Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005045.1 Hibiscus syriacus cultivar Beakdansim tig00011327_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: 53558
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:257 original size:29 final size:29
Alignment explanation
Indices: 183--263 Score: 112
Period size: 27 Copynumber: 2.8 Consensus size: 29
173 CAAACTAAAT
183 TGATGTCATTACTTACATCATTTAAGTAA
1 TGATGTCATTACTTACATCATTTAAGTAA
* *
212 AGA--TCATTACTTACATCATTTAATTAA
1 TGATGTCATTACTTACATCATTTAAGTAA
*
239 TGATGTCATTGCTTACATCAATTTA
1 TGATGTCATTACTTACATC-ATTTA
264 GTTAGGTGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
27 25 0.56
29 15 0.33
30 5 0.11
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.42
Consensus pattern (29 bp):
TGATGTCATTACTTACATCATTTAAGTAA
Found at i:1584 original size:20 final size:18
Alignment explanation
Indices: 1549--1603 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 18
1539 ATTTGTTTAT
*
1549 TATTA-TTATTAGTATTA
1 TATTATTTATTATTATTA
*
1566 TTTTATTTATACTATTATTA
1 TATTATTTAT--TATTATTA
1586 TATTATTTATTATTATTA
1 TATTATTTATTATTATTA
1604 AAAAAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.12
18 12 0.38
20 16 0.50
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
TATTATTTATTATTATTA
Found at i:1619 original size:3 final size:3
Alignment explanation
Indices: 1545--1603 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
1535 ATCAATTTGT
* *
1545 TTA TTA TTA TTA TTA GTA TTA TT- TTA TT- TATA CTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
1588 TTA TTTA TTA TTA TTA
1 TTA -TTA TTA TTA TTA
1604 AAAAAAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
2 5 0.11
3 39 0.83
4 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3087 original size:25 final size:23
Alignment explanation
Indices: 3042--3105 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 23
3032 TAGTTTTAAT
* * * * *
3042 TTTATTTATTTAATCATTGTTTA
1 TTTATATATTTAATTATTATATG
3065 TTTATAT-TTTAATT-TTATATG
1 TTTATATATTTAATTATTATATG
3086 TTTATATATTTAATTATTAT
1 TTTATATATTTAATTATTAT
3106 TATTATTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
21 11 0.32
22 13 0.38
23 10 0.29
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (23 bp):
TTTATATATTTAATTATTATATG
Found at i:3106 original size:3 final size:3
Alignment explanation
Indices: 3098--3138 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
3088 TATATATTTA
3098 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
3139 AAAAATATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3436 original size:134 final size:136
Alignment explanation
Indices: 3246--3489 Score: 399
Period size: 134 Copynumber: 1.8 Consensus size: 136
3236 TAATCATATT
3246 TTAATATTTATTTATTTTTTAATTTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTTCTTTTCT
1 TTAATATTTATTTATTTTTTAATTTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTTCTTTTCT
*
3311 GATA-TTCTTAAAT-AATAAATATCCTATTTTTATAAAT-TATATATTTTAATTATTTTAGAGAA
66 GATATTTC-TAAATAAATAAATATCCTATTTATA-AAATATATATATTTTAATTATTTTAGAGAA
3373 ATGTTTTA
129 ATGTTTTA
3381 TTAATATTTATTTA-TTTTTAATATTAAGAAAT-GGCTGTCTTAAAGCACCTAGAAGTTCTTTTC
1 TTAATATTTATTTATTTTTTAAT-TTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTTCTTTTC
* *
3444 TGATATTTCTAAGTAAATAAATATCTTATTTATAAAATATATATAT
65 TGATATTTCTAAATAAATAAATATCCTATTTATAAAATATATATAT
3490 AGATATAGAT
Statistics
Matches: 102, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
134 52 0.51
135 50 0.49
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.48
Consensus pattern (136 bp):
TTAATATTTATTTATTTTTTAATTTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTTCTTTTCT
GATATTTCTAAATAAATAAATATCCTATTTATAAAATATATATATTTTAATTATTTTAGAGAAAT
GTTTTA
Found at i:5464 original size:43 final size:44
Alignment explanation
Indices: 5403--5489 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 44
5393 TGGCTTTAGA
* * *
5403 GAAGTTAGGAGGGAAAGTTATCCCTTATATAT-AAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATATAAAAGTTTTGTT
* * *
5446 GAAGTTAGGACTGAAAGTTGTCCCCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGACGGAAAGTTATCCCCTACATATAAAAGTTTTGTT
5490 TGATGCACGG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 26 0.70
44 11 0.30
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGTTATCCCCTACATATAAAAGTTTTGTT
Found at i:6902 original size:18 final size:18
Alignment explanation
Indices: 6879--6916 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
6869 CTTCAAACGA
*
6879 GTGGTTCAATAACTCTTG
1 GTGGTTCAAGAACTCTTG
*
6897 GTGGTTTAAGAACTCTTG
1 GTGGTTCAAGAACTCTTG
6915 GT
1 GT
6917 TCAGGGAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.39
Consensus pattern (18 bp):
GTGGTTCAAGAACTCTTG
Found at i:8197 original size:71 final size:72
Alignment explanation
Indices: 8114--8248 Score: 238
Period size: 71 Copynumber: 1.9 Consensus size: 72
8104 ATACAATAAC
*
8114 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAAT-A-CCTCGGCTTTATGGATAATATTTAGCTAA
1 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATCACCCT-GGCTTTATGGATAATATTCAGCTAA
8177 TCTGTTAA
65 TCTGTTAA
8185 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATCACCCTGGCTTTATGGATAATATTCAGCTAA
1 GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATCACCCTGGCTTTATGGATAATATTCAGCTAA
8249 CTTATTATAC
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
71 33 0.54
72 25 0.41
73 3 0.05
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (72 bp):
GCTTGAGTTATCCCCCTAAAGCAATTGGTTAATCACCCTGGCTTTATGGATAATATTCAGCTAAT
CTGTTAA
Found at i:11418 original size:75 final size:70
Alignment explanation
Indices: 11330--11503 Score: 206
Period size: 75 Copynumber: 2.4 Consensus size: 70
11320 ATCAATAAGA
11330 AGCAAATACTGGGGCATGCTGAAAGCCCATTTCAATAAAAAATTGGAATATTGGCACATTTTGAA
1 AGCAAATACTGGGGCATGCTGAAAGCCCATTTCAATAAAAAATTGGAATA-----ACATTTTGAA
* *
11395 CG-TCTGTATT
61 CGTTC-ATATC
* * * * *
11405 AGCAAATGCTGGGGCATGTTGAAAGCCTATTTCAATCAGAAATTGGAATAACATTTTGAACGTTC
1 AGCAAATACTGGGGCATGCTGAAAGCCCATTTCAATAAAAAATTGGAATAACATTTTGAACGTTC
11470 ATATC
66 ATATC
* *
11475 AGTAAATACTGGGGCATGCTGAAGGCCCA
1 AGCAAATACTGGGGCATGCTGAAAGCCCA
11504 CATCATTATG
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
70 39 0.45
71 2 0.02
75 45 0.52
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (70 bp):
AGCAAATACTGGGGCATGCTGAAAGCCCATTTCAATAAAAAATTGGAATAACATTTTGAACGTTC
ATATC
Found at i:12436 original size:54 final size:54
Alignment explanation
Indices: 12370--12587 Score: 251
Period size: 54 Copynumber: 4.0 Consensus size: 54
12360 TCAATAATTG
* *
12370 AACATCTAAGCAGAAGCCATAGGAAATGATGAATATGTTGTCAAATG-TTTACGA
1 AACATCTGAGCAGAAGCCACAGGAAATGATGAATATGTTGTCAAATGCTTTAC-A
* * *
12424 AACATCTGAGCAGAAACCACAGAAAATGATGAATATGTTGTCAAATGTTTTACA
1 AACATCTGAGCAGAAGCCACAGGAAATGATGAATATGTTGTCAAATGCTTTACA
* * * * * * **
12478 AACATTTGTGCAGAAGTCACATGAAAAGATGAATGTGTTGTCAAATGCTTTATG
1 AACATCTGAGCAGAAGCCACAGGAAATGATGAATATGTTGTCAAATGCTTTACA
* * * *
12532 AACATCTG-GCCAGAAGCCACAAGAAATGATGAATGTGTTATCAAAAGCTTTACA
1 AACATCTGAG-CAGAAGCCACAGGAAATGATGAATATGTTGTCAAATGCTTTACA
12586 AA
1 AA
12588 AATCCAAGCA
Statistics
Matches: 139, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
53 1 0.01
54 133 0.96
55 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (54 bp):
AACATCTGAGCAGAAGCCACAGGAAATGATGAATATGTTGTCAAATGCTTTACA
Found at i:12603 original size:54 final size:54
Alignment explanation
Indices: 12370--12619 Score: 209
Period size: 54 Copynumber: 4.6 Consensus size: 54
12360 TCAATAATTG
* * *
12370 AACATCTAAGCAGAAGCCATAGGAAATGATGAATATGTTGTCAAATG-TTTACGA
1 AACATCCAAGCAGAAGCCACAAGAAATGATGAATATGTTGTCAAATGCTTTAC-A
** * *
12424 AACATCTGAGCAGAAACCAC-AGAAAATGATGAATATGTTGTCAAATGTTTTACA
1 AACATCCAAGCAGAAGCCACAAG-AAATGATGAATATGTTGTCAAATGCTTTACA
**** * * * * **
12478 AACATTTGTGCAGAAGTCACATGAAAAGATGAATGTGTTGTCAAATGCTTTATG
1 AACATCCAAGCAGAAGCCACAAGAAATGATGAATATGTTGTCAAATGCTTTACA
** * * *
12532 AACAT-CTGGCCAGAAGCCACAAGAAATGATGAATGTGTTATCAAAAGCTTTACA
1 AACATCCAAG-CAGAAGCCACAAGAAATGATGAATATGTTGTCAAATGCTTTACA
* * ** *
12586 AAAATCCAAGCAAAAGCCATGAGAAAGGATGAAT
1 AACATCCAAGCAGAAGCCACAAGAAATGATGAAT
12620 TGTCACATGT
Statistics
Matches: 160, Mismatches: 31, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
53 2 0.01
54 150 0.94
55 8 0.05
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (54 bp):
AACATCCAAGCAGAAGCCACAAGAAATGATGAATATGTTGTCAAATGCTTTACA
Found at i:12617 original size:108 final size:107
Alignment explanation
Indices: 12377--12619 Score: 262
Period size: 108 Copynumber: 2.2 Consensus size: 107
12367 TTGAACATCT
12377 AAGCAGAAGCCAT-AGGAAATGATGAATATGTTGTCAAATGTTTACGAAACATCTGAGCAGAAAC
1 AAGCAGAAGCCATGA-GAAA-GATGAATATGTTGTCAAATGTTTACGAAACATCTGAGCAGAAAC
* * * * **
12441 CACAGAAAATGATGAATATGTTGTCAAATGTTTTACAAACATTT
64 CACAGAAAATGATGAATATGTTATCAAAAGCTTTACAAAAATCC
** * *
12485 GTGCAGAAGTCACATGA-AAAGATGAATGTGTTGTCAAATGCTTTATG-AACATCTG-GCCAGAA
1 AAGCAGAAG-C-CATGAGAAAGATGAATATGTTGTCAAATG-TTTACGAAACATCTGAG-CAGAA
* *
12547 GCCACA-AGAAATGATGAATGTGTTATCAAAAGCTTTACAAAAATCC
62 ACCACAGA-AAATGATGAATATGTTATCAAAAGCTTTACAAAAATCC
*
12593 AAGCAAAAGCCATGAGAAAGGATGAAT
1 AAGCAGAAGCCATGAGAAA-GATGAAT
12620 TGTCACATGT
Statistics
Matches: 112, Mismatches: 15, Indels: 16
0.78 0.10 0.11
Matches are distributed among these distances:
106 5 0.04
107 6 0.05
108 88 0.79
109 9 0.08
110 3 0.03
111 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (107 bp):
AAGCAGAAGCCATGAGAAAGATGAATATGTTGTCAAATGTTTACGAAACATCTGAGCAGAAACCA
CAGAAAATGATGAATATGTTATCAAAAGCTTTACAAAAATCC
Found at i:13032 original size:22 final size:22
Alignment explanation
Indices: 13004--13082 Score: 122
Period size: 22 Copynumber: 3.6 Consensus size: 22
12994 ACATCTACAT
*
13004 TCTTCAAAGATAATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
13026 TCTTCAAAAATGATAGATTCAC
1 TCTTCAAAGATGATAGATTCTC
13048 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
13070 TTTTCAAAGATGA
1 TCTTCAAAGATGA
13083 AAGCTTTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.35
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:13666 original size:113 final size:112
Alignment explanation
Indices: 13468--13910 Score: 540
Period size: 113 Copynumber: 3.9 Consensus size: 112
13458 CATGTCGGGT
* *
13468 AGAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAACTTGT
* * *
13533 TCAAACTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCTGAG
65 TCAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAG
* *
13581 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAATAATTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAACTTGT
13646 TCAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAG
65 TCAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAG
*
13694 -GAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAA-AAAGTTCATAATAAGAAGAACTTG
1 AG-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAA-TTCATAATGAGAAGAACTTG
* ** *
13757 TTCAACCTTTTGC-TCAATTCTATCACAGAAGGAGATAGATCAACATCAACGTTTCCAGATG
64 TTCAACCTTTTGCTTGAATTC-ATCAC-----TCGATGGATCAAC-T-----TTTCCAGA-G
*
13818 A-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTT
* * *
13882 CGACC-TTAGCTTG-ATTCATCA-TCTATGGA
66 CAACCTTTTGCTTGAATTCATCACTCGATGGA
13911 GTTGAATGAA
Statistics
Matches: 289, Mismatches: 23, Indels: 34
0.84 0.07 0.10
Matches are distributed among these distances:
111 9 0.03
112 44 0.15
113 135 0.47
115 4 0.01
117 10 0.03
118 1 0.00
121 4 0.01
122 8 0.03
123 71 0.25
124 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (112 bp):
AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTT
CAACCTTTTGCTTGAATTCATCACTCGATGGATCAACTTTTCCAGAG
Found at i:14155 original size:131 final size:133
Alignment explanation
Indices: 13816--14156 Score: 476
Period size: 137 Copynumber: 2.5 Consensus size: 133
13806 CGTTTCCAGA
13816 TGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 TGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * ** *
13881 TCGACCTTAGCTTGATTCATCATCTATGGAGTTGAATGAAAGAAGAACCTCCCTGGAGGATCAAC
66 TCAACCTTAGCTTAATTCATCATCTATAAAGTTGAATCAAAG-AGAACCTCCCTGGAGGATCAAC
13946 ATTT
130 ATTT
13950 TCAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACT
1 T--GA-AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACT
* * ** *
14015 TGTTTAACCTT-GCCTTAATTCATCA-CATATAAAGTTGAATCAACG-GAACCTCTTTTGAGGAT
63 TGTTCAACCTTAG-CTTAATTCATCATC-TATAAAGTTGAATCAAAGAGAACCTCCCTGGAGGAT
14077 CAACA-TT
126 CAACATTT
* *
14084 TGAAGTTCACAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAAT-ATGAAGAACTTA
1 TGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGA-GAAGAACTTG
14148 TTCAACCTT
65 TTCAACCTT
14157 TTACTCGACT
Statistics
Matches: 188, Mismatches: 13, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
130 1 0.01
131 65 0.35
132 2 0.01
134 4 0.02
135 19 0.10
136 4 0.02
137 93 0.49
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26
Consensus pattern (133 bp):
TGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTAGCTTAATTCATCATCTATAAAGTTGAATCAAAGAGAACCTCCCTGGAGGATCAACA
TTT
Found at i:14471 original size:26 final size:26
Alignment explanation
Indices: 14442--14534 Score: 120
Period size: 26 Copynumber: 3.7 Consensus size: 26
14432 TTTGTTTTTT
* *
14442 TATTATTTTTGTTATTATTATTATTA
1 TATTATTATTATTATTATTATTATTA
*
14468 TATTATTATTAGTATTATT-TTATTTA
1 TATTATTATTATTATTATTATTA-TTA
*
14494 TACTATTATTATTATT-TTATTATT-
1 TATTATTATTATTATTATTATTATTA
14518 TATTATTATTATTATTA
1 TATTATTATTATTATTA
14535 ATAAAAAATA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
24 15 0.26
25 7 0.12
26 36 0.62
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.67
Consensus pattern (26 bp):
TATTATTATTATTATTATTATTATTA
Found at i:14550 original size:3 final size:3
Alignment explanation
Indices: 14441--14534 Score: 106
Period size: 3 Copynumber: 32.0 Consensus size: 3
14431 ATTTGTTTTT
* * *
14441 TTA TTA TTT TTG TTA TTA TTA TTA TTA -TA TTA TTA TTA GTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
14487 TTA TT- TATA CTA TTA TTA TTA TT- TTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
14532 TTA
1 TTA
14535 ATAAAAAATA
Statistics
Matches: 78, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
2 7 0.09
3 68 0.87
4 3 0.04
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:15677 original size:28 final size:28
Alignment explanation
Indices: 15646--15738 Score: 96
Period size: 30 Copynumber: 3.2 Consensus size: 28
15636 ATTTTGATCC
15646 TTTTAATTCGGTCTCTTAATTTTATTTA
1 TTTTAATTCGGTCTCTTAATTTTATTTA
** * * * *
15674 TTTTATAATTTAGTCACTGACTTATTTATATA
1 -TTT-TAATTCGGTCTCTTA-AT-TTTATTTA
15706 TTTTAATTCGGTCTCTTAATTTTATTTA
1 TTTTAATTCGGTCTCTTAATTTTATTTA
15734 TTTTA
1 TTTTA
15739 TAAATTATAT
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
28 12 0.24
29 4 0.08
30 22 0.45
31 4 0.08
32 7 0.14
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.59
Consensus pattern (28 bp):
TTTTAATTCGGTCTCTTAATTTTATTTA
Found at i:17041 original size:21 final size:22
Alignment explanation
Indices: 16997--17043 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
16987 AATTTAATTT
** *
16997 TAATCTTTGATATTTTTATTAA
1 TAATCTTTGATATTTAAATAAA
17019 TAAT-TTTGATATTTAAATAAA
1 TAATCTTTGATATTTAAATAAA
17040 TAAT
1 TAAT
17044 ATTTTACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (22 bp):
TAATCTTTGATATTTAAATAAA
Found at i:18753 original size:14 final size:15
Alignment explanation
Indices: 18722--18754 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
18712 TTAATCATGA
18722 TATTGTTCATGATAT
1 TATTGTTCATGATAT
*
18737 TATTGTT-ATGGTAT
1 TATTGTTCATGATAT
18751 TATT
1 TATT
18755 ACCATATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.58
Consensus pattern (15 bp):
TATTGTTCATGATAT
Found at i:19068 original size:45 final size:46
Alignment explanation
Indices: 18969--19072 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 46
18959 GATTATTGTG
* *
18969 TTGTCAAAACTAAAATCAAAATATTAGTTCATTTCGATTATTGGATT
1 TTGT-AAAATTAAAATCAAAAGATTAGTTCATTTCGATTATTGGATT
** * * * *
19016 GCG-AAAATTAAAATCAAAGGATTAGTTCCTTTTGA-TATTGGGTT
1 TTGTAAAATTAAAATCAAAAGATTAGTTCATTTCGATTATTGGATT
19060 TTGTAAAATTAAA
1 TTGTAAAATTAAA
19073 GGATTAATTC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
44 9 0.20
45 36 0.78
47 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.38
Consensus pattern (46 bp):
TTGTAAAATTAAAATCAAAAGATTAGTTCATTTCGATTATTGGATT
Found at i:19318 original size:61 final size:59
Alignment explanation
Indices: 19210--19322 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 59
19200 TCATCATTAG
* * *
19210 AATCTTGCATTGATTCTAACTTTGTAAGGAAAATAGATTGTTGAATTTATTTCCTTGGA
1 AATCTTGCATTGATTCTAACTTTGTAAGAAAAATAAATTGTCGAATTTATTTCCTTGGA
*
19269 AATCTTG-ATTGATTTTAACTTTGTAAGAAAAATAATAAATTGTCGAATTTATTT
1 AATCTTGCATTGATTCTAACTTTGTAAG--AAA-AATAAATTGTCGAATTTATTT
19323 TTTTGAGATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
58 19 0.40
59 7 0.15
60 2 0.04
61 19 0.40
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (59 bp):
AATCTTGCATTGATTCTAACTTTGTAAGAAAAATAAATTGTCGAATTTATTTCCTTGGA
Found at i:19611 original size:39 final size:39
Alignment explanation
Indices: 19557--19637 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
19547 ATGAATCTTA
19557 TATGATTCTAATATGTAAAAGAAAATAAATCGTTGGATT
1 TATGATTCTAATATGTAAAAGAAAATAAATCGTTGGATT
*
19596 TATGATTCTAATATGTAAAAGGAAATAAATCGTTGGATT
1 TATGATTCTAATATGTAAAAGAAAATAAATCGTTGGATT
19635 TAT
1 TAT
19638 TTTCGTATTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (39 bp):
TATGATTCTAATATGTAAAAGAAAATAAATCGTTGGATT
Found at i:19654 original size:39 final size:39
Alignment explanation
Indices: 19572--19705 Score: 130
Period size: 39 Copynumber: 3.4 Consensus size: 39
19562 TTCTAATATG
* * * * *
19572 TAAAAGAAAATAAATCGTTGGATTTATGATTC-TAATATG
1 TAAAAGGAAATAAATCGTTGGATTTAT-TTTCGTATTGTA
19611 TAAAAGGAAATAAATCGTTGGATTTATTTTCGTATTGTA
1 TAAAAGGAAATAAATCGTTGGATTTATTTTCGTATTGTA
* * * *
19650 TAAAATGAAATAAATCGTAGAATTTATTTTCCTGTTTTG-A
1 TAAAAGGAAATAAATCGTTGGATTTATTTT-C-GTATTGTA
*
19690 -AAAAGGAAATACATCG
1 TAAAAGGAAATAAATCG
19706 GTAAATTTAT
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
38 3 0.04
39 71 0.88
40 2 0.02
41 5 0.06
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.37
Consensus pattern (39 bp):
TAAAAGGAAATAAATCGTTGGATTTATTTTCGTATTGTA
Found at i:19660 original size:127 final size:128
Alignment explanation
Indices: 19424--19665 Score: 292
Period size: 127 Copynumber: 1.9 Consensus size: 128
19414 GAATACATTT
* * * * *
19424 TCTTATATGATTCTATCTTTTAAAAAGAAAATAAATCGTCCGATTTATTTTCCTATTTTGGAAAA
1 TCTTATATGATTCTATCATGTAAAAAGAAAATAAATCGTCCGATTTATATTCCTAATATGGAAAA
* * * * *
19489 AGAAATAAATCATTGAATTTATTTTCTTGTTTTGTACAAGGAAATAAATCTTTTTCCTATGAA
66 AGAAATAAATCATTGAATTTATTTTCGTATTGTATAAAAGGAAATAAATCTTTTTCCTATGAA
** *
19552 TCTTATATGATTCTAAT-ATGT-AAAAGAAAATAAATCGTTGGATTTATGATT-CTAATATGTAA
1 TCTTATATGATTCT-ATCATGTAAAAAGAAAATAAATCGTCCGATTTAT-ATTCCTAATATGGAA
* * * *
19614 AAGGAAATAAATCGTTGGATTTATTTTCGTATTGTATAAAATGAAATAAATC
64 AAAGAAATAAATCATTGAATTTATTTTCGTATTGTATAAAAGGAAATAAATC
19666 GTAGAATTTA
Statistics
Matches: 95, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
127 75 0.79
128 18 0.19
129 2 0.02
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (128 bp):
TCTTATATGATTCTATCATGTAAAAAGAAAATAAATCGTCCGATTTATATTCCTAATATGGAAAA
AGAAATAAATCATTGAATTTATTTTCGTATTGTATAAAAGGAAATAAATCTTTTTCCTATGAA
Found at i:19713 original size:39 final size:39
Alignment explanation
Indices: 19611--19718 Score: 114
Period size: 39 Copynumber: 2.8 Consensus size: 39
19601 TTCTAATATG
* **
19611 TAAAAGGAAATAAATCGTTGGATTTATTTTCGTATTGTA
1 TAAAAGGAAATAAATCGGTAAATTTATTTTCGTATTGTA
* *
19650 TAAAATGAAATAAATC-GTAGAATTTATTTTCCTGTTTTG-A
1 TAAAAGGAAATAAATCGGTA-AATTTATTTT-C-GTATTGTA
*
19690 -AAAAGGAAATACATCGGTAAATTTATTTT
1 TAAAAGGAAATAAATCGGTAAATTTATTTT
19719 TTCAAGAATC
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
38 1 0.02
39 47 0.81
40 5 0.09
41 5 0.09
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (39 bp):
TAAAAGGAAATAAATCGGTAAATTTATTTTCGTATTGTA
Found at i:19801 original size:39 final size:39
Alignment explanation
Indices: 19747--19837 Score: 137
Period size: 39 Copynumber: 2.3 Consensus size: 39
19737 TTCTATATGT
* * * *
19747 AAAAGGAAATAAATCATTGGATTTATTTTCCTATTTTGA
1 AAAAGAAAATAAATCATAGAATTTAGTTTCCTATTTTGA
*
19786 AAAAGAAAATAAATCATAGAATTTAGTTTCCTATTTTGT
1 AAAAGAAAATAAATCATAGAATTTAGTTTCCTATTTTGA
19825 AAAAGAAAATAAA
1 AAAAGAAAATAAA
19838 CCGAAATAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (39 bp):
AAAAGAAAATAAATCATAGAATTTAGTTTCCTATTTTGA
Found at i:19837 original size:174 final size:173
Alignment explanation
Indices: 19549--19984 Score: 428
Period size: 183 Copynumber: 2.5 Consensus size: 173
19539 TTTTTCCTAT
* * * * *
19549 GAATCTTATATGATTCTAATATGTAAAAGAAAATAAATCGTTGGATTTATGATT-CTAATATGTA
1 GAATCTTGTATGATTCT-ATATGTAAAAGGAAATAAATCATTGGATTTAT-TTTCCT-ATTTGTA
* * * * * *
19613 AAAGGAAATAAATCGTTGGATTTATTTTCGTATTGTATAAAATG--AAATAAATCGTAGAATTTA
63 AAAGAAAATAAATCATAGAATTTAGTTTCCTATTGTATAAAATGACAAATAAATCGTAGAATTTA
* * * *
19676 TTTTCCTGTTTTGAAAAAGGAAATACATCGGTAAATTTATTTTTTCAA
128 TTTTCCT-ATTTGAAAAAGGAAATAAATCAGTAAATTCATTTTTT-AA
*
19724 GAATCTTGTATGATTCTATATGTAAAAGGAAATAAATCATTGGATTTATTTTCCTATTTTGAAAA
1 GAATCTTGTATGATTCTATATGTAAAAGGAAATAAATCATTGGATTTATTTTCCTA-TTTGTAAA
* * *
19789 AGAAAATAAATCATAGAATTTAGTTTCCTATTTTGTAAAAGAAAATAAACCGAAATAAATCGTTG
65 AGAAAATAAATCATAGAATTTAGTTTCCTA--TTGT---ATAAAAT-GA-C-AAATAAATCGTAG
* * * * * ** *
19854 GATTTATTTTCCTATTTGTAAAGGGAAATAAATTATTGGATTCATTTTTTGA
122 AATTTATTTTCCTATTTGAAAAAGGAAATAAATCAGTAAATTCATTTTTTAA
* * * * *
19906 GAATCTTGTATGATTCTTCTTTGTAAAAAGAAACAAATCATTGGATTTATTTTCCTAATTGTAAA
1 GAATCTTGTATGATTC-TATATGTAAAAGGAAATAAATCATTGGATTTATTTTCCTATTTGTAAA
19971 AGAAAATAAATCAT
65 AGAAAATAAATCAT
19985 TGGATATTTT
Statistics
Matches: 215, Mismatches: 33, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
173 3 0.01
174 62 0.29
175 16 0.07
176 4 0.02
179 6 0.03
182 37 0.17
183 63 0.29
184 24 0.11
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (173 bp):
GAATCTTGTATGATTCTATATGTAAAAGGAAATAAATCATTGGATTTATTTTCCTATTTGTAAAA
GAAAATAAATCATAGAATTTAGTTTCCTATTGTATAAAATGACAAATAAATCGTAGAATTTATTT
TCCTATTTGAAAAAGGAAATAAATCAGTAAATTCATTTTTTAA
Found at i:19846 original size:49 final size:48
Alignment explanation
Indices: 19792--19885 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 48
19782 TTGAAAAAGA
19792 AAATAAATCATAGAATTTAGTTTCCTATTTTGTAAAAGAAAATAAACCG
1 AAATAAATCATAGAATTTAGTTTCCTA-TTTGTAAAAGAAAATAAACCG
* * * * * *
19841 AAATAAATCGTTGGATTTATTTTCCTATTTGTAAAGGGAAATAAA
1 AAATAAATCATAGAATTTAGTTTCCTATTTGTAAAAGAAAATAAA
19886 TTATTGGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
48 16 0.41
49 23 0.59
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.35
Consensus pattern (48 bp):
AAATAAATCATAGAATTTAGTTTCCTATTTGTAAAAGAAAATAAACCG
Found at i:20046 original size:93 final size:94
Alignment explanation
Indices: 19840--20076 Score: 336
Period size: 93 Copynumber: 2.5 Consensus size: 94
19830 AAAATAAACC
* * * *
19840 GAAATAAATCGTTGGATTTATTTTCCTATTTGTAAAGGGAAATAAATTATTGGATTCATTTTTTG
1 GAAATAAATCATTGGATTTATTTTCCTATTTGTAAAAGAAAATAAATCATTGGATT-ATTTTTTG
19905 AGAATCTTGTATGATTCTTCTTTGTAAAAA
65 AGAATCTTGTATGATTCTTCTTTGTAAAAA
* *
19935 GAAACAAATCATTGGATTTATTTTCCTAATTGTAAAAGAAAATAAATCATTGGA-TATTTTTTTG
1 GAAATAAATCATTGGATTTATTTTCCTATTTGTAAAAGAAAATAAATCATTGGATTA-TTTTTTG
* *
19999 -GAATCTTGTATGATTCTTGTTTGT-GAAA
65 AGAATCTTGTATGATTCTTCTTTGTAAAAA
*
20027 GAAAATAAATCATTGGATTTATTTTCATGATTTGTAAAAGAAAATAAATC
1 G-AAATAAATCATTGGATTTATTTTCCT-ATTTGTAAAAGAAAATAAATC
20077 GGTGGATTGT
Statistics
Matches: 128, Mismatches: 11, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
92 4 0.03
93 48 0.38
94 28 0.22
95 48 0.38
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (94 bp):
GAAATAAATCATTGGATTTATTTTCCTATTTGTAAAAGAAAATAAATCATTGGATTATTTTTTGA
GAATCTTGTATGATTCTTCTTTGTAAAAA
Found at i:25452 original size:497 final size:497
Alignment explanation
Indices: 24518--25514 Score: 1985
Period size: 497 Copynumber: 2.0 Consensus size: 497
24508 AATAAAATTC
24518 ATAATAATATAAAATAATATATTTAAAAGGTTAAGGTATTTTATTAGTCATTTATTAGTCATATA
1 ATAATAATATAAAATAATATATTTAAAAGGTTAAGGTATTTTATTAGTCATTTATTAGTCATATA
24583 GTCGTTGTATAATTTGGATTTTTATAGACATTTAAAATTTTAAAATGTATACAAATTAAAATTGA
66 GTCGTTGTATAATTTGGATTTTTATAGACATTTAAAATTTTAAAATGTATACAAATTAAAATTGA
24648 TCAAATTAGAGCATAATAAATTAAACCACAATTTGCACATAGTATAGATACTAATAACAAAATTT
131 TCAAATTAGAGCATAATAAATTAAACCACAATTTGCACATAGTATAGATACTAATAACAAAATTT
24713 TACCTTTTGACAAACTAGTTTATCTTAACAAAAATTTTAATTATTATTGATGTCAATATTTATCA
196 TACCTTTTGACAAACTAGTTTATCTTAACAAAAATTTTAATTATTATTGATGTCAATATTTATCA
24778 CAATAAAAAGTAAAAAATTAAGTGTCAATAAACTTTATTGTCACAAAAAATATCAAATAATATTG
261 CAATAAAAAGTAAAAAATTAAGTGTCAATAAACTTTATTGTCACAAAAAATATCAAATAATATTG
24843 ATCACTTTATATTTTGTCACCGTCGTATCATTTATCGTCAAGAAAATAATTGGCATCAATTTGCG
326 ATCACTTTATATTTTGTCACCGTCGTATCATTTATCGTCAAGAAAATAATTGGCATCAATTTGCG
24908 TATTATAATAGTGTCAAAAAAATTTTAACGGTGAAATTTGTATCAAAATTATATACTTATAATGA
391 TATTATAATAGTGTCAAAAAAATTTTAACGGTGAAATTTGTATCAAAATTATATACTTATAATGA
24973 GAATTTAATTATTAAAAAAATATAATCATCATAGTTATTACT
456 GAATTTAATTATTAAAAAAATATAATCATCATAGTTATTACT
25015 ATAATAATATAAAATAATATATTTAAAAGGTTAAGGTATTTTATTAGTCATTTATTAGTCATATA
1 ATAATAATATAAAATAATATATTTAAAAGGTTAAGGTATTTTATTAGTCATTTATTAGTCATATA
25080 GTCGTTGTATAATTTGGATTTTTATAGACATTTAAAATTTTAAAATGTATACAAATTAAAATTGA
66 GTCGTTGTATAATTTGGATTTTTATAGACATTTAAAATTTTAAAATGTATACAAATTAAAATTGA
25145 TCAAATTAGAGCATAATAAATTAAACCACAATTTGCACATAGTATAGATACTAATAACAAAATTT
131 TCAAATTAGAGCATAATAAATTAAACCACAATTTGCACATAGTATAGATACTAATAACAAAATTT
25210 TACCTTTTGACAAACTAGTTTATCTTAACAAAAATTTTAATTATTATTGATGTCAATATTTATCA
196 TACCTTTTGACAAACTAGTTTATCTTAACAAAAATTTTAATTATTATTGATGTCAATATTTATCA
25275 CAATAAAAAGTAAAAAATTAAGTGTCAATAAACTTTATTGTCACAAAAAATATCAAATAATATTG
261 CAATAAAAAGTAAAAAATTAAGTGTCAATAAACTTTATTGTCACAAAAAATATCAAATAATATTG
*
25340 ATCACTTTATATTTTGTCACCGTCGTATCATTTATCGTCAAGAAAATAATTGGCATTAATTTGCG
326 ATCACTTTATATTTTGTCACCGTCGTATCATTTATCGTCAAGAAAATAATTGGCATCAATTTGCG
25405 TATTATAATAGTGTCAAAAAAATTTTAACGGTGAAATTTGTATCAAAATTATATACTTATAATGA
391 TATTATAATAGTGTCAAAAAAATTTTAACGGTGAAATTTGTATCAAAATTATATACTTATAATGA
25470 GAATTTAATTATTAAAAAAATATAATCATCATAGTTATTACT
456 GAATTTAATTATTAAAAAAATATAATCATCATAGTTATTACT
25512 ATA
1 ATA
25515 GTAGTGACGA
Statistics
Matches: 499, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
497 499 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.38
Consensus pattern (497 bp):
ATAATAATATAAAATAATATATTTAAAAGGTTAAGGTATTTTATTAGTCATTTATTAGTCATATA
GTCGTTGTATAATTTGGATTTTTATAGACATTTAAAATTTTAAAATGTATACAAATTAAAATTGA
TCAAATTAGAGCATAATAAATTAAACCACAATTTGCACATAGTATAGATACTAATAACAAAATTT
TACCTTTTGACAAACTAGTTTATCTTAACAAAAATTTTAATTATTATTGATGTCAATATTTATCA
CAATAAAAAGTAAAAAATTAAGTGTCAATAAACTTTATTGTCACAAAAAATATCAAATAATATTG
ATCACTTTATATTTTGTCACCGTCGTATCATTTATCGTCAAGAAAATAATTGGCATCAATTTGCG
TATTATAATAGTGTCAAAAAAATTTTAACGGTGAAATTTGTATCAAAATTATATACTTATAATGA
GAATTTAATTATTAAAAAAATATAATCATCATAGTTATTACT
Found at i:25935 original size:40 final size:41
Alignment explanation
Indices: 25870--25962 Score: 134
Period size: 40 Copynumber: 2.3 Consensus size: 41
25860 TTCACTTTAA
* * * *
25870 TAGTGATAAAAGTATTTGTCGTCACAAATCACAAATTAA-AC
1 TAGTGA-AAAAATAATTGTCATCACAAATCACAAACTAAGAC
25911 TAGTGAAAAAATAATTGTCATCACAAATCACAAACTAAGAC
1 TAGTGAAAAAATAATTGTCATCACAAATCACAAACTAAGAC
25952 TAGTGAAAAAA
1 TAGTGAAAAAA
25963 ATATTTTGTC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
40 28 0.60
41 19 0.40
ACGTcount: A:0.49, C:0.14, G:0.12, T:0.25
Consensus pattern (41 bp):
TAGTGAAAAAATAATTGTCATCACAAATCACAAACTAAGAC
Found at i:25975 original size:40 final size:39
Alignment explanation
Indices: 25870--25976 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 39
25860 TTCACTTTAA
* * *
25870 TAGTGATAAAAGTATTTGTCGTCACAAATCACAAATTAAAC
1 TAGTGAAAAAAATATTT-T-GTCACAAATCACAAACTAAAC
**
25911 TAGTG-AAAAAATAATTGTCATCACAAATCACAAACTAAGAC
1 TAGTGAAAAAAAT-ATT-TTGTCACAAATCACAAACTAA-AC
25952 TAGTGAAAAAAATATTTTGTCACAA
1 TAGTGAAAAAAATATTTTGTCACAA
25977 TTATACATAA
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
40 29 0.53
41 18 0.33
42 8 0.15
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (39 bp):
TAGTGAAAAAAATATTTTGTCACAAATCACAAACTAAAC
Found at i:29637 original size:207 final size:212
Alignment explanation
Indices: 29196--29924 Score: 1095
Period size: 216 Copynumber: 3.4 Consensus size: 212
29186 ATTTTATGAA
* * * *
29196 AAATACAAATTTAAGAATTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAA-AAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAA
*
29260 ACAACACACATTGATGAGGGATCAAATTGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAA
66 ACAACACACA--GA-GAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAA
29325 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAGTAATAA
128 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATT-AAAAATATAAATAAGTAATAA
*
29390 GTATGGGTCAATTTCAGATGC
192 GTATGGGACAATTTCAGATGC
* *
29411 AAATAGAA-TTTAGAGGACTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTA
1 AAATATAATTTTA-AGGACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTA
* *
29475 AAC-A-ACACA-A-AGGGATCAAATCGAAATAATTTTAAGTTGTGAGGTTGAAATTAATTC-AAA
65 AACAACACACAGAGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAA
* * * *
29535 AAGTACTAAATTATACCTATTTAAAAAGTTCTCGGCCAATTAAAAATATAAATAATTAATAAGTA
130 AAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAATATAAATAAGTAATAAGTA
* *
29600 TTGGCCAATTTCAGATGC
195 TGGGACAATTTCAGATGC
29618 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAA
* *
29683 ACAACACACATAGATGAGGGATCAAATCAAAATAATTTTAAATTGTGAGGTTTAAATTAATACAA
66 ACAACACAC--AGA-GAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAA
29748 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAA-ATAGATATAAGTAATA
128 AAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAATATA-A-ATAAGTAATA
* *
29812 AGTATGGGATAATTTTAGATGC
191 AGTATGGGACAATTTCAGATGC
*
29834 AAATATAATTTTAAGGACTAAATTGAACAAATATAAAATTACAAATTAAAATTTAAATAAATTAA
1 AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAA
29899 AC-A-ACACA-A-AGGGATCAAATCGAAAT
66 ACAACACACAGAGAGGGATCAAATCGAAAT
29925 GATCGCAAAA
Statistics
Matches: 472, Mismatches: 29, Indels: 32
0.89 0.05 0.06
Matches are distributed among these distances:
207 99 0.21
208 46 0.10
209 64 0.14
211 3 0.01
212 2 0.00
214 59 0.12
215 97 0.21
216 102 0.22
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.29
Consensus pattern (212 bp):
AAATATAATTTTAAGGACTAAATTGAACAAATATGAAATTACAAATTAAAATTTAAATAAATTAA
ACAACACACAGAGAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAA
AGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAATATAAATAAGTAATAAGTAT
GGGACAATTTCAGATGC
Found at i:30016 original size:2 final size:2
Alignment explanation
Indices: 30005--30086 Score: 53
Period size: 2 Copynumber: 40.5 Consensus size: 2
29995 TTGAAAGAAC
* * *
30005 TA TA -A TA TA TA TA TA TA TA TA AA CTA TA TA AA GTA TA TG TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA
* * *
30047 TA TA TA TA TA AA CTA TA TA T- TA TG TA TA AA CTA TA TA TA T
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA T
30087 CATGTATAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
1 3 0.05
2 54 0.89
3 4 0.07
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:30067 original size:20 final size:19
Alignment explanation
Indices: 30005--30160 Score: 85
Period size: 20 Copynumber: 8.2 Consensus size: 19
29995 TTGAAAGAAC
*
30005 TATA-ATATATATA-TATA
1 TATATATATATAAACTATA
* *
30022 TATAAACTATATAAAGTATA
1 TATATA-TATATAAACTATA
30042 TGTATTATATATATAAACTATA
1 --TA-TATATATATAAACTATA
*
30064 TAT-TATGTATAAACTATA
1 TATATATATATAAACTATA
* *
30082 TATATCATGTATAAACTA-G
1 TATAT-ATATATAAACTATA
*
30101 T-T-TATATATGAACTAT-
1 TATATATATATAAACTATA
* *
30117 TGA-ACTATATAGAAACTACA
1 T-ATA-TATATATAAACTATA
* *
30137 TAGTTTATATATAAATTATA
1 TA-TATATATATAAACTATA
30157 TATA
1 TATA
30161 AACTATACAA
Statistics
Matches: 108, Mismatches: 15, Indels: 30
0.71 0.10 0.20
Matches are distributed among these distances:
16 11 0.10
17 5 0.05
18 19 0.18
19 23 0.21
20 33 0.31
22 14 0.13
23 3 0.03
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (19 bp):
TATATATATATAAACTATA
Found at i:30076 original size:18 final size:20
Alignment explanation
Indices: 30053--30099 Score: 80
Period size: 18 Copynumber: 2.5 Consensus size: 20
30043 GTATTATATA
30053 TATAAACTATATAT-T-ATG
1 TATAAACTATATATATCATG
30071 TATAAACTATATATATCATG
1 TATAAACTATATATATCATG
30091 TATAAACTA
1 TATAAACTA
30100 GTTTATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 14 0.52
19 1 0.04
20 12 0.44
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (20 bp):
TATAAACTATATATATCATG
Found at i:30082 original size:31 final size:30
Alignment explanation
Indices: 30016--30086 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
30006 ATAATATATA
* *
30016 TATATATATAAACTATATAAAGTATATGTAT
1 TATATATATAAACTATATAAAGTATA-GAAC
*
30047 TATATATATAAACTATATATTATGTATA-AAC
1 TATATATATAAACTATATA--AAGTATAGAAC
30078 TATATATAT
1 TATATATAT
30087 CATGTATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 29 0.83
33 6 0.17
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (30 bp):
TATATATATAAACTATATAAAGTATAGAAC
Found at i:30305 original size:14 final size:14
Alignment explanation
Indices: 30269--30307 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
30259 ATATATATAA
*
30269 TATGGTTTAAGGTT
1 TATGGTTTAGGGTT
*
30283 TAGGGTTTAGGGTT
1 TATGGTTTAGGGTT
*
30297 TATGATTTAGG
1 TATGGTTTAGG
30308 ATTAATTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (14 bp):
TATGGTTTAGGGTT
Found at i:30529 original size:27 final size:26
Alignment explanation
Indices: 30495--30551 Score: 96
Period size: 27 Copynumber: 2.2 Consensus size: 26
30485 ATATATAAAT
30495 TATAGTTTATATTTATATACTACATA
1 TATAGTTTATATTTATATACTACATA
*
30521 CTATAGTTTATATTTATATACTATATA
1 -TATAGTTTATATTTATATACTACATA
30548 TATA
1 TATA
30552 TACACTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 4 0.14
27 25 0.86
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.51
Consensus pattern (26 bp):
TATAGTTTATATTTATATACTACATA
Found at i:30546 original size:60 final size:58
Alignment explanation
Indices: 30466--30623 Score: 187
Period size: 60 Copynumber: 2.7 Consensus size: 58
30456 TATATAAACT
* *
30466 ATTTATATAGTAT-TACTATATATATAAATTATAGTTTATA-T-TTATATACTACATACTATA
1 ATTTATAT-TTATATACTATATATATAAACTATAGTTTATACTATT-TATA-TA-A-ACTATA
* *
30526 GTTTATATTTATATACTATATATATATACACTATATTTTATACTATTTATATAAACTATA
1 ATTTATATTTATATACTATATATATA-A-ACTATAGTTTATACTATTTATATAAACTATA
*
30586 ATTTATATTTATATACTATATATATGAACTATAGTTTA
1 ATTTATATTTATATACTATATATATAAACTATAGTTTA
30624 CATATGAACT
Statistics
Matches: 86, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
58 10 0.12
59 4 0.05
60 50 0.58
61 2 0.02
62 13 0.15
63 5 0.06
64 2 0.02
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (58 bp):
ATTTATATTTATATACTATATATATAAACTATAGTTTATACTATTTATATAAACTATA
Found at i:30583 original size:25 final size:27
Alignment explanation
Indices: 30529--30607 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 27
30519 TACTATAGTT
*
30529 TATATTTATATACTATATATATATACAC
1 TATATTT-TATACTATATATATATAAAC
30557 TATATTTTATACTAT-T-TATATAAAC
1 TATATTTTATACTATATATATATAAAC
* *
30582 TATAATTTATATTTATATACTATATA
1 TATATTTTATA-CTATATA-TATATA
30608 TATGAACTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
25 18 0.41
26 4 0.09
27 9 0.20
28 7 0.16
29 6 0.14
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.51
Consensus pattern (27 bp):
TATATTTTATACTATATATATATAAAC
Found at i:30610 original size:33 final size:33
Alignment explanation
Indices: 30466--30697 Score: 142
Period size: 33 Copynumber: 7.5 Consensus size: 33
30456 TATATAAACT
* *
30466 ATTTATATAGTAT-TACTATATATATAAATTATA
1 ATTTATAT-TTATATACTATATATATAAACTATA
* *
30499 GTTTATATTTATATAC----TACAT--ACTATA
1 ATTTATATTTATATACTATATATATAAACTATA
* *
30526 GTTTATATTTATATACTATATATAT--A-TA-C
1 ATTTATATTTATATACTATATATATAAACTATA
* *
30555 A-CTATATTT-TATACTATTTATATAAACTATA
1 ATTTATATTTATATACTATATATATAAACTATA
*
30586 ATTTATATTTATATACTATATATATGAACTATA
1 ATTTATATTTATATACTATATATATAAACTATA
* * *
30619 GTTTACA--TATGA-ACTGTATATATAAACTATA
1 ATTTATATTTAT-ATACTATATATATAAACTATA
* *
30650 TAGTTTACA--TATGA-ACTATATATATACACTATA
1 -A-TTTATATTTAT-ATACTATATATATAAACTATA
* *
30683 GTTGATATTTATATA
1 ATTTATATTTATATA
30698 TGAACTATAG
Statistics
Matches: 159, Mismatches: 23, Indels: 34
0.74 0.11 0.16
Matches are distributed among these distances:
27 34 0.21
28 7 0.04
29 5 0.03
30 4 0.03
31 30 0.19
32 12 0.08
33 67 0.42
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.47
Consensus pattern (33 bp):
ATTTATATTTATATACTATATATATAAACTATA
Found at i:30628 original size:18 final size:18
Alignment explanation
Indices: 30607--30766 Score: 93
Period size: 18 Copynumber: 8.7 Consensus size: 18
30597 TATACTATAT
30607 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
*
30625 ATATGAAC--T-G--TAT
1 ATATGAACTATAGTTTAC
*
30638 ATATAAACTATATAGTTTAC
1 ATATGAAC--TATAGTTTAC
30658 ATATGAACTATA-TATATAC
1 ATATGAACTATAGT-T-TAC
** *
30677 ACTAT-AGTTGATA-TTTAT
1 A-TATGAACT-ATAGTTTAC
30695 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
* *
30713 ATATAAACTATTGTTGATATTTAC
1 ATATGAACTA----T-A-GTTTAC
30737 ATATGAACTATAGTTTAC
1 ATATGAACTATAGTTTAC
30755 ATATGAACTATA
1 ATATGAACTATA
30767 TATATAATTT
Statistics
Matches: 109, Mismatches: 14, Indels: 38
0.68 0.09 0.24
Matches are distributed among these distances:
13 9 0.08
15 1 0.01
16 1 0.01
17 8 0.07
18 49 0.45
19 8 0.07
20 17 0.16
22 1 0.01
23 1 0.01
24 14 0.13
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (18 bp):
ATATGAACTATAGTTTAC
Found at i:30729 original size:42 final size:42
Alignment explanation
Indices: 30653--30766 Score: 157
Period size: 42 Copynumber: 2.8 Consensus size: 42
30643 AACTATATAG
*
30653 TTTACATATGAACTATA---T--ATATACACTATAGTTGATA
1 TTTACATATGAACTATAGTTTACATATAAACTATAGTTGATA
* *
30690 TTTATATATGAACTATAGTTTACATATAAACTATTGTTGATA
1 TTTACATATGAACTATAGTTTACATATAAACTATAGTTGATA
*
30732 TTTACATATGAACTATAGTTTACATATGAACTATA
1 TTTACATATGAACTATAGTTTACATATAAACTATA
30767 TATATAATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
37 16 0.24
40 1 0.02
42 49 0.74
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.42
Consensus pattern (42 bp):
TTTACATATGAACTATAGTTTACATATAAACTATAGTTGATA
Found at i:30872 original size:20 final size:20
Alignment explanation
Indices: 30856--31170 Score: 92
Period size: 20 Copynumber: 15.4 Consensus size: 20
30846 ATTCTATAGT
* *
30856 TTATATTTATATACTATATA
1 TTATATATATAAACTATATA
30876 TTATATATATAAACTATATA
1 TTATATATATAAACTATATA
30896 TACTATATAGTATAATTTAC-ATATGAA
1 T--TATATA-TATAA---ACTATAT--A
* * *
30923 CTATATATAAAAACCATATA
1 TTATATATATAAACTATATA
* * *
30943 -AACTATATACTATAGT-TGATA
1 TTA-TATATA-TAAACTAT-ATA
30964 TTTATATACTATATAA-TATA-A
1 -TTATATA-TATA-AACTATATA
30985 TT-TATACTAT--ACTATACTA
1 TTATATA-TATAAACTATA-TA
*
31004 TAATATATATAAACTATATA
1 TTATATATATAAACTATATA
31024 --ATATATATAAACTATATA
1 TTATATATATAAACTATATA
31042 TTATATAGTTCATTAGAA-TATATA
1 TTATATA--T-A-TA-AACTATATA
* * * *
31066 -AACTATATGGTATA-TATAAA
1 TTA-TATAT-ATAAACTATATA
* * * *
31086 CTATACAT-TATA-TAGTTTA
1 TTATATATATAAACTA-TATA
31105 TTAGTATATATAAACTATATA
1 TTA-TATATATAAACTATATA
31126 --ATATATATAAAC--TATA
1 TTATATATATAAACTATATA
* * *
31142 TGATATATCTAAACTATACA
1 TTATATATATAAACTATATA
31162 TTATATATA
1 TTATATATA
31171 GTTCATTAGT
Statistics
Matches: 226, Mismatches: 29, Indels: 80
0.67 0.09 0.24
Matches are distributed among these distances:
16 5 0.02
17 4 0.02
18 46 0.20
19 19 0.08
20 64 0.28
21 23 0.10
22 22 0.10
23 12 0.05
24 16 0.07
25 12 0.05
26 2 0.01
27 1 0.00
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (20 bp):
TTATATATATAAACTATATA
Found at i:30875 original size:2 final size:2
Alignment explanation
Indices: 30857--31248 Score: 63
Period size: 2 Copynumber: 188.5 Consensus size: 2
30847 TTCTATAGTT
* *
30857 TA TA TT TA TA TA CTA TA TA T- TA TA TA TA TA AA CTA TA TA TA CTA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA
* * * * *
30901 TA TA GTA TA -A TT TA CA TA TGA -A CTA TA TA TA AA AA CCA TA TA
1 TA TA -TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA TA -TA TA TA
* *
30943 AA CTA TA TA CTA TA GT- TGA TA TT TA TA TA CTA TA TA -A TA TA -A
1 TA -TA TA TA -TA TA -TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA
* *
30985 TT TA TA CTA TA CTA TA CTA TA -A TA TA TA TA AA CTA TA TA -A TA
1 TA TA TA -TA TA -TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
31027 TA TA TA AA CTA TA TA T- TA TA TA GT- TCA T- TA GA -A TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA
* * * * *
31066 AA CTA TA TGG TA TA TA TA AA CTA TA CA T- TA TA TA GTT TA T- TA
1 TA -TA TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA
* * *
31108 GTA TA TA TA AA CTA TA TA -A TA TA TA TA AA CTA TA TGA TA TA TC
1 -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA T-A TA TA TA
* * *
31151 TA AA CTA TA CA T- TA TA TA TA GT- TCA T- TA GTA TA TA TA AA CTA
1 TA TA -TA TA TA TA TA TA TA TA -TA T-A TA TA -TA TA TA TA TA -TA
*
31193 TA TA T- TA TA TA GT- TCA T- TA GTA TA TA TA AA CTA TA TA GTA TA
1 TA TA TA TA TA TA -TA T-A TA TA -TA TA TA TA TA -TA TA TA -TA TA
*
31235 TA TA AA T- TA TA TA T
1 TA TA TA TA TA TA TA T
31249 TGAAAAGTTC
Statistics
Matches: 283, Mismatches: 48, Indels: 118
0.63 0.11 0.26
Matches are distributed among these distances:
1 22 0.08
2 211 0.75
3 50 0.18
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (2 bp):
TA
Found at i:30882 original size:9 final size:9
Alignment explanation
Indices: 30863--31042 Score: 70
Period size: 9 Copynumber: 20.6 Consensus size: 9
30853 AGTTTATATT
30863 TATATACTA
1 TATATACTA
30872 TATATTA-TA
1 TATA-TACTA
30881 TATATAAACTA
1 TATAT--ACTA
30892 TATATACTA
1 TATATACTA
30901 TATAGTA-TA
1 TATA-TACTA
*
30910 -ATTTAC-A
1 TATATACTA
30917 TATGA-ACTA
1 TAT-ATACTA
30926 TATATA--A
1 TATATACTA
*
30933 -A-A-ACCA
1 TATATACTA
*
30939 TATAAAC--
1 TATATACTA
30946 TATATACTA
1 TATATACTA
*
30955 TAGTTGATA-TT
1 TA--T-ATACTA
30966 TATATACTA
1 TATATACTA
30975 TATAATA-TAA
1 TAT-ATACT-A
*
30985 TTTATACTA
1 TATATACTA
30994 TACTATACTA
1 TA-TATACTA
31004 TA-ATA-TA
1 TATATACTA
*
31011 TATAAACTA
1 TATATACTA
31020 TATAATA-TA
1 TAT-ATACTA
*
31029 TATAAACTA
1 TATATACTA
31038 TATAT
1 TATAT
31043 TATATAGTTC
Statistics
Matches: 131, Mismatches: 11, Indels: 58
0.65 0.05 0.29
Matches are distributed among these distances:
4 1 0.01
5 1 0.01
6 2 0.02
7 15 0.11
8 19 0.15
9 56 0.43
10 23 0.18
11 11 0.08
12 3 0.02
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (9 bp):
TATATACTA
Found at i:30905 original size:51 final size:50
Alignment explanation
Indices: 30850--31238 Score: 172
Period size: 51 Copynumber: 7.7 Consensus size: 50
30840 TACTACATTC
30850 TATAGTTTATATTTATATACTATATATTATATATATAAACTATATATACTA
1 TATAGTTTATATTTATATACTATATATTATATATATAAACTATATATA-TA
* * * * *
30901 TATAGTATA-ATTTACATATGAACTATATATAAAAACCATATAAAC--TATATA-C
1 TATAGTTTATATTT--ATAT--ACTATATAT-TATA-TATATAAACTATATATATA
* * * *
30953 TATAGTTGATATTTATATACTATATAATATA-ATTTATACTATACTATACTA
1 TATAGTTTATATTTATATACTATATATTATATATATAAACTATA-TATA-TA
*
31004 TA-A---TATA--TATAAACTATATA--ATATATATAAACTATATAT-TA
1 TATAGTTTATATTTATATACTATATATTATATATATAAACTATATATATA
* ** * ** *
31045 TATAGTTCATTAGAATATATA-AACTATATGGTATATATAAACTATACAT-TA
1 TATAGTTTA-TA-TTTATATACTA-TATATTATATATATAAACTATATATATA
*
31096 TATAGTTTATTAGTATATATAAACTATATA--ATATATATAAACTATATGATATA
1 TATAGTTTA-TA-T-T-TATATACTATATATTATATATATAAACTATAT-ATATA
* *** *
31149 TCTAAACTATACATTATATA-TAGT-TCATTAGTATATATAAACTATATAT-TA
1 TATAGTTTATA-TTTATATACTA-TAT-ATTA-TATATATAAACTATATATATA
* * *
31200 TATAGTTCATTAGTATATATAAACTATATAGTATATATA
1 TATAG-T--TTA-TATTTATATACTATATATTATATATA
31239 AATTATATAT
Statistics
Matches: 254, Mismatches: 44, Indels: 78
0.68 0.12 0.21
Matches are distributed among these distances:
41 4 0.02
42 1 0.00
43 6 0.02
44 10 0.04
45 13 0.05
46 8 0.03
47 3 0.01
48 5 0.02
49 24 0.09
50 12 0.05
51 66 0.26
52 18 0.07
53 42 0.17
54 27 0.11
55 7 0.03
56 8 0.03
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (50 bp):
TATAGTTTATATTTATATACTATATATTATATATATAAACTATATATATA
Found at i:30926 original size:34 final size:36
Alignment explanation
Indices: 30863--30931 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 36
30853 AGTTTATATT
*
30863 TATATACTATATATTATATATATAAACTATATATAC
1 TATATACTATATATTATACATATAAACTATATATAC
* *
30899 TATATAGTATA-ATT-TACATATGAACTATATATA
1 TATATACTATATATTATACATATAAACTATATATA
30932 AAAACCATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 17 0.57
35 3 0.10
36 10 0.33
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (36 bp):
TATATACTATATATTATACATATAAACTATATATAC
Found at i:30978 original size:7 final size:6
Alignment explanation
Indices: 30961--31248 Score: 54
Period size: 7 Copynumber: 46.7 Consensus size: 6
30951 ACTATAGTTG
* *
30961 ATATTT ATATACT ATATA- ATATA- ATTTAT ACTATACT ATACTAT A-ATAT
1 ATATAT ATATA-T ATATAT ATATAT ATATAT A-TATA-T ATA-TAT ATATAT
* * *
31010 ATATAA ACTATAT A-ATAT ATATAA ACTATAT AT-TAT ATAGT-T CAT-TAG
1 ATATAT A-TATAT ATATAT ATATAT A-TATAT ATATAT ATA-TAT -ATATAT
* * * * *
31058 A-ATAT ATAAACT ATATGGT ATATAT AAACTAT ACAT-T ATATAGT TTAT-T
1 ATATAT ATATA-T ATAT-AT ATATAT ATA-TAT ATATAT ATATA-T ATATAT
* * * *
31107 AGTATAT ATAAACT ATATA- ATATAT ATAAACT ATATGAT ATATCT AAACTAT
1 A-TATAT ATATA-T ATATAT ATATAT ATATA-T ATAT-AT ATATAT ATA-TAT
* *
31159 ACAT-T ATATAT AGT-TCAT -TAGTAT ATATAA ACTATAT AT-TAT ATAGT-T
1 ATATAT ATATAT A-TAT-AT ATA-TAT ATATAT A-TATAT ATATAT ATA-TAT
* *
31207 CAT-TAGT ATATAT AAACTAT ATAGTAT ATATAA AT-TAT ATAT
1 -ATATA-T ATATAT ATA-TAT ATA-TAT ATATAT ATATAT ATAT
31249 TGAAAAGTTC
Statistics
Matches: 206, Mismatches: 34, Indels: 84
0.64 0.10 0.26
Matches are distributed among these distances:
5 53 0.26
6 56 0.27
7 92 0.45
8 5 0.02
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (6 bp):
ATATAT
Found at i:31006 original size:74 final size:71
Alignment explanation
Indices: 30892--31028 Score: 177
Period size: 74 Copynumber: 1.9 Consensus size: 71
30882 ATATAAACTA
* *
30892 TATATACTATATAGTATAATTTACATATGAACTATATATAAAAACCATATAAACTATATACTATA
1 TATATACTATATAATATAATTTACATAT-AACTATATAT-AAAA-CATATAAACTATATAATATA
30957 GTTGATATT
63 GTTGATATT
* * *
30966 TATATACTATATAATATAATTTATACTAT-ACTATACTATAATATATATAAACTATATAATATA
1 TATATACTATATAATATAATTTACA-TATAACTATA-TATAAAACATATAAACTATATAATATA
31029 TATAAACTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
72 18 0.32
73 9 0.16
74 26 0.46
75 3 0.05
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (71 bp):
TATATACTATATAATATAATTTACATATAACTATATATAAAACATATAAACTATATAATATAGTT
GATATT
Found at i:31046 original size:18 final size:18
Alignment explanation
Indices: 31002--31247 Score: 187
Period size: 18 Copynumber: 14.2 Consensus size: 18
30992 TATACTATAC
*
31002 TATAATATATATAAACTA
1 TATAGTATATATAAACTA
*
31020 TATAATATATATAAACTA
1 TATAGTATATATAAACTA
**
31038 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
*
31054 T-TAGAATATATAAACTA
1 TATAGTATATATAAACTA
*
31071 TATGGTATATATAAACTA
1 TATAGTATATATAAACTA
* ***
31089 TACA-T-TATATAGTTTA
1 TATAGTATATATAAACTA
31105 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
*
31122 TATAATATATATAAACTA
1 TATAGTATATATAAACTA
*
31140 TAT-GATATATCTAAACTA
1 TATAG-TATATATAAACTA
* * **
31158 TACATTATATAT-AGTTCA
1 TATAGTATATATAAACT-A
31176 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
**
31193 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
31209 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
*
31226 TATAGTATATATAAATTA
1 TATAGTATATATAAACTA
31244 TATA
1 TATA
31248 TTGAAAAGTT
Statistics
Matches: 177, Mismatches: 33, Indels: 36
0.72 0.13 0.15
Matches are distributed among these distances:
15 9 0.05
16 25 0.14
17 38 0.21
18 105 0.59
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:31098 original size:69 final size:68
Alignment explanation
Indices: 31006--31248 Score: 196
Period size: 69 Copynumber: 3.6 Consensus size: 68
30996 CTATACTATA
* * * *
31006 ATATATATAAACTATATAATATATATAAACTA-TATATTATATAGT-TCATTAGA-ATATATAAA
1 ATATATATAAACTATACATTATATATAAACTAGTATA-TATAAACTAT-A-TA-ATATATATAAA
31068 CTATATG
62 CTATATG
* ** *
31075 GTATATATAAACTATACATTATATAGTTTATTAGTATATATAAACTATATAATATATATAAACTA
1 ATATATATAAACTATACATTATATA-TAAACTAGTATATATAAACTATATAATATATATAAACTA
31140 TATG
65 TATG
* * * * **
31144 ATATATCTAAACTATACATTATATATAGTTCATTAGTATATATAAACTATATATTATATAGTTCA
1 ATATATATAAACTATACATTATATATA---AACTAGTATATATAAACTATATAATATATA-TAAA
31209 -T-TA-G
62 CTATATG
* * *
31213 -TATATATAAACTATATAGTATATATAAATTA-TATAT
1 ATATATATAAACTATACATTATATATAAACTAGTATAT
31249 TGAAAAGTTC
Statistics
Matches: 147, Mismatches: 19, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
64 5 0.03
65 4 0.03
68 25 0.17
69 64 0.44
70 13 0.09
71 34 0.23
72 2 0.01
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (68 bp):
ATATATATAAACTATACATTATATATAAACTAGTATATATAAACTATATAATATATATAAACTAT
ATG
Found at i:31179 original size:71 final size:69
Alignment explanation
Indices: 31059--31203 Score: 236
Period size: 71 Copynumber: 2.1 Consensus size: 69
31049 GTTCATTAGA
* *
31059 ATATATAAACTATATGGTATATATAAACTATACATTATATAGTTTATTAGTATATATAAACTATA
1 ATATATAAACTATATGATATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTATA
31124 TAAT
66 TAAT
*
31128 ATATATAAACTATATGATATATCTAAACTATACATTATATATAGTTCATTAGTATATATAAACTA
1 ATATATAAACTATATGATATATATAAACTATACA-T-TATATAGTTCATTAGTATATATAAACTA
*
31193 TATATT
64 TATAAT
31199 ATATA
1 ATATA
31204 GTTCATTAGT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
69 32 0.46
70 1 0.01
71 37 0.53
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (69 bp):
ATATATAAACTATATGATATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTATA
TAAT
Found at i:31185 original size:17 final size:17
Alignment explanation
Indices: 31163--31220 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
31153 AACTATACAT
31163 TATATATAGTTCATTAG
1 TATATATAGTTCATTAG
**
31180 TATATATA-AAC-TATA-
1 TATATATAGTTCAT-TAG
31195 TATTATATAGTTCATTAG
1 TA-TATATAGTTCATTAG
31213 TATATATA
1 TATATATA
31221 AACTATATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 3 0.09
16 9 0.28
17 17 0.53
18 3 0.09
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (17 bp):
TATATATAGTTCATTAG
Found at i:31206 original size:104 final size:102
Alignment explanation
Indices: 31007--31249 Score: 312
Period size: 104 Copynumber: 2.4 Consensus size: 102
30997 TATACTATAA
** *
31007 TATATATAAACTATATAATATATATAAACTATATATTATATAGTTCATTAGAATATATAAACTAT
1 TATATATAAACTATATAATATATATAAACTATATATTATATAACTCATTACAATATATAAACTAT
* *
31072 ATGGTATATATAAACTATACATTATATAGTTTATTAG
66 ATAGTATATATAAACTATACATTATATAGTTCATTAG
* * * *
31109 TATATATAAACTATATAATATATATAAACTATATGATATATCTAAACT-A-TACATTATATATAG
1 TATATATAAACTATATAATATATATAAACTATAT-AT-TATAT-AACTCATTACAATATATAAAC
*
31172 T-TCATTAGTATATATAAACTATATATTATATAGTTCATTAG
63 TAT-A-TAGTATATATAAACTATACATTATATAGTTCATTAG
* *
31213 TATATATAAACTATATAGTATATATAAATTATATATT
1 TATATATAAACTATATAATATATATAAACTATATATT
31250 GAAAAGTTCA
Statistics
Matches: 124, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
102 36 0.29
103 16 0.13
104 70 0.56
105 2 0.02
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (102 bp):
TATATATAAACTATATAATATATATAAACTATATATTATATAACTCATTACAATATATAAACTAT
ATAGTATATATAAACTATACATTATATAGTTCATTAG
Found at i:31248 original size:51 final size:51
Alignment explanation
Indices: 31007--31280 Score: 326
Period size: 51 Copynumber: 5.3 Consensus size: 51
30997 TATACTATAA
*
31007 TATATATAAACTATATAATATATATAAACTATATATTATATAGTTCATTAG
1 TATATATAAACTATATAGTATATATAAACTATATATTATATAGTTCATTAG
* * * *
31058 AATATATAAACTATATGGTATATATAAACTATACATTATATAGTTTATTAG
1 TATATATAAACTATATAGTATATATAAACTATATATTATATAGTTCATTAG
* * *
31109 TATATATAAACTATATAATATATATAAACTATATGATATATCTAAACTATACATTA-
1 TATATATAAACTATATAGTATATATAAACTATAT-AT-TA--TATAGT-T-CATTAG
*
31165 TATATAGT--TC-AT-TAGTATATATAAACTATATATTATATAGTTCATTAG
1 TATATA-TAAACTATATAGTATATATAAACTATATATTATATAGTTCATTAG
* *
31213 TATATATAAACTATATAGTATATATAAATTATATATTGA-AAAGTTCATTAG
1 TATATATAAACTATATAGTATATATAAACTATATATT-ATATAGTTCATTAG
*
31264 TATATATAACCTATATA
1 TATATATAAACTATATA
31281 TTTATTTATT
Statistics
Matches: 190, Mismatches: 20, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
47 6 0.03
48 7 0.04
49 5 0.03
50 2 0.01
51 126 0.66
52 5 0.03
53 20 0.11
54 2 0.01
55 5 0.03
56 7 0.04
57 5 0.03
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (51 bp):
TATATATAAACTATATAGTATATATAAACTATATATTATATAGTTCATTAG
Found at i:31930 original size:101 final size:101
Alignment explanation
Indices: 31688--32030 Score: 458
Period size: 101 Copynumber: 3.4 Consensus size: 101
31678 TTCATCCGTG
* * * *
31688 TTCATCACTTGTTCATCCCAGTTCTTCCCCAAAACTCTCTTTTGATCTTCAAAAATACCAAAACC
1 TTCATC-CGTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCAAAACC
* * ** *
31753 AAAACCATTTCGTGTTTTTTTCCAATCAAATGCCAAAACA
65 CAAACCATTTCATGTTTTTTT---ATCAAACACCAAAAAA
*
31793 TTCATCCGTGTTCATCCCAGCTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCAAAACCC
1 TTCATCCGTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCAAAACCC
31858 AAACCATTTCATGTTTTTTTATCAAACACCAAAAAA
66 AAACCATTTCATGTTTTTTTATCAAACACCAAAAAA
31894 TTCATCCGTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCAAAACCC
1 TTCATCCGTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCAAAACCC
** *
31959 AAACCATTTCAT-TTTTTCGATCAAACACTC-ACAAA
66 AAACCATTTCATGTTTTTTTATCAAACAC-CAAAAAA
* * **
31994 TTCATCCATTATTCATCCGTGTTCTTCCCC-AAACCCT
1 TTCATCC-GTGTTCATCCCAGTTCTTCCCCAAAACCCT
32031 TATAAACACC
Statistics
Matches: 218, Mismatches: 18, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
100 32 0.15
101 108 0.50
104 72 0.33
105 6 0.03
ACGTcount: A:0.32, C:0.32, G:0.05, T:0.31
Consensus pattern (101 bp):
TTCATCCGTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCAAAACCC
AAACCATTTCATGTTTTTTTATCAAACACCAAAAAA
Found at i:32238 original size:6 final size:6
Alignment explanation
Indices: 32202--32277 Score: 89
Period size: 6 Copynumber: 12.7 Consensus size: 6
32192 ACCCTAAGTA
* * * * *
32202 AAACCC AATCCC GAACCC AAACCC GATCCC AAACCC AAACCC AAACCT
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC
* *
32250 AAACCC AAACCC AAACCC GAATCC AAAC
1 AAACCC AAACCC AAACCC AAACCC AAAC
32278 TGAACCCCGA
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.45, C:0.46, G:0.04, T:0.05
Consensus pattern (6 bp):
AAACCC
Found at i:32599 original size:2 final size:2
Alignment explanation
Indices: 32592--32622 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
32582 TATATTCTTG
32592 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32623 CGGGTATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44261 original size:65 final size:65
Alignment explanation
Indices: 44164--44370 Score: 276
Period size: 65 Copynumber: 3.2 Consensus size: 65
44154 TTTGAAATTA
* * *
44164 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAACCATCTTTGAGTCT
1 TTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATCATCTTTGAGT-T
44229 -
65 G
* * * * *
44229 TTTCCCTTGGAACGAATTTTATCTCTCGTGAGATATTTTCTCTTGAAACAATCATCTTTGAGTTG
1 TTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATCATCTTTGAGTTG
* *
44294 TTTCCATTGAAACGAATTTTGTCTCTTTTGAGACAGTTTCTCTTG-AA-AATCATCTTTGAGTAT
1 TTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATCATCTTTGAGT-T
44357 G
65 G
*
44358 TTTTCCTTGAAAC
1 TTTCCCTTGAAAC
44371 ATTATCCCTA
Statistics
Matches: 123, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
63 14 0.11
64 16 0.13
65 93 0.76
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (65 bp):
TTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATCATCTTTGAGTTG
Found at i:44506 original size:48 final size:48
Alignment explanation
Indices: 44435--44553 Score: 193
Period size: 48 Copynumber: 2.5 Consensus size: 48
44425 CGACCAGACC
*
44435 TCCTCATCACGTAGGAACTGTGTTATCATCCCTAAAGATGATCTACCA
1 TCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGATCTACCA
* * *
44483 TCCTCATCACGTAGGAACCGTGTTATTATCCCTAAAGATGGTTTACCA
1 TCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGATCTACCA
*
44531 TCCTCATCACGTAGGAATCGTGT
1 TCCTCATCACGTAGGAACCGTGT
44554 CATCCACTGA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (48 bp):
TCCTCATCACGTAGGAACCGTGTTATCATCCCTAAAGATGATCTACCA
Found at i:44935 original size:3 final size:3
Alignment explanation
Indices: 44929--44964 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
44919 CTAAAAAAAT
*
44929 ATA ATA AAA ATA ATA ATA ATTA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA AT
44965 TATTATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:44953 original size:13 final size:13
Alignment explanation
Indices: 44937--44961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44927 ATATAATAAA
44937 AATAATAATAATT
1 AATAATAATAATT
44950 AATAATAATAAT
1 AATAATAATAAT
44962 AATTATTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATAATAATAATT
Found at i:44954 original size:19 final size:19
Alignment explanation
Indices: 44930--44969 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
44920 TAAAAAAATA
44930 TAATAAAAATAATAATAAT
1 TAATAAAAATAATAATAAT
* *
44949 TAATAATAATAATAATTAT
1 TAATAAAAATAATAATAAT
44968 TA
1 TA
44970 TTATTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAATAAAAATAATAATAAT
Found at i:50098 original size:16 final size:16
Alignment explanation
Indices: 50065--50098 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
50055 TTACTATTCA
**
50065 CGTGAATAGTGATCTT
1 CGTGAATAGTGAAATT
50081 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
50097 CG
1 CG
50099 GTCGGTGATA
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:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Done.