Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006225.1 Hibiscus syriacus cultivar Beakdansim tig00014836_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: 157934
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8021 original size:15 final size:16
Alignment explanation
Indices: 7991--8023 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
7981 AAGTGTAACG
*
7991 AAAAAAATATTATTTA
1 AAAAAAATAATATTTA
8007 AAAAAAATAAT-TTTA
1 AAAAAAATAATATTTA
8022 AA
1 AA
8024 TATAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAAAATAATATTTA
Found at i:13959 original size:59 final size:60
Alignment explanation
Indices: 13846--13978 Score: 171
Period size: 59 Copynumber: 2.2 Consensus size: 60
13836 TTAAGGGTAA
* * *
13846 TTACATAAATGGTCCCCTGACTATAGAGAATTACTTCATTAAGTCTTCTAACTATTAAAAG
1 TTACA-AAATGGTCCACTGACTATAGAGAATTACTTCATTAAGTCATATAACTATTAAAAG
* * * *
13907 TTATAAAATGGTTCACTGACTATA-AGACGTTACTT-TTTAAGTCATATAACTATTAAAAG
1 TTACAAAATGGTCCACTGACTATAGAGA-ATTACTTCATTAAGTCATATAACTATTAAAAG
13966 TTACAAAATGGTC
1 TTACAAAATGGTC
13979 ACCAGACTCT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 35 0.56
60 23 0.37
61 4 0.06
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (60 bp):
TTACAAAATGGTCCACTGACTATAGAGAATTACTTCATTAAGTCATATAACTATTAAAAG
Found at i:17651 original size:69 final size:69
Alignment explanation
Indices: 17565--17695 Score: 194
Period size: 69 Copynumber: 1.9 Consensus size: 69
17555 AAGTTTAACT
*
17565 GTCAAAACTCCAATGTTTGTCCCATTATTGACTGTG-TTCAAATA-TATTTTAGATAATCAATTA
1 GTCAAAACTCCAATGTTTGTCCCATTATTAACTG-GATTCAAA-AGTATTTTAGATAATCAATTA
17628 TAAGTC
64 TAAGTC
* *
17634 GTCAATACTCCAATGTTTGTCCCATTATTAAGTGGATTTCAAAAGTATTTTAGATAATCAAT
1 GTCAAAACTCCAATGTTTGTCCCATTATTAACTGGA-TTCAAAAGTATTTTAGATAATCAAT
17696 GTCGGTCCAA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
68 1 0.02
69 32 0.57
70 23 0.41
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (69 bp):
GTCAAAACTCCAATGTTTGTCCCATTATTAACTGGATTCAAAAGTATTTTAGATAATCAATTATA
AGTC
Found at i:21252 original size:18 final size:18
Alignment explanation
Indices: 21225--21303 Score: 54
Period size: 18 Copynumber: 4.4 Consensus size: 18
21215 TACTAAGGGG
*
21225 TTCCTAACGTGACAGAGA
1 TTCCTGACGTGACAGAGA
*** *
21243 TTCCTGACGTGGGGGACA
1 TTCCTGACGTGACAGAGA
* *
21261 TTCTTGACATAGA-AGAGA
1 TTCCTGACGT-GACAGAGA
*
21279 TTCCTGACGT-ACCAGGGA
1 TTCCTGACGTGA-CAGAGA
21297 TTCCTGA
1 TTCCTGA
21304 AGTGGAAGCA
Statistics
Matches: 45, Mismatches: 13, Indels: 6
0.70 0.20 0.09
Matches are distributed among these distances:
16 1 0.02
18 43 0.96
19 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.25
Consensus pattern (18 bp):
TTCCTGACGTGACAGAGA
Found at i:21949 original size:17 final size:17
Alignment explanation
Indices: 21924--21974 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
21914 TTATTCAAGG
*
21924 ATAACTTAAACAAATTA
1 ATAATTTAAACAAATTA
***
21941 ATAATTTAAAGTTGATTA
1 ATAATTTAAA-CAAATTA
21959 ATAATTTAAACAAATT
1 ATAATTTAAACAAATT
21975 TTAAAAGAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (17 bp):
ATAATTTAAACAAATTA
Found at i:28201 original size:23 final size:23
Alignment explanation
Indices: 28175--28219 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
28165 CACCACAGCT
* *
28175 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATACACCGAAGTGCCC
* *
28198 CGTAGAATTACACCGTAGTGCC
1 CGTAGAAATACACCGAAGTGCC
28220 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCC
Found at i:28468 original size:149 final size:149
Alignment explanation
Indices: 28198--28501 Score: 554
Period size: 149 Copynumber: 2.0 Consensus size: 149
28188 CGAAGTGCCC
28198 CGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
* *
28263 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
* *
28328 TATATGTCCTAAAGAACCG
131 CATATGTCCCAAAGAACCG
*
28347 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
28412 CATATATATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
28477 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
28496 CGTAGA
1 CGTAGA
28502 CCCTCTACCC
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:29018 original size:20 final size:21
Alignment explanation
Indices: 28977--29017 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
28967 TTTTTTCTCA
*
28977 TGGGGGAATCGGTTCCCCCCC
1 TGGGGGAATCGATTCCCCCCC
*
28998 TGGGGGTATCGATTCCCCCC
1 TGGGGGAATCGATTCCCCCC
29018 TAGCATTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.37, G:0.32, T:0.22
Consensus pattern (21 bp):
TGGGGGAATCGATTCCCCCCC
Found at i:29088 original size:67 final size:67
Alignment explanation
Indices: 28978--29129 Score: 268
Period size: 67 Copynumber: 2.3 Consensus size: 67
28968 TTTTTCTCAT
* *
28978 GGGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCCCTAGCATTCTGGAATTTCATATTCGT
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCCCTAGCATTCTGGAAATTCATATTCGT
29043 TGA
65 TGA
*
29046 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCCCTAGCATTCTGGAAATTCATATTCGTT
29111 GA
66 GA
29113 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
29130 TTGAATGGGT
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
67 69 0.85
68 12 0.15
ACGTcount: A:0.15, C:0.27, G:0.28, T:0.30
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCCCTAGCATTCTGGAAATTCATATTCGTT
GA
Found at i:31149 original size:31 final size:31
Alignment explanation
Indices: 31111--31199 Score: 90
Period size: 31 Copynumber: 2.9 Consensus size: 31
31101 TCATATCCCT
* **
31111 ACAAACAAACAAATAAATAAATAATTTTG-AA
1 ACAAACAAACAAATAAA-AAATAACTAAGCAA
* **
31142 ACAAACAAATAAATTCAAAATAACTAAGCAA
1 ACAAACAAACAAATAAAAAATAACTAAGCAA
**
31173 ACAAACAAACAAATTTAAAATAACTAA
1 ACAAACAAACAAATAAAAAATAACTAA
31200 ATAAATAAGT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
30 8 0.16
31 41 0.84
ACGTcount: A:0.65, C:0.13, G:0.02, T:0.19
Consensus pattern (31 bp):
ACAAACAAACAAATAAAAAATAACTAAGCAA
Found at i:31204 original size:4 final size:4
Alignment explanation
Indices: 31190--31301 Score: 66
Period size: 4 Copynumber: 27.0 Consensus size: 4
31180 AACAAATTTA
* * **
31190 AAAT AACT AAAT AAAT AAGT TCA- AAAT AAAT AAAT AAAT AAAT AAATTT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA--T
** * * * *
31239 GAGTT GAAT AAAT AAAT AAAT AAAT AAA- ACAT AAAT GAAT ATAT AAATT
1 -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T
31288 CGAAAT AAAT AAAT
1 --AAAT AAAT AAAT
31302 TGTAACACCC
Statistics
Matches: 80, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
3 3 0.04
4 69 0.86
5 2 0.03
6 2 0.03
7 4 0.05
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:31225 original size:31 final size:30
Alignment explanation
Indices: 31190--31266 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 30
31180 AACAAATTTA
*
31190 AAATAACTAAATAAA-TAAGTTCAAAATAAAT
1 AAATAAATAAATAAATTAAGTT--AAATAAAT
* *
31221 AAATAAATAAATAAATTTGAGTTGAATAAAT
1 AAATAAATAAATAAA-TTAAGTTAAATAAAT
31252 AAATAAATAAATAAA
1 AAATAAATAAATAAA
31267 ACATAAATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 36 0.88
33 5 0.12
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (30 bp):
AAATAAATAAATAAATTAAGTTAAATAAAT
Found at i:31278 original size:31 final size:32
Alignment explanation
Indices: 31214--31300 Score: 88
Period size: 31 Copynumber: 2.7 Consensus size: 32
31204 ATAAGTTCAA
** **
31214 AATAAATAAATAAATAAAT-AAATTTGAGTTG
1 AATAAATAAATAAATAAATAAAACATGAAATG
31245 AATAAATAAATAAATAAATAAAACAT-AAATG
1 AATAAATAAATAAATAAATAAAACATGAAATG
*
31276 AATATATAAATTCGAAATAAATAAA
1 AATAAATAAA-T--AAATAAATAAA
31301 TTGTAACACC
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
31 31 0.66
32 5 0.11
34 11 0.23
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (32 bp):
AATAAATAAATAAATAAATAAAACATGAAATG
Found at i:31299 original size:27 final size:27
Alignment explanation
Indices: 31190--31301 Score: 106
Period size: 27 Copynumber: 4.3 Consensus size: 27
31180 AACAAATTTA
* * *
31190 AAATAACTAAATAAATAAGTTCAAAAT
1 AAATAAATAAATAAATAAATTCGAAAT
* **
31217 AAATAAATAAATAAATAAATTTGAGTT
1 AAATAAATAAATAAATAAATTCGAAAT
*
31244 GAATAAATAAATAAATAAA-T--AAA-
1 AAATAAATAAATAAATAAATTCGAAAT
* * *
31267 ACATAAATGAATATATAAATTCGAAAT
1 AAATAAATAAATAAATAAATTCGAAAT
31294 AAATAAAT
1 AAATAAAT
31302 TGTAACACCC
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
23 15 0.22
24 2 0.03
26 4 0.06
27 46 0.69
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (27 bp):
AAATAAATAAATAAATAAATTCGAAAT
Found at i:31685 original size:2 final size:2
Alignment explanation
Indices: 31678--31706 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31668 TCAATTATTC
31678 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31707 GATAACAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32336 original size:38 final size:38
Alignment explanation
Indices: 32258--32336 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
32248 GTATATATAT
****
32258 ATTTAAATTAAATATATAAATATTATATATATTTTTTA
1 ATTTAAATTAAATATATAAATATTATATATATAAAATA
* * *
32296 ATTTAATTTAAATTTATTAATATTATATATATAAAATA
1 ATTTAAATTAAATATATAAATATTATATATATAAAATA
32334 ATT
1 ATT
32337 ATTTTTAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (38 bp):
ATTTAAATTAAATATATAAATATTATATATATAAAATA
Found at i:34713 original size:60 final size:60
Alignment explanation
Indices: 34594--34716 Score: 140
Period size: 60 Copynumber: 2.0 Consensus size: 60
34584 GCTCTCAAAG
* * * * * * * *
34594 TATGACTCTCATTTTAAATTTGTTCTTAAACTTTTAAATGTTTCAATTTTATCTATAAAC
1 TATGACTATCATTCTAAATTAGTCCTCAAACTTTTAAATATTCCAATTTTAACTATAAAC
* *
34654 TATGACTATCATTCTAAATTAGTCCTCAAACGTTTTGAATATTCCAATTTTAAC-CTAAAC
1 TATGACTATCATTCTAAATTAGTCCTCAAAC-TTTTAAATATTCCAATTTTAACTATAAAC
34714 TAT
1 TAT
34717 ATGTATATAC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 34 0.65
61 18 0.35
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (60 bp):
TATGACTATCATTCTAAATTAGTCCTCAAACTTTTAAATATTCCAATTTTAACTATAAAC
Found at i:45698 original size:32 final size:32
Alignment explanation
Indices: 45651--45714 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
45641 GAGTCGGGTA
* * *
45651 GAGATTATATATTTTTTGGGTC-AGATCGAGTT
1 GAGAATATAAATTTTTTGAGTCGA-ATCGAGTT
45683 GAGAATATAAATTTTTTGAGTCGAATCGAGTT
1 GAGAATATAAATTTTTTGAGTCGAATCGAGTT
45715 TGGGTAGAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.30, C:0.06, G:0.23, T:0.41
Consensus pattern (32 bp):
GAGAATATAAATTTTTTGAGTCGAATCGAGTT
Found at i:46038 original size:20 final size:20
Alignment explanation
Indices: 46009--46067 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
45999 AAATAATCAA
46009 CAAATTCGCAACGCGAATTC
1 CAAATTCGCAACGCGAATTC
* * * *
46029 CAATTTCGCAATGCGATTTT
1 CAAATTCGCAACGCGAATTC
*
46049 CAAATTCGCAACGCTAATT
1 CAAATTCGCAACGCGAATT
46068 ACCGATATAG
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTC
Found at i:46197 original size:20 final size:20
Alignment explanation
Indices: 46174--46218 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
46164 ATAAATCAGT
46174 TTTCAAATTCGCAACGCGAA
1 TTTCAAATTCGCAACGCGAA
*** *
46194 TTTCGTTTTCGCAACTCGAA
1 TTTCAAATTCGCAACGCGAA
46214 TTTCA
1 TTTCA
46219 CAACGCTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (20 bp):
TTTCAAATTCGCAACGCGAA
Found at i:53352 original size:17 final size:18
Alignment explanation
Indices: 53330--53369 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
53320 GAATGCTTGT
53330 TTAAATAA-ATTTAATCA
1 TTAAATAATATTTAATCA
*
53347 TTAAATAATCTTTAATCA
1 TTAAATAATATTTAATCA
*
53365 CTAAA
1 TTAAA
53370 ATTATATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAATAATATTTAATCA
Found at i:57136 original size:29 final size:29
Alignment explanation
Indices: 57094--57169 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
57084 GGAGCAGGAG
57094 GGAGTGCATGGCGACCTACAAGGTCGCCA
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
* *
57123 GGAGTGCATGGCGACCTACAAGGTCTCCC
1 GGAGTGCATGGCGACCTACAAGGTCGCCA
*
57152 GGAGTGCATGACGACCTA
1 GGAGTGCATGGCGACCTA
57170 TTCTTGGGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.24, C:0.28, G:0.33, T:0.16
Consensus pattern (29 bp):
GGAGTGCATGGCGACCTACAAGGTCGCCA
Found at i:57739 original size:24 final size:24
Alignment explanation
Indices: 57703--57758 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
57693 TGATCTTTAA
57703 TTGAATTTCGTTCCAACAAATCAC
1 TTGAATTTCGTTCCAACAAATCAC
*
57727 TTGAATTTTGTTCCAACAAATCAC
1 TTGAATTTCGTTCCAACAAATCAC
57751 TTGAATTT
1 TTGAATTT
57759 ATCTAAAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (24 bp):
TTGAATTTCGTTCCAACAAATCAC
Found at i:58926 original size:2 final size:2
Alignment explanation
Indices: 58919--58948 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
58909 GTGGTACATT
58919 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58949 TTGTTCCGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:62116 original size:2 final size:2
Alignment explanation
Indices: 62109--62143 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
62099 ATCCAGCCCC
62109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
62144 CATTGAAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:83918 original size:198 final size:199
Alignment explanation
Indices: 83574--83958 Score: 538
Period size: 198 Copynumber: 1.9 Consensus size: 199
83564 AGATCGCATG
* * * *
83574 ACAATGAATGTGTACTGTGTCATGCCTACAAAAGAGAACTACATTCATTTCATTTATAGCTTGGA
1 ACAATGAATGTGTACTGTATCAAGCCTACAAAAGAGAACTACATGCATCTCATTTATAGCTTGGA
* * * * * * *
83639 TTTACGCAATAAAAACTCTTTATTTCAATACTCCAGAAGAAGCTAGTAGGGGCTCTAATTTCATA
66 TATAAGCAATAAAAACTATTTATTTCAAGACTCCAGAAGAAGCTACTAGGGACTCTAATGTCATA
* * *
83704 TGCAAATCTGTTTATTTACCATGAGATCTATATCAAACCCCTCAAAATAGAAATAGAGGCATAAA
131 TGCAAATCTATTTATTTACCATGAGATCTATAACAAACCCATCAAAATAGAAATAGAGGCATAAA
83769 CCTA
196 CCTA
* *
83773 ACAATGAATGTGTTCTGTATCAAGCCTAC-AAAGAGAACTCCATGCATCTCATTTATAGCTTGGA
1 ACAATGAATGTGTACTGTATCAAGCCTACAAAAGAGAACTACATGCATCTCATTTATAGCTTGGA
* ** *
83837 TATAAGCAATAAAAACTATTTGTTTCAAGACTCCAGAAGATTCTACTAGGGACTCTACTGTCATA
66 TATAAGCAATAAAAACTATTTATTTCAAGACTCCAGAAGAAGCTACTAGGGACTCTAATGTCATA
* * * **
83902 TTCGAATCTATTTATTTACCATGAGTTCTATAACAAGTCCATCAAAATAGAAATAGA
131 TGCAAATCTATTTATTTACCATGAGATCTATAACAAACCCATCAAAATAGAAATAGA
83959 TATGTTCACA
Statistics
Matches: 161, Mismatches: 25, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
198 135 0.84
199 26 0.16
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (199 bp):
ACAATGAATGTGTACTGTATCAAGCCTACAAAAGAGAACTACATGCATCTCATTTATAGCTTGGA
TATAAGCAATAAAAACTATTTATTTCAAGACTCCAGAAGAAGCTACTAGGGACTCTAATGTCATA
TGCAAATCTATTTATTTACCATGAGATCTATAACAAACCCATCAAAATAGAAATAGAGGCATAAA
CCTA
Found at i:90234 original size:2 final size:2
Alignment explanation
Indices: 90227--90251 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
90217 TATTAAAATT
90227 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
90252 TTGATTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:90775 original size:31 final size:31
Alignment explanation
Indices: 90721--90781 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
90711 TTTAGTTGAA
* * *
90721 TTTAATAATCAAATTAATGTTTTATCTAAAG
1 TTTAAAAATCAAAATAATATTTTATCTAAAG
*
90752 TTTAAAAATTAAAATAATATTTTATCTAAA
1 TTTAAAAATCAAAATAATATTTTATCTAAA
90782 CTTCAATGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (31 bp):
TTTAAAAATCAAAATAATATTTTATCTAAAG
Found at i:94809 original size:31 final size:30
Alignment explanation
Indices: 94774--94881 Score: 105
Period size: 31 Copynumber: 3.6 Consensus size: 30
94764 GCTTTAGTTG
94774 AATTCAATGATCAAATTGATATTTTATCTAA
1 AATTCAATGATCAAATTGATATTTTAT-TAA
*
94805 AATTC-ATGGATCAAAATGATATTTTATATAA
1 AATTCAAT-GATCAAATTGATATTTTAT-TAA
* * *
94836 AATTCAA-GGTCTAATT-AGTATTCTATTAA
1 AATTCAATGATCAAATTGA-TATTTTATTAA
* *
94865 AGTTCAATGATAAAATT
1 AATTCAATGATCAAATT
94882 AAAGGTTATC
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
29 10 0.16
30 21 0.33
31 31 0.49
32 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (30 bp):
AATTCAATGATCAAATTGATATTTTATTAA
Found at i:98621 original size:21 final size:21
Alignment explanation
Indices: 98595--98638 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
98585 ATTCTGGGCT
* *
98595 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
98616 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
98637 AG
1 AG
98639 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:98709 original size:23 final size:22
Alignment explanation
Indices: 98665--98709 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
98655 AATGTCATGG
*
98665 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
98687 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
98710 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:99990 original size:11 final size:12
Alignment explanation
Indices: 99950--99993 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
99940 TATTTAAACG
*
99950 GGTATTGGGCCA
1 GGTATTGGGTCA
*
99962 GGTATTGGGTCG
1 GGTATTGGGTCA
99974 GGTATTGGGTC-
1 GGTATTGGGTCA
99985 GGTATTGGG
1 GGTATTGGG
99994 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:99992 original size:23 final size:24
Alignment explanation
Indices: 99948--99993 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
99938 ATTATTTAAA
99948 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
99972 CGGGTATTGGGTC-GGTATTGGG
1 CGGGTATTGGGCCAGGTATTGGG
99994 CTGGGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.30
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:100567 original size:18 final size:18
Alignment explanation
Indices: 100544--100579 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
100534 AGGAATGATA
100544 TGTGGTCATTCGGGACAT
1 TGTGGTCATTCGGGACAT
*
100562 TGTGGTCCTTCGGGACAT
1 TGTGGTCATTCGGGACAT
100580 ATATGTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.19, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCATTCGGGACAT
Found at i:100600 original size:121 final size:121
Alignment explanation
Indices: 100441--100925 Score: 898
Period size: 121 Copynumber: 4.0 Consensus size: 121
100431 CGAGGGTCTA
* *
100441 TGTGGTCCTTCGAGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
100506 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCATTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
100562 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
*
100627 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
100683 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
100748 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
*
100804 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCATACTT
1 TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
* **
100869 GATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACAT
66 GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
100925 T
1 T
100926 ATTATATGGC
Statistics
Matches: 355, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 355 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (121 bp):
TGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTT
GATCCCTAGCATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTCGGGACAT
Found at i:100688 original size:18 final size:18
Alignment explanation
Indices: 100665--100700 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
100655 AGGAATGATA
100665 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
100683 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
100701 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:100809 original size:18 final size:18
Alignment explanation
Indices: 100786--100821 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
100776 AGGAATGATA
100786 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
100804 TGTGGTCCTTCGGGACAT
1 TGTGGTCCTTCGGGACAT
100822 ATATGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.33, T:0.33
Consensus pattern (18 bp):
TGTGGTCCTTCGGGACAT
Found at i:101000 original size:23 final size:23
Alignment explanation
Indices: 100932--100992 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
100922 CATTATTATA
100932 TGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
100955 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
100978 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
100993 TTTATATGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:107615 original size:18 final size:19
Alignment explanation
Indices: 107594--107630 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 19
107584 ATATATAATC
107594 ATTAAATTA-TTTTAAAAA
1 ATTAAATTAGTTTTAAAAA
107612 ATTAAATTAGTTTTTAAAA
1 ATTAAATTAG-TTTTAAAA
107631 TAAAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
20 8 0.47
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTAAATTAGTTTTAAAAA
Found at i:113534 original size:35 final size:35
Alignment explanation
Indices: 113494--113566 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
113484 CGGAGGATAG
*
113494 TCAACACAGAACAAGATTTGCATCAACTCGGATTA
1 TCAACACAGAACAAGATTTGCATCAACTCGAATTA
*
113529 TCAACACAGAACAAGATTTGCATTAACTCGAATTA
1 TCAACACAGAACAAGATTTGCATCAACTCGAATTA
113564 TCA
1 TCA
113567 CGCTGTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (35 bp):
TCAACACAGAACAAGATTTGCATCAACTCGAATTA
Found at i:117859 original size:85 final size:85
Alignment explanation
Indices: 117770--117943 Score: 215
Period size: 85 Copynumber: 2.0 Consensus size: 85
117760 ATCATGGGTC
* * ** *
117770 AAAAAGGCTCC-TAACGTTTGAATAAATGATCATTTTAAATCTTATTTTTTGGAGCATCTTGGCC
1 AAAAAGGC-CCTTAACGTTTGAATAAATAATCATTTTAAACCACATTTTTTAGAGCATCTTGGCC
* *
117834 TCTAATGTTTCATTTTAGAGT
65 CCTAATATTTCATTTTAGAGT
* * *
117855 AAAAAGGCCCTTATCGTTTGAATAAATAATCATTTTAGACCACATTTTTTAGAGCATTTTGGCCC
1 AAAAAGGCCCTTAACGTTTGAATAAATAATCATTTTAAACCACATTTTTTAGAGCATCTTGGCCC
** *
117920 CTAATATTTTGTTTTAGGGT
66 CTAATATTTCATTTTAGAGT
117940 AAAA
1 AAAA
117944 GGTCTTTATT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
84 2 0.03
85 73 0.97
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (85 bp):
AAAAAGGCCCTTAACGTTTGAATAAATAATCATTTTAAACCACATTTTTTAGAGCATCTTGGCCC
CTAATATTTCATTTTAGAGT
Found at i:127637 original size:3 final size:3
Alignment explanation
Indices: 127618--127669 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
127608 TTGGTTTTAA
* * **
127618 ATT ATT TTT ACT ATT ATT ATT ATT ATT ATT GCT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
127666 ATT A
1 ATT A
127670 ATTTACATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:135226 original size:17 final size:17
Alignment explanation
Indices: 135192--135243 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
135182 ACCGGACAAA
* *
135192 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
135209 TTTATTAATTTACCGAG
1 TTTATTAATTTACAGAG
*
135226 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
135241 TTT
1 TTT
135244 CTACTGTACA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:146019 original size:16 final size:16
Alignment explanation
Indices: 146000--146030 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
145990 CCTTTCAAAC
146000 GACCCCATTTTCTAAG
1 GACCCCATTTTCTAAG
146016 GACCCCATTTTCTAA
1 GACCCCATTTTCTAA
146031 ATGAGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.32
Consensus pattern (16 bp):
GACCCCATTTTCTAAG
Found at i:147643 original size:2 final size:2
Alignment explanation
Indices: 147636--147673 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
147626 CCATGCAATA
*
147636 AT AT AT AT AT AT AT CT 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
147674 TTCAAAAGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:150140 original size:2 final size:2
Alignment explanation
Indices: 150133--150166 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
150123 TACAACAATG
150133 TA TA TA TA T- TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
150167 AACTAGGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:152451 original size:24 final size:24
Alignment explanation
Indices: 152411--152461 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
152401 ATTGTGAATG
*
152411 TTTTATTTATTTA-TTTTAGTATTA
1 TTTTATATATTTATTTTTA-TATTA
152435 TTTTATAT-TTTATTTTTTATATTA
1 TTTTATATATTTA-TTTTTATATTA
152459 TTT
1 TTT
152462 ATTTAATTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.17
24 15 0.62
25 5 0.21
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTATATATTTATTTTTATATTA
Found at i:152464 original size:16 final size:16
Alignment explanation
Indices: 152412--152465 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
152402 TTGTGAATGT
*
152412 TTTATTTATTTATTTTA
1 TTTATTT-TTTATATTA
*
152429 -GTATTATTTTATA-T-
1 TTTATT-TTTTATATTA
152443 TTTATTTTTTATATTA
1 TTTATTTTTTATATTA
152459 TTTATTT
1 TTTATTT
152466 AATTAGGGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
14 7 0.23
15 6 0.20
16 16 0.53
17 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTATTTTTTATATTA
Found at i:152470 original size:12 final size:12
Alignment explanation
Indices: 152411--152470 Score: 52
Period size: 12 Copynumber: 4.8 Consensus size: 12
152401 ATTGTGAATG
152411 TTTTAT-TTATTT
1 TTTTATATTA-TT
152423 ATTTTAGTATTATT
1 -TTTTA-TATTATT
* *
152437 TTATATTTTATT
1 TTTTATATTATT
152449 TTTTATATTATT
1 TTTTATATTATT
152461 TATTTA-ATTA
1 T-TTTATATTA
152471 GGGGAATGAC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 21 0.52
13 13 0.32
14 3 0.08
15 3 0.08
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (12 bp):
TTTTATATTATT
Found at i:154149 original size:21 final size:21
Alignment explanation
Indices: 154116--154156 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
154106 TACATGGGTA
*
154116 CACCGCAGCCATTTCAGATGG
1 CACCACAGCCATTTCAGATGG
* *
154137 CACCACAGTCATTTTAGATG
1 CACCACAGCCATTTCAGATG
154157 CCACTGCAGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (21 bp):
CACCACAGCCATTTCAGATGG
Found at i:154745 original size:14 final size:14
Alignment explanation
Indices: 154686--154747 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
154676 TTTCTTAATG
*
154686 TTGTTATTATTTAA
1 TTGTTTTTATTTAA
**
154700 TTGTTTGAATTGTAA
1 TTGTTTTTATT-TAA
*
154715 -TGTTTGTATTT-A
1 TTGTTTTTATTTAA
154727 TTGTTTTTATTTAA
1 TTGTTTTTATTTAA
154741 TTGTTTT
1 TTGTTTT
154748 AATTGTTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 1 0.03
13 11 0.28
14 25 0.62
15 3 0.08
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.66
Consensus pattern (14 bp):
TTGTTTTTATTTAA
Found at i:154752 original size:23 final size:23
Alignment explanation
Indices: 154718--154788 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 23
154708 ATTGTAATGT
154718 TTGTATTT-ATTGTTTTTATTTAA
1 TTGT-TTTAATTGTTTTTATTTAA
* *
154741 TTGTTTTAATTGTTTTTA-CTAT
1 TTGTTTTAATTGTTTTTATTTAA
154763 TTAGTTTGTAA-TGTTTTTATTTAA
1 TT-GTTT-TAATTGTTTTTATTTAA
154787 TT
1 TT
154789 TTCACTTGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 7 0.17
23 26 0.65
24 7 0.17
ACGTcount: A:0.21, C:0.01, G:0.10, T:0.68
Consensus pattern (23 bp):
TTGTTTTAATTGTTTTTATTTAA
Found at i:156280 original size:31 final size:31
Alignment explanation
Indices: 156226--156292 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
156216 ATTTTAAAAG
*
156226 TTATAAAATAATTATTAATTTTATCAAACTA
1 TTATAAAATAAATATTAATTTTATCAAACTA
* * *
156257 TTATGAAATAAATATTGAA-TTTATCGAACTG
1 TTATAAAATAAATATT-AATTTTATCAAACTA
156288 TTATA
1 TTATA
156293 TAATGATCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (31 bp):
TTATAAAATAAATATTAATTTTATCAAACTA
Done.