Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005791.1 Hibiscus syriacus cultivar Beakdansim tig00013578_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: 52236
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2924 original size:86 final size:86
Alignment explanation
Indices: 2780--2940 Score: 243
Period size: 85 Copynumber: 1.9 Consensus size: 86
2770 TATGTTATAT
*
2780 CATTTAACCGAAAATATTATCAAGCACAACAAATATTAGGTAGCGCTTATATAATGTAAT-GGTA
1 CATTTAACCGAAAATATTATCAAGCACAACAAAAATTAGGTAGCGCTTATATAATGTAATAGGTA
*
2844 ACGCTTATATAATAAAATAGA
66 ACACTTATATAATAAAATAGA
* * * *
2865 CATTTAACCGAAAATATTATTAAGTACAATAATAAATTAGGTAGCGTTTATATAATGTAATAGGT
1 CATTTAACCGAAAATATTATCAAGCACAACAA-AAATTAGGTAGCGCTTATATAATGTAATAGGT
*
2930 AGCACTTATAT
65 AACACTTATAT
2941 TGATCTATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
85 29 0.43
86 26 0.39
87 12 0.18
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.32
Consensus pattern (86 bp):
CATTTAACCGAAAATATTATCAAGCACAACAAAAATTAGGTAGCGCTTATATAATGTAATAGGTA
ACACTTATATAATAAAATAGA
Found at i:3391 original size:200 final size:197
Alignment explanation
Indices: 2962--3413 Score: 450
Period size: 197 Copynumber: 2.3 Consensus size: 197
2952 TTCATAAAAT
* * * * * * * *
2962 CGGTAAATTTAAACCGGTTACATT-ATAAATTGACATATTATATTAT-GTATATCGGTTTCGATG
1 CGGTATATTTTAACCGGTTACATTGA-AAATTTACCTATTACATAATAAT-TATCGATTTCGATG
* * * * *
3025 TTTTCAGGATCGATACAATTTTAAATGTATTGACACTTTATGCGTGCAATTCGTTTGTGCTTTAT
64 TTTTCAGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCCTTCAT
* * * * * *
3090 TTTGGAAAAACGTATCGATACATATTTAAAGAGTGTCGATACATAATATAGACCTATTTGCTAAT
129 TTTGAAAAAACGTATCGACACAAATTAAAAAAGTGTCGATACATAATATAGACATATTTGCTAAT
*
3155 TAAC
194 GAAC
* * *
3159 CGGTATATTTTAACCTGTTACATTGAAAATTTATCTGTTACATAATAATTATCGATTTCGATG-T
1 CGGTATATTTTAACCGGTTACATTGAAAATTTACCTATTACATAATAATTATCGATTTCGATGTT
* * * *
3223 TTCGAGGATCGATAC-TTTTTACAAATGTATCGATATTTTATGCGTACACCTCGTTT-TCCATTC
66 TTC-AGGATCGATACAATTTT--AAATGTATCGACACTTTATGCGTACAACTCGTTTGTCC-TTC
* * * * *
3286 ATTTTGAAAAAATGTATCGACACAAATTAAACAAAGTGTCGATACTTTATGTTGACATATTCT-C
127 ATTTTGAAAAAACGTATCGACACAAATTAAA-AAAGTGTCGATACATAATATAGACATATT-TGC
*
3350 TCATGAACC
190 TAATGAA-C
* *
3359 CGGTATATTTCT-ACCGGTTACATTGGAAATTTACCTATTACATTATAATTATCGA
1 CGGTATATTT-TAACCGGTTACATTGAAAATTTACCTATTACATAATAATTATCGA
3414 CACAAAATCT
Statistics
Matches: 207, Mismatches: 38, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
196 8 0.04
197 61 0.29
198 58 0.28
199 29 0.14
200 50 0.24
201 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (197 bp):
CGGTATATTTTAACCGGTTACATTGAAAATTTACCTATTACATAATAATTATCGATTTCGATGTT
TTCAGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTACAACTCGTTTGTCCTTCATTT
TGAAAAAACGTATCGACACAAATTAAAAAAGTGTCGATACATAATATAGACATATTTGCTAATGA
AC
Found at i:6772 original size:21 final size:22
Alignment explanation
Indices: 6746--6792 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
6736 TAGTATGGAC
*
6746 ATAAAGTGTCGACACA-AATGT
1 ATAAAGTATCGACACATAATGT
* *
6767 ATAAAGTATCGATACATTATGT
1 ATAAAGTATCGACACATAATGT
6789 ATAA
1 ATAA
6793 CTTTTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.30
Consensus pattern (22 bp):
ATAAAGTATCGACACATAATGT
Found at i:6896 original size:198 final size:197
Alignment explanation
Indices: 6547--7453 Score: 1024
Period size: 201 Copynumber: 4.5 Consensus size: 197
6537 CGTAATTTTA
* * *
6547 AAAAGTATCGACACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTATTATGTCATAA-AAC
1 AAAAGTATCGACACAAATGTATAAAGTGTCGATACATTA-TGTATACCT-TT-T-TTATAATAAC
* * * * ** *
6610 CAGTATATTTCAACCGGTTACATTGTAAAGTGGCCTATTACATTATCATTACGGGTTTCGATGTT
62 CGGTATATTTAAACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTT
* * * * ** *
6675 TTTAGGATAGACACTTTTTATAAATGTATCGACACTTTTTCATGAACTTGTTTGGAAAATTTAGT
127 TTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATACATT
6740 ATGGAC
192 ATGGAC
* * * *
6746 ATAAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATAACTTTTTTTTAATAACCGG
1 A-AAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACCTTTTTTATAATAACCGG
* * *
6811 TATGTTTAAACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTT
65 TATATTTAAACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTT
* * **
6876 GGGATCGACACTGGTTATAAATGTATCGACACATTTTCGTGAACTTGTTTGGAAAATTTATTATG
130 GGGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATACATTATG
6941 GAC
195 GAC
* * *
6944 ---A-TGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAATAACCG
1 AAAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACC-TT-TTTTATAATAACCG
* * * *
7005 GTATATTTAGACCGGTTATATTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTT
64 GTATATTTAAACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTT
*
7070 TGGGATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGCACTTGGTTTGG-AAATACATT
129 TGGGATCGACACTTGTTATAAATGTATCGACAC-TTTTTCGTGAACTT-GTTTGGAAAATACATT
7134 ATGGAC
192 ATGGAC
* * * *
7140 AACATGTATCGGCACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTATTTTCTCATAA-AA
1 AA-AAGTATCGACACAAATGTATAAAGTGTCGATACATTA-TGTATACCT-TTTT-T-ATAATAA
** * * * * *
7203 CATGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTCGATGT
61 CCGGTATATTTAAACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGT
* * *
7268 TTTTGGGATCGACACTTGATATAAATGTGTCAACACTTATTT-GTGAACTTGTTTTGGTTGGAAA
126 TTTTGGGATCGACACTTGTTATAAATGTATCGACACTT-TTTCGTGAACTTG---T--TTGGAAA
7332 ATACATTATGGAC
185 ATACATTATGGAC
* * * * *
7345 ACAAAGTATCGACACAAATGTATAAAGTGTCGACACTTTATGTATACCTCTTTTCTCATAAACCG
1 A-AAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACCTTTTTTATAAT-AACCG
* * *
7410 GTATATTTAGACTGGTTACATTGTTATTTTACCTATTACATTAT
64 GTATATTTAAACCGGTTACATTGTTATGTTACCTATTACATTAT
7454 GTTGAGTTAA
Statistics
Matches: 608, Mismatches: 73, Indels: 49
0.83 0.10 0.07
Matches are distributed among these distances:
193 41 0.07
194 3 0.00
195 108 0.18
196 25 0.04
197 10 0.02
198 123 0.20
199 4 0.01
200 54 0.09
201 130 0.21
202 6 0.01
203 1 0.00
204 47 0.08
205 53 0.09
206 3 0.00
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.38
Consensus pattern (197 bp):
AAAAGTATCGACACAAATGTATAAAGTGTCGATACATTATGTATACCTTTTTTATAATAACCGGT
ATATTTAAACCGGTTACATTGTTATGTTACCTATTACATTATAATTACGGGTTTCGATGTTTTTG
GGATCGACACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATACATTATGG
AC
Found at i:7348 original size:393 final size:389
Alignment explanation
Indices: 6552--7353 Score: 897
Period size: 393 Copynumber: 2.0 Consensus size: 389
6542 TTTTAAAAAG
* *
6552 TATCGACACAAATGAATAAAGTGTCGATACATATTGTAGACCTATTATGTCATAAAACCAGTATA
1 TATCGACACAAATGTATAAAGTATCGATACATATTGTAGACCTATTATGTCATAAAACCAGTATA
* *
6617 TTTCAACCGGTTACATTGTAAAGTGGCCTATTACATTATCATTACGGGTTTCGATGTTTTTAGGA
66 TTTCAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTTAGGA
* **
6682 TAGACACTTTTTATAAATGTATCGACACTTTTTCATGAACTTGTTTGGAAAATTTAGTATGGACA
131 TAGACACTTGTTATAAATGTATCGACACTTTTTCATGAACTTGTTTGGAAAATACAGTATGGACA
* * * * *
6747 TAAAGTGTCGACACAAATGTATAAAGTATCGATACATTATGTATAACTTTTTTTTAATAACCGGT
196 TAAAGTATCGACACAAATGAATAAAGTATCGATACATTATGTAGAACTTTTTTATAATAACAGGT
** * * * * *
6812 ATGTTTAAACCGGTTACATTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTG
261 AAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTTG
* * * **
6877 GGATCGACACTGGTTATAAATGTATCGACACATTTTCGTGAACTTGTTTGGAAAATTTATTATGG
326 GGATCGACACTGGATATAAATGTATCAACACATTTTCGTGAACTTGTTTGG---ATTGAAAAT-G
6942 ACA
387 ACA
* * * * ** *
6945 TGTCGACACAAATGTATAAAGTATCGATACAT-TATGTATACCT-TTCTTTTTTAATAACCGGTA
1 TATCGACACAAATGTATAAAGTATCGATACATAT-TGTAGACCTATTATGTCATAA-AACCAGTA
* * * * * * *
7008 TATTT-AGACCGGTTATATTGTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTG
64 TATTTCA-ACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTTA
* * * *
7072 GGATCGACACTTGTTATAAATGTATCGACACTTTTTTCGTGCACTTGGTTTGG-AAATACATTAT
128 GGATAGACACTTGTTATAAATGTATCGACAC-TTTTTCATGAACTT-GTTTGGAAAATACAGTAT
* * * *
7136 GGACA-ACATGTATCGGCACAAATGAATAAAGTGTCGATACA-TATTGTAGACCTATTTTCTCAT
191 GGACATA-AAGTATCGACACAAATGAATAAAGTATCGATACATTA-TGTAGAACT-TTTT-T-AT
* *
7199 AA-AACATGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAGTTACGGGTTTC
251 AATAACAGGTAAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTC
* * *
7263 GATGTTTTTGGGATCGACACTTGATATAAATGTGTCAACAC-TTATTTGTGAACTTGTTTTGG-T
316 GATGTTTTTGGGATCGACACTGGATATAAATGTATCAACACATT-TTCGTGAACTTG-TTTGGAT
7326 TGGAAAAT-ACA
379 T-GAAAATGACA
*
7337 TTATGGACACAAA-GTAT
1 -TATCGACACAAATGTAT
7354 CGACACAAAT
Statistics
Matches: 342, Mismatches: 53, Indels: 29
0.81 0.12 0.07
Matches are distributed among these distances:
392 16 0.05
393 141 0.41
394 64 0.19
395 12 0.04
396 101 0.30
397 8 0.02
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.38
Consensus pattern (389 bp):
TATCGACACAAATGTATAAAGTATCGATACATATTGTAGACCTATTATGTCATAAAACCAGTATA
TTTCAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTTAGGA
TAGACACTTGTTATAAATGTATCGACACTTTTTCATGAACTTGTTTGGAAAATACAGTATGGACA
TAAAGTATCGACACAAATGAATAAAGTATCGATACATTATGTAGAACTTTTTTATAATAACAGGT
AAATTTAAACCGGTTACATTGTAAAGTGACCTATTACATTATAATTACGGGTTTCGATGTTTTTG
GGATCGACACTGGATATAAATGTATCAACACATTTTCGTGAACTTGTTTGGATTGAAAATGACA
Found at i:8207 original size:18 final size:17
Alignment explanation
Indices: 8153--8201 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
8143 TTGGACTCCT
* *
8153 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
8171 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
8189 AGTGCATTCGATG
1 AGTGCA-TCGATG
8202 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:8267 original size:45 final size:42
Alignment explanation
Indices: 8170--8276 Score: 124
Period size: 45 Copynumber: 2.4 Consensus size: 42
8160 CGGTGCACTA
* *
8170 AGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAAT
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAAT
* *
8212 AGCCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAAT
1 AG---AGTGCATCGATGCATCAAATGCATTCGATGTTTGAA--AAAT
8259 CAGAGTGCATCGATGCAT
1 -AGAGTGCATCGATGCAT
8277 GAAGAGTGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.04
45 46 0.85
47 4 0.07
48 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (42 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAAAT
Found at i:8284 original size:19 final size:19
Alignment explanation
Indices: 8260--8310 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
8250 TAATTAAATC
8260 AGAGTGCATCGATGCATGA
1 AGAGTGCATCGATGCATGA
* *
8279 AGAGTGCATCGGTACATGA
1 AGAGTGCATCGATGCATGA
8298 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
8311 TTTCAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 5 0.19
19 18 0.67
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGA
Found at i:8286 original size:64 final size:64
Alignment explanation
Indices: 8218--8342 Score: 171
Period size: 64 Copynumber: 1.9 Consensus size: 64
8208 AAATAGCCTG
* *
8218 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCA-GAGTGCATCGATGCATGAAGA
1 GTGCATCGATACATCAAATGCATTCGATGTTTCAATTAAATCATGA-TGCATCGATGCATGAAGA
* * * *
8282 GTGCATCGGTACATGAAATGCATTCGATGTTTCAATTTATTCATTGATGCATCGATGCATG
1 GTGCATCGATACATCAAATGCATTCGATGTTTCAATTAAATCA-TGATGCATCGATGCATG
8343 GTATTGATGC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 37 0.70
65 14 0.26
66 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (64 bp):
GTGCATCGATACATCAAATGCATTCGATGTTTCAATTAAATCATGATGCATCGATGCATGAAGA
Found at i:8348 original size:21 final size:21
Alignment explanation
Indices: 8324--8363 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
8314 CAATTTATTC
8324 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
* *
8345 ATTGATGCATTGGTGCATG
1 ATTGATGCATCGATGCATG
8364 CCTTTGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.30, T:0.35
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:10982 original size:24 final size:23
Alignment explanation
Indices: 10911--10990 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 23
10901 CATGGTTTTG
* *
10911 TGCATCGATGCATATTCAAGGCA
1 TGCATCGATGCACATTCAAGGGA
* *
10934 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
10955 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
*
10979 TGCATTGATGCA
1 TGCATCGATGCA
10991 TTGTAAAGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 4 0.09
21 12 0.27
23 11 0.24
24 16 0.36
25 2 0.04
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:16863 original size:64 final size:63
Alignment explanation
Indices: 16788--16950 Score: 195
Period size: 64 Copynumber: 2.6 Consensus size: 63
16778 CAGTGCACTT
* *
16788 AGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AGCCTGGTGCATCGATGCATG
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAATCAG---AGTGCATCGATGCATG
*
16851 G
63 A
*** * *
16852 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGA
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAA-TAAATCAGAGTGCATCGATGCATGA
*
16916 AGAGTGCATCGGTGCATGAAATGCATTCGATGTTT
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTT
16951 CAATTTATTC
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
64 77 0.93
66 4 0.05
67 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (63 bp):
AGAGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAATCAGAGTGCATCGATGCATGA
Found at i:16921 original size:19 final size:19
Alignment explanation
Indices: 16897--16947 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
16887 TAATTAAATC
16897 AGAGTGCATCGATGCATGA
1 AGAGTGCATCGATGCATGA
*
16916 AGAGTGCATCGGTGCATGA
1 AGAGTGCATCGATGCATGA
16935 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
16948 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGA
Found at i:16985 original size:21 final size:21
Alignment explanation
Indices: 16961--17000 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
16951 CAATTTATTC
16961 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
16982 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
17001 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:18415 original size:15 final size:15
Alignment explanation
Indices: 18395--18429 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
18385 ATATCCTCAA
18395 AAGAGGTGGGTTGAG
1 AAGAGGTGGGTTGAG
18410 AAGAGGTGGGTTGAG
1 AAGAGGTGGGTTGAG
18425 AAGAG
1 AAGAG
18430 CCCCGATTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.51, T:0.17
Consensus pattern (15 bp):
AAGAGGTGGGTTGAG
Found at i:19118 original size:198 final size:198
Alignment explanation
Indices: 18852--19984 Score: 1774
Period size: 198 Copynumber: 5.7 Consensus size: 198
18842 AATTTCATTG
* * * * ** * ** **
18852 TTTTAGGATCGATACTTTTTATAAATGTATCGACACTTTTTTGTG-CACTTTTTGACCATTTACA
1 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGAC-CTTGGTAAGGAAAT-CA
* *
18916 TTCTGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTTATGTACACCTATTTTCTC
64 TTCTGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTC
* * *
18981 ATAAACCGGTGTATTTAGACTGGTTAGATTGATAATTTACCTATTACATTATAATTATGGGTCTT
129 ATAAACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATAACATTATAATTATGGGTCTC
19046 GATGT
194 GATGT
19051 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
1 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
*
19116 CTGGACACAAAGTATCGACACAAATTAAAAAAGTGTTGATACTTCATGTACACCTGTTTTCTCAT
66 CTGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCAT
*
19181 AAACCGGTGTATTTAGACCAGTTAGATTGATAATTTACCTATAACATTATAATTATGGGTCTCGA
131 AAACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATAACATTATAATTATGGGTCTCGA
19246 TGT
196 TGT
19249 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
1 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
* *
19314 CTGGACACAAAGTATCGACACAAATTAAAAAAAGTGTCGATATTTCATGTACACATGTTTTCTCA
66 CTGGACACAAAGTATCGACACAAATT-AAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCA
* *
19379 TAAACCAGTGTATTTAGA-CGGTTAGATTGATAATTTACCTATTACATTATAATTATGGGTCTCG
130 TAAACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATAACATTATAATTATGGGTCTCG
19443 ATGT
195 ATGT
* *
19447 TTTTGGGATCGATACTTTTTATAAATATATCGACACATTATGGTAACCTTGGTAAGGAAATCATT
1 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
*
19512 TTGGTA-ACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCA
66 CTGG-ACACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCA
19576 TAAACCGGTGTATTTA-ACCGGTTAGATTGATAATTTACCTATAACATTATAATTATGGGTCTCG
130 TAAACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATAACATTATAATTATGGGTCTCG
19640 ATGT
195 ATGT
19644 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
1 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
* * * *
19709 CTAGACACAAAGTATCGACACAAATTAAAAAAGTATCGATACTTCGTGTACACCTATTTTCTCAT
66 CTGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCAT
*
19774 AAACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATAACATTATAATTATAGGTCTCGA
131 AAACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATAACATTATAATTATGGGTCTCGA
19839 TGT
196 TGT
* * * * **
19842 TTTTAGGATCGATACTTTGTATAAATATATCGACATATT-TCCATG-CACTTGGTAAGGAAATCA
1 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTAT-GGTGAC-CTTGGTAAGGAAATCA
* * *
19905 TTATGGACACAAAGTATGGGATCGACACAAATTAAACAAGTGTCGATACTTTATGTACACCTGTT
64 TTCTGGACACAAAG--T---ATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACCTGTT
19970 TTCTCATAAACCGGT
124 TTCTCATAAACCGGT
19985 ATACTTGGAC
Statistics
Matches: 869, Mismatches: 52, Indels: 22
0.92 0.06 0.02
Matches are distributed among these distances:
196 2 0.00
197 238 0.27
198 471 0.54
199 101 0.12
200 2 0.00
203 55 0.06
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (198 bp):
TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
CTGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACCTGTTTTCTCAT
AAACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATAACATTATAATTATGGGTCTCGA
TGT
Found at i:19837 original size:395 final size:396
Alignment explanation
Indices: 18852--19984 Score: 1794
Period size: 395 Copynumber: 2.8 Consensus size: 396
18842 AATTTCATTG
* * * * ** * ** **
18852 TTTTAGGATCGATACTTTTTATAAATGTATCGACACTTTTTTGTG-CACTTTTTGACCATTTACA
1 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGAC-CTTGGTAAGGAAAT-CA
*
18916 TTCTGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTTATGTACACCTATTTTCTC
64 TTCTGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACCTATTTTCTC
* *
18981 ATAAACCGGTGTATTTAGACTGGTTAGATTGATAATTTACCTATTACATTATAATTATGGGTCTT
129 ATAAACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATTACATTATAATTATGGGTCTC
* *
19046 GATGTTTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAA
194 GATGTTTTTGGGATCGATACTTTTTATAAATATATCGACACATTATGGTAACCTTGGTAAGGAAA
* *
19111 TCATTCTGGACACAAAGTATCGACACAAATTAAAAAAGTGTTGATACTTCATGTACACCTGTTTT
259 TCATTATGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACCTGTTTT
19176 CTCATAAACCGGTGTATTTAGACCAGTTAGATTGATAATTTACCTATAACATTATAATTATGGGT
324 CTCATAAACCGGTGTATTTAGACCAGTTAGATTGATAATTTACCTATAACATTATAATTATGGGT
19241 CTCGATGT
389 CTCGATGT
19249 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
1 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
* * *
19314 CTGGACACAAAGTATCGACACAAATTAAAAAAAGTGTCGATATTTCATGTACACATGTTTTCTCA
66 CTGGACACAAAGTATCGACACAAATT-AAAAAAGTGTCGATACTTCATGTACACCTATTTTCTCA
*
19379 TAAACCAGTGTATTTAGA-CGGTTAGATTGATAATTTACCTATTACATTATAATTATGGGTCTCG
130 TAAACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATTACATTATAATTATGGGTCTCG
19443 ATGTTTTTGGGATCGATACTTTTTATAAATATATCGACACATTATGGTAACCTTGGTAAGGAAAT
195 ATGTTTTTGGGATCGATACTTTTTATAAATATATCGACACATTATGGTAACCTTGGTAAGGAAAT
*
19508 CATTTTGGTA-ACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACCTGTTTT
260 CATTATGG-ACACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACCTGTTTT
*
19572 CTCATAAACCGGTGTATTTA-ACCGGTTAGATTGATAATTTACCTATAACATTATAATTATGGGT
324 CTCATAAACCGGTGTATTTAGACCAGTTAGATTGATAATTTACCTATAACATTATAATTATGGGT
19636 CTCGATGT
389 CTCGATGT
19644 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
1 TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
* * *
19709 CTAGACACAAAGTATCGACACAAATTAAAAAAGTATCGATACTTCGTGTACACCTATTTTCTCAT
66 CTGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACCTATTTTCTCAT
* *
19774 AAACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATAACATTATAATTATAGGTCTCGA
131 AAACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATTACATTATAATTATGGGTCTCGA
* * * *
19839 TGTTTTTAGGATCGATACTTTGTATAAATATATCGACATATTTCCAT-G-CA-CTTGGTAAGGAA
196 TGTTTTTGGGATCGATACTTTTTATAAATATATCGACACA-TT--ATGGTAACCTTGGTAAGGAA
* *
19901 ATCATTATGGACACAAAGTATGGGATCGACACAAATTAAACAAGTGTCGATACTTTATGTACACC
258 ATCATTATGGACACAAAG--T---ATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACC
19966 TGTTTTCTCATAAACCGGT
318 TGTTTTCTCATAAACCGGT
19985 ATACTTGGAC
Statistics
Matches: 684, Mismatches: 39, Indels: 23
0.92 0.05 0.03
Matches are distributed among these distances:
394 51 0.07
395 250 0.37
396 220 0.32
397 102 0.15
398 3 0.00
400 58 0.08
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (396 bp):
TTTTGGGATCGATACTTTTTATAAATGTATCGACACATTATGGTGACCTTGGTAAGGAAATCATT
CTGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACCTATTTTCTCAT
AAACCGGTGTATTTAGACCGGTTAGATTGATAATTTACCTATTACATTATAATTATGGGTCTCGA
TGTTTTTGGGATCGATACTTTTTATAAATATATCGACACATTATGGTAACCTTGGTAAGGAAATC
ATTATGGACACAAAGTATCGACACAAATTAAAAAAGTGTCGATACTTCATGTACACCTGTTTTCT
CATAAACCGGTGTATTTAGACCAGTTAGATTGATAATTTACCTATAACATTATAATTATGGGTCT
CGATGT
Found at i:20286 original size:19 final size:19
Alignment explanation
Indices: 20262--20311 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
20252 TTACATTCAC
*
20262 ATACAAAATTATAAATCGT
1 ATACAAAATTAAAAATCGT
*
20281 ATACAAAATTAAAAATCTT
1 ATACAAAATTAAAAATCGT
20300 ATACAAAATTAA
1 ATACAAAATTAA
20312 CCCTATATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (19 bp):
ATACAAAATTAAAAATCGT
Found at i:21476 original size:17 final size:17
Alignment explanation
Indices: 21454--21489 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
21444 GAATCATTAG
21454 GATTAATATCTTTTCAT
1 GATTAATATCTTTTCAT
21471 GATTAATATCTTTTCAT
1 GATTAATATCTTTTCAT
21488 GA
1 GA
21490 AATATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.11, G:0.08, T:0.50
Consensus pattern (17 bp):
GATTAATATCTTTTCAT
Found at i:22489 original size:22 final size:24
Alignment explanation
Indices: 22461--22516 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
22451 AACCTGCATT
22461 TATAATAAAAT-TA-ATCATTTTA
1 TATAATAAAATATACATCATTTTA
*
22483 TATAAT-AACTATACCATCATTTTA
1 TATAATAAAATATA-CATCATTTTA
*
22507 TATAAAAAAA
1 TATAATAAAA
22517 CAAAAACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 3 0.11
22 8 0.30
24 14 0.52
25 2 0.07
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (24 bp):
TATAATAAAATATACATCATTTTA
Found at i:25600 original size:44 final size:46
Alignment explanation
Indices: 25550--25659 Score: 143
Period size: 47 Copynumber: 2.4 Consensus size: 46
25540 GTAACCATGC
* *
25550 AAATAAGCTTATGAGCTTACGGAA-T-AATGGCAAGTATATTGGAA
1 AAATAAGCTTACGAGCTTACAGAATTAAATGGCAAGTATATTGGAA
* * * *
25594 AAATAAGCTTACGAGCTTATAGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTACAGAA-TTAAATGGCAAGTATATTGGAA
25641 AAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
25660 TGGGATAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 21 0.37
46 1 0.02
47 35 0.61
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTACAGAATTAAATGGCAAGTATATTGGAA
Found at i:32741 original size:44 final size:46
Alignment explanation
Indices: 32691--32800 Score: 134
Period size: 47 Copynumber: 2.4 Consensus size: 46
32681 GTAACCATGC
* *
32691 AAATAAGCTTATGAGCTTACGGAA-T-AATGGCAAATATATTGGAA
1 AAATAAGCTTACGAGCTTACAGAATTAAATGGCAAATATATTGGAA
* * * * *
32735 AAATAAGCTTACGAGCTTATAGAATTTAAATGGTAATTATTTTGGTA
1 AAATAAGCTTACGAGCTTACAGAA-TTAAATGGCAAATATATTGGAA
32782 AAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTA
32801 TGGGATAAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
44 21 0.38
46 1 0.02
47 34 0.61
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTACAGAATTAAATGGCAAATATATTGGAA
Found at i:34607 original size:182 final size:182
Alignment explanation
Indices: 34404--35368 Score: 1507
Period size: 182 Copynumber: 5.3 Consensus size: 182
34394 TACGCGTACT
* *
34404 TATTAAAGTACCGACACTTTCAACATAACCGGTAGCACTTTACCGGTTTTGTCATTTCGATATCG
1 TATTAAAGTACCGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCG
* *
34469 GTTTTGTTATATTTTTACCTATTATATTGTTATGGATCGATACATTTGTATACAGTATCGACACT
66 GTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTGTATAAAGTATCGACACT
*
34534 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTATGAAAGTGTCGATACTTA
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTA
34586 TATTAAAGTACCGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCG
1 TATTAAAGTACCGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCG
* *
34651 GTTTTATCATATTTTTACATATTATATTGTTATGGATCGATACATTTGTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTGTATAAAGTATCGACACT
* * **
34716 TTTTAGGCGCTATAATTTATTCTCTTTTAAATTACGAAAGTGTTAATACTTA
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTA
**
34768 TATTAAAGTACTAACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCG
1 TATTAAAGTACCGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCG
34833 GTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTGTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTGTATAAAGTATCGACACT
* *
34898 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGAAAATGCCGATACTTA
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTA
34950 TATTAAAGTACCGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCG
1 TATTAAAGTACCGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCG
35015 GTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTGTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTGTATAAAGTATCGACACT
* *
35080 TTTTATGCGCTATAACTTCTTCTCTTTTAAATTACAAAAGTGTCGATACTTA
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTA
** * * * * ** * * *
35132 TATTAATTTATCGACACTTTCAATATATCTGGTAGCTTTTTACCGGTTTTATCATTTCGAGACCT
1 TATTAAAGTACCGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCG
* * * * * *
35197 ATTTTGTCATATTATTACCTGTTATATTGCTATGGATCGACACATTTTTATAAAGTATCGACACT
66 GTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTGTATAAAGTATCGACACT
* * * *
35262 TTTTCGGCGCTATAACTTCTTCTATTTTAAATTACAAAATTGTCGATACTTA
131 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTA
** * * **** *
35314 TATTAATTTATCGACACTTTCAATATATTTAGTAGCGCTTTACCGGTTTTATCAT
1 TATTAAAGTACCGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCAT
35369 ATTTTTAGCT
Statistics
Matches: 731, Mismatches: 52, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
182 731 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
TATTAAAGTACCGACACTTTCAACATAACCGGTAGCGCTTTACCGGTTTTGTCATTTCGATACCG
GTTTTGTCATATTTTTACCTATTATATTGTTATGGATCGATACATTTGTATAAAGTATCGACACT
TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTACGAAAGTGTCGATACTTA
Found at i:34851 original size:20 final size:20
Alignment explanation
Indices: 34805--34851 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
34795 ACCGGTAGCG
34805 CTTTACCGGTTTTGTCATTT
1 CTTTACCGGTTTTGTCATTT
**
34825 CGATACCGGTTTTGTCATATT
1 CTTTACCGGTTTTGTCAT-TT
34846 -TTTACC
1 CTTTACC
34852 TATTATATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49
Consensus pattern (20 bp):
CTTTACCGGTTTTGTCATTT
Found at i:35033 original size:20 final size:20
Alignment explanation
Indices: 34987--35033 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
34977 ACCGGTAGCG
34987 CTTTACCGGTTTTGTCATTT
1 CTTTACCGGTTTTGTCATTT
**
35007 CGATACCGGTTTTGTCATATT
1 CTTTACCGGTTTTGTCAT-TT
35028 -TTTACC
1 CTTTACC
35034 TATTATATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.15, C:0.21, G:0.15, T:0.49
Consensus pattern (20 bp):
CTTTACCGGTTTTGTCATTT
Found at i:36050 original size:2 final size:2
Alignment explanation
Indices: 36043--36076 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
36033 TTTAACCATA
36043 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
36077 TATTTCATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36531 original size:156 final size:156
Alignment explanation
Indices: 36362--36689 Score: 421
Period size: 155 Copynumber: 2.1 Consensus size: 156
36352 AGCATGTGGT
* *
36362 TCAAATTTAGTAAAAGAATGACTTAAAATAAATCACAAATTGAAGGAATAAGAAAATTATGAAAA
1 TCAAATTTGGTAAAA-AATGACTTAAAATAAATCACAAATTGAAGAAATAAGAAAATTATGAAAA
* *
36427 ATTGAACAACT-A-TGAAAAATAAAAAAAATTGTTATCAAAAAGAGAAATTGAAAGTACACATGT
65 ATTGAACAACTAATTGAAAAAT-AAAAAAATTATTATCAAAAAGAGAAATTGAAAGTACACATAT
*
36490 ATTCTATTATGGTTTAGGAGAACGTGAC
129 ATTCTACTATGGTTTAGGAGAACGTGAC
* * ** * * *
36518 TCAAATTTGGTAAAAAA--ACTTAAAATAAGTGATGAATTGAATAAATAAGGAGATTATGAAAAA
1 TCAAATTTGGTAAAAAATGACTTAAAATAAATCACAAATTGAAGAAATAAGAAAATTATGAAAAA
** * *
36581 TTGAAGGACTAAATTGAAAAATAAAAAATTTATTATCAAAAAGATAAATTGAAAGTACACATATA
66 TTGAACAACT-AATTGAAAAATAAAAAAATTATTATCAAAAAGAGAAATTGAAAGTACACATATA
* * **
36646 TTCTACTATGGTTTAGGAGCATGTGGT
130 TTCTACTATGGTTTAGGAGAACGTGAC
36673 TCAAATTTGGTAAAAAA
1 TCAAATTTGGTAAAAAA
36690 ATGGAATGAA
Statistics
Matches: 149, Mismatches: 20, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
153 46 0.31
155 81 0.54
156 22 0.15
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (156 bp):
TCAAATTTGGTAAAAAATGACTTAAAATAAATCACAAATTGAAGAAATAAGAAAATTATGAAAAA
TTGAACAACTAATTGAAAAATAAAAAAATTATTATCAAAAAGAGAAATTGAAAGTACACATATAT
TCTACTATGGTTTAGGAGAACGTGAC
Found at i:40745 original size:30 final size:30
Alignment explanation
Indices: 40631--40867 Score: 151
Period size: 30 Copynumber: 7.9 Consensus size: 30
40621 TACAAGGACC
* * * *
40631 AAATAGCAAAAACATAAACTCAAAGGACCA
1 AAATAGTAAAAACAGAAACTTAAAGGACTA
* *
40661 AAATAGTACAAACATG-AATTTAAAGGACTA
1 AAATAGTAAAAACA-GAAACTTAAAGGACTA
** *
40691 AAATGGAAAAAAAACAAAAAACTTAAATGG-CTA
1 AAAT--AGTAAAAAC-AGAAACTTAAA-GGACTA
* *
40724 AAATAGTAAAAACAGAAACTTAAGGGTCT-
1 AAATAGTAAAAACAGAAACTTAAAGGACTA
* * * *
40753 AAATAATAAATACAGACATTTAAAGGACTA
1 AAATAGTAAAAACAGAAACTTAAAGGACTA
* ** * *
40783 GAATAACAAAAATAGAAACTTAAGGGACT-
1 AAATAGTAAAAACAGAAACTTAAAGGACTA
* * * *
40812 AAATAGCAAAAATAGAAAGTTAAAGGACCA
1 AAATAGTAAAAACAGAAACTTAAAGGACTA
* * *
40842 AAATAGCACAAACA-AAATTTAAAGGA
1 AAATAGTAAAAACAGAAACTTAAAGGA
40868 TTGAATCATA
Statistics
Matches: 162, Mismatches: 36, Indels: 19
0.75 0.17 0.09
Matches are distributed among these distances:
29 60 0.37
30 72 0.44
31 7 0.04
32 6 0.04
33 15 0.09
34 2 0.01
ACGTcount: A:0.58, C:0.11, G:0.14, T:0.17
Consensus pattern (30 bp):
AAATAGTAAAAACAGAAACTTAAAGGACTA
Found at i:40767 original size:29 final size:29
Alignment explanation
Indices: 40724--40839 Score: 106
Period size: 29 Copynumber: 4.0 Consensus size: 29
40714 TAAATGGCTA
* *
40724 AAATAGTAAAAACAGAAACTTAAGGGTCT
1 AAATAATAAAAACAGAAACTTAAGGGACT
* * * *
40753 AAATAATAAATACAGACATTTAAAGGACT
1 AAATAATAAAAACAGAAACTTAAGGGACT
* *
40782 AGAATAACAAAAATAGAAACTTAAGGGACT
1 A-AATAATAAAAACAGAAACTTAAGGGACT
** * * *
40812 AAATAGCAAAAATAGAAAGTTAAAGGAC
1 AAATAATAAAAACAGAAACTTAAGGGAC
40840 CAAAATAGCA
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
29 48 0.68
30 23 0.32
ACGTcount: A:0.56, C:0.09, G:0.16, T:0.19
Consensus pattern (29 bp):
AAATAATAAAAACAGAAACTTAAGGGACT
Found at i:43006 original size:30 final size:30
Alignment explanation
Indices: 42970--43035 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
42960 AGTGAATCGG
* **
42970 CGGTTCAAACCGGTTTTGTCGATTTTCAGC
1 CGGTTCAAACCGATTTTCCCGATTTTCAGC
**
43000 CGGTTCACCCCGATTTTCCCGATTTTCAGC
1 CGGTTCAAACCGATTTTCCCGATTTTCAGC
43030 CGGTTC
1 CGGTTC
43036 TTCCGATTCT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.14, C:0.30, G:0.21, T:0.35
Consensus pattern (30 bp):
CGGTTCAAACCGATTTTCCCGATTTTCAGC
Found at i:43241 original size:30 final size:30
Alignment explanation
Indices: 43207--43300 Score: 179
Period size: 30 Copynumber: 3.1 Consensus size: 30
43197 ACATTTTAAT
43207 TAATAAAAAGTTTTAAATAAATAATATAAA
1 TAATAAAAAGTTTTAAATAAATAATATAAA
*
43237 TAATAAAAAGTTTTAAATAAATAATAAAAA
1 TAATAAAAAGTTTTAAATAAATAATATAAA
43267 TAATAAAAAGTTTTAAATAAATAATATAAA
1 TAATAAAAAGTTTTAAATAAATAATATAAA
43297 TAAT
1 TAAT
43301 TACATAATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 62 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (30 bp):
TAATAAAAAGTTTTAAATAAATAATATAAA
Found at i:43255 original size:17 final size:17
Alignment explanation
Indices: 43200--43286 Score: 66
Period size: 17 Copynumber: 5.6 Consensus size: 17
43190 AATTTTCACA
*
43200 TTTTAATTAATAAAAAG
1 TTTTAAATAATAAAAAG
*
43217 TTTTAAAT-A-AATAA-
1 TTTTAAATAATAAAAAG
*
43231 -TATAAATAATAAAAAG
1 TTTTAAATAATAAAAAG
*
43247 TTTTAAATAAATAATAA-
1 TTTTAAAT-AATAAAAAG
43264 ----AAATAATAAAAAG
1 TTTTAAATAATAAAAAG
43277 TTTTAAATAA
1 TTTTAAATAA
43287 ATAATATAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 20
0.66 0.09 0.25
Matches are distributed among these distances:
12 7 0.13
13 10 0.19
14 1 0.02
15 8 0.15
16 1 0.02
17 19 0.36
18 7 0.13
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TTTTAAATAATAAAAAG
Found at i:51735 original size:32 final size:32
Alignment explanation
Indices: 51671--51735 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
51661 GTTGGAAAAT
*
51671 ATTTATATATTTTTAAAAAATTAAATTAATAA
1 ATTTATATATTTTTAAAAAATTAAAATAATAA
* *
51703 ATTTATATTTTTTTACAAAATTGAAAAT-ATAA
1 ATTTATATATTTTTAAAAAATT-AAAATAATAA
51735 A
1 A
51736 AAAGTTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 25 0.86
33 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (32 bp):
ATTTATATATTTTTAAAAAATTAAAATAATAA
Done.