Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015157.1 Kokia drynarioides strain JFW-HI SEQ_130201, 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: 303618
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 217 characters in sequence are not A, C, G, or T
Found at i:7525 original size:18 final size:18
Alignment explanation
Indices: 7502--7538 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
7492 CAAGAAGGCG
7502 AACTTATCTATGCATGTT
1 AACTTATCTATGCATGTT
7520 AACTTATCTATGCATGTT
1 AACTTATCTATGCATGTT
7538 A
1 A
7539 TGTTACAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (18 bp):
AACTTATCTATGCATGTT
Found at i:12433 original size:21 final size:21
Alignment explanation
Indices: 12404--12450 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
12394 GAACCTAATT
*
12404 AATGGCTCCAATGGTAAATAG
1 AATGTCTCCAATGGTAAATAG
12425 AATGTCTCCAATGGTAAATAG
1 AATGTCTCCAATGGTAAATAG
12446 AATGT
1 AATGT
12451 TGTTCATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (21 bp):
AATGTCTCCAATGGTAAATAG
Found at i:13308 original size:31 final size:33
Alignment explanation
Indices: 13258--13318 Score: 83
Period size: 31 Copynumber: 1.9 Consensus size: 33
13248 ATTATAATTC
13258 TAAAATTTTCAAAGAAATATA-TAA-AAATAAA
1 TAAAATTTTCAAAGAAATATAGTAACAAATAAA
*
13289 TAAATATTTTCTAA-AAATATAGTAACAAAT
1 TAAA-ATTTTCAAAGAAATATAGTAACAAAT
13319 TTAAAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 11 0.42
32 11 0.42
33 4 0.15
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (33 bp):
TAAAATTTTCAAAGAAATATAGTAACAAATAAA
Found at i:15607 original size:15 final size:16
Alignment explanation
Indices: 15587--15627 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
15577 TCTTTTTAAA
*
15587 AATATTTATT-TATTT
1 AATATTTATTATATTC
15602 AATATTTTATTATATTC
1 AATA-TTTATTATATTC
15619 AATATTTAT
1 AATATTTAT
15628 CAATTTCTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 11 0.48
17 8 0.35
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (16 bp):
AATATTTATTATATTC
Found at i:15622 original size:17 final size:16
Alignment explanation
Indices: 15587--15625 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
15577 TCTTTTTAAA
*
15587 AATA-TTTATTTATTT
1 AATATTTTATTTATTC
15602 AATATTTTATTATATTC
1 AATATTTTATT-TATTC
15619 AATATTT
1 AATATTT
15626 ATCAATTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 6 0.29
17 11 0.52
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
AATATTTTATTTATTC
Found at i:29085 original size:59 final size:60
Alignment explanation
Indices: 28979--29100 Score: 151
Period size: 60 Copynumber: 2.0 Consensus size: 60
28969 ATAAATTTTC
* * *
28979 TTTATGCAAGAAAATAAACATACTTAAAATAACAAAAAAATACCT-AAATAACATAAACT
1 TTTATACAAGAAAATAAACATACTTAAAACAACAAAAAAATACCTAAAATAACACAAACT
* * *
29038 TTTATACAAGAAAATGAAACATACTTAAAAGCAAC-ATAAAAT-GCTAAAATAACACCAACT
1 TTTATACAAGAAAAT-AAACATACTTAAAA-CAACAAAAAAATACCTAAAATAACACAAACT
29098 TTT
1 TTT
29101 CTAATGATTC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
59 16 0.30
60 35 0.65
61 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.05, T:0.25
Consensus pattern (60 bp):
TTTATACAAGAAAATAAACATACTTAAAACAACAAAAAAATACCTAAAATAACACAAACT
Found at i:30992 original size:14 final size:15
Alignment explanation
Indices: 30969--31011 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
30959 AAATTCAGTG
30969 CTTAATTTTTCAACA
1 CTTAATTTTTCAACA
* *
30984 CTTATTTTTTCAGCA
1 CTTAATTTTTCAACA
*
30999 TTTAATTTTTCAA
1 CTTAATTTTTCAA
31012 TTTACCAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.28, C:0.16, G:0.02, T:0.53
Consensus pattern (15 bp):
CTTAATTTTTCAACA
Found at i:32734 original size:30 final size:30
Alignment explanation
Indices: 32650--32734 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 30
32640 GGGTTACCTA
* *
32650 ATAT-ATGTCAGT-TTGTGTGAGCAAACTTG
1 ATATAATGTCA-TCTTGTGTGAGCAACCCTG
* *
32679 ATATAATGCCAGCTTGTGTGAGCAACCCTG
1 ATATAATGTCATCTTGTGTGAGCAACCCTG
*
32709 ATATAATGTCATCTTGTGCGAGCAAC
1 ATATAATGTCATCTTGTGTGAGCAAC
32735 TTATTCACCC
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 4 0.09
30 43 0.91
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (30 bp):
ATATAATGTCATCTTGTGTGAGCAACCCTG
Found at i:39443 original size:13 final size:14
Alignment explanation
Indices: 39413--39450 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
39403 TGTAGGTGAA
39413 AAATAATTATATTTG
1 AAATAATTA-ATTTG
39428 AAATAATTAA-TTG
1 AAATAATTAATTTG
*
39441 AAATATTTAA
1 AAATAATTAA
39451 CATATAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
14 1 0.05
15 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (14 bp):
AAATAATTAATTTG
Found at i:39487 original size:45 final size:46
Alignment explanation
Indices: 39414--39526 Score: 156
Period size: 45 Copynumber: 2.4 Consensus size: 46
39404 GTAGGTGAAA
* *
39414 AATAATTATATTTGAAATAATTAATTGAAATATTTAACATAT-AAC
1 AATAATGATATTTGAAATAACTAATTGAAATATTTAACATATAAAC
* *
39459 AATAGTGATATTTGAAATAACTATTTGAAATATTTAACATATAAAAAC
1 AATAATGATATTTGAAATAACTAATTGAAATATTTAACATAT--AAAC
*
39507 AATAATGATATTTTAAATAA
1 AATAATGATATTTGAAATAA
39527 TGGGGATTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
45 38 0.64
48 21 0.36
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.38
Consensus pattern (46 bp):
AATAATGATATTTGAAATAACTAATTGAAATATTTAACATATAAAC
Found at i:52215 original size:169 final size:169
Alignment explanation
Indices: 51936--52278 Score: 668
Period size: 169 Copynumber: 2.0 Consensus size: 169
51926 TACAAGTGAG
51936 CAAAATCTGATTTGATTTGAAAAATTCAAAAAATAATTTAAATTTTGAATTAAATAGCTGAAATT
1 CAAAATCTGATTTGATTTGAAAAATTCAAAAAATAATTTAAATTTTGAATTAAATAGCTGAAATT
52001 ATTTGAGTTAATCGAGTTATTTGAATCAACTCGAATAAAAAATTAAGTTTTTCGGTTTAACTCGA
66 ATTTGAGTTAATCGAGTTATTTGAATCAACTCGAATAAAAAATTAAGTTTTTCGGTTTAACTCGA
52066 ACATGAATTACACAATTCGAGTTATCCGAAAATCCGAAT
131 ACATGAATTACACAATTCGAGTTATCCGAAAATCCGAAT
52105 CAAAATCTGATTTGATTTGAAAAATTCAAAAAATAATTTAAATTTTGAATTAAATAGCTGAAATT
1 CAAAATCTGATTTGATTTGAAAAATTCAAAAAATAATTTAAATTTTGAATTAAATAGCTGAAATT
*
52170 ATTTGAGTTAATCGAGTTATTTGAATCAACTTGAATAAAAAATTAAGTTTTTCGGTTTAACTCGA
66 ATTTGAGTTAATCGAGTTATTTGAATCAACTCGAATAAAAAATTAAGTTTTTCGGTTTAACTCGA
52235 ACATGAATTACACAATTCGAGTTATCCGAAAATCCGAAT
131 ACATGAATTACACAATTCGAGTTATCCGAAAATCCGAAT
*
52274 AAAAA
1 CAAAA
52279 AAGATAAAAC
Statistics
Matches: 172, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
169 172 1.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (169 bp):
CAAAATCTGATTTGATTTGAAAAATTCAAAAAATAATTTAAATTTTGAATTAAATAGCTGAAATT
ATTTGAGTTAATCGAGTTATTTGAATCAACTCGAATAAAAAATTAAGTTTTTCGGTTTAACTCGA
ACATGAATTACACAATTCGAGTTATCCGAAAATCCGAAT
Found at i:53051 original size:32 final size:33
Alignment explanation
Indices: 53025--53096 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 33
53015 TTTTTCAAGT
53025 TTTTAAAGGGCCCAAAA-AATTATTTTTCCAAC
1 TTTTAAAGGGCCCAAAACAATTATTTTTCCAAC
* * * *
53057 TTTTAAGGGGCCTAAAACAA-T-TTTCTCTAAC
1 TTTTAAAGGGCCCAAAACAATTATTTTTCCAAC
53088 TTTTAAAGG
1 TTTTAAAGG
53097 ATCTAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 16 0.47
32 16 0.47
33 2 0.06
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (33 bp):
TTTTAAAGGGCCCAAAACAATTATTTTTCCAAC
Found at i:53103 original size:31 final size:30
Alignment explanation
Indices: 53046--53104 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
53036 CCAAAAAATT
* *
53046 ATTTTTCCAACTTTTAAGGGGCCTAAAACA
1 ATTTTTCCAACTTTTAAAGGACCTAAAACA
* *
53076 ATTTTCTCTAACTTTTAAAGGATCTAAAA
1 ATTTT-TCCAACTTTTAAAGGACCTAAAA
53105 TTCAATTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 5 0.21
31 19 0.79
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (30 bp):
ATTTTTCCAACTTTTAAAGGACCTAAAACA
Found at i:57735 original size:13 final size:13
Alignment explanation
Indices: 57717--57766 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
57707 TATAAGCAAG
57717 TTTTGGATTTTAA
1 TTTTGGATTTTAA
57730 TTTTGGAATATTT--
1 TTTTGG-AT-TTTAA
* *
57743 TTTTCGAATTTAA
1 TTTTGGATTTTAA
57756 TTTTGGATTTT
1 TTTTGGATTTT
57767 GGTTTCATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
11 3 0.10
12 1 0.03
13 20 0.69
14 2 0.07
15 3 0.10
ACGTcount: A:0.22, C:0.02, G:0.14, T:0.62
Consensus pattern (13 bp):
TTTTGGATTTTAA
Found at i:60122 original size:21 final size:19
Alignment explanation
Indices: 60076--60122 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
60066 GTACTATCAT
*
60076 TTTG-TTTCTTTCTTTCTC
1 TTTGTTTTCTTTCTTTATC
*
60094 TTTATTTTCTATTCTTTTATC
1 TTTGTTTTCT-TTC-TTTATC
60115 TTTGTTTT
1 TTTGTTTT
60123 TGTTCTTGAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 3 0.13
19 5 0.22
20 3 0.13
21 12 0.52
ACGTcount: A:0.06, C:0.15, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTGTTTTCTTTCTTTATC
Found at i:66739 original size:43 final size:42
Alignment explanation
Indices: 66678--66821 Score: 155
Period size: 43 Copynumber: 3.4 Consensus size: 42
66668 TAGTTATTAT
*
66678 TAAATGGAAGACTTATGTCTCGGGTAGAGCATAAGATTGTTTA
1 TAAATGGAAAACTTATGTCTCGGGTAGAGCATAAGATT-TTTA
* *
66721 TAAATGGAAAACTTATGTCTCGGGTAAAGCATAAGATTATTA
1 TAAATGGAAAACTTATGTCTCGGGTAGAGCATAAGATTTTTA
* ** ** * *
66763 TAAAT-GAAAGACCTATGTCTTAGCAAGAGCATAGGATTATTTG
1 TAAATGGAAA-ACTTATGTCTCGGGTAGAGCATAAGATT-TTTA
66806 TAAATGGAAGAACTTA
1 TAAATGGAA-AACTTA
66822 AGGCTCGGTG
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.05
42 29 0.35
43 43 0.51
44 7 0.08
45 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.31
Consensus pattern (42 bp):
TAAATGGAAAACTTATGTCTCGGGTAGAGCATAAGATTTTTA
Found at i:70149 original size:21 final size:21
Alignment explanation
Indices: 70125--70173 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
70115 TTTCGTCTCA
* **
70125 CGACCATCGCCAAGCTGTCGT
1 CGACCACCGCCAAGCCATCGT
70146 CGACCACCGCCAAGCCATCGT
1 CGACCACCGCCAAGCCATCGT
70167 CGACCAC
1 CGACCAC
70174 ACCGTCGAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.22, C:0.45, G:0.20, T:0.12
Consensus pattern (21 bp):
CGACCACCGCCAAGCCATCGT
Found at i:72251 original size:56 final size:56
Alignment explanation
Indices: 72169--72356 Score: 161
Period size: 56 Copynumber: 3.3 Consensus size: 56
72159 ACAATATATG
* *
72169 CACATAGTCTGACACATGCCCATGTGTCCAGCCCGTGTGTTCCAATACAGTATACA
1 CACACAGTCTGACACATGCCCGTGTGTCCAGCCCGTGTGTTCCAATACAGTATACA
* ** * * *
72225 CACACAGTCTG-CGACACGCCCGTGTGTCC--CCTATATGCTATTTCCAAAATAGTA-AGCA
1 CACACAGTCTGAC-ACATGCCCGTGTGTCCAGCC--CGTG-T-GTTCCAATACAGTATA-CA
* * *
72283 CACACGGTCTGACACATGCCCGTTTGTCTAGCCCGTGTGTTCCAAGT-CAGTATACA
1 CACACAGTCTGACACATGCCCGTGTGTCCAGCCCGTGTGTTCCAA-TACAGTATACA
* *
72339 CACACGGTCTAACACATG
1 CACACAGTCTGACACATG
72357 TCCATGGGTC
Statistics
Matches: 103, Mismatches: 18, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
54 2 0.02
55 1 0.01
56 55 0.53
57 4 0.04
58 38 0.37
59 1 0.01
60 2 0.02
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (56 bp):
CACACAGTCTGACACATGCCCGTGTGTCCAGCCCGTGTGTTCCAATACAGTATACA
Found at i:74431 original size:93 final size:93
Alignment explanation
Indices: 74259--74431 Score: 213
Period size: 93 Copynumber: 1.9 Consensus size: 93
74249 AACGTTCAAG
* * * * *
74259 TAGAATGAGCAACAATACAAGGTTTTAGAATGCCTTAAACTTAGTTACCCAAATTTGTTGAAAGC
1 TAGAATGAACAACAATACAAGGTTTTAAAATGCCTTAAACTTAGTTACCAAAATCTGTTCAAAGC
* *
74324 CGTAAGTTTGGGGTTTTAGTTTTGACTT
66 CGTAACTTTAGGGTTTTAGTTTTGACTT
* * * * *
74352 TAGAATGAACATCAATAGATGGTTTTAAAAAT-CCTTCAATTTAGTTACCAAAATCTGTTCAAAG
1 TAGAATGAACAACAATACAAGGTTTT-AAAATGCCTTAAACTTAGTTACCAAAATCTGTTCAAAG
*
74416 CCTTAACTTTAGGGTT
65 CCGTAACTTTAGGGTT
74432 ACAAATTTGA
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
93 62 0.94
94 4 0.06
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (93 bp):
TAGAATGAACAACAATACAAGGTTTTAAAATGCCTTAAACTTAGTTACCAAAATCTGTTCAAAGC
CGTAACTTTAGGGTTTTAGTTTTGACTT
Found at i:78472 original size:22 final size:20
Alignment explanation
Indices: 78438--78479 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 20
78428 GTCAAAGTTC
78438 AAGGGTTAGGTTTAGGGGTT
1 AAGGGTTAGGTTTAGGGGTT
78458 AAGGGATTAGGGTTTAGGGGTT
1 AAGGG-TTA-GGTTTAGGGGTT
78480 GGGATTTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 3 0.15
22 12 0.60
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.33
Consensus pattern (20 bp):
AAGGGTTAGGTTTAGGGGTT
Found at i:78644 original size:90 final size:90
Alignment explanation
Indices: 78491--78671 Score: 335
Period size: 90 Copynumber: 2.0 Consensus size: 90
78481 GGATTTAAGG
*
78491 CGTTAAAGGTAACCCATTGACGAAATCCATCGTCACCCACTCCTACTTCTACCAGGGAATCTTAA
1 CGTTAAAGGTAACCCACTGACGAAATCCATCGTCACCCACTCCTACTTCTACCAGGGAATCTTAA
78556 CCAGTTGCAGCAACTCCAAAGGTAC
66 CCAGTTGCAGCAACTCCAAAGGTAC
*
78581 CGTTAAAGGTAACCCACTGACGAAATCCATCGTCACCCACTCTTACTTCTACCAGGGAATCTTAA
1 CGTTAAAGGTAACCCACTGACGAAATCCATCGTCACCCACTCCTACTTCTACCAGGGAATCTTAA
*
78646 CCAGTTGCAGCAACTCCNAAGGTAC
66 CCAGTTGCAGCAACTCCAAAGGTAC
78671 C
1 C
78672 TGATGCTCGG
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 88 1.00
ACGTcount: A:0.30, C:0.31, G:0.15, T:0.22
Consensus pattern (90 bp):
CGTTAAAGGTAACCCACTGACGAAATCCATCGTCACCCACTCCTACTTCTACCAGGGAATCTTAA
CCAGTTGCAGCAACTCCAAAGGTAC
Found at i:80097 original size:51 final size:51
Alignment explanation
Indices: 79976--80210 Score: 337
Period size: 51 Copynumber: 4.6 Consensus size: 51
79966 GCTATAGACG
*
79976 AAAGTGTCCGATGACTGAGTGTCATCGTGAGTAAATGAATCCTTTAT-GATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
* * *
80027 AAAGATCCGATGACTAAGTGTTATTGTGAGTAAATGAATCCTTTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
* * * *
80078 AAAGGTCCGATTACTAAGTGTCATCATGAGTGAATAAATCCTTTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
* * * *
80129 AATGGTCCGATGACTAAGTGTCATTGTGAGTAAATGAATTCTGTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
*
80180 AAACGTCCGATGACTAAGTGTCATCGTGAGT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGT
80211 TTATAGATTC
Statistics
Matches: 161, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
50 38 0.24
51 123 0.76
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
Found at i:87365 original size:51 final size:51
Alignment explanation
Indices: 87287--87520 Score: 339
Period size: 51 Copynumber: 4.6 Consensus size: 51
87277 GCTATAGACG
* * *
87287 AAAGGTTCTGATGACTAAGTGTCATCATGAGTAAATGAATCATTTATGGATT
1 AAAGG-TCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
* * *
87339 AAAGGTCCGACGACTAAGTGTTATCATGAGTAAATGAAT-CTTGTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTT-TATGGATT
* *
87390 AAAGGTCCGATGACT-A-TGTCATCGTGAGTGAATGAATCCTTTATGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
* *
87439 AATGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTGTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
87490 AAAGGTCCGATGACTAAGTGTCATCGTGAGT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGT
87521 TATAGATTCC
Statistics
Matches: 164, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
49 39 0.24
50 7 0.04
51 113 0.69
52 5 0.03
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
Found at i:87484 original size:100 final size:102
Alignment explanation
Indices: 87287--87520 Score: 355
Period size: 100 Copynumber: 2.3 Consensus size: 102
87277 GCTATAGACG
* * *
87287 AAAGGTTCTGATGACTAAGTGTCATCATGAGTAAATGAATCATTTATGGATTAAAGGTCCGACGA
1 AAAGG-TCCGATGACTAAGTGTCATCGTGAGTAAATGAATCATTTATGAATTAAAGGTCCGACGA
* *
87352 CTAAGTGTTATCATGAGTAAATGAATCTTGTATGGATT
65 CTAAGTGTCATCATGAGTAAATGAATCCTGTATGGATT
* * * *
87390 AAAGGTCCGATGACT-A-TGTCATCGTGAGTGAATGAATCCTTTATGAATTAATGGTCCGATGAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCATTTATGAATTAAAGGTCCGACGAC
*
87453 TAAGTGTCATCGTGAGTAAATGAATCCTGTATGGATT
66 TAAGTGTCATCATGAGTAAATGAATCCTGTATGGATT
87490 AAAGGTCCGATGACTAAGTGTCATCGTGAGT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGT
87521 TATAGATTCC
Statistics
Matches: 119, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
100 90 0.76
101 2 0.02
102 22 0.18
103 5 0.04
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.32
Consensus pattern (102 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCATTTATGAATTAAAGGTCCGACGAC
TAAGTGTCATCATGAGTAAATGAATCCTGTATGGATT
Found at i:98716 original size:46 final size:49
Alignment explanation
Indices: 98659--98765 Score: 139
Period size: 49 Copynumber: 2.2 Consensus size: 49
98649 CAATATAATG
** * *
98659 GTTTTGTCTTTTAAC-TT-AATGA-GTAAATATTTATTAAAACAACGTA
1 GTTTTGTCTTTTAACTTTAAAAAAGGTAAACATTTATCAAAACAACGTA
* *
98705 GTTTTGACTTTTAACTTTAAAAAAGGTAAACATTTATCAAAACGACGTA
1 GTTTTGTCTTTTAACTTTAAAAAAGGTAAACATTTATCAAAACAACGTA
98754 GTTTTGTCTTTT
1 GTTTTGTCTTTT
98766 CTTATTCAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
46 14 0.27
47 2 0.04
48 3 0.06
49 32 0.63
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (49 bp):
GTTTTGTCTTTTAACTTTAAAAAAGGTAAACATTTATCAAAACAACGTA
Found at i:99446 original size:29 final size:31
Alignment explanation
Indices: 99397--99457 Score: 99
Period size: 29 Copynumber: 2.0 Consensus size: 31
99387 CAAATTTTTT
*
99397 ACTTTCCCTCCAAAATTTTTACTCCC-TCTC
1 ACTTTCCCTCCAAAACTTTTACTCCCATCTC
99427 ACTTTCCCT-CAAAACTTTTACTCCCATCTC
1 ACTTTCCCTCCAAAACTTTTACTCCCATCTC
99457 A
1 A
99458 TCCCATTCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.23, C:0.39, G:0.00, T:0.38
Consensus pattern (31 bp):
ACTTTCCCTCCAAAACTTTTACTCCCATCTC
Found at i:101115 original size:17 final size:18
Alignment explanation
Indices: 101095--101130 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
101085 TTTACATATA
101095 AAAATAATTATTT-TTTT
1 AAAATAATTATTTATTTT
101112 AAAATAATTATTTATTTT
1 AAAATAATTATTTATTTT
101130 A
1 A
101131 TAATTTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AAAATAATTATTTATTTT
Found at i:106764 original size:44 final size:43
Alignment explanation
Indices: 106693--106776 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 43
106683 ACATTACTCA
106693 ATTTACAATTTTAAATATTTTTATTATTTATAAAATTTATTAC
1 ATTTACAATTTTAAATATTTTTATTATTTATAAAATTTATTAC
* * *
106736 ATTTATAATTTTATATAATTTTTATTATTTATATAATTTAT
1 ATTTACAATTTTAAAT-ATTTTTATTATTTATAAAATTTAT
106777 ATTTAAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 14 0.38
44 23 0.62
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (43 bp):
ATTTACAATTTTAAATATTTTTATTATTTATAAAATTTATTAC
Found at i:106768 original size:18 final size:18
Alignment explanation
Indices: 106708--106779 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 18
106698 CAATTTTAAA
* * *
106708 TATTTTTATTATTTATAA
1 TATTTATATAATTTATAT
* *
106726 AATTTAT-TACATTTATAA
1 TATTTATATA-ATTTATAT
*
106744 T-TTTATATAATTTTTAT
1 TATTTATATAATTTATAT
106761 TATTTATATAATTTATAT
1 TATTTATATAATTTATAT
106779 T
1 T
106780 TAAATTATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
17 13 0.30
18 31 0.70
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTTATATAATTTATAT
Found at i:106778 original size:9 final size:9
Alignment explanation
Indices: 106718--106778 Score: 63
Period size: 9 Copynumber: 6.9 Consensus size: 9
106708 TATTTTTATT
*
106718 ATTTATAAA
1 ATTTATATA
106727 ATTTAT-TA
1 ATTTATATA
106735 CATTTATA-A
1 -ATTTATATA
*
106744 TTTTATATA
1 ATTTATATA
* *
106753 ATTTTTATT
1 ATTTATATA
106762 ATTTATATA
1 ATTTATATA
106771 ATTTATAT
1 ATTTATAT
106779 TTAAATTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
8 7 0.17
9 35 0.83
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
ATTTATATA
Found at i:107441 original size:21 final size:22
Alignment explanation
Indices: 107394--107434 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
107384 AATATGGTAC
* *
107394 AAATGTTTTAATTATGATTTGA
1 AAATTTTTTAATAATGATTTGA
107416 AAATTTTTTAATAAT-ATTT
1 AAATTTTTTAATAATGATTT
107435 ATAAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (22 bp):
AAATTTTTTAATAATGATTTGA
Found at i:117009 original size:52 final size:52
Alignment explanation
Indices: 116942--117087 Score: 186
Period size: 52 Copynumber: 2.8 Consensus size: 52
116932 TTAATTTAAG
* * *
116942 TTACTTTATAAATTCAAAACTCAATTTTAATTTTTAATAGTTTAAATTTTCAT
1 TTACTTTAT-AATTCAAAAGTCAATTTTAATTTTTAATAATTTAAATTTTCAA
* *
116995 TTACTTTATAATTCAAGAGTCAATTTT-ATTTTTAATAATTTAAATTTTTAA
1 TTACTTTATAATTCAAAAGTCAATTTTAATTTTTAATAATTTAAATTTTCAA
* * * *
117046 TTACTTAACAAATTCAAAAGTCAATTTTAGTCTTTAATAATT
1 TTACTTTA-TAATTCAAAAGTCAATTTTAATTTTTAATAATT
117088 GTTTTTCAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
51 28 0.35
52 33 0.41
53 20 0.25
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.49
Consensus pattern (52 bp):
TTACTTTATAATTCAAAAGTCAATTTTAATTTTTAATAATTTAAATTTTCAA
Found at i:129155 original size:99 final size:98
Alignment explanation
Indices: 128984--129180 Score: 367
Period size: 99 Copynumber: 2.0 Consensus size: 98
128974 TCCTCTCCAC
*
128984 CGAAACATCATTGATTGGGCCTTTATTTTCCAAAGTCTCCTCCCCTTCACGAGGCATAATGCCTC
1 CGAAACATCATTGATTGGGCCTTTATTTTCCAAAGTCTCCTCCCCTTCACGAGGCACAATGCCTC
129049 TTTGTTTACACAACAACATTATTAGAGAAGGGA
66 TTTGTTTACACAACAACATTATTAGAGAAGGGA
129082 NCGAAACATCATTGATTGGGCCTTTATTTTCCAAAGTCTCCTCCCCTTCACGAGGCACAATGCCT
1 -CGAAACATCATTGATTGGGCCTTTATTTTCCAAAGTCTCCTCCCCTTCACGAGGCACAATGCCT
*
129147 CTTTGTTTACATAACAACATTATTAGAGAAGGGA
65 CTTTGTTTACACAACAACATTATTAGAGAAGGGA
129181 AGGGTAGGAT
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 96 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.30
Consensus pattern (98 bp):
CGAAACATCATTGATTGGGCCTTTATTTTCCAAAGTCTCCTCCCCTTCACGAGGCACAATGCCTC
TTTGTTTACACAACAACATTATTAGAGAAGGGA
Found at i:143631 original size:19 final size:18
Alignment explanation
Indices: 143616--143650 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
143606 TTTTAAAATT
143616 TAAAAAT-TAATTTAAAA
1 TAAAAATATAATTTAAAA
143633 TAAAAATCATAATTTAAA
1 TAAAAAT-ATAATTTAAA
143651 GACGTTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAAATATAATTTAAAA
Found at i:145019 original size:20 final size:21
Alignment explanation
Indices: 144994--145044 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 21
144984 CAAACAATGA
144994 AAAAAAGTATCGATACC-TTT
1 AAAAAAGTATCGATACCTTTT
145014 AAAAAAGTATCGATACCTTTT
1 AAAAAAGTATCGATACCTTTT
*
145035 CAAAAAGTAT
1 AAAAAAGTAT
145045 TAATACATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (21 bp):
AAAAAAGTATCGATACCTTTT
Found at i:148090 original size:31 final size:31
Alignment explanation
Indices: 148055--148191 Score: 124
Period size: 31 Copynumber: 4.5 Consensus size: 31
148045 TTAATATAAC
*
148055 ATTTGATACTTTAACTTGACATTTTTTTTTA
1 ATTTGATACTTAAACTTGACATTTTTTTTTA
* **
148086 ATTTGGTACTTAAA--T---ATTTTTTGTCCA
1 ATTTGATACTTAAACTTGACATTTTTT-TTTA
* * *
148113 ATTTGATACTCAAACTTAACATTTTTTCTTA
1 ATTTGATACTTAAACTTGACATTTTTTTTTA
* *
148144 ATTTGGTACTTAAACTTGACACTTTTTTTTA
1 ATTTGATACTTAAACTTGACATTTTTTTTTA
*
148175 AATT-AGTACTTAAACTT
1 ATTTGA-TACTTAAACTT
148192 TCTGGAGTCC
Statistics
Matches: 83, Mismatches: 16, Indels: 14
0.73 0.14 0.12
Matches are distributed among these distances:
26 7 0.08
27 14 0.17
29 2 0.02
31 53 0.64
32 7 0.08
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.51
Consensus pattern (31 bp):
ATTTGATACTTAAACTTGACATTTTTTTTTA
Found at i:148229 original size:89 final size:89
Alignment explanation
Indices: 148055--148241 Score: 209
Period size: 89 Copynumber: 2.1 Consensus size: 89
148045 TTAATATAAC
* * * * * ***
148055 ATTTGATACTTTAACTTGACATTTTTTTTTAATTTGGTACTTAAATATTTTTTGTCCAATTTGAT
1 ATTTGGTACTTAAACTTGACACTTTTTTTTAAATTAGTACTTAAATATTTGGAGTCCAATTTGAT
* *
148120 ACTCAAACTTAACATTTTTTCTTA
66 ACTCAAACTTAACATCTTTTCCTA
148144 ATTTGGTACTTAAACTTGACACTTTTTTTTAAATTAGTACTTAAACT-TTCTGGAGTCCAATTTG
1 ATTTGGTACTTAAACTTGACACTTTTTTTTAAATTAGTACTTAAA-TATT-TGGAGTCCAATTTG
* * *
148208 GTAC-CTGAACTTGAC-TCTTTTCCTA
64 ATACTC-AAACTTAACATCTTTTCCTA
148233 ATTTGGTAC
1 ATTTGGTAC
148242 CTAATATTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
89 60 0.73
90 22 0.27
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (89 bp):
ATTTGGTACTTAAACTTGACACTTTTTTTTAAATTAGTACTTAAATATTTGGAGTCCAATTTGAT
ACTCAAACTTAACATCTTTTCCTA
Found at i:148489 original size:29 final size:29
Alignment explanation
Indices: 148409--148552 Score: 96
Period size: 29 Copynumber: 4.8 Consensus size: 29
148399 AATTGAATCT
* *
148409 AAAAAAAAGCTTAGGTACCAAATTAGG--
1 AAAAAAAAGTTTAGGTACCAAATTGGGTC
* * *
148436 AAAAATGCCAAGTTTAGGGATCAAATTGGGTCC
1 AAAAA---AAAGTTTAGGTACCAAATTGGGT-C
** **
148469 AAAAAAAA-TTTAGGTACCAAATTAAGAA
1 AAAAAAAAGTTTAGGTACCAAATTGGGTC
* *
148497 AAAAATATCAAGTTCAGGTATCAAATTGGGTC
1 AAAAA-A--AAGTTTAGGTACCAAATTGGGTC
*
148529 AAAAAAAAGTTTAAGTACCAAATT
1 AAAAAAAAGTTTAGGTACCAAATT
148553 AAAAAAAAAA
Statistics
Matches: 86, Mismatches: 21, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
27 5 0.06
28 5 0.06
29 30 0.35
30 19 0.22
31 3 0.03
32 19 0.22
33 5 0.06
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.24
Consensus pattern (29 bp):
AAAAAAAAGTTTAGGTACCAAATTGGGTC
Found at i:148520 original size:61 final size:61
Alignment explanation
Indices: 148409--148583 Score: 212
Period size: 61 Copynumber: 2.9 Consensus size: 61
148399 AATTGAATCT
* * ** * *
148409 AAAAAAAAGCTTAGGTACCAAATT-AG-GAAAAATGCCAAGTTTAGGGATCAAATTGGGTCC
1 AAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATATCAAGTTCAGGTATCAAATTGGGT-C
148469 AAAAAAAA-TTTAGGTACCAAATTAAGAAAAAAATATCAAGTTCAGGTATCAAATTGGGTC
1 AAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATATCAAGTTCAGGTATCAAATTGGGTC
* * * * * *
148529 AAAAAAAAGTTTAAGTACCAAATTAAAAAAAAAATTTCAAATTCAGATACCAAAT
1 AAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATATCAAGTTCAGGTATCAAAT
148584 GTTATATTAA
Statistics
Matches: 100, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
59 14 0.14
60 19 0.19
61 67 0.67
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.23
Consensus pattern (61 bp):
AAAAAAAAGTTTAGGTACCAAATTAAGAAAAAAATATCAAGTTCAGGTATCAAATTGGGTC
Found at i:148914 original size:92 final size:93
Alignment explanation
Indices: 148781--148965 Score: 246
Period size: 93 Copynumber: 2.0 Consensus size: 93
148771 TTAAAATTTT
* * * * * * *
148781 CTCTTCACATCTGTACAACTGCTTCCTGCTGCTATTATTTTTTGTT-TTTCGGCAACTGGTGGTT
1 CTCTTCACATCTCTACAAATGCTCCCCGCTGCTATTATTTTTTGTTGTTTCGACAAATGGTGGCT
148845 GCTACAATTGGTTCTATTCAATTGTTGG
66 GCTACAATTGGTTCTATTCAATTGTTGG
* * * *
148873 CTCTTCACGTCTCTGCAAATGCTCCCCGCTGCTATTTTTTTTTGTTGTTTCGATAAATGGTGGCT
1 CTCTTCACATCTCTACAAATGCTCCCCGCTGCTATTATTTTTTGTTGTTTCGACAAATGGTGGCT
**
148938 GCTGTAATTGGTTCTATTCAATTGTTGG
66 GCTACAATTGGTTCTATTCAATTGTTGG
148966 TTGTTGTTGC
Statistics
Matches: 79, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
92 39 0.49
93 40 0.51
ACGTcount: A:0.16, C:0.21, G:0.19, T:0.44
Consensus pattern (93 bp):
CTCTTCACATCTCTACAAATGCTCCCCGCTGCTATTATTTTTTGTTGTTTCGACAAATGGTGGCT
GCTACAATTGGTTCTATTCAATTGTTGG
Found at i:152952 original size:13 final size:12
Alignment explanation
Indices: 152925--152965 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
152915 TTAGCAACCA
152925 TTTTCTTCTTCT
1 TTTTCTTCTTCT
152937 TTTTC-TC-TCT
1 TTTTCTTCTTCT
* *
152947 TTTTTTTCTTTT
1 TTTTCTTCTTCT
152959 TTTTCTT
1 TTTTCTT
152966 TTCGAACCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
10 7 0.29
11 4 0.17
12 13 0.54
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTCTTCTTCT
Found at i:152986 original size:9 final size:9
Alignment explanation
Indices: 152933--152967 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
152923 CATTTTCTTC
152933 TTCTTTTTCT
1 TTCTTTTT-T
*
152943 CTCTTTTTT
1 TTCTTTTTT
152952 TTCTTTTTT
1 TTCTTTTTT
152961 TTCTTTT
1 TTCTTTT
152968 CGAACCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:166307 original size:22 final size:22
Alignment explanation
Indices: 166235--166304 Score: 65
Period size: 21 Copynumber: 3.2 Consensus size: 22
166225 AAAAATTATA
166235 TTGTTGTTTTGG-TGCTT-TTTT
1 TTGTTGTTTTGGATG-TTGTTTT
** *
166256 TTACTGTTTTGGTTGTTGTTTT
1 TTGTTGTTTTGGATGTTGTTTT
166278 TTGTTGTTTT-GATGTTGCTTTT
1 TTGTTGTTTTGGATGTTG-TTTT
166300 ATTGT
1 -TTGT
166305 GTTGGTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 18 0.45
22 18 0.45
23 4 0.10
ACGTcount: A:0.04, C:0.04, G:0.23, T:0.69
Consensus pattern (22 bp):
TTGTTGTTTTGGATGTTGTTTT
Found at i:166337 original size:20 final size:20
Alignment explanation
Indices: 166312--166362 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
166302 TGTGTTGGTT
166312 TTTTTACTGTTTTGGTGCTA
1 TTTTTACTGTTTTGGTGCTA
* *
166332 TTTTTACTGTTTTGGTGTTG
1 TTTTTACTGTTTTGGTGCTA
*
166352 TTTTTAATGTT
1 TTTTTACTGTT
166363 ATTTTTGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.06, G:0.20, T:0.65
Consensus pattern (20 bp):
TTTTTACTGTTTTGGTGCTA
Found at i:172183 original size:27 final size:27
Alignment explanation
Indices: 172108--172184 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
172098 AGTAATCTAT
* *
172108 TTCTAGCTTGAAAGAGGGTTATTATGA
1 TTCTAGCTCGAAAGAGCGTTATTATGA
* *
172135 TTTTAGCTCGAAAGAACGTTATTATGA
1 TTCTAGCTCGAAAGAGCGTTATTATGA
*
172162 TTCT-GTCTCGAAAGAGCATTATT
1 TTCTAG-CTCGAAAGAGCGTTATT
172185 CTGTCTGGGC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.38
Consensus pattern (27 bp):
TTCTAGCTCGAAAGAGCGTTATTATGA
Found at i:172215 original size:26 final size:26
Alignment explanation
Indices: 172184--172286 Score: 118
Period size: 26 Copynumber: 4.0 Consensus size: 26
172174 AGAGCATTAT
172184 TCTGTCTGGGCTCGTAAGAGTTAAAC
1 TCTGTCTGGGCTCGTAAGAGTTAAAC
* * *
172210 TTTGTCTGGGCTCATAAGAGCTAAAC
1 TCTGTCTGGGCTCGTAAGAGTTAAAC
* *
172236 TCTATTTGGGCTCGTAAGA-TCTAAAC
1 TCTGTCTGGGCTCGTAAGAGT-TAAAC
* * *
172262 TCTGTCTAGGCTCGTATGAGATAAA
1 TCTGTCTGGGCTCGTAAGAGTTAAA
172287 TTTTGTTATG
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
26 62 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (26 bp):
TCTGTCTGGGCTCGTAAGAGTTAAAC
Found at i:174189 original size:93 final size:92
Alignment explanation
Indices: 174080--174413 Score: 365
Period size: 93 Copynumber: 3.6 Consensus size: 92
174070 CAGCAACCAT
174080 CAATTGAATAGAACCAATTGCAGCAACCACCAGTTGCTGAAAAAACAAAAAATAATAGAAGGAGA
1 CAATTGAATAGAACCAATTGCAGCAACCACCAGTTGCTGAAAAAACAAAAAATAATAGAAGGAGA
* * * *
174145 GAACAATTGCAAAAACATGAAGAGCCAA
66 GAA-AATTGCAAAGACGTGAAGAGCTAG
* * * *
174173 CAATTGAATAGAACCAATTACAGCAACCACCAGTTGCTAAAAAAACAAAAAATAATAGCAGTAG-
1 CAATTGAATAGAACCAATTGCAGCAACCACCAGTTGCTGAAAAAACAAAAAATAATAGAAGGAGA
*
174237 GAAGTAGTTGCAAAGACGTGAAGAGCTAG
66 GAA--AATTGCAAAGACGTGAAGAGCTAG
* * ** * *
174266 CAATTGAATAGAACAAATTGCAGCAGCCACCAACTG-TCAAAAAACAATAAA-AATAGCAACAGG
1 CAATTGAATAGAACCAATTGCAGCAACCACCAGTTGCTGAAAAAACAAAAAATAATAG--A-AGG
* * *
174329 -GAG-AATTTTCAAAGATGTGAAGAGCTAG
63 AGAGAAAATTGCAAAGACGTGAAGAGCTAG
* * * * *
174357 CAATTGAATAGAACCAACTGCAGTAGCCACCAGTTGCCG-AAAAACAAAAAGTAATAG
1 CAATTGAATAGAACCAATTGCAGCAACCACCAGTTGCTGAAAAAACAAAAAATAATAG
174414 CAATAGGAAG
Statistics
Matches: 203, Mismatches: 31, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
91 67 0.33
92 21 0.10
93 112 0.55
94 3 0.01
ACGTcount: A:0.48, C:0.17, G:0.18, T:0.16
Consensus pattern (92 bp):
CAATTGAATAGAACCAATTGCAGCAACCACCAGTTGCTGAAAAAACAAAAAATAATAGAAGGAGA
GAAAATTGCAAAGACGTGAAGAGCTAG
Found at i:175435 original size:3 final size:3
Alignment explanation
Indices: 175427--175483 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
175417 TTTTTATTTT
175427 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
175474 TAA TAA TAA T
1 TAA TAA TAA T
175484 CATCATCATC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:175674 original size:32 final size:32
Alignment explanation
Indices: 175637--175703 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
175627 TGAATTACTT
* * *
175637 ATTACAATTTTATTCTATTAAAGCTTTATTCC
1 ATTACAACTATATTCTATTAAAGCTCTATTCC
* *
175669 ATTACAACTATATTTTATTACAGCTCTATTCC
1 ATTACAACTATATTCTATTAAAGCTCTATTCC
175701 ATT
1 ATT
175704 TCAGTGAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.18, G:0.03, T:0.48
Consensus pattern (32 bp):
ATTACAACTATATTCTATTAAAGCTCTATTCC
Found at i:175976 original size:16 final size:16
Alignment explanation
Indices: 175956--176010 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
175946 GTTTGGTTTA
175956 CTGTAATGGAATAG-G
1 CTGTAATGGAATAGAG
175971 ACTGTAATGGAATAGAG
1 -CTGTAATGGAATAGAG
*
175988 TTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
176004 CTGTAAT
1 CTGTAAT
176011 CAGTAATTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 35 0.97
17 1 0.03
ACGTcount: A:0.36, C:0.05, G:0.29, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:176216 original size:26 final size:26
Alignment explanation
Indices: 176181--176272 Score: 76
Period size: 26 Copynumber: 3.3 Consensus size: 26
176171 GTTATTAAAA
176181 TTTAATAAAATTATTATTAAATATAT
1 TTTAATAAAATTATTATTAAATATAT
* *
176207 TTTAATAAAAAATAATAAATATTTAATTATAT
1 TTTAAT--AAAAT--T-ATTA-TTAAATATAT
* * * *
176239 TTTAACATAATTATTATTAAATACAA
1 TTTAATAAAATTATTATTAAATATAT
176265 TTTAATAA
1 TTTAATAA
176273 CATTCTTAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
26 19 0.38
27 3 0.06
28 6 0.12
30 5 0.10
31 3 0.06
32 14 0.28
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
TTTAATAAAATTATTATTAAATATAT
Found at i:176330 original size:23 final size:21
Alignment explanation
Indices: 176304--176345 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
176294 TAAAATATGA
176304 ATTAAAAAATTATAATATATATT
1 ATTAAAAAA--ATAATATATATT
*
176327 ATTATAAAAATAATATATA
1 ATTAAAAAAATAATATATA
176346 ACCTACGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTAAAAAAATAATATATATT
Found at i:184481 original size:45 final size:45
Alignment explanation
Indices: 184411--184900 Score: 517
Period size: 45 Copynumber: 11.0 Consensus size: 45
184401 TACATCATCT
* * * *
184411 CGTCCAATCTTTTACCGCTAGTCAAGAGGGGTAAATTGAAGCCAT
1 CGTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAC
** * * * *
184456 ATTCCAATCTTTTATCCCTAATCAAGATGGGCAGATTGAAGCCAT
1 CGTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAC
** * *
184501 ATTCCAATCTTTTATCCCTAATCAAGAGGGGCAGATTGAAGCCAC
1 CGTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAC
* * * * *
184546 TGCCCAATCTTTTATCCCTAGTCAAGAGGAGCAGATTGAAGTCAC
1 CGTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAC
* *
184591 CGTCCAATCTTTTACCCCTAATCCAA-AGGGGCAGA-TGAA---AGT
1 CGTCCAATCTTTTACCCCTAGT-CAAGAGGGGCAGATTGAAGCCA-C
** * * *
184633 CGTCCAATCTTTTACCTTTAGTTAAGAGGGG-AAATTGAAGTCAC
1 CGTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAC
* * * *
184677 CATCCAATCTTTT-CCCCATAATCCAGAGGGGCAGATTGAAGCAAC
1 CGTCCAATCTTTTACCCC-TAGTCAAGAGGGGCAGATTGAAGCCAC
* * * *
184722 CTTCTAATCTTTTACCCCTAGTCAAGTGGGGTAGATTGAAGCCAC
1 CGTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAC
* * * **
184767 CATCCAATCATCTACCCCTAGTCAAGAGGGATAGATTGAAGCCAC
1 CGTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAC
* * *
184812 CGACCAATCCTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCAC
1 CGTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAC
*
184857 CTTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCA
1 CGTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCA
184901 TCTAATTTGT
Statistics
Matches: 374, Mismatches: 61, Indels: 20
0.82 0.13 0.04
Matches are distributed among these distances:
41 5 0.01
42 28 0.07
43 2 0.01
44 26 0.07
45 306 0.82
46 7 0.02
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (45 bp):
CGTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCAC
Found at i:184794 original size:221 final size:222
Alignment explanation
Indices: 184410--184900 Score: 589
Period size: 221 Copynumber: 2.2 Consensus size: 222
184400 ATACATCATC
* *
184410 TCGTCCAATCTTTTACCGCTAGTCAAGAGGGGTAAATTGAAGCCATATTCCAATCTTTTATCCCT
1 TCGTCCAATCTTTTACCGCTAGTCAAGAGGGGTAAATTGAAGCCACATTCCAATCTTTTACCCCT
* * * *
184475 AATCAAGATGGGCAGATTGAAGCCATATTCCAATCTTTTATCCCTAATCAAGAGGGGCAGATTGA
66 AATCAAGAGGGGCAGATTGAAGCAACATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGA
** * * * * * *
184540 AGCCACTGCCCAATCTTTTATCCCTAGTCAAGA-GGAGCAGATTGAAGTCACCGTCCAATCTTTT
131 AGCCACCACCCAATCATCTACCCCTAGTCAAGAGGGA-CAGATTGAAGCCACCGACCAATCCTTT
184604 ACCCCTAATCCAA-AGGGGCAGATGAAAG
195 ACCCCTAAT-CAAGAGGGGCAGATGAAAG
** * *
184632 TCGTCCAATCTTTTACCTTTAGTTAAGAGGGG-AAATTGAAGTCACCA-TCCAATCTTTT-CCCC
1 TCGTCCAATCTTTTACCGCTAGTCAAGAGGGGTAAATTGAAGCCA-CATTCCAATCTTTTACCCC
* * * * * *
184694 ATAATCCAGAGGGGCAGATTGAAGCAACCTTCTAATCTTTTACCCCTAGTCAAGTGGGGTAGATT
65 -TAATCAAGAGGGGCAGATTGAAGCAACATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATT
* *
184759 GAAGCCACCATCCAATCATCTACCCCTAGTCAAGAGGGATAGATTGAAGCCACCGACCAATCCTT
129 GAAGCCACCACCCAATCATCTACCCCTAGTCAAGAGGGACAGATTGAAGCCACCGACCAATCCTT
184824 TACCCCTAATCAAGAGGGGCAGATTG-AAG
194 TACCCCTAATCAAGAGGGGCAGA-TGAAAG
* * * * *
184853 CCACCTTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCA
1 ---TCGTCCAATCTTTTACCGCTAGTCAAGAGGGGTAAATTGAAGCCA
184901 TCTAATTTGT
Statistics
Matches: 227, Mismatches: 33, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
220 6 0.03
221 149 0.66
222 35 0.15
224 27 0.12
225 10 0.04
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (222 bp):
TCGTCCAATCTTTTACCGCTAGTCAAGAGGGGTAAATTGAAGCCACATTCCAATCTTTTACCCCT
AATCAAGAGGGGCAGATTGAAGCAACATTCCAATCTTTTACCCCTAATCAAGAGGGGCAGATTGA
AGCCACCACCCAATCATCTACCCCTAGTCAAGAGGGACAGATTGAAGCCACCGACCAATCCTTTA
CCCCTAATCAAGAGGGGCAGATGAAAG
Found at i:184934 original size:42 final size:40
Alignment explanation
Indices: 184413--185019 Score: 311
Period size: 45 Copynumber: 13.8 Consensus size: 40
184403 CATCATCTCG
* * * *
184413 TCCAATCTTTTACCGCTAGTCAAGAGGGGTAAATTGAAGCCATA
1 TCCAATCTTTTACCCCTAATCAA-A-GGGCAGATTGAAGCC--A
*
184457 TTCCAATCTTTTATCCCTAATCAAGATGGGCAGATTGAAGCCATA
1 -TCCAATCTTTTACCCCTAATCAA-A-GGGCAGATTGAAGCC--A
*
184502 TTCCAATCTTTTATCCCTAATCAAGAGGGGCAGATTGAAGCCA
1 -TCCAATCTTTTACCCCTAATCAA-A-GGGCAGATTGAAGCCA
* * *
184545 CTGCCCAATCTTTTATCCCTAGTCAAGAGGAGCAGATTGAAGTCACCG
1 -T--CCAATCTTTTACCCCTAATCAA-AGG-GCAGATTGAAG---CCA
* *
184593 TCCAATCTTTTACCCCTAATCCAAAGGGGCAGA-TGAAAGTCG
1 TCCAATCTTTTACCCCTAAT-CAAA-GGGCAGATTG-AAGCCA
** * * * *
184635 TCCAATCTTTTACCTTTAGTTAAGAGGGGAAATTGAAGTCACCA
1 TCCAATCTTTTACCCCTAATCAA-AGGGCAGATTGAAG---CCA
* *
184679 TCCAATCTTTT-CCCCATAATCCAGAGGGGCAGATTGAAGCAACCT
1 TCCAATCTTTTACCCC-TAAT-CA-AAGGGCAGATTGAAG---CCA
* * * *
184724 TCTAATCTTTTACCCCTAGTCAAGTGGGGTAGATTGAAGCCACCA
1 TCCAATCTTTTACCCCTAATCAA--AGGGCAGATTGAAG---CCA
* * * *
184769 TCCAATCATCTACCCCTAGTCAAGAGGGATAGATTGAAGCCA
1 TCCAATCTTTTACCCCTAATCAA-AGGG-CAGATTGAAGCCA
* *
184811 CCGACCAATCCTTTACCCCTAATCAAGAGGGGCAGATTGAAGCCA
1 ---TCCAATCTTTTACCCCTAATCAA-A-GGGCAGATTGAAGCCA
*
184856 CCTTCCAATCTTTTACCCCTAGTCAAGAGGGGCAGATTGAAGCCA
1 ---TCCAATCTTTTACCCCTAATCAA-A-GGGCAGATTGAAGCCA
* * *
184901 TCTAAT-TTGTTACCCTTAATCCAAAGGGACAGATTAAAGCCA
1 TCCAATCTT-TTACCCCTAAT-CAAAGGG-CAGATTGAAGCCA
* * * * *
184943 TCTAGTCTTTTACCCCTAATATAGAAAGGTAGATTGAAGCCA
1 TCCAATCTTTTACCCCTAAT-CA-AAGGGCAGATTGAAGCCA
* * *
184985 TCCACTCTTTTACCCTTGATCCAAAAGGGCAGATT
1 TCCAATCTTTTACCCCTAAT-C-AAAGGGCAGATT
185020 AAAGTCACAC
Statistics
Matches: 462, Mismatches: 69, Indels: 65
0.78 0.12 0.11
Matches are distributed among these distances:
41 15 0.03
42 104 0.23
43 15 0.03
44 24 0.05
45 288 0.62
46 13 0.03
47 1 0.00
48 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (40 bp):
TCCAATCTTTTACCCCTAATCAAAGGGCAGATTGAAGCCA
Found at i:191542 original size:135 final size:134
Alignment explanation
Indices: 191284--191549 Score: 365
Period size: 135 Copynumber: 2.0 Consensus size: 134
191274 AATTGTTTTT
* *
191284 GATTAATCACGAATTTAATGAATTTTTTGATTTAATAATAAAAATTTAAAAAAAGCACCTATAGT
1 GATTAATCACGAATTTAATGAATTTTTTGATTTAATAATAAAAATTAAAAAAAAACACCTATAGT
* *
191349 TGATGACATAATAATAATATTATATATACACACACATAACTTGACTAATGCATAAGAATATGACA
66 TGATGACATAATAATAATATTATATATACACACACATAACGTGACTAATACATAAGAATATGACA
191414 AATA
131 AATA
* * *
191418 GATTAATCACTAATTTAATGAATTTTGTTGATTTAATAATAATAATTAAAAAAAAACACCTATAT
1 GATTAATCACGAATTTAATGAATTTT-TTGATTTAATAATAAAAATTAAAAAAAAACACCTATAG
* ** * * * *
191483 TTTATGGTATAATAATAATCTTA-A-ATATACACACATAACGTGACTAGTACAATATAGAATATT
65 TTGATGACATAATAATAATATTATATATACACACACATAACGTGACTAATAC-ATA-AGAATATG
191546 ACAA
128 ACAA
191550 GATAAAATGA
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
133 22 0.19
134 29 0.25
135 64 0.56
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.34
Consensus pattern (134 bp):
GATTAATCACGAATTTAATGAATTTTTTGATTTAATAATAAAAATTAAAAAAAAACACCTATAGT
TGATGACATAATAATAATATTATATATACACACACATAACGTGACTAATACATAAGAATATGACA
AATA
Found at i:195616 original size:60 final size:59
Alignment explanation
Indices: 195523--195662 Score: 190
Period size: 60 Copynumber: 2.3 Consensus size: 59
195513 GGGATTTTAG
* * *
195523 ATTTTTTGCGAAGTTCAAGGGTCAAAATGTGATTTTTGAGAAGTTCGAGGGTCAAAATGT
1 ATTTTTTGCGAAGTT-TAGGGTCAAAATGTGATTTTTAAGAAGTTCAAGGGTCAAAATGT
* * *
195583 ATTTTTTGCGAAGTTTGAGGGTTAAAATGTGATTTTTAAGAAGTTTAAGGGTTAAAATGT
1 ATTTTTTGCGAAGTTT-AGGGTCAAAATGTGATTTTTAAGAAGTTCAAGGGTCAAAATGT
* *
195643 AATTTTTGAGAAGTTTAGGG
1 ATTTTTTGCGAAGTTTAGGG
195663 ACCTCTTGAG
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
59 4 0.06
60 67 0.94
ACGTcount: A:0.31, C:0.04, G:0.26, T:0.39
Consensus pattern (59 bp):
ATTTTTTGCGAAGTTTAGGGTCAAAATGTGATTTTTAAGAAGTTCAAGGGTCAAAATGT
Found at i:195658 original size:30 final size:30
Alignment explanation
Indices: 195525--195659 Score: 162
Period size: 30 Copynumber: 4.5 Consensus size: 30
195515 GATTTTAGAT
* * *
195525 TTTTTGCGAAGTTCAAGGGTCAAAATGTGA
1 TTTTTGAGAAGTTTAAGGGTCAAAATGTAA
** *
195555 TTTTTGAGAAGTTCGAGGGTCAAAATGTAT
1 TTTTTGAGAAGTTTAAGGGTCAAAATGTAA
* * * *
195585 TTTTTGCGAAGTTTGAGGGTTAAAATGTGA
1 TTTTTGAGAAGTTTAAGGGTCAAAATGTAA
* *
195615 TTTTTAAGAAGTTTAAGGGTTAAAATGTAA
1 TTTTTGAGAAGTTTAAGGGTCAAAATGTAA
195645 TTTTTGAGAAGTTTA
1 TTTTTGAGAAGTTTA
195660 GGGACCTCTT
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 91 1.00
ACGTcount: A:0.31, C:0.04, G:0.25, T:0.39
Consensus pattern (30 bp):
TTTTTGAGAAGTTTAAGGGTCAAAATGTAA
Found at i:198070 original size:29 final size:29
Alignment explanation
Indices: 198036--198096 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
198026 GAAGCTTGGA
198036 TTCGAAGTTTCGCTCACATGGAGCTTTGT
1 TTCGAAGTTTCGCTCACATGGAGCTTTGT
*
198065 TTCGAAGTTTCGCTCACATTGAGCTTTGT
1 TTCGAAGTTTCGCTCACATGGAGCTTTGT
198094 TTC
1 TTC
198097 ATTAATTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.41
Consensus pattern (29 bp):
TTCGAAGTTTCGCTCACATGGAGCTTTGT
Found at i:200324 original size:3 final size:3
Alignment explanation
Indices: 200311--200342 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
200301 TGGGCGACCA
*
200311 TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
200343 AATATCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:208942 original size:20 final size:20
Alignment explanation
Indices: 208917--208957 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
208907 GCACTGAGGT
*
208917 GAAAACCTCATGAAGGAGTA
1 GAAAACCTCACGAAGGAGTA
208937 GAAAACCTCACGAAGGAGTA
1 GAAAACCTCACGAAGGAGTA
208957 G
1 G
208958 TTTCCCGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.17, G:0.27, T:0.12
Consensus pattern (20 bp):
GAAAACCTCACGAAGGAGTA
Found at i:225323 original size:8 final size:8
Alignment explanation
Indices: 225300--225348 Score: 53
Period size: 9 Copynumber: 5.6 Consensus size: 8
225290 ATTGCACCCA
225300 AAAAAAAG
1 AAAAAAAG
*
225308 AGGAAAAAAA
1 A--AAAAAAG
225318 ATAAAAAAG
1 A-AAAAAAG
225327 AAAAGAAAG
1 AAAA-AAAG
225336 AAAAAAAG
1 AAAAAAAG
225344 AAAAA
1 AAAAA
225349 GAAAAAAGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
8 13 0.37
9 15 0.43
10 7 0.20
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:225348 original size:25 final size:25
Alignment explanation
Indices: 225301--225357 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
225291 TTGCACCCAA
*
225301 AAAAAAG-AGGAAAAAAAATAAAA-
1 AAAAAAGAAAGAAAAAAAATAAAAG
225324 AAGAAAAGAAAGAAAAAAAGA-AAAAG
1 AA-AAAAGAAAGAAAAAAA-ATAAAAG
225350 AAAAAAGA
1 AAAAAAGA
225358 GAGGTTGAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
23 2 0.07
24 5 0.17
25 19 0.66
26 3 0.10
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (25 bp):
AAAAAAGAAAGAAAAAAAATAAAAG
Found at i:226420 original size:43 final size:43
Alignment explanation
Indices: 226264--226466 Score: 171
Period size: 43 Copynumber: 4.6 Consensus size: 43
226254 AGTTAAGAGG
* *
226264 GGCAGATTGAAGCCACCGTCCAATCTTTTACCCCTAATCCAGTA-A
1 GGCAGATTGAAGTCA---TCCAGTCTTTTACCCCTAATCCAGTAGA
* * * * * *
226309 GAGTAGATTGAAGCCACCATCCAATCTTTTACCCCTAGTCAAG-AGG
1 G-GCAGATTGAAG---TCATCCAGTCTTTTACCCCTAATCCAGTAGA
* *
226355 GGCAAATTGAAGTCATCTAGTCTTTTACCCCTAATCCAGTAGA
1 GGCAGATTGAAGTCATCCAGTCTTTTACCCCTAATCCAGTAGA
* **
226398 GGCAGATTGAAGTCATTCAGTCTTTTACATCTAATCCAGTAG-
1 GGCAGATTGAAGTCATCCAGTCTTTTACCCCTAATCCAGTAGA
*
226440 GGATAGATTGAAG-CTATCCAGTCTTTT
1 GG-CAGATTGAAGTC-ATCCAGTCTTTT
226467 TGAAGCCATC
Statistics
Matches: 131, Mismatches: 19, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
42 25 0.19
43 59 0.45
45 11 0.08
46 33 0.25
49 3 0.02
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (43 bp):
GGCAGATTGAAGTCATCCAGTCTTTTACCCCTAATCCAGTAGA
Found at i:226471 original size:19 final size:19
Alignment explanation
Indices: 226447--226485 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
226437 TAGGGATAGA
* *
226447 TTGAAGCTATCCAGTCTTT
1 TTGAAGCCATCCAATCTTT
226466 TTGAAGCCATCCAATCTTT
1 TTGAAGCCATCCAATCTTT
226485 T
1 T
226486 ACCCCTAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.41
Consensus pattern (19 bp):
TTGAAGCCATCCAATCTTT
Found at i:226494 original size:62 final size:62
Alignment explanation
Indices: 226404--226528 Score: 155
Period size: 62 Copynumber: 2.0 Consensus size: 62
226394 TAGAGGCAGA
* * * * * *
226404 TTGAAGTCATTCAGTCTTTTACATCTAATCCAGTAG-GGATAGATTGAAG-CTATCCAGTCTTT
1 TTGAAGCCATCCAATCTTTTACACCTAATCCAGTAGAGG-TAAATTGAAGTC-ATCCAATCTTT
*
226466 TTGAAGCCATCCAATCTTTTACCCCTAATCCAGTAGAGGTAAATTGAAGTCATCCAATCTTT
1 TTGAAGCCATCCAATCTTTTACACCTAATCCAGTAGAGGTAAATTGAAGTCATCCAATCTTT
226528 T
1 T
226529 ACCTCTAATC
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 51 0.94
63 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (62 bp):
TTGAAGCCATCCAATCTTTTACACCTAATCCAGTAGAGGTAAATTGAAGTCATCCAATCTTT
Found at i:226514 original size:43 final size:43
Alignment explanation
Indices: 226466--226847 Score: 348
Period size: 43 Copynumber: 8.9 Consensus size: 43
226456 TCCAGTCTTT
* * * *
226466 TTGAAGCCATCCAATCTTTTACCCCTAATCCAGTAGAGGTAAA
1 TTGAAGTCATCCAATCTTTTACCCCTAATCCAGTAGGGGCAGA
* **
226509 TTGAAGTCATCCAATCTTTTACCTCTAATCCAGTAAAGGCAGA
1 TTGAAGTCATCCAATCTTTTACCCCTAATCCAGTAGGGGCAGA
* *
226552 TTGAAGTCATCCAGTCTTTTACCCCTAATCTAG-AGGGGCAGA
1 TTGAAGTCATCCAATCTTTTACCCCTAATCCAGTAGGGGCAGA
* *
226594 TTGAAGTCATTCAATCTTTTACCCTTAATCCAGTAGGGGCAGA
1 TTGAAGTCATCCAATCTTTTACCCCTAATCCAGTAGGGGCAGA
* * * * * **
226637 TTAAAGTCTTCTAATATTTTACCCTTAATTTAG-AGGGGCAGA
1 TTGAAGTCATCCAATCTTTTACCCCTAATCCAGTAGGGGCAGA
* * * * *
226679 TTGAAGCCCTCCAATCTTTTACCCCTAATCTAGTAAGGGCAAA
1 TTGAAGTCATCCAATCTTTTACCCCTAATCCAGTAGGGGCAGA
* ** *
226722 TTGAAGCCACCATCCAATCTTTTATTCCTAAGTCAAG-AGGGGCAGA
1 TTGAAG---TCATCCAATCTTTTACCCCTAA-TCCAGTAGGGGCAGA
** * * *
226768 TTGAAAACATTAGCCAATCTCTTACCCC-GA-CCA-T-GGGGCAAA
1 TTGAAGTCA-T--CCAATCTTTTACCCCTAATCCAGTAGGGGCAGA
*
226810 TTGAAGTCATCCAATCTTTTACCCCTAATCGAG-AGGGG
1 TTGAAGTCATCCAATCTTTTACCCCTAATCCAGTAGGGG
226848 AAAATTGAGA
Statistics
Matches: 276, Mismatches: 49, Indels: 29
0.78 0.14 0.08
Matches are distributed among these distances:
39 14 0.05
40 1 0.00
41 3 0.01
42 89 0.32
43 120 0.43
44 1 0.00
45 1 0.00
46 43 0.16
47 4 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (43 bp):
TTGAAGTCATCCAATCTTTTACCCCTAATCCAGTAGGGGCAGA
Found at i:226543 original size:105 final size:105
Alignment explanation
Indices: 226361--226571 Score: 300
Period size: 105 Copynumber: 2.0 Consensus size: 105
226351 GAGGGGCAAA
* * * * * *
226361 TTGAAGTCATCTAGTCTTTTACCCCTAATCCAGTAGAGGCAGATTGAAGTCATTCAGTCTTTTAC
1 TTGAAGCCATCCAATCTTTTACCCCTAATCCAGTAGAGGCAAATTGAAGTCATCCAATCTTTTAC
* *
226426 ATCTAATCCAGT-AGGGATAGATTGAAG-CTATCCAGTCTTT
66 ATCTAATCCAGTAAAGG-CAGATTGAAGTC-ATCCAGTCTTT
*
226466 TTGAAGCCATCCAATCTTTTACCCCTAATCCAGTAGAGGTAAATTGAAGTCATCCAATCTTTTAC
1 TTGAAGCCATCCAATCTTTTACCCCTAATCCAGTAGAGGCAAATTGAAGTCATCCAATCTTTTAC
*
226531 CTCTAATCCAGTAAAGGCAGATTGAAGTCATCCAGTCTTT
66 ATCTAATCCAGTAAAGGCAGATTGAAGTCATCCAGTCTTT
226571 T
1 T
226572 ACCCCTAATC
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
105 90 0.96
106 4 0.04
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (105 bp):
TTGAAGCCATCCAATCTTTTACCCCTAATCCAGTAGAGGCAAATTGAAGTCATCCAATCTTTTAC
ATCTAATCCAGTAAAGGCAGATTGAAGTCATCCAGTCTTT
Found at i:226623 original size:85 final size:85
Alignment explanation
Indices: 226466--226847 Score: 360
Period size: 85 Copynumber: 4.4 Consensus size: 85
226456 TCCAGTCTTT
* * * * *
226466 TTGAAGCCATCCAATCTTTTACCCCTAATCCAGTAGAGGTAAATTGAAGTCATCCAATCTTTTA-
1 TTGAAGTCATCCAATCTTTTACCCCTAATCTAG-AGGGGCAGATTGAAGTCATCCAATCTTTTAC
* *
226530 CCTCTAATCCAGTAAAGGCAGA
65 CCT-TAATCCAGTAAGGGCAAA
* *
226552 TTGAAGTCATCCAGTCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGTCATTCAATCTTTTACC
1 TTGAAGTCATCCAATCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGTCATCCAATCTTTTACC
* *
226617 CTTAATCCAGTAGGGGCAGA
66 CTTAATCCAGTAAGGGCAAA
* * * * * * * *
226637 TTAAAGTCTTCTAATATTTTACCCTTAATTTAGAGGGGCAGATTGAAGCCCTCCAATCTTTTACC
1 TTGAAGTCATCCAATCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGTCATCCAATCTTTTACC
* *
226702 CCTAATCTAGTAAGGGCAAA
66 CTTAATCCAGTAAGGGCAAA
* ** * **
226722 TTGAAGCCACCATCCAATCTTTTATTCCTAAGTCAAGAGGGGCAGATTGAAAACATTAGCCAATC
1 TTGAAG---TCATCCAATCTTTTACCCCTAA-TCTAGAGGGGCAGATTGAAGTCA-T--CCAATC
* ** *
226787 TCTTACCC-CGA-CCA-T-GGGGCAAA
59 TTTTACCCTTAATCCAGTAAGGGCAAA
*
226810 TTGAAGTCATCCAATCTTTTACCCCTAATCGAGAGGGG
1 TTGAAGTCATCCAATCTTTTACCCCTAATCTAGAGGGG
226848 AAAATTGAGA
Statistics
Matches: 243, Mismatches: 45, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
84 9 0.04
85 137 0.56
86 33 0.14
88 28 0.12
89 19 0.08
90 3 0.01
91 1 0.00
92 13 0.05
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (85 bp):
TTGAAGTCATCCAATCTTTTACCCCTAATCTAGAGGGGCAGATTGAAGTCATCCAATCTTTTACC
CTTAATCCAGTAAGGGCAAA
Found at i:227519 original size:32 final size:32
Alignment explanation
Indices: 227457--227520 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
227447 ATAATAAACA
* **
227457 AAATAAAAAAATTTCAAATAAAAATTCATTTC
1 AAATAAAAAAATTTCAAAAAAAAAAACATTTC
227489 AAAT-AAAAAATTTCATAAAAAAAAAACATTTC
1 AAATAAAAAAATTTCA-AAAAAAAAAACATTTC
227521 GACATCCACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (32 bp):
AAATAAAAAAATTTCAAAAAAAAAAACATTTC
Found at i:229065 original size:28 final size:29
Alignment explanation
Indices: 229012--229081 Score: 99
Period size: 28 Copynumber: 2.4 Consensus size: 29
229002 ACTATACCAA
*
229012 TTAAAGATATTATAGCTATTTAGAATATAT
1 TTAAAAATATTA-AGCTATTTAGAATATAT
*
229042 TTAAAAATATTAA-CTATTTAGAATGTAT
1 TTAAAAATATTAAGCTATTTAGAATATAT
229070 TTAAAAAT-TTAA
1 TTAAAAATATTAA
229082 ATTAATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 4 0.11
28 22 0.58
29 1 0.03
30 11 0.29
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (29 bp):
TTAAAAATATTAAGCTATTTAGAATATAT
Found at i:229109 original size:32 final size:32
Alignment explanation
Indices: 229067--229129 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
229057 ATTTAGAATG
*
229067 TATTTAAAAATTTAAATTAATTTATATATTTAC
1 TATTTAAAAATTTAAATTAATTCATAT-TTTAC
*
229100 TATTT-AAAATTTATATTAATTCATATTTTA
1 TATTTAAAAATTTAAATTAATTCATATTTTA
229130 TCAATCATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 4 0.14
32 19 0.68
33 5 0.18
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (32 bp):
TATTTAAAAATTTAAATTAATTCATATTTTAC
Found at i:230013 original size:37 final size:37
Alignment explanation
Indices: 229937--230022 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
229927 AAATTGCTTT
* *
229937 AATTTAAATTCTCAGTTACTTTATAAATTCAAAACTC
1 AATTTTAATTTTCAGTTACTTTATAAATTCAAAACTC
* * * *
229974 AATTTTAATTTTCATTTACTTTATAAATTCTAGAGTC
1 AATTTTAATTTTCAGTTACTTTATAAATTCAAAACTC
*
230011 AATTTTAGTTTT
1 AATTTTAATTTT
230023 TAATAATTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (37 bp):
AATTTTAATTTTCAGTTACTTTATAAATTCAAAACTC
Found at i:230037 original size:53 final size:53
Alignment explanation
Indices: 229974--230083 Score: 166
Period size: 53 Copynumber: 2.1 Consensus size: 53
229964 TTCAAAACTC
* * * * * *
229974 AATTTTAATTTTCATTTACTTTATAAATTCTAGAGTCAATTTTAGTTTTTAAT
1 AATTTAAATTTTCAATTACTTAACAAATTCAAAAGTCAATTTTAGTTTTTAAT
230027 AATTTAAATTTTCAATTACTTAACAAATTCAAAAGTCAATTTTAGTTTTTAAT
1 AATTTAAATTTTCAATTACTTAACAAATTCAAAAGTCAATTTTAGTTTTTAAT
230080 AATT
1 AATT
230084 GTTTTTCAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (53 bp):
AATTTAAATTTTCAATTACTTAACAAATTCAAAAGTCAATTTTAGTTTTTAAT
Found at i:230327 original size:25 final size:24
Alignment explanation
Indices: 230288--230344 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 24
230278 AACAACAGGT
* *
230288 CAAAAGAAA-TAACCCTAAAAACC
1 CAAAAGAAACAAACCCGAAAAACC
*
230311 CAAAATGAAACAAACCCGAAATACC
1 CAAAA-GAAACAAACCCGAAAAACC
*
230336 TAAAAGAAA
1 CAAAAGAAA
230345 AGCCCAGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 5 0.18
24 8 0.29
25 15 0.54
ACGTcount: A:0.61, C:0.23, G:0.07, T:0.09
Consensus pattern (24 bp):
CAAAAGAAACAAACCCGAAAAACC
Found at i:235652 original size:27 final size:27
Alignment explanation
Indices: 235622--235676 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
235612 ATCACTATCA
*
235622 CTATCTCCCTTTAGAACAACTTCCTCC
1 CTATCTCCCTCTAGAACAACTTCCTCC
* * *
235649 CTATCTCCCTCTGGAACAGCTTTCTCC
1 CTATCTCCCTCTAGAACAACTTCCTCC
235676 C
1 C
235677 CTCTTTCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.18, C:0.42, G:0.07, T:0.33
Consensus pattern (27 bp):
CTATCTCCCTCTAGAACAACTTCCTCC
Found at i:235816 original size:48 final size:48
Alignment explanation
Indices: 235743--235860 Score: 166
Period size: 48 Copynumber: 2.5 Consensus size: 48
235733 TATATTCACA
* *
235743 CCCTTATCTAAACCCTCTCCTATATTT-AGGTTGCTATTGACAGGATTG
1 CCCTTATCTAAACCCTCTCCTATATTTGA-GCTACTATTGACAGGATTG
* *
235791 CTCTTATCTAAACCCTCTCTTATATTTGAGCTACTATTGACAGGATTG
1 CCCTTATCTAAACCCTCTCCTATATTTGAGCTACTATTGACAGGATTG
* *
235839 CCCTTATCTAAACTCTCACCTA
1 CCCTTATCTAAACCCTCTCCTA
235861 AGTTAATATT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
48 60 0.98
49 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.37
Consensus pattern (48 bp):
CCCTTATCTAAACCCTCTCCTATATTTGAGCTACTATTGACAGGATTG
Found at i:236956 original size:26 final size:26
Alignment explanation
Indices: 236924--236977 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
236914 TTTTAAAATC
236924 TCAATTTTTTTAAACCTTCTCTTATT
1 TCAATTTTTTTAAACCTTCTCTTATT
236950 TCAATTTTTTTAAACCTTCTCTTATT
1 TCAATTTTTTTAAACCTTCTCTTATT
236976 TC
1 TC
236978 TTCTTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.00, T:0.57
Consensus pattern (26 bp):
TCAATTTTTTTAAACCTTCTCTTATT
Found at i:237000 original size:160 final size:160
Alignment explanation
Indices: 236829--237135 Score: 605
Period size: 160 Copynumber: 1.9 Consensus size: 160
236819 ACTCACATGG
*
236829 TTGAATTTTGAAATTTACTTTTTTGCATACAAATTATTTGCTTCTACCACAGTTTACATTTTCTT
1 TTGAATTTTGAAATTTACTTTTCTGCATACAAATTATTTGCTTCTACCACAGTTTACATTTTCTT
236894 CTCAAATTTTAAATTGAAATTTTTAAAATCTCAATTTTTTTAAACCTTCTCTTATTTCAATTTTT
66 CTCAAATTTTAAATTGAAATTTTTAAAATCTCAATTTTTTTAAACCTTCTCTTATTTCAATTTTT
236959 TTAAACCTTCTCTTATTTCTTCTTCTTTTT
131 TTAAACCTTCTCTTATTTCTTCTTCTTTTT
236989 TTGAATTTTGAAATTTACTTTTCTGCATACAAATTATTTGCTTCTACCACAGTTTACATTTTCTT
1 TTGAATTTTGAAATTTACTTTTCTGCATACAAATTATTTGCTTCTACCACAGTTTACATTTTCTT
237054 CTCAAATTTTAAATTGAAATTTTTAAAATCTCAATTTTTTTAAACCTTCTCTTATTTCAATTTTT
66 CTCAAATTTTAAATTGAAATTTTTAAAATCTCAATTTTTTTAAACCTTCTCTTATTTCAATTTTT
237119 TTAAACCTTCTCTTATT
131 TTAAACCTTCTCTTATT
237136 CCAATTTTTT
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 146 1.00
ACGTcount: A:0.27, C:0.16, G:0.04, T:0.52
Consensus pattern (160 bp):
TTGAATTTTGAAATTTACTTTTCTGCATACAAATTATTTGCTTCTACCACAGTTTACATTTTCTT
CTCAAATTTTAAATTGAAATTTTTAAAATCTCAATTTTTTTAAACCTTCTCTTATTTCAATTTTT
TTAAACCTTCTCTTATTTCTTCTTCTTTTT
Found at i:237116 original size:26 final size:26
Alignment explanation
Indices: 237084--237189 Score: 169
Period size: 26 Copynumber: 4.1 Consensus size: 26
237074 TTTTAAAATC
237084 TCAATTTTTTTAAACCTTCTCTTATT
1 TCAATTTTTTTAAACCTTCTCTTATT
237110 TCAATTTTTTTAAACCTTCTCTTATT
1 TCAATTTTTTTAAACCTTCTCTTATT
*
237136 CCAA-TTTTTTAAACCTTCTCTTATT
1 TCAATTTTTTTAAACCTTCTCTTATT
* *
237161 TCAAAATTTTTTAAACCATCTCTTATT
1 TC-AATTTTTTTAAACCTTCTCTTATT
237188 TC
1 TC
237190 TTCTTCTTTT
Statistics
Matches: 75, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
25 22 0.29
26 31 0.41
27 22 0.29
ACGTcount: A:0.25, C:0.21, G:0.00, T:0.54
Consensus pattern (26 bp):
TCAATTTTTTTAAACCTTCTCTTATT
Found at i:237148 original size:51 final size:52
Alignment explanation
Indices: 237089--237187 Score: 173
Period size: 51 Copynumber: 1.9 Consensus size: 52
237079 AAATCTCAAT
* *
237089 TTTTTTAAACCTTCTCTTATTTC-AATTTTTTTAAACCTTCTCTTATTCCAA
1 TTTTTTAAACCTTCTCTTATTTCAAAATTTTTTAAACCATCTCTTATTCCAA
237140 TTTTTTAAACCTTCTCTTATTTCAAAATTTTTTAAACCATCTCTTATT
1 TTTTTTAAACCTTCTCTTATTTCAAAATTTTTTAAACCATCTCTTATT
237188 TCTTCTTCTT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 23 0.51
52 22 0.49
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (52 bp):
TTTTTTAAACCTTCTCTTATTTCAAAATTTTTTAAACCATCTCTTATTCCAA
Found at i:237199 original size:27 final size:27
Alignment explanation
Indices: 237089--237189 Score: 154
Period size: 27 Copynumber: 3.9 Consensus size: 27
237079 AAATCTCAAT
*
237089 TTTTTTAAACCTTCTCTTATTTC-AAT
1 TTTTTTAAACCTTCTCTTATTTCAAAA
*
237115 TTTTTTAAACCTTCTCTTA-TTC-CAA
1 TTTTTTAAACCTTCTCTTATTTCAAAA
237140 TTTTTTAAACCTTCTCTTATTTCAAAA
1 TTTTTTAAACCTTCTCTTATTTCAAAA
*
237167 TTTTTTAAACCATCTCTTATTTC
1 TTTTTTAAACCTTCTCTTATTTC
237190 TTCTTCTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
25 23 0.33
26 22 0.32
27 24 0.35
ACGTcount: A:0.25, C:0.21, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTTTTAAACCTTCTCTTATTTCAAAA
Found at i:240220 original size:22 final size:23
Alignment explanation
Indices: 240181--240237 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
240171 ACCCTTTTAT
*
240181 TTTTATTTTTATTAAAATTTAACCC
1 TTTTA-TTTT-TTAAAATTGAACCC
*
240206 TTTTATTTTTT-AAATTGAATCC
1 TTTTATTTTTTAAAATTGAACCC
*
240228 TTTCATTTTT
1 TTTTATTTTT
240238 CTTTCTGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 18 0.62
23 2 0.07
24 4 0.14
25 5 0.17
ACGTcount: A:0.26, C:0.11, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTATTTTTTAAAATTGAACCC
Found at i:241898 original size:20 final size:20
Alignment explanation
Indices: 241861--241898 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
241851 TTTTTAAGAC
*
241861 TTTAATTAACCCCTTTTAAT
1 TTTAATTAACACCTTTTAAT
241881 TTTAATTAA-ACCTATTTA
1 TTTAATTAACACCT-TTTA
241899 CGCTTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAATTAACACCTTTTAAT
Found at i:246102 original size:44 final size:44
Alignment explanation
Indices: 246047--246132 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
246037 ATAATTATAA
* * * *
246047 ATTAAATTATAATTATTTTTAAATGTGTAATTATCACAAATTAT
1 ATTAAACTATAAATATTTTTAAATATATAATTATCACAAATTAT
*
246091 ATTAAACTATAAATATTTTTAAATATATAATTATCTCAAATT
1 ATTAAACTATAAATATTTTTAAATATATAATTATCACAAATT
246133 TTAATTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (44 bp):
ATTAAACTATAAATATTTTTAAATATATAATTATCACAAATTAT
Found at i:247404 original size:6 final size:6
Alignment explanation
Indices: 247390--247419 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
247380 AAGGCCCAGC
247390 AAAAA- AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
247420 GAAATTGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:248095 original size:2 final size:2
Alignment explanation
Indices: 248088--248127 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
248078 GCAACAAATA
248088 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
248128 GAACTTGGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:253212 original size:20 final size:20
Alignment explanation
Indices: 253159--253205 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
253149 CTCCAGTAAG
* *
253159 ACTTCTACCGGTAGAACTCC
1 ACTTCTACCGATACAACTCC
253179 ACTTCTACCGATACAACTCC
1 ACTTCTACCGATACAACTCC
253199 ACTTCTA
1 ACTTCTA
253206 TTGATACCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.36, G:0.09, T:0.28
Consensus pattern (20 bp):
ACTTCTACCGATACAACTCC
Found at i:263579 original size:433 final size:433
Alignment explanation
Indices: 262773--263640 Score: 1468
Period size: 433 Copynumber: 2.0 Consensus size: 433
262763 CATGGAGGTC
*
262773 TGTCATTGACATTGAGATCATTTAGCCCACATGAGCTGGCCCGATTCAGAGAGCTGTTGGTCAAG
1 TGTCATTGACATTGAGATCATTTAGCCCACATGAGCTGGCCCGATTCAGAGAGCTATTGGTCAAG
**
262838 CCTATCAGTTTGAAGCCTAGGTGGCCCAATAATGAAGCTTTGGCAACTTAAGGCATCTTGGAAAA
66 CCTATCAAATTGAAGCCTAGGTGGCCCAATAATGAAGCTTTGGCAACTTAAGGCATCTTGGAAAA
*
262903 TATGGGAACTAATCCTAGAAGATAAGGGAGAATCATATCTTTAGGATTAGATAGGATTTGATTTG
131 TATGGGAACTAATCCTAGAAGATAAGGAAGAATCATATCTTTAGGATTAGATAGGATTTGATTTG
* * * * * *
262968 GATGTAATCTTTGTAAATCCCATAATTTAAGGGATAGGCTAATCTCATYCGTCGATGTAATTCGA
196 AATGTAATCCTTGTAAATCCCATAATGTAAGGGATAGGCCAATATCATCCGTCGATGTAATTCGA
* * * * *
263033 TCCTGAYCGTYGGTTGTGGGGGAGCTCAACTATAAATAGGGAGCCTCCCCTCATTTGTAACACAC
261 TCCTGACCGTCGATTGTGGGGGAGCTCAACTATAAATAGAGAGCCTCCCCTCATTAGTAACACAC
263098 TCCATTCTTTGTATTGTTTCTTTGTGAATACAATAGAGAGCATTTACTCAAACTCTTCTCCTTTG
326 TCCATTCTTTGTATTGTTTCTTTGTGAATACAATAGAGAGCATTTACTCAAACTCTTCTCCTTTG
* *
263163 TTCTTATTT-GTATTGGCTTTCTGTTGTCTTTTGAGTCTTCGTT
391 TTCTTATTTACT-TTGGCTTTCTGTTGTCTTTTGAGCCTTCGTT
*
263206 TGTCATTGACATTGGGATCATTTAGCCCACATGAGCTGGCCCGATTCAGAGAGCTATTGGTCAAG
1 TGTCATTGACATTGAGATCATTTAGCCCACATGAGCTGGCCCGATTCAGAGAGCTATTGGTCAAG
* * * *
263271 CCTATCAAATTGAAGCTTGGGTGGCCCAATGATGAAGCTTTGGCAACTTAAGGCATCTTGGCAAA
66 CCTATCAAATTGAAGCCTAGGTGGCCCAATAATGAAGCTTTGGCAACTTAAGGCATCTTGGAAAA
263336 TATGGGAACTAATCCTAGAAGATAAGGAAGAATCATATCTTTAGGATTAGATAGGATTTGATTTG
131 TATGGGAACTAATCCTAGAAGATAAGGAAGAATCATATCTTTAGGATTAGATAGGATTTGATTTG
263401 AATGTAATCCTTGTAAATCCCATAATGTAAGGGATAGGCCAATATCATCCGTCGATGTAATTCGA
196 AATGTAATCCTTGTAAATCCCATAATGTAAGGGATAGGCCAATATCATCCGTCGATGTAATTCGA
* * * *
263466 TCTTGACCGTCTATTGTGGGGGAGCTCAACTATAAATAGAGAGCCTTCCCTTATTAGTAACACAC
261 TCCTGACCGTCGATTGTGGGGGAGCTCAACTATAAATAGAGAGCCTCCCCTCATTAGTAACACAC
*
263531 TCCATTCTTTGTATTGTTTCTTTGTGAATACAATAGAGAGCATTTACTCAAACTCTTCTCTTTTG
326 TCCATTCTTTGTATTGTTTCTTTGTGAATACAATAGAGAGCATTTACTCAAACTCTTCTCCTTTG
*
263596 TTCTTATTTACTTTGGCTTTCTGTTGTCTTTTGAGCCTTCTTT
391 TTCTTATTTACTTTGGCTTTCTGTTGTCTTTTGAGCCTTCGTT
263639 TG
1 TG
263641 GCTAATCGCT
Statistics
Matches: 406, Mismatches: 28, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
433 405 1.00
434 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (433 bp):
TGTCATTGACATTGAGATCATTTAGCCCACATGAGCTGGCCCGATTCAGAGAGCTATTGGTCAAG
CCTATCAAATTGAAGCCTAGGTGGCCCAATAATGAAGCTTTGGCAACTTAAGGCATCTTGGAAAA
TATGGGAACTAATCCTAGAAGATAAGGAAGAATCATATCTTTAGGATTAGATAGGATTTGATTTG
AATGTAATCCTTGTAAATCCCATAATGTAAGGGATAGGCCAATATCATCCGTCGATGTAATTCGA
TCCTGACCGTCGATTGTGGGGGAGCTCAACTATAAATAGAGAGCCTCCCCTCATTAGTAACACAC
TCCATTCTTTGTATTGTTTCTTTGTGAATACAATAGAGAGCATTTACTCAAACTCTTCTCCTTTG
TTCTTATTTACTTTGGCTTTCTGTTGTCTTTTGAGCCTTCGTT
Found at i:265714 original size:2 final size:2
Alignment explanation
Indices: 265707--265737 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
265697 ATTTAATGAA
265707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
265738 ATTATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:266112 original size:15 final size:16
Alignment explanation
Indices: 266092--266125 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
266082 AATTTTTTAA
266092 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
266107 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
266123 AAA
1 AAA
266126 AAAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Found at i:266262 original size:18 final size:18
Alignment explanation
Indices: 266231--266265 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
266221 TGTTTAGCAA
**
266231 CATTTTTGGGATAAAAAG
1 CATTTTTGAAATAAAAAG
266249 CATTTTTGAAATAAAAA
1 CATTTTTGAAATAAAAA
266266 TATTACTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (18 bp):
CATTTTTGAAATAAAAAG
Found at i:267092 original size:25 final size:26
Alignment explanation
Indices: 267038--267099 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
267028 AATTATAACT
* *
267038 ATTTAAAAATATTTTTTCATATTTTA
1 ATTTTAAAATATTTTATCATATTTTA
*
267064 ATTTTATAATATTTTAT-AT-TTTTA
1 ATTTTAAAATATTTTATCATATTTTA
267088 GATTTTAAAATA
1 -ATTTTAAAATA
267100 AATATTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 5 0.16
25 12 0.39
26 14 0.45
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (26 bp):
ATTTTAAAATATTTTATCATATTTTA
Found at i:267561 original size:14 final size:13
Alignment explanation
Indices: 267525--267572 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
267515 CATGTTTAAG
*
267525 TTAATTAAAACAA
1 TTAATTAAAAAAA
267538 TT-ATTCAAAAAAA
1 TTAATT-AAAAAAA
267551 GTTAATTAAAACAAA
1 -TTAATTAAAA-AAA
267566 TTAATTA
1 TTAATTA
267573 CATATTAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
12 3 0.10
13 8 0.27
14 13 0.43
15 6 0.20
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.33
Consensus pattern (13 bp):
TTAATTAAAAAAA
Found at i:270727 original size:21 final size:18
Alignment explanation
Indices: 270684--270728 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
270674 AGAACCCTTA
270684 TATGTTGTTATGCGAACC
1 TATGTTGTTATGCGAACC
*
270702 TATGTTGTTATGTGAACC
1 TATGTTGTTATGCGAACC
*
270720 TATGATGTT
1 TATGTTGTT
270729 CGCAAACCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.44
Consensus pattern (18 bp):
TATGTTGTTATGCGAACC
Found at i:274842 original size:20 final size:20
Alignment explanation
Indices: 274804--274843 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
274794 ATTTTTTCTC
*
274804 TCAAAAGGCCCTATGGTCGG
1 TCAAAAGGCCCTATCGTCGG
274824 TCAAAAGGCACC-ATCGTCGG
1 TCAAAAGGC-CCTATCGTCGG
274844 CCACCGTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (20 bp):
TCAAAAGGCCCTATCGTCGG
Found at i:275827 original size:25 final size:25
Alignment explanation
Indices: 275797--275879 Score: 130
Period size: 25 Copynumber: 3.3 Consensus size: 25
275787 CTTCGAAGTT
275797 TGGCTCGAAAGAGCGTAATTCTGTC
1 TGGCTCGAAAGAGCGTAATTCTGTC
* * *
275822 TAGCTCAAAAGAGCGTAATTTTGTC
1 TGGCTCGAAAGAGCGTAATTCTGTC
*
275847 TGGCTCGAAAGAGCATAATTCTGTC
1 TGGCTCGAAAGAGCGTAATTCTGTC
275872 TGGCTCGA
1 TGGCTCGA
275880 GAAAGTAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (25 bp):
TGGCTCGAAAGAGCGTAATTCTGTC
Found at i:275891 original size:25 final size:25
Alignment explanation
Indices: 275797--275921 Score: 117
Period size: 25 Copynumber: 5.0 Consensus size: 25
275787 CTTCGAAGTT
**
275797 TGGCTCGAAAGAGCGTAATTCTGTC
1 TGGCTCGAAAGAGCAAAATTCTGTC
* * ** *
275822 TAGCTCAAAAGAGCGTAATTTTGTC
1 TGGCTCGAAAGAGCAAAATTCTGTC
*
275847 TGGCTCGAAAGAGCATAATTCTGTC
1 TGGCTCGAAAGAGCAAAATTCTGTC
* *
275872 TGGCTCGAGAA-AGTAAAATTCTATC
1 TGGCTCGA-AAGAGCAAAATTCTGTC
* *
275897 TGGGCTCGTAAGAGCTAAATTCTGT
1 T-GGCTCGAAAGAGCAAAATTCTGT
275922 TTGGGCTCCT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
25 65 0.78
26 18 0.22
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (25 bp):
TGGCTCGAAAGAGCAAAATTCTGTC
Found at i:275948 original size:26 final size:26
Alignment explanation
Indices: 275887--275941 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
275877 CGAGAAAGTA
* * *
275887 AAATTCTATCTGGGCTCGTAAGAGCT
1 AAATTCTGTTTGGGCTCCTAAGAGCT
275913 AAATTCTGTTTGGGCTCCTAAGAGCT
1 AAATTCTGTTTGGGCTCCTAAGAGCT
275939 AAA
1 AAA
275942 CTTTGTTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (26 bp):
AAATTCTGTTTGGGCTCCTAAGAGCT
Found at i:278128 original size:50 final size:49
Alignment explanation
Indices: 278074--278227 Score: 136
Period size: 51 Copynumber: 3.1 Consensus size: 49
278064 CTCAATCAAA
* *
278074 TCCACTATAACTTTAGGGATATAGCATTTGATTTTGTAGCTTTATCTTGT
1 TCCACTACAACTTAAGGGATATAG-ATTTGATTTTGTAGCTTTATCTTGT
* * * *
278124 TCCACTACAACTTCATGGAGATAAAGATTTGCTTTCATG-A-CTTTAT-TTCGA
1 TCCACTACAACTT-AAGG-GATATAGATTTGATTT--TGTAGCTTTATCTT-GT
* *
278175 TCCACTACAACTTCAAGGG-TATAGGATTTGGTTTTGTAGCTTCATCTTGT
1 TCCACTACAACTT-AAGGGATATA-GATTTGATTTTGTAGCTTTATCTTGT
278225 TCC
1 TCC
278228 GATTAGTTTT
Statistics
Matches: 84, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
48 2 0.02
49 4 0.05
50 33 0.39
51 36 0.43
52 7 0.08
53 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.41
Consensus pattern (49 bp):
TCCACTACAACTTAAGGGATATAGATTTGATTTTGTAGCTTTATCTTGT
Found at i:289585 original size:16 final size:17
Alignment explanation
Indices: 289553--289590 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
289543 TTCATTCATT
289553 TTCTTTTATAATTTTTC
1 TTCTTTTATAATTTTTC
*
289570 TTCTTTT-TATTTTTTC
1 TTCTTTTATAATTTTTC
289586 -TCTTT
1 TTCTTT
289591 GCTAAAAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 8 0.40
17 7 0.35
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCTTTTATAATTTTTC
Found at i:290459 original size:18 final size:18
Alignment explanation
Indices: 290438--290497 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
290428 AGAATAAAAT
* *
290438 TATAATAAGTATTAGAAG
1 TATAATAAGTAATAGAAA
*
290456 TAT-ATAAAG-AATAAAAA
1 TATAAT-AAGTAATAGAAA
290473 TATAATAAGTAATAGAAA
1 TATAATAAGTAATAGAAA
290491 TAATAAT
1 T-ATAAT
290498 GCGTATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
17 13 0.38
18 16 0.47
19 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (18 bp):
TATAATAAGTAATAGAAA
Found at i:290461 original size:35 final size:35
Alignment explanation
Indices: 290421--290489 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
290411 TATAGATATT
* *
290421 TATATAAAGAATAAAATTATAATAAGTATTAGAAG
1 TATATAAAGAATAAAAATATAATAAGTAATAGAAG
290456 TATATAAAGAATAAAAATATAATAAGTAATAGAA
1 TATATAAAGAATAAAAATATAATAAGTAATAGAA
290490 ATAATAATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (35 bp):
TATATAAAGAATAAAAATATAATAAGTAATAGAAG
Found at i:290476 original size:17 final size:17
Alignment explanation
Indices: 290421--290476 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
290411 TATAGATATT
*
290421 TATATAAAGAATAAAAT
1 TATATAAAGAATAAAAA
* * *
290438 TATA-ATAAGTATTAGAAG
1 TATATA-AAG-AATAAAAA
290456 TATATAAAGAATAAAAA
1 TATATAAAGAATAAAAA
290473 TATA
1 TATA
290477 ATAAGTAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 1 0.03
17 16 0.53
18 12 0.40
19 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (17 bp):
TATATAAAGAATAAAAA
Found at i:290717 original size:15 final size:14
Alignment explanation
Indices: 290675--290741 Score: 64
Period size: 15 Copynumber: 4.6 Consensus size: 14
290665 TGGTGCGAGA
* *
290675 AAAGTAAATACAAA
1 AAAGTAAATGCAAG
*
290689 AAATTAAATGCAAG
1 AAAGTAAATGCAAG
290703 AAAGTAAAGTGCAAG
1 AAAGTAAA-TGCAAG
290718 AATA-TAAATTGCAAG
1 AA-AGTAAA-TGCAAG
*
290733 AAAATAAAT
1 AAAGTAAAT
290742 TGGTAAACAG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
14 20 0.44
15 24 0.53
16 1 0.02
ACGTcount: A:0.61, C:0.06, G:0.13, T:0.19
Consensus pattern (14 bp):
AAAGTAAATGCAAG
Found at i:290742 original size:15 final size:15
Alignment explanation
Indices: 290688--290743 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
290678 GTAAATACAA
290688 AAAATTAAA-TGCAAG
1 AAAA-TAAATTGCAAG
* *
290703 AAAGTAAAGTGCAAG
1 AAAATAAATTGCAAG
*
290718 AATATAAATTGCAAG
1 AAAATAAATTGCAAG
290733 AAAATAAATTG
1 AAAATAAATTG
290744 GTAAACAGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 4 0.11
15 31 0.89
ACGTcount: A:0.57, C:0.05, G:0.16, T:0.21
Consensus pattern (15 bp):
AAAATAAATTGCAAG
Found at i:293386 original size:3 final size:3
Alignment explanation
Indices: 293374--293403 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
293364 ATTCCTTATC
293374 TCT T-T TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
293404 AGTGTTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:293864 original size:18 final size:18
Alignment explanation
Indices: 293838--293887 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
293828 ATATATAAAG
*
293838 AATAAAAATATAATAAGT
1 AATAGAAATATAATAAGT
*
293856 ATTAGAAATATAATAAGT
1 AATAGAAATATAATAAGT
293874 AATAG--ATATAATAA
1 AATAGAAATATAATAA
293888 CGCGTATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 9 0.31
18 20 0.69
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (18 bp):
AATAGAAATATAATAAGT
Found at i:293982 original size:82 final size:82
Alignment explanation
Indices: 293815--293965 Score: 209
Period size: 82 Copynumber: 1.9 Consensus size: 82
293805 ATGGCAAAAT
* * *
293815 AATATATATATATATATATAAAGAATAAAAATATAATAAGTATTAGAAATATAATAAGTAATAGA
1 AATATATATATATATATATAAAGAATAAAAATATAAAAAATATTAGAAATATAATAAGTAATAAA
*
293880 TATAATAACGCGTATTA
66 AATAATAACGCGTATTA
* *
293897 AATATATATATATATATATAAAGAATAAAGATA-AACAAAATAGTTA-AAATAT-ATAATTAATA
1 AATATATATATATATATATAAAGAATAAAAATATAA-AAAATA-TTAGAAATATAATAAGTAATA
293959 AAAATAA
64 AAAATAA
293966 ACTAAGTACG
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
81 16 0.26
82 42 0.69
83 3 0.05
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.32
Consensus pattern (82 bp):
AATATATATATATATATATAAAGAATAAAAATATAAAAAATATTAGAAATATAATAAGTAATAAA
AATAATAACGCGTATTA
Done.