Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003446.1 Hibiscus syriacus cultivar Beakdansim tig00007271_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: 98604
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:49 original size:19 final size:21
Alignment explanation
Indices: 11--52 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1 GTTGCTTGCT
11 GTTGTCATGTAAATATTGTTG
1 GTTGTCATGTAAATATTGTTG
32 GTTGTCATGT-AA-ATTGTTG
1 GTTGTCATGTAAATATTGTTG
51 GT
1 GT
53 CTGACTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.43
20 2 0.10
21 10 0.48
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.48
Consensus pattern (21 bp):
GTTGTCATGTAAATATTGTTG
Found at i:503 original size:15 final size:17
Alignment explanation
Indices: 496--529 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
486 AATAAAATCA
496 TGTTTAAT-AAATAAAT
1 TGTTTAATAAAATAAAT
*
512 TGTTTAATAAAATTAAT
1 TGTTTAATAAAATAAAT
529 T
1 T
530 TAATGATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
TGTTTAATAAAATAAAT
Found at i:1852 original size:32 final size:32
Alignment explanation
Indices: 1816--1879 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
1806 CCCTATTTTT
*
1816 CATTATCTGAATGTAATACTAACTCTGATGTG
1 CATTATCTGAATGCAATACTAACTCTGATGTG
* * *
1848 CATTATCTGAATGCAATATTGACTCTGTTGTG
1 CATTATCTGAATGCAATACTAACTCTGATGTG
1880 ATTCATACAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (32 bp):
CATTATCTGAATGCAATACTAACTCTGATGTG
Found at i:2847 original size:22 final size:22
Alignment explanation
Indices: 2819--2862 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2809 ATGCACAGTT
*
2819 AGGCATTTACCCTTCCATCTAA
1 AGGCATTTAACCTTCCATCTAA
*
2841 AGGCATTTAACCTTTCATCTAA
1 AGGCATTTAACCTTCCATCTAA
2863 CTTGCATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (22 bp):
AGGCATTTAACCTTCCATCTAA
Found at i:2932 original size:81 final size:80
Alignment explanation
Indices: 2771--3088 Score: 474
Period size: 81 Copynumber: 3.9 Consensus size: 80
2761 ATGCACTGTT
* * * *
2771 TTTCATCTAACTTGCATTAGTGGTACCTTTCTGCCAAAATGCACAGTTAGGCATTTACCCTTCCA
1 TTTCATCTAACTTGCATTAGTGGCACCTTTCTGCC-AAATGCACAGTTAGGCAATTAACCTTTCA
2836 TCTAAAGGCATTTAACC
65 TCTAAA-GCATTTAACC
* * * *
2853 TTTCATCTAACTTGCATTATTGACACCTTTCTGCCAAATGCATAGTTAGGCAATTAACTTTTCAT
1 TTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAATGCACAGTTAGGCAATTAACCTTTCAT
2918 CTAAAGTCATTTAACC
66 CTAAAG-CATTTAACC
* *
2934 TTTCATCTAACTTGCATTAGTGGCACCTTTTTGCCAAATGCACAGTTAGGCAATTAACTTTTCAT
1 TTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAATGCACAGTTAGGCAATTAACCTTTCAT
2999 CTAAAAGCATTTAACC
66 CT-AAAGCATTTAACC
* * *
3015 TTTCATCTAACTTGTATTAGTGGTACGTTTCTGCCAAATGCACAGTTAGGCAATTAACCTTTCAT
1 TTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAATGCACAGTTAGGCAATTAACCTTTCAT
3080 CTTAAAGCA
66 C-TAAAGCA
3089 GTTTTTACTC
Statistics
Matches: 216, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
80 1 0.00
81 178 0.82
82 37 0.17
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.36
Consensus pattern (80 bp):
TTTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAATGCACAGTTAGGCAATTAACCTTTCAT
CTAAAGCATTTAACC
Found at i:4686 original size:37 final size:36
Alignment explanation
Indices: 4631--4708 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 36
4621 AGAATTTTAG
* * * *
4631 AATTTAATATTTTTTAATTAAAAAATAAT-TGTCAATT
1 AATTTAATAATATATAATT-AAAAATAATATCT-AATT
*
4668 AATTTAATAATATATAATTATAAATAATATCTAATT
1 AATTTAATAATATATAATTAAAAATAATATCTAATT
4704 AATTT
1 AATTT
4709 GATTCAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
36 17 0.49
37 18 0.51
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (36 bp):
AATTTAATAATATATAATTAAAAATAATATCTAATT
Found at i:6431 original size:22 final size:24
Alignment explanation
Indices: 6398--6441 Score: 58
Period size: 22 Copynumber: 1.9 Consensus size: 24
6388 CAAGAAACGG
6398 GAAAAGAGTAAG-AGA-GAAAAAT
1 GAAAAGAGTAAGAAGATGAAAAAT
6420 GAAAAG-GATAAGAAGATGAAAA
1 GAAAAGAG-TAAGAAGATGAAAA
6442 GATAATAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.05
22 10 0.53
23 3 0.16
24 5 0.26
ACGTcount: A:0.64, C:0.00, G:0.27, T:0.09
Consensus pattern (24 bp):
GAAAAGAGTAAGAAGATGAAAAAT
Found at i:6904 original size:15 final size:15
Alignment explanation
Indices: 6880--6911 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6870 TGAAAATATG
6880 ACTATCTGATACTAT
1 ACTATCTGATACTAT
*
6895 ACTATTTGATACTAT
1 ACTATCTGATACTAT
6910 AC
1 AC
6912 GCTCGGAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (15 bp):
ACTATCTGATACTAT
Found at i:22612 original size:22 final size:22
Alignment explanation
Indices: 22586--22643 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
22576 GACATCCTAG
* *
22586 TTGTTACTGTTT-TTAGTCGTTA
1 TTGTTACTGTTTCTGACT-GTTA
22608 TTGTTACTGTTTCTGACTGTTA
1 TTGTTACTGTTTCTGACTGTTA
*
22630 TTGTTATTGTTTCT
1 TTGTTACTGTTTCT
22644 AGCTATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 29 0.91
23 3 0.09
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.60
Consensus pattern (22 bp):
TTGTTACTGTTTCTGACTGTTA
Found at i:22652 original size:22 final size:22
Alignment explanation
Indices: 22605--22652 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
22595 TTTTTAGTCG
*
22605 TTATTGTTACTGTTTCTGACTG
1 TTATTGTTACTGTTTCTGACTA
*
22627 TTATTGTTATTGTTTCT-AGCTA
1 TTATTGTTACTGTTTCTGA-CTA
22649 TTAT
1 TTAT
22653 AAGTGATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.17, C:0.10, G:0.15, T:0.58
Consensus pattern (22 bp):
TTATTGTTACTGTTTCTGACTA
Found at i:24913 original size:14 final size:12
Alignment explanation
Indices: 24885--24926 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
24875 AACCCCAATT
*
24885 TTATT-TATTTT
1 TTATTATATTTA
24896 TTATTATAGTTATA
1 TTATTATA-TT-TA
24910 TTATTATATTTA
1 TTATTATATTTA
24922 TTATT
1 TTATT
24927 TAATATGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 5 0.19
12 9 0.33
13 4 0.15
14 9 0.33
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTATTATATTTA
Found at i:30394 original size:32 final size:32
Alignment explanation
Indices: 30358--30420 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
30348 TTTTTTGTTT
*
30358 AGATTAAATTTAATTCGAGTTAAATTCGGTTC
1 AGATTAAATTTAATTCGAGTTAAATTAGGTTC
*** *
30390 AGATTGTTTTTGATTCGAGTTAAATTAGGTT
1 AGATTAAATTTAATTCGAGTTAAATTAGGTT
30421 TTTGTTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.44
Consensus pattern (32 bp):
AGATTAAATTTAATTCGAGTTAAATTAGGTTC
Found at i:30785 original size:94 final size:94
Alignment explanation
Indices: 30624--30812 Score: 378
Period size: 94 Copynumber: 2.0 Consensus size: 94
30614 GATTGCAGAT
30624 AAGCCAGCGTGGGATGAAGAGAAGGTCTACACTACATTTATAGCATCTGATACATAACTAATTCT
1 AAGCCAGCGTGGGATGAAGAGAAGGTCTACACTACATTTATAGCATCTGATACATAACTAATTCT
30689 AGCTATTTCTATCGCTCCAAATGATATAG
66 AGCTATTTCTATCGCTCCAAATGATATAG
30718 AAGCCAGCGTGGGATGAAGAGAAGGTCTACACTACATTTATAGCATCTGATACATAACTAATTCT
1 AAGCCAGCGTGGGATGAAGAGAAGGTCTACACTACATTTATAGCATCTGATACATAACTAATTCT
30783 AGCTATTTCTATCGCTCCAAATGATATAG
66 AGCTATTTCTATCGCTCCAAATGATATAG
30812 A
1 A
30813 GGCAATTATT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 95 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (94 bp):
AAGCCAGCGTGGGATGAAGAGAAGGTCTACACTACATTTATAGCATCTGATACATAACTAATTCT
AGCTATTTCTATCGCTCCAAATGATATAG
Found at i:37740 original size:17 final size:18
Alignment explanation
Indices: 37718--37751 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
37708 TTAGTCGGTC
37718 CGGTTCT-AACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
37735 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
37752 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Found at i:39773 original size:3 final size:3
Alignment explanation
Indices: 39749--39810 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
39739 TCTACAAAAA
39749 TAT T-T TAT TA- TAT TA- TATT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
*
39792 TAT TAT TAT TTT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
39811 TTTGCAGGCC
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 6 0.11
3 45 0.85
4 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:39940 original size:33 final size:33
Alignment explanation
Indices: 39870--39945 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 33
39860 AAATCAACGT
* * *
39870 ATTTGAGTCTTATTGAAACACTAAAACTAATGT
1 ATTTGAGTCCTATTGAAACACTAAAACGAATGC
*
39903 ATTTGAGTCCTATTGAAATACTAAAATCGAA-GC
1 ATTTGAGTCCTATTGAAACACTAAAA-CGAATGC
39936 ATTTGAGTCC
1 ATTTGAGTCC
39946 AAGTAGGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 35 0.92
34 3 0.08
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.34
Consensus pattern (33 bp):
ATTTGAGTCCTATTGAAACACTAAAACGAATGC
Found at i:40441 original size:11 final size:11
Alignment explanation
Indices: 40417--40451 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
40407 ATGATAATAC
40417 ATTATTTA-TT
1 ATTATTTATTT
40427 ATTATTTATTT
1 ATTATTTATTT
40438 ATTATTTATTT
1 ATTATTTATTT
40449 ATT
1 ATT
40452 TTGTTTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTATTTATTT
Found at i:40795 original size:28 final size:28
Alignment explanation
Indices: 40722--41106 Score: 135
Period size: 30 Copynumber: 13.0 Consensus size: 28
40712 ATAGTAATTT
* *
40722 AAAATCAAGATAAAAATAAATATATTTTT
1 AAAATTAAGAT-AAAATAAATATATTTTA
* *
40751 ATAGTTAAGATAAAATAAATAT-TTTTA
1 AAAATTAAGATAAAATAAATATATTTTA
* *
40778 AAAATTAAAATAAGAATAAAATATACACTTT-
1 AAAATTAAGATAA-AAT-AAATAT--ATTTTA
* *
40809 -AAATTAATATTAAAACAAATTATACATTTT-
1 AAAATTAAGA-TAAAATAAA-TAT--ATTTTA
* * *
40839 TAAGTTAAGATAAGAATAGATCATA-TTTA
1 AAAATTAAGATAA-AATAAAT-ATATTTTA
* *
40868 ATAATTTAAGGTAACAATATAATATA-TTTA
1 A-AAATTAAGATAA-AATA-AATATATTTTA
* * *
40898 ATAATTTAAGCTAAGAATATAATATA--TGA
1 A-AAATTAAGATAA-AATA-AATATATTTTA
40927 AATAAGTTAAGATAAAAATAAAATATATTTTTA
1 AA-AA-TTAAGAT-AAAAT-AAATATA-TTTTA
* *
40960 AAAGTTAAGATAATAATAAAATATATTTTT
1 AAAATTAAGATAA-AAT-AAATATATTTTA
* * *
40990 TAAGTTAAGGTAGAAATAAAATATATTTTA
1 AAAATTAAGATA-AAAT-AAATATATTTTA
** * *
41020 TGAGTTAAGATAAGATTAAAATATATTTT-
1 AAAATTAAGATAA-AAT-AAATATATTTTA
* *
41049 -TAGTTAAGATAAGAATAAA-ATATATTTA
1 AAAATTAAGATAA-AATAAATATAT-TTTA
* *
41077 ATAAGTTAAAATAAAAATAAATTATATTTT
1 A-AAATTAAGAT-AAAATAAA-TATATTTT
41107 TTTAATGTTA
Statistics
Matches: 288, Mismatches: 38, Indels: 58
0.75 0.10 0.15
Matches are distributed among these distances:
26 4 0.01
27 20 0.07
28 32 0.11
29 23 0.08
30 152 0.53
31 45 0.16
32 8 0.03
33 4 0.01
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (28 bp):
AAAATTAAGATAAAATAAATATATTTTA
Found at i:40877 original size:30 final size:30
Alignment explanation
Indices: 40843--41105 Score: 187
Period size: 30 Copynumber: 8.8 Consensus size: 30
40833 CATTTTTAAG
*
40843 TTAAGATAAGAATA-GATCATATTTAATAAT
1 TTAAGATAAGAATATAAT-ATATTTAATAAT
* *
40873 TTAAGGTAACAATATAATATATTTAATAAT
1 TTAAGATAAGAATATAATATATTTAATAAT
* ** *
40903 TTAAGCTAAGAATATAATATATGAAATAAG
1 TTAAGATAAGAATATAATATATTTAATAAT
* * *
40933 TTAAGATAAAAATAAAATATATTTTTAA-AAG
1 TTAAGATAAGAATATAATATA--TTTAATAAT
* * ** *
40964 TTAAGATAATAATAAAATATATTTTTTAAG
1 TTAAGATAAGAATATAATATATTTAATAAT
* * * * *
40994 TTAAGGT-AGAAATAAAATATATTTTATGAG
1 TTAAGATAAG-AATATAATATATTTAATAAT
* * * *
41024 TTAAGATAAGATTAAAATATATTT--TTAG
1 TTAAGATAAGAATATAATATATTTAATAAT
* *
41052 TTAAGATAAGAATAAAATATATTTAATAAG
1 TTAAGATAAGAATATAATATATTTAATAAT
* *
41082 TTAAAATAAAAATA-AATTATATTT
1 TTAAGATAAGAATATAA-TATATTT
41106 TTTTAATGTT
Statistics
Matches: 197, Mismatches: 27, Indels: 18
0.81 0.11 0.07
Matches are distributed among these distances:
28 26 0.13
29 6 0.03
30 135 0.69
31 27 0.14
32 3 0.02
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.38
Consensus pattern (30 bp):
TTAAGATAAGAATATAATATATTTAATAAT
Found at i:40998 original size:91 final size:91
Alignment explanation
Indices: 40839--41103 Score: 265
Period size: 91 Copynumber: 3.0 Consensus size: 91
40829 TATACATTTT
* * * *
40839 TAAGTTAAGATAAGAAT-AGATCATA--TTTAATAATTTAAGGTAACAATATAATATATTTAATA
1 TAAGTTAAGATAAGAATAAAAT-ATATTTTTAA-AAGTTAAGATAACAATAAAATATATTTAATA
* *
40901 ATTTAAGCTA-AGAATATAATATATGAAA
64 AGTTAAGCTAGA-AATAAAATATATGAAA
* * **
40929 TAAGTTAAGATAAAAATAAAATATATTTTTAAAAGTTAAGATAATAATAAAATATATTTTTTAAG
1 TAAGTTAAGATAAGAATAAAATATATTTTTAAAAGTTAAGATAACAATAAAATATATTTAATAAG
* ***
40994 TTAAGGTAGAAATAAAATATATTTTA
66 TTAAGCTAGAAATAAAATATATGAAA
* * *
41020 TGAGTTAAGATAAGATTAAAATATATTTTT---AGTTAAGATAAGAATAAAATATATTTAATAAG
1 TAAGTTAAGATAAGAATAAAATATATTTTTAAAAGTTAAGATAACAATAAAATATATTTAATAAG
** * *
41082 TTAAAATAAAAATAAATTATAT
66 TTAAGCTAGAAATAAAATATAT
41104 TTTTTTAATG
Statistics
Matches: 147, Mismatches: 24, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
88 47 0.32
90 19 0.13
91 75 0.51
92 6 0.04
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.37
Consensus pattern (91 bp):
TAAGTTAAGATAAGAATAAAATATATTTTTAAAAGTTAAGATAACAATAAAATATATTTAATAAG
TTAAGCTAGAAATAAAATATATGAAA
Found at i:42057 original size:3 final size:3
Alignment explanation
Indices: 42049--42126 Score: 95
Period size: 3 Copynumber: 26.0 Consensus size: 3
42039 TTTTATTTAT
* * * *
42049 TTA TTA TTA TTA TTA CTA TAA TTA TTA TTA TTA TAA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
42097 TAA TTA TTA TATA TT- TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
42127 AAAAATAATT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
2 2 0.03
3 58 0.92
4 3 0.05
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:43529 original size:28 final size:27
Alignment explanation
Indices: 43455--43530 Score: 64
Period size: 29 Copynumber: 2.7 Consensus size: 27
43445 GTTCTAATTG
** *
43455 TATTTTTATTATTGTT-TATTTATGTTT
1 TATTTTTATTATT-TTATATTTAAATAT
* *
43482 TAATTTTACTTGTTTATATATTTAAATAT
1 TATTTTTA-TTATTT-TATATTTAAATAT
43511 TATTTTTATTATTATTATAT
1 TATTTTTATTATT-TTATAT
43531 AGTCATATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
27 8 0.21
28 14 0.37
29 16 0.42
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (27 bp):
TATTTTTATTATTTTATATTTAAATAT
Found at i:54825 original size:17 final size:16
Alignment explanation
Indices: 54802--54888 Score: 101
Period size: 17 Copynumber: 5.5 Consensus size: 16
54792 AATAAAAAAT
*
54802 GAAAAGAAGAAAAGAA
1 GAAAAAAAGAAAAGAA
54818 GAAAAAGAAGAAAA-AA
1 GAAAAA-AAGAAAAGAA
54834 G-AAAAAAGAAAAGAA
1 GAAAAAAAGAAAAGAA
*
54849 AAAGAAAAAGAAAA-AA
1 GAA-AAAAAGAAAAGAA
54865 G-AAAAAAGAAAAAGAA
1 GAAAAAAAG-AAAAGAA
54881 GAAAAAAA
1 GAAAAAAA
54889 AGAGAAAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
14 13 0.21
15 11 0.18
16 14 0.23
17 23 0.38
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
GAAAAAAAGAAAAGAA
Found at i:54846 original size:31 final size:31
Alignment explanation
Indices: 54795--54897 Score: 145
Period size: 31 Copynumber: 3.2 Consensus size: 31
54785 ATGCTTGAAT
*
54795 AAAAAATGAAAAGAAGAAAAGAAGAAAAAGAAG
1 AAAAAA-GAAAA-AAGAAAAGAAGAAAAAAAAG
54828 AAAAAAGAAAAAAGAAAAGAA-AAAGAAAAAG
1 AAAAAAGAAAAAAGAAAAGAAGAAA-AAAAAG
54859 AAAAAAGAAAAAAGAAAAAGAAGAAAAAAAAG
1 AAAAAAGAAAAAAG-AAAAGAAGAAAAAAAAG
54891 AGAAAAA
1 A-AAAAA
54898 AAGGGGGTCA
Statistics
Matches: 65, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
30 3 0.05
31 29 0.45
32 19 0.29
33 14 0.22
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (31 bp):
AAAAAAGAAAAAAGAAAAGAAGAAAAAAAAG
Found at i:54897 original size:12 final size:12
Alignment explanation
Indices: 54814--54899 Score: 68
Period size: 13 Copynumber: 6.8 Consensus size: 12
54804 AAAGAAGAAA
54814 AGAAGAAAAAGAAG
1 AGAA-AAAAA-AAG
*
54828 A-AAAAAGAAAAA
1 AGAAAAA-AAAAG
54840 AGAAAAGAAAAAG
1 AGAAAA-AAAAAG
*
54853 AAAAAGAAAAAAG
1 AGAAA-AAAAAAG
*
54866 AAAAAAGAAAAAG
1 AGAAAA-AAAAAG
54879 A-AGAAAAAAAAG
1 AGA-AAAAAAAAG
54891 AGAAAAAAA
1 AGAAAAAAA
54900 GGGGGTCAAG
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
12 21 0.34
13 38 0.61
14 3 0.05
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAG
Found at i:56588 original size:113 final size:113
Alignment explanation
Indices: 56390--57170 Score: 1159
Period size: 113 Copynumber: 7.0 Consensus size: 113
56380 GCAAAGATTA
* *
56390 AAATCCATCATTCAATGGATCAACATTTCCAGTTCGAGTTCATATTAAGAAGAACTCATCTGAAG
1 AAATCCATCATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* *
56455 AAGGAAGAAGAAGTTCATAATGAGACGAACTTGTTCAACTTTTTACTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
56503 AAATCCATCATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
56568 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
* * * *
56616 GAATTCATGATTCAATGGATCAACATTTCCAGTTCTAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
56681 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
56729 AAATCCATCATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
56794 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
* * * *
56842 GAATTCATGATTCAATGGATCAACATTTCCAGCTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
56907 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
* ** * * * *
56955 AAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATAAGAA-AACTCGTCATCTG
1 AAATCCATCATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAA--C-TCATCTG
* * * *
57019 AAGAA-GAA-AA-AA-TTCATAATGAGAATAATTTGTTCAACCTTTTGCTC
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
* * * ****
57066 AAATCCATCACTT-GATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---
1 AAATCCATCA-TTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
* * *
57127 GAA-GAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTT
57171 AATAATTTTA
Statistics
Matches: 620, Mismatches: 40, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
106 6 0.01
107 2 0.00
108 2 0.00
109 33 0.05
110 1 0.00
111 71 0.11
112 8 0.01
113 481 0.78
114 4 0.01
115 12 0.02
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (113 bp):
AAATCCATCATTCAATGGATCAACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
Found at i:57230 original size:118 final size:121
Alignment explanation
Indices: 57091--57377 Score: 390
Period size: 118 Copynumber: 2.4 Consensus size: 121
57081 TGGATCAGCT
57091 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG-AAGAAGTTCACAATGAGAAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGTTCACAATGAGAAGA
* * * * * * *
57155 GCTTGTTCAACCTTTT-AATAATTTTATCACAGAA-GAAATATATTAGCATTAACC
66 GCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
*
57209 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA-AAGAAAGAAGTTCATAATGAGAAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGTTCACAATGAGAAGA
* * *
57273 GCTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAACATCATCC
66 GCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
*
57329 ---CCAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAGAAGAA
1 TTTCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AAGA-AAGAA
57378 TTTATTCAAC
Statistics
Matches: 150, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
117 7 0.05
118 105 0.70
119 15 0.10
120 18 0.12
121 5 0.03
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.24
Consensus pattern (121 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGTTCACAATGAGAAGA
GCTTATTCAACCTTTTGAATAACTCTATCACAGAAGGAAATAGATCAACATCAACC
Found at i:57534 original size:3 final size:3
Alignment explanation
Indices: 57526--57587 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
57516 TTTTATTTAT
* * *
57526 TTA TTA TTA TTA TTA CTA TAA TTA TTA TTA TTA TAA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
57572 TATA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA
57588 AAAAATAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 45 0.87
4 7 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:58939 original size:28 final size:27
Alignment explanation
Indices: 58865--58940 Score: 64
Period size: 29 Copynumber: 2.7 Consensus size: 27
58855 GTTCTAATTG
** *
58865 TATTTTTATTATTGTT-TATTTATGTTT
1 TATTTTTATTATT-TTATATTTAAATAT
* *
58892 TAATTTTACTTGTTTATATATTTAAATAT
1 TATTTTTA-TTATTT-TATATTTAAATAT
58921 TATTTTTATTATTATTATAT
1 TATTTTTATTATT-TTATAT
58941 AGTCATATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
27 8 0.21
28 14 0.37
29 16 0.42
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (27 bp):
TATTTTTATTATTTTATATTTAAATAT
Found at i:59110 original size:120 final size:119
Alignment explanation
Indices: 59003--59242 Score: 304
Period size: 121 Copynumber: 2.0 Consensus size: 119
58993 ATTTTTATCA
* * *
59003 TATTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGGGCAATCTTAAAACAACTGGATGTT
1 TATTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAATCTTAAAACAACTAGAAGTT
*
59067 CATTTTATGATATTTTTAAATAAATAAATATCTTATTTTATAAATTATATATTAAT
66 C-TTTTATGATATTTCTAAATAAATAAATATCTTA-TTTATAAATTATATATTAAT
* * * ** *** *
59123 TGTTTTAATTATTTATTTATTTTTTAATATTGAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGTT
1 TATTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAATCTTAAAACAACTAGAAGTT
* * *
59188 CTTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAA-TATATATAAAT
66 CTTTTATGATATTTCTAAATAAATAAATATCTTATTTATAAATTATATATTAAT
59241 TA
1 TA
59243 ATATATTTTT
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
118 11 0.11
119 8 0.08
120 37 0.36
121 46 0.45
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (119 bp):
TATTTTAATTATTTATTTATTTTTCAATATCGAAGAAAAGAGCAATCTTAAAACAACTAGAAGTT
CTTTTATGATATTTCTAAATAAATAAATATCTTATTTATAAATTATATATTAAT
Found at i:59134 original size:20 final size:19
Alignment explanation
Indices: 59109--59150 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
59099 TTATTTTATA
59109 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
59129 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
59148 AAT
1 AAT
59151 ATTGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:64963 original size:3 final size:3
Alignment explanation
Indices: 64955--65026 Score: 94
Period size: 3 Copynumber: 24.3 Consensus size: 3
64945 GGGTTATGTA
*
64955 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* *
65001 -AT AAT AAT -AT AGT AAT AAT AGT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
65027 TAAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
2 4 0.07
3 53 0.88
4 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:65277 original size:36 final size:36
Alignment explanation
Indices: 65199--65400 Score: 253
Period size: 36 Copynumber: 5.6 Consensus size: 36
65189 GATATGTTCC
* ****
65199 TACTTCACTACTCTTTCGTGAAGGCTAGGTTTGCA-T
1 TACTTCACTACTCTTCCGTGAAGGCTAAAAATG-ATT
* * *
65235 TGCTTCAATACTCTTCCATGAAGGCTAAAAATGATT
1 TACTTCACTACTCTTCCGTGAAGGCTAAAAATGATT
65271 TACTTCACTACTCTTCCGTGAAGGCTAAAAATGATT
1 TACTTCACTACTCTTCCGTGAAGGCTAAAAATGATT
65307 TACTTCACTACTCTTCCGTGAAGGCTAAAAATGATT
1 TACTTCACTACTCTTCCGTGAAGGCTAAAAATGATT
** *** *
65343 TACTTCACTACTCTTCCGTGAAGGAGAATTTTGCTT
1 TACTTCACTACTCTTCCGTGAAGGCTAAAAATGATT
*
65379 TACTTCATTACTCTTCCGTGAA
1 TACTTCACTACTCTTCCGTGAA
65401 AGTTGGGTTG
Statistics
Matches: 147, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
35 1 0.01
36 146 0.99
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (36 bp):
TACTTCACTACTCTTCCGTGAAGGCTAAAAATGATT
Found at i:74398 original size:3 final size:3
Alignment explanation
Indices: 74390--74457 Score: 93
Period size: 3 Copynumber: 22.3 Consensus size: 3
74380 GGATTATGTA
*
74390 AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT -AT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
74435 AAT AAT AAT AAAT AAT AGT AAT A
1 AAT AAT AAT -AAT AAT AAT AAT A
74458 TAAAACGAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
2 2 0.03
3 50 0.86
4 6 0.10
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:74437 original size:33 final size:33
Alignment explanation
Indices: 74395--74459 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
74385 ATGTAAATAA
74395 TAATAATAATAATAA-ATAATAATAATAATATAG
1 TAATAATAATAATAATA-AATAATAATAATATAG
*
74428 TAATAATAATAATAATAAATAATAGTAATATA
1 TAATAATAATAATAATAAATAATAATAATATA
74460 AAACGAAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (33 bp):
TAATAATAATAATAATAAATAATAATAATATAG
Found at i:75093 original size:21 final size:21
Alignment explanation
Indices: 75067--75109 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
75057 CCCCTTCGCG
75067 TATCCATCATTGAATATGAGT
1 TATCCATCATTGAATATGAGT
75088 TATCCATCATTGAATATGAGT
1 TATCCATCATTGAATATGAGT
75109 T
1 T
75110 GGAGATGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (21 bp):
TATCCATCATTGAATATGAGT
Found at i:75240 original size:20 final size:20
Alignment explanation
Indices: 75215--75305 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
75205 TAAATTAAAT
*
75215 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
75235 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
75255 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
75267 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
75287 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
75306 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:75276 original size:52 final size:52
Alignment explanation
Indices: 75214--75361 Score: 271
Period size: 53 Copynumber: 2.8 Consensus size: 52
75204 CTAAATTAAA
*
75214 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
75266 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
75319 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATT
75362 ATGTTGCTAA
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 8 0.09
52 35 0.37
53 51 0.54
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:75345 original size:20 final size:20
Alignment explanation
Indices: 75320--75359 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
75310 TCTATTAGTT
*
75320 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
75340 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
75360 TTATGTTGCT
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:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:79951 original size:20 final size:20
Alignment explanation
Indices: 79926--80016 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
79916 TAAATTAAAT
*
79926 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
79946 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
* *
79966 ATT--CT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
79978 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
79998 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
80017 TTATTCTATT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 3 0.06
13 2 0.04
14 1 0.02
15 4 0.07
17 3 0.06
18 1 0.02
19 2 0.04
20 38 0.70
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:80003 original size:52 final size:52
Alignment explanation
Indices: 79925--80072 Score: 271
Period size: 53 Copynumber: 2.8 Consensus size: 52
79915 CTAAATTAAA
*
79925 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
79977 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
80030 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATT
80073 ATGTTGCTAA
Statistics
Matches: 94, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
51 8 0.09
52 35 0.37
53 51 0.54
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:80056 original size:20 final size:20
Alignment explanation
Indices: 80031--80070 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
80021 TCTATTAGTT
*
80031 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
80051 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
80071 TTATGTTGCT
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:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:80547 original size:24 final size:25
Alignment explanation
Indices: 80502--80549 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
80492 TTAGTGAGGC
**
80502 ATAATCAATAATAAAAGTAAACATA
1 ATAATCAATAATAAAACCAAACATA
*
80527 ATAA-CAATAATAATACCAAACAT
1 ATAATCAATAATAAAACCAAACAT
80550 TTCATATGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.23
Consensus pattern (25 bp):
ATAATCAATAATAAAACCAAACATA
Found at i:93444 original size:74 final size:74
Alignment explanation
Indices: 93323--93471 Score: 298
Period size: 74 Copynumber: 2.0 Consensus size: 74
93313 CCTATCTTCT
93323 TAAAAAATATTCTTATTTTCATTTGATTTATATAACACTTTCACTTCTAAAGGTGTATGAAAACA
1 TAAAAAATATTCTTATTTTCATTTGATTTATATAACACTTTCACTTCTAAAGGTGTATGAAAACA
93388 AACATCTAG
66 AACATCTAG
93397 TAAAAAATATTCTTATTTTCATTTGATTTATATAACACTTTCACTTCTAAAGGTGTATGAAAACA
1 TAAAAAATATTCTTATTTTCATTTGATTTATATAACACTTTCACTTCTAAAGGTGTATGAAAACA
93462 AACATCTAG
66 AACATCTAG
93471 T
1 T
93472 GAGAGGTAGG
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 75 1.00
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.40
Consensus pattern (74 bp):
TAAAAAATATTCTTATTTTCATTTGATTTATATAACACTTTCACTTCTAAAGGTGTATGAAAACA
AACATCTAG
Found at i:95918 original size:24 final size:24
Alignment explanation
Indices: 95868--95917 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
95858 TGAAACAAGT
*
95868 AAATAAAATATAAACATAAATATA
1 AAATAAAAGATAAACATAAATATA
* *
95892 AAATAAAAGGTAAAC-TAATTATA
1 AAATAAAAGATAAACATAAATATA
95915 AAA
1 AAA
95918 AGGAAACACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.24
Consensus pattern (24 bp):
AAATAAAAGATAAACATAAATATA
Done.