Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000521.1 Hibiscus syriacus cultivar Beakdansim tig00000999_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: 1347562
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:2998 original size:15 final size:15
Alignment explanation
Indices: 2976--3017 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
2966 TAAAATATAT
2976 TAATTATAATATTAA
1 TAATTATAATATTAA
* *
2991 TTATTATAATAATAA
1 TAATTATAATATTAA
3006 TAATTA-AATATT
1 TAATTATAATATT
3018 TTATAATTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATTATAATATTAA
Found at i:13249 original size:2 final size:2
Alignment explanation
Indices: 13242--13269 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13232 CACGGCAAGT
13242 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
13270 AAAACTTATT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:27965 original size:21 final size:21
Alignment explanation
Indices: 27939--27984 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
27929 GGCAGAGGAT
27939 GCCAAAGATAAGCTAGTATCA
1 GCCAAAGATAAGCTAGTATCA
27960 GCCAAAGATAAGCTAGTATCA
1 GCCAAAGATAAGCTAGTATCA
27981 GCCA
1 GCCA
27985 GAGAATTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (21 bp):
GCCAAAGATAAGCTAGTATCA
Found at i:43510 original size:17 final size:17
Alignment explanation
Indices: 43488--43527 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
43478 CTCAAGATTA
43488 TTAAACCTTCTAATGAG
1 TTAAACCTTCTAATGAG
43505 TTAAACCTTCTAATGAG
1 TTAAACCTTCTAATGAG
43522 TTAAAC
1 TTAAAC
43528 TCTGATACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (17 bp):
TTAAACCTTCTAATGAG
Found at i:59574 original size:2 final size:2
Alignment explanation
Indices: 59567--59591 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59557 TTCCAAATTC
59567 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
59592 CCAGGTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:59724 original size:40 final size:40
Alignment explanation
Indices: 59673--59753 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
59663 TAGCTTCCAA
* *
59673 CACTAACAAAAACATCAAAATAAACATTAACCTTTGGCTT
1 CACTAACAAAAACAGCAAAAGAAACATTAACCTTTGGCTT
*
59713 CACTAACAAAAACAGCAAAAGAATCATTAACCTTTGGCTT
1 CACTAACAAAAACAGCAAAAGAAACATTAACCTTTGGCTT
59753 C
1 C
59754 CAAGTTCTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.23
Consensus pattern (40 bp):
CACTAACAAAAACAGCAAAAGAAACATTAACCTTTGGCTT
Found at i:60027 original size:2 final size:2
Alignment explanation
Indices: 60022--60050 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60012 CTCAAAAAAT
60022 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60051 GTAAACAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61710 original size:44 final size:44
Alignment explanation
Indices: 61659--61761 Score: 161
Period size: 44 Copynumber: 2.3 Consensus size: 44
61649 CAATGGTTCC
*
61659 ATCTTTGGCTTCCAACACTACTAAAAACAGCAAAATAAACATTA
1 ATCTTTGGCTTCCAACACTACTAAAAACAGCAAAAGAAACATTA
*
61703 ATCTTTGGCTTCCAACACTACTAAAAACAGCAAAAGAATCATTA
1 ATCTTTGGCTTCCAACACTACTAAAAACAGCAAAAGAAACATTA
* * *
61747 ACCTGTGGCTCCCAA
1 ATCTTTGGCTTCCAA
61762 GTTCTGAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (44 bp):
ATCTTTGGCTTCCAACACTACTAAAAACAGCAAAAGAAACATTA
Found at i:62051 original size:29 final size:28
Alignment explanation
Indices: 62019--62081 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
62009 TTTTGAAACA
*
62019 TTTATAATTTTATGATAATAAATTTAATC
1 TTTATAATTATAT-ATAATAAATTTAATC
** *
62048 TTTAATAATTATATATTTTAAATTTAATT
1 TTT-ATAATTATATATAATAAATTTAATC
62077 TTTAT
1 TTTAT
62082 GAGTTAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 2 0.07
29 18 0.62
30 9 0.31
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTATAATTATATATAATAAATTTAATC
Found at i:67573 original size:13 final size:13
Alignment explanation
Indices: 67555--67580 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67545 TCTATTTAGT
67555 GTATAATTTAGAG
1 GTATAATTTAGAG
67568 GTATAATTTAGAG
1 GTATAATTTAGAG
67581 TCTAAATCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
GTATAATTTAGAG
Found at i:70456 original size:20 final size:20
Alignment explanation
Indices: 70431--70482 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
70421 ACTATAGACT
* *
70431 ATCGCAACGTGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
70451 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
70471 ATCGCAACGCGA
1 ATCGCAACGCGA
70483 TTTTCAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:70563 original size:20 final size:20
Alignment explanation
Indices: 70540--70604 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
70530 AGATCGCGTT
70540 GCGATTTCAACTATCGCAAC
1 GCGATTTCAACTATCGCAAC
* ** * *
70560 GCGAAATGGAA-AATCGCAAA
1 GCG-ATTTCAACTATCGCAAC
70580 GCGATTTTCAACTATCGCAAC
1 GCGA-TTTCAACTATCGCAAC
70601 GCGA
1 GCGA
70605 AATGGAACGC
Statistics
Matches: 32, Mismatches: 10, Indels: 5
0.68 0.21 0.11
Matches are distributed among these distances:
19 1 0.03
20 16 0.50
21 15 0.47
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
GCGATTTCAACTATCGCAAC
Found at i:70573 original size:101 final size:101
Alignment explanation
Indices: 70451--70637 Score: 338
Period size: 101 Copynumber: 1.9 Consensus size: 101
70441 GAAATGGAAA
*
70451 ATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGA
1 ATCGCAACGCGAAATGAAAAATCGCAAAGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGA
*
70516 ATTTGTGATAGTGGAGATCGCGTTGCGATTTCAACT
66 ATTTGCGATAGTGGAGATCGCGTTGCGATTTCAACT
* *
70552 ATCGCAACGCGAAATGGAAAATCGCAAAGCGATTTTCAACTATCGCAACGCGAAATGGAACGCGA
1 ATCGCAACGCGAAATGAAAAATCGCAAAGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGA
70617 ATTTGCGATAGTGGAGATCGC
66 ATTTGCGATAGTGGAGATCGC
70638 AATGCGAATT
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 82 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (101 bp):
ATCGCAACGCGAAATGAAAAATCGCAAAGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGA
ATTTGCGATAGTGGAGATCGCGTTGCGATTTCAACT
Found at i:102164 original size:23 final size:23
Alignment explanation
Indices: 102113--102169 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
102103 TTATTTAGGA
**
102113 TATTATTATTAAATTTAGTTTTT
1 TATTATTATTAAATAAAGTTTTT
*
102136 TTTTATTA-TAAATAAAGTTTTAT
1 TATTATTATTAAATAAAGTTTT-T
102159 TATTATT-TTAA
1 TATTATTATTAA
102170 TTTTTTCAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 11 0.39
23 17 0.61
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
TATTATTATTAAATAAAGTTTTT
Found at i:104583 original size:18 final size:15
Alignment explanation
Indices: 104560--104601 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
104550 ATGCATAAAT
104560 GATATATGTATGAAATTA
1 GATATATGTA-G-AA-TA
104578 GATATATG-AGAATA
1 GATATATGTAGAATA
104592 GATATATGTA
1 GATATATGTA
104602 ACATGTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 10 0.43
15 3 0.13
16 1 0.04
17 1 0.04
18 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (15 bp):
GATATATGTAGAATA
Found at i:104929 original size:23 final size:23
Alignment explanation
Indices: 104896--104939 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
104886 GAGTCGAGGG
104896 TCTACGCGGTCCTACGGGACAAT
1 TCTACGCGGTCCTACGGGACAAT
* *
104919 TCTACGTGGTCCTTCGGGACA
1 TCTACGCGGTCCTACGGGACA
104940 TATATGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.30, G:0.27, T:0.25
Consensus pattern (23 bp):
TCTACGCGGTCCTACGGGACAAT
Found at i:105044 original size:18 final size:18
Alignment explanation
Indices: 105021--105073 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
105011 ATTCTTAAGG
105021 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
105039 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
*
105057 AGTGGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
105074 AATATTCAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:106159 original size:23 final size:23
Alignment explanation
Indices: 106133--106193 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
106123 CTCGTATAAA
*
106133 TGCACCTAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
106156 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
106179 TACACCGAAGTGCCA
1 TGCACCGAAGTGCCA
106194 TATAAAATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:113850 original size:23 final size:22
Alignment explanation
Indices: 113807--113850 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
113797 TACTGTATGA
**
113807 GGGAATCGGTTCCCTGTAGCAG
1 GGGAATCGGTTCCCTCAAGCAG
113829 GGGAATCGGTTCCCCTCAAGCA
1 GGGAATCGGTT-CCCTCAAGCA
113851 ATCTGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.20, C:0.27, G:0.32, T:0.20
Consensus pattern (22 bp):
GGGAATCGGTTCCCTCAAGCAG
Found at i:126349 original size:168 final size:168
Alignment explanation
Indices: 126071--126407 Score: 665
Period size: 168 Copynumber: 2.0 Consensus size: 168
126061 CATGTCCATT
126071 TTCACTTGTAAAAAGCTCTACTACAATTGATGGTGAAATATCAGTAAAAGTATAGGCAATTATGA
1 TTCACTTGTAAAAAGCTCTACTACAATTGATGGTGAAATATCAGTAAAAGTATAGGCAATTATGA
126136 ATTCTTAATTCTTATATGTACATGAAATCCTTTTTCTTTGATATCTTAAACCCCATGAATATATT
66 ATTCTTAATTCTTATATGTACATGAAATCCTTTTTCTTTGATATCTTAAACCCCATGAATATATT
126201 TAGTCTCGTTAACAAGAAACTTGTCGATCAAATAGTTA
131 TAGTCTCGTTAACAAGAAACTTGTCGATCAAATAGTTA
126239 TTCACTTGTAAAAAGCTCTACTACAATTGATGGTGAAATATCAGTAAAAGTATAGGCAATTATGA
1 TTCACTTGTAAAAAGCTCTACTACAATTGATGGTGAAATATCAGTAAAAGTATAGGCAATTATGA
126304 ATTCTTAATTCTTATATGTACATGAAATCCTTTTTCTTTGATATCTTAAACCCCATGAATATATT
66 ATTCTTAATTCTTATATGTACATGAAATCCTTTTTCTTTGATATCTTAAACCCCATGAATATATT
*
126369 TAGTCTTGTTAACAAGAAACTTGTCGATCAAATAGTTA
131 TAGTCTCGTTAACAAGAAACTTGTCGATCAAATAGTTA
126407 T
1 T
126408 GGATTATGTC
Statistics
Matches: 168, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
168 168 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (168 bp):
TTCACTTGTAAAAAGCTCTACTACAATTGATGGTGAAATATCAGTAAAAGTATAGGCAATTATGA
ATTCTTAATTCTTATATGTACATGAAATCCTTTTTCTTTGATATCTTAAACCCCATGAATATATT
TAGTCTCGTTAACAAGAAACTTGTCGATCAAATAGTTA
Found at i:127582 original size:24 final size:21
Alignment explanation
Indices: 127531--127574 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
127521 ATCGTGATTG
* *
127531 CGGTCGTCGCAGGCGTTATTA
1 CGGTCGTCGCAGACGCTATTA
127552 CGGTCGTCGCAGACGCTATTA
1 CGGTCGTCGCAGACGCTATTA
127573 CG
1 CG
127575 ACTGTCGTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.27, G:0.32, T:0.25
Consensus pattern (21 bp):
CGGTCGTCGCAGACGCTATTA
Found at i:131745 original size:76 final size:76
Alignment explanation
Indices: 131619--131770 Score: 304
Period size: 76 Copynumber: 2.0 Consensus size: 76
131609 TCCGAATCGG
131619 GTCTCGCCCAAGAAGGGAGATTTTCTTCAGACTTGCTGGACTTGGCAGAACCTTCAGTTGCATTT
1 GTCTCGCCCAAGAAGGGAGATTTTCTTCAGACTTGCTGGACTTGGCAGAACCTTCAGTTGCATTT
131684 AACACAAGAAA
66 AACACAAGAAA
131695 GTCTCGCCCAAGAAGGGAGATTTTCTTCAGACTTGCTGGACTTGGCAGAACCTTCAGTTGCATTT
1 GTCTCGCCCAAGAAGGGAGATTTTCTTCAGACTTGCTGGACTTGGCAGAACCTTCAGTTGCATTT
131760 AACACAAGAAA
66 AACACAAGAAA
131771 CCTACCAGAT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (76 bp):
GTCTCGCCCAAGAAGGGAGATTTTCTTCAGACTTGCTGGACTTGGCAGAACCTTCAGTTGCATTT
AACACAAGAAA
Found at i:136016 original size:23 final size:25
Alignment explanation
Indices: 135989--136037 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
135979 TATTTTTCTC
135989 AATATACT-TTT-TTT-AATAATAAT
1 AATATACTATTTCTTTGAAT-ATAAT
136012 AATATACTATTTCTTTGAATATAAT
1 AATATACTATTTCTTTGAATATAAT
136037 A
1 A
136038 CATTTAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 8 0.35
24 3 0.13
25 9 0.39
26 3 0.13
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (25 bp):
AATATACTATTTCTTTGAATATAAT
Found at i:136090 original size:2 final size:2
Alignment explanation
Indices: 136083--136115 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
136073 TATATTATTC
136083 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
136116 AAAAAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:147613 original size:58 final size:58
Alignment explanation
Indices: 147544--147659 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
147534 GGAAGAATCA
147544 AATCCAAATTAGGTAAAGTGGTTTTTTTGGTTAAAAATGTTTGATTACTTGAATAAAG
1 AATCCAAATTAGGTAAAGTGGTTTTTTTGGTTAAAAATGTTTGATTACTTGAATAAAG
147602 AATCCAAATTAGGTAAAGTGGTTTTTTTGGTTAAAAATGTTTGATTACTTGAATAAAG
1 AATCCAAATTAGGTAAAGTGGTTTTTTTGGTTAAAAATGTTTGATTACTTGAATAAAG
147660 TTGTCAGGGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (58 bp):
AATCCAAATTAGGTAAAGTGGTTTTTTTGGTTAAAAATGTTTGATTACTTGAATAAAG
Found at i:147832 original size:27 final size:27
Alignment explanation
Indices: 147801--147854 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
147791 ATTTAGTGTA
147801 GAAATTAAAGGGAATATTATTTTCACT
1 GAAATTAAAGGGAATATTATTTTCACT
147828 GAAATTAAAGGGAATATTATTTTCACT
1 GAAATTAAAGGGAATATTATTTTCACT
147855 TGAGGTCCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (27 bp):
GAAATTAAAGGGAATATTATTTTCACT
Found at i:150135 original size:14 final size:14
Alignment explanation
Indices: 150116--150155 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
150106 TTCATATTAT
150116 TTATTTATTTAAAA
1 TTATTTATTTAAAA
* *
150130 TTATTTATTTATAT
1 TTATTTATTTAAAA
*
150144 TTATTCATTTAA
1 TTATTTATTTAA
150156 TTTTATAGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTATTTAAAA
Found at i:150160 original size:14 final size:14
Alignment explanation
Indices: 150115--150161 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
150105 ATTCATATTA
*
150115 TTTATTTATTTAAA
1 TTTATTTATTTAAT
*
150129 ATTATTTATTT-AT
1 TTTATTTATTTAAT
*
150142 ATTTATTCATTTAAT
1 -TTTATTTATTTAAT
150157 TTTAT
1 TTTAT
150162 AGATAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 1 0.04
14 24 0.89
15 2 0.07
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTATTTATTTAAT
Found at i:150388 original size:43 final size:44
Alignment explanation
Indices: 150325--150411 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 44
150315 CTCCAATCCA
150325 AGGTTCACGCCTGATCACGATCAGT-AGGGCATTAGACTTCACT
1 AGGTTCACGCCTGATCACGATCAGTAAGGGCATTAGACTTCACT
* *
150368 AGGTTTACGCCTGATTACGATCAGTAAGGGCATTAGACTTCACT
1 AGGTTCACGCCTGATCACGATCAGTAAGGGCATTAGACTTCACT
150412 TGAAATTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 23 0.56
44 18 0.44
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (44 bp):
AGGTTCACGCCTGATCACGATCAGTAAGGGCATTAGACTTCACT
Found at i:152625 original size:58 final size:58
Alignment explanation
Indices: 152555--152670 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
152545 TTGAGTTTTA
152555 TTGGTGTCCTCACTTTCTATTCAGAGCTTGCAGTTGAGAAAGATGAAAATGATGAGTT
1 TTGGTGTCCTCACTTTCTATTCAGAGCTTGCAGTTGAGAAAGATGAAAATGATGAGTT
152613 TTGGTGTCCTCACTTTCTATTCAGAGCTTGCAGTTGAGAAAGATGAAAATGATGAGTT
1 TTGGTGTCCTCACTTTCTATTCAGAGCTTGCAGTTGAGAAAGATGAAAATGATGAGTT
152671 ATCAAATATT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (58 bp):
TTGGTGTCCTCACTTTCTATTCAGAGCTTGCAGTTGAGAAAGATGAAAATGATGAGTT
Found at i:153914 original size:20 final size:20
Alignment explanation
Indices: 153889--153926 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
153879 CTGATAGTCC
153889 TTGTCTTTATTCTGTATATT
1 TTGTCTTTATTCTGTATATT
153909 TTGTCTTTATTCTGTATA
1 TTGTCTTTATTCTGTATA
153927 ATGCAACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.63
Consensus pattern (20 bp):
TTGTCTTTATTCTGTATATT
Found at i:157053 original size:72 final size:74
Alignment explanation
Indices: 156950--157087 Score: 217
Period size: 73 Copynumber: 1.9 Consensus size: 74
156940 AAACTAACGA
* * *
156950 AAGTTAACGTTTTAGTAACTACATCTTAATTAAAA-AAAACAAAAGTGACTACGAATTAACGTTT
1 AAGTTAACGTTTCAGTAACTACATCTTAATTAAAACAAAACAAAAATAACTACGAATTAACGTTT
157014 TTGAATCGG
66 TTGAATCGG
* *
157023 AAGTTAACGTTTCAGTGAC-ACATCTTAATTAAAACAAAATAAAAATAACTACGAATTAACGTTT
1 AAGTTAACGTTTCAGTAACTACATCTTAATTAAAACAAAACAAAAATAACTACGAATTAACGTTT
157087 T
66 T
157088 GATTTGATAG
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
72 15 0.25
73 44 0.75
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (74 bp):
AAGTTAACGTTTCAGTAACTACATCTTAATTAAAACAAAACAAAAATAACTACGAATTAACGTTT
TTGAATCGG
Found at i:165013 original size:23 final size:23
Alignment explanation
Indices: 164968--165013 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
164958 GAGTTTATTT
* *
164968 TTTAAAATTAAAATTATTTTAAA
1 TTTAAAATTAAAAATATTATAAA
164991 TTTAAAATATAAAAATA-TATAAA
1 TTTAAAAT-TAAAAATATTATAAA
165014 CATTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTAAAATTAAAAATATTATAAA
Found at i:165803 original size:39 final size:41
Alignment explanation
Indices: 165757--165845 Score: 128
Period size: 39 Copynumber: 2.2 Consensus size: 41
165747 AATCAATATT
* * *
165757 TTAATTAAAAATTTATCTGAAATTTT-ATTTTA-AATTATA
1 TTAATTAAAAAATTATATAAAATTTTAATTTTATAATTATA
165796 TTAATTAAAAAATTATATAAAATTTTAATTTTATAATTATA
1 TTAATTAAAAAATTATATAAAATTTTAATTTTATAATTATA
*
165837 TTATTTAAA
1 TTAATTAAA
165846 TTAATTGTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 23 0.52
40 6 0.14
41 15 0.34
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (41 bp):
TTAATTAAAAAATTATATAAAATTTTAATTTTATAATTATA
Found at i:165878 original size:216 final size:223
Alignment explanation
Indices: 165576--166026 Score: 744
Period size: 225 Copynumber: 2.0 Consensus size: 223
165566 CTAAATCTAT
165576 ATTA-ATTAATTAAAAAATTATAAAATTTTAATTTTATAATTATATTTATTTAAATTAATTGTAA
1 ATTATATTAATTAAAAAATTATAAAATTTTAATTTTATAATTATATTTATTTAAATTAATTGTAA
165640 ATTGTTTTTTTTAATT-A-A-A-A-ATATTATATATATTATATATAACATATGAGCTCAACCCAA
66 ATTGTTTTTTTTAATTAATATATATATATTATATATATTATATATAACATATGAGCTCAACCCAA
165700 ACTA-TTAAAACTCAATT-TAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATT-TTAAT
131 ACTATTTAAAACTCAATTATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTATTAAT
165762 TAAAAATTTATCTGAAATTTTATTTTAA
196 TAAAAATTTATCTGAAATTTTATTTTAA
165790 ATTATATTAATTAAAAAATTATATAAAATTTTAATTTTATAATTATA-TTATTTAAATTAATTGT
1 ATTATATTAATTAAAAAA-T-TATAAAATTTTAATTTTATAATTATATTTATTTAAATTAATTGT
165854 AAATTG-TTTTTTTAATTAAAAAATATTATATATATTATATATATTATATATAACATATGAGCTC
64 AAATTGTTTTTTTTAATT----AATA-TATATATATTATATATATTATATATAACATATGAGCTC
165918 AACCCAAACTATTTAAAACTCAATTAATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATA
124 AACCCAAACTATTTAAAACTCAATT-ATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATA
165983 TTAATTAATTAAAAATTTATCTGAAATTTTATTTTAA
188 TT-ATTAATTAAAAATTTATCTGAAATTTTATTTTAA
166020 ATTATAT
1 ATTATAT
166027 ATTATTTAAA
Statistics
Matches: 219, Mismatches: 0, Indels: 20
0.92 0.00 0.08
Matches are distributed among these distances:
214 4 0.02
215 24 0.11
216 24 0.11
217 26 0.12
220 1 0.00
221 1 0.00
223 1 0.00
224 1 0.00
225 44 0.20
226 13 0.06
228 40 0.18
230 40 0.18
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (223 bp):
ATTATATTAATTAAAAAATTATAAAATTTTAATTTTATAATTATATTTATTTAAATTAATTGTAA
ATTGTTTTTTTTAATTAATATATATATATTATATATATTATATATAACATATGAGCTCAACCCAA
ACTATTTAAAACTCAATTATAATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTATTAAT
TAAAAATTTATCTGAAATTTTATTTTAA
Found at i:165896 original size:11 final size:9
Alignment explanation
Indices: 165876--165905 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
165866 TAATTAAAAA
165876 ATATTATAT
1 ATATTATAT
165885 ATATTATAT
1 ATATTATAT
165894 ATATTATAT
1 ATATTATAT
165903 ATA
1 ATA
165906 ACATATGAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
ATATTATAT
Found at i:165911 original size:18 final size:18
Alignment explanation
Indices: 165876--165911 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
165866 TAATTAAAAA
**
165876 ATATTATATATATTATAT
1 ATATTATATATAACATAT
165894 ATATTATATATAACATAT
1 ATATTATATATAACATAT
165912 GAGCTCAACC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTATATATAACATAT
Found at i:173945 original size:25 final size:26
Alignment explanation
Indices: 173892--173945 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
173882 AATTATATAT
* * *
173892 TAAACTTATACAATTTTAAGAGGGGA
1 TAAACTTACAAAATTTTAAGAGGGAA
*
173918 TAAACTTACAAAATTTT-AGAGGTAA
1 TAAACTTACAAAATTTTAAGAGGGAA
173943 TAA
1 TAA
173946 CAGTTTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.31
Consensus pattern (26 bp):
TAAACTTACAAAATTTTAAGAGGGAA
Found at i:182424 original size:24 final size:24
Alignment explanation
Indices: 182407--182452 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
182397 TCTGTTCTGG
182407 ATTCTGTTCTGATATCTGATATGA
1 ATTCTGTTCTGATATCTGATATGA
* *
182431 ATTCTGTTTTGATTTCTGATAT
1 ATTCTGTTCTGATATCTGATAT
182453 CTCCGTTTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.52
Consensus pattern (24 bp):
ATTCTGTTCTGATATCTGATATGA
Found at i:190757 original size:111 final size:111
Alignment explanation
Indices: 190563--190784 Score: 410
Period size: 111 Copynumber: 2.0 Consensus size: 111
190553 GAAACTATCG
* *
190563 AAGAGAAATTCACTCACAAAGCAAGCACCGAAATCACTATATTCATGTTTCATTGCCATCTTCAT
1 AAGAGAAATTCACTCACAAAGCAAGCACCGAAATCACTAAATTCATGCTTCATTGCCATCTTCAT
190628 GAAGTATAATCCGTTTTCTAATTTAGATTAGACTGAGCTAAGTTGT
66 GAAGTATAATCCGTTTTCTAATTTAGATTAGACTGAGCTAAGTTGT
190674 AAGAGAAATTCACT-AGCAAAGCAAGCACCGAAATCACTAAATTCATGCTTCATTGCCATCTTCA
1 AAGAGAAATTCACTCA-CAAAGCAAGCACCGAAATCACTAAATTCATGCTTCATTGCCATCTTCA
190738 TGAAGTATAATCCGTTTTCTAATTTAGATTAGACTGAGCTAAGTTGT
65 TGAAGTATAATCCGTTTTCTAATTTAGATTAGACTGAGCTAAGTTGT
190785 TGAGTTTGGT
Statistics
Matches: 108, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
110 1 0.01
111 107 0.99
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (111 bp):
AAGAGAAATTCACTCACAAAGCAAGCACCGAAATCACTAAATTCATGCTTCATTGCCATCTTCAT
GAAGTATAATCCGTTTTCTAATTTAGATTAGACTGAGCTAAGTTGT
Found at i:193619 original size:2 final size:2
Alignment explanation
Indices: 193612--193640 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
193602 AATAATGACA
193612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
193641 CATAACCCAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:196023 original size:19 final size:19
Alignment explanation
Indices: 195999--196042 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
195989 CGACTTAAAG
195999 TTAAATAATAATAAATTAT
1 TTAAATAATAATAAATTAT
196018 TTAAATAATAATAAATTAT
1 TTAAATAATAATAAATTAT
196037 TTAAAT
1 TTAAAT
196043 TTAATTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTAAATAATAATAAATTAT
Found at i:197832 original size:2 final size:2
Alignment explanation
Indices: 197821--197851 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
197811 ATCTCAACAA
197821 AT AT -T 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
197852 TAGAGGATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:198859 original size:25 final size:25
Alignment explanation
Indices: 198831--198889 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
198821 CAGAAGAATA
198831 TGCTGCTTTTATTTTGAAATATGAT
1 TGCTGCTTTTATTTTGAAATATGAT
198856 TGCTGCTTTTATTTTGAAATATGAT
1 TGCTGCTTTTATTTTGAAATATGAT
*
198881 TGCTACTTT
1 TGCTGCTTT
198890 GCATAGCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.22, C:0.10, G:0.15, T:0.53
Consensus pattern (25 bp):
TGCTGCTTTTATTTTGAAATATGAT
Found at i:204662 original size:164 final size:161
Alignment explanation
Indices: 204461--204785 Score: 575
Period size: 164 Copynumber: 2.0 Consensus size: 161
204451 TCTGTTTGAA
204461 GGGAATCGGGAAATGTGGAGTTCTTTTTGCTTTCTTTTCCTTTTTATGTGAGCTTTGGGATCACA
1 GGGAATCGGGAAATGTGGAGTTCTTTTTGCTTTCTTTTCCTTTTTATGTGAGCTTT-GGATCACA
204526 AAATCATGAACATTGC-TTAAATTATA-TTTTTCCTATAAAATAAAGTTACAAATGATAAATTTT
65 AAATCATGAACATTGCTTTAAATTATATTTTTTCCTATAAAATAAAGTTACAAATGAT-AATTTT
204589 GAA-TTTAGACAGTTGATCTGCTTACAGATCAGATT
129 GAATTTTAGACAGTT--T-TGCTTACAGATCAGATT
204624 GGGAATCGGGAAATGTGGATGTTCTTTTTGCTTTCTTTTCCTTTTTATGTGAGCTTTGGATCACA
1 GGGAATCGGGAAATGTGGA-GTTCTTTTTGCTTTCTTTTCCTTTTTATGTGAGCTTTGGATCACA
204689 AAATCATGAACATTGCTTTAAATTATATTTTTTCCTATAAAATAAAGTTACAAATGATAATTTTG
65 AAATCATGAACATTGCTTTAAATTATATTTTTTCCTATAAAATAAAGTTACAAATGATAATTTTG
204754 AATTTTAGACAGTTTTGCTTACAGATCAGATT
130 AATTTTAGACAGTTTTGCTTACAGATCAGATT
204786 ATTTGTTAAA
Statistics
Matches: 158, Mismatches: 0, Indels: 9
0.95 0.00 0.05
Matches are distributed among these distances:
162 17 0.11
163 44 0.28
164 56 0.35
165 41 0.26
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (161 bp):
GGGAATCGGGAAATGTGGAGTTCTTTTTGCTTTCTTTTCCTTTTTATGTGAGCTTTGGATCACAA
AATCATGAACATTGCTTTAAATTATATTTTTTCCTATAAAATAAAGTTACAAATGATAATTTTGA
ATTTTAGACAGTTTTGCTTACAGATCAGATT
Found at i:206335 original size:20 final size:21
Alignment explanation
Indices: 206310--206361 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
206300 TTTTCCCAAT
*
206310 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
206330 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
206351 TCGCAATGCGA
1 TCGCAATGCGA
206362 TATGACTATC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:206374 original size:19 final size:20
Alignment explanation
Indices: 206350--206461 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
206340 AATTGGGAAA
206350 ATCGCAATGCGATA-TGACT
1 ATCGCAATGCGATACTGACT
*
206369 ATCGC-ATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
206388 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
206409 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
206429 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
206449 TTCGCAACGCGAT
1 ATCGCAATGCGAT
206462 TTACATAGCG
Statistics
Matches: 78, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
18 8 0.10
19 16 0.21
20 39 0.50
21 13 0.17
22 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:206399 original size:20 final size:19
Alignment explanation
Indices: 206350--206401 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
206340 AATTGGGAAA
206350 ATCGCAATGCGATATGACT
1 ATCGCAATGCGATATGACT
*
206369 ATCGC-ATGCGATACTTACT
1 ATCGCAATGCGATA-TGACT
206388 ATCGCAATGCGATA
1 ATCGCAATGCGATA
206402 ATACAAAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 8 0.27
19 14 0.47
20 8 0.27
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (19 bp):
ATCGCAATGCGATATGACT
Found at i:206454 original size:61 final size:59
Alignment explanation
Indices: 206347--206461 Score: 140
Period size: 61 Copynumber: 1.9 Consensus size: 59
206337 GCGAATTGGG
* * * * *
206347 AAAATCGCAATGCGATATGACTATCGCATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATATGACTATCGCACGCGATACTGACTATCGCAACGCGATAATAC
* * *
206406 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATA-TGACTATCGC-ACGCGATACTGACTATCGCAACGCGAT
206462 TTACATAGCG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 15 0.33
60 9 0.20
61 22 0.48
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (59 bp):
AAAATCGCAACGAGATATGACTATCGCACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:207022 original size:26 final size:27
Alignment explanation
Indices: 206975--207029 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
206965 GAATGAAAAT
**
206975 CGCAACGCGGAAATAACTATCGCAACG
1 CGCAACGCGGAAATAAAAATCGCAACG
207002 CGCAACGC-GAAATAAAAATCGCAACG
1 CGCAACGCGGAAATAAAAATCGCAACG
207028 CG
1 CG
207030 AAACCAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.40, C:0.29, G:0.22, T:0.09
Consensus pattern (27 bp):
CGCAACGCGGAAATAAAAATCGCAACG
Found at i:207038 original size:19 final size:19
Alignment explanation
Indices: 207002--207041 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
206992 TATCGCAACG
*
207002 CGCAACGCGAAATAAAAAT
1 CGCAACGCGAAACAAAAAT
*
207021 CGCAACGCGAAACCAAAAT
1 CGCAACGCGAAACAAAAAT
207040 CG
1 CG
207042 ATTGCGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.07
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAT
Found at i:207073 original size:19 final size:19
Alignment explanation
Indices: 207043--207122 Score: 114
Period size: 18 Copynumber: 4.4 Consensus size: 19
207033 CCAAAATCGA
*
207043 TTGCGA-TTTCATTTCACG
1 TTGCGATTTTCATTTCGCG
207061 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
207080 -TGCGATTTTTATTTCGCG
1 TTGCGATTTTCATTTCGCG
207098 TTGCGATTTTCA-TT-GCG
1 TTGCGATTTTCATTTCGCG
207115 TTGCGATT
1 TTGCGATT
207123 GTCTGTCGCG
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
17 11 0.19
18 25 0.44
19 21 0.37
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:207141 original size:30 final size:29
Alignment explanation
Indices: 207107--207186 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 29
207097 GTTGCGATTT
*
207107 TCATTGCGTTGCGATTGTCTGTCGCGATAG
1 TCATTGCGTTGCGATTCTC-GTCGCGATAG
*
207137 TCATTCGCGTTGCGATTCTCGTTGCGATAG
1 TCATT-GCGTTGCGATTCTCGTCGCGATAG
*
207167 TCATTTCCGTTGCGATTCTC
1 TCA-TTGCGTTGCGATTCTC
207187 ATTATCTCGT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
30 30 0.67
31 15 0.33
ACGTcount: A:0.12, C:0.24, G:0.25, T:0.39
Consensus pattern (29 bp):
TCATTGCGTTGCGATTCTCGTCGCGATAG
Found at i:207189 original size:48 final size:48
Alignment explanation
Indices: 207059--207189 Score: 115
Period size: 48 Copynumber: 2.7 Consensus size: 48
207049 TTTCATTTCA
* * * *
207059 CGTTGCGATTTTCATTTCGCG-TGCGATTTTTATTTCGCGTTGCGATTTT
1 CGTTGCGATTGTCATTTC-CGTTGCGATTCTCA-TTCGCGTTGCGATTCT
* * * **
207108 CATTGCG-TTG-CGATTGTCTGTCGCGATAGTCATTCGCGTTGCGATTCT
1 CGTTGCGATTGTC-ATT-TCCGTTGCGATTCTCATTCGCGTTGCGATTCT
*
207156 CGTTGCGATAGTCATTTCCGTTGCGATTCTCATT
1 CGTTGCGATTGTCATTTCCGTTGCGATTCTCATT
207190 ATCTCGTTGA
Statistics
Matches: 63, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
47 1 0.02
48 41 0.65
49 20 0.32
50 1 0.02
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.43
Consensus pattern (48 bp):
CGTTGCGATTGTCATTTCCGTTGCGATTCTCATTCGCGTTGCGATTCT
Found at i:208297 original size:25 final size:23
Alignment explanation
Indices: 208262--208312 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 23
208252 ATCATATATA
208262 AACAAGTTTAATAGTAGACGTTT
1 AACAAGTTTAATAGTAGACGTTT
208285 AACAAGTTATTAATAGTAGACGTTT
1 AACAAG-T-TTAATAGTAGACGTTT
208310 AAC
1 AAC
208313 TTTGTTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 6 0.23
24 1 0.04
25 19 0.73
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (23 bp):
AACAAGTTTAATAGTAGACGTTT
Found at i:209243 original size:42 final size:42
Alignment explanation
Indices: 209183--209305 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
209173 GCCCGACTCG
* * *
209183 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
209225 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
209267 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
209306 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:209263 original size:21 final size:21
Alignment explanation
Indices: 209239--209305 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
209229 TCATTCCTCG
209239 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
209260 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
209281 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
209302 AGAG
1 AGAG
209306 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:210680 original size:13 final size:12
Alignment explanation
Indices: 210640--210681 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
210630 TTGCTTATTT
210640 TTGA-TTGTTAA
1 TTGATTTGTTAA
*
210651 TTGATTTGTAAA
1 TTGATTTGTTAA
210663 GTTGATTTGTTTAA
1 -TTGATTTG-TTAA
210677 TTGAT
1 TTGAT
210682 GTTACATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 6 0.23
13 13 0.50
14 3 0.12
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (12 bp):
TTGATTTGTTAA
Found at i:210843 original size:33 final size:33
Alignment explanation
Indices: 210784--210909 Score: 177
Period size: 33 Copynumber: 3.8 Consensus size: 33
210774 TATCGCTTCG
*
210784 CGTTGCGATTTTCATTTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
* **
210818 CGTTGCGATTTTCATTTCGCATTGCGAAAT-TAG
1 CGTTGCGATTTTCATTTCGCATTGCG-ATTCTCT
210851 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
210884 C-TT-CGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
210910 AGTTAATTTC
Statistics
Matches: 83, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
31 23 0.28
32 4 0.05
33 40 0.48
34 16 0.19
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:210844 original size:19 final size:19
Alignment explanation
Indices: 210780--210909 Score: 69
Period size: 14 Copynumber: 7.7 Consensus size: 19
210770 GTACTATCGC
*
210780 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
*
210800 TTCGCGTTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
210816 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
210833 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
210847 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
210866 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
*
210881 -TCTC-TT-CGATTTTCAT
1 TTCGCATTGCGATTTTCAT
210897 TTCGCATTGCGAT
1 TTCGCATTGCGAT
210910 AGTTAATTTC
Statistics
Matches: 83, Mismatches: 10, Indels: 35
0.65 0.08 0.27
Matches are distributed among these distances:
12 3 0.04
13 2 0.02
14 23 0.28
16 7 0.08
17 10 0.12
18 5 0.06
19 21 0.25
20 12 0.14
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:210905 original size:64 final size:67
Alignment explanation
Indices: 210783--210908 Score: 222
Period size: 64 Copynumber: 1.9 Consensus size: 67
210773 CTATCGCTTC
*
210783 GCGTTGCGATTTTCATTTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAAAT
1 GCGTTGCGATTTTCATTTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAAAT
210848 TA
66 TA
210850 GCGTTGCGATTTTCA-TTTCGCATTGCGATTCTCTC-TT-CGATTTTCATTTCGCATTGCGA
1 GCGTTGCGATTTTCATTTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGA
210909 TAGTTAATTT
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
64 22 0.38
65 2 0.03
66 19 0.33
67 15 0.26
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.44
Consensus pattern (67 bp):
GCGTTGCGATTTTCATTTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGAAAT
TA
Found at i:214310 original size:20 final size:20
Alignment explanation
Indices: 214281--214331 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
214271 ATTCATTTGA
*
214281 CTATCACAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
214301 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
214321 TTATCGCAACG
1 CTATCGCAACG
214332 AAAATCGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:214404 original size:18 final size:18
Alignment explanation
Indices: 214355--214419 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
214345 GAAATGAAAA
*
214355 TCGCATTGCGATTT--TC
1 TCGCATTGCGATTTCATT
214371 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
214388 TCGCATTGTGATTTCATT
1 TCGCATTGCGATTTCATT
214406 TCGCATTGCGATTT
1 TCGCATTGCGATTT
214420 TCTCATTGCG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
14 6 0.15
15 3 0.07
16 3 0.07
17 4 0.10
18 20 0.49
19 5 0.12
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:214557 original size:14 final size:14
Alignment explanation
Indices: 214538--214574 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
214528 CATCAATTAA
214538 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
214552 ACAAATCATCTTTT
1 ACAAATCAACATTT
214566 ACAAATCAA
1 ACAAATCAA
214575 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:216437 original size:16 final size:16
Alignment explanation
Indices: 216416--216495 Score: 67
Period size: 16 Copynumber: 4.9 Consensus size: 16
216406 GAAACTTAAA
216416 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
216432 ATCGCAACGCGAAATGG
1 ATCGCAACGCGAAAT-G
* * *
216449 CTAGCAATGCGAAATG
1 ATCGCAACGCGAAATG
216465 AAAATCGCAACGAC-AAA--
1 ---ATCGCAACG-CGAAATG
216482 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
216496 CACAAATCGC
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
13 1 0.02
14 12 0.23
16 16 0.31
17 13 0.25
19 9 0.17
20 1 0.02
ACGTcount: A:0.42, C:0.24, G:0.23, T:0.11
Consensus pattern (16 bp):
ATCGCAACGCGAAATG
Found at i:216494 original size:33 final size:29
Alignment explanation
Indices: 216413--216495 Score: 76
Period size: 33 Copynumber: 2.6 Consensus size: 29
216403 CACGAAACTT
216413 AAAATCGCAACGCGAAATGATCGCAACGC
1 AAAATCGCAACGCGAAATGATCGCAACGC
* *
216442 GAAATGGCTAGCAATGCGAAATGAAAATCGCAACGAC
1 AAAAT--C--GCAACGCGAAATG---ATCGCAACG-C
216479 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
216496 CACAAATCGC
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
29 4 0.10
31 1 0.02
33 22 0.52
35 1 0.02
36 9 0.21
37 5 0.12
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.11
Consensus pattern (29 bp):
AAAATCGCAACGCGAAATGATCGCAACGC
Found at i:216526 original size:14 final size:14
Alignment explanation
Indices: 216507--216562 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
216497 ACAAATCGCA
216507 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
216521 TTGCGATTTCATTTCG
1 TTGCGATTT--TGTCG
216537 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
*
216553 TTGCAATTTT
1 TTGCGATTTT
216563 CATTTCGTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 18 0.51
16 8 0.23
18 9 0.26
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.50
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:216543 original size:32 final size:33
Alignment explanation
Indices: 216502--216578 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 33
216492 GAAACACAAA
*
216502 TCGCATTGCGATTTTGTCGTTGCGA-TTTCATT
1 TCGCATTGCGATTTTGTCGTTGCAATTTTCATT
216534 TCGCATTGCGATTTTGTCGTTGCAATTTTCATT
1 TCGCATTGCGATTTTGTCGTTGCAATTTTCATT
*
216567 TCGTATTGCGAT
1 TCGCATTGCGAT
216579 AGCCATTTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
32 24 0.57
33 18 0.43
ACGTcount: A:0.14, C:0.18, G:0.21, T:0.47
Consensus pattern (33 bp):
TCGCATTGCGATTTTGTCGTTGCAATTTTCATT
Found at i:216544 original size:18 final size:16
Alignment explanation
Indices: 216502--216552 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
216492 GAAACACAAA
216502 TCGCATTGCGATTTTG
1 TCGCATTGCGATTTTG
*
216518 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTT--TG
216534 TCGCATTGCGATTTTG
1 TCGCATTGCGATTTTG
216550 TCG
1 TCG
216553 TTGCAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.31
16 11 0.38
18 9 0.31
ACGTcount: A:0.12, C:0.20, G:0.24, T:0.45
Consensus pattern (16 bp):
TCGCATTGCGATTTTG
Found at i:216585 original size:19 final size:19
Alignment explanation
Indices: 216563--216616 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
216553 TTGCAATTTT
*
216563 CATTTCGTATTGCGATAGC
1 CATTTCGTGTTGCGATAGC
* *
216582 CATTTCCGCGTTGCGATAGT
1 CATTT-CGTGTTGCGATAGC
216602 CATTTCGTGTTGCGA
1 CATTTCGTGTTGCGA
216617 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (19 bp):
CATTTCGTGTTGCGATAGC
Found at i:217119 original size:18 final size:18
Alignment explanation
Indices: 217098--217135 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
217088 GATCAGATGA
*
217098 TCTGGGTGAGGTGATAGC
1 TCTGGGCGAGGTGATAGC
*
217116 TCTGGGCGAGGTGATGGC
1 TCTGGGCGAGGTGATAGC
217134 TC
1 TC
217136 CCGAAGTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.16, G:0.45, T:0.26
Consensus pattern (18 bp):
TCTGGGCGAGGTGATAGC
Found at i:218668 original size:20 final size:21
Alignment explanation
Indices: 218643--218690 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
218633 TCTGAGAGAT
218643 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
218663 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
218685 -GAGATG
1 GGAGATG
218691 GGTGAGAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 7 0.29
21 5 0.21
22 12 0.50
ACGTcount: A:0.23, C:0.15, G:0.42, T:0.21
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:218690 original size:21 final size:22
Alignment explanation
Indices: 218650--218692 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
218640 GATGGAGATA
218650 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
218672 GACGGATTTCGTC-GAGATGGG
1 GACGGATTTCGCCGGAGATGGG
218693 TGAGAGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.19, C:0.16, G:0.44, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:218944 original size:20 final size:20
Alignment explanation
Indices: 218919--218972 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
218909 GATTTTTTAT
218919 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
218939 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTCAG
218959 TATCGCATTGCGAT
1 TATCGCATTGCGAT
218973 TTTCCCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTCAG
Found at i:218973 original size:61 final size:62
Alignment explanation
Indices: 218858--218975 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 62
218848 CGCTTTGAAA
* * * *
218858 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTAAGTATCTCGTTACGATTTTTTATT
1 ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTAAGTATCGCATTACGATTTTTTATT
* * *
218920 ATCGCATTGCGA-TA-GTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGATTATGT-AGTATCGCATTGCGAAAGTAAGTATCGCATTACGATTTT
218976 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 2 0.04
61 34 0.71
62 12 0.25
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (62 bp):
ATCGCATTGCGATTATGTAGTATCGCATTGCGAAAGTAAGTATCGCATTACGATTTTTTATT
Found at i:219006 original size:41 final size:41
Alignment explanation
Indices: 218961--219053 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
218951 ATAGTCAGTA
*
218961 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTATTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
219002 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
219043 TCGCATTGCGA
1 TCGCATTGCGA
219054 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:219026 original size:21 final size:21
Alignment explanation
Indices: 218961--219053 Score: 93
Period size: 20 Copynumber: 4.5 Consensus size: 21
218951 ATAGTCAGTA
218961 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* **
218982 TCGCGTTGCGATTTAT--TTAT
1 TCGCATTGCGATTT-TCCCAAT
219002 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
219023 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
219043 TCGCATTGCGA
1 TCGCATTGCGA
219054 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 7
0.76 0.14 0.09
Matches are distributed among these distances:
19 1 0.02
20 31 0.53
21 25 0.43
22 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:221682 original size:59 final size:58
Alignment explanation
Indices: 221608--221778 Score: 183
Period size: 60 Copynumber: 3.0 Consensus size: 58
221598 TCAGTTACAT
*
221608 GTACTC-GAGTGTTGAGCATTTTAT-AGAATAGATCTAATATGTTACAGTCTAGATAAAAA
1 GTACTCAG-GTGTTGAGCATTTTATAAAAATA-ATCTAATATGTTACAGT-TAGATAAAAA
* * * *
221667 GTACTCAGGTGTTGAGCGTTTTATAAAAATAAATCTAATATGTTGCAATTTAGATAAAAG
1 GTACTCAGGTGTTGAGCATTTTATAAAAAT-AATCTAATATGTTAC-AGTTAGATAAAAA
* * *
221727 GAACTCA--AGTT-AGAATTTTATAAAAATAA-CTAATATGTTACAGTTAGATAAA
1 GTACTCAGGTGTTGAGCATTTTATAAAAATAATCTAATATGTTACAGTTAGATAAA
221779 GGTAAAAATA
Statistics
Matches: 97, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
54 10 0.10
55 11 0.11
56 2 0.02
57 14 0.14
58 3 0.03
59 21 0.22
60 33 0.34
61 3 0.03
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (58 bp):
GTACTCAGGTGTTGAGCATTTTATAAAAATAATCTAATATGTTACAGTTAGATAAAAA
Found at i:224877 original size:209 final size:212
Alignment explanation
Indices: 224517--224939 Score: 809
Period size: 209 Copynumber: 2.0 Consensus size: 212
224507 AATAGCTTCT
224517 TTTCCTGCATGTGATTATGTTTACTTCTTATTCTCTTTTAAACATATACTGCTTATGCCTAACTA
1 TTTCCTGCATGTGATTATGTTTACTTCTTATTCTCTTTTAAACATATACTGCTTATGCCTAACTA
224582 AGAATAACATATTACAATATTCACCTTTCATTACTTGAATTTTAAGATATAAATCTAACTCAAAC
66 AGAATAACATATTACAATATTCACCTTTCATTACTTGAATTTTAAGATATAAATCTAACTCAAAC
224647 CTGCTAATGCTTATAAGAAT-AATC-TGAATTTGTT-GTCCAGGAATCCTAG-AAAGATGAAGAG
131 CTGCTAATGCTTATAAGAATAAATCTTGAATTTGTTGGTCCAGGAATCCTAGAAAAGATGAAGAG
224708 GGATATTGTGTTATCTA
196 GGATATTGTGTTATCTA
224725 TTTCCTGCATGTGATTATGTTTTACTTCTTATTCTCTTTTAAACATATACTGCTTATGCCTAACT
1 TTTCCTGCATGTGATTATG-TTTACTTCTTATTCTCTTTTAAACATATACTGCTTATGCCTAACT
224790 AAGAATAACATATTACAATATTCACCTTTCATTACTTGAATTTTAAGATATAAATCTAACTCAAA
65 AAGAATAACATATTACAATATTCACCTTTCATTACTTGAATTTTAAGATATAAATCTAACTCAAA
224855 CCTGCTAATGCTTATAAGAATAAATCTTGAATTTGTTGGTCCAGGAATCCTAGAAAAGATGAAGA
130 CCTGCTAATGCTTATAAGAATAAATCTTGAATTTGTTGGTCCAGGAATCCTAGAAAAGATGAAGA
224920 GGGATATTGTGTTATCTA
195 GGGATATTGTGTTATCTA
224938 TT
1 TT
224940 GCTAGAACAG
Statistics
Matches: 210, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
208 19 0.09
209 131 0.62
210 4 0.02
211 10 0.05
212 15 0.07
213 31 0.15
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (212 bp):
TTTCCTGCATGTGATTATGTTTACTTCTTATTCTCTTTTAAACATATACTGCTTATGCCTAACTA
AGAATAACATATTACAATATTCACCTTTCATTACTTGAATTTTAAGATATAAATCTAACTCAAAC
CTGCTAATGCTTATAAGAATAAATCTTGAATTTGTTGGTCCAGGAATCCTAGAAAAGATGAAGAG
GGATATTGTGTTATCTA
Found at i:231676 original size:27 final size:28
Alignment explanation
Indices: 231617--231678 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
231607 TTTTTTTTAG
* * *
231617 AATAATGAGTTGGTAAAAAGTGGTCAAT
1 AATAATAATTTGGTAAAAAGTGGTAAAT
*
231645 AATAATAATTTGGTAAGAA-TGGTAAAT
1 AATAATAATTTGGTAAAAAGTGGTAAAT
*
231672 CATAATA
1 AATAATA
231679 TCAATAATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.31
Consensus pattern (28 bp):
AATAATAATTTGGTAAAAAGTGGTAAAT
Found at i:234592 original size:17 final size:18
Alignment explanation
Indices: 234557--234589 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
234547 ATGTTTTTGA
234557 TATAAAATAGAACTAAAT
1 TATAAAATAGAACTAAAT
234575 TATAAAA-AGAA-TAAA
1 TATAAAATAGAACTAAA
234590 ATTGTTGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 4 0.27
18 7 0.47
ACGTcount: A:0.67, C:0.03, G:0.06, T:0.24
Consensus pattern (18 bp):
TATAAAATAGAACTAAAT
Found at i:242529 original size:24 final size:23
Alignment explanation
Indices: 242501--242550 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
242491 TTTGTGTTTC
242501 TTTTTAAAATATATATAATTTTAT
1 TTTTTAAAATATATATAATTTT-T
* *
242525 TTTTTAAATTTTATATAATTTTT
1 TTTTTAAAATATATATAATTTTT
242548 TTT
1 TTT
242551 AAATTATCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTTAAAATATATATAATTTTT
Found at i:250909 original size:2 final size:2
Alignment explanation
Indices: 250902--250949 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
250892 AAATCTATTA
250902 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
250944 AT AT AT
1 AT AT AT
250950 TACTTTATCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:252239 original size:29 final size:29
Alignment explanation
Indices: 252184--252240 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
252174 AGTGTTAGCC
* *
252184 GTAGGTCGTCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGAGCGACCTT
*
252213 GTAGGTCGCCATGCACTCCGAGTGACCT
1 GTAGGTCGCCATGCACTCCGAGCGACCT
252241 ACCCTTGCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.23
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGAGCGACCTT
Found at i:252430 original size:23 final size:21
Alignment explanation
Indices: 252394--252451 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 21
252384 GCTCGGTTGC
**
252394 CTTCGGATTCCCTCGCATAGCT
1 CTTCGGATGGCCTCGCAT-GCT
*
252416 CGTTCGGATGGCCTCGGATGCT
1 C-TTCGGATGGCCTCGCATGCT
252438 C-TCGGATGGCCTCG
1 CTTCGGATGGCCTCG
252452 GTCGGATGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 13 0.41
22 5 0.16
23 14 0.44
ACGTcount: A:0.10, C:0.33, G:0.29, T:0.28
Consensus pattern (21 bp):
CTTCGGATGGCCTCGCATGCT
Found at i:252433 original size:33 final size:33
Alignment explanation
Indices: 252362--252464 Score: 109
Period size: 33 Copynumber: 3.1 Consensus size: 33
252352 CCTACCCTCG
* *
252362 CTCGGCTTCCCTCGCATAGCTCGCTCGG-TTGC
1 CTCGGATTCCCTCGCATAGCTCGCTCGGATGGC
*
252394 CTTCGGATTCCCTCGCATAGCTCGTTCGGATGGC
1 C-TCGGATTCCCTCGCATAGCTCGCTCGGATGGC
* * * * *
252428 CTCGGATGCTCTCGGATGGCCTCGGTCGGATGGC
1 CTCGGATTCCCTCGCATAG-CTCGCTCGGATGGC
252462 CTC
1 CTC
252465 AGATGCCCAG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
32 1 0.02
33 39 0.65
34 20 0.33
ACGTcount: A:0.09, C:0.35, G:0.29, T:0.27
Consensus pattern (33 bp):
CTCGGATTCCCTCGCATAGCTCGCTCGGATGGC
Found at i:252434 original size:10 final size:10
Alignment explanation
Indices: 252419--252452 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
252409 CATAGCTCGT
252419 TCGGATGGCC
1 TCGGATGGCC
252429 TCGGAT-GCTC
1 TCGGATGGC-C
252439 TCGGATGGCC
1 TCGGATGGCC
252449 TCGG
1 TCGG
252453 TCGGATGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.09
10 18 0.82
11 2 0.09
ACGTcount: A:0.09, C:0.29, G:0.38, T:0.24
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:252546 original size:29 final size:29
Alignment explanation
Indices: 252509--252566 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
252499 GCAATCTCTT
* * *
252509 GTAGTTCGCCGGGAATACATGGCGACCTA
1 GTAGGTCGCCCGGAAGACATGGCGACCTA
* *
252538 GTAGGTCGCCCGTAAGGCATGGCGACCTA
1 GTAGGTCGCCCGGAAGACATGGCGACCTA
252567 CGGCCAACAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.22, C:0.26, G:0.33, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCCGGAAGACATGGCGACCTA
Found at i:253464 original size:42 final size:41
Alignment explanation
Indices: 253398--253561 Score: 152
Period size: 42 Copynumber: 3.9 Consensus size: 41
253388 AGGTGAGTTC
* *
253398 CATAATTATTTTAATCTAACTTTTTATATTTATAGTTAAGACT
1 CATAATT-TTTTCATCTAACTTTTTA-ATTTATAATTAAGACT
* * * *
253441 CTTAATTTTTTCATCTCATTTTTTAATTTTATAATTGAGGA-T
1 CATAATTTTTTCATCTAACTTTTTAA-TTTATAATT-AAGACT
*
253483 CATAATTTTTTCAATCTAACTTTTTACATTTATAATTAAGACC
1 CATAATTTTTTC-ATCTAACTTTTTA-ATTTATAATTAAGACT
* * *
253526 CCTAATTTTTTCAT-TCCACTTTTTACCTTTATAATT
1 CATAATTTTTTCATCT-AACTTTTTA-ATTTATAATT
253562 GAGTCCCCTT
Statistics
Matches: 101, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
41 2 0.02
42 58 0.57
43 40 0.40
44 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.04, T:0.52
Consensus pattern (41 bp):
CATAATTTTTTCATCTAACTTTTTAATTTATAATTAAGACT
Found at i:253507 original size:85 final size:85
Alignment explanation
Indices: 253398--254131 Score: 263
Period size: 85 Copynumber: 8.6 Consensus size: 85
253388 AGGTGAGTTC
* * * * *
253398 CATAATTATTTTAATCTAACTTTTTATATTTATAGTTAAGACTCTTAATTTTTTCA-TCTCATTT
1 CATAATTATTTTAATCTAACTTTTTACATTTATAATTAAGACCCCTAATTTTTTCATTC-CACTT
*
253462 TTTAATTTTATAATTGAGGAT
65 TTTAACTTTATAATTGAGGAT
253483 CATAATT-TTTTCAATCTAACTTTTTACATTTATAATTAAGACCCCTAATTTTTTCATTCCACTT
1 CATAATTATTTT-AATCTAACTTTTTACATTTATAATTAAGACCCCTAATTTTTTCATTCCACTT
* ***
253547 TTTACCTTTATAATTGAGTCC
65 TTTAACTTTATAATTGAGGAT
* * * ** * * * * * *
253568 CCTTATT-TTGTTCATCCCACGTTTTA-ATTTTATATTTGAGGCCCTTAATTTTTTTTAATAT-C
1 CATAATTATT-TTAATCTAACTTTTTACA-TTTATAATTAAGACCCCTAA--TTTTTTCAT-TCC
* * * * **
253630 ACTTTCTACCTTTATGATTGAAGCC
61 ACTTTTTAACTTTATAATTGAGGAT
* * * * * * ** * *
253655 CTTAATTTTTTTTATTCTCACTTTTTACTTTTATAATTGAGGTCCTTAATTTTTTCAATCTCACT
1 CATAA-TTATTTTAATCTAACTTTTTACATTTATAATTAAGACCCCTAATTTTTTCATTC-CACT
* * * *
253720 TTATAGCTTTATAATTGA-AAC
64 TTTTAACTTTATAATTGAGGAT
* * * * *** * *
253741 CTATAATT-TTTTGAATCTCACTTTTTACCTTTACAGCTT-AGGTTCCTAA-TTTTTGAATCTCA
1 C-ATAATTATTTT-AATCTAACTTTTTACATTTATA-ATTAAGACCCCTAATTTTTTCATTC-CA
* * * **
253803 CTTTTTATCTTTATAATTAATGCC
62 CTTTTTAACTTTATAATTGAGGAT
* * * * * * *
253827 CCTAATT-TTTTGAATTTCACTTTCTATC-TTTATAATTGAAG--CCCTAATTTTTGCAATCTAC
1 CATAATTATTTT-AATCTAACTTTTTA-CATTTATAATT-AAGACCCCTAATTTTTTCATTCCAC
* * * *
253888 ATTTTACCTTTATAATCGAAG-T
63 TTTTTAACTTTATAATTGAGGAT
* * * * *** ** * *
253910 CCCTAATTTTTTTAATCTTACTTTTTATATTTATAACCGAGACCATTCATTTTTTCAATCTCACT
1 -CATAATTATTTTAATCTAACTTTTTACATTTATAATTAAGACCCCTAATTTTTTCATTC-CACT
* * *
253975 TTTTATCTTTATAACTAAGG-T
64 TTTTAACTTTATAATTGAGGAT
* * * * *
253996 CCTTAATT-TTTTCAATCTAACATTCTATC-TTTATAATTGAAG-CCCATAGTTCTTTT-ATAT-
1 -CATAATTATTTT-AATCTAACTTTTTA-CATTTATAATT-AAGACCCCTAATT-TTTTCAT-TC
*
254056 CACTTTTTAGCTTTATAATTGAGG-T
60 CACTTTTTAACTTTATAATTGAGGAT
* * * *
254081 CCCA-AATT-TTCTAATCCAACTTTTTACTTTTATAATTTAGACCCCTAATTT
1 --CATAATTATTTTAATCTAACTTTTTACATTTATAATTAAGACCCCTAATTT
254132 AATCATTTTT
Statistics
Matches: 504, Mismatches: 111, Indels: 70
0.74 0.16 0.10
Matches are distributed among these distances:
83 6 0.01
84 82 0.16
85 219 0.43
86 98 0.19
87 64 0.13
88 33 0.07
89 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (85 bp):
CATAATTATTTTAATCTAACTTTTTACATTTATAATTAAGACCCCTAATTTTTTCATTCCACTTT
TTAACTTTATAATTGAGGAT
Found at i:253650 original size:87 final size:86
Alignment explanation
Indices: 253511--253737 Score: 237
Period size: 87 Copynumber: 2.6 Consensus size: 86
253501 ACTTTTTACA
* * * *
253511 TTTATAATTAAGACCCCTAATTTTTTC-AT-TCCACTTTTTACCTTTATAATTGAGTCCCCTT-A
1 TTTATAATTGAGGCCCTTAATTTTTTCAATAT-CACTTTATACCTTTATAATTGAG--CCCTTAA
253573 TTTTGTTCA-TCCCACGTTTTAAT
63 TTTTGTTCATTCCCACGTTTTAAT
* * * *
253596 TTTATATTTGAGGCCCTTAATTTTTTTTAATATCACTTTCTACCTTTATGATTGAAGCCCTTAAT
1 TTTATAATTGAGGCCCTTAA-TTTTTTCAATATCACTTTATACCTTTATAATTG-AGCCCTTAAT
* * * * *
253661 TTTTTTTATTCTCACTTTTTACT
64 TTTGTTCATTCCCACGTTTTAAT
* * *
253684 TTTATAATTGAGGTCCTTAATTTTTTCAATCTCACTTTATAGCTTTATAATTGA
1 TTTATAATTGAGGCCCTTAATTTTTTCAATATCACTTTATACCTTTATAATTGA
253738 AACCTATAAT
Statistics
Matches: 117, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
85 16 0.14
86 12 0.10
87 57 0.49
88 32 0.27
ACGTcount: A:0.24, C:0.18, G:0.07, T:0.51
Consensus pattern (86 bp):
TTTATAATTGAGGCCCTTAATTTTTTCAATATCACTTTATACCTTTATAATTGAGCCCTTAATTT
TGTTCATTCCCACGTTTTAAT
Found at i:253656 original size:44 final size:43
Alignment explanation
Indices: 253400--254117 Score: 422
Period size: 43 Copynumber: 16.8 Consensus size: 43
253390 GTGAGTTCCA
* ** * *
253400 TAATTATTTT-AATCTAACTTTTTATATTTATAGTT-AAGACTCT
1 TAATT-TTTTGAATCTCACTTTTTACCTTTATAATTGAAG-CCCT
* * ** * ** *
253443 TAATTTTTT-CATCTCATTTTTTAATTTTATAATTGAGGATCA
1 TAATTTTTTGAATCTCACTTTTTACCTTTATAATTGAAGCCCT
* * * *
253485 TAATTTTTTCAATCTAACTTTTTACATTTATAATT-AAGACCCC
1 TAATTTTTTGAATCTCACTTTTTACCTTTATAATTGAAG-CCCT
* *
253528 TAATTTTTTCATTC-CACTTTTTACCTTTATAATTG-AGTCCCCT
1 TAATTTTTTGAATCTCACTTTTTACCTTTATAATTGAAG--CCCT
* * * ** * *
253571 T-ATTTTGTT-CATCCCACGTTTTAATTTTATATTTGAGGCCCT
1 TAATTTT-TTGAATCTCACTTTTTACCTTTATAATTGAAGCCCT
* * * *
253613 TAATTTTTTTTAATATCACTTTCTACCTTTATGATTGAAGCCCT
1 TAA-TTTTTTGAATCTCACTTTTTACCTTTATAATTGAAGCCCT
* * * * *
253657 TAATTTTTTTTATTCTCACTTTTTACTTTTATAATTGAGGTCCT
1 TAA-TTTTTTGAATCTCACTTTTTACCTTTATAATTGAAGCCCT
* * * *
253701 TAATTTTTTCAATCTCACTTTATAGCTTTATAATTGAA-ACCT
1 TAATTTTTTGAATCTCACTTTTTACCTTTATAATTGAAGCCCT
* * * *
253743 ATAATTTTTTGAATCTCACTTTTTACCTTTACAGCTT-AGGTTCC-
1 -TAATTTTTTGAATCTCACTTTTTACCTTTATA-ATTGAAG-CCCT
* *
253787 TAA-TTTTTGAATCTCACTTTTTATCTTTATAATT-AATGCCCC
1 TAATTTTTTGAATCTCACTTTTTACCTTTATAATTGAA-GCCCT
* * *
253829 TAATTTTTTGAATTTCACTTTCTATCTTTATAATTGAAGCCC-
1 TAATTTTTTGAATCTCACTTTTTACCTTTATAATTGAAGCCCT
* *
253871 TAA-TTTTTGCAATCT-ACATTTTACCTTTATAATCGAAGTCCC-
1 TAATTTTTTG-AATCTCACTTTTTACCTTTATAATTGAAG-CCCT
* * ** ** *
253913 TAATTTTTTTAATCTTACTTTTTATATTTATAACCG-AGACCAT
1 TAATTTTTTGAATCTCACTTTTTACCTTTATAATTGAAG-CCCT
* * * * *
253956 TCATTTTTTCAATCTCACTTTTTATCTTTATAACT-AAGGTCCT
1 TAATTTTTTGAATCTCACTTTTTACCTTTATAATTGAA-GCCCT
* * * * * *
253999 TAATTTTTTCAATCTAACATTCTATCTTTATAATTGAAGCCCA
1 TAATTTTTTGAATCTCACTTTTTACCTTTATAATTGAAGCCCT
* * * *
254042 TAGTTCTTTT--ATATCACTTTTTAGCTTTATAATTGAGGTCCC-
1 TAATT-TTTTGAATCTCACTTTTTACCTTTATAATTGAAG-CCCT
* * *
254084 AAATTTTCT-AATC-CAACTTTTTACTTTTATAATT
1 TAATTTTTTGAATCTC-ACTTTTTACCTTTATAATT
254118 TAGACCCCTA
Statistics
Matches: 537, Mismatches: 107, Indels: 63
0.76 0.15 0.09
Matches are distributed among these distances:
41 34 0.06
42 167 0.31
43 255 0.47
44 79 0.15
45 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (43 bp):
TAATTTTTTGAATCTCACTTTTTACCTTTATAATTGAAGCCCT
Found at i:253833 original size:128 final size:126
Alignment explanation
Indices: 253670--253899 Score: 311
Period size: 128 Copynumber: 1.8 Consensus size: 126
253660 TTTTTTTTAT
* * *
253670 TCTCACTTTTTACTTTTATAATTGAGGTCCTTAATTTTTTCAATCTCACTTTATAGCTTTATAAT
1 TCTCACTTTTTACTTTTATAATTAAGGCCCCTAATTTTTTCAATCTCACTTTATAGCTTTATAAT
*
253735 TGAAACCTATAATTTTTTG-AATCTCACTTTTTACCTTTACAGCTTAGGTTCCTAATTTTTGAA
66 TGAAACC-ATAA-TTTTTGCAATCT-ACATTTTACCTTTACAGCTTAGGTTCCTAATTTTTGAA
* * * * *
253798 TCTCACTTTTTA-TCTTTATAATTAATGCCCCTAATTTTTTGAATTTCACTTTCTATCTTTATAA
1 TCTCACTTTTTACT-TTTATAATTAAGGCCCCTAATTTTTTCAATCTCACTTTATAGCTTTATAA
* *
253862 TTGAAGCCCTAATTTTTGCAATCTACATTTTACCTTTA
65 TTGAAACCATAATTTTTGCAATCTACATTTTACCTTTA
253900 TAATCGAAGT
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
126 19 0.21
127 9 0.10
128 61 0.69
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.50
Consensus pattern (126 bp):
TCTCACTTTTTACTTTTATAATTAAGGCCCCTAATTTTTTCAATCTCACTTTATAGCTTTATAAT
TGAAACCATAATTTTTGCAATCTACATTTTACCTTTACAGCTTAGGTTCCTAATTTTTGAA
Found at i:253964 original size:212 final size:215
Alignment explanation
Indices: 253618--254077 Score: 522
Period size: 212 Copynumber: 2.2 Consensus size: 215
253608 GCCCTTAATT
* ** * *
253618 TTTTTTAATATCACTTTCTACCTTTATGATTGAAGCCCTTAATTTTTTTTATTCTCACTTTTTAC
1 TTTTTTAATATCACTTTCTACCTTTATAATTGAAGCCCTTAATTTTTTGCAATCTCACATTTTAC
* * * * * **
253683 TTTTATAATTGAGGTCCTTAATTTTTTCAATCTCACTTTATAGCTTTATAATTGAAACCTATAAT
66 CTTTATAATCGAAGTCCCTAATTTTTTCAATCTCACTTTATAGATTTATAACCGAAACCTATAAT
* * * * * * *
253748 TTTTTGAATCTCACTTTTTACCTTTACAGCTTAGGTTCC-TAA-TTTTTGAATCTCACTTTTTAT
131 TTTTTCAATCTCACTTTTTACCTTTACAACTAAGG-TCCTTAATTTTTTCAATCTAACATTCTAT
*
253811 CTTTATAATT-AATGCCCCTAA
195 CTTTATAATTGAA-GCCCATAA
* *
253832 TTTTTTGAATTTCACTTTCTATCTTTATAATTGAAGCCC-TAA-TTTTTGCAATCT-ACATTTTA
1 TTTTTT-AATATCACTTTCTACCTTTATAATTGAAGCCCTTAATTTTTTGCAATCTCACATTTTA
* * * * * *
253894 CCTTTATAATCGAAGTCCCTAATTTTTTTAATCTTACTTTTTATATTTATAACCGAGACC-ATTC
65 CCTTTATAATCGAAGTCCCTAATTTTTTCAATCTCACTTTATAGATTTATAACCGAAACCTA-TA
* *
253958 ATTTTTTCAATCTCACTTTTTATCTTTATAACTAAGGTCCTTAATTTTTTCAATCTAACATTCTA
129 ATTTTTTCAATCTCACTTTTTACCTTTACAACTAAGGTCCTTAATTTTTTCAATCTAACATTCTA
*
254023 TCTTTATAATTGAAGCCCATAG
194 TCTTTATAATTGAAGCCCATAA
* *
254045 TTCTTTT-ATATCACTTTTTAGCTTTATAATTGA
1 TT-TTTTAATATCACTTTCTACCTTTATAATTGA
254078 GGTCCCAAAT
Statistics
Matches: 206, Mismatches: 34, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
211 4 0.02
212 114 0.55
213 44 0.21
214 15 0.07
215 29 0.14
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.50
Consensus pattern (215 bp):
TTTTTTAATATCACTTTCTACCTTTATAATTGAAGCCCTTAATTTTTTGCAATCTCACATTTTAC
CTTTATAATCGAAGTCCCTAATTTTTTCAATCTCACTTTATAGATTTATAACCGAAACCTATAAT
TTTTTCAATCTCACTTTTTACCTTTACAACTAAGGTCCTTAATTTTTTCAATCTAACATTCTATC
TTTATAATTGAAGCCCATAA
Found at i:254105 original size:170 final size:170
Alignment explanation
Indices: 253790--254115 Score: 417
Period size: 170 Copynumber: 1.9 Consensus size: 170
253780 AGGTTCCTAA
* * * * * * *
253790 TTTTTGAATCTCACTTTTTATCTTTATAATTAATGCCCCTAATTTTTTGAATTTCACTTTCTATC
1 TTTTTCAATCTCACTTTTTATCTTTATAACTAAGGCCCCTAATTTTTTCAATCTAACATTCTATC
*
253855 TTTATAATTGAAGCCCTAATTTTTGCAATCTACATTTTACCTTTATAATCGAAGTCCCTAATTTT
66 TTTATAATTGAAGCCCTAATTTTTGCAATCTACATTTTACCTTTATAATCGAAGTCCCTAAATTT
* **
253920 TTTAATCTTACTTTTTA-TATTTATAACCGAGACCATTCAT
131 TCTAATCCAACTTTTTACT-TTTATAACCGAGACCATTCAT
* *
253960 TTTTTCAATCTCACTTTTTATCTTTATAACTAAGGTCCTTAATTTTTTCAATCTAACATTCTATC
1 TTTTTCAATCTCACTTTTTATCTTTATAACTAAGGCCCCTAATTTTTTCAATCTAACATTCTATC
* * * * * *
254025 TTTATAATTGAAGCCCATAGTTCTTT-TATATC-ACTTTTTAGCTTTATAATTGAGGTCCC-AAA
66 TTTATAATTGAAGCCC-TAATT-TTTGCA-ATCTACATTTTACCTTTATAATCGAAGTCCCTAAA
254087 TTTTCTAATCCAACTTTTTACTTTTATAA
128 TTTTCTAATCCAACTTTTTACTTTTATAA
254116 TTTAGACCCC
Statistics
Matches: 133, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
170 98 0.74
171 29 0.22
172 6 0.05
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (170 bp):
TTTTTCAATCTCACTTTTTATCTTTATAACTAAGGCCCCTAATTTTTTCAATCTAACATTCTATC
TTTATAATTGAAGCCCTAATTTTTGCAATCTACATTTTACCTTTATAATCGAAGTCCCTAAATTT
TCTAATCCAACTTTTTACTTTTATAACCGAGACCATTCAT
Found at i:254496 original size:22 final size:24
Alignment explanation
Indices: 254439--254497 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
254429 TATATTTTTA
* *
254439 TTAAAATTTAAAATATAAATTATT
1 TTAATATTTTAAATATAAATTATT
**
254463 TTAATAAATTAAATATAAA-TA-T
1 TTAATATTTTAAATATAAATTATT
254485 TTAATATTTTAAA
1 TTAATATTTTAAA
254498 ATTTATTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
22 12 0.41
23 2 0.07
24 15 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TTAATATTTTAAATATAAATTATT
Found at i:260487 original size:29 final size:29
Alignment explanation
Indices: 260435--260557 Score: 120
Period size: 29 Copynumber: 4.1 Consensus size: 29
260425 AATTTAATAC
* *
260435 TTGTACTTTGACAGAATATTTAATGTGATAT
1 TTGTACTTTTA-A-AATATCTAATGTGATAT
* *
260466 TTATACTTTTAAAATATCTAATTTGATAT
1 TTGTACTTTTAAAATATCTAATGTGATAT
* * * *
260495 TTGTATTTTTAAAATGTCTAATATAATAT
1 TTGTACTTTTAAAATATCTAATGTGATAT
* *
260524 TTGTACTTTAAAGAAAATCTAATGTGATACT
1 TTGTACTTTTAA-AATATCTAATGTGATA-T
260555 TTG
1 TTG
260558 ACAAAATATT
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
29 49 0.65
30 13 0.17
31 13 0.17
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (29 bp):
TTGTACTTTTAAAATATCTAATGTGATAT
Found at i:266831 original size:35 final size:35
Alignment explanation
Indices: 266768--266853 Score: 111
Period size: 35 Copynumber: 2.5 Consensus size: 35
266758 AGAAAGGAAG
* *
266768 CAAAACCCTAATT-CAAGTAACTCGTCGTAAATTA
1 CAAAACCCTAATTCCAAGTAAATCATCGTAAATTA
* *
266802 CAAAACTCTAATTCCAAGTAAATCATCGTAAATTG
1 CAAAACCCTAATTCCAAGTAAATCATCGTAAATTA
* *
266837 CGAAACCCTAAATCCAA
1 CAAAACCCTAATTCCAA
266854 ATGGATCAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
34 12 0.27
35 32 0.73
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.24
Consensus pattern (35 bp):
CAAAACCCTAATTCCAAGTAAATCATCGTAAATTA
Found at i:267934 original size:25 final size:26
Alignment explanation
Indices: 267898--267949 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
267888 CTCATTTTAA
*
267898 AAAACTATTTGTTCAACTA-AAAAAC
1 AAAACTATTTGTTCAAATAGAAAAAC
*
267923 AAAA-TATATTGTTTAAATAGAAAAAC
1 AAAACTAT-TTGTTCAAATAGAAAAAC
267949 A
1 A
267950 TTTTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 3 0.13
25 13 0.57
26 7 0.30
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.29
Consensus pattern (26 bp):
AAAACTATTTGTTCAAATAGAAAAAC
Found at i:272720 original size:24 final size:23
Alignment explanation
Indices: 272693--272737 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
272683 GGTGAACGGT
*
272693 TAAATACATACAGAAATTAACTGC
1 TAAAAACATACAGAAA-TAACTGC
*
272717 TAAAAACATTCAGAAATAACT
1 TAAAAACATACAGAAATAACT
272738 TACTTTTCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.53, C:0.16, G:0.07, T:0.24
Consensus pattern (23 bp):
TAAAAACATACAGAAATAACTGC
Found at i:276493 original size:4 final size:4
Alignment explanation
Indices: 276484--276534 Score: 75
Period size: 4 Copynumber: 12.5 Consensus size: 4
276474 TATTATCACA
* *
276484 TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC TACC ATCC TTTCC
1 TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC TTCC -TTCC
276533 TT
1 TT
276535 TCAATATTTG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
4 39 0.93
5 3 0.07
ACGTcount: A:0.04, C:0.47, G:0.00, T:0.49
Consensus pattern (4 bp):
TTCC
Found at i:286223 original size:124 final size:127
Alignment explanation
Indices: 285987--286357 Score: 637
Period size: 124 Copynumber: 2.9 Consensus size: 127
285977 GTATTTTTAT
285987 TTTTTATG-TT-TTGTA-TTTTATGTTTCAAAAAATTAGTATGTTTATTTATCTAATTTCAATGT
1 TTTTTATGTTTGTTGTATTTTTATGTTTCAAAAAATTAGTATGTTTATTTATCTAATTTCAATGT
286049 ATTTTTATCTATCTTGCAATTTAATCTACTTTAATCTAATTTAATCATTAAAAAAATTCTATG
66 A-TTTTATCTATCTTGCAATTTAATCTACTTTAATCTAATTTAATCATTAAAAAAATTCTATG
*
286112 TTTTTATGTTTGTTGTATTTTTATGTTTCAAAAAATTAATATGTTTATTTATCTAATTTCAATGT
1 TTTTTATGTTTGTTGTATTTTTATGTTTCAAAAAATTAGTATGTTTATTTATCTAATTTCAATGT
*
286177 A-TTT-T-TATCTTACAATTTAATCTACTTTAATCTAATTTAATCATTAAAAAAATTCTATG
66 ATTTTATCTATCTTGCAATTTAATCTACTTTAATCTAATTTAATCATTAAAAAAATTCTATG
*
286236 TTTTTATGTTTGTTGTATTTTTATGTTTCAAAAAATTAGTATATTTATTTATCTAATTTCAATGT
1 TTTTTATGTTTGTTGTATTTTTATGTTTCAAAAAATTAGTATGTTTATTTATCTAATTTCAATGT
*
286301 ATTTTCTATCTATCTTGCAATTTAATCTACTTCAATCTAATTTAATCATTAAAAAAA
66 A-TTT-TATCTATCTTGCAATTTAATCTACTTTAATCTAATTTAATCATTAAAAAAA
286358 ATATTTTTTT
Statistics
Matches: 232, Mismatches: 6, Indels: 12
0.93 0.02 0.05
Matches are distributed among these distances:
124 117 0.50
125 9 0.04
126 7 0.03
127 6 0.03
128 48 0.21
129 45 0.19
ACGTcount: A:0.33, C:0.09, G:0.06, T:0.53
Consensus pattern (127 bp):
TTTTTATGTTTGTTGTATTTTTATGTTTCAAAAAATTAGTATGTTTATTTATCTAATTTCAATGT
ATTTTATCTATCTTGCAATTTAATCTACTTTAATCTAATTTAATCATTAAAAAAATTCTATG
Found at i:287250 original size:30 final size:30
Alignment explanation
Indices: 287216--287273 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
287206 TTCTTTTTTC
*
287216 AAATTCCTAATTTCCTAACTCACAATCCCT
1 AAATTCCCAATTTCCTAACTCACAATCCCT
*
287246 AAATTCCCAATTTCCTGACTCACAATCC
1 AAATTCCCAATTTCCTAACTCACAATCC
287274 TTAATTCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.34, G:0.02, T:0.31
Consensus pattern (30 bp):
AAATTCCCAATTTCCTAACTCACAATCCCT
Found at i:287285 original size:21 final size:20
Alignment explanation
Indices: 287261--287299 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
287251 CCCAATTTCC
*
287261 TGACTCACAATCCTTAATTCT
1 TGAC-CACAATCCCTAATTCT
*
287282 TGACCCCAATCCCTAATT
1 TGACCACAATCCCTAATT
287300 TCTCCTCCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.28, C:0.33, G:0.05, T:0.33
Consensus pattern (20 bp):
TGACCACAATCCCTAATTCT
Found at i:287302 original size:21 final size:22
Alignment explanation
Indices: 287250--287302 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
287240 ATCCCTAAAT
*
287250 TCCC-AATTTCCTGACTCACAA
1 TCCCTAATTTCTTGACTCACAA
* *
287271 TCCTTAA-TTCTTGAC-CCCAA
1 TCCCTAATTTCTTGACTCACAA
287291 TCCCTAATTTCT
1 TCCCTAATTTCT
287303 CCTCCAGGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 10 0.38
21 14 0.54
22 2 0.08
ACGTcount: A:0.25, C:0.36, G:0.04, T:0.36
Consensus pattern (22 bp):
TCCCTAATTTCTTGACTCACAA
Found at i:292496 original size:30 final size:30
Alignment explanation
Indices: 292462--292523 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
292452 TTCTTTTTTC
292462 AAATTCCCAATTTCCTAACTCACAATCCCT
1 AAATTCCCAATTTCCTAACTCACAATCCCT
* **
292492 AAATTCCCAATTTCCTGACTCGTAATCCCT
1 AAATTCCCAATTTCCTAACTCACAATCCCT
292522 AA
1 AA
292524 TTCTTGACCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.34, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATTCCCAATTTCCTAACTCACAATCCCT
Found at i:297014 original size:21 final size:21
Alignment explanation
Indices: 296988--297032 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
296978 GATTTCTGGG
* *
296988 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
297009 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
297030 CAA
1 CAA
297033 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:298904 original size:103 final size:104
Alignment explanation
Indices: 298720--298929 Score: 404
Period size: 103 Copynumber: 2.0 Consensus size: 104
298710 TCTACGCGAT
298720 CTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCC
1 CTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCC
*
298785 TAGTATATGTATATGATTCTTAAGGAATGATATGTGGTC
66 TAGTATATGTATATGATTCTTAAGGAATGATATGTAGTC
298824 CTTT-GGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCC
1 CTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCC
298888 TAGTATATGTATATGATTCTTAAGGAATGATATGTAGTC
66 TAGTATATGTATATGATTCTTAAGGAATGATATGTAGTC
298927 CTT
1 CTT
298930 ATGTACATTA
Statistics
Matches: 105, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
103 101 0.96
104 4 0.04
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.37
Consensus pattern (104 bp):
CTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCC
TAGTATATGTATATGATTCTTAAGGAATGATATGTAGTC
Found at i:298985 original size:23 final size:23
Alignment explanation
Indices: 298946--299013 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
298936 ATTATTATAT
* *
298946 GGCATTACGATGCAATTCTACGC
1 GGCATTTCGGTGCAATTCTACGC
* *
298969 GGCACTTT-GGTGTAATTCTACGT
1 GGCA-TTTCGGTGCAATTCTACGC
*
298992 GGCATTTCGGTGCAATTATACG
1 GGCATTTCGGTGCAATTCTACG
299014 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
22 3 0.08
23 32 0.86
24 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (23 bp):
GGCATTTCGGTGCAATTCTACGC
Found at i:299237 original size:16 final size:16
Alignment explanation
Indices: 299186--299238 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
299176 TGTATGTGAT
*
299186 ATATGTATATGATTTGTG
1 ATATG-ATAT-ATGTGTG
* **
299204 ATATGATGTATGCATG
1 ATATGATATATGTGTG
299220 ATATGATATATGTGTG
1 ATATGATATATGTGTG
299236 ATA
1 ATA
299239 GGGGTTATGG
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
16 20 0.71
17 3 0.11
18 5 0.18
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.43
Consensus pattern (16 bp):
ATATGATATATGTGTG
Found at i:303733 original size:11 final size:11
Alignment explanation
Indices: 303709--303758 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 11
303699 TTCCTTAGAT
303709 AAAAATTATTTAA
1 AAAAATTA--TAA
303722 AAAAATTATAA
1 AAAAATTATAA
*
303733 AATAAAGTAATAA
1 AA-AAA-TTATAA
303746 AAAAATTATAA
1 AAAAATTATAA
303757 AA
1 AA
303759 TAAAGTAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
11 12 0.36
12 6 0.18
13 15 0.45
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:303775 original size:24 final size:24
Alignment explanation
Indices: 303719--303767 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
303709 AAAAATTATT
303719 TAAAAAAATTATAAAATAAAGTAA
1 TAAAAAAATTATAAAATAAAGTAA
303743 TAAAAAAATTATAAAATAAAGTAA
1 TAAAAAAATTATAAAATAAAGTAA
303767 T
1 T
303768 CACAAAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (24 bp):
TAAAAAAATTATAAAATAAAGTAA
Found at i:312988 original size:16 final size:16
Alignment explanation
Indices: 312947--313002 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
312937 AGATATTAAT
312947 TATATTATT-TAAAATA
1 TATATT-TTATAAAATA
*
312963 TTTAATTTTTATAAAATA
1 TAT-A-TTTTATAAAATA
312981 TATATTTTA-AAATATA
1 TATATTTTATAAA-ATA
312997 TATATT
1 TATATT
313003 ATTTTATAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 3 0.09
16 16 0.47
17 4 0.12
18 11 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTTTATAAAATA
Found at i:313668 original size:2 final size:2
Alignment explanation
Indices: 313661--313742 Score: 164
Period size: 2 Copynumber: 41.0 Consensus size: 2
313651 TCTATTACAC
313661 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
313703 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
313743 AGCTCAAGGG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:316284 original size:7 final size:7
Alignment explanation
Indices: 316272--316325 Score: 58
Period size: 7 Copynumber: 8.0 Consensus size: 7
316262 TTAATATAAG
316272 AAAATAT
1 AAAATAT
316279 AAAATAT
1 AAAATAT
316286 AAAATAT
1 AAAATAT
* *
316293 TATATAT
1 AAAATAT
*
316300 ATAAT-T
1 AAAATAT
*
316306 AATATA-
1 AAAATAT
316312 AAAATAT
1 AAAATAT
316319 AAAATAT
1 AAAATAT
316326 TATATATATG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
6 9 0.24
7 28 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
AAAATAT
Found at i:316303 original size:33 final size:33
Alignment explanation
Indices: 316265--316334 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
316255 TATATAATTA
316265 ATATAAGAAAATAT-AAAATATAAAATATTATAT
1 ATATAA-AAAATATAAAAATATAAAATATTATAT
**
316298 ATATAATTAATATAAAAATATAAAATATTATAT
1 ATATAAAAAATATAAAAATATAAAATATTATAT
316331 ATAT
1 ATAT
316335 GATTAATCGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 5 0.15
33 29 0.85
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (33 bp):
ATATAAAAAATATAAAAATATAAAATATTATAT
Found at i:316340 original size:33 final size:32
Alignment explanation
Indices: 316274--316341 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 32
316264 AATATAAGAA
316274 AATATAAAATATAAAATATTATATATATAATT
1 AATATAAAATATAAAATATTATATATATAATT
*
316306 AATATAAAAATATAAAATATTATATATATGATT
1 AATAT-AAAATATAAAATATTATATATATAATT
316339 AAT
1 AAT
316342 CGGGGGCGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 5 0.15
33 29 0.85
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (32 bp):
AATATAAAATATAAAATATTATATATATAATT
Found at i:326355 original size:20 final size:20
Alignment explanation
Indices: 326329--326406 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
326319 TTTGGTTCAC
326329 GGAATGTAAAATTACCAGTG
1 GGAATGTAAAATTACCAGTG
* **
326349 TGAATGTAAAATTATAAGTG
1 GGAATGTAAAATTACCAGTG
*
326369 GGAATATAAAATTACCAGTG
1 GGAATGTAAAATTACCAGTG
*
326389 GGAATGTAAGATTACCAG
1 GGAATGTAAAATTACCAG
326407 GTAATATGAT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (20 bp):
GGAATGTAAAATTACCAGTG
Found at i:334188 original size:14 final size:14
Alignment explanation
Indices: 334171--334204 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
334161 ATGTAATTCG
334171 TTTTCCGGAAAATA
1 TTTTCCGGAAAATA
* *
334185 TTTTTCGGAAAATG
1 TTTTCCGGAAAATA
334199 TTTTCC
1 TTTTCC
334205 CGTGTTTGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (14 bp):
TTTTCCGGAAAATA
Found at i:334236 original size:42 final size:42
Alignment explanation
Indices: 334185--334278 Score: 172
Period size: 42 Copynumber: 2.3 Consensus size: 42
334175 CCGGAAAATA
334185 TTTTT-CGGAAAATGTTTTCCCGTGTTTGTTTCACGTAATTC
1 TTTTTCCGGAAAATGTTTTCCCGTGTTTGTTTCACGTAATTC
334226 TTTTTCCGGAAAATGTTTTCCCGTGTTTGTTTCACGTAATTC
1 TTTTTCCGGAAAATGTTTTCCCGTGTTTGTTTCACGTAATTC
*
334268 GTTTTCCGGAA
1 TTTTTCCGGAA
334279 CGTAATTCAT
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 5 0.10
42 46 0.90
ACGTcount: A:0.17, C:0.18, G:0.18, T:0.47
Consensus pattern (42 bp):
TTTTTCCGGAAAATGTTTTCCCGTGTTTGTTTCACGTAATTC
Done.