAGTCCTTCG
438073 CAACGTAGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 39 1.00
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:438660 original size:19 final size:18
Alignment explanation
Indices: 438632--438667 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
438622 TATGTAAATT
438632 AAAGTATTTTGTTTTAAAC
1 AAAGTATTTT-TTTTAAAC
*
438651 AAAGTTTTTTTTTTAAA
1 AAAGTATTTTTTTTAAA
438668 TTCCCGGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (18 bp):
AAAGTATTTTTTTTAAAC
Found at i:438664 original size:18 final size:19
Alignment explanation
Indices: 438632--438667 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
438622 TATGTAAATT
438632 AAAGTATTTTGTTTTAAAC
1 AAAGTATTTTGTTTTAAAC
*
438651 AAAGT-TTTTTTTTTAAA
1 AAAGTATTTTGTTTTAAA
438668 TTCCCGGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (19 bp):
AAAGTATTTTGTTTTAAAC
Found at i:439947 original size:19 final size:19
Alignment explanation
Indices: 439919--439956 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
439909 AAATTGAAGC
*
439919 AGGAAAATAATTATTTTAA
1 AGGAAAATAATGATTTTAA
*
439938 AGGAATATAATGATTTTAA
1 AGGAAAATAATGATTTTAA
439957 GTATGTGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (19 bp):
AGGAAAATAATGATTTTAA
Found at i:446388 original size:14 final size:15
Alignment explanation
Indices: 446371--446399 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
446361 TGCATGATAT
446371 GCAT-AAACATAAGA
1 GCATAAAACATAAGA
446385 GCATAAAACATAAGA
1 GCATAAAACATAAGA
446400 TATATGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (15 bp):
GCATAAAACATAAGA
Found at i:446693 original size:15 final size:15
Alignment explanation
Indices: 446675--446709 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
446665 CGAGGGTATT
446675 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
446690 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
446705 GTAGT
1 GTAGT
446710 GGTCCTACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:448739 original size:19 final size:20
Alignment explanation
Indices: 448715--448759 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 20
448705 GTGTGGTTGC
448715 AATTGAAT-ATGTCGTGGCA
1 AATTGAATAATGTCGTGGCA
448734 AATTGAATGAAATGTCGTGGCA
1 AATTGAAT--AATGTCGTGGCA
448756 AATT
1 AATT
448760 CAATTGTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.35
22 15 0.65
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (20 bp):
AATTGAATAATGTCGTGGCA
Found at i:453167 original size:7 final size:7
Alignment explanation
Indices: 453155--453181 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
453145 ATAAAGATCG
453155 GTTTACT
1 GTTTACT
453162 GTTTACT
1 GTTTACT
453169 GTTTACT
1 GTTTACT
453176 GTTTAC
1 GTTTAC
453182 ACTAAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (7 bp):
GTTTACT
Found at i:464090 original size:19 final size:18
Alignment explanation
Indices: 464066--464102 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
464056 AACATAGGGT
*
464066 TAATCAATATCGATATAAA
1 TAATCAATA-CGAAATAAA
464085 TAATCAATACGAAATAAA
1 TAATCAATACGAAATAAA
464103 AATGAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (18 bp):
TAATCAATACGAAATAAA
Found at i:466367 original size:15 final size:16
Alignment explanation
Indices: 466343--466377 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
466333 ATTAAATTAT
*
466343 TATTATAATAATAA-A
1 TATTAAAATAATAATA
466358 TATTAAAATAATAATA
1 TATTAAAATAATAATA
466374 TATT
1 TATT
466378 TTTATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTAAAATAATAATA
Found at i:467027 original size:85 final size:84
Alignment explanation
Indices: 466904--467193 Score: 316
Period size: 85 Copynumber: 3.4 Consensus size: 84
466894 TCGTGGTGTT
* * * * *
466904 TTTTTGGAACAAACGCCACAAAATGTCGATATCTATAGCGGTGTTTTTGTAACAAACGCCGCAAA
1 TTTTTGGAACAAAAGCCACAAAAGGTCAAGATCTATAGCGGCGTTTTTG-AACAAACGCCGCAAA
*
466969 AGGTCAGATATATAGCGGCG
65 AGGTCAGATCTATAGCGGCG
* * * *
466989 TTTTTGGATACAAAAGCCGCAAAAGGTC-AGACCTATAGCGGCGTTTTTGGAACAAACGCAGTAA
1 TTTTTGGA-ACAAAAGCCACAAAAGGTCAAGATCTATAGCGGCGTTTTT-GAACAAACGCCGCAA
* *
467053 AATGTCAG-TCTATAGCGTCG
64 AAGGTCAGATCTATAGCGGCG
* * * * * *
467073 TTTTTTGGAACAAACGTCGCAAAAGGTCAATATCTATAGCGGCGTTTTAGATCAAACGCCGCAAA
1 -TTTTTGGAACAAAAGCCACAAAAGGTCAAGATCTATAGCGGCGTTTTTGAACAAACGCCGCAAA
*
467138 AGGACAGATCTATAGCGGCG
65 AGGTCAGATCTATAGCGGCG
** * *
467158 TTTTTATATCAAAAGCCACAAAAGGGC-AGATCTATA
1 TTTTTGGAACAAAAGCCACAAAAGGTCAAGATCTATA
467194 ATAAATTAAA
Statistics
Matches: 170, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
83 8 0.05
84 65 0.38
85 80 0.47
86 17 0.10
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (84 bp):
TTTTTGGAACAAAAGCCACAAAAGGTCAAGATCTATAGCGGCGTTTTTGAACAAACGCCGCAAAA
GGTCAGATCTATAGCGGCG
Found at i:467163 original size:42 final size:42
Alignment explanation
Indices: 466904--467193 Score: 323
Period size: 42 Copynumber: 6.9 Consensus size: 42
466894 TCGTGGTGTT
* * * *
466904 TTTTTGGAACAAACGCCACAAAATGTCGATATCTATAGCGGTG
1 TTTTTGGAACAAACGCCGCAAAAGGTC-AGATCTATAGCGGCG
* *
466947 TTTTTGTAACAAACGCCGCAAAAGGTCAGATATATAGCGGCG
1 TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
* *
466989 TTTTTGGATACAAAAGCCGCAAAAGGTCAGACCTATAGCGGCG
1 TTTTTGGA-ACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
* * * *
467032 TTTTTGGAACAAACGCAGTAAAATGTCAG-TCTATAGCGTCG
1 TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
* *
467073 TTTTTTGGAACAAACGTCGCAAAAGGTCAATATCTATAGCGGCG
1 -TTTTTGGAACAAACGCCGCAAAAGGTC-AGATCTATAGCGGCG
* * *
467117 -TTTTAGATCAAACGCCGCAAAAGGACAGATCTATAGCGGCG
1 TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
** * * * *
467158 TTTTTATATCAAAAGCCACAAAAGGGCAGATCTATA
1 TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATA
467194 ATAAATTAAA
Statistics
Matches: 211, Mismatches: 31, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
41 24 0.11
42 112 0.53
43 64 0.30
44 11 0.05
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (42 bp):
TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
Found at i:469136 original size:24 final size:24
Alignment explanation
Indices: 469100--469154 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
469090 TATGGCAACT
469100 TGAAAAAAAAAACTGCAGTAGCTA
1 TGAAAAAAAAAACTGCAGTAGCTA
*
469124 TGAAAAAACAAACTGCAGTAGCTA
1 TGAAAAAAAAAACTGCAGTAGCTA
*
469148 AGAAAAA
1 TGAAAAA
469155 TCACAGCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.56, C:0.13, G:0.16, T:0.15
Consensus pattern (24 bp):
TGAAAAAAAAAACTGCAGTAGCTA
Done.