Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015162.1 Kokia drynarioides strain JFW-HI SEQ_130206, 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: 88138
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:6324 original size:18 final size:18
Alignment explanation
Indices: 6301--6335 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
6291 GAGATAAACA
6301 AATCGAGTTATTTGAGTT
1 AATCGAGTTATTTGAGTT
6319 AATCGAGTTATTTGAGT
1 AATCGAGTTATTTGAGT
6336 CAACTCGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.43
Consensus pattern (18 bp):
AATCGAGTTATTTGAGTT
Found at i:6619 original size:23 final size:23
Alignment explanation
Indices: 6585--6630 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
6575 CTGACATGAC
6585 ATCCAATCAGCAGCTTCTAGAAG
1 ATCCAATCAGCAGCTTCTAGAAG
*
6608 ATCCAATTAGCAGCTTCTAGAAG
1 ATCCAATCAGCAGCTTCTAGAAG
6631 GTCTAGTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (23 bp):
ATCCAATCAGCAGCTTCTAGAAG
Found at i:11156 original size:5 final size:6
Alignment explanation
Indices: 11096--11161 Score: 51
Period size: 6 Copynumber: 10.2 Consensus size: 6
11086 ATTATTTCTA
* * * *
11096 TTTATT TTTATTT TTGGTATT TTAAATT TTTATT TATAAAT ATTATT TTTATT
1 TTTATT TTTA-TT TT--TATT TT-TATT TTTATT T-TTATT TTTATT TTTATT
11149 TTTATT TTTATT T
1 TTTATT TTTATT T
11162 CAGACTCAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 8
0.73 0.14 0.12
Matches are distributed among these distances:
6 29 0.62
7 12 0.26
8 4 0.09
9 2 0.04
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (6 bp):
TTTATT
Found at i:12002 original size:15 final size:16
Alignment explanation
Indices: 11982--12014 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
11972 AAGGAGTTCG
11982 AATAAAGAAGAAA-AA
1 AATAAAGAAGAAAGAA
11997 AATAAAGAAGAAAGAA
1 AATAAAGAAGAAAGAA
12013 AA
1 AA
12015 GAACAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (16 bp):
AATAAAGAAGAAAGAA
Found at i:12101 original size:14 final size:15
Alignment explanation
Indices: 12082--12114 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
12072 AAAAGGTTCG
12082 AAAAGAAAAA-AAAA
1 AAAAGAAAAAGAAAA
12096 AAAAGAAAAAGAAAA
1 AAAAGAAAAAGAAAA
12111 AAAA
1 AAAA
12115 AACATGGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAGAAAA
Found at i:12884 original size:23 final size:23
Alignment explanation
Indices: 12848--12893 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
12838 CTGACGTGGC
*
12848 ATCCAGTCAGCAGCTTCTAGAAG
1 ATCCAGTCAACAGCTTCTAGAAG
*
12871 ATCCAGTTAACAGCTTCTAGAAG
1 ATCCAGTCAACAGCTTCTAGAAG
12894 GTTTAGTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (23 bp):
ATCCAGTCAACAGCTTCTAGAAG
Found at i:22373 original size:27 final size:28
Alignment explanation
Indices: 22332--22390 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
22322 CAATCTTCAA
**
22332 TTAATGATTATTTCCTTTGATCCTCCTT
1 TTAATGATTATTTCCTTCAATCCTCCTT
* *
22360 TTAAT-ATTGTTTCCTTCAATCCTCTTT
1 TTAATGATTATTTCCTTCAATCCTCCTT
22387 TTAA
1 TTAA
22391 CAGGATTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.54
Consensus pattern (28 bp):
TTAATGATTATTTCCTTCAATCCTCCTT
Found at i:23416 original size:205 final size:206
Alignment explanation
Indices: 22988--23923 Score: 1073
Period size: 205 Copynumber: 4.6 Consensus size: 206
22978 TCCTGACCAT
* * * * * * *
22988 CTTCCCGATGAGGTACAGAGAAGTGGACCAAATTCGTTTTCCTGATGAGATACAGAGAAGCGAAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAGT
* * * * * * * * *
23053 TGTAGCAGATGACGCGGTTATCTTCCTGATGAGATACTGAGAAGAAGACC---CCAAA-CGAGGC
66 TGAAACAAACGGCGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATGC
** * * * * * * *
23114 TTAAAGTGAGCGAAATCTTCAAAAT-CCAGCTTCCTGATGAGACACCGAGAAGCAGGTGGAAGTA
131 TCGATGTGAGCAAAATCTTC-GAATCCCAGCTTCCGGATGACACACCGAGAAGCAGATGGAAGCA
23178 ATAAATGGTTAG
195 ATAAATGGTTAG
* **
23190 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATGCAGAGAAGCGAGT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAGT
*
23255 TGAAACAAACGGCGCAGTCATCTTCCTGATGAGATACTGAGAAAAAGACCAAACCAAACCCATGC
66 TGAAACAAACGGCGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATGC
** * * *
23320 TCGATGTGAGC-AGGTCTTCGGATCCCAGCTTCCGGATGACACACTGAGAAGCAGGTGGAAGCAA
131 TCGATGTGAGCAAAATCTTCGAATCCCAGCTTCCGGATGACACACCGAGAAGCAGATGGAAGCAA
*
23384 TAAATGGTTAA
196 TAAATGGTTAG
* *
23395 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGCCTTCCTGATGAGATGTAGAGAAGCGAGT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAGT
* * * * *
23460 TGAAACAAACGGTGC-GATCATCTTCCTGATGAGATATTGAGAAAAAGATCAAACCAAACCCACG
66 TGAAACAAACGGCGCAG-TCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATG
* * ** * * * *
23524 CTCGATGTAATC-AGGTCTTCGGATCCCAGCTTCCGGATGAGACACCAAGAAGCAGATTGAAGCA
130 CTCGATGTGAGCAAAATCTTCGAATCCCAGCTTCCGGATGACACACCGAGAAGCAGATGGAAGCA
*
23588 ATAAACGGTTAG
195 ATAAATGGTTAG
* * *
23600 CTTCCTGATGAGATACGGAGAAGT-AGACCAAATTCGTTTTCCTAATGAGATATAGAGAAGCG-G
1 CTTCCTGATGAGATACTGAGAAGTGA-ACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAG
* *
23663 AATGAAACAAACGGCGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCAT
65 -TTGAAACAAACGGCGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCAT
** ** *
23728 GCTCGACATGAGCAAAATCTTCGAATCCCAGCTTCCTAATGACACACCGAGAAGCAGATCGAAGC
129 GCTCGATGTGAGCAAAATCTTCGAATCCCAGCTTCCGGATGACACACCGAGAAGCAGATGGAAGC
* *
23793 AGTAAAAGGTTAG
194 AATAAATGGTTAG
* * * * * * *
23806 CTTCCTGATGAGATACTGAGAAGTAAACCAAACTCGTATTCCTAATGAGGTATAAAGAAGCGAAT
1 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAGT
* * * ** * *
23871 CGAAGCAAATGATGCAGTTATCTTCCTGATAAGATACTGAGAAGAAGACCAAA
66 TGAAACAAACGGCGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAA
23924 TCAGTAAAAT
Statistics
Matches: 638, Mismatches: 84, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
202 99 0.16
204 5 0.01
205 366 0.57
206 167 0.26
207 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.21
Consensus pattern (206 bp):
CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCGAGT
TGAAACAAACGGCGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAACCAAACCCATGC
TCGATGTGAGCAAAATCTTCGAATCCCAGCTTCCGGATGACACACCGAGAAGCAGATGGAAGCAA
TAAATGGTTAG
Found at i:24185 original size:17 final size:17
Alignment explanation
Indices: 24163--24224 Score: 97
Period size: 17 Copynumber: 3.6 Consensus size: 17
24153 GGAAATTGAA
24163 TTTATTTTAAATTTAAG
1 TTTATTTTAAATTTAAG
24180 TTTATTTTAAATTTAAG
1 TTTATTTTAAATTTAAG
* *
24197 TTTATTTGAAATTTAAA
1 TTTATTTTAAATTTAAG
*
24214 TTTATTATAAA
1 TTTATTTTAAA
24225 ACTAAATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TTTATTTTAAATTTAAG
Found at i:24201 original size:34 final size:33
Alignment explanation
Indices: 24155--24224 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 33
24145 GGCCCTTTGG
* * *
24155 AAATTGAATTTATTTTAAATTTAAGTTTATTTT
1 AAATTGAATTTATTTGAAATTTAAATTTATTAT
*
24188 AAATTTAAGTTTATTTGAAATTTAAATTTATTAT
1 AAATTGAA-TTTATTTGAAATTTAAATTTATTAT
24222 AAA
1 AAA
24225 ACTAAATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 7 0.22
34 25 0.78
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (33 bp):
AAATTGAATTTATTTGAAATTTAAATTTATTAT
Found at i:26072 original size:59 final size:59
Alignment explanation
Indices: 25994--26479 Score: 699
Period size: 59 Copynumber: 8.3 Consensus size: 59
25984 CCCCGAAGGT
*
25994 CCCCGAACCTTCTGAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* *
26053 CCCCGAACATTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * * *
26112 CCCCAAACCTTCTAAAAATTACCATTTTA-CCCTGAACTTCCAAAAATCCCATTCTTAA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * *
26170 CCCTGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
**
26229 CCCCGAACCTTCTAAAAATTACCATTTTACCCCAAAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* ** * * * *
26288 CCCCAAAATTTTTGAAAATTACCATTTTACCCCCGAACTCCCAAAAATCTCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* *
26347 CCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* * ** *
26406 CCCAGAACCTTCTAAAAATAACCATTTTACCCCTTAACTTCCAAAAAT--CAATTTTGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
* *
26463 CTCCGAACCTTCCAAAA
1 CCCCGAACCTTCTAAAA
26480 CTACCTATTT
Statistics
Matches: 379, Mismatches: 47, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
57 22 0.06
58 52 0.14
59 305 0.80
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.29
Consensus pattern (59 bp):
CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
Found at i:26292 original size:176 final size:177
Alignment explanation
Indices: 25994--26479 Score: 726
Period size: 176 Copynumber: 2.8 Consensus size: 177
25984 CCCCGAAGGT
*
25994 CCCCGAACCTTCTGAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGA
* *
26059 ACATTCTAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTC
66 ACCTTCTAAAAATTACCATTTTACCCCAAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTC
* *
26124 TAAAAATTACCATTTTA-CCCTGAACTTCCAAAAATCCCATTCTTAA
131 TAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTCTTAA
* * *
26170 CCCTGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCCCGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGA
** *
26235 ACCTTCTAAAAATTACCATTTTACCCCAAAACTTCCAAAAATCCCATTTTTGACCCCAAAATTTT
66 ACCTTCTAAAAATTACCATTTTACCCCAAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTC
* * * *
26300 TGAAAATTACCATTTTACCCCCGAACTCCCAAAAATCTCATTTTTGA
131 TAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTCTTAA
* * *
26347 CCCCGAACCTTCCAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTGACCCAGA
1 CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGA
* ** * * *
26412 ACCTTCTAAAAATAACCATTTTACCCCTTAACTTCCAAAAAT--CAATTTTGACTCCGAACCTTC
66 ACCTTCTAAAAATTACCATTTTACCCCAAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTC
*
26475 CAAAA
131 TAAAA
26480 CTACCTATTT
Statistics
Matches: 277, Mismatches: 32, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
175 18 0.06
176 137 0.49
177 122 0.44
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.29
Consensus pattern (177 bp):
CCCCGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGA
ACCTTCTAAAAATTACCATTTTACCCCAAAACTTCCAAAAATCCCATTTTTGACCCCAAACCTTC
TAAAAATTACCATTTTACCCCCGAACTCCCAAAAATCCCATTCTTAA
Found at i:26446 original size:29 final size:27
Alignment explanation
Indices: 25994--26490 Score: 332
Period size: 29 Copynumber: 17.0 Consensus size: 27
25984 CCCCGAAGGT
* *
25994 CCCCGAACCTTCTGAAAATTACCATTTTA
1 CCCCGAA-CTTC-CAAAAATACCATTTTA
*
26023 CCCCCGAACTTCCAAAAATCCCATTTTTGA
1 -CCCCGAACTTCCAAAAATACCA-TTTT-A
*
26053 CCCCGAACATTCTAAAAATTACCATTTTA
1 CCCCGAAC-TTCCAAAAA-TACCATTTTA
* *
26082 CCCCCAAACTTCCAAAAATCCCATTTTTGA
1 -CCCCGAACTTCCAAAAATACCA-TTTT-A
* *
26112 CCCCAAACCTTCTAAAAATTACCATTTTA
1 CCCCGAA-CTTCCAAAAA-TACCATTTTA
* *
26141 CCCTGAACTTCCAAAAATCCCATTCTTAA
1 CCCCGAACTTCCAAAAATACCATT-TT-A
* *
26170 CCCTGAACCTTCTAAAAATTACCATTTTA
1 CCCCGAA-CTTCCAAAAA-TACCATTTTA
* *
26199 CCCTCGAACTTCTAAAAATCCCATTTTTGA
1 CCC-CGAACTTCCAAAAATACCA-TTTT-A
*
26229 CCCCGAACCTTCTAAAAATTACCATTTTA
1 CCCCGAA-CTTCCAAAAA-TACCATTTTA
* *
26258 CCCCAAAACTTCCAAAAATCCCATTTTTGA
1 CCCC-GAACTTCCAAAAATACCA-TTTT-A
* * ** *
26288 CCCCAAAATTTTTGAAAATTACCATTTTA
1 CCCC-GAA-CTTCCAAAAATACCATTTTA
*
26317 CCCCCGAACTCCCAAAAAT-CTCATTTTTGA
1 -CCCCGAACTTCCAAAAATAC-CA-TTTT-A
26347 CCCCGAACCTTCCAAAAATTACCATTTTA
1 CCCCGAA-CTTCCAAAAA-TACCATTTTA
* *
26376 CCCCCGAACTCCCAAAAATCCCATTTTTGA
1 -CCCCGAACTTCCAAAAATACCA-TTTT-A
* *
26406 CCCAGAACCTTCTAAAAATAACCATTTTA
1 CCCCGAA-CTTCCAAAAAT-ACCATTTTA
* *
26435 CCCCTTAACTTCCAAAAAT-CAATTTTGA
1 CCCC-GAACTTCCAAAAATACCATTTT-A
* *
26463 CTCCGAACCTTCCAAAACTACCTATTTT
1 CCCCGAA-CTTCCAAAAATACC-ATTTT
26491 GCCTCCATGC
Statistics
Matches: 380, Mismatches: 48, Indels: 78
0.75 0.09 0.15
Matches are distributed among these distances:
27 15 0.04
28 57 0.15
29 139 0.37
30 134 0.35
31 34 0.09
32 1 0.00
ACGTcount: A:0.34, C:0.32, G:0.04, T:0.30
Consensus pattern (27 bp):
CCCCGAACTTCCAAAAATACCATTTTA
Found at i:27683 original size:27 final size:26
Alignment explanation
Indices: 27593--27693 Score: 71
Period size: 28 Copynumber: 3.7 Consensus size: 26
27583 TAAAATTCGT
*
27593 CACAAAGGCAATTCTTTCA-ATAGTGTGC
1 CACAAAGGC-ATTCTTTCAGA-A-TTTGC
* *
27621 CACAAAGACATTTCTTTTAG-ATTATCGC
1 CACAAAGGCA-TTCTTTCAGAATT-T-GC
*
27649 CATAAAGGCATTCCTTTCAGAATTTGC
1 CACAAAGGCATT-CTTTCAGAATTTGC
*
27676 CACAAAGGTTATTCTTTC
1 CACAAAGG-CATTCTTTC
27694 CTATCATGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 15
0.72 0.10 0.19
Matches are distributed among these distances:
26 1 0.02
27 19 0.33
28 35 0.60
29 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (26 bp):
CACAAAGGCATTCTTTCAGAATTTGC
Found at i:37970 original size:42 final size:42
Alignment explanation
Indices: 37924--38012 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
37914 TGAGTCAAAG
* *
37924 GTCTTCCGTCAATCATAATCTCGTGCTAATCCCGA-ACCATGA
1 GTCTTCCGTCAAACATAATCTCATGCTAATCCCGAGA-CATGA
* * * * *
37966 GTCTTCCTTTAAACATAATTTCATTCTCATCCCGAGACATGA
1 GTCTTCCGTCAAACATAATCTCATGCTAATCCCGAGACATGA
38008 GTCTT
1 GTCTT
38013 TCATTTACAC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 38 0.97
43 1 0.03
ACGTcount: A:0.26, C:0.28, G:0.12, T:0.34
Consensus pattern (42 bp):
GTCTTCCGTCAAACATAATCTCATGCTAATCCCGAGACATGA
Found at i:55859 original size:6 final size:6
Alignment explanation
Indices: 55850--55874 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55840 ATAATTTTTA
55850 TTTTCT TTTTCT TTTTCT TTTTCT T
1 TTTTCT TTTTCT TTTTCT TTTTCT T
55875 CATTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:57228 original size:39 final size:39
Alignment explanation
Indices: 56960--57602 Score: 609
Period size: 39 Copynumber: 16.4 Consensus size: 39
56950 TTCTGATTAA
* *
56960 GGTAAAAGATTGGAT-GCTTCAATCTGCCCCATGATCGA
1 GGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCGG
* * *
56998 GGTAAGAGACTGGAT-GCTTTAATCTGCCCCATGATCAG
1 GGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCGG
* * * * *
57036 GGTAATAGATTGGAT-GCTTTAATCTGCCCCACGACCAG
1 GGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCGG
* ** **** ***
57074 TGTAAGAGATTGGATCATCTTCAATCTGCTTTTTGATTAA
1 GGTAAGAGATTGGAT-GGCTTCAATCTGCCCCATGATCGG
*
57114 GGTAAAAGATTGGAT-GCTTCAATCTGCCCCATGATCGG
1 GGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCGG
* * *
57152 GGTAAGAGATTGGATTGTCTTTAATCTACCCCATGATCGG
1 GGTAAGAGATTGGA-TGGCTTCAATCTGCCCCATGATCGG
*
57192 GGTAAGAGATTGGATGGCTTAAATCTGCCCCATGATCGG
1 GGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCGG
* *
57231 GGTAAGAGATTAGATGATGTCTTTAATCTGCCCCATGATCGG
1 GGTAAGAGATT-G--GATGGCTTCAATCTGCCCCATGATCGG
* * * *
57273 GATAAGAGATTGGATGACTTCAA-CTAGCCCAATGATCAG
1 GGTAAGAGATTGGATGGCTTCAATCT-GCCCCATGATCGG
* * *
57312 GGTAAGAGATTGGATGGCTTTACTCTGCCTCATGATCGG
1 GGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCGG
* ** *
57351 GGTAAGAGATTGGATGATGGCTGCAATCTGCCTTATGATTGG
1 GGTAAGAGATT-G--GATGGCTTCAATCTGCCCCATGATCGG
*** * * *
57393 GGTAAGAGATTGGACAACTGCAATCTACCTCATGATCGG
1 GGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCGG
** * *
57432 GGTAAGAGATTGGAAAGCTGT-AATCGGCCCCATGATTGG
1 GGTAAGAGATTGGATGGCT-TCAATCTGCCCCATGATCGG
* * *
57471 GGTAAGAGATTGGATGGCTGCAATCTGCCTCATGATCGA
1 GGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCGG
* * * *
57510 GATAAGAGATTGGA-AGATTACAATCTGCCCCATGATCGA
1 GGTAAGAGATTGGATGGCTT-CAATCTGCCCCATGATCGG
*
57549 GGTAAGAGATTGGATGGCTGT-AATCTACCCCATGATCGG
1 GGTAAGAGATTGGATGGCT-TCAATCTGCCCCATGATCGG
*
57588 GATAAGAGATTGGAT
1 GGTAAGAGATTGGAT
57603 TGGTGACGTA
Statistics
Matches: 500, Mismatches: 88, Indels: 33
0.81 0.14 0.05
Matches are distributed among these distances:
38 112 0.22
39 251 0.50
40 66 0.13
41 3 0.01
42 68 0.14
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (39 bp):
GGTAAGAGATTGGATGGCTTCAATCTGCCCCATGATCGG
Found at i:57348 original size:120 final size:117
Alignment explanation
Indices: 56960--57602 Score: 622
Period size: 120 Copynumber: 5.5 Consensus size: 117
56950 TTCTGATTAA
* * * * *
56960 GGTAAAAGATTGGAT-GCTTCAATCTGCCCCATGATCGAGGTAAGAGACTGGATGCTTTAATCTG
1 GGTAAGAGATTGGATGGCTTTAATCTGCCCCATGATCGGGGTAAGAGATTGGATGCTTCAATCTG
* * * *
57024 CCCCATGATCAGGG-TAATAGATTGGATG-CTTTAATCT-GCCCCACGACCAG
66 CCCCATGATC-GGGATAAGAGATTGGATGACTTCAATCTAGCCCCATGATCAG
* ** * **** *** *
57074 TGTAAGAGATTGGATCATCTTCAATCTGCTTTTTGATTAAGGTAAAAGATTGGATGCTTCAATCT
1 GGTAAGAGATTGGAT-GGCTTTAATCTGCCCCATGATCGGGGTAAGAGATTGGATGCTTCAATCT
* * * *
57139 GCCCCATGATCGGGGTAAGAGATTGGATTGTCTTTAATCTA-CCCCATGATCGG
65 GCCCCATGATCGGGATAAGAGATTGGA-TGACTTCAATCTAGCCCCATGATCAG
* *
57192 GGTAAGAGATTGGATGGCTTAAATCTGCCCCATGATCGGGGTAAGAGATTAGATGATGTCTTTAA
1 GGTAAGAGATTGGATGGCTTTAATCTGCCCCATGATCGGGGTAAGAGATT-G--GATG-CTTCAA
*
57257 TCTGCCCCATGATCGGGATAAGAGATTGGATGACTTCAA-CTAGCCCAATGATCAG
62 TCTGCCCCATGATCGGGATAAGAGATTGGATGACTTCAATCTAGCCCCATGATCAG
* * *
57312 GGTAAGAGATTGGATGGCTTTACTCTGCCTCATGATCGGGGTAAGAGATTGGATGATGGCTGCAA
1 GGTAAGAGATTGGATGGCTTTAATCTGCCCCATGATCGGGGTAAGAGATT-G--GAT-GCTTCAA
** * * ** * * *
57377 TCTGCCTTATGATTGGGGTAAGAGATTGGACAACTGCAATCTA-CCTCATGATCGG
62 TCTGCCCCATGATCGGGATAAGAGATTGGATGACTTCAATCTAGCCCCATGATCAG
** * * * *
57432 GGTAAGAGATTGGAAAGCTGTAATCGGCCCCATGATTGGGGTAAGAGATTGGATGGCTGCAATCT
1 GGTAAGAGATTGGATGGCTTTAATCTGCCCCATGATCGGGGTAAGAGATTGGAT-GCTTCAATCT
* * *
57497 GCCTCATGATCGAGATAAGAGATTGGAAGA-TTACAATCT-GCCCCATGATC-G
65 GCCCCATGATCGGGATAAGAGATTGGATGACTT-CAATCTAGCCCCATGATCAG
* * *
57548 AGGTAAGAGATTGGATGGCTGTAATCTACCCCATGATCGGGATAAGAGATTGGAT
1 -GGTAAGAGATTGGATGGCTTTAATCTGCCCCATGATCGGGGTAAGAGATTGGAT
57603 TGGTGACGTA
Statistics
Matches: 442, Mismatches: 71, Indels: 29
0.82 0.13 0.05
Matches are distributed among these distances:
114 13 0.03
115 3 0.01
116 62 0.14
117 127 0.29
118 33 0.07
119 4 0.01
120 162 0.37
121 38 0.09
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (117 bp):
GGTAAGAGATTGGATGGCTTTAATCTGCCCCATGATCGGGGTAAGAGATTGGATGCTTCAATCTG
CCCCATGATCGGGATAAGAGATTGGATGACTTCAATCTAGCCCCATGATCAG
Found at i:58183 original size:49 final size:49
Alignment explanation
Indices: 58123--58409 Score: 211
Period size: 49 Copynumber: 5.8 Consensus size: 49
58113 GGTATCAGGT
* ** * * *
58123 TTTACCATTACGGTCTCAACCTTTCCCTTCATATCTTTATGGTATCGGG
1 TTTACCATTGCGACCTCAACCTTTCCCTTCACATCTTTATGGTACCGGA
* * * * * ** *
58172 TTTACCGTTACGGCCTCAACATTTCCCGTCATGTCTTCATGGTACCGGA
1 TTTACCATTGCGACCTCAACCTTTCCCTTCACATCTTTATGGTACCGGA
*** * * *
58221 TTCGTCATTGCGACCTCAATCC-TTCTCATCACATCTTCTAAGGTACCGGA
1 TTTACCATTGCGACCTCAA-CCTTTCCCTTCACATCTT-TATGGTACCGGA
* * * *
58271 TTTGCCGTTGCGGCCTCAACCTTTCCCTTCAAAT-TTTCATGGTACCGGA
1 TTTACCATTGCGACCTCAACCTTTCCCTTCACATCTTT-ATGGTACCGGA
** * * * * *
58320 TTCGCCATTGCGACCTCAACCTTTCCCATCACGTCTTTTAAGGTATCGGG
1 TTTACCATTGCGACCTCAACCTTTCCCTTCACATC-TTTATGGTACCGGA
* * *
58370 TTTACCGTTGCGACCTCTACCTTTCCCTTCA-ATCTCTATG
1 TTTACCATTGCGACCTCAACCTTTCCCTTCACATCTTTATG
58410 TTTTCTCGGT
Statistics
Matches: 186, Mismatches: 46, Indels: 13
0.76 0.19 0.05
Matches are distributed among these distances:
48 5 0.03
49 109 0.59
50 69 0.37
51 3 0.02
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (49 bp):
TTTACCATTGCGACCTCAACCTTTCCCTTCACATCTTTATGGTACCGGA
Found at i:58272 original size:50 final size:50
Alignment explanation
Indices: 58185--58404 Score: 196
Period size: 50 Copynumber: 4.5 Consensus size: 50
58175 ACCGTTACGG
* * ** * *
58185 CCTCAACATTTCCCGTCATGTCTTC-ATGGTACCGGATTCGTCATTGCGA
1 CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCATTGCGA
* * * *
58234 CCTCAATCC-TTCTCATCACATCTTCTAAGGTACCGGATTTGCCGTTGCGG
1 CCTCAA-CCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCATTGCGA
* * * *
58284 CCTCAACCTTTCCCTTCAAATTTTC-ATGGTACCGGATTCGCCATTGCGA
1 CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCATTGCGA
* * * * ** *
58333 CCTCAACCTTTCCCATCACGTCTTTTAAGGTATCGGGTTTACCGTTGCGA
1 CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCATTGCGA
* *
58383 CCTCTACCTTTCCCTTCA-ATCT
1 CCTCAACCTTTCCCATCACATCT
58405 CTATGTTTTC
Statistics
Matches: 135, Mismatches: 32, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
49 63 0.47
50 72 0.53
ACGTcount: A:0.18, C:0.33, G:0.15, T:0.34
Consensus pattern (50 bp):
CCTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTCGCCATTGCGA
Found at i:58290 original size:99 final size:99
Alignment explanation
Indices: 58137--58401 Score: 318
Period size: 99 Copynumber: 2.7 Consensus size: 99
58127 CCATTACGGT
* * * * * * *
58137 CTCAACCTTTCCCTTCATATCTT-TATGGTATCGGGTTTACCGTTACGGCCTCAACATTTCCCGT
1 CTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTTACCGTTGCGGCCTCAACCTTTCCCGT
** *
58201 CATGTCTTCATGGTACCGGATTCGTCATTGCGAC
66 CAAATCTTCATGGTACCGGATTCGCCATTGCGAC
* * *
58235 CTCAATCC-TTCTCATCACATCTTCTAAGGTACCGGATTTGCCGTTGCGGCCTCAACCTTTCCCT
1 CTCAA-CCTTTCCCATCACATCTTCTAAGGTACCGGATTTACCGTTGCGGCCTCAACCTTTCCCG
*
58299 TCAAATTTTCATGGTACCGGATTCGCCATTGCGAC
65 TCAAATCTTCATGGTACCGGATTCGCCATTGCGAC
* * * * * * *
58334 CTCAACCTTTCCCATCACGTCTTTTAAGGTATCGGGTTTACCGTTGCGACCTCTACCTTTCCCTT
1 CTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTTACCGTTGCGGCCTCAACCTTTCCCGT
58399 CAA
66 CAA
58402 TCTCTATGTT
Statistics
Matches: 142, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
98 19 0.13
99 123 0.87
ACGTcount: A:0.18, C:0.32, G:0.16, T:0.34
Consensus pattern (99 bp):
CTCAACCTTTCCCATCACATCTTCTAAGGTACCGGATTTACCGTTGCGGCCTCAACCTTTCCCGT
CAAATCTTCATGGTACCGGATTCGCCATTGCGAC
Found at i:59426 original size:6 final size:6
Alignment explanation
Indices: 59417--59473 Score: 55
Period size: 6 Copynumber: 9.2 Consensus size: 6
59407 CGACCTCTCA
*
59417 TTTTCT TTTTCGT TCTTT-T TTTTCT TTCT-T TTTTCT TTTTCT CTTCTTCT
1 TTTTCT TTTTC-T T-TTTCT TTTTCT TTTTCT TTTTCT TTTTCT -TT-TTCT
59467 TTTTCT T
1 TTTTCT T
59474 ATTTTTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
5 7 0.16
6 23 0.53
7 6 0.14
8 7 0.16
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:59479 original size:30 final size:30
Alignment explanation
Indices: 59417--59479 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
59407 CGACCTCTCA
* * *
59417 TTTTCTTTTTCGTTCTTTTTTTTCTTTCTT
1 TTTTCTTTTTCCTTCTTCTTTTTCTTTATT
59447 TTTTCTTTTTCTCTTCTTCTTTTTC-TTATT
1 TTTTCTTTTTC-CTTCTTCTTTTTCTTTATT
59477 TTT
1 TTT
59480 ATTTTTTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (30 bp):
TTTTCTTTTTCCTTCTTCTTTTTCTTTATT
Found at i:69496 original size:14 final size:14
Alignment explanation
Indices: 69477--69511 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
69467 GAAAATTAAT
69477 TCATTTTTCAGAAA
1 TCATTTTTCAGAAA
*
69491 TCATTTTTCGGAAA
1 TCATTTTTCAGAAA
*
69505 CCATTTT
1 TCATTTT
69512 CAGTCAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.46
Consensus pattern (14 bp):
TCATTTTTCAGAAA
Found at i:70583 original size:17 final size:16
Alignment explanation
Indices: 70553--70586 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
70543 ATTTTCAACT
70553 TCTTTATTTATCTCTC
1 TCTTTATTTATCTCTC
*
70569 TCTTATATTTTTCTCTC
1 TCTT-TATTTATCTCTC
70586 T
1 T
70587 ATTTTCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (16 bp):
TCTTTATTTATCTCTC
Found at i:70957 original size:19 final size:18
Alignment explanation
Indices: 70929--70965 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
70919 CGGAATTGAG
*
70929 GTTTATTTTTTTTTTATT
1 GTTTATTTTTATTTTATT
70947 GTTTGATTTTTATTTTATT
1 GTTT-ATTTTTATTTTATT
70966 TGGTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (18 bp):
GTTTATTTTTATTTTATT
Found at i:71509 original size:17 final size:15
Alignment explanation
Indices: 71482--71520 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
71472 AATTTTTTAA
*
71482 TTTTTAAACTTATTAT
1 TTTTTATACTTATT-T
71498 TTGTTTATACTTATTT
1 TT-TTTATACTTATTT
71514 TTTTTAT
1 TTTTTAT
71521 TGAACTCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 5 0.24
17 11 0.52
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTTTATACTTATTT
Found at i:72308 original size:6 final size:6
Alignment explanation
Indices: 72297--72323 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
72287 GTTTATTTAT
72297 AAATTA AAATTA AAATTA AAATTA AAA
1 AAATTA AAATTA AAATTA AAATTA AAA
72324 ACTGATTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTA
Found at i:72866 original size:11 final size:11
Alignment explanation
Indices: 72850--72898 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
72840 ATTAGCAAAA
72850 TTAAAAATTAT
1 TTAAAAATTAT
*
72861 TTAAAAACTAT
1 TTAAAAATTAT
*
72872 TTAAACATTAT
1 TTAAAAATTAT
* *
72883 AT-AAAATTAC
1 TTAAAAATTAT
72893 TTAAAA
1 TTAAAA
72899 TTGAATATGA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
10 7 0.23
11 23 0.77
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (11 bp):
TTAAAAATTAT
Found at i:74052 original size:6 final size:6
Alignment explanation
Indices: 74043--74102 Score: 70
Period size: 6 Copynumber: 10.2 Consensus size: 6
74033 TAGATTTATT
** *
74043 TTTAAA TTTAAA TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA TTT-AG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
74089 TTTAAA TTTGAAA T
1 TTTAAA TTT-AAA T
74103 AATTTTAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
5 7 0.16
6 34 0.76
7 4 0.09
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:74052 original size:18 final size:18
Alignment explanation
Indices: 74031--74102 Score: 85
Period size: 17 Copynumber: 4.1 Consensus size: 18
74021 TAGATTAATT
**
74031 TTTAGATTTATTTTTAAA
1 TTTAGATTTAAATTTAAA
*
74049 TTTAAATTTAAATTTAAA
1 TTTAGATTTAAATTTAAA
*
74067 TTT-GTTTTAAATTTAAA
1 TTTAGATTTAAATTTAAA
74084 TTTAG-TTTAAATTTGAAA
1 TTTAGATTTAAATTT-AAA
74102 T
1 T
74103 AATTTTAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
17 24 0.51
18 23 0.49
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAGATTTAAATTTAAA
Found at i:74065 original size:12 final size:12
Alignment explanation
Indices: 74043--74102 Score: 70
Period size: 11 Copynumber: 5.1 Consensus size: 12
74033 TAGATTTATT
74043 TTTAAATTTAAA
1 TTTAAATTTAAA
74055 TTTAAATTTAAA
1 TTTAAATTTAAA
**
74067 TTT-GTTTTAAA
1 TTTAAATTTAAA
*
74078 TTTAAATTT-AG
1 TTTAAATTTAAA
74089 TTTAAATTTGAAA
1 TTTAAATTT-AAA
74102 T
1 T
74103 AATTTTAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
11 19 0.49
12 18 0.46
13 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:74109 original size:17 final size:17
Alignment explanation
Indices: 74043--74117 Score: 71
Period size: 17 Copynumber: 4.4 Consensus size: 17
74033 TAGATTTATT
*
74043 TTTAAATTTAAATTTAAA
1 TTTAAA-TTAATTTTAAA
**
74061 TTTAAATTTGTTTTAAA
1 TTTAAATTAATTTTAAA
* *
74078 TTTAAATTTAGTTTAAA
1 TTTAAATTAATTTTAAA
74095 TTTGAAA-TAATTTTAAA
1 TTT-AAATTAATTTTAAA
*
74112 CTTAAA
1 TTTAAA
74118 ACTTTCAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
16 3 0.06
17 36 0.75
18 9 0.19
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (17 bp):
TTTAAATTAATTTTAAA
Found at i:74940 original size:24 final size:24
Alignment explanation
Indices: 74911--74956 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
74901 TTATATATTA
74911 AATAATTTCATTAATGATAATAAT
1 AATAATTTCATTAATGATAATAAT
*
74935 AATAATTTTATTAATGATAATA
1 AATAATTTCATTAATGATAATA
74957 TTTATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.43
Consensus pattern (24 bp):
AATAATTTCATTAATGATAATAAT
Found at i:74949 original size:18 final size:18
Alignment explanation
Indices: 74928--74976 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
74918 TCATTAATGA
74928 TAATAATAATAATTTTAT
1 TAATAATAATAATTTTAT
*
74946 TAATGATAAT-A-TTTAT
1 TAATAATAATAATTTTAT
74962 TAAATAATTAATAAT
1 T-AATAA-TAATAAT
74977 AATAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 6 0.24
17 5 0.20
18 13 0.52
19 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TAATAATAATAATTTTAT
Found at i:74975 original size:21 final size:21
Alignment explanation
Indices: 74928--74996 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
74918 TCATTAATGA
74928 TAATAATAATAATT--T-TAT
1 TAATAATAATAATTAATATAT
*
74946 TAATGATAATATTTATTAA-ATAAT
1 TAATAATAATA---ATTAATAT-AT
74970 TAATAATAATAATTAATATAT
1 TAATAATAATAATTAATATAT
74991 TAATAA
1 TAATAA
74997 AAAGAAAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
18 10 0.24
21 16 0.39
22 2 0.05
23 1 0.02
24 12 0.29
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (21 bp):
TAATAATAATAATTAATATAT
Found at i:76067 original size:29 final size:30
Alignment explanation
Indices: 75988--76243 Score: 171
Period size: 29 Copynumber: 8.7 Consensus size: 30
75978 AAGGTCCCTA
**
75988 AACTATCCAAAAATTCCATTTTTGACCCTAA
1 AACT-TCCAAAAATTCCATTTTTGACCCTCG
* ***
76019 AACTTTCAAAAATGATATTTTT-ACCCTCG
1 AACTTCCAAAAATTCCATTTTTGACCCTCG
*
76048 AACTTCCAAAAAATCCATTTTTGA--CTACG
1 AACTTCCAAAAATTCCATTTTTGACCCT-CG
* *
76077 AAACTTCCAAAAATTACATTTTT-ACCCTCA
1 -AACTTCCAAAAATTCCATTTTTGACCCTCG
* *
76107 AACCTCCAAAAATTCCATTTTTGATCC-CG
1 AACTTCCAAAAATTCCATTTTTGACCCTCG
76136 AAAC-TCTCAAAAATTACCA-TTTTG-CCCTCG
1 -AACTTC-CAAAAATT-CCATTTTTGACCCTCG
* * *
76166 AA-TGTCCAAAAATTCCGTTTTTTA-TCTCG
1 AACT-TCCAAAAATTCCATTTTTGACCCTCG
** *
76195 ATTTTCTAAAAATTACCA-TTTT-ACCCTCG
1 AACTTCCAAAAATT-CCATTTTTGACCCTCG
*
76224 GA-TGT-CAAAAATTCCATTTT
1 AACT-TCCAAAAATTCCATTTT
76244 AAACCCCAAA
Statistics
Matches: 177, Mismatches: 29, Indels: 41
0.72 0.12 0.17
Matches are distributed among these distances:
27 3 0.02
28 16 0.09
29 87 0.49
30 62 0.35
31 9 0.05
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (30 bp):
AACTTCCAAAAATTCCATTTTTGACCCTCG
Found at i:76088 original size:59 final size:58
Alignment explanation
Indices: 75983--76187 Score: 195
Period size: 59 Copynumber: 3.5 Consensus size: 58
75973 CCATGAAGGT
* *
75983 CCCT-AAACTATCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATGATATTTTTA
1 CCCTCAAACT-TCCAAAAATTCCATTTTTGA-CCTAAAACTTCCAAAAATGACATTTTTA
* * *
76042 CCCTCGAACTTCCAAAAAATCCATTTTTGA-CTACGAAACTTCCAAAAATTACATTTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTGACCTA--AAACTTCCAAAAATGACATTTTTA
* ** * *
76101 CCCTCAAACCTCCAAAAATTCCATTTTTGATCCCGAAAC-TCTCAAAAATTACCA-TTTTG
1 CCCTCAAACTTCCAAAAATTCCATTTTTGA-CCTAAAACTTC-CAAAAATGA-CATTTTTA
* *
76160 CCCTCGAA-TGTCCAAAAATTCCGTTTTT
1 CCCTCAAACT-TCCAAAAATTCCATTTTT
76188 TATCTCGATT
Statistics
Matches: 124, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
57 3 0.02
58 2 0.02
59 112 0.90
60 6 0.05
61 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.33
Consensus pattern (58 bp):
CCCTCAAACTTCCAAAAATTCCATTTTTGACCTAAAACTTCCAAAAATGACATTTTTA
Found at i:77606 original size:29 final size:28
Alignment explanation
Indices: 77580--77677 Score: 106
Period size: 28 Copynumber: 3.4 Consensus size: 28
77570 AATTTTTACT
*
77580 ATTTTTAATAACTTTTACAATATTTTATA
1 ATTTCTAATAA-TTTTACAATATTTTATA
* *
77609 ATTTCTAATAATTTTACAACATTGTATA
1 ATTTCTAATAATTTTACAATATTTTATA
* * *
77637 ATTTCTAATATTTTTATAATTTTTTGATA
1 ATTTCTAATAATTTTACAATATTTT-ATA
* *
77666 TTTTCAAATAAT
1 ATTTCTAATAAT
77678 AATAATTTTT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 35 0.61
29 22 0.39
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (28 bp):
ATTTCTAATAATTTTACAATATTTTATA
Found at i:82040 original size:87 final size:86
Alignment explanation
Indices: 81932--82095 Score: 233
Period size: 87 Copynumber: 1.9 Consensus size: 86
81922 TACATGCATA
* * *
81932 AGGTTGAGTTGTCACTCTTAAT-AAGTTCATATCTCA-ATATTTGAGTGGTCCTATTGAGACGGA
1 AGGTTGAGTTATCACTCTTAATGAA-TTCATATCCCAGA-ATTTGAGTGGTCCTATTGAGACAGA
81995 CTTGATGAATTCACCGACATGAG
64 CTTGATGAATTCACCGACATGAG
* * *
82018 AGGTTGAGTTTATTACTCTTAATGAATTCATATCCCAGAGTTTGGGTGGTCCTATTGAGACAGAC
1 AGGTTGAG-TTATCACTCTTAATGAATTCATATCCCAGAATTTGAGTGGTCCTATTGAGACAGAC
82083 TTGATGAATTCAC
65 TTGATGAATTCAC
82096 TGAACTTAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
86 8 0.12
87 58 0.84
88 3 0.04
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (86 bp):
AGGTTGAGTTATCACTCTTAATGAATTCATATCCCAGAATTTGAGTGGTCCTATTGAGACAGACT
TGATGAATTCACCGACATGAG
Found at i:83126 original size:23 final size:24
Alignment explanation
Indices: 83090--83147 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 24
83080 CTTCCACCAT
83090 TCTTCACTATGTTTTTTCCCTCCC
1 TCTTCACTATGTTTTTTCCCTCCC
83114 TCTTC-CTATGTTTTTTCCCTCCC
1 TCTTCACTATGTTTTTTCCCTCCC
*
83137 TCTTCAATATG
1 TCTTCACTATG
83148 GCATTTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 23 0.72
24 9 0.28
ACGTcount: A:0.10, C:0.34, G:0.05, T:0.50
Consensus pattern (24 bp):
TCTTCACTATGTTTTTTCCCTCCC
Found at i:84052 original size:40 final size:40
Alignment explanation
Indices: 83976--84073 Score: 106
Period size: 40 Copynumber: 2.5 Consensus size: 40
83966 CGTTTGGACA
* * * *
83976 ATAAACGCCGCAAAAGGTGAAGCAATAGCGGGGTTTTTCC
1 ATAAACGCCGCAAAAGGTAAAGCAATAACAGGGTTTTTAC
* * *
84016 ATAAACGCCGCAAAAGGTAAAGTATTAACAGTGTTTTTAC
1 ATAAACGCCGCAAAAGGTAAAGCAATAACAGGGTTTTTAC
* * *
84056 ATAAGCGCTGCTAAAGGT
1 ATAAACGCCGCAAAAGGT
84074 CAGAGCATTA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (40 bp):
ATAAACGCCGCAAAAGGTAAAGCAATAACAGGGTTTTTAC
Found at i:84111 original size:41 final size:40
Alignment explanation
Indices: 84065--84337 Score: 248
Period size: 41 Copynumber: 6.7 Consensus size: 40
84055 CATAAGCGCT
84065 GCTAAAGGTCAGAGCATTAGCGGCGTTTATGGGGAAAAGCC
1 GCTAAAGGTCAGAGCATTAGCGGCGTTTAT-GGGAAAAGCC
* * *
84106 GCTAAA-GTCAGAGCATTAGTGACGTTTATGGGAAAGCGCC
1 GCTAAAGGTCAGAGCATTAGCGGCGTTTATGGGAAA-AGCC
* *
84146 GCTAAAGGTCAAAGCATTAGCGGCGTTTATGGGAAAGCGCC
1 GCTAAAGGTCAGAGCATTAGCGGCGTTTATGGGAAA-AGCC
* * * *
84187 GCTAAAGGTCAGAGTAATAGCGACGTTTACGGG-AAAGCACC
1 GCTAAAGGTCAGAGCATTAGCGGCGTTTATGGGAAAAG--CC
* * * * *
84228 GTTAAAGGTCAGAGTAATAGCGGGGTTTATGTGGAAGCA-CC
1 GCTAAAGGTCAGAGCATTAGCGGCGTTTATG-GGAA-AAGCC
* * * * *
84269 GCTAATGGTCAGAGTAATT-GCGACATTTATGAGAAAACGCC
1 GCTAAAGGTCAGAG-CATTAGCGGCGTTTATGGGAAAA-GCC
* *
84310 GCTAAAGGTCAGAGTAATAGCGGCGTTT
1 GCTAAAGGTCAGAGCATTAGCGGCGTTT
84338 TTCTATAAAC
Statistics
Matches: 190, Mismatches: 31, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
39 8 0.04
40 37 0.19
41 139 0.73
42 4 0.02
43 1 0.01
44 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.22
Consensus pattern (40 bp):
GCTAAAGGTCAGAGCATTAGCGGCGTTTATGGGAAAAGCC
Found at i:84237 original size:82 final size:82
Alignment explanation
Indices: 84058--84337 Score: 341
Period size: 82 Copynumber: 3.4 Consensus size: 82
84048 GTTTTTACAT
* * * *
84058 AAGCGCTGCTAAAGGTCAGAGCATTAGCGGCGTTTATGGGGAAA-AGCCGCTAAA-GTCAGAGCA
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGTTTAT-GGGAAAGCGCCGCTAAAGGTCAGAGTA
* *
84121 TTAGTGACGTTTATGGGA
65 ATAGCGACGTTTATGGGA
* *
84139 AAGCGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAGAGTAA
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAGAGTAA
*
84204 TAGCGACGTTTACGGGA
66 TAGCGACGTTTATGGGA
* * * * * *
84221 AAGCACCGTTAAAGGTCAGAGTAATAGCGGGGTTTATGTGG-AAGCACCGCTAATGGTCAGAGTA
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGTTTATG-GGAAAGCGCCGCTAAAGGTCAGAGTA
* * *
84285 ATTGCGACATTTATGAGA
65 ATAGCGACGTTTATGGGA
* *
84303 AAACGCCGCTAAAGGTCAGAGTAATAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGTTT
84338 TTCTATAAAC
Statistics
Matches: 173, Mismatches: 23, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
80 6 0.03
81 44 0.25
82 121 0.70
83 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (82 bp):
AAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGTTTATGGGAAAGCGCCGCTAAAGGTCAGAGTAA
TAGCGACGTTTATGGGA
Found at i:84348 original size:41 final size:41
Alignment explanation
Indices: 83976--84349 Score: 165
Period size: 41 Copynumber: 9.2 Consensus size: 41
83966 CGTTTGGACA
* * * * *
83976 ATAAACGCCGCAAAAGGTGA-AGCAATAGCGGGGTTTTTCC
1 ATAAACGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTTTCG
* * * * * *
84016 ATAAACGCCGCAAAAGGT-AAAGTATTAACAGTGTTTTTAC-
1 ATAAACGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTTT-CG
* * * * * *
84056 ATAAGCGCTGCTAAAGGTCAGAGCATTAGCGGCGTTTATGG
1 ATAAACGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTTTCG
** * * * * * **
84097 GGAAAAGCCGCTAAA-GTCAGAGCATTAGTGACGTTTATGGG
1 ATAAACGCCGCTAAAGGTCAGAGTAATAGCGGCGTTT-TTCG
* * * * **
84138 A-AAGCGCCGCTAAAGGTCAAAGCATTAGCGGCGTTTATGGG
1 ATAAACGCCGCTAAAGGTCAGAGTAATAGCGGCGTTT-TTCG
* * *
84179 A-AAGCGCCGCTAAAGGTCAGAGTAATAGCGACG-TTTACG
1 ATAAACGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTTTCG
** * * *
84218 GGAAAGCACCGTTAAAGGTCAGAGTAATAGCGGGGTTTATGT-G
1 ATAAA-CGCCGCTAAAGGTCAGAGTAATAGCGGCGTTT-T-TCG
* * * * * * * *
84261 -GAAGCACCGCTAATGGTCAGAGTAATTGCGACATTTAT-G
1 ATAAACGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTTTCG
* *
84300 AGAAAACGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTTTCT
1 A-TAAACGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTTTCG
84342 ATAAACGC
1 ATAAACGC
84350 GATTAATTTA
Statistics
Matches: 259, Mismatches: 61, Indels: 27
0.75 0.18 0.08
Matches are distributed among these distances:
39 5 0.02
40 80 0.31
41 166 0.64
42 6 0.02
43 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.22
Consensus pattern (41 bp):
ATAAACGCCGCTAAAGGTCAGAGTAATAGCGGCGTTTTTCG
Found at i:85751 original size:41 final size:40
Alignment explanation
Indices: 85705--85893 Score: 193
Period size: 41 Copynumber: 4.6 Consensus size: 40
85695 TCCCATAAAC
*
85705 ACCGCTAAAGGTGAGAGCATTAGCGGCGCTTGTAGGAAAG
1 ACCGCTAAAGGTCAGAGCATTAGCGGCGCTTGTAGGAAAG
* *
85745 ATCCGCTAAAGGTCAGAGAATTAGCGGCGCTTGTGGGAAAG
1 A-CCGCTAAAGGTCAGAGCATTAGCGGCGCTTGTAGGAAAG
* *
85786 CGCCGCTAAAGGTCAGAGCATTAGCGGTGCTTGT-GTGAAAG
1 -ACCGCTAAAGGTCAGAGCATTAGCGGCGCTTGTAG-GAAAG
* * * * *
85827 CACCACTAAAGGTCAGAGCATTAACGACGCTTATAAGAAAG
1 -ACCGCTAAAGGTCAGAGCATTAGCGGCGCTTGTAGGAAAG
* * *
85868 -CGTCGTTAAAGATCAAAGCATTAGCG
1 AC--CGCTAAAGGTCAGAGCATTAGCG
85894 ACGTTTTTAA
Statistics
Matches: 125, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
39 1 0.01
40 2 0.02
41 122 0.98
ACGTcount: A:0.32, C:0.19, G:0.30, T:0.20
Consensus pattern (40 bp):
ACCGCTAAAGGTCAGAGCATTAGCGGCGCTTGTAGGAAAG
Found at i:85819 original size:82 final size:82
Alignment explanation
Indices: 85706--85893 Score: 227
Period size: 82 Copynumber: 2.3 Consensus size: 82
85696 CCCATAAACA
* * *
85706 CCGCTAAAGGTGAGAGCATTAGCGGCGCTTGTAG-GAAAG-ATCCGCTAAAGGTCAGAGAATTAG
1 CCGCTAAAGGTCAGAGCATTAGCGGCGCTTGT-GTGAAAGCA-CCACTAAAGGTCAGAGAATTAA
* * **
85769 CGGCGCTTGTGGGAAAGCG
64 CGACGCTTATAAGAAAGCG
* *
85788 CCGCTAAAGGTCAGAGCATTAGCGGTGCTTGTGTGAAAGCACCACTAAAGGTCAGAGCATTAACG
1 CCGCTAAAGGTCAGAGCATTAGCGGCGCTTGTGTGAAAGCACCACTAAAGGTCAGAGAATTAACG
85853 ACGCTTATAAGAAAGCG
66 ACGCTTATAAGAAAGCG
* * * *
85870 TCGTTAAAGATCAAAGCATTAGCG
1 CCGCTAAAGGTCAGAGCATTAGCG
85894 ACGTTTTTAA
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
81 1 0.01
82 89 0.98
83 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.30, T:0.20
Consensus pattern (82 bp):
CCGCTAAAGGTCAGAGCATTAGCGGCGCTTGTGTGAAAGCACCACTAAAGGTCAGAGAATTAACG
ACGCTTATAAGAAAGCG
Found at i:86031 original size:19 final size:20
Alignment explanation
Indices: 86002--86045 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
85992 TTATATAAAC
*
86002 TAAAAATAATTCTAAAATTT
1 TAAAAATAATTCAAAAATTT
86022 TAAAAA-AATTCAAAAATTT
1 TAAAAATAATTCAAAAATTT
86041 TAAAA
1 TAAAA
86046 CTTATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TAAAAATAATTCAAAAATTT
Done.