Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001278.1 Hibiscus syriacus cultivar Beakdansim tig00002508_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: 93985
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:13098 original size:14 final size:15
Alignment explanation
Indices: 13059--13095 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
13049 ATCATTATAT
*
13059 GTACTTTTCATGTGA
1 GTACTTTTCAAGTGA
13074 GTACTTTTCAAGTGA
1 GTACTTTTCAAGTGA
13089 GTACTTT
1 GTACTTT
13096 CAAACTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.46
Consensus pattern (15 bp):
GTACTTTTCAAGTGA
Found at i:15966 original size:122 final size:123
Alignment explanation
Indices: 15727--15977 Score: 398
Period size: 122 Copynumber: 2.0 Consensus size: 123
15717 TAGAATTGGC
* * * *
15727 CGATGAAGAATAGGAAGTCTTGGCTTTCGATAATTCTACTGATGCCTCGTTACTCTCTTTTTTAG
1 CGATGAAGAAGAGGAAGTCTTGGCTTTCGATAATTCTACTGATGCCCCGTTACTCTCTCTTTGAG
15792 AACTGCTTGGTGGGTCGGTTCCTATCTTCTGGGAATATTAACTGTCAGGCTATGAAAA
66 AACTGCTTGGTGGGTCGGTTCCTATCTTCTGGGAATATTAACTGTCAGGCTATGAAAA
*
15850 TGATGAAGAAGAGGAAGTCTTGGCTTTCGATAATTCTACTGCA-GCCCCGTTACTCTC-CTTTGA
1 CGATGAAGAAGAGGAAGTCTTGGCTTTCGATAATTCTACTG-ATGCCCCGTTACTCTCTCTTTGA
* * * *
15913 TAACTGCTTGGTGGGTTGGTTCCTATCTTCTGGGAATATTAACTTTTAGGCTATGAAAA
65 GAACTGCTTGGTGGGTCGGTTCCTATCTTCTGGGAATATTAACTGTCAGGCTATGAAAA
15972 CGATGA
1 CGATGA
15978 TGGTGAACGT
Statistics
Matches: 117, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
122 64 0.55
123 52 0.44
124 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (123 bp):
CGATGAAGAAGAGGAAGTCTTGGCTTTCGATAATTCTACTGATGCCCCGTTACTCTCTCTTTGAG
AACTGCTTGGTGGGTCGGTTCCTATCTTCTGGGAATATTAACTGTCAGGCTATGAAAA
Found at i:17725 original size:18 final size:18
Alignment explanation
Indices: 17702--17745 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
17692 TTAAAGAGTC
17702 ATCTTGAGGCTTTGAAGA
1 ATCTTGAGGCTTTGAAGA
17720 ATCTTGAGGCTTTGAAGA
1 ATCTTGAGGCTTTGAAGA
*
17738 AGCTTGAG
1 ATCTTGAG
17746 CCTAACGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.11, G:0.30, T:0.32
Consensus pattern (18 bp):
ATCTTGAGGCTTTGAAGA
Found at i:18734 original size:7 final size:7
Alignment explanation
Indices: 18722--18759 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
18712 ACCAGAGGGC
18722 ATGAAGA
1 ATGAAGA
18729 ATGAAGA
1 ATGAAGA
18736 ATGAAGA
1 ATGAAGA
18743 ATGAAGA
1 ATGAAGA
18750 ATGAAGA
1 ATGAAGA
18757 ATG
1 ATG
18760 TGATCTTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.16
Consensus pattern (7 bp):
ATGAAGA
Found at i:29751 original size:20 final size:20
Alignment explanation
Indices: 29726--29765 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
29716 AAATTAATAG
29726 TACTCGTCGTTAATGATGCT
1 TACTCGTCGTTAATGATGCT
*
29746 TACTCGTCGTTAGTGATGCT
1 TACTCGTCGTTAATGATGCT
29766 CATCGTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (20 bp):
TACTCGTCGTTAATGATGCT
Found at i:32233 original size:24 final size:24
Alignment explanation
Indices: 32200--32253 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
32190 GACGGTTCCT
*
32200 GGAAGTGGACACTTAGGGTCACCC
1 GGAAGCGGACACTTAGGGTCACCC
*
32224 GGAAGCGGACCCTTAGGGTCACCC
1 GGAAGCGGACACTTAGGGTCACCC
32248 GGAAGC
1 GGAAGC
32254 ATGGTTAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.28, G:0.35, T:0.13
Consensus pattern (24 bp):
GGAAGCGGACACTTAGGGTCACCC
Found at i:33773 original size:2 final size:2
Alignment explanation
Indices: 33768--33801 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
33758 TTTTGTCATA
33768 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33802 CATTTTTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34658 original size:146 final size:144
Alignment explanation
Indices: 34479--34808 Score: 504
Period size: 146 Copynumber: 2.3 Consensus size: 144
34469 GAAAACCCCT
* *
34479 ACCCTCTCTCTGCATGCAACGTGATTGGTTCTTCCCACCCCATTTGCATGAACAC-CGAATGAAA
1 ACCCTCTCTCTGCATGCAACGTGATTGGCTCTTCCCACCCCATTTGCATAAACACAC-AATGAAA
*
34543 A-CCCTCTCATTCCTCTCTGTATGCATGCACCGACACCCAAGGAAAACCC-CCCGAAGACGCATG
65 ACCCCTCTCATTCCTCTCTGCATGCATGCACCGACACCCAAGGAAAACCCTCCCGAAGACGCATG
* *
34606 GCATTCCAAACATCTTCTC
130 GCATT-C---CATATTATC
* * *
34625 ACCCCCTCTCTACATGCAACATGATTGGCTCTTCCCACCCCATTTGCATAAACACACAATGAAAA
1 ACCCTCTCTCTGCATGCAACGTGATTGGCTCTTCCCACCCCATTTGCATAAACACACAATGAAAA
*
34690 CCCCTCTCATTCCTCTCTGCATGCATGCACCGACACCCAAGGAAAACCCTCTCGAAGACGCATGG
66 CCCCTCTCATTCCTCTCTGCATGCATGCACCGACACCCAAGGAAAACCCTCCCGAAGACGCATGG
34755 CATTCCATATTATC
131 CATTCCATATTATC
*
34769 ACCCTTTCTCTGCATGCAACGTGATTGGCTCTTCCCACCC
1 ACCCTCTCTCTGCATGCAACGTGATTGGCTCTTCCCACCC
34809 AACGAAAAAC
Statistics
Matches: 168, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
144 43 0.26
146 58 0.35
147 49 0.29
148 18 0.11
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.24
Consensus pattern (144 bp):
ACCCTCTCTCTGCATGCAACGTGATTGGCTCTTCCCACCCCATTTGCATAAACACACAATGAAAA
CCCCTCTCATTCCTCTCTGCATGCATGCACCGACACCCAAGGAAAACCCTCCCGAAGACGCATGG
CATTCCATATTATC
Found at i:35158 original size:3 final size:3
Alignment explanation
Indices: 35152--35208 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
35142 GAGGAGAACA
*
35152 AAG AAG -AG AA- AAG AGG AAG AAAG AAG AAG AAG -AG AAG AAAG AAG
1 AAG AAG AAG AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG -AAG AAG
35196 AAG AAG -AG AAG AA
1 AAG AAG AAG AAG AA
35209 AGTTAAAGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
2 8 0.17
3 32 0.70
4 6 0.13
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:35158 original size:18 final size:18
Alignment explanation
Indices: 35132--35210 Score: 104
Period size: 18 Copynumber: 4.2 Consensus size: 18
35122 ACTGGGAGTA
* *
35132 AAAGAAAGAAGAGGAGAAC
1 AAAG-AAGAAGAAGAGAAG
*
35151 AAAGAAGAGAAAAGAGGAAG
1 AAAGAAGA-AGAAGA-GAAG
35171 AAAGAAGAAGAAGAGAAG
1 AAAGAAGAAGAAGAGAAG
35189 AAAGAAGAAGAAGAGAAG
1 AAAGAAGAAGAAGAGAAG
35207 AAAG
1 AAAG
35211 TTAAAGTTGT
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
18 30 0.56
19 13 0.24
20 11 0.20
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.00
Consensus pattern (18 bp):
AAAGAAGAAGAAGAGAAG
Found at i:35927 original size:18 final size:18
Alignment explanation
Indices: 35904--35943 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
35894 CAGTGTTATT
*
35904 ATTATTTAATAAAATATA
1 ATTATTTAAGAAAATATA
* *
35922 ATTATTTGAGAAAATATT
1 ATTATTTAAGAAAATATA
35940 ATTA
1 ATTA
35944 GTAAATGGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (18 bp):
ATTATTTAAGAAAATATA
Found at i:36980 original size:5 final size:5
Alignment explanation
Indices: 36908--36976 Score: 129
Period size: 5 Copynumber: 13.8 Consensus size: 5
36898 GAAAAAATGT
36908 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
*
36958 ATATG ATATG ATATA ATAT
1 ATATG ATATG ATATG ATAT
36977 AATAATAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 63 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.41
Consensus pattern (5 bp):
ATATG
Found at i:37002 original size:10 final size:9
Alignment explanation
Indices: 36989--37034 Score: 58
Period size: 10 Copynumber: 4.9 Consensus size: 9
36979 TAATAATACT
36989 ATTTAATTTA
1 ATTT-ATTTA
36999 ATTTATTTAA
1 ATTTATTT-A
37009 ATTTATTT-
1 ATTTATTTA
37017 ATTTATTTA
1 ATTTATTTA
37026 TATTTATTT
1 -ATTTATTT
37035 CTTAATCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.24
9 4 0.12
10 21 0.64
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
ATTTATTTA
Found at i:37007 original size:14 final size:14
Alignment explanation
Indices: 36988--37034 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
36978 ATAATAATAC
36988 TATTTAATTTAATT
1 TATTTAATTTAATT
37002 TATTTAAATTT-ATT
1 TATTT-AATTTAATT
37016 TATTT-ATTTATATT
1 TATTTAATTTA-ATT
37030 TATTT
1 TATTT
37035 CTTAATCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.13
14 21 0.70
15 5 0.17
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTAATTTAATT
Found at i:45667 original size:32 final size:32
Alignment explanation
Indices: 45591--45695 Score: 93
Period size: 32 Copynumber: 3.3 Consensus size: 32
45581 GATTCAAGGG
* * * * *
45591 TTGACTTGAACTAAAAACTGACCAATCTTATA
1 TTGACTCGAACTAAAAACTAAACGATCTAATA
* * * *
45623 TTAACCCAAACTAAAAACTAAATGATCTAATA
1 TTGACTCGAACTAAAAACTAAACGATCTAATA
* * * *
45655 TTGATTCGAACTAAAAATTGACCGATCTAATA
1 TTGACTCGAACTAAAAACTAAACGATCTAATA
45687 TTGACTCGA
1 TTGACTCGA
45696 TCCATATGTC
Statistics
Matches: 55, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.30
Consensus pattern (32 bp):
TTGACTCGAACTAAAAACTAAACGATCTAATA
Found at i:45696 original size:16 final size:16
Alignment explanation
Indices: 45646--45697 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
45636 AAAACTAAAT
*
45646 GATCTAATATTGATTC
1 GATCTAATATTGACTC
* *
45662 GAACTAAAAATTGAC-C
1 GATCT-AATATTGACTC
45678 GATCTAATATTGACTC
1 GATCTAATATTGACTC
45694 GATC
1 GATC
45698 CATATGTCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
15 8 0.28
16 14 0.48
17 7 0.24
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (16 bp):
GATCTAATATTGACTC
Found at i:46187 original size:24 final size:23
Alignment explanation
Indices: 46143--46187 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
46133 GTACTCAACG
**
46143 TGTAATTAAATTTTAGTTGAAAA
1 TGTAATTAAATTTTAAATGAAAA
*
46166 TGTAATTGTAATTTTAAATGAA
1 TGTAATT-AAATTTTAAATGAA
46188 TCACAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (23 bp):
TGTAATTAAATTTTAAATGAAAA
Found at i:48145 original size:18 final size:18
Alignment explanation
Indices: 48122--48163 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
48112 GTCATAACCT
*
48122 GACCCGACCCGTTTACCC
1 GACCCGACCCGTTGACCC
*
48140 GACCCGACCTGTTGACCC
1 GACCCGACCCGTTGACCC
48158 GACCCG
1 GACCCG
48164 TTGACCGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.48, G:0.21, T:0.14
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:48156 original size:13 final size:13
Alignment explanation
Indices: 48140--48169 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
48130 CCGTTTACCC
*
48140 GACCCGACCTGTT
1 GACCCGACCCGTT
48153 GACCCGACCCGTT
1 GACCCGACCCGTT
48166 GACC
1 GACC
48170 GTTGACCGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:50664 original size:24 final size:23
Alignment explanation
Indices: 50611--50682 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 23
50601 ATACGTTACC
* *
50611 TGAATTCTGTTCTGATTTTGATT
1 TGAATTCTGTTTTGATTTTGATA
* *
50634 TGGATTCTGTTTTGATATATGATA
1 TGAATTCTGTTTTGAT-TTTGATA
50658 TGAATTCTGTTTTGATTTTTGATA
1 TGAATTCTGTTTTGA-TTTTGATA
50682 T
1 T
50683 CTCCGTTTAC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
23 14 0.34
24 26 0.63
25 1 0.02
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.56
Consensus pattern (23 bp):
TGAATTCTGTTTTGATTTTGATA
Found at i:52671 original size:9 final size:9
Alignment explanation
Indices: 52657--52686 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
52647 GCCGGAAGGG
*
52657 GCCCCACGT
1 GCCCCACGC
52666 GCCCCACGC
1 GCCCCACGC
52675 GCCCCACGC
1 GCCCCACGC
52684 GCC
1 GCC
52687 GCCATTGCGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.10, C:0.63, G:0.23, T:0.03
Consensus pattern (9 bp):
GCCCCACGC
Found at i:55329 original size:24 final size:23
Alignment explanation
Indices: 55276--55347 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 23
55266 ATACGTTACC
* *
55276 TGAATTCTGTTCTGATTCTGATT
1 TGAATTCTATTCTGATTCTGATA
*
55299 TGGATTCTATTCTGATATCTGATA
1 TGAATTCTATTCTGAT-TCTGATA
*
55323 TGAATTCTATTTTGATTTCTGATA
1 TGAATTCTATTCTGA-TTCTGATA
55347 T
1 T
55348 CTCCGTTTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 14 0.33
24 27 0.64
25 1 0.02
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.51
Consensus pattern (23 bp):
TGAATTCTATTCTGATTCTGATA
Found at i:57366 original size:18 final size:18
Alignment explanation
Indices: 57343--57396 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
57333 ACCGATCATA
57343 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
57361 -----ACCCGACCCGTTT
1 ACCCGACCCGACCCGTTT
*
57374 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTT
57392 ACCCG
1 ACCCG
57397 TTGACCGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 10
0.73 0.02 0.24
Matches are distributed among these distances:
13 13 0.43
18 17 0.57
ACGTcount: A:0.17, C:0.50, G:0.19, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTT
Found at i:57396 original size:13 final size:13
Alignment explanation
Indices: 57348--57383 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
57338 TCATAACCCG
57348 ACCCGACCCGTTT
1 ACCCGACCCGTTT
57361 ACCCGACCCGTTT
1 ACCCGACCCGTTT
57374 ACCCGACCCG
1 ACCCGACCCG
57384 ACCCGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.17, C:0.50, G:0.17, T:0.17
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:57406 original size:15 final size:16
Alignment explanation
Indices: 57386--57419 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
57376 CCGACCCGAC
57386 CCGTTGACC-CGTTGA
1 CCGTTGACCACGTTGA
57401 CCGTTGACCGACGTTGA
1 CCGTTGACC-ACGTTGA
57418 CC
1 CC
57420 ACTCTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (16 bp):
CCGTTGACCACGTTGA
Found at i:59762 original size:24 final size:23
Alignment explanation
Indices: 59709--59780 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 23
59699 ATACGTTACC
* * *
59709 TGAATTCTGTTCTGATTCTGATT
1 TGAATTCTATTATGATTCTGATA
59732 TCG-ATTCTATTATGATATCTGATA
1 T-GAATTCTATTATGAT-TCTGATA
*
59756 TGAATTCTATTTTGATTTCTGATA
1 TGAATTCTATTATGA-TTCTGATA
59780 T
1 T
59781 CTCCATTTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
23 13 0.32
24 27 0.66
25 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.51
Consensus pattern (23 bp):
TGAATTCTATTATGATTCTGATA
Found at i:61882 original size:8 final size:8
Alignment explanation
Indices: 61871--61918 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 8
61861 CCTGTTGACC
61871 TGACCCGT
1 TGACCCGT
61879 TGACCCGT
1 TGACCCGT
61887 TGA-CCGT
1 TGACCCGT
61894 TGACCGACGT
1 TGACC--CGT
61904 TGACCACTGT
1 TGACC-C-GT
61914 TGACC
1 TGACC
61919 AAAACTTTGA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.19
8 12 0.33
9 2 0.06
10 15 0.42
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.25
Consensus pattern (8 bp):
TGACCCGT
Found at i:61895 original size:15 final size:16
Alignment explanation
Indices: 61875--61908 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
61865 TTGACCTGAC
61875 CCGTTGACC-CGTTGA
1 CCGTTGACCACGTTGA
61890 CCGTTGACCGACGTTGA
1 CCGTTGACC-ACGTTGA
61907 CC
1 CC
61909 ACTGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (16 bp):
CCGTTGACCACGTTGA
Found at i:64404 original size:24 final size:24
Alignment explanation
Indices: 64327--64422 Score: 88
Period size: 24 Copynumber: 4.0 Consensus size: 24
64317 ATTTCCGAAT
* * *
64327 TGAATTCTGTTCTGATA-CGTTATC
1 TGAATTCTATTCTGATATC-TGATA
* * *
64351 TGAATTCTGTACTGAT-TCTGATT
1 TGAATTCTATTCTGATATCTGATA
*
64374 TGGATTCTATTCTGATATCTGATA
1 TGAATTCTATTCTGATATCTGATA
* *
64398 TGAATTCTATTTTGATTTCTGATA
1 TGAATTCTATTCTGATATCTGATA
64422 T
1 T
64423 CTCCGTTTAC
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 16 0.27
24 44 0.73
ACGTcount: A:0.23, C:0.12, G:0.16, T:0.49
Consensus pattern (24 bp):
TGAATTCTATTCTGATATCTGATA
Found at i:66506 original size:13 final size:14
Alignment explanation
Indices: 66490--66521 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
66480 CCGTTTTCTC
66490 GACCCGAA-CTGTT
1 GACCCGAACCTGTT
66503 GACCC-AACCTGTT
1 GACCCGAACCTGTT
66516 GACCCG
1 GACCCG
66522 TTGATCGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.12
13 15 0.88
ACGTcount: A:0.22, C:0.38, G:0.22, T:0.19
Consensus pattern (14 bp):
GACCCGAACCTGTT
Found at i:69052 original size:24 final size:23
Alignment explanation
Indices: 68999--69070 Score: 90
Period size: 24 Copynumber: 3.0 Consensus size: 23
68989 ATACGTTATC
* *
68999 TGAATTCTGTTCTGATTCTGATT
1 TGAATTCTATTCTGATTCTGATA
*
69022 TGGATTCTATTCTGATATCTGATA
1 TGAATTCTATTCTGAT-TCTGATA
*
69046 TGAATTCTATTTTGATTTCTGATA
1 TGAATTCTATTCTGA-TTCTGATA
69070 T
1 T
69071 CTCCGTTTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 14 0.33
24 27 0.64
25 1 0.02
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.51
Consensus pattern (23 bp):
TGAATTCTATTCTGATTCTGATA
Found at i:70697 original size:12 final size:12
Alignment explanation
Indices: 70659--70750 Score: 59
Period size: 12 Copynumber: 7.8 Consensus size: 12
70649 ATTTCTGAAT
70659 TGAATTCTGTTC
1 TGAATTCTGTTC
*
70671 TG-ATAC-GTTACC
1 TGAATTCTGTT--C
70683 TGAATTCTGTTC
1 TGAATTCTGTTC
70695 TG-ATTCTGATT-
1 TGAATTCTG-TTC
*
70706 TGGATTCTGTTC
1 TGAATTCTGTTC
* *
70718 TG-ATATCTGATA
1 TGAAT-TCTGTTC
*
70730 TGAATTCTGTTT
1 TGAATTCTGTTC
*
70742 TGATTTCTG
1 TGAATTCTG
70751 ATATCTCCGT
Statistics
Matches: 64, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
10 3 0.05
11 15 0.23
12 38 0.59
13 5 0.08
14 3 0.05
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.49
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:70713 original size:47 final size:48
Alignment explanation
Indices: 70649--70752 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 48
70639 ATTTTATCTA
* *
70649 ATTTCTGAATTGAATTCTGTTCTGATA-C-GTTACCTGAATTCTGTTCTG
1 ATTTCTGATTTGAATTCTGTTCTGATATCTGATA--TGAATTCTGTTCTG
* *
70697 A-TTCTGATTTGGATTCTGTTCTGATATCTGATATGAATTCTGTTTTG
1 ATTTCTGATTTGAATTCTGTTCTGATATCTGATATGAATTCTGTTCTG
70744 ATTTCTGAT
1 ATTTCTGAT
70753 ATCTCCGTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
47 37 0.76
48 9 0.18
49 3 0.06
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.49
Consensus pattern (48 bp):
ATTTCTGATTTGAATTCTGTTCTGATATCTGATATGAATTCTGTTCTG
Found at i:70736 original size:24 final size:24
Alignment explanation
Indices: 70659--70754 Score: 108
Period size: 24 Copynumber: 4.0 Consensus size: 24
70649 ATTTCTGAAT
*
70659 TGAATTCTGTTCTGATA-C-GTTA
1 TGAATTCTGTTCTGATATCTGATA
*
70681 CCTGAATTCTGTTCTGAT-TCTGATT
1 --TGAATTCTGTTCTGATATCTGATA
*
70706 TGGATTCTGTTCTGATATCTGATA
1 TGAATTCTGTTCTGATATCTGATA
* *
70730 TGAATTCTGTTTTGATTTCTGATA
1 TGAATTCTGTTCTGATATCTGATA
70754 T
1 T
70755 CTCCGTTTAC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
23 15 0.24
24 45 0.73
25 2 0.03
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.49
Consensus pattern (24 bp):
TGAATTCTGTTCTGATATCTGATA
Found at i:73046 original size:17 final size:18
Alignment explanation
Indices: 73020--73058 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
73010 TAAGATAAAG
73020 ATAAAGTAGAA-ATAAATA
1 ATAAAGTAGAATA-AAATA
73038 ATAAA-TAGAATAAAATA
1 ATAAAGTAGAATAAAATA
73055 ATAA
1 ATAA
73059 TTGGAGTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (18 bp):
ATAAAGTAGAATAAAATA
Found at i:73524 original size:24 final size:24
Alignment explanation
Indices: 73492--73541 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
73482 GTTTTGATTT
73492 GAAAATAAGCCCAGAAAACTGAGA
1 GAAAATAAGCCCAGAAAACTGAGA
73516 GAAAATAAGCCCAGAAAACTGAGA
1 GAAAATAAGCCCAGAAAACTGAGA
73540 GA
1 GA
73542 GATATTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.16, G:0.22, T:0.08
Consensus pattern (24 bp):
GAAAATAAGCCCAGAAAACTGAGA
Found at i:74336 original size:54 final size:54
Alignment explanation
Indices: 74208--74708 Score: 605
Period size: 54 Copynumber: 9.3 Consensus size: 54
74198 CTTTCGTGGG
* * *
74208 TTGCACACATAGTGCCAAAACGGTTATTCATCAACATA-GATGAATTCCATACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* * *
74261 TTGCACACTTAGTACCAAAACGGTTATTCATCAACATATGATGAATTCCGTGA-A
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGT-ACT
* * * *
74315 TTGAACGCTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTGA-A
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGT-ACT
* ** * * **
74369 TTGCACACTTAGTTCTAAAATGGTTATTCAT-AGACATATAATGAATTTTGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCA-ACATATGATGAATTCCGTACT
* * * * * * *
74423 TTACATACTTAGTGTCGAAATGGTTATTAATTAACATATGATGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* *
74477 TTGCACACTTAGTGTCGAAACGGTTATTCATCAACATATGATGAATTCTGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* ** *
74531 TTGCACACTTAGTTCCGAAACGGTTATTCATCAACATATGATGAATTCAATAGT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* * *
74585 TTGTAAACTTAGTGCTGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* * * *
74639 TTGCACACTTAGTGCCAAAACGATTATTCACCAACATATGATGAATTTCGTACT
1 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
*
74693 TTGCACTCTTAGTGCC
1 TTGCACACTTAGTGCC
74709 TATTTAGTAA
Statistics
Matches: 387, Mismatches: 56, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
53 38 0.10
54 347 0.90
55 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (54 bp):
TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
Found at i:74629 original size:26 final size:26
Alignment explanation
Indices: 74547--74629 Score: 60
Period size: 27 Copynumber: 3.1 Consensus size: 26
74537 ACTTAGTTCC
74547 GAAACGGTTATTCATCAACATATGAT
1 GAAACGGTTATTCATCAACATATGAT
* ** ** * * *
74573 GAATTC-AATAGTTTGTAAACTTAGTGCT
1 GAA-ACGGTTA-TTCATCAACATA-TGAT
74601 GAAACGGTTATTCATCAACATATGAT
1 GAAACGGTTATTCATCAACATATGAT
74627 GAA
1 GAA
74630 TTCCGTACTT
Statistics
Matches: 37, Mismatches: 16, Indels: 8
0.61 0.26 0.13
Matches are distributed among these distances:
26 11 0.30
27 18 0.49
28 8 0.22
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (26 bp):
GAAACGGTTATTCATCAACATATGAT
Found at i:81163 original size:54 final size:54
Alignment explanation
Indices: 81104--81655 Score: 368
Period size: 54 Copynumber: 10.3 Consensus size: 54
81094 TTCGTTACAA
* * * * *
81104 TGCACACGTAGTGCCTATACGATCATTCATAAAC-TCATTATGAATTTTGTAAGT
1 TGCACACATAGTGCCGAAACGATCATTCATAAACAT-ATGATGAATTTCGTAAGT
* * * **
81158 TGCACACATAGTGCCGAAACTATTATTCATCAACATATGATGAATTTCGTACTT
1 TGCACACATAGTGCCGAAACGATCATTCATAAACATATGATGAATTTCGTAAGT
* * * * *
81212 TGCACACTTAGTGCCAAAATGGTTATTC---AACATATGATGAATTTCGTGAA-T
1 TGCACACATAGTGCCGAAACGATCATTCATAAACATATGATGAATTTCGT-AAGT
* * * * * **
81263 TGCACACTTAGTGCCGAAATGATTATTCATCAACGTATGATGAA-TTCTGTACTT
1 TGCACACATAGTGCCGAAACGATCATTCATAAACATATGATGAATTTC-GTAAGT
* * * ** * * * * **
81317 TGTATACTTAGTGTTGAAACGGTTATTCATCAACATATGATGAATTCCGTACTT
1 TGCACACATAGTGCCGAAACGATCATTCATAAACATATGATGAATTTCGTAAGT
* * * * * * **
81371 TGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGGTGAATTCCGTACTT
1 TGCACACATAGTGCCGAAACGATCATTCATAAACATATGATGAATTTCGTAAGT
* ** * * * * **
81425 TGCACACTTAGTGCTAAAACGGTTATTCATCAACATATGATGAATTCCGTACTT
1 TGCACACATAGTGCCGAAACGATCATTCATAAACATATGATGAATTTCGTAAGT
* * * * **
81479 TGCACACTTAGTGCCGAAATGATTATTCATCAACATATGATG-ATTTCCGTACTT
1 TGCACACATAGTGCCGAAACGATCATTCATAAACATATGATGAATTT-CGTAAGT
* * * **
81533 TGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAA-TTCTGTACTT
1 TGCACACATAGTGCCGAAACGATCATTCATAAACATATGATGAATTTC-GTAAGT
* * * * *
81587 TGCACACTTAGTGCCGACACGATTATTTATCAACATATGATGAA-TTCTGTGAA-T
1 TGCACACATAGTGCCGAAACGATCATTCATAAACATATGATGAATTTC-GT-AAGT
*
81641 TGCACACTTAGTGCC
1 TGCACACATAGTGCC
81656 TATTTAGTAA
Statistics
Matches: 441, Mismatches: 45, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
51 46 0.10
52 1 0.00
53 8 0.02
54 381 0.86
55 5 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (54 bp):
TGCACACATAGTGCCGAAACGATCATTCATAAACATATGATGAATTTCGTAAGT
Found at i:81401 original size:108 final size:108
Alignment explanation
Indices: 81157--81655 Score: 704
Period size: 108 Copynumber: 4.6 Consensus size: 108
81147 ATTTTGTAAG
* *
81157 TTGCACACATAGTGCCGAAACTATTATTCATCAACATATGATGAATT-TCGTACTTTGCACACTT
1 TTGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCT-GTACTTTGCACACTT
* * *
81221 AGTGCCAAAATGGTTA-T--TCAACATATGATGAATTTCGTGA-A
65 AGTGCCAAAACGGTTATTCATCAACATATGATGAATTCCGT-ACT
* * * *
81262 TTGCACACTTAGTGCCGAAATGATTATTCATCAACGTATGATGAATTCTGTACTTTGTATACTTA
1 TTGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTACTTTGCACACTTA
***
81327 GTGTTGAAACGGTTATTCATCAACATATGATGAATTCCGTACT
66 GTGCCAAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* * *
81370 TTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATGGTGAATTCCGTACTTTGCACACTTA
1 TTGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTACTTTGCACACTTA
*
81435 GTGCTAAAACGGTTATTCATCAACATATGATGAATTCCGTACT
66 GTGCCAAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* * *
81478 TTGCACACTTAGTGCCGAAATGATTATTCATCAACATATGATGATTTCCGTACTTTGCACACTTA
1 TTGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTACTTTGCACACTTA
* * *
81543 GTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTACT
66 GTGCCAAAACGGTTATTCATCAACATATGATGAATTCCGTACT
* * *
81586 TTGCACACTTAGTGCCGACACGATTATTTATCAACATATGATGAATTCTGTGA-ATTGCACACTT
1 TTGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGT-ACTTTGCACACTT
81650 AGTGCC
65 AGTGCC
81656 TATTTAGTAA
Statistics
Matches: 353, Mismatches: 35, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
105 68 0.19
106 2 0.01
107 1 0.00
108 281 0.80
109 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (108 bp):
TTGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTACTTTGCACACTTA
GTGCCAAAACGGTTATTCATCAACATATGATGAATTCCGTACT
Found at i:81490 original size:162 final size:162
Alignment explanation
Indices: 81104--81655 Score: 720
Period size: 162 Copynumber: 3.4 Consensus size: 162
81094 TTCGTTACAA
* * * * * * * ** *
81104 TGCACACGTAGTGCCTATACGATCATTCATAAAC-TCATTATGAATTTTGTAAGTTGCACACATA
1 TGCACACTTAGTGCCGAAACGATTATTCATCAACAT-ATGATGAATTCTGTACTTTGCACACTTA
* * * *
81168 GTGCCGAAACTATTATTCATCAACATATGATGAATTTCGTACTTTGCACACTTAGTGCCAAAATG
65 GTGCCGAAACGATTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACG
* *
81233 GTTA-T--TCAACATATGATGAATTTCGTGA-AT
130 GTTATTCATCAACATATGATGAATTCCGT-ACTT
* * * *
81263 TGCACACTTAGTGCCGAAATGATTATTCATCAACGTATGATGAATTCTGTACTTTGTATACTTAG
1 TGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTACTTTGCACACTTAG
** *
81328 TGTTGAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGG
66 TGCCGAAACGATTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGG
*
81393 TTATTCATCAACATATGGTGAATTCCGTACTT
131 TTATTCATCAACATATGATGAATTCCGTACTT
** * *
81425 TGCACACTTAGTGCTAAAACGGTTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAG
1 TGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTACTTTGCACACTTAG
* * *
81490 TGCCGAAATGATTATTCATCAACATATGATGATTTCCGTACTTTGCACACTTAGTGCCGAAACGA
66 TGCCGAAACGATTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGG
*
81555 TTATTCATCAACATATGATGAATTCTGTACTT
131 TTATTCATCAACATATGATGAATTCCGTACTT
* * *
81587 TGCACACTTAGTGCCGACACGATTATTTATCAACATATGATGAATTCTGTGA-ATTGCACACTTA
1 TGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGT-ACTTTGCACACTTA
81651 GTGCC
65 GTGCC
81656 TATTTAGTAA
Statistics
Matches: 341, Mismatches: 46, Indels: 9
0.86 0.12 0.02
Matches are distributed among these distances:
159 111 0.33
160 2 0.01
161 1 0.00
162 226 0.66
163 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (162 bp):
TGCACACTTAGTGCCGAAACGATTATTCATCAACATATGATGAATTCTGTACTTTGCACACTTAG
TGCCGAAACGATTATTCATCAACATATGATGAATTCCGTACTTTGCACACTTAGTGCCGAAACGG
TTATTCATCAACATATGATGAATTCCGTACTT
Found at i:87946 original size:4 final size:4
Alignment explanation
Indices: 87937--87966 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
87927 GATAAGGATA
87937 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
87967 TAATTATAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:88041 original size:21 final size:21
Alignment explanation
Indices: 88015--88075 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
88005 TTGTTTAAAG
*
88015 AAATAAAATGAGATAAAGATT
1 AAATAAAATGAGATAAAGATA
88036 AAATAAACA--A-ATAAATAGATA
1 AAATAAA-ATGAGAT-AA-AGATA
*
88057 AAATAAATTGAGATAAAGA
1 AAATAAAATGAGATAAAGA
88076 AAACTTATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 21 0.66
22 4 0.12
23 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.11, T:0.21
Consensus pattern (21 bp):
AAATAAAATGAGATAAAGATA
Found at i:88849 original size:19 final size:20
Alignment explanation
Indices: 88813--88850 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
88803 AACAAGGTAA
88813 AAATAAATACTAAATTAAAG
1 AAATAAATACTAAATTAAAG
*
88833 AAATAAATCCT-AATTAAA
1 AAATAAATACTAAATTAAA
88851 ATATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.63, C:0.08, G:0.03, T:0.26
Consensus pattern (20 bp):
AAATAAATACTAAATTAAAG
Found at i:92180 original size:21 final size:21
Alignment explanation
Indices: 92156--92203 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
92146 CAATAGATAG
92156 AGATTGCAAATCGTCTTCCTT
1 AGATTGCAAATCGTCTTCCTT
** *
92177 AGATTGTGATTCGTCTTCCTT
1 AGATTGCAAATCGTCTTCCTT
92198 AGATTG
1 AGATTG
92204 TGATTCACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (21 bp):
AGATTGCAAATCGTCTTCCTT
Found at i:92204 original size:21 final size:21
Alignment explanation
Indices: 92166--92209 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
92156 AGATTGCAAA
92166 TCGTCTTCCTTAGATTGTGAT
1 TCGTCTTCCTTAGATTGTGAT
92187 TCGTCTTCCTTAGATTGTGAT
1 TCGTCTTCCTTAGATTGTGAT
92208 TC
1 TC
92210 ACCTTCCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (21 bp):
TCGTCTTCCTTAGATTGTGAT
Found at i:92215 original size:21 final size:21
Alignment explanation
Indices: 92170--92216 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
92160 TGCAAATCGT
**
92170 CTTCCTTAGATTGTGATTCGT
1 CTTCCTTAGATTGTGATTCAC
92191 CTTCCTTAGATTGTGATTCAC
1 CTTCCTTAGATTGTGATTCAC
92212 CTTCC
1 CTTCC
92217 AAATCCTCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.45
Consensus pattern (21 bp):
CTTCCTTAGATTGTGATTCAC
Done.