Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001104.1 Hibiscus syriacus cultivar Beakdansim tig00002185_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: 105997
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:634 original size:20 final size:20
Alignment explanation
Indices: 591--634 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
581 TTTAAATATT
*
591 AAAGTTGAAGTTTTAAAAAT
1 AAAGTTGAAGTTTTAAAAAG
* * *
611 AAAGTTTAATTTTTTAAAAG
1 AAAGTTGAAGTTTTAAAAAG
631 AAAG
1 AAAG
635 AAACATTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (20 bp):
AAAGTTGAAGTTTTAAAAAG
Found at i:3307 original size:3 final size:3
Alignment explanation
Indices: 3286--3339 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
3276 TAAAAAACAA
* * *
3286 AAT AAT AAAT ATT AGT AAT AAT AAT -AT AAT -AT AAT GAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3330 AAT AAT AAT A
1 AAT AAT AAT A
3340 GTGGACCCCA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:3326 original size:22 final size:20
Alignment explanation
Indices: 3286--3339 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 20
3276 TAAAAAACAA
*
3286 AATAATA-AATATTAGTAAT
1 AATAATATAATATAAGTAAT
3305 AATAATATAATATAATGATAAT
1 AATAATATAATATAA-G-TAAT
3327 AATAATAATAATA
1 AATAAT-ATAATA
3340 GTGGACCCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 7 0.23
20 6 0.20
21 1 0.03
22 10 0.33
23 6 0.20
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
AATAATATAATATAAGTAAT
Found at i:3963 original size:133 final size:131
Alignment explanation
Indices: 3529--3971 Score: 484
Period size: 131 Copynumber: 3.4 Consensus size: 131
3519 AGTATGGAAG
* * * * * * * *
3529 AGATTTGGAAATATTGATTCATTCCACT-TCTCTACAAGAAAGATTGAATCGA--AGACTTGTTC
1 AGATCTGGAAATGTTGATTCATTCCAATGT-TCTTCAGGGAAGATTGAATCGAGGCGACATGTTC
* *
3591 CACTATTCCTCAGGGAAGATCAAATTTGAAAAAAGGGATTTGTTCTGTTGCTTCTTAAGGGAATA
65 CACTATTCCTCAGGGAAGATCAAATTTGAAAAAAGGGATATGTTCTGTTGCTTCTTAAGGGAAAA
*
3656 TT
130 TC
* * *
3658 AGATCTGGTAATGTTGATTCATT-CAATGTTCTTCAGGGAAGATTGAATCGAGGCGACTTGTTTC
1 AGATCTGGAAATGTTGATTCATTCCAATGTTCTTCAGGGAAGATTGAATCGAGGCGACATGTTCC
* * * *
3722 ATTATTCCTCAGGGAAGGTCAAATCTTGAAAAAAGGGATATGTTATGTTGCTTCTTAAGAGAAAA
66 ACTATTCCTCAGGGAAGATCAAAT-TTGAAAAAAGGGATATGTTCTGTTGCTTCTTAAGGGAAAA
3787 TC
130 TC
* * * * *
3789 AGGTCTAGAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATTGAGGCATACATGTTC
1 AGATCTGGAAATGTTGATTCATTCCAATGTTCTTCAGGGAAGATTGAATCGAGGC-GACATGTTC
** *** * *
3854 CACTATTCCTCATAGAAGATCAAATTTGGAATAAATAGGGATATGTTCCCCTCCTTCTTGAGGGA
65 CACTATTCCTCAGGGAAGATCAAATTT-GAA-AAA-AGGGATATGTTCTGTTGCTTCTTAAGGGA
*
3919 AAAAC
127 AAATC
* * *
3924 AGATCTGGAAATATTAATTC-TTCCATTG-TCTTCAGGGAAGATTGAATC
1 AGATCTGGAAATGTTGATTCATTCCAATGTTCTTCAGGGAAGATTGAATC
3972 AAGTTCAATT
Statistics
Matches: 263, Mismatches: 42, Indels: 14
0.82 0.13 0.04
Matches are distributed among these distances:
128 22 0.08
129 21 0.08
130 31 0.12
131 57 0.22
132 31 0.12
133 49 0.19
134 10 0.04
135 42 0.16
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (131 bp):
AGATCTGGAAATGTTGATTCATTCCAATGTTCTTCAGGGAAGATTGAATCGAGGCGACATGTTCC
ACTATTCCTCAGGGAAGATCAAATTTGAAAAAAGGGATATGTTCTGTTGCTTCTTAAGGGAAAAT
C
Found at i:5642 original size:2 final size:2
Alignment explanation
Indices: 5635--5695 Score: 108
Period size: 2 Copynumber: 31.5 Consensus size: 2
5625 GCTTTATTGC
5635 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5676 AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT A
5696 ATCGCCTTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 55 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9455 original size:6 final size:6
Alignment explanation
Indices: 9444--9470 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
9434 GCAAAATAAG
9444 AATGCA AATGCA AATGCA AATGCA AAT
1 AATGCA AATGCA AATGCA AATGCA AAT
9471 AAACAAGGTA
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:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (6 bp):
AATGCA
Found at i:11064 original size:128 final size:131
Alignment explanation
Indices: 10724--11065 Score: 430
Period size: 129 Copynumber: 2.7 Consensus size: 131
10714 AGAAAATGAT
* *
10724 AATATCTAATTATTTCCAATCGAGAAT-AATGAGCTCTCATGCCTTAAAGCAGTCATTTATTACT
1 AATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTAATTTATTACT
* *
10788 CCAACCGAAATG-AGAGATATCACTCTTTAGTCTTAAAATTCAATATTGATTTGAAAGAAAACAA
66 CCAACCGAAATGAAGAGATATCACTCATTAGTCTTAAAATTCAATATTGATTCGAAAGAAAACAA
10852 A
131 A
* * *
10853 AATATCTAATTATTTCCAATCGA-AATAAATGACCTCTCAT-CCGTTAAAACAATAATTTATTAT
1 AATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCC-TTAAAGCAGTAATTTATTAC
* ** * * *
10916 TCTAATTGAAATGAAAAGATATCACT-ATTCGTCTTACAAA-TCAATATTGATTCGAGAGAAAAC
65 TCCAACCGAAATGAAGAGATATCACTCATTAGTCTTA-AAATTCAATATTGATTCGAAAGAAAAC
**
10979 -GT
129 AAA
* * * *
10981 TATATCTAGTTATTTCCAATCGAGAATAAATGACCTCTCCTGCCTT-AAGCAGTTATTTATTACT
1 AATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTAATTTATTACT
*
11045 CCAACCAAAATGAAGAGATAT
66 CCAACCGAAATGAAGAGATAT
11066 TATTATTTTC
Statistics
Matches: 180, Mismatches: 27, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
128 56 0.31
129 108 0.60
130 16 0.09
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (131 bp):
AATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTAATTTATTACT
CCAACCGAAATGAAGAGATATCACTCATTAGTCTTAAAATTCAATATTGATTCGAAAGAAAACAA
A
Found at i:12887 original size:31 final size:31
Alignment explanation
Indices: 12820--12890 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
12810 GCCTGAGAGA
* * *
12820 CTACCCAAGATAATTTTCGGGCCATAGAGGC
1 CTACCCAAGATAAATCTCGGGCCACAGAGGC
* *
12851 TTACCCAAGATAAATCTCGAGGCCACATA-GC
1 CTACCCAAGATAAATCTCG-GGCCACAGAGGC
12882 CTACCCAAG
1 CTACCCAAG
12891 GCTCGCCTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (31 bp):
CTACCCAAGATAAATCTCGGGCCACAGAGGC
Found at i:13641 original size:17 final size:17
Alignment explanation
Indices: 13615--13648 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13605 TGAAAAATAT
13615 AAAATATGACTTTTCAG
1 AAAATATGACTTTTCAG
*
13632 AAAATTTGACTTTTCAG
1 AAAATATGACTTTTCAG
13649 TTCAAAGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAATATGACTTTTCAG
Found at i:13674 original size:16 final size:16
Alignment explanation
Indices: 13650--13692 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
13640 ACTTTTCAGT
*
13650 TCAAAGTCAACTCTAG
1 TCAAAGTCAACTATAG
* *
13666 TCAAGGTCAACTATGG
1 TCAAAGTCAACTATAG
13682 TCAAAGTCAAC
1 TCAAAGTCAAC
13693 GGGTCAGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (16 bp):
TCAAAGTCAACTATAG
Found at i:17081 original size:32 final size:31
Alignment explanation
Indices: 17032--17098 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 31
17022 GGAGTACGTT
*
17032 GGGGCCTGAGAGCTTACCCAA-AACAATTCTC
1 GGGGCCTGAGAGCTTACCCAAGAA-AAATCTC
*
17063 GGGGCCTTAGAGGCTTACCCAAGAAAAATCTC
1 GGGGCCTGAGA-GCTTACCCAAGAAAAATCTC
17095 GGGG
1 GGGG
17099 GCGTAGATCC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 10 0.31
32 20 0.62
33 2 0.06
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.18
Consensus pattern (31 bp):
GGGGCCTGAGAGCTTACCCAAGAAAAATCTC
Found at i:21048 original size:12 final size:12
Alignment explanation
Indices: 21028--21077 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
21018 AAACTTCATT
*
21028 AATATAAATGCA
1 AATACAAATGCA
21040 AATACAAATGCA
1 AATACAAATGCA
*
21052 AATACAAATCCA
1 AATACAAATGCA
**
21064 AATGTAAATGCA
1 AATACAAATGCA
21076 AA
1 AA
21078 AGGGAAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.58, C:0.14, G:0.08, T:0.20
Consensus pattern (12 bp):
AATACAAATGCA
Found at i:21059 original size:18 final size:18
Alignment explanation
Indices: 21033--21077 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
21023 TCATTAATAT
21033 AAATGCAAATACAAATGC
1 AAATGCAAATACAAATGC
* * *
21051 AAATACAAATCCAAATGT
1 AAATGCAAATACAAATGC
21069 AAATGCAAA
1 AAATGCAAA
21078 AGGGAAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.58, C:0.16, G:0.09, T:0.18
Consensus pattern (18 bp):
AAATGCAAATACAAATGC
Found at i:31472 original size:32 final size:32
Alignment explanation
Indices: 31429--31513 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 32
31419 AATTATTGAT
* *
31429 GTGACATATGTC-TCATCATCATTTTTGCTAAC
1 GTGACAAATGTCAT-ATCATCATTTCTGCTAAC
* *
31461 GTGACAAATGTCATATCATCATTTCTGGTGAC
1 GTGACAAATGTCATATCATCATTTCTGCTAAC
* * *
31493 GTGACACATGTTATATTATCA
1 GTGACAAATGTCATATCATCA
31514 CTTTTGTTGA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 44 0.98
33 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (32 bp):
GTGACAAATGTCATATCATCATTTCTGCTAAC
Found at i:31822 original size:2 final size:2
Alignment explanation
Indices: 31815--31843 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31805 TACTTGTATC
31815 TA TA 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 TA TA T
31844 TTCAAGGCCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33355 original size:16 final size:16
Alignment explanation
Indices: 33336--33369 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
33326 AAAAAAAATT
33336 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
33352 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
33368 TA
1 TA
33370 TAATACATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:33619 original size:11 final size:11
Alignment explanation
Indices: 33537--33620 Score: 55
Period size: 11 Copynumber: 7.3 Consensus size: 11
33527 TTATATACTT
*
33537 TAATAGTAAAA
1 TAATATTAAAA
*
33548 TAATAATAAATA
1 TAATATTAAA-A
33560 TAATAGTTATAAA
1 TAATA-TTA-AAA
*
33573 TATATATATATAA
1 TA-ATAT-TAAAA
33586 TAACT-TTAAAA
1 TAA-TATTAAAA
*
33597 -AACATTAAAA
1 TAATATTAAAA
*
33607 TAATATTAGAA
1 TAATATTAAAA
33618 TAA
1 TAA
33621 AAATAATTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
10 8 0.14
11 24 0.41
12 8 0.14
13 11 0.19
14 7 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (11 bp):
TAATATTAAAA
Found at i:34133 original size:35 final size:37
Alignment explanation
Indices: 34063--34162 Score: 114
Period size: 35 Copynumber: 2.8 Consensus size: 37
34053 GTGCTTGTGG
* * * * *
34063 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATTCT
*
34100 ATCCTA-TTTTAAGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATTCT
* *
34135 ATCTTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTTAAGAGTTTGAATCCTAG
34163 TAGGACGAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 21 0.40
36 15 0.28
37 17 0.32
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATTCT
Found at i:35028 original size:109 final size:105
Alignment explanation
Indices: 34678--35563 Score: 593
Period size: 109 Copynumber: 8.5 Consensus size: 105
34668 TGGGAAATTG
** * * * *
34678 TTTGTTGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGT-CTA--ATA
1 TTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGC-ACGATA
* * * * *
34740 TCCTTCAC-T-GTGAAGATGAAATTGACTCTG-AA-CG-AAAT
65 TCC-TC-CGTCGTGGAGTTGAAATCGGCTCTGAAATTGAAAAT
* * *
34778 CTTGTTGACAATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-C-CAATAT
1 TTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACGATAT
* *
34841 CCTTCG-C-TGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAAT
66 CCTCCGTCGTG-G-AGTTGAAATCGGCTCTGAAA-TTG-AAAAT
34883 GTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACGAT
1 -TTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCACGAT
* ** *
34948 ATCCTCCGTCGTGGAGTTAAAATC-GCGAATGAAACTGAAAAGT
64 ATCCTCCGTCGTGGAGTTGAAATCGGC-TCTGAAATTGAAAA-T
*
34991 TATTCGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGA
1 T-TT-GTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT-GCACGA
* * *
35056 TATCCTCTGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATT
63 TATCCTCCGTCGTGGAGTTGAAATCGGCTCTGAAATT--GAAAAT
* * * *
35101 GTTTGTTGACAACCAGCCATCCCTTCGCTGTGAAGCTGAACTTGTGTTGTCTCGAGT-C-CAATA
1 -TTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACGATA
* * * * *
35164 TCCTTCG-CTGTGAAGTTGAGATTGGCTCCGAAATT----A-
65 TCCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAATTGAAAAT
* * ** * * * * * * *
35200 CTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGT-C-CAATAT
1 TTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACGATAT
* * * * * * *
35263 CCTTCG-CTGTGAACTTGAAATTGGCCCTGAAACTAGGAAAT
66 CCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAA-TTGAAAAT
*
35304 TATTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTCA--ATA
1 T-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACGATA
* * * * * *
35367 TCTTTCG-CTGTGAAGTTGAGATTGGCTCCGAAATTG-----
65 TCCTCCGTC-GTGGAGTTGAAATCGGCTCTGAAATTGAAAAT
* ** * * * * * * * *
35403 TTTGTCGACAGTCAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTGCTGTCTTGGGT-C-CAATAT
1 TTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACGATAT
* * * * *
35466 CCTTCAC-T-GTGAAGTTAAAATTGGCCCTGAAATTGGGAAAT
66 CC-TC-CGTCGTGGAGTTGAAATCGGCTCTGAAATT-GAAAAT
** *
35507 TATTGTTGACAACCAGCTATCTCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
1 T-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT
35564 CCAATATCCT
Statistics
Matches: 636, Mismatches: 103, Indels: 89
0.77 0.12 0.11
Matches are distributed among these distances:
97 1 0.00
98 155 0.24
99 5 0.01
100 73 0.11
101 2 0.00
103 2 0.00
104 3 0.00
105 124 0.19
106 85 0.13
107 6 0.01
108 8 0.01
109 158 0.25
110 7 0.01
111 7 0.01
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (105 bp):
TTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCACGATAT
CCTCCGTCGTGGAGTTGAAATCGGCTCTGAAATTGAAAAT
Found at i:35264 original size:98 final size:97
Alignment explanation
Indices: 35121--35593 Score: 462
Period size: 105 Copynumber: 4.7 Consensus size: 97
35111 AACCAGCCAT
* * *
35121 CCCTTCGCTGTGAAGCTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAGAT
1 CCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
35186 TGGCTCCGAAATTACTTGTCGACAGTCAGCCGC
66 TGGCTCCGAAATTA-TTGTCGACAGTCAGCCGC
* * * *
35219 CCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGCTGTGAACTTGAAAT
1 CCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
* * ** *
35284 TGGCCCTGAAACTAGGAAATTATTGTTGACAACCAGCCGT
66 TGG--CT----C--CGAAATTATTGTCGACAGTCAGCCGC
* * * * *
35324 CCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTCAATATCTTTCGCTGTGAAGTTGAGAT
1 CCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
*
35389 TGGCTCCGAAATTGTTTGTCGACAGTCAGCCGC
66 TGGCTCCGAAATT-ATTGTCGACAGTCAGCCGC
* * * * * *
35422 CCCTTCGCTATGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCACTGTGAAGTTAAAAT
1 CCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
* ** ***
35487 TGGC-CCTGAAATTGGGAAATTATTGTTGACAACCAGCTAT
66 TGGCTCC---------GAAATTATTGTCGACAGTCAGCCGC
* * * *
35527 CTCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTCGAAAT
1 CCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
35592 TG
66 TG
35594 ACTCTAGATA
Statistics
Matches: 302, Mismatches: 55, Indels: 29
0.78 0.14 0.08
Matches are distributed among these distances:
97 8 0.03
98 133 0.44
99 1 0.00
100 2 0.01
103 2 0.01
104 1 0.00
105 142 0.47
106 13 0.04
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (97 bp):
CCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAAT
TGGCTCCGAAATTATTGTCGACAGTCAGCCGC
Found at i:35348 original size:105 final size:103
Alignment explanation
Indices: 34623--35593 Score: 769
Period size: 98 Copynumber: 9.3 Consensus size: 103
34613 AATATTGTTC
* * ** * * *
34623 CGAGTCCAATATCGTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCT-GAAAT-GGAAATT-ATTGTCGACA
** *
34688 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
63 ACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * * * * * *
34729 CGAGTCTAATATCCTTCACTGTGAAGATGAAATTGACTCTG-AA-CGAAA-TCTTGTTGACAATC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAATGGAAATTATTGTCGACAACC
* * *
34791 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 AGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * *
34829 CGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGT-TTGTTGAC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAA--TG-GAAAT-TATTGTCGAC
* * *
34893 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
62 AACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * * ** *
34935 CGAGTGGCACGATATCCTCCG-TCGTGGAGTT-AAAATCGCGAATGAAACTGAAAAGTTATTCGT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGC-CCTGAAA-TGGAAA-TTATT-GT
* * * *
34998 TGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
58 CGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * * * *
35044 CGGGTAGCACGATATCC-TCTG-TCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGT
1 CGAGT--C-CAATATCCTTC-GCT-GTGAAGTTGAAATTGGCCCT-GAAAT-GGAAATT-ATTGT
* ** * *
35107 TGACAACCAGCCATCCCTTCGCTGTGAAGCTGAACTTGTGTTGTCT
58 CGACAACCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* *
35153 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCC-------GAAATTACTTGTCGACAG
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC-CCTGAAATGGAAATTA-TTGTCGACAA
* *
35211 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
64 CCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * *
35251 TGGGTCCAATATCCTTCGCTGTGAACTTGAAATTGGCCCTGAAACTAGGAAATTATTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAA-T-GGAAATTATTGTCGACAA
* * *
35316 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 CCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * **
35356 CGAGTTCAATATCTTTCGCTGTGAAGTTGAGATTGGCTCC-GAAATTG----T-TTGTCGACAGT
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC-CCTGAAATGGAAATTATTGTCGACAAC
* *
35415 CAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTGCTGTCT
65 CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * *
35454 TGGGTCCAATATCCTTCACTGTGAAGTTAAAATTGGCCCTGAAATTGGGAAATTATTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAA-T-GGAAATTATTGTCGACAA
*** * * *
35519 CCAGCTATCTCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 CCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
*
35559 CGAGTCCAATATCCTTCGCTGTGAAGTCGAAATTG
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
35594 ACTCTAGATA
Statistics
Matches: 712, Mismatches: 111, Indels: 85
0.78 0.12 0.09
Matches are distributed among these distances:
97 4 0.01
98 157 0.22
99 2 0.00
100 82 0.12
101 3 0.00
102 4 0.01
103 1 0.00
104 3 0.00
105 151 0.21
106 118 0.17
107 11 0.02
108 14 0.02
109 148 0.21
110 14 0.02
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (103 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCCTGAAATGGAAATTATTGTCGACAACC
AGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
Found at i:35410 original size:203 final size:203
Alignment explanation
Indices: 34626--35593 Score: 1041
Period size: 203 Copynumber: 4.7 Consensus size: 203
34616 ATTGTTCCGA
* * * * * * **
34626 GTCCAATATCGTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAGTC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT-ATTGTTGACAACC
* * * * * * *
34691 AGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCACTGTGAAGA
65 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGT
* * * *
34756 TGAAATTGACTCTGAACGAAA-T-CTTGTTGACAATCAGCCGTCCCTTCGTTGTGAAGTTGAACT
130 TGAAATTGGCTC----CGAAATTACTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAACT
* *
34819 TGTGTTGTCTCGA
191 TGTGCTGTCTCGG
* **
34832 GTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGT-TTGTTGACAAC
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTGGGAAAT-TATTGTTGACAAC
* *
34896 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGGCACGATATCCTCCG-TCGT
64 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT--C-CAATATCCTTCGCT-GT
* * * * * * * * *
34960 GGAGTTAAAATCGCGAATGAAACTGAAAAGTTA-TTCGTTGACAACCAGCCGTCCCTTCGTTGTG
125 GAAGTTGAAATTG-G-CT----CCG-AAA-TTACTT-GTCGACAATCAGCCGCCCCTTCGCTGTG
*
35024 AAGTTGAACTTGTGTTGTCTCGG
181 AAGTTGAACTTGTGCTGTCTCGG
* * * * *
35047 GTAGCACGATATCC-TCTG-TCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTTGA
1 GT--C-CAATATCCTTC-GCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT-ATTGTTGA
* * *
35110 CAACCAGCCATCCCTTCGCTGTGAAGCTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGT
60 CAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGT
* * *
35175 GAAGTTGAGATTGGCTCCGAAATTACTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGC
125 GAAGTTGAAATTGGCTCCGAAATTACTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAAC
*
35240 TTGTGCTGTCTTGG
190 TTGTGCTGTCTCGG
* * * *
35254 GTCCAATATCCTTCGCTGTGAACTTGAAATTGGCCCTGAAACTAGGAAATTATTGTTGACAACCA
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTGTTGACAACCA
* *
35319 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTCAATATCTTTCGCTGTGAAGTT
66 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTT
* ** * * *
35384 GAGATTGGCTCCGAAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTATGAAGTTGAGCTTGTGC
131 GAAATTGGCTCCGAAATTACTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGC
*
35449 TGTCTTGG
196 TGTCTCGG
* * *
35457 GTCCAATATCCTTCACTGTGAAGTTAAAATTGGCCCTGAAATTGGGAAATTATTGTTGACAACCA
1 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTGTTGACAACCA
** * *
35522 GCTATCTCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTC
66 GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTT
35587 GAAATTG
131 GAAATTG
35594 ACTCTAGATA
Statistics
Matches: 652, Mismatches: 82, Indels: 59
0.82 0.10 0.07
Matches are distributed among these distances:
203 268 0.41
204 35 0.05
205 4 0.01
206 85 0.13
207 54 0.08
208 8 0.01
209 21 0.03
211 2 0.00
212 3 0.00
213 1 0.00
214 4 0.01
215 73 0.11
216 3 0.00
217 11 0.02
218 80 0.12
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (203 bp):
GTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTGTTGACAACCA
GCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTT
GAAATTGGCTCCGAAATTACTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGC
TGTCTCGG
Found at i:36151 original size:65 final size:65
Alignment explanation
Indices: 36047--36227 Score: 299
Period size: 65 Copynumber: 2.8 Consensus size: 65
36037 GACAAAATTT
36047 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
36112 TGTTTCAAGAGAATCTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * **
36177 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA-TTCATTTCAAGGGAAA
36228 ATATCTCAAG
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
65 93 0.87
66 14 0.13
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:36218 original size:102 final size:102
Alignment explanation
Indices: 36112--36467 Score: 586
Period size: 102 Copynumber: 3.5 Consensus size: 102
36102 TCAATGTTTA
* * *
36112 TGTTTCAAGAGAATCTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
36177 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
36214 TGTTTCAAGGGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
36279 TGTTTCAAGAGAAACTGTCTCAATGGAGACAGAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
36316 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAGTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* * *
36381 TGTTTCAAGAGAAACTGTCTCAAGGGAAAAAAAAATT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * **
36418 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
36468 CTGTCTCAAG
Statistics
Matches: 236, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 236 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:36235 original size:37 final size:36
Alignment explanation
Indices: 36177--36485 Score: 116
Period size: 37 Copynumber: 8.9 Consensus size: 36
36167 TCAATGTTTA
* * * *
36177 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAAATATCTCAAGAGAGACAAAA-TT
36214 TGTTTCAAGGGAAAATATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAAATATCTCAAGAGAGACAAAATT
** * * * *
36250 CATTTCAAGGG-AAATGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAAAT-ATCTCAAGAGAGACAAAATT
* * * *
36278 ATGTTTCAAGAGAAACTGTCTCAATG-GAGACAGAATTT
1 -TGTTTCAAGGGAAAATATCTCAA-GAGAGACA-AAATT
* *
36316 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAGT
1 TGTTTCAAGGGAAAATATCTCAAGAGAGACAAAATT
** * * * *
36352 CATTTCAAGGG-AAATGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAAAT-ATCTCAAGAGAGACAAAATT
* * * * * *
36380 ATGTTTCAAGAGAAACTGTCTCAAGGGAAAAAAAAATT
1 -TGTTTCAAGGGAAAATATCTCAAGAG-AGACAAAATT
* * *
36418 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAAATATCTCAAGAGAGACAAAATT
* *
36454 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAAATATCTCAAGAGAGACAA
36486 TGGTGAGCAC
Statistics
Matches: 202, Mismatches: 44, Indels: 53
0.68 0.15 0.18
Matches are distributed among these distances:
28 3 0.01
29 22 0.11
30 8 0.04
32 1 0.00
33 2 0.01
34 2 0.01
35 9 0.04
36 69 0.34
37 81 0.40
38 5 0.02
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAAATATCTCAAGAGAGACAAAATT
Found at i:36287 original size:50 final size:50
Alignment explanation
Indices: 36233--36392 Score: 117
Period size: 50 Copynumber: 3.2 Consensus size: 50
36223 GGAAAATATC
36233 TCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
1 TCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
*** * ** ** * * * *** * *
36283 TCAAGAGA-A-ACTGTCTCAATGGAGACAGAATTTTGTTTCAAGGGAAACTATC
1 TCAAGAGAGACAAAAT-TCATTTCA-AGGGAAATGT-TTTCAATGTTTA-TGTT
*
36335 TCAAGAGAGACAAAAGTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
1 TCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
36385 TCAAGAGA
1 TCAAGAGA
36393 AACTGTCTCA
Statistics
Matches: 71, Mismatches: 33, Indels: 12
0.61 0.28 0.10
Matches are distributed among these distances:
48 2 0.03
49 6 0.08
50 24 0.34
51 16 0.23
52 16 0.23
53 6 0.08
54 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (50 bp):
TCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
Found at i:36463 original size:36 final size:36
Alignment explanation
Indices: 36381--36485 Score: 156
Period size: 36 Copynumber: 2.9 Consensus size: 36
36371 TCAATGTTTA
* * * *
36381 TGTTTCAAGAGAAACTGTCTCAAGGGAAAAAAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAG-AGACAAAATT
*
36418 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
36454 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
36486 TGGTGAGCAC
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
36 39 0.62
37 24 0.38
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:38008 original size:20 final size:21
Alignment explanation
Indices: 37982--38043 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
37972 CTTTTTGTTC
*
37982 CCTTTTTTATTTTTGTTCTTT
1 CCTTTTTTATTCTTGTTCTTT
* *
38003 -CTTTTTTGTTCTTGTTTTTT
1 CCTTTTTTATTCTTGTTCTTT
*
38023 CCTTTTTTGCTTCTT-TTCTTT
1 CCTTTTTT-ATTCTTGTTCTTT
38044 TTTCTTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 12 0.35
22 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.76
Consensus pattern (21 bp):
CCTTTTTTATTCTTGTTCTTT
Found at i:38054 original size:22 final size:22
Alignment explanation
Indices: 38000--38052 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
37990 ATTTTTGTTC
38000 TTTCTTTTTTG-TTCTTGTTTT
1 TTTCTTTTTTGCTTCTTGTTTT
* *
38021 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTCTTTTTTGCTTCTTGT-TTT
38044 TTTCTTTTT
1 TTTCTTTTT
38053 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTGCTTCTTGTTTT
Found at i:41415 original size:16 final size:16
Alignment explanation
Indices: 41394--41431 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41384 AAAAATAATT
41394 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
41410 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
41426 T-ATAAA
1 TAATAAA
41432 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:42198 original size:35 final size:37
Alignment explanation
Indices: 42124--42223 Score: 105
Period size: 35 Copynumber: 2.8 Consensus size: 37
42114 GTGCTTGTGG
* * * * * *
42124 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATGCT
*
42161 ATCCTA-TTTTAAGAG-TTGAATCCTAGCAGAATGCT
1 ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATGCT
* *
42196 ATCTTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTTAAGAGTTTGAATCCTAG
42224 TAGGACGAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
35 20 0.38
36 15 0.29
37 17 0.33
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (37 bp):
ATCCTATTTTTAAGAGTTTGAATCCTAGCAAAATGCT
Found at i:46400 original size:93 final size:95
Alignment explanation
Indices: 46266--46459 Score: 232
Period size: 93 Copynumber: 2.1 Consensus size: 95
46256 GTTGAGGTGG
* * * * * **
46266 GTATCGATAC-AATGAGGAAGGTATTGATTCCATTGATTCCAGAATGCATAAATGGTATCGATAC
1 GTATCGGTACTAA-GAGAAAGGTATTGATACCAATGATTCCAGAATGCAAAAATGAAATCGATAC
* * * *
46330 TGTAATAGAGTATCGATACCATAGTATAGAA
65 TGAAAGAGAATATCGATACCAGAGTATAGAA
*
46361 -TATCGGTACTAAGAGAAAGGTATTGATACCAATGA-TCCAGAATGCAAAAATGAAATCGATATT
1 GTATCGGTACTAAGAGAAAGGTATTGATACCAATGATTCCAGAATGCAAAAATGAAATCGATACT
* *
46424 GAAAGGGAATATCGGTACCAGAGTATAGAA
66 GAAAGAGAATATCGATACCAGAGTATAGAA
46454 GTATCG
1 GTATCG
46460 ATACCATGGT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
93 48 0.58
94 33 0.40
95 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.26
Consensus pattern (95 bp):
GTATCGGTACTAAGAGAAAGGTATTGATACCAATGATTCCAGAATGCAAAAATGAAATCGATACT
GAAAGAGAATATCGATACCAGAGTATAGAA
Found at i:46867 original size:54 final size:54
Alignment explanation
Indices: 46803--47305 Score: 679
Period size: 54 Copynumber: 9.3 Consensus size: 54
46793 GATTACCGAA
* * * **
46803 TGGCACTATGTATGCAACCTAAGAAATTTATAATGAGTTTATGAATTTCTATAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
*
46857 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * **
46911 TGGCACTATGTGCGCAACCTAAGAAATTAATAATAAGTTTATGAATTTTTGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * * * *
46965 CGACATTATGTGTGCAACCTAAGAAATTTATAATAAGTTTATGAATTTCCATAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * *
47019 TGGCACTATGTGAGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCATAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * *
47073 TGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTAT-TATTTTCGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* *
47126 TGGCACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATAAATGTT-CGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT-TTCCGTAT
47180 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * * * * * *
47234 TGGTACTGTGTGTGCAACCCCACGTAATTCATGATAAGTTTGTGAATTAT-CGTAT
1 TGGCACTATGTGTGCAA-CCTAAGAAATTCATAATAAGTTTATGAATT-TCCGTAT
*
47289 TGGCACTACGTGTGCAA
1 TGGCACTATGTGTGCAA
47306 ACAATAGAGG
Statistics
Matches: 404, Mismatches: 40, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
53 50 0.12
54 307 0.76
55 46 0.11
56 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (54 bp):
TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
Found at i:53637 original size:22 final size:21
Alignment explanation
Indices: 53612--53652 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
53602 TGAGAAATTG
*
53612 TTTTTAAAATATAAAAATGATA
1 TTTTGAAAATA-AAAAATGATA
*
53634 TTTTGAAATTAAAAAATGA
1 TTTTGAAAATAAAAAATGA
53653 AAATAATCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTTGAAAATAAAAAATGATA
Found at i:57527 original size:23 final size:22
Alignment explanation
Indices: 57482--57528 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
57472 GGAATCGATA
*
57482 CCCCCTTGAAGGGAAACTGATT
1 CCCCCTTGAAGGGAAACTAATT
57504 CCCCCTTTGAAGGGGAAA-TAATT
1 CCCCC-TTGAA-GGGAAACTAATT
57527 CC
1 CC
57529 ACCTGGAGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 11 0.50
24 6 0.27
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (22 bp):
CCCCCTTGAAGGGAAACTAATT
Found at i:62853 original size:54 final size:54
Alignment explanation
Indices: 62771--63429 Score: 838
Period size: 54 Copynumber: 12.2 Consensus size: 54
62761 GAATGATACA
*
62771 ATGTGTGCAACCTAAGAAATTCATAATAAGTTTACGAATTTCCATATTGGCACT
1 ATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACT
* *
62825 ATGTGTGCAACCTAAGAAAATCATAATAAGTTTATGAATTT--ATGCATTAGCACT
1 ATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCAT--ATTGGCACT
*
62879 ACGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACT
1 ATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACT
* * * * *
62933 ATGTGTGCAACCTAATAAATTCATAATAAGTTTATGATTTTACGTATTGTCACT
1 ATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACT
* *
62987 ACGTGTACAACCTAAGAAATTCATAATGAA-TTTATGAATTTCCATATTGGCACT
1 ATGTGTGCAACCTAAGAAATTCATAAT-AAGTTTATGAATTTCCATATTGGCACT
** * * * *
63041 ATGTGTATAACCTAATAAATTCATAATGAGTTTATGAATTTCCGTATTGGAACT
1 ATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACT
* * ***
63095 ATGTGTGCAACCTAATAAATTCATAATAAGTTTAAGAATTTATGTATTGGCACT
1 ATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACT
* * *
63149 ATGTTTTCAACCTAAGAAATTCATAATAAGCTTATGAATTTCCATATTGGCACT
1 ATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACT
** ***
63203 ATGTACGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGCACT
1 ATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACT
* * * * *
63257 ATGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTTCGTATTGGTATT
1 ATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACT
* * *
63311 ATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCATT
1 ATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACT
* * * * * * * *
63365 GTGTGTGCAACCCCACGTAATTCATAATAAGTTTATGAATTGCTATATTGGTATT
1 ATGTGTGCAA-CCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACT
*
63420 CTGTGTGCAA
1 ATGTGTGCAA
63430 ACTATAGGGT
Statistics
Matches: 533, Mismatches: 65, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
52 2 0.00
53 1 0.00
54 481 0.90
55 47 0.09
56 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (54 bp):
ATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGCACT
Found at i:76953 original size:36 final size:36
Alignment explanation
Indices: 76899--77037 Score: 199
Period size: 36 Copynumber: 3.9 Consensus size: 36
76889 ACGAAAGAAA
76899 GCATC-GCACTTCCAATTCAAATCGAACGGAATGAG
1 GCATCGGCACTTCCAATTCAAATCGAACGGAATGAG
* *
76934 GCATCGACACTTCCGATTCAAATCGAACGGAATGAG
1 GCATCGGCACTTCCAATTCAAATCGAACGGAATGAG
* * * * *
76970 GCATCGGTACTTCCGATTCAAATTGAACGGAAGGAA
1 GCATCGGCACTTCCAATTCAAATCGAACGGAATGAG
*
77006 GCATCGGCACTTCCAATTCAAATCAAACGGAA
1 GCATCGGCACTTCCAATTCAAATCGAACGGAA
77038 AGATGTATCG
Statistics
Matches: 92, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 5 0.05
36 87 0.95
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (36 bp):
GCATCGGCACTTCCAATTCAAATCGAACGGAATGAG
Found at i:80337 original size:7 final size:7
Alignment explanation
Indices: 80325--80354 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
80315 AGAAGATAGT
80325 TGAGTGA
1 TGAGTGA
80332 TGAGTGA
1 TGAGTGA
80339 TGAGTGA
1 TGAGTGA
*
80346 TGAATGA
1 TGAGTGA
80353 TG
1 TG
80355 TAATTTACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.40, T:0.30
Consensus pattern (7 bp):
TGAGTGA
Found at i:85457 original size:15 final size:16
Alignment explanation
Indices: 85439--85471 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
85429 AAAAAATAGT
85439 AAATAAA-ATAAAATA
1 AAATAAACATAAAATA
*
85454 AAATAAACATAAATTA
1 AAATAAACATAAAATA
85470 AA
1 AA
85472 GGACATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (16 bp):
AAATAAACATAAAATA
Found at i:87373 original size:91 final size:91
Alignment explanation
Indices: 87012--87361 Score: 488
Period size: 91 Copynumber: 3.9 Consensus size: 91
87002 GCGATGAAGC
* * ** *
87012 GAGCTAAGGTTAAACAAGTTC-TCTCATTATGAACTTATTCTCCCTCATCAAATGAGTTATTTTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTATTCTC
*
87076 ATTATGAACTCTCCA-TCGAAAATATT
66 ATTATGAACTCTCCACT-GAAAATGTT
* * * *
87102 GAGCCAAGGTTGAAGAAGTTCTTCTCATTAAGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTATTCTC
* *
87167 ATTATGAATTCTCCACTGGAAATGTT
66 ATTATGAACTCTCCACTGAAAATGTT
* * * *
87193 GAGCCAACGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTATTCTC
* *
87258 ATTATGAACTCCCCACTGGAAATGTT
66 ATTATGAACTCTCCACTGAAAATGTT
* * *
87284 CAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTATTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTATTCTC
87349 ATTATGAACTCTC
66 ATTATGAACTCTC
87362 TATCGAAAAT
Statistics
Matches: 234, Mismatches: 24, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
90 18 0.08
91 215 0.92
92 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (91 bp):
GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTATTCTC
ATTATGAACTCTCCACTGAAAATGTT
Found at i:90702 original size:7 final size:7
Alignment explanation
Indices: 90687--90754 Score: 50
Period size: 7 Copynumber: 9.9 Consensus size: 7
90677 TTGATCAGTT
*
90687 TTCTCTC
1 TTCTTTC
90694 TTCTTTC
1 TTCTTTC
*
90701 TTTTTTC
1 TTCTTTC
*
90708 -TCTTTT
1 TTCTTTC
*
90714 TTCTTTT
1 TTCTTTC
*
90721 TTCTTTT
1 TTCTTTC
*
90728 TTCTCTC
1 TTCTTTC
90735 TT-TTTC
1 TTCTTTC
*
90741 TTTTTTC
1 TTCTTTC
90748 TTTCTTT
1 -TTCTTT
90755 TCTATATTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
6 9 0.18
7 36 0.72
8 5 0.10
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (7 bp):
TTCTTTC
Found at i:90721 original size:17 final size:16
Alignment explanation
Indices: 90685--90750 Score: 82
Period size: 16 Copynumber: 4.2 Consensus size: 16
90675 ATTTGATCAG
* *
90685 TTTTCTCTCTTCTTTC
1 TTTTTTCTCTTTTTTC
90701 TTTTTTCTCTTTTTTC
1 TTTTTTCTCTTTTTTC
90717 TTTTTTCT-TTTTTCTC
1 TTTTTTCTCTTTTT-TC
*
90733 TCTTTT-TCTTTTTTC
1 TTTTTTCTCTTTTTTC
90748 TTT
1 TTT
90751 CTTTTCTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
15 10 0.23
16 34 0.77
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTCTCTTTTTTC
Found at i:90723 original size:23 final size:24
Alignment explanation
Indices: 90692--90750 Score: 102
Period size: 23 Copynumber: 2.5 Consensus size: 24
90682 CAGTTTTCTC
*
90692 TCTTCTTTCTTTTTTCTCT-TTTT
1 TCTTTTTTCTTTTTTCTCTCTTTT
90715 TCTTTTTTCTTTTTTCTCTCTTTT
1 TCTTTTTTCTTTTTTCTCTCTTTT
90739 TCTTTTTTCTTT
1 TCTTTTTTCTTT
90751 CTTTTCTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 18 0.53
24 16 0.47
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (24 bp):
TCTTTTTTCTTTTTTCTCTCTTTT
Found at i:90753 original size:17 final size:17
Alignment explanation
Indices: 90694--90755 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
90684 GTTTTCTCTC
*
90694 TTCTTTCTTTTT-TCTCT
1 TTCTTTCTTTTTCT-TTT
90711 TT-TTTCTTTTTTCTTTT
1 TTCTTTC-TTTTTCTTTT
*
90728 TTCTCTCTTTTTCTTTT
1 TTCTTTCTTTTTCTTTT
90745 TTCTTTCTTTT
1 TTCTTTCTTTT
90756 CTATATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
16 4 0.10
17 31 0.79
18 4 0.10
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTCTTTCTTTTTCTTTT
Found at i:90755 original size:16 final size:15
Alignment explanation
Indices: 90692--90757 Score: 80
Period size: 16 Copynumber: 4.2 Consensus size: 15
90682 CAGTTTTCTC
*
90692 TCTTCTTTCTTTTTT
1 TCTTTTTTCTTTTTT
90707 CTCTTTTTTC-TTTTT
1 -TCTTTTTTCTTTTTT
90722 TCTTTTTTCTCTCTTTT
1 TCTTTTTTCT-T-TTTT
90739 TCTTTTTTCTTTCTTT
1 TCTTTTTTCTTT-TTT
90755 TCT
1 TCT
90758 ATATTTTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 9 0.20
15 6 0.13
16 16 0.36
17 14 0.31
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TCTTTTTTCTTTTTT
Found at i:90795 original size:16 final size:16
Alignment explanation
Indices: 90692--90796 Score: 76
Period size: 16 Copynumber: 6.5 Consensus size: 16
90682 CAGTTTTCTC
*
90692 TCTTCTTTCTT-TTTT
1 TCTTTTTTCTTCTTTT
90707 CTCTTTTTTC-T-TTTT
1 -TCTTTTTTCTTCTTTT
90722 TCTTTTTTCTCTCTTTT
1 TCTTTTTTCT-TCTTTT
90739 TCTTTTTTCTT-TCTTT
1 TCTTTTTTCTTCT-TTT
*
90755 TCTATATTTT-TTCTGTGT
1 TCT-T-TTTTCTTCT-TTT
**
90773 GATTTTTTCTTCTTTT
1 TCTTTTTTCTTCTTTT
*
90789 TCCTTTTT
1 TCTTTTTT
90797 GGTATATCTC
Statistics
Matches: 72, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
14 9 0.12
15 6 0.08
16 27 0.38
17 22 0.31
18 8 0.11
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (16 bp):
TCTTTTTTCTTCTTTT
Found at i:94148 original size:18 final size:18
Alignment explanation
Indices: 94122--94156 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
94112 TCGAAAGGAC
*
94122 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
94140 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
94157 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:96069 original size:18 final size:18
Alignment explanation
Indices: 96046--96080 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
96036 TTCCATCCGG
*
96046 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
96064 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
96081 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:99589 original size:16 final size:16
Alignment explanation
Indices: 99568--99600 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
99558 AAAAAACAAT
99568 AATAAA-ATAAATATAA
1 AATAAACATAAAT-TAA
99584 AATAAACATAAATTAA
1 AATAAACATAAATTAA
99600 A
1 A
99601 GGACCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
AATAAACATAAATTAA
Found at i:100756 original size:2 final size:2
Alignment explanation
Indices: 100749--100796 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
100739 AACTACTACA
100749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
100791 AT AT AT
1 AT AT AT
100797 TACATACATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:100908 original size:22 final size:22
Alignment explanation
Indices: 100883--100925 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
100873 CAATTATTCA
100883 CAATTCAAACAACTCAAAAACT
1 CAATTCAAACAACTCAAAAACT
100905 CAATTCAAACAACTCAAAAAC
1 CAATTCAAACAACTCAAAAAC
100926 AAATGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (22 bp):
CAATTCAAACAACTCAAAAACT
Found at i:102023 original size:45 final size:45
Alignment explanation
Indices: 101972--102268 Score: 278
Period size: 45 Copynumber: 6.6 Consensus size: 45
101962 TAATCCAAGG
* * *
101972 CTTTTGATTATTGGGTTTCCAAAAGTAAAATCAAATGATTAGTTC
1 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAGTTC
** * *
102017 CTTTTGATTATTGTATTAG-CAAAAGTAAATTCAAAGGATTAGCTT-
1 CTTTTGATTATTGGGTT-GCCAAAATTAAAATCAAAGGATTAG-TTC
* *
102062 CTTTTGATTATTGGGTTGCCGATATTAAAATCAAAGGATTAGTTTC
1 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAG-TTC
* * *** *
102108 C-TTTGGTTACTGGGTTGAGGAAATTAAAATCAAAAGATTAGTTC
1 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAGTTC
* * * *
102152 ATTTTGATTACTAGGTTGCAAAAAATTAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTGGGTTGC-CAAAATTAAAATCAAAGGATTAGTTC
* * * * * *
102198 CTTTTGATTATTGGGTTTG-GAAAATTAAAATATAAATGATCAATTT
1 CTTTTGATTATTGGG-TTGCCAAAATTAAAAT-CAAAGGATTAGTTC
*
102244 CTTTTGATTATTGGGTTGCTAAAAT
1 CTTTTGATTATTGGGTTGCCAAAAT
102269 CAAATGATTA
Statistics
Matches: 208, Mismatches: 35, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
44 4 0.02
45 134 0.64
46 67 0.32
47 3 0.01
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.40
Consensus pattern (45 bp):
CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAGTTC
Found at i:102491 original size:58 final size:58
Alignment explanation
Indices: 102375--102492 Score: 141
Period size: 58 Copynumber: 2.0 Consensus size: 58
102365 GTGTTGATTC
* * *
102375 TAACTTTGTAAAGAAAATAAATTGGTGAATTTATTTTATTGAAAATATTTAATGATTA
1 TAACTTTGTAAAGAAAATAAATCGGTGAATTTATTTTATTGAAAATATTGAATAATTA
* * * *
102433 TAACTTTGT-AAGTAAAATAAATCGTTGAATTTATTTTCTTGAGAAT-TGTGGATAATTA
1 TAACTTTGTAAAG-AAAATAAATCGGTGAATTTATTTTATTGAAAATAT-TGAATAATTA
102491 TA
1 TA
102493 TTTTATTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
57 4 0.08
58 47 0.92
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (58 bp):
TAACTTTGTAAAGAAAATAAATCGGTGAATTTATTTTATTGAAAATATTGAATAATTA
Found at i:102670 original size:32 final size:35
Alignment explanation
Indices: 102620--102690 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 35
102610 TTTATAAAAG
* *
102620 AAAATAAATCGTTTAA-TTTATTTCCCTGTTTTGT
1 AAAATAAATCGTTGAATTTTATTTCCCTGTTTTAT
*
102654 AAAA-AAA-CGTTGAATTTTATTTTCCTGTTTTAT
1 AAAATAAATCGTTGAATTTTATTTCCCTGTTTTAT
102687 AAAA
1 AAAA
102691 CAAAATAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 6 0.18
33 23 0.70
34 4 0.12
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.46
Consensus pattern (35 bp):
AAAATAAATCGTTGAATTTTATTTCCCTGTTTTAT
Done.