Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007306.1 Hibiscus syriacus cultivar Beakdansim tig00019461_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: 65890
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:371 original size:21 final size:21
Alignment explanation
Indices: 345--428 Score: 141
Period size: 21 Copynumber: 4.0 Consensus size: 21
335 CAATTAAGAA
* *
345 TCAAGGAGCTTTACTTCAAAG
1 TCAAGGCGCCTTACTTCAAAG
*
366 TCAAGGCGCATTACTTCAAAG
1 TCAAGGCGCCTTACTTCAAAG
387 TCAAGGCGCCTTACTTCAAAG
1 TCAAGGCGCCTTACTTCAAAG
408 TCAAGGCGCCTTACTTCAAAG
1 TCAAGGCGCCTTACTTCAAAG
429 CCATAGCTTG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 60 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
TCAAGGCGCCTTACTTCAAAG
Found at i:16251 original size:24 final size:24
Alignment explanation
Indices: 16224--16276 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
16214 TGATCCGACT
16224 CCTGATCAGCACCATTCTGAGACA
1 CCTGATCAGCACCATTCTGAGACA
* *
16248 CCTGATCAGCATCATTCTGAGACC
1 CCTGATCAGCACCATTCTGAGACA
16272 CCTGA
1 CCTGA
16277 ATATCCACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.23
Consensus pattern (24 bp):
CCTGATCAGCACCATTCTGAGACA
Found at i:19277 original size:21 final size:20
Alignment explanation
Indices: 19253--19301 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
19243 AATATAGAGC
19253 AAAGAAAAACAAAGAGAAAAA
1 AAAGAAAAACAAA-AGAAAAA
*
19274 AAAGAAGAAAGAAAAGAAAAA
1 AAAGAA-AAACAAAAGAAAAA
*
19295 GAAGAAA
1 AAAGAAA
19302 TAAAATGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 18 0.72
22 6 0.24
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAGAAAAACAAAAGAAAAA
Found at i:19293 original size:18 final size:17
Alignment explanation
Indices: 19263--19306 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
19253 AAAGAAAAAC
19263 AAAGAGAAAAAAAAGAAG
1 AAAGA-AAAAAAAAGAAG
19281 AAAGAAAAGAAAAAGAAG
1 AAAGAAAA-AAAAAGAAG
*
19299 AAATAAAA
1 AAAGAAAA
19307 TGGATCAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (17 bp):
AAAGAAAAAAAAAGAAG
Found at i:19306 original size:12 final size:12
Alignment explanation
Indices: 19254--19291 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
19244 ATATAGAGCA
19254 AAGAAAAACAAAG
1 AAGAAAAA-AAAG
19267 -AGAAAAAAAAG
1 AAGAAAAAAAAG
*
19278 AAGAAAGAAAAG
1 AAGAAAAAAAAG
19290 AA
1 AA
19292 AAAGAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 4 0.17
12 19 0.83
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAG
Found at i:22261 original size:37 final size:34
Alignment explanation
Indices: 22219--22301 Score: 85
Period size: 37 Copynumber: 2.3 Consensus size: 34
22209 AATTGATCTT
* *
22219 ACTTGAGATTGTTTTCTCTAAAAACAAATTTTGTCTC
1 ACTTGAGATT-TATT-T-TAAAAACAAATTTCGTCTC
*
22256 GCTTGAGTCAATTTATTTTAAAAACAAATTTCGTCTC
1 ACTTGAG---ATTTATTTTAAAAACAAATTTCGTCTC
22293 ACTTGAGAT
1 ACTTGAGAT
22302 AGTCTTCCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
34 2 0.05
37 30 0.77
38 1 0.03
39 3 0.08
40 3 0.08
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (34 bp):
ACTTGAGATTTATTTTAAAAACAAATTTCGTCTC
Found at i:22388 original size:67 final size:66
Alignment explanation
Indices: 22273--22402 Score: 163
Period size: 67 Copynumber: 2.0 Consensus size: 66
22263 TCAATTTATT
* * * * *
22273 TTAAAAACAAATTTCGTCTCACTTGAGATAGTCTTCCTTAAGACACAAACATTTGATATTGTTTT
1 TTAAAAACAAATTTCGTCTCACTTAAGACAGTCTTCCCTAAAACACAAA-ATTTGAAATTGTTTT
22338 TC
65 TC
* * *
22340 TTAAAAACAAATTTTGTCTCACTTAAGACAGT-TTCCCTAGAAATACAAATTTTGAAATTGTTT
1 TTAAAAACAAATTTCGTCTCACTTAAGACAGTCTTCCCTA-AAACACAAAATTTGAAATTGTTT
22403 CACTTGAAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
66 18 0.33
67 36 0.67
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.38
Consensus pattern (66 bp):
TTAAAAACAAATTTCGTCTCACTTAAGACAGTCTTCCCTAAAACACAAAATTTGAAATTGTTTTT
C
Found at i:22513 original size:99 final size:100
Alignment explanation
Indices: 22336--22616 Score: 316
Period size: 99 Copynumber: 2.8 Consensus size: 100
22326 TGATATTGTT
* ** * * *
22336 TTTCTTAAAAACAAATTTTGTCTCACTTAAGACAGTTTCCCTAGAAATACAAATTTTGAAATTGT
1 TTTCTTAAAAACAAATTTTGTCTCACTTGAGACAGTTTTTCTTGAAACACAAATTTTGAAGTTGT
* ***
22401 TTCACTTGAAACAAAATTTATCTTACTTGAGATTG
66 TTCACTTGAAACAAAATTGATAGCACTTGAGATTG
* **
22436 -TTC-TCAAAACAAATTTCATCTCACTTGAGACAGTTTTTCTTCGAAACACAAATTTTGAAGTTG
1 TTTCTTAAAAACAAATTTTGTCTCACTTGAGACAGTTTTTCTT-GAAACACAAATTTTGAAGTTG
*
22499 TTTCACTTGAAACAAAATTGATAGCATTTGAGATTG
65 TTTCACTTGAAACAAAATTGATAGCACTTGAGATTG
* * * *
22535 TTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTG-AGA
1 --TTTCTTAAAAACAAATTTTGTCTCACTTGAGACAGTTTTTCTTGAAACACAAA-TTTTGAAG-
* *
22599 TTGTTTCTCTTTAAACAA
62 TTGTTTCACTTGAAACAA
22617 TTGTATCGCT
Statistics
Matches: 151, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
98 31 0.21
99 53 0.35
102 14 0.09
103 53 0.35
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (100 bp):
TTTCTTAAAAACAAATTTTGTCTCACTTGAGACAGTTTTTCTTGAAACACAAATTTTGAAGTTGT
TTCACTTGAAACAAAATTGATAGCACTTGAGATTG
Found at i:22782 original size:65 final size:66
Alignment explanation
Indices: 22525--22936 Score: 591
Period size: 67 Copynumber: 6.3 Consensus size: 66
22515 ATTGATAGCA
* *
22525 TTTGAGATTGTTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAA
1 TTTGAGATTGTTTCTCTT-GAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAA
22590 CC
65 CC
* * * * * *
22592 TTTGAGATTGTTTCTCTTTAAAC-AA--TTGTATCGCTTGAGACCGTTTCTATGGAAACATAAAT
1 TTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAC
22654 C
66 C
*
22655 TTTGAGATCGTTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTC-CTTTGAAACATAA
1 TTTGAGATTGTTTCTCTTGAAACAAA-TTTTGTCTCGCTTGAGACAGTTTCTC-TTGAAACATAA
22719 ACC
64 ACC
*
22722 TTTGATATTGTTTCTCTTGAAACAAA-TTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAC
22786 C
66 C
*
22787 TTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACATAAAA
1 TTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACAT-AAA
22852 CC
65 CC
* ** * * *
22854 TTTGAGATTGTTTCTCTTGAAACAAATTTTGTATCTTTTGAGACATTTTCTTTTGAAACATAAGC
1 TTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAC
22919 C
66 C
*
22920 TTTAAGATTGTTTCTCT
1 TTTGAGATTGTTTCTCT
22937 CAAAATAAAT
Statistics
Matches: 311, Mismatches: 26, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
63 54 0.17
64 2 0.01
65 64 0.21
66 58 0.19
67 133 0.43
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.41
Consensus pattern (66 bp):
TTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAC
C
Found at i:22853 original size:132 final size:131
Alignment explanation
Indices: 22525--22962 Score: 603
Period size: 132 Copynumber: 3.3 Consensus size: 131
22515 ATTGATAGCA
*
22525 TTTGAGATTGTTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAA
1 TTTGAGATTGTTTCTCTT-AAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAA
* * *
22590 CCTTTGAGATTGTTTCTCTTTAAAC-AA-TTGTATCGCTTGAGACCGTTTCTATGGAAACATAAA
65 CCTTTGAGATTGTTTCTCTTGAAACAAATTTGTATCGCTTGAGACAGTTTCTATTGAAACATAAA
*
22653 TC
130 CC
* *
22655 TTTGAGATCGTTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGACAGTTTC-CTTTGAAACATAA
1 TTTGAGATTGTTTCTCTTAAAACAAA-TTTTGTCTCGCTTGAGACAGTTTCTC-TTGAAACATAA
* * *
22719 ACCTTTGATATTGTTTCTCTTGAAACAAATTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAA
64 ACCTTTGAGATTGTTTCTCTTGAAACAAATTTGTATCGCTTGAGACAGTTTCTATTGAAACATAA
22784 ACC
129 ACC
* *
22787 TTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACATAAAA
1 TTTGAGATTGTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACAT-AAA
** * *
22852 CCTTTGAGATTGTTTCTCTTGAAACAAATTTTGTATCTTTTGAGACATTTTCTTTTGAAACATAA
65 CCTTTGAGATTGTTTCTCTTGAAACAAA-TTTGTATCGCTTGAGACAGTTTCTATTGAAACATAA
*
22917 GCC
129 ACC
* * * ** *
22920 TTTAAGATTGTTTCTCTCAAAATAAATTTCATCTCACTTGAGA
1 TTTGAGATTGTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGA
22963 TAATTTTCCC
Statistics
Matches: 275, Mismatches: 26, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
129 8 0.03
130 75 0.27
131 34 0.12
132 89 0.32
133 69 0.25
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.41
Consensus pattern (131 bp):
TTTGAGATTGTTTCTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCTCTTGAAACATAAAC
CTTTGAGATTGTTTCTCTTGAAACAAATTTGTATCGCTTGAGACAGTTTCTATTGAAACATAAAC
C
Found at i:23634 original size:139 final size:139
Alignment explanation
Indices: 23249--23892 Score: 907
Period size: 139 Copynumber: 4.6 Consensus size: 139
23239 ATCATCATCA
* * *
23249 ACCGACTAGATCTCCTCAACACGTAGGAGCAGCGTCATCCTCAGACAACCAGACTTCCTCATCAC
1 ACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCAC
* * * *
23314 GTAAGAACCGTGTTGTCTCCAAGTTATCCCTAAAGACAGCTAGACGTCCTCATCACGTAGGAAAA
66 GTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCATCACATAGGAACA
*
23379 ATGTCTTCC
131 ATGTCGTCC
* * * * *
23388 ACCGACCAGATCTCCTTAACGCGTAGGAGTA--GTCATCCTCATACAATTAGACTTCCTCATCAT
1 ACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCAC
* * * * *
23451 GTAAGAACTGTGTTGTCACCAAATCATCCCTAAAGACGGCTAGACGTCCTCATCACATAGGAACA
66 GTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCATCACATAGGAACA
23516 ATGTCGTCC
131 ATGTCGTCC
* *
23525 ACCGACCAAATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAAACTTCCTCATCAC
1 ACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCAC
* * * * * *
23590 ATAGGAACCGTGTTGTCTCCAAATTATCCCTAGAGACGGCTAGACGACCTCATAACGTAGGAACA
66 GTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCATCACATAGGAACA
23655 ATGTCGTCC
131 ATGTCGTCC
* *
23664 ACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTTAGGCAATCAGACTTCCTCATCAC
1 ACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCAC
* *
23729 GTAGGAACTGTGTTGTCTCCAAATTATCCCTAAAGACAGCTAGACATCCTCATCACGA-AGGAAC
66 GTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCATCAC-ATAGGAAC
* *
23793 AATTTCGTTC
130 AATGTCGTCC
* * ** * *
23803 ACCGACCAGATCTCCTCAACGCGAATGAGCAATGTCATCCTCAGACAATCAGTCTTCCTTATCAC
1 ACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCAC
*
23868 GTAGGAACCGTGTTGTCACCAAATT
66 GTAGGAACCGTGTTGTCTCCAAATT
23893 GTCTCTAGAT
Statistics
Matches: 446, Mismatches: 56, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
137 122 0.27
139 324 0.73
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (139 bp):
ACCGACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCAC
GTAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCATCACATAGGAACA
ATGTCGTCC
Found at i:24459 original size:20 final size:20
Alignment explanation
Indices: 24426--24464 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24416 GTGGTGATGA
24426 TTGGGAAGTAAGGTCGTCGG
1 TTGGGAAGTAAGGTCGTCGG
* *
24446 TTGGGGAGTGAGGTCGTCG
1 TTGGGAAGTAAGGTCGTCG
24465 TTTAGGGTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.10, G:0.49, T:0.26
Consensus pattern (20 bp):
TTGGGAAGTAAGGTCGTCGG
Found at i:25077 original size:4 final size:4
Alignment explanation
Indices: 25068--25092 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
25058 TTAACCATTA
25068 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
25093 CATTGTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:25342 original size:225 final size:221
Alignment explanation
Indices: 25076--25636 Score: 627
Period size: 225 Copynumber: 2.5 Consensus size: 221
25066 TATTATTTAT
* *
25076 TTATTTA-TTTA-TTTATTCATTGTTTCTAATATTTTATTCGACCTTGTGGTAACTAGATCTGGG
1 TTATTTATTTTATTTTATTAATTGTTTCTAATATTCTATTCGACCTTGTGGTAACTAGATCTGGG
*
25139 ATATGATCCACATTATTATGGTTCGGACTCTGTTAACCACTAATTTTTTTTATTTTATTTTACTT
66 -TATGATCCACATTATTATGGTTCGGACTCTGTTAACCACTAA-CTTTTTTATTTTA---T--TT
* * * *
25204 TATTAATTTGTTT-ATAATATTCTATTCAACTTTGTGGTGACCAGATTCGGGATATGATCAAACA
124 TATTAATTTGTTTGA-AATATTCGATTCAACCTTGTGGTGACCAGATCCGGGACATGATC-AACA
*
25268 TTATTATGGTTCGGACTCTGCTAACCACT-A-A-C
187 TTATTATGGTTCAGACTCTGCTAACCACTAATATC
*
25300 TT-TTTATTTTATTTTATTAATTGTTTCTAATATTCTATTCGACCTTGTGGTAA-TCAGATCCAG
1 TTATTTATTTTATTTTATTAATTGTTTCTAATATTCTATTCGACCTTGTGGTAACT-AGAT-CTG
* * * *
25363 GGTATGATCCACATTATTATGATTTGGACTCTCTTAACCGCTAACTTTTTTATTTTATTTTATTA
64 GGTATGATCCACATTATTATGGTTCGGACTCTGTTAACCACTAACTTTTTTATTTTATTTTATTA
* * * * *
25428 ATTTGTTTGAATTGTTCGATTCGACCTTGTGGTGACCAGATCCGGGGCATGATCCACATTATTAT
129 ATTTGTTTGAAATATTCGATTCAACCTTGTGGTGACCAGATCCGGGACATGATCAACATTATTAT
* *
25493 GGTTCAGACTCTGTTAACCACTAATTTTTTATTTT
194 GGTTCAGACTCTGCTAACCACTAA-----TA--TC
* * * *
25528 TTATTGTATTTTATTTTATTAATTTGTTT-GAATTATTCGATTCGACCTTGTGGTGACCAGATCT
1 TTATT-TATTTTATTTTATTAA-TTGTTTCTAA-TATTCTATTCGACCTTGTGGTAACTAGATCT
*
25592 GGGGGTATGATCCACATTATTATGGTTCGGACTCTGCTAACCACT
63 --GGGTATGATCCACATTATTATGGTTCGGACTCTGTTAACCACT
25637 GACCGCTAAC
Statistics
Matches: 285, Mismatches: 30, Indels: 36
0.81 0.09 0.10
Matches are distributed among these distances:
218 30 0.11
219 52 0.18
220 1 0.00
221 1 0.00
223 4 0.01
224 19 0.07
225 82 0.29
226 4 0.01
228 2 0.01
229 2 0.01
230 19 0.07
231 31 0.11
232 38 0.13
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (221 bp):
TTATTTATTTTATTTTATTAATTGTTTCTAATATTCTATTCGACCTTGTGGTAACTAGATCTGGG
TATGATCCACATTATTATGGTTCGGACTCTGTTAACCACTAACTTTTTTATTTTATTTTATTAAT
TTGTTTGAAATATTCGATTCAACCTTGTGGTGACCAGATCCGGGACATGATCAACATTATTATGG
TTCAGACTCTGCTAACCACTAATATC
Found at i:25480 original size:110 final size:111
Alignment explanation
Indices: 25111--25636 Score: 564
Period size: 110 Copynumber: 4.6 Consensus size: 111
25101 CTAATATTTT
* * * * *
25111 ATTCGACCTTGTGGTAACTAGATCTGGGATATGATCCACATTATTATGGTTCGGACTCTGTTAAC
1 ATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCGGACTCTCTTAAC
* * *
25176 CACTAATTTTTTTTATTTTATTTTACTTTATTAATTTGTTT-ATAATATTCT
66 CACTAATCTTTTTTATTTTA---T--TTTATTAATTTGTTTGA-ATTATTCG
* * * * *
25227 ATTCAACTTTGTGGTGACCAGATTCGGGATATGATCAAACATTATTATGGTTCGGACTCTGC-TA
1 ATTCGACCTTGTGGTGACCAGATCCGGGGTATGATC-CACATTATTATGGTTCGGACTCT-CTTA
* *
25291 ACCACTAA-C-TTTTTATTTTATTTTATTAA-TTGTTTCTAA-TATTCT
64 ACCACTAATCTTTTTTATTTTATTTTATTAATTTGTTT-GAATTATTCG
* * * * *
25336 ATTCGACCTTGTGGTAATCAGATCCAGGGTATGATCCACATTATTATGATTTGGACTCTCTTAAC
1 ATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCGGACTCTCTTAAC
* *
25401 CGCTAA-CTTTTTTATTTTATTTTATTAATTTGTTTGAATTGTTCG
66 CACTAATCTTTTTTATTTTATTTTATTAATTTGTTTGAATTATTCG
* * *
25446 ATTCGACCTTGTGGTGACCAGATCCGGGGCATGATCCACATTATTATGGTTCAGACTCTGTTAAC
1 ATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCGGACTCTCTTAAC
*
25511 CACTAATTTTTTATTTTTTATTGTATTTTATTTTATTAATTTGTTTGAATTATTCG
66 CACT-A------A-TCTTT-TT-TATTTTATTTTATTAATTTGTTTGAATTATTCG
*
25567 ATTCGACCTTGTGGTGACCAGATCTGGGGGTATGATCCACATTATTATGGTTCGGACTCTGC-TA
1 ATTCGACCTTGTGGTGACCAGATC-CGGGGTATGATCCACATTATTATGGTTCGGACTCT-CTTA
25631 ACCACT
64 ACCACT
25637 GACCGCTAAC
Statistics
Matches: 351, Mismatches: 38, Indels: 36
0.83 0.09 0.08
Matches are distributed among these distances:
107 1 0.00
108 30 0.09
109 63 0.18
110 79 0.23
111 2 0.01
112 1 0.00
115 11 0.03
116 30 0.09
117 33 0.09
119 3 0.01
120 2 0.01
121 56 0.16
122 40 0.11
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (111 bp):
ATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCGGACTCTCTTAAC
CACTAATCTTTTTTATTTTATTTTATTAATTTGTTTGAATTATTCG
Found at i:27392 original size:21 final size:21
Alignment explanation
Indices: 27368--27458 Score: 80
Period size: 21 Copynumber: 4.3 Consensus size: 21
27358 TCCCCATCCC
27368 CCACCTCCACCTCCACCACCA
1 CCACCTCCACCTCCACCACCA
* *
27389 CCACCTCCTCCTCCTCCACCA
1 CCACCTCCACCTCCACCACCA
*
27410 CC-CCATCC-CCATGCC-CAACCA
1 CCACC-TCCACC-T-CCACCACCA
* *
27431 CCACCTCCACCCCCACCCCCA
1 CCACCTCCACCTCCACCACCA
*
27452 CCTCCTC
1 CCACCTC
27459 TATTCTTGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
20 6 0.11
21 45 0.79
22 6 0.11
ACGTcount: A:0.19, C:0.68, G:0.01, T:0.12
Consensus pattern (21 bp):
CCACCTCCACCTCCACCACCA
Found at i:27416 original size:57 final size:57
Alignment explanation
Indices: 27331--27458 Score: 175
Period size: 57 Copynumber: 2.2 Consensus size: 57
27321 ATTTATACCA
* * * * *
27331 ACCACCACCACCTCCTCCTCCTCCCCATCCCCATCCCCCACCTCCACCTCCACCACC
1 ACCACCACCTCCTCCTCCACCACCCCATCCCCATCCCCAACCACCACCTCCACCACC
* * *
27388 ACCACCTCCTCCTCCTCCACCACCCCATCCCCATGCCCAACCACCACCTCCACCCCC
1 ACCACCACCTCCTCCTCCACCACCCCATCCCCATCCCCAACCACCACCTCCACCACC
*
27445 ACCCCCACCTCCTC
1 ACCACCACCTCCTC
27459 TATTCTTGTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 61 1.00
ACGTcount: A:0.18, C:0.68, G:0.01, T:0.13
Consensus pattern (57 bp):
ACCACCACCTCCTCCTCCACCACCCCATCCCCATCCCCAACCACCACCTCCACCACC
Found at i:27435 original size:51 final size:51
Alignment explanation
Indices: 27331--27441 Score: 147
Period size: 51 Copynumber: 2.2 Consensus size: 51
27321 ATTTATACCA
* *
27331 ACCACCACCACCTCCTCCTCCTCCCCATCCCCATCCCCCACCTCCACCTCC
1 ACCACCACCACCTCCTCCTCCTCCCCATCCCCATCCCCCACCTCAACCACC
27382 ACCACCACCACCTCCTCCTCCTCCACCA-CCCCAT-CCCCATGCC-CAACCACC
1 ACCACCACCACCTCCTCCTCCTCC-CCATCCCCATCCCCCA--CCTCAACCACC
*
27433 ACCTCCACC
1 ACCACCACC
27442 CCCACCCCCA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
50 5 0.09
51 44 0.81
52 5 0.09
ACGTcount: A:0.19, C:0.67, G:0.01, T:0.14
Consensus pattern (51 bp):
ACCACCACCACCTCCTCCTCCTCCCCATCCCCATCCCCCACCTCAACCACC
Found at i:27738 original size:2 final size:2
Alignment explanation
Indices: 27731--27758 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27721 AACCCTCACC
27731 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27759 CTCGGGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29203 original size:16 final size:16
Alignment explanation
Indices: 29182--29213 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
29172 ACATTTTTAA
29182 AAGTCGGATTTGATTT
1 AAGTCGGATTTGATTT
29198 AAGTCGGATTTGATTT
1 AAGTCGGATTTGATTT
29214 TAGGTGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (16 bp):
AAGTCGGATTTGATTT
Found at i:35593 original size:17 final size:16
Alignment explanation
Indices: 35571--35607 Score: 58
Period size: 15 Copynumber: 2.3 Consensus size: 16
35561 ATATGTCGAT
35571 GATATTATAATTACAAG
1 GATATT-TAATTACAAG
35588 GATA-TTAATTACAAG
1 GATATTTAATTACAAG
35603 GATAT
1 GATAT
35608 CTGCTGAAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 14 0.74
16 1 0.05
17 4 0.21
ACGTcount: A:0.46, C:0.05, G:0.14, T:0.35
Consensus pattern (16 bp):
GATATTTAATTACAAG
Found at i:35598 original size:15 final size:15
Alignment explanation
Indices: 35578--35607 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
35568 GATGATATTA
35578 TAATTACAAGGATAT
1 TAATTACAAGGATAT
35593 TAATTACAAGGATAT
1 TAATTACAAGGATAT
35608 CTGCTGAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (15 bp):
TAATTACAAGGATAT
Found at i:35823 original size:14 final size:14
Alignment explanation
Indices: 35804--35835 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
35794 GCACTCGGAT
35804 ACAACAAGTTGATG
1 ACAACAAGTTGATG
35818 ACAACAAGTTGATG
1 ACAACAAGTTGATG
35832 ACAA
1 ACAA
35836 TAAGGGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (14 bp):
ACAACAAGTTGATG
Found at i:38677 original size:6 final size:6
Alignment explanation
Indices: 38666--38691 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
38656 TCACTCCTAT
38666 TGAAGA TGAAGA TGAAGA TGAAGA TG
1 TGAAGA TGAAGA TGAAGA TGAAGA TG
38692 CAGCAATCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.35, T:0.19
Consensus pattern (6 bp):
TGAAGA
Found at i:45680 original size:21 final size:20
Alignment explanation
Indices: 45636--45681 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
45626 TGAATGGTCA
*
45636 TTTTATGATAAAATGATAAT
1 TTTTATGATAAAATGATAAC
45656 TTTTATTGATCAAAATG-TAAC
1 TTTTA-TGAT-AAAATGATAAC
45677 TTTTA
1 TTTTA
45682 AAGTTGAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 12 0.52
22 6 0.26
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (20 bp):
TTTTATGATAAAATGATAAC
Found at i:50669 original size:21 final size:20
Alignment explanation
Indices: 50645--50684 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
50635 TTGATTAAAT
*
50645 ATTTAATAAATTTTTTTTTAA
1 ATTTAA-AAATTTATTTTTAA
*
50666 ATTTAAATATTTATTTTTA
1 ATTTAAAAATTTATTTTTA
50685 CTTGAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTAAAAATTTATTTTTAA
Found at i:54886 original size:29 final size:29
Alignment explanation
Indices: 54844--54932 Score: 178
Period size: 29 Copynumber: 3.1 Consensus size: 29
54834 CTACAGTGGT
54844 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
54873 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
54902 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
54931 CT
1 CT
54933 GTGTGTATTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.13, C:0.31, G:0.37, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:54991 original size:18 final size:18
Alignment explanation
Indices: 54954--55007 Score: 101
Period size: 18 Copynumber: 3.1 Consensus size: 18
54944 AGAATAGGGC
54954 CATGCAATCAACAT-GGA
1 CATGCAATCAACATGGGA
54971 CATGCAATCAACATGGGA
1 CATGCAATCAACATGGGA
54989 CATGCAATCAACATGGGA
1 CATGCAATCAACATGGGA
55007 C
1 C
55008 GTGGGAATGC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 14 0.39
18 22 0.61
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (18 bp):
CATGCAATCAACATGGGA
Found at i:55041 original size:45 final size:45
Alignment explanation
Indices: 54990--55078 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
54980 AACATGGGAC
54990 ATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCT
1 ATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCT
55035 ATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGC
1 ATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGC
55079 ATGGGGTGGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.27, C:0.13, G:0.43, T:0.17
Consensus pattern (45 bp):
ATGCAATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCT
Found at i:55093 original size:15 final size:15
Alignment explanation
Indices: 55053--55232 Score: 137
Period size: 15 Copynumber: 11.1 Consensus size: 15
55043 AACATGGGAC
55053 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* *
55069 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
55084 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
* *
55099 G-GAGGGATCAACATGGG
1 GTG-GGAAT--GCATGGG
55116 ATGTGGGAATGCATGGGG
1 --GTGGGAATGCAT-GGG
* *
55134 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
55149 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
55166 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* * *
55182 GAGGGGATGGTGCATTGGAC
1 G-TGGGA--ATGCA-TGG-G
55202 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
55217 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
55232 G
1 G
55233 GAGGGGATGG
Statistics
Matches: 131, Mismatches: 18, Indels: 31
0.73 0.10 0.17
Matches are distributed among these distances:
14 1 0.01
15 52 0.40
16 27 0.21
17 30 0.23
18 3 0.02
19 15 0.11
20 3 0.02
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:55115 original size:65 final size:66
Alignment explanation
Indices: 55040--55166 Score: 229
Period size: 65 Copynumber: 1.9 Consensus size: 66
55030 ATGCTATGCA
55040 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGG-GTGGGAATGCATGGGGGAGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
55104 G
66 G
*
55105 ATCAACATGGGATGTGGGAATGCATGGGGGAGGGGATGCATGGGACGTGGGAATGCATGGGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGA-GTGGGAATGCATGGGG
55167 TGGGAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 43 0.73
67 16 0.27
ACGTcount: A:0.24, C:0.09, G:0.50, T:0.17
Consensus pattern (66 bp):
ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
G
Found at i:55171 original size:82 final size:83
Alignment explanation
Indices: 55055--55231 Score: 234
Period size: 82 Copynumber: 2.2 Consensus size: 83
55045 CATGGGACGT
* * *
55055 GGGAATGCATGGG-GGAGGGGATGCATGGGGTGGGAATGCATGGGGGA-GGGAT-CAACATGGGA
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
*
55117 TGTGGGAATGCATGGGGGA
66 CGTGGGAATGCAT-GGGGA
* *** *
55136 GGGGATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTGCATTGGA
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
*
55201 CGTGGGAATGCATGGGGT
66 CGTGGGAATGCATGGGGA
55219 GGGAATGCATGGG
1 GGGAATGCATGGG
55232 GGAGGGGATG
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
81 12 0.15
82 31 0.38
83 21 0.26
84 18 0.22
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (83 bp):
GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGCAACATGGGA
CGTGGGAATGCATGGGGA
Found at i:55179 original size:65 final size:64
Alignment explanation
Indices: 55043--55236 Score: 207
Period size: 65 Copynumber: 3.0 Consensus size: 64
55033 CTATGCAATC
*
55043 AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGGAT
1 AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGAAT
*
55107 CAACATGGGATGTGGGAATGCATGGGGGAGGGGATGCATGGGACGTGGGAATGCATGGGGTG-GG
1 -AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGG--GTGGGAATGCATGGGG-GAGG
55171 AAT
62 AAT
* * ** * *
55174 -GCATGGGGGA-G-GGGATGGTGCATTGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAG
1 AACAT--GGGACGTGGGA--ATGCA-TGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAG
55236 G
61 G
55237 GGATGGTGCA
Statistics
Matches: 112, Mismatches: 8, Indels: 17
0.82 0.06 0.12
Matches are distributed among these distances:
65 48 0.43
66 19 0.17
67 28 0.25
68 17 0.15
ACGTcount: A:0.22, C:0.08, G:0.53, T:0.17
Consensus pattern (64 bp):
AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGAAT
Found at i:55217 original size:51 final size:51
Alignment explanation
Indices: 55118--55256 Score: 248
Period size: 51 Copynumber: 2.8 Consensus size: 51
55108 AACATGGGAT
*
55118 GTGGGAATGCATGGGGGAGGGGA---TGCATGGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
55166 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
55217 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGG
55257 AACTGTGCAT
Statistics
Matches: 87, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
48 23 0.26
51 64 0.74
ACGTcount: A:0.19, C:0.08, G:0.54, T:0.19
Consensus pattern (51 bp):
GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
Found at i:55372 original size:32 final size:32
Alignment explanation
Indices: 55331--55394 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
55321 AAGGTCCTGC
55331 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1 TGCATGCATGCGTTGCATCATAGCTCATAGCT
55363 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1 TGCATGCATGCGTTGCATCATAGCTCATAGCT
55395 CAGAGATTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (32 bp):
TGCATGCATGCGTTGCATCATAGCTCATAGCT
Found at i:55752 original size:21 final size:21
Alignment explanation
Indices: 55704--55752 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
55694 ACTAAAATCT
*
55704 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTGTAAGTATA
* *
55726 AATTATTAGTTTGTAAGTTTA
1 AGTTATTAGTTTGTAAGTATA
55747 AGTTAT
1 AGTTAT
55753 ATTATATTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
AGTTATTAGTTTGTAAGTATA
Found at i:55762 original size:28 final size:30
Alignment explanation
Indices: 55729--55791 Score: 94
Period size: 28 Copynumber: 2.2 Consensus size: 30
55719 TAGTATAAAT
*
55729 TATTAGTTTGTAAGTTTAAG-T-TATATTA
1 TATTAGTTTATAAGTTTAAGTTATATATTA
*
55757 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATAAGTTTAAGTTATATATTA
55787 TATTA
1 TATTA
55792 TATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 18 0.58
29 1 0.03
30 12 0.39
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (30 bp):
TATTAGTTTATAAGTTTAAGTTATATATTA
Found at i:56625 original size:26 final size:25
Alignment explanation
Indices: 56596--56654 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
56586 AAATCATATT
*
56596 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
56622 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
56648 ATTATTA
1 ATTATTA
56655 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:59554 original size:26 final size:26
Alignment explanation
Indices: 59525--59838 Score: 219
Period size: 26 Copynumber: 12.8 Consensus size: 26
59515 TTTGATGATT
59525 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
59551 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
59577 TAATAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * *
59599 TA--ACT-ATTTAATGAACAAAT-ATT-
1 TAGTAATGATTTGAT-AA-TAATCATTA
59622 TAGTAATGA-TTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
59647 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
59673 TAATAATGATTT-ATTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** * * *
59699 TAAAAATGATTTAATAATGAATTA-AA
1 TAGTAATGATTTGATAAT-AATCATTA
* *
59725 TATTTAATGATTTG------ATGATT-
1 TA-GTAATGATTTGATAATAATCATTA
*
59745 TAGTAATGATTTGATAATGAT--TTA
1 TAGTAATGATTTGATAATAATCATTA
* * * * * * *
59769 -AATATTTA-ATGAT-TTGATGATT-
1 TAGTAATGATTTGATAATAATCATTA
59791 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
59817 TAGTAATGATTTGATAATAATC
1 TAGTAATGATTTGATAATAATC
59839 TGTGCATGGC
Statistics
Matches: 230, Mismatches: 29, Indels: 58
0.73 0.09 0.18
Matches are distributed among these distances:
19 11 0.05
20 9 0.04
21 4 0.02
22 7 0.03
23 34 0.15
24 12 0.05
25 26 0.11
26 114 0.50
27 13 0.06
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:59664 original size:122 final size:120
Alignment explanation
Indices: 59522--59834 Score: 386
Period size: 122 Copynumber: 2.6 Consensus size: 120
59512 TGATTTGATG
59522 ATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGAT
1 ATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGAT
* *
59587 TTAATAATGATTTAACTATTTAATGAACAAAT-ATTTAGTAATGATTGATAATAATC
66 TTAATAATGAATTAAATATTTAATGAACAAATGATTTAGTAATGATT--TAATAATC
* *
59643 ATTATAGTAATGATTTGATAATAATCATTATAATAATGATTT-ATTAATAATCATTATAAAAATG
1 ATT-TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGA-TAATAATCATTATAATAATG
**** * *
59707 ATTTAATAATGAATTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATG
64 ATTTAATAATGAATTAAATATTTAATGAACAAATGATTTAGTAATGATTTAATAATC
* * * * *
59764 ATTTA--AAT-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAATAATCATTATAGTAATG
1 ATTTAGTAATGATTTGAT-A-ATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATG
*
59825 ATTTGATAAT
64 ATTTAATAAT
59835 AATCTGTGCA
Statistics
Matches: 168, Mismatches: 18, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
117 6 0.04
118 42 0.25
119 7 0.04
120 2 0.01
121 13 0.08
122 84 0.50
123 14 0.08
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.44
Consensus pattern (120 bp):
ATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGAT
TTAATAATGAATTAAATATTTAATGAACAAATGATTTAGTAATGATTTAATAATC
Found at i:59673 original size:96 final size:98
Alignment explanation
Indices: 59470--59690 Score: 365
Period size: 96 Copynumber: 2.3 Consensus size: 98
59460 ATGTATTTAT
* ****
59470 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
59535 TTGATAATAATCATTATAGTAATGATTTGATAA
66 TTGATAATAATCATTATAGTAATGATTTGATAA
*
59568 TAATCATTATAATAATGATTTAATAATGATTTAACTATTTAATGAACAAAT-ATTTAGTAATGA-
1 TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
59631 TTGATAATAATCATTATAGTAATGATTTGATAA
66 TTGATAATAATCATTATAGTAATGATTTGATAA
*
59664 TAATCATTATAATAATGATTTATTAAT
1 TAATCATTATAATAATGATTTAATAAT
59691 AATCATTATA
Statistics
Matches: 116, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
96 59 0.51
97 12 0.10
98 45 0.39
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (98 bp):
TAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGAACAAATGATTTAGTAATGAT
TTGATAATAATCATTATAGTAATGATTTGATAA
Found at i:59751 original size:19 final size:19
Alignment explanation
Indices: 59729--59805 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
59719 ATTAAATATT
59729 TAATGATTTGATGATTTAG
1 TAATGATTTGATGATTTAG
*
59748 TAATGATTTGATAATGATTTAAATATT
1 TAATGATTTG---ATGA-TT---TA-G
59775 TAATGATTTGATGATTTAG
1 TAATGATTTGATGATTTAG
59794 TAATGATTTGAT
1 TAATGATTTGAT
59806 AATAATCATT
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
19 22 0.46
20 2 0.04
22 4 0.08
23 4 0.08
24 4 0.08
26 2 0.04
27 10 0.21
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (19 bp):
TAATGATTTGATGATTTAG
Found at i:59753 original size:46 final size:46
Alignment explanation
Indices: 59703--59808 Score: 194
Period size: 46 Copynumber: 2.3 Consensus size: 46
59693 TCATTATAAA
*
59703 AATGATTTAATAATGAATTAAATATTTAATGATTTGATGATTTAGT
1 AATGATTTGATAATGAATTAAATATTTAATGATTTGATGATTTAGT
*
59749 AATGATTTGATAATGATTTAAATATTTAATGATTTGATGATTTAGT
1 AATGATTTGATAATGAATTAAATATTTAATGATTTGATGATTTAGT
59795 AATGATTTGATAAT
1 AATGATTTGATAAT
59809 AATCATTATA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (46 bp):
AATGATTTGATAATGAATTAAATATTTAATGATTTGATGATTTAGT
Found at i:59801 original size:11 final size:10
Alignment explanation
Indices: 59729--59808 Score: 59
Period size: 11 Copynumber: 8.4 Consensus size: 10
59719 ATTAAATATT
59729 TAATGATTTG
1 TAATGATTTG
59739 --ATGATTTAG
1 TAATGATTT-G
59748 TAATGATTTG
1 TAATGATTTG
59758 ATAATGATTT-
1 -TAATGATTTG
*
59768 AAAT-A-TT-
1 TAATGATTTG
59775 TAATGATTTG
1 TAATGATTTG
59785 --ATGATTTAG
1 TAATGATTT-G
59794 TAATGATTTG
1 TAATGATTTG
59804 ATAAT
1 -TAAT
59809 AATCATTATA
Statistics
Matches: 57, Mismatches: 2, Indels: 21
0.71 0.03 0.26
Matches are distributed among these distances:
7 5 0.09
8 16 0.28
9 7 0.12
10 2 0.04
11 27 0.47
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.47
Consensus pattern (10 bp):
TAATGATTTG
Found at i:61774 original size:43 final size:45
Alignment explanation
Indices: 61701--61787 Score: 126
Period size: 43 Copynumber: 2.0 Consensus size: 45
61691 AACAAACAAA
61701 TATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 TATAACTTAACTATTTAACTAACACAAACTAATT-AATAATTTTTT
* *
61747 TATAAC-TAACTA-TTAAC-AATACAAACTAATTAATTATTTTT
1 TATAACTTAACTATTTAACTAACACAAACTAATTAATAATTTTT
61788 AACTATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
42 9 0.23
43 13 0.33
44 5 0.13
45 6 0.15
46 6 0.15
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (45 bp):
TATAACTTAACTATTTAACTAACACAAACTAATTAATAATTTTTT
Found at i:62016 original size:4 final size:4
Alignment explanation
Indices: 61989--62045 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
61979 TTTCGAATTC
* * **
61989 TTCT TACT TTCCT TTC- TCCT TTCT TTCT TTCT TTCCT TTCT CCCT TTCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTCT
62038 TTCT TTCT
1 TTCT TTCT
62046 CGATGGCAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
3 2 0.05
4 32 0.76
5 8 0.19
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (4 bp):
TTCT
Found at i:62022 original size:24 final size:25
Alignment explanation
Indices: 61989--62045 Score: 98
Period size: 24 Copynumber: 2.3 Consensus size: 25
61979 TTTCGAATTC
*
61989 TTCTTACTTTCCTTTCT-CCTTTCT
1 TTCTTTCTTTCCTTTCTCCCTTTCT
62013 TTCTTTCTTTCCTTTCTCCCTTTCT
1 TTCTTTCTTTCCTTTCTCCCTTTCT
62038 TTCTTTCT
1 TTCTTTCT
62046 CGATGGCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 16 0.52
25 15 0.48
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (25 bp):
TTCTTTCTTTCCTTTCTCCCTTTCT
Found at i:62027 original size:17 final size:17
Alignment explanation
Indices: 62005--62046 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
61995 CTTTCCTTTC
**
62005 TCCTTTCTTTCTTTCTT
1 TCCTTTCTCCCTTTCTT
62022 TCCTTTCTCCCTTTCTT
1 TCCTTTCTCCCTTTCTT
62039 T-CTTTCTC
1 TCCTTTCTC
62047 GATGGCAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
TCCTTTCTCCCTTTCTT
Found at i:62139 original size:25 final size:25
Alignment explanation
Indices: 62111--62162 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
62101 TTTCTTTTAT
*
62111 AACCGGCTGCCTCAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
*
62136 AACCGACTGCCTTAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
62161 AA
1 AA
62163 TAATTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (25 bp):
AACCGACTGCCTCAATTATTTCACC
Found at i:62303 original size:23 final size:23
Alignment explanation
Indices: 62273--62332 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
62263 ACACGTGAAG
62273 GAATGGATGATGGGGCTGCATGT
1 GAATGGATGATGGGGCTGCATGT
62296 GAATGGATGATGGGGCTGCATGT
1 GAATGGATGATGGGGCTGCATGT
62319 GAATGGATGATGGG
1 GAATGGATGATGGG
62333 AATGGCGCCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.23, C:0.07, G:0.45, T:0.25
Consensus pattern (23 bp):
GAATGGATGATGGGGCTGCATGT
Found at i:62432 original size:28 final size:29
Alignment explanation
Indices: 62338--62446 Score: 211
Period size: 29 Copynumber: 3.8 Consensus size: 29
62328 ATGGGAATGG
62338 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
62367 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
62396 CGCCGGGACTACATGGCGACCTAT-AGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
62424 CGCCGGGACTACATGGCGACCTA
1 CGCCGGGACTACATGGCGACCTA
62447 CACCCTATTC
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
28 27 0.34
29 53 0.66
ACGTcount: A:0.23, C:0.29, G:0.31, T:0.17
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTATAAGGT
Found at i:62444 original size:57 final size:58
Alignment explanation
Indices: 62338--62446 Score: 211
Period size: 57 Copynumber: 1.9 Consensus size: 58
62328 ATGGGAATGG
62338 CGCCGGGACTACATGGCGACCTATAAGGTCGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGTCGCCGGGACTACATGGCGACCTATAAGGT
62396 CGCCGGGACTACATGGCGACCTAT-AGGTCGCCGGGACTACATGGCGACCTA
1 CGCCGGGACTACATGGCGACCTATAAGGTCGCCGGGACTACATGGCGACCTA
62447 CACCCTATTC
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 27 0.53
58 24 0.47
ACGTcount: A:0.23, C:0.29, G:0.31, T:0.17
Consensus pattern (58 bp):
CGCCGGGACTACATGGCGACCTATAAGGTCGCCGGGACTACATGGCGACCTATAAGGT
Found at i:62494 original size:15 final size:15
Alignment explanation
Indices: 62471--62539 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
62461 GCATGGCCAC
62471 CTCGCATGGCTCGCA
1 CTCGCATGGCTCGCA
* *
62486 CTCGTATGGCTCGTA
1 CTCGCATGGCTCGCA
*
62501 -T-GCATGG---GGA
1 CTCGCATGGCTCGCA
62511 CCTCGCATGGCTCGCA
1 -CTCGCATGGCTCGCA
*
62527 CTCGTATGGCTCG
1 CTCGCATGGCTCG
62540 TATGCATGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
10 2 0.05
12 1 0.02
13 11 0.26
14 1 0.02
15 25 0.60
16 2 0.05
ACGTcount: A:0.13, C:0.32, G:0.30, T:0.25
Consensus pattern (15 bp):
CTCGCATGGCTCGCA
Found at i:62506 original size:41 final size:41
Alignment explanation
Indices: 62460--62630 Score: 179
Period size: 41 Copynumber: 4.1 Consensus size: 41
62450 CCTATTCCAC
62460 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
**
62501 TGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
** *** * *
62542 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTAT---TC-CA
1 TGCATGGCCACCTCGCATGGCTCG--C-A-CTC-GTATGGCTCGTA
62584 CTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 -TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
62626 TGCAT
1 TGCAT
62631 CTATTCCACT
Statistics
Matches: 106, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
38 3 0.03
39 3 0.03
40 1 0.01
41 68 0.64
42 2 0.02
43 22 0.21
44 1 0.01
45 3 0.03
46 3 0.03
ACGTcount: A:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (41 bp):
TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
Found at i:62640 original size:55 final size:55
Alignment explanation
Indices: 62575--62685 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
62565 GAACGACCTC
62575 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
62630 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
62685 T
1 T
62686 GGGGACCTCG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.16, C:0.34, G:0.22, T:0.28
Consensus pattern (55 bp):
TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
Found at i:62655 original size:139 final size:139
Alignment explanation
Indices: 62501--62769 Score: 520
Period size: 139 Copynumber: 1.9 Consensus size: 139
62491 ATGGCTCGTA
**
62501 TGCATGGGGACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCATGGGGAG
1 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCATGGGGAG
62566 AACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCAT
66 AACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCAT
62631 CTATTCCAC
131 CTATTCCAC
62640 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCATGGGGAG
1 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCATGGGGAG
62705 AACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCAT
66 AACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCAT
62770 GGGGAGAACC
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
139 128 1.00
ACGTcount: A:0.17, C:0.32, G:0.27, T:0.24
Consensus pattern (139 bp):
TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCATGGGGAG
AACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCAT
CTATTCCAC
Found at i:62667 original size:27 final size:27
Alignment explanation
Indices: 62582--62667 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
62572 CTCTCTATTC
62582 CACTGCATGGCCACCTCGCATGGCTCG
1 CACTGCATGGCCACCTCGCATGGCTCG
* * * * ***
62609 CACTCGTATGG-CTCGTATGCATCTATTC-
1 CACT-GCATGGCCACCT-CGCAT-GGCTCG
62637 CACTGCATGGCCACCTCGCATGGCTCG
1 CACTGCATGGCCACCTCGCATGGCTCG
62664 CACT
1 CACT
62668 CGTATGGCTC
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 2 0.05
27 20 0.50
28 16 0.40
29 2 0.05
ACGTcount: A:0.16, C:0.37, G:0.22, T:0.24
Consensus pattern (27 bp):
CACTGCATGGCCACCTCGCATGGCTCG
Found at i:62694 original size:41 final size:41
Alignment explanation
Indices: 62640--62771 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 41
62630 TCTATTCCAC
62640 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
** *** * *
62681 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTAT---TC-CA
1 TGCATGGCCACCTCGCATGGCTCG--C-A-CTC-GTATGGCTCGTA
62723 CTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 -TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
62765 TGCATGG
1 TGCATGG
62772 GGAGAACCAG
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 1 0.01
41 29 0.43
42 2 0.03
43 22 0.33
44 1 0.01
45 3 0.04
46 3 0.04
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.23
Consensus pattern (41 bp):
TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
Found at i:63044 original size:43 final size:41
Alignment explanation
Indices: 62983--63300 Score: 187
Period size: 44 Copynumber: 7.4 Consensus size: 41
62973 GGTTTTTAAT
* * *
62983 TTTTTAAATCTTATTTTTTAACTTTATAATTGAGGTCCTAA
1 TTTTTCAATCTCACTTTTTAACTTTATAATTGAGGTCCTAA
* * *
63024 TATTATTCAATCTCACTTTTTATCTTTATAATTGAAGTCTCTATT
1 T-TT-TTCAATCTCACTTTTTAACTTTATAATTGAGGTC-CTA-A
* * * *
63069 TTTTTCAAT-T-TCTTTTTCACCTTTATAACTGATGTCCTAA
1 TTTTTCAATCTCACTTTTT-AACTTTATAATTGAGGTCCTAA
* **
63109 TTTTGT-AATTTCAC-TTTTAACTTTATAATTGAGGCTTTTAA
1 TTTT-TCAATCTCACTTTTTAACTTTATAATTGAGG-TCCTAA
* * * * * *
63150 TTTTTTTCGATCTCAATTTCTACCTTT-TCAACTGAGGCCCCTAA
1 --TTTTTCAATCTCACTTTTTAACTTTAT-AATTGAGG-TCCTAA
* * * **
63194 GTTTTTCCAATCTCAATTTTTACCTTCATAATTGATGCCCCTAA
1 -TTTTT-CAATCTCACTTTTTAACTTTATAATTGA-GGTCCTAA
* *
63238 TTTTTTATTCTCACTTTTTTTAACTTTATAATTGAGGTCCTTAA
1 TTTTTCAATCTCAC--TTTTTAACTTTATAATTGAGGTCC-TAA
*
63282 GTTTTTTTAATCTCACTTT
1 --TTTTTCAATCTCACTTT
63301 CTAATTGAGA
Statistics
Matches: 215, Mismatches: 40, Indels: 41
0.73 0.14 0.14
Matches are distributed among these distances:
40 20 0.09
41 20 0.09
42 26 0.12
43 58 0.27
44 75 0.35
45 3 0.01
46 13 0.06
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.52
Consensus pattern (41 bp):
TTTTTCAATCTCACTTTTTAACTTTATAATTGAGGTCCTAA
Found at i:63331 original size:36 final size:36
Alignment explanation
Indices: 63260--63332 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
63250 ACTTTTTTTA
*
63260 ACTTTATAATTGAGGTCCTTAAGTTTTTTTAATCTC
1 ACTTTATAATTGAGGTCCTTAAGTTTTTTCAATCTC
* *
63296 ACTTTCTAATTGAGAG-CCTTGAA-TTTTTTCGATCTC
1 ACTTTATAATTGAG-GTCCTT-AAGTTTTTTCAATCTC
63332 A
1 A
63333 ATTATACCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 29 0.91
37 3 0.09
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (36 bp):
ACTTTATAATTGAGGTCCTTAAGTTTTTTCAATCTC
Found at i:64882 original size:18 final size:18
Alignment explanation
Indices: 64859--64900 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
64849 AGTATATTTT
64859 ATAATTTTAATTATTTAA
1 ATAATTTTAATTATTTAA
64877 ATAATTTTAATTATTTAA
1 ATAATTTTAATTATTTAA
64895 ATAATT
1 ATAATT
64901 AAAATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATAATTTTAATTATTTAA
Found at i:64906 original size:18 final size:18
Alignment explanation
Indices: 64867--64906 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
64857 TTATAATTTT
**
64867 AATTATTTAAATAATTTT
1 AATTATTTAAATAATTAA
64885 AATTATTTAAATAATTAA
1 AATTATTTAAATAATTAA
64903 AATT
1 AATT
64907 TATAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTATTTAAATAATTAA
Done.