Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003740.1 Hibiscus syriacus cultivar Beakdansim tig00008002_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: 78313
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:9119 original size:13 final size:13
Alignment explanation
Indices: 9098--9157 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
9088 ATTTTGTTAG
9098 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
9111 TATTGTA-TTATT
1 TATTTTATTTAAT
9123 TAATTTT-TTT-AT
1 T-ATTTTATTTAAT
9135 TATTTTATTTAAT
1 TATTTTATTTAAT
9148 TATTTTATTT
1 TATTTTATTT
9158 TTTTACAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 5 0.13
12 10 0.26
13 24 0.62
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:9123 original size:21 final size:20
Alignment explanation
Indices: 9098--9162 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
9088 ATTTTGTTAG
9098 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAATTATT-TAT
*
9119 TA-TTTAATT--TT-TTTAT
1 TATTTTATTTAATTATTTAT
9135 TATTTTATTTAATTATTTTAT
1 TATTTTATTTAATTA-TTTAT
*
9156 TTTTTTA
1 TATTTTA
9163 CAGTTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 5 0.14
17 8 0.22
18 2 0.06
19 2 0.06
20 6 0.17
21 13 0.36
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TATTTTATTTAATTATTTAT
Found at i:9133 original size:29 final size:29
Alignment explanation
Indices: 9100--9162 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
9090 TTTGTTAGTA
9100 TTTTATT-TAATTATTGT-ATTATTTAATTT
1 TTTTATTAT-ATTATT-TAATTATTTAATTT
* *
9129 TTTTATTATTTTATTTAATTATTTTATTT
1 TTTTATTATATTATTTAATTATTTAATTT
9158 TTTTA
1 TTTTA
9163 CAGTTATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 1 0.03
29 28 0.93
30 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (29 bp):
TTTTATTATATTATTTAATTATTTAATTT
Found at i:9144 original size:16 final size:16
Alignment explanation
Indices: 9102--9144 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
9092 TGTTAGTATT
* *
9102 TTATTTAATTATTGTA
1 TTATTTAATTTTTTTA
9118 TTATTTAATTTTTTTA
1 TTATTTAATTTTTTTA
*
9134 TTATTTTATTT
1 TTATTTAATTT
9145 AATTATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTTTA
Found at i:9438 original size:16 final size:16
Alignment explanation
Indices: 9409--9465 Score: 53
Period size: 16 Copynumber: 3.5 Consensus size: 16
9399 TTTATAACTG
*
9409 TAAA-AAAATAAATAAT
1 TAAATAAAAT-AATAAA
9425 TAAATAAAATAATAAA
1 TAAATAAAATAATAAA
* *
9441 AAAATTAAATAATACAA
1 TAAATAAAATAATA-AA
*
9458 TAATTAAA
1 TAAATAAA
9466 TAAATACTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 21 0.64
17 12 0.36
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAATAAAATAATAAA
Found at i:9466 original size:16 final size:16
Alignment explanation
Indices: 9426--9468 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
9416 ATAAATAATT
*
9426 AAATAAAATAATAAAA
1 AAATTAAATAATAAAA
*
9442 AAATTAAATAATACAA
1 AAATTAAATAATAAAA
*
9458 TAATTAAATAA
1 AAATTAAATAA
9469 ATACTAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATTAAATAATAAAA
Found at i:9466 original size:21 final size:21
Alignment explanation
Indices: 9409--9460 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
9399 TTTATAACTG
* *
9409 TAAAAAAAT-AAATAATTAAA
1 TAAAACAATAAAAAAATTAAA
*
9429 TAAAATAATAAAAAAATTAAA
1 TAAAACAATAAAAAAATTAAA
*
9450 TAATACAATAA
1 TAAAACAATAA
9461 TTAAATAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (21 bp):
TAAAACAATAAAAAAATTAAA
Found at i:10264 original size:51 final size:52
Alignment explanation
Indices: 10204--10308 Score: 135
Period size: 53 Copynumber: 2.0 Consensus size: 52
10194 TAAATTAAAA
* * *
10204 TTTTGATTTAT-TATAGTTT-TACGCAAATGACTTAATATA-ATTTTCTATTAT
1 TTTTAATTTATATATAGTTTATACACAAATAACTTAATATATATTTT-T-TTAT
*
10255 TTTTAATTTATATATATTTTATACACAAATAACTTAATATATATTTTTTTAT
1 TTTTAATTTATATATAGTTTATACACAAATAACTTAATATATATTTTTTTAT
10307 TT
1 TT
10309 CTTTGAAAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
51 10 0.21
52 13 0.28
53 19 0.40
54 5 0.11
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.55
Consensus pattern (52 bp):
TTTTAATTTATATATAGTTTATACACAAATAACTTAATATATATTTTTTTAT
Found at i:11956 original size:3 final size:3
Alignment explanation
Indices: 11943--12028 Score: 136
Period size: 3 Copynumber: 28.7 Consensus size: 3
11933 TTTTTATCCA
*
11943 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
11991 TAT TAT TAT TAT TAT TAT CAT CAT CAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12029 ATAAATATAT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:12043 original size:14 final size:14
Alignment explanation
Indices: 12024--12064 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
12014 TCATTATTAT
12024 TATTAATAAATATA
1 TATTAATAAATATA
12038 TATTAAATAAATATA
1 TATT-AATAAATATA
*
12053 TATAAATAAATA
1 TATTAATAAATA
12065 ATTACAGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATTAATAAATATA
Found at i:12048 original size:15 final size:15
Alignment explanation
Indices: 12024--12064 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
12014 TCATTATTAT
12024 TATT-AATAAATATA
1 TATTAAATAAATATA
12038 TATTAAATAAATATA
1 TATTAAATAAATATA
12053 TA-TAAATAAATA
1 TATTAAATAAATA
12065 ATTACAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATTAAATAAATATA
Found at i:12498 original size:17 final size:17
Alignment explanation
Indices: 12475--12511 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
12465 CCAACCTGAA
12475 AAAAAAAACCAGAGACAG
1 AAAAAAAA-CAGAGACAG
*
12493 AAAAAAAAGAGAGACAG
1 AAAAAAAACAGAGACAG
12510 AA
1 AA
12512 CCGGAGAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.70, C:0.11, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAAAAACAGAGACAG
Found at i:24813 original size:8 final size:7
Alignment explanation
Indices: 24800--24845 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
24790 GCTTGAAGAA
24800 AAAAAAG
1 AAAAAAG
*
24807 CAAAAAAA
1 -AAAAAAG
24815 AAAAAAG
1 AAAAAAG
*
24822 AAAAGA-
1 AAAAAAG
24828 AAAAAAG
1 AAAAAAG
24835 -AAAAAG
1 AAAAAAG
24841 AAAAA
1 AAAAA
24846 GGGGGGTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
6 11 0.34
7 15 0.47
8 6 0.19
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:24816 original size:13 final size:12
Alignment explanation
Indices: 24795--24846 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
24785 ATTATGCTTG
*
24795 AAGAAAAAAAAGC
1 AAGAAAAAAAA-A
24808 AA-AAAAAAAAA
1 AAGAAAAAAAAA
24819 AAGAAAAGAAAAA
1 AAGAAAA-AAAAA
*
24832 AAGAAAAAGAAA
1 AAGAAAAAAAAA
24844 AAG
1 AAG
24847 GGGGGTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
11 2 0.06
12 19 0.54
13 14 0.40
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:24817 original size:14 final size:13
Alignment explanation
Indices: 24798--24845 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
24788 ATGCTTGAAG
24798 AAAAAAAAGCAAAAA
1 AAAAAAAAG--AAAA
24813 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
*
24826 GAAAAAAAGAAAA
1 AAAAAAAAGAAAA
*
24839 AGAAAAA
1 AAAAAAA
24846 GGGGGGTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 21 0.70
15 9 0.30
ACGTcount: A:0.88, C:0.02, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:24830 original size:19 final size:20
Alignment explanation
Indices: 24798--24844 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
24788 ATGCTTGAAG
24798 AAAA-AAAAGCAAAAAAAAA
1 AAAAGAAAAGCAAAAAAAAA
*
24817 AAAAGAAAAG-AAAAAAAGA
1 AAAAGAAAAGCAAAAAAAAA
24836 AAAAGAAAA
1 AAAAGAAAA
24845 AGGGGGGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.87, C:0.02, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAGCAAAAAAAAA
Found at i:25192 original size:16 final size:17
Alignment explanation
Indices: 25173--25218 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
25163 CTATTTCAAG
*
25173 TTCAATTTATT-GGAGA
1 TTCAATTTATTGGGAAA
25189 TTCAATTTATTTTGGGAAA
1 TTCAATTTA--TTGGGAAA
25208 TTCAATTTATT
1 TTCAATTTATT
25219 CTTCTATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 9 0.35
17 2 0.08
18 2 0.08
19 13 0.50
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (17 bp):
TTCAATTTATTGGGAAA
Found at i:26112 original size:82 final size:83
Alignment explanation
Indices: 25996--26448 Score: 745
Period size: 83 Copynumber: 5.5 Consensus size: 83
25986 GATTGTGTTC
25996 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CAATCATTGAGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAGTT
26060 TAGAAGATGAATTTGTCA
66 TAGAAGATGAATTTGTCA
26078 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAA-CAATCATTGAGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAGTT
*
26142 TAGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGTCA
*
26160 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAACCAATCATTGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCAATCATTGAGT
** *
26224 TCGGAAGATGAATGTGTCA
65 TTAGAAGATGAATTTGTCA
*
26243 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGGCAGAACCAATCATTGAGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAGTT
*
26308 TAGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGTCA
*
26326 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGA-AGAACCAATCATTGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAACCAATCATTGAGT
** *
26390 TCGGAAGATGAATGTGTTC-
65 TTAGAAGATGAATTTG-TCA
26409 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
26449 ATTCAGTAGG
Statistics
Matches: 349, Mismatches: 17, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
82 131 0.38
83 213 0.61
84 5 0.01
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACCAATCATTGAGTT
TAGAAGATGAATTTGTCA
Found at i:27405 original size:116 final size:115
Alignment explanation
Indices: 27192--27483 Score: 495
Period size: 116 Copynumber: 2.6 Consensus size: 115
27182 TCGAATCCAC
*
27192 TTGATGGATCA-TTTCTTCCAGAGAAAGTTCATAATGAGAAGAACT-CT-TCTGAAGAAGGAAGA
1 TTGATGGATCAGTTT-TTCCAGAGAAAGTTCATAATGAGAAGAACTCCTCTATGAAGAAGGAAGA
27254 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
65 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
27305 TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCCTCATATGAAGAAGGAAGA
1 TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCCTC-TATGAAGAAGGAAGA
*
27370 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACTTGAATCCATCAT
65 AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
* *
27421 TTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTA--AAGAAGGAAGAA
1 TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCCTCTATGAAGAAGGAAGAA
27484 TTTGTTCAAA
Statistics
Matches: 171, Mismatches: 4, Indels: 8
0.93 0.02 0.04
Matches are distributed among these distances:
113 53 0.31
114 5 0.03
115 2 0.01
116 111 0.65
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (115 bp):
TTGATGGATCAGTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCCTCTATGAAGAAGGAAGAA
GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATCAT
Found at i:27519 original size:94 final size:94
Alignment explanation
Indices: 27385--27563 Score: 261
Period size: 94 Copynumber: 1.9 Consensus size: 94
27375 TTCATAATGA
* * * * **
27385 GAAGAATTTGTTCAACCTTTTACTTGAATCCATCATTTGATGGATCAGCTTTTCCAG-AGAAAGT
1 GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGCAGAAAGT
27449 TCATAATGAGAAGAACTCATCTAAAGAAG
66 TCATAATGAGAAGAACTCATCTAAAGAAG
* * *
27478 GAAGAATTTGTTCAAACCTTTTACATGAATCCATTACTTGATGGAGCATCATCCCCAGCGGAAAG
1 GAAGAATTTGTTC-AACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGCAGAAAG
27543 TTCATAATGAGAAGAACTCAT
65 TTCATAATGAGAAGAACTCAT
27564 ATGAAAAAGA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
93 13 0.17
94 36 0.48
95 26 0.35
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (94 bp):
GAAGAATTTGTTCAACCTTTTACATGAATCCATCACTTGATGGAGCAGCATCCCCAGCAGAAAGT
TCATAATGAGAAGAACTCATCTAAAGAAG
Found at i:27906 original size:116 final size:117
Alignment explanation
Indices: 27538--27964 Score: 548
Period size: 114 Copynumber: 3.7 Consensus size: 117
27528 ATCCCCAGCG
** * *
27538 GAAAGTTCATAATGAGAAGAACTCAT-ATGAAAAAGAAAGAAGAAGAAGTTCATAATGAGGAGAA
1 GAAAGTTCATAATGAGAAGAACTCATCAT-ATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
**
27602 CTTGTTCAATTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-
65 CTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGA
* * *
27654 GTAGAGTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAAAAGAAGTTCATAAT---AAGAA
1 G-AAAGTTCATAATGAGAAGAACTCATCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
27716 CTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGA
65 CTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGA
* *
27769 -AAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
1 GAA-AGTTCATAATGAGAAGAACTCATCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
* * * * * * *
27833 TTTGTTCAACCTTTT-ATCTGAATTCATCACTGGATGGATTATTTC-TT-CCAGA
65 CTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCA--ACATTGCCAGA
* * *
27885 GAAAGTTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAAC
1 GAAAGTTCATAATGAGAAGAACTCATCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
*
27950 TTGTTCAACTTTTTG
66 TTGTTCAACCTTTTG
27965 CATAATTCTA
Statistics
Matches: 275, Mismatches: 25, Indels: 21
0.86 0.08 0.07
Matches are distributed among these distances:
113 1 0.00
114 105 0.38
116 97 0.35
117 69 0.25
118 3 0.01
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (117 bp):
GAAAGTTCATAATGAGAAGAACTCATCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAAC
TTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGA
Found at i:27978 original size:116 final size:117
Alignment explanation
Indices: 27478--27978 Score: 496
Period size: 114 Copynumber: 4.3 Consensus size: 117
27468 TCTAAAGAAG
* * * * * * * ** *
27478 GAAGAATTTGTTCAAACC-TTTTACATGAATCCATTACTTGATGGAGCATCATCCCCAGCGGAAA
1 GAAGAACTTGTTC-AACCTTTTTGCTTGAATTCATCACTTGATGGATCAACATTGCCAG-AGAAA
*
27542 GTTCATAATGAGAAGAA---CTCATATGAAAAAGAAAGAAGAAGAAGTTCATAATGA
64 GTTCATAATGAGAAGAACTCCTCATATGAAGAAG--A-AAGAAGAAGTTCATAATGA
* * * * *
27596 GGAGAACTTGTTCAA-TTTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAG-GTAGA
1 GAAGAACTTGTTCAACCTTTTT-GCTTGAATTCATCACTTGATGGATCAACATTGCCAGAG-AAA
* *
27659 GTTCATAATGAGAAGAACTCATCATCTGAAGAAGGAAA-AAGAAGTTCATAAT--
64 GTTCATAATGAGAAGAACTCCTCATATGAAGAA-GAAAGAAGAAGTTCATAATGA
* * *
27711 -AAGAACTTGTTCAACCTTTTGGTTTGAATTCATCATTTGATGGATCAACATTGCCAGA-AAGAG
1 GAAGAACTTGTTCAACCTTTTTGCTTGAATTCATCACTTGATGGATCAACATTGCCAGAGAA-AG
* * *
27774 TTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
65 TTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATGA
* * * *
27827 GAAGAATTTGTTCAACCTTTTAT-C-TGAATTCATCACTGGATGGATTATTTC-TT-CCAGAGAA
1 GAAGAACTTGTTCAACCTTTT-TGCTTGAATTCATCACTTGATGGATCA--ACATTGCCAGAGAA
*
27888 AGTTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATAA
63 AGTTCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATGA
*
27943 GAAGAACTTGTTCAA-CTTTTTGCAT-AATTCTATCAC
1 GAAGAACTTGTTCAACCTTTTTGCTTGAATTC-ATCAC
27979 AGAAGGAGAT
Statistics
Matches: 327, Mismatches: 35, Indels: 44
0.81 0.09 0.11
Matches are distributed among these distances:
113 4 0.01
114 97 0.30
115 15 0.05
116 97 0.30
117 62 0.19
118 40 0.12
119 1 0.00
120 10 0.03
121 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (117 bp):
GAAGAACTTGTTCAACCTTTTTGCTTGAATTCATCACTTGATGGATCAACATTGCCAGAGAAAGT
TCATAATGAGAAGAACTCCTCATATGAAGAAGAAAGAAGAAGTTCATAATGA
Found at i:28203 original size:3 final size:3
Alignment explanation
Indices: 28190--28260 Score: 106
Period size: 3 Copynumber: 23.7 Consensus size: 3
28180 TTTTTATCCA
*
28190 TAT TTT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
28238 TAT TAT CAT CAT CAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
28261 ATAAATATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:28275 original size:14 final size:14
Alignment explanation
Indices: 28256--28296 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 14
28246 TCATCATTAT
28256 TATTAATAAATATA
1 TATTAATAAATATA
28270 TATTAAATAAATATA
1 TATT-AATAAATATA
*
28285 TATAAATAAATA
1 TATTAATAAATA
28297 ATTACAGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TATTAATAAATATA
Found at i:28280 original size:15 final size:15
Alignment explanation
Indices: 28256--28296 Score: 68
Period size: 14 Copynumber: 2.9 Consensus size: 15
28246 TCATCATTAT
28256 TATT-AATAAATATA
1 TATTAAATAAATATA
28270 TATTAAATAAATATA
1 TATTAAATAAATATA
28285 TA-TAAATAAATA
1 TATTAAATAAATA
28297 ATTACAGACC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TATTAAATAAATATA
Found at i:28715 original size:20 final size:20
Alignment explanation
Indices: 28690--28732 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
28680 CTACCAACCT
*
28690 GAAAAAAAAAACCAGAGACA
1 GAAAAAAAAAAACAGAGACA
*
28710 GAAAAAAAAAAAGAGAGACA
1 GAAAAAAAAAAACAGAGACA
28730 GAA
1 GAA
28733 CCGGAGAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.72, C:0.09, G:0.19, T:0.00
Consensus pattern (20 bp):
GAAAAAAAAAAACAGAGACA
Found at i:28716 original size:16 final size:16
Alignment explanation
Indices: 28690--28765 Score: 64
Period size: 16 Copynumber: 4.8 Consensus size: 16
28680 CTACCAACCT
28690 GAAA-AAAAAAACCAGA
1 GAAAGAAAAAAA-CAGA
* * *
28706 GACAGAAAAAAAAAAA
1 GAAAGAAAAAAACAGA
* * * * *
28722 GAGAGACAGAACCGGA
1 GAAAGAAAAAAACAGA
28738 GAAAGAAAAAAACAGA
1 GAAAGAAAAAAACAGA
28754 GAAAGAAAAAAA
1 GAAAGAAAAAAA
28766 AACTATTAAA
Statistics
Matches: 44, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
16 37 0.84
17 7 0.16
ACGTcount: A:0.71, C:0.09, G:0.20, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAAAACAGA
Found at i:31542 original size:21 final size:21
Alignment explanation
Indices: 31516--31570 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
31506 GCACCGGAAC
*
31516 GGTTCCGATGAACCATAGACA
1 GGTTCCGATGAACCACAGACA
31537 GGTTCCGATGAACCACAGACA
1 GGTTCCGATGAACCACAGACA
* *
31558 GATTCCGACGAAC
1 GGTTCCGATGAAC
31571 TTTTGGATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (21 bp):
GGTTCCGATGAACCACAGACA
Found at i:32051 original size:31 final size:31
Alignment explanation
Indices: 32013--32074 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
32003 AACTCTTGAA
32013 AAATAGGTAATTGATGCATTCTAATATATTT
1 AAATAGGTAATTGATGCATTCTAATATATTT
32044 AAATAGGTAATTGATGCATTCTAATATATTT
1 AAATAGGTAATTGATGCATTCTAATATATTT
32075 CTCAATTGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (31 bp):
AAATAGGTAATTGATGCATTCTAATATATTT
Found at i:35532 original size:21 final size:21
Alignment explanation
Indices: 35507--35551 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 21
35497 AAACAAAGTA
35507 AAAGTAGGACTCTC-ATCGATT
1 AAAGTAGGACTCTCAAT-GATT
35528 AAAGTAGGACTCTCAATGATT
1 AAAGTAGGACTCTCAATGATT
35549 AAA
1 AAA
35552 AGATCGCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.27
Consensus pattern (21 bp):
AAAGTAGGACTCTCAATGATT
Found at i:38938 original size:22 final size:20
Alignment explanation
Indices: 38912--38965 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
38902 AATTTTTATT
*
38912 TATTTTTAAAATTTCAAAAG
1 TATTTTTAAAATTTCAAAAA
* *
38932 TATATTTTATCAATTTTAAAAA
1 TAT-TTTTA-AAATTTCAAAAA
38954 TATTTTTAAAAT
1 TATTTTTAAAAT
38966 ACAATTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 6 0.21
21 10 0.36
22 12 0.43
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (20 bp):
TATTTTTAAAATTTCAAAAA
Found at i:39734 original size:20 final size:21
Alignment explanation
Indices: 39696--39735 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
39686 TCGAAAATTA
*
39696 GATAATAAAATTAACATTTTT
1 GATAATAAAAATAACATTTTT
*
39717 GATAA-AAAAATAATATTTT
1 GATAATAAAAATAACATTTT
39736 AAATAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (21 bp):
GATAATAAAAATAACATTTTT
Found at i:39741 original size:12 final size:12
Alignment explanation
Indices: 39724--39748 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39714 TTTGATAAAA
39724 AAATAATATTTT
1 AAATAATATTTT
39736 AAATAATATTTT
1 AAATAATATTTT
39748 A
1 A
39749 CCAAAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:42393 original size:54 final size:54
Alignment explanation
Indices: 42311--42474 Score: 274
Period size: 54 Copynumber: 3.0 Consensus size: 54
42301 ATCGATCCAT
* *
42311 GATATCAATGATACATATATGATAGAAAAGTTGTACAGAATTTACCTTAAAGTA
1 GATATCAATGATACATATATGATAGAAAAGTTGTACATAATTTGCCTTAAAGTA
*
42365 GATATCAATGATGCATATATGATAGAAAAGTTGTACATAATTTGCCTTAAAGTA
1 GATATCAATGATACATATATGATAGAAAAGTTGTACATAATTTGCCTTAAAGTA
* * *
42419 GATATCAATGATACATATATGATAGAAAACTTATACATAATTTGCCTCAAAGTA
1 GATATCAATGATACATATATGATAGAAAAGTTGTACATAATTTGCCTTAAAGTA
42473 GA
1 GA
42475 AATAGTTCTA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 103 1.00
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (54 bp):
GATATCAATGATACATATATGATAGAAAAGTTGTACATAATTTGCCTTAAAGTA
Found at i:44268 original size:16 final size:16
Alignment explanation
Indices: 44247--44296 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
44237 TTACCCGACC
*
44247 TGTTTTCAATCTGACA
1 TGTTTTCAACCTGACA
*
44263 TGTTTTCAACCTGACC
1 TGTTTTCAACCTGACA
44279 TGTTTT-AACCTGACA
1 TGTTTTCAACCTGACA
44294 TGT
1 TGT
44297 AAATGATCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
15 11 0.35
16 20 0.65
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (16 bp):
TGTTTTCAACCTGACA
Found at i:44585 original size:23 final size:24
Alignment explanation
Indices: 44551--44600 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
44541 ATGCAAAGGA
44551 AAATTAATATAGCTTAATTTATAT
1 AAATTAATATAGCTTAATTTATAT
*
44575 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGCTTAATTTATAT
44598 AAA
1 AAA
44601 GAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (24 bp):
AAATTAATATAGCTTAATTTATAT
Found at i:45117 original size:18 final size:17
Alignment explanation
Indices: 45085--45118 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
45075 TTACTTCTAA
*
45085 ATTCTAAATTTTCCTAT
1 ATTCTAAAATTTCCTAT
45102 ATTCTCAAAATTTCCTA
1 ATTCT-AAAATTTCCTA
45119 ATTTCCCAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTCTAAAATTTCCTAT
Found at i:45652 original size:2 final size:2
Alignment explanation
Indices: 45645--45669 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
45635 TATGTTTAAT
45645 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
45670 TATTCAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45770 original size:29 final size:30
Alignment explanation
Indices: 45736--45813 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 30
45726 TTTTGATTTT
45736 ATTTGAGAATTTAGAGGGAAATT-A-GGAA
1 ATTTGAGAATTTAGAGGGAAATTAAGGGAA
*
45764 ATTTTGAGAA--TATAGGGAAATTAGAGGGAA
1 A-TTTGAGAATTTAGAGGGAAATTA-AGGGAA
45794 A-TTGAGAAATTTAGAGGGAA
1 ATTTGAG-AATTTAGAGGGAA
45814 TAGAAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
27 11 0.27
28 6 0.15
29 11 0.27
30 5 0.12
31 8 0.20
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.27
Consensus pattern (30 bp):
ATTTGAGAATTTAGAGGGAAATTAAGGGAA
Found at i:45809 original size:20 final size:20
Alignment explanation
Indices: 45738--45813 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
45728 TTGATTTTAT
45738 TTGAG-AATTTAGAGGGAAA
1 TTGAGAAATTTAGAGGGAAA
*
45757 TT-AGGAAATTTTGA--GAATA
1 TTGA-GAAATTTAGAGGGAA-A
* *
45776 TAGGGAAA-TTAGAGGGAAA
1 TTGAGAAATTTAGAGGGAAA
45795 TTGAGAAATTTAGAGGGAA
1 TTGAGAAATTTAGAGGGAA
45814 TAGAAAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
18 8 0.18
19 16 0.36
20 20 0.45
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.26
Consensus pattern (20 bp):
TTGAGAAATTTAGAGGGAAA
Found at i:46230 original size:2 final size:2
Alignment explanation
Indices: 46157--46221 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
46147 ACACACACAC
*
46157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
46199 AC AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
46222 AACTATATAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:46405 original size:15 final size:15
Alignment explanation
Indices: 46385--46420 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
46375 CTATATATTT
46385 TATATAGTTTATACA
1 TATATAGTTTATACA
* *
46400 TATATAGTTTTTATA
1 TATATAGTTTATACA
46415 TATATA
1 TATATA
46421 TATACACACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:46429 original size:2 final size:2
Alignment explanation
Indices: 46424--46448 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46414 ATATATATAT
46424 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
46449 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:46453 original size:2 final size:2
Alignment explanation
Indices: 46448--46524 Score: 145
Period size: 2 Copynumber: 38.0 Consensus size: 2
46438 ACACACACAC
46448 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
46490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
46525 TAATATAAAT
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 72 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46530 original size:6 final size:6
Alignment explanation
Indices: 46448--46535 Score: 50
Period size: 6 Copynumber: 14.5 Consensus size: 6
46438 ACACACACAC
* * * * * * * *
46448 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
* * * * *
46496 ATATAT ATATAT ATATAT ATATACT ATATTA ATATAA ATA
1 ATATAA ATATAA ATATAA ATATA-A ATATAA ATATAA ATA
46536 ATATTTTATA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
6 73 0.94
7 5 0.06
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATAA
Found at i:46562 original size:18 final size:18
Alignment explanation
Indices: 46539--46581 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
46529 ATAAATAATA
46539 TTTTATAAACTATATACT
1 TTTTATAAACTATATACT
***
46557 TTTTATAGTTTATATACT
1 TTTTATAAACTATATACT
46575 TTTTATA
1 TTTTATA
46582 GTTTATACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTTATAAACTATATACT
Found at i:46582 original size:18 final size:18
Alignment explanation
Indices: 46549--46588 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
46539 TTTTATAAAC
46549 TATATACTTTTTATAGTT
1 TATATACTTTTTATAGTT
46567 TATATACTTTTTATAGTT
1 TATATACTTTTTATAGTT
46585 TATA
1 TATA
46589 CATATATAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (18 bp):
TATATACTTTTTATAGTT
Found at i:46610 original size:13 final size:13
Alignment explanation
Indices: 46578--46813 Score: 76
Period size: 15 Copynumber: 17.2 Consensus size: 13
46568 ATATACTTTT
46578 TATAGTTTATACATA
1 TATAGTTTAT--ATA
46593 TATAGTTTATATA
1 TATAGTTTATATA
*
46606 CATAGTTTATATA
1 TATAGTTTATATA
* *
46619 TATAGTTCACATAAA
1 TATAGTT--TATATA
* *
46634 CATAATTTATATA
1 TATAGTTTATATA
46647 TATAGCTTATAATAATTA
1 TATAG-TT-T-AT-A-TA
46665 TATAGTTTATA-A
1 TATAGTTTATATA
** *
46677 TATA-AATATAGTT
1 TATAGTTTATA-TA
*
46690 TATAATTTTATATA
1 TAT-AGTTTATATA
* *
46704 CATAG-TT-GATA
1 TATAGTTTATATA
* *
46715 TATAGTTCACATAAA
1 TATAGTT--TATATA
*
46730 TATA-ATT-TATA
1 TATAGTTTATATA
46741 TATAGTTTATAACAATTA
1 TATAGTTTAT----A-TA
46759 TATAGTTTATAATA
1 TATAGTTTAT-ATA
46773 TAAATAGTTTATATA
1 T--ATAGTTTATATA
*
46788 TA-ATTTTATAT-
1 TATAGTTTATATA
*
46799 TATA-TATATATA
1 TATAGTTTATATA
46811 TAT
1 TAT
46814 TATATTTTTT
Statistics
Matches: 166, Mismatches: 29, Indels: 55
0.66 0.12 0.22
Matches are distributed among these distances:
11 26 0.16
12 22 0.13
13 34 0.20
14 11 0.07
15 38 0.23
16 12 0.07
17 4 0.02
18 19 0.11
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:46636 original size:28 final size:26
Alignment explanation
Indices: 46579--46651 Score: 83
Period size: 28 Copynumber: 2.7 Consensus size: 26
46569 TATACTTTTT
* *
46579 ATAGTTTATACATATATAGTTTATATAC
1 ATAGTTTAT--ATATATAGTTCATAAAC
46607 ATAGTTTATATATATAGTTCACATAAAC
1 ATAGTTTATATATATAGTT--CATAAAC
*
46635 ATAATTTATATATATAG
1 ATAGTTTATATATATAG
46652 CTTATAATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
26 10 0.25
28 30 0.75
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (26 bp):
ATAGTTTATATATATAGTTCATAAAC
Found at i:46658 original size:26 final size:25
Alignment explanation
Indices: 46590--46658 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 25
46580 TAGTTTATAC
* *
46590 ATATATAGTTTATATACATAGTTTAT
1 ATATATAG-TTATAAACATAATTTAT
46616 ATATATAGTTCACATAAACATAATTTAT
1 ATATATAGTT---ATAAACATAATTTAT
46644 ATATATAGCTTATAA
1 ATATATAG-TTATAA
46659 TAATTATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
25 2 0.05
26 12 0.32
28 21 0.57
29 2 0.05
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (25 bp):
ATATATAGTTATAAACATAATTTAT
Found at i:46685 original size:18 final size:18
Alignment explanation
Indices: 46641--46789 Score: 96
Period size: 18 Copynumber: 8.2 Consensus size: 18
46631 AAACATAATT
*
46641 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
46659 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
*
46677 TATAAATATAGTTTATAA
1 TATATATATAGTTTATAA
* *
46695 TTTTATATACATAGTTGAT-A
1 ---TATATATATAGTTTATAA
* **
46715 TATAGTTCACATA-AATATAA
1 TATA--T-ATATAGTTTATAA
*
46735 TTTATATATAGTTTATAA
1 TATATATATAGTTTATAA
*
46753 CA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
46771 TATA-A-ATAGTTTAT-A
1 TATATATATAGTTTATAA
46786 TATA
1 TATA
46790 ATTTTATATT
Statistics
Matches: 104, Mismatches: 15, Indels: 27
0.71 0.10 0.18
Matches are distributed among these distances:
15 5 0.05
16 9 0.09
17 11 0.11
18 51 0.49
19 5 0.05
20 10 0.10
21 13 0.12
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:46790 original size:96 final size:100
Alignment explanation
Indices: 46579--46798 Score: 301
Period size: 94 Copynumber: 2.2 Consensus size: 100
46569 TATACTTTTT
* *
46579 ATAGTTTATACATATATAGTTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTAT
1 ATAGTTTAT--ATATA-ATTTTATATACATAGTTTAGATATATAGTTCACATAAACATAATTTAT
*
46644 ATATATAGCTTATAATAATTATATAGTTTATAATATAA
63 ATATATAGCTTATAACAATTATATAGTTTATAATATAA
* *
46682 ATA---TAGTTTATAATTTTATATACATAG-TT-GATATATAGTTCACATAAATATAA-TT-TAT
1 ATAGTTTA-TATATAATTTTATATACATAGTTTAGATATATAGTTCACATAAACATAATTTATAT
*
46740 ATATAGTTTATAACAATTATATAGTTTATAATATAA
65 ATATAGCTTATAACAATTATATAGTTTATAATATAA
46776 ATAGTTTATATATAATTTTATAT
1 ATAGTTTATATATAATTTTATAT
46799 TATATATATA
Statistics
Matches: 106, Mismatches: 7, Indels: 15
0.83 0.05 0.12
Matches are distributed among these distances:
94 40 0.38
95 2 0.02
96 36 0.34
97 4 0.04
98 14 0.13
99 4 0.04
100 2 0.02
101 1 0.01
103 3 0.03
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (100 bp):
ATAGTTTATATATAATTTTATATACATAGTTTAGATATATAGTTCACATAAACATAATTTATATA
TATAGCTTATAACAATTATATAGTTTATAATATAA
Found at i:46812 original size:96 final size:96
Alignment explanation
Indices: 46598--46813 Score: 289
Period size: 96 Copynumber: 2.2 Consensus size: 96
46588 ACATATATAG
*
46598 TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
1 TTTATATACATAG--TATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAACAAT
*
46663 TATATAGTTTATAATATAAATATAGTTTATAAT
64 TATATAGTTTATAATATAAATATAGTATATAAT
* *
46696 TTTATATACATAGT-TGATATATAGTTCACATAAATATAA-TT-TATATATAGTTTATAACAATT
1 TTTATATACATAGTAT-ATATATAGTTCACATAAACATAATTTATATATATAGCTTATAACAATT
46758 ATATAGTTTATAATATAAATAGTTTA-TATATAAT
65 ATATAGTTTATAATATAAATA---TAGTATATAAT
*
46792 TTTATATTATATA-TATATATAT
1 TTTATA-TACATAGTATATATAT
46814 TATATTTTTT
Statistics
Matches: 107, Mismatches: 5, Indels: 14
0.85 0.04 0.11
Matches are distributed among these distances:
94 40 0.37
95 3 0.03
96 43 0.40
97 8 0.07
98 13 0.12
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (96 bp):
TTTATATACATAGTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAACAATTA
TATAGTTTATAATATAAATATAGTATATAAT
Found at i:46817 original size:28 final size:29
Alignment explanation
Indices: 46755--46822 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 29
46745 GTTTATAACA
* *
46755 ATTATATAGTTTATAATATAAATAGTTTAT
1 ATTATA-ATTTTATAATATAAATAGTATAT
* *
46785 A-TATAATTTTATATTATATATA-TATAT
1 ATTATAATTTTATAATATAAATAGTATAT
*
46812 ATTATATTTTT
1 ATTATAATTTT
46823 TCAATTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
27 5 0.16
28 22 0.69
29 4 0.12
30 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (29 bp):
ATTATAATTTTATAATATAAATAGTATAT
Found at i:49234 original size:40 final size:40
Alignment explanation
Indices: 49174--49252 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
49164 TGCAATTTTT
49174 TTATCTGGTATAAAACCCCATTGAATTCACATTCACATAA
1 TTATCTGGTATAAAACCCCATTGAATTCACATTCACATAA
* *
49214 TTATTTGGTATAATACCCCATTGAATTCACATTCACATA
1 TTATCTGGTATAAAACCCCATTGAATTCACATTCACATA
49253 CTGTTATTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (40 bp):
TTATCTGGTATAAAACCCCATTGAATTCACATTCACATAA
Found at i:58474 original size:34 final size:35
Alignment explanation
Indices: 58424--58502 Score: 124
Period size: 34 Copynumber: 2.3 Consensus size: 35
58414 AACACAATCA
*
58424 TCAATTACATTCTAAACCCCAAA-TCCAAAATACT
1 TCAATTACATTATAAACCCCAAATTCCAAAATACT
* *
58458 TCAATTATATTATAAACCTCAAATTCCAAAATACT
1 TCAATTACATTATAAACCCCAAATTCCAAAATACT
58493 TCAATTACAT
1 TCAATTACAT
58503 GTCCAACCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 20 0.50
35 20 0.50
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (35 bp):
TCAATTACATTATAAACCCCAAATTCCAAAATACT
Found at i:58517 original size:35 final size:34
Alignment explanation
Indices: 58424--58518 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 34
58414 AACACAATCA
*
58424 TCAATTACATTCTAAACCCCAAA-TCCAAAATACT
1 TCAATTACATTC-AAACCCTAAATTCCAAAATACT
* *
58458 TCAATTATATT-ATAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCA-AACCCT-AAATTCCAAAATACT
*
58493 TCAATTACATGTCCAACCCTAAATTC
1 TCAATTACAT-TCAAACCCTAAATTC
58519 ATAATCCATT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
32 1 0.02
33 4 0.08
34 13 0.26
35 26 0.52
36 6 0.12
ACGTcount: A:0.42, C:0.26, G:0.01, T:0.31
Consensus pattern (34 bp):
TCAATTACATTCAAACCCTAAATTCCAAAATACT
Found at i:59188 original size:148 final size:148
Alignment explanation
Indices: 58995--59287 Score: 460
Period size: 148 Copynumber: 2.0 Consensus size: 148
58985 AAACTATTTA
* * * *
58995 AATTAGAATCAAATAATATTATAGTATTATAAATATTTATGATTAAATTTAAACATAAACTCAAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* *
59060 AATTTAATTCAATTTGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCAAGTCAACT
66 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCAAGTCAACT
59125 ATTTTATAAACTGAACTG
131 ATTTTATAAACTGAACTG
*
59143 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAAGAGAAACTCAAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
* * ** * *
59208 AATTCAATTCAATTCGATTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTTGATTCAAGT
66 AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCAAGTCAACT
*
59273 ATTTTATAAATTGAA
131 ATTTTATAAACTGAA
59288 TTAAATATTT
Statistics
Matches: 131, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
148 131 1.00
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (148 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCAAA
AATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAATTCAAGTCAACT
ATTTTATAAACTGAACTG
Found at i:68029 original size:21 final size:18
Alignment explanation
Indices: 67992--68030 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 18
67982 TTGTAAGATA
67992 ATTTTTTTAATATATTAT
1 ATTTTTTTAATATATTAT
68010 ATTTATTTTATATATGATTAT
1 ATTT-TTTTA-ATAT-ATTAT
68031 TTGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
20 4 0.22
21 5 0.28
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTTTTTTAATATATTAT
Found at i:69075 original size:18 final size:18
Alignment explanation
Indices: 69048--69086 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
69038 TTAAATGAAA
69048 GGCGCAGATCACCTTACT
1 GGCGCAGATCACCTTACT
*
69066 GGCGCGGATCACCTTACT
1 GGCGCAGATCACCTTACT
69084 GGC
1 GGC
69087 CCGTTTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.33, G:0.28, T:0.21
Consensus pattern (18 bp):
GGCGCAGATCACCTTACT
Found at i:70710 original size:23 final size:23
Alignment explanation
Indices: 70684--70796 Score: 129
Period size: 23 Copynumber: 5.0 Consensus size: 23
70674 GAGTCGAGGG
70684 TTCTATGCGGTCCTTCGGGACAA
1 TTCTATGCGGTCCTTCGGGACAA
70707 TTCTATGCGGTCCTTCGGGACAA
1 TTCTATGCGGTCCTTCGGGACAA
* * * *
70730 TTCTACGTGGTCCTTCCGG-CAT
1 TTCTATGCGGTCCTTCGGGACAA
* *
70752 TTCTACGCAGTCCTTCGGGACAA
1 TTCTATGCGGTCCTTCGGGACAA
* ** *
70775 TACTATATGGTCTTTCGGGACA
1 TTCTATGCGGTCCTTCGGGACA
70797 TTTTTATGTG
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
22 18 0.24
23 57 0.76
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.32
Consensus pattern (23 bp):
TTCTATGCGGTCCTTCGGGACAA
Found at i:70786 original size:45 final size:46
Alignment explanation
Indices: 70692--70796 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 46
70682 GGTTCTATGC
* * * * *
70692 GGTCCTTCGGGACAATTCTATGCGGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCCGGACAATTCTACGCAGTCCTTCGGGACAATACTACAT
* *
70738 GGTCCTTCCGG-CATTTCTACGCAGTCCTTCGGGACAATACTATAT
1 GGTCCTTCCGGACAATTCTACGCAGTCCTTCGGGACAATACTACAT
* *
70783 GGTCTTTCGGGACA
1 GGTCCTTCCGGACA
70797 TTTTTATGTG
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
45 37 0.76
46 12 0.24
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (46 bp):
GGTCCTTCCGGACAATTCTACGCAGTCCTTCGGGACAATACTACAT
Found at i:70977 original size:30 final size:31
Alignment explanation
Indices: 70942--71000 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
70932 GCATAATGTG
** *
70942 ATATGTTCTTGTTGGTTAAAT-TATGATGAT
1 ATATGTTCTTGACGATTAAATATATGATGAT
70972 ATATGTTCTTGACGATTAAATATATGATG
1 ATATGTTCTTGACGATTAAATATATGATG
71001 TTTCCTATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.46
Consensus pattern (31 bp):
ATATGTTCTTGACGATTAAATATATGATGAT
Found at i:77247 original size:24 final size:24
Alignment explanation
Indices: 77220--77276 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
77210 ATGAGGTGAA
77220 AAACAAG-CTAAGAAATAAAGTTAT
1 AAACAAGTC-AAGAAATAAAGTTAT
* * * *
77244 AAACGAGTCGATAAATAAATTTAT
1 AAACAAGTCAAGAAATAAAGTTAT
77268 AAACAAGTC
1 AAACAAGTC
77277 GATAATAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.54, C:0.11, G:0.12, T:0.23
Consensus pattern (24 bp):
AAACAAGTCAAGAAATAAAGTTAT
Found at i:77277 original size:24 final size:24
Alignment explanation
Indices: 77232--77281 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
77222 ACAAGCTAAG
*
77232 AAATAAAGTTATAAACGAGTCGAT
1 AAATAAAGTTATAAACAAGTCGAT
*
77256 AAATAAATTTATAAACAAGTCGAT
1 AAATAAAGTTATAAACAAGTCGAT
77280 AA
1 AA
77282 TAACTTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.08, G:0.12, T:0.26
Consensus pattern (24 bp):
AAATAAAGTTATAAACAAGTCGAT
Done.