Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003728.1 Hibiscus syriacus cultivar Beakdansim tig00007972_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: 111283
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:13598 original size:60 final size:58
Alignment explanation
Indices: 13477--13600 Score: 140
Period size: 59 Copynumber: 2.1 Consensus size: 58
13467 TAAAGTATAT
* * * *
13477 AAATGGTCCTCAAATATAAGATACTACTTTATTGAGTCCACGACTATTAAAAGTTATA
1 AAATGATCCTCAAATATAAGATACTACTTTATTAAGTCCACGAATATTAAAAGTTACA
* ** * * *
13535 AAATGATCCTCTAACTATAAGATGTTACTTTGTTAAGTCTCTCGAATATTACAAGTTACA
1 AAATGATCCTC-AAATATAAGATACTACTTTATTAAGTC-CACGAATATTAAAAGTTACA
13595 AAATGA
1 AAATGA
13601 CCACTCAATT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
58 10 0.19
59 22 0.41
60 22 0.41
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (58 bp):
AAATGATCCTCAAATATAAGATACTACTTTATTAAGTCCACGAATATTAAAAGTTACA
Found at i:13884 original size:60 final size:59
Alignment explanation
Indices: 13807--13925 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 59
13797 AACATAATGA
* * * * *
13807 ATAGGCGAGTGACCATTTTGTAACTTTTTATAATTAGAGGACACAACAAAGTAACATCCT
1 ATAGGCGAGGGACCATTTTGTAACTATTAATAATCAGAGGACACAACAAAGCAAC-TCCT
* * *
13867 ATAGTCGAGGGACCATTTTGTAACTATTAATAGTCAGAGGACTCAACAAAGCAACTCCT
1 ATAGGCGAGGGACCATTTTGTAACTATTAATAATCAGAGGACACAACAAAGCAACTCCT
13926 TATAATCAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 4 0.08
60 47 0.92
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (59 bp):
ATAGGCGAGGGACCATTTTGTAACTATTAATAATCAGAGGACACAACAAAGCAACTCCT
Found at i:18054 original size:21 final size:21
Alignment explanation
Indices: 18030--18175 Score: 132
Period size: 21 Copynumber: 6.7 Consensus size: 21
18020 TGCCTGTCGC
*
18030 CTCTCCACCACCACCAGTTTA
1 CTCTCCACCACCACCAGTCTA
* *
18051 CTCTCCACCTCCTCCAGTCTA
1 CTCTCCACCACCACCAGTCTA
* * * *
18072 CTCACCACCTCCGCCTGTCTA
1 CTCTCCACCACCACCAGTCTA
* *
18093 CTCACCACCACCACCCGTCTA
1 CTCTCCACCACCACCAGTCTA
18114 CTCTCCACCCCACCACCTCCAGTTCT-
1 CTCTCCA--CCACCA---CCAG-TCTA
* *
18140 CTCACCCCCACCACCAGTCTA
1 CTCTCCACCACCACCAGTCTA
18161 CTCTCCACCACCACC
1 CTCTCCACCACCACC
18176 TCCTCCAGTC
Statistics
Matches: 103, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.03
21 77 0.75
23 6 0.06
24 6 0.06
26 8 0.08
27 3 0.03
ACGTcount: A:0.19, C:0.55, G:0.05, T:0.21
Consensus pattern (21 bp):
CTCTCCACCACCACCAGTCTA
Found at i:18127 original size:47 final size:47
Alignment explanation
Indices: 18074--18203 Score: 181
Period size: 47 Copynumber: 2.7 Consensus size: 47
18064 CCAGTCTACT
* * *
18074 CACCACCTCCGCCTGTCTACTCACCACCACCACCCGTCTACTCTCCAC
1 CACCACCTCCTCCAGTCT-CTCACCCCCACCACCCGTCTACTCTCCAC
* *
18122 C-CCACCACCTCCAGTTCTCTCACCCCCACCACCAGTCTACTCTCCAC
1 CACCACCTCCTCCAG-TCTCTCACCCCCACCACCCGTCTACTCTCCAC
18169 CACCACCTCCTCCAGTCCTCTCACCCCCACCACCC
1 CACCACCTCCTCCAGT-CTCTCACCCCCACCACCC
18204 CCGCCAGTTC
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
47 39 0.54
48 33 0.46
ACGTcount: A:0.18, C:0.59, G:0.05, T:0.18
Consensus pattern (47 bp):
CACCACCTCCTCCAGTCTCTCACCCCCACCACCCGTCTACTCTCCAC
Found at i:18183 original size:27 final size:26
Alignment explanation
Indices: 18095--18229 Score: 106
Period size: 27 Copynumber: 5.4 Consensus size: 26
18085 CCTGTCTACT
*
18095 CACCACCACCACCCGTCTACTCTCCAC
1 CACCACCACCACCAGTCT-CTCTCCAC
*
18122 C-CCACCACCTCCAGT-TCTCT-CA-
1 CACCACCACCACCAGTCTCTCTCCAC
18144 C-CC-CCACCACCAGTCTACTCTCCAC
1 CACCACCACCACCAGTCT-CTCTCCAC
* * * *
18169 CACCACCTCCTCCAGTCCTCTCACCCC
1 CACCACCACCACCAGT-CTCTCTCCAC
* * *
18196 CACCACCCCCGCCAGT-TCGCTCC-C
1 CACCACCACCACCAGTCTCTCTCCAC
18220 CACCACCACC
1 CACCACCACC
18230 CGTCCATTCT
Statistics
Matches: 89, Mismatches: 12, Indels: 17
0.75 0.10 0.14
Matches are distributed among these distances:
21 10 0.11
22 4 0.04
23 6 0.07
24 16 0.18
25 7 0.08
26 14 0.16
27 30 0.34
28 2 0.02
ACGTcount: A:0.19, C:0.61, G:0.05, T:0.16
Consensus pattern (26 bp):
CACCACCACCACCAGTCTCTCTCCAC
Found at i:18193 original size:24 final size:24
Alignment explanation
Indices: 18114--18202 Score: 87
Period size: 24 Copynumber: 3.7 Consensus size: 24
18104 CACCCGTCTA
*
18114 CTCTCCACCCCACCACCTCCAGTT
1 CTCTCCACCCCACCACCTCCAGTC
*
18138 CTCT-CA-CCC-CCACCACCAGTC
1 CTCTCCACCCCACCACCTCCAGTC
*
18159 TACTCTCCACCACCACCTCCTCCAGTC
1 --CTCTCCACC-CCACCACCTCCAGTC
18186 CTCT-CACCCCCACCACC
1 CTCTCCA-CCCCACCACC
18203 CCCGCCAGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
21 10 0.19
22 3 0.06
23 6 0.11
24 15 0.28
25 7 0.13
26 2 0.04
27 10 0.19
ACGTcount: A:0.18, C:0.61, G:0.03, T:0.18
Consensus pattern (24 bp):
CTCTCCACCCCACCACCTCCAGTC
Found at i:18267 original size:21 final size:21
Alignment explanation
Indices: 18034--18268 Score: 77
Period size: 21 Copynumber: 10.4 Consensus size: 21
18024 TGTCGCCTCT
* *
18034 CCACCACCACCAGTT-TACTCT
1 CCACCACCCCCAGTTCT-CTCA
* *
18055 CCACCTCCTCCAG-TCTACTCA
1 CCACCACCCCCAGTTCT-CTCA
* * *
18076 CCACCTCCGCCTG-TCTACTCA
1 CCACCACCCCCAGTTCT-CTCA
18097 CCACCACCACCC-GTCTACTCTCCA
1 CCACCACC-CCCAGT-T-CTCT-CA
*
18121 CCCCACCACCTCCAGTTCTCTCA
1 --CCACCACCCCCAGTTCTCTCA
* *
18144 CCCCCACCACCAGTCTACTCTCCA
1 CCACCACCCCCAGT-T-CTCT-CA
*
18168 CCACCACCTCCTCCAGTCCTCTCA
1 CCACCA-C-CC-CCAGTTCTCTCA
* *
18192 CCCCCACCACCCCCGCCAGTTCGCTCC
1 ---CCACCA--CCC-CCAGTTCTCTCA
* *
18219 CCACCACCACCC-GTCCAT-TCT
1 CCACCACC-CCCAGTTC-TCTCA
*
18240 CCTCCACCCCCAGTTCTCTCA
1 CCACCACCCCCAGTTCTCTCA
18261 CCACCACC
1 CCACCACC
18269 ACTGGTTCAC
Statistics
Matches: 167, Mismatches: 24, Indels: 46
0.70 0.10 0.19
Matches are distributed among these distances:
20 5 0.03
21 79 0.47
22 7 0.04
23 10 0.06
24 23 0.14
25 8 0.05
26 11 0.07
27 22 0.13
28 2 0.01
ACGTcount: A:0.18, C:0.57, G:0.06, T:0.19
Consensus pattern (21 bp):
CCACCACCCCCAGTTCTCTCA
Found at i:18276 original size:21 final size:21
Alignment explanation
Indices: 18252--18291 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
18242 TCCACCCCCA
* *
18252 GTTCTCTCACCACCACCACTG
1 GTTCACTCACAACCACCACTG
*
18273 GTTCACTCACAACCGCCAC
1 GTTCACTCACAACCACCAC
18292 CCGTCCACTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.47, G:0.10, T:0.20
Consensus pattern (21 bp):
GTTCACTCACAACCACCACTG
Found at i:34251 original size:20 final size:20
Alignment explanation
Indices: 34226--34263 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34216 TATTTTTAAA
34226 ATTTTTAA-TAATAAAAATTT
1 ATTTTTAATTAA-AAAAATTT
34246 ATTTTTAATTAAAAAAAT
1 ATTTTTAATTAAAAAAAT
34264 AAGAAAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTTTAATTAAAAAAATTT
Found at i:34281 original size:29 final size:29
Alignment explanation
Indices: 34232--34292 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
34222 TAAAATTTTT
* *
34232 AATAATAAAAATTTATTTTTAATTAAAAA
1 AATAAGAAAAATTTATATTTAATTAAAAA
* *
34261 AATAAGAAAAAGTTTA-ATTTATTTATAAA
1 AATAAGAAAAA-TTTATATTTAATTAAAAA
34290 AAT
1 AAT
34293 CCCCCACTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (29 bp):
AATAAGAAAAATTTATATTTAATTAAAAA
Found at i:34751 original size:18 final size:19
Alignment explanation
Indices: 34719--34755 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
34709 TTCTTTTAAT
34719 TTTTTAATAATAAAAAATA
1 TTTTTAATAATAAAAAATA
*
34738 TTTTTAATTA-AAAAAATA
1 TTTTTAATAATAAAAAATA
34756 AAAAATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTTAATAATAAAAAATA
Found at i:35220 original size:17 final size:17
Alignment explanation
Indices: 35151--35210 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 17
35141 TCAATTTAAA
*
35151 TATAGTAAAAATATAA-
1 TATAATAAAAATATAAT
*
35167 AAT-ATAAAAA-ATAA-
1 TATAATAAAAATATAAT
35181 -A-AATAAAAATATAAT
1 TATAATAAAAATATAAT
35196 TATAATAAAAATATA
1 TATAATAAAAATATA
35211 TTTTATATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 8 0.22
14 8 0.22
15 6 0.16
16 3 0.08
17 12 0.32
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (17 bp):
TATAATAAAAATATAAT
Found at i:38477 original size:6 final size:6
Alignment explanation
Indices: 38468--38503 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
38458 TGAATGTTTA
* *
38468 AATTTT AATTTA AATTTT AATTTA AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
38504 CGCAACTAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (6 bp):
AATTTT
Found at i:38481 original size:12 final size:12
Alignment explanation
Indices: 38464--38502 Score: 78
Period size: 12 Copynumber: 3.2 Consensus size: 12
38454 GAATTGAATG
38464 TTTAAATTTTAA
1 TTTAAATTTTAA
38476 TTTAAATTTTAA
1 TTTAAATTTTAA
38488 TTTAAATTTTAA
1 TTTAAATTTTAA
38500 TTT
1 TTT
38503 TCGCAACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTAAATTTTAA
Found at i:47528 original size:31 final size:31
Alignment explanation
Indices: 47493--47600 Score: 189
Period size: 31 Copynumber: 3.5 Consensus size: 31
47483 CCATAAATAC
* *
47493 AAACCGATTGTTTAGGTATTAAAATCGATTA
1 AAACCGATTGTTTAGGTATTAAAATAGACTA
*
47524 AAACCGATTGTTTAGGTATTAAAATATACTA
1 AAACCGATTGTTTAGGTATTAAAATAGACTA
47555 AAACCGATTGTTTAGGTATTAAAATAGACTA
1 AAACCGATTGTTTAGGTATTAAAATAGACTA
47586 AAACCGATTGTTTAG
1 AAACCGATTGTTTAG
47601 ATGCAAAACG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (31 bp):
AAACCGATTGTTTAGGTATTAAAATAGACTA
Found at i:48215 original size:18 final size:18
Alignment explanation
Indices: 48191--48236 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 18
48181 GAGGATGTCA
48191 ACAATATGGTTCTTGAAT
1 ACAATATGGTTCTTGAAT
*
48209 TCAATATAATGGTTCTTGAAT
1 AC-A-AT-ATGGTTCTTGAAT
48230 ACAATAT
1 ACAATAT
48237 TCAATTGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
18 3 0.13
19 3 0.13
20 3 0.13
21 14 0.61
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (18 bp):
ACAATATGGTTCTTGAAT
Found at i:48220 original size:21 final size:21
Alignment explanation
Indices: 48196--48236 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
48186 TGTCAACAAT
*
48196 ATGGTTCTTGAATTCAATATA
1 ATGGTTCTTGAATACAATATA
48217 ATGGTTCTTGAATACAATAT
1 ATGGTTCTTGAATACAATAT
48237 TCAATTGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.41
Consensus pattern (21 bp):
ATGGTTCTTGAATACAATATA
Found at i:55097 original size:15 final size:15
Alignment explanation
Indices: 55077--55109 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
55067 GCGTAATCTT
*
55077 TGGCAACTTTTGATC
1 TGGCAACTTCTGATC
55092 TGGCAACTTCTGATC
1 TGGCAACTTCTGATC
55107 TGG
1 TGG
55110 TTGATCTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.36
Consensus pattern (15 bp):
TGGCAACTTCTGATC
Found at i:56928 original size:287 final size:288
Alignment explanation
Indices: 56409--56988 Score: 1047
Period size: 287 Copynumber: 2.0 Consensus size: 288
56399 CGACTGAGTC
*
56409 ATCCGTCCTTCTAGAAATGTTGAATTGACCTTCTAGAAGCTGTTGACTAGATGCAATCATGCCCA
1 ATCCGTCCTTCTAGAAATGTTGAATTGACCTTCTAGAAGCTGCTGACTAGATGCAATCATGCCCA
*
56474 CTAATCCAACATTGACTCCAGAAAATAAAAAAAAAACTACAGAAGTACACCATTTTAGCTATGTT
66 CTAATCCAACATTGACTCCAGAAAAT--AAAAAAAACTACAGAAGTACACCATTGTAGCTATGTT
*
56539 TCTATAATCCAACATCCTGCATAGCAAATGGATAGAAAAGTCTAAACCAGTAACAAAAATCGACG
129 TCTATAATCCAACATCCTGCATAGCAAATGGATAGAAAAGCCTAAACCAGTAACAAAAATCGACG
*
56604 AACAAAGAGTAATTAAAGATAAAATAGTAACTAATTAAACCACTCATAAGGAACTATCTCTTATC
194 AACAAAGAGTAATTAAAGATAAAATAGTAACTAATTAAACCACTCAAAAGGAACTATCTCTTATC
56669 ATGGATTCATCCCTTAGTTGGCTATGCATA
259 ATGGATTCATCCCTTAGTTGGCTATGCATA
56699 ATCCGTCCTTCTAGAAATGTTGAA-TGAACCTTCTAGAAGCTGCTGACTAGATGCAATCATGCCC
1 ATCCGTCCTTCTAGAAATGTTGAATTG-ACCTTCTAGAAGCTGCTGACTAGATGCAATCATGCCC
* * *
56763 ACTAATCCATCCTTGACTCCAGAAAAT-AAAAAAACTGCAGAAGTACACCATTGTAGCTATGTTT
65 ACTAATCCAACATTGACTCCAGAAAATAAAAAAAACTACAGAAGTACACCATTGTAGCTATGTTT
56827 CTATAATCCAACATCCTGCATAGCAAATGGATAGAAAAGCCTAAACCAGTAACAAAAATCGACGA
130 CTATAATCCAACATCCTGCATAGCAAATGGATAGAAAAGCCTAAACCAGTAACAAAAATCGACGA
*
56892 ACAAAGTGTAATTAAAGATAAAATAGTAACTAATTAAACCACTCAAAAGGAACTATCTCTTATCA
195 ACAAAGAGTAATTAAAGATAAAATAGTAACTAATTAAACCACTCAAAAGGAACTATCTCTTATCA
56957 TGGATTCATCCCTTAGTTGGCTATGCATA
260 TGGATTCATCCCTTAGTTGGCTATGCATA
56986 ATC
1 ATC
56989 GGCTGCCTAC
Statistics
Matches: 281, Mismatches: 8, Indels: 5
0.96 0.03 0.02
Matches are distributed among these distances:
287 194 0.69
289 2 0.01
290 85 0.30
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (288 bp):
ATCCGTCCTTCTAGAAATGTTGAATTGACCTTCTAGAAGCTGCTGACTAGATGCAATCATGCCCA
CTAATCCAACATTGACTCCAGAAAATAAAAAAAACTACAGAAGTACACCATTGTAGCTATGTTTC
TATAATCCAACATCCTGCATAGCAAATGGATAGAAAAGCCTAAACCAGTAACAAAAATCGACGAA
CAAAGAGTAATTAAAGATAAAATAGTAACTAATTAAACCACTCAAAAGGAACTATCTCTTATCAT
GGATTCATCCCTTAGTTGGCTATGCATA
Found at i:63464 original size:182 final size:182
Alignment explanation
Indices: 63156--63504 Score: 470
Period size: 182 Copynumber: 1.9 Consensus size: 182
63146 CCATTCAAAA
* *
63156 TTAAATAGGTATTATTTTAATTCAAAATATACAAAACTATATAATTATCTTTAATATTCAAAGTT
1 TTAAATAGATATTATTTTAATTCAAAATATACAAAACTATATAATTATCTTTAATATTCAAAATT
* * * * * *
63221 AAAAAGATAACAAATATATTTTTAAATTAACATATTCAAAGTGTGATTATCCTACTAATATTCAA
66 AAAAAGATAACAAATACATTTTTAAATGAACATACTAAAAGAGTAATTATCCTACTAATATTCAA
*
63286 ATTAAATAA-TAT-GTTTAATTTACAATGGTCAAAAAGTAAACTCCTTTAATC
131 ATTAAA-AATTATCGTTTAATTTACAATAGTCAAAAAGTAAACTCCTTTAATC
* * * * *
63337 TTAAATATATATTATTTTAATGT-GAAATATACAAAAGTCTATAGTTATCTTTTAATATTCAAAA
1 TTAAATAGATATTATTTTAAT-TCAAAATATACAAAACTATATAATTATC-TTTAATATTCAAAA
* * * * *
63401 TTAAAAAGATAACAAATACATTTTTAAATGGACTTACTAAAAGAGTAATTCTCTTATTAATATTC
64 TTAAAAAGATAACAAATACATTTTTAAATGAACATACTAAAAGAGTAATTATCCTACTAATATTC
*
63466 AAATTAAAAATTATCTTTTAATTTACAATAGTCAAAAAG
129 AAATTAAAAATTATCGTTTAATTTACAATAGTCAAAAAG
63505 ACTATGAATT
Statistics
Matches: 144, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
181 43 0.30
182 79 0.55
183 22 0.15
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.39
Consensus pattern (182 bp):
TTAAATAGATATTATTTTAATTCAAAATATACAAAACTATATAATTATCTTTAATATTCAAAATT
AAAAAGATAACAAATACATTTTTAAATGAACATACTAAAAGAGTAATTATCCTACTAATATTCAA
ATTAAAAATTATCGTTTAATTTACAATAGTCAAAAAGTAAACTCCTTTAATC
Found at i:65406 original size:61 final size:61
Alignment explanation
Indices: 65336--65460 Score: 250
Period size: 61 Copynumber: 2.0 Consensus size: 61
65326 CTTCATTCTC
65336 TTTTATGACTCGTCGATGTAATTAGATTTGTTCGTATTTACTTTTTATCTGAGTTTATTTG
1 TTTTATGACTCGTCGATGTAATTAGATTTGTTCGTATTTACTTTTTATCTGAGTTTATTTG
65397 TTTTATGACTCGTCGATGTAATTAGATTTGTTCGTATTTACTTTTTATCTGAGTTTATTTG
1 TTTTATGACTCGTCGATGTAATTAGATTTGTTCGTATTTACTTTTTATCTGAGTTTATTTG
65458 TTT
1 TTT
65461 AAGTTTTTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 64 1.00
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (61 bp):
TTTTATGACTCGTCGATGTAATTAGATTTGTTCGTATTTACTTTTTATCTGAGTTTATTTG
Found at i:65580 original size:14 final size:14
Alignment explanation
Indices: 65561--65589 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
65551 TTACCATAGT
65561 TTAATTTAAAATTG
1 TTAATTTAAAATTG
65575 TTAATTTAAAATTG
1 TTAATTTAAAATTG
65589 T
1 T
65590 GATCGTAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTAATTTAAAATTG
Found at i:66118 original size:36 final size:36
Alignment explanation
Indices: 66078--66215 Score: 258
Period size: 36 Copynumber: 3.8 Consensus size: 36
66068 GAACACGAAT
66078 TCGAATTTTAACTATAACAAACGTCCATTAGTGAGA
1 TCGAATTTTAACTATAACAAACGTCCATTAGTGAGA
*
66114 TCGAATTTTAACTATAACAAACTTCCATTAGTGAGA
1 TCGAATTTTAACTATAACAAACGTCCATTAGTGAGA
66150 TCGAATTTTAACTATAACAAACGTCCATTAGTGAGA
1 TCGAATTTTAACTATAACAAACGTCCATTAGTGAGA
*
66186 TCGAATTTTAACTATAACAAACTTCCATTA
1 TCGAATTTTAACTATAACAAACGTCCATTA
66216 AGCTCGCTAG
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 99 1.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (36 bp):
TCGAATTTTAACTATAACAAACGTCCATTAGTGAGA
Found at i:66849 original size:55 final size:55
Alignment explanation
Indices: 66790--66899 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
66780 CAAACGAAAT
66790 TTGATGTCTCTTAAAAAATGTAAATAAAATATTCATTGTCGAGTTTTTTTCTAAG
1 TTGATGTCTCTTAAAAAATGTAAATAAAATATTCATTGTCGAGTTTTTTTCTAAG
66845 TTGATGTCTCTTAAAAAATGTAAATAAAATATTCATTGTCGAGTTTTTTTCTAAG
1 TTGATGTCTCTTAAAAAATGTAAATAAAATATTCATTGTCGAGTTTTTTTCTAAG
66900 GAGATAAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.44
Consensus pattern (55 bp):
TTGATGTCTCTTAAAAAATGTAAATAAAATATTCATTGTCGAGTTTTTTTCTAAG
Found at i:67760 original size:14 final size:14
Alignment explanation
Indices: 67735--67770 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
67725 ACCTTTCTAA
*
67735 ATTTTAATTTTTTTC
1 ATTTT-ATTTTTCTC
67750 ATTTTATTTTTCTC
1 ATTTTATTTTTCTC
67764 ATTTTAT
1 ATTTTAT
67771 ATTATTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTTATTTTTCTC
Found at i:70620 original size:10 final size:10
Alignment explanation
Indices: 70605--70629 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
70595 ATCTACCGTC
70605 CCTTCTTCCA
1 CCTTCTTCCA
70615 CCTTCTTCCA
1 CCTTCTTCCA
70625 CCTTC
1 CCTTC
70630 GTCATCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.52, G:0.00, T:0.40
Consensus pattern (10 bp):
CCTTCTTCCA
Found at i:74334 original size:40 final size:40
Alignment explanation
Indices: 74290--74373 Score: 141
Period size: 40 Copynumber: 2.1 Consensus size: 40
74280 CTGTAACACG
* * *
74290 CCTTCCCTCCACGTATGCAAGGCGCGTTCCCTGCCACGCA
1 CCTTCCCTCCACATATGCAAGGCGCATTCCCTACCACGCA
74330 CCTTCCCTCCACATATGCAAGGCGCATTCCCTACCACGCA
1 CCTTCCCTCCACATATGCAAGGCGCATTCCCTACCACGCA
74370 CCTT
1 CCTT
74374 ATTATCACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.18, C:0.45, G:0.15, T:0.21
Consensus pattern (40 bp):
CCTTCCCTCCACATATGCAAGGCGCATTCCCTACCACGCA
Found at i:82405 original size:13 final size:14
Alignment explanation
Indices: 82387--82460 Score: 59
Period size: 13 Copynumber: 5.4 Consensus size: 14
82377 TTAAAATCAC
82387 TAATAAATAAT-TA
1 TAATAAATAATATA
82400 TAATAAATAATATA
1 TAATAAATAATATA
*
82414 TAATTACTATAA-ATA
1 TAA-TA-AATAATATA
82429 TTAAT-AATAA-ATAA
1 -TAATAAATAATAT-A
*
82443 TAATATATAATATA
1 TAATAAATAATATA
82457 -AATA
1 TAATA
82461 CTATGTAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 14
0.75 0.04 0.21
Matches are distributed among these distances:
13 25 0.49
14 11 0.22
15 8 0.16
16 7 0.14
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATAAATAATATA
Found at i:82442 original size:26 final size:26
Alignment explanation
Indices: 82402--82478 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 26
82392 AATAATTATA
* *
82402 ATAAATAATATATAATTACTATA-AAT
1 ATAAATAATAAATAA-TAATATATAAT
*
82428 ATTAATAATAAATAATAATATATAAT
1 ATAAATAATAAATAATAATATATAAT
* ** *
82454 ATAAATACTATGTAATAAAATATAA
1 ATAAATAATAAATAATAATATATAA
82479 ATTAGGATCC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 6 0.14
26 36 0.86
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (26 bp):
ATAAATAATAAATAATAATATATAAT
Found at i:82452 original size:7 final size:7
Alignment explanation
Indices: 82387--82460 Score: 59
Period size: 7 Copynumber: 10.7 Consensus size: 7
82377 TTAAAATCAC
*
82387 TAATAAA
1 TAATATA
82394 TAAT-TA
1 TAATATA
*
82400 TAATAAA
1 TAATATA
82407 TAATATA
1 TAATATA
82414 TAATTACTA
1 TAA-TA-TA
82423 TAA-ATA
1 TAATATA
82429 TTAATA-A
1 -TAATATA
82436 TAA-ATAA
1 TAATAT-A
82443 TAATATA
1 TAATATA
82450 TAATATA
1 TAATATA
82457 -AATA
1 TAATA
82461 CTATGTAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
5 1 0.02
6 14 0.25
7 31 0.55
8 5 0.09
9 5 0.09
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (7 bp):
TAATATA
Found at i:85081 original size:18 final size:19
Alignment explanation
Indices: 85044--85081 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
85034 TCTTAAACTT
* *
85044 TCTATTATTTTATTATAAA
1 TCTAATATTTTATAATAAA
85063 TCTAATATTTT-TAATAAA
1 TCTAATATTTTATAATAAA
85081 T
1 T
85082 TATCAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (19 bp):
TCTAATATTTTATAATAAA
Found at i:85239 original size:16 final size:16
Alignment explanation
Indices: 85218--85269 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
85208 CATGTTAAAA
*
85218 TTCGGTTCGGGTTACT
1 TTCGGTTCGGGTTAAT
85234 TTCGGTTCGGGTTAAT
1 TTCGGTTCGGGTTAAT
* *
85250 TTCAGTTCAGGTTAAT
1 TTCGGTTCGGGTTAAT
85266 TTCG
1 TTCG
85270 ATTCTGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.13, C:0.15, G:0.27, T:0.44
Consensus pattern (16 bp):
TTCGGTTCGGGTTAAT
Found at i:87797 original size:12 final size:12
Alignment explanation
Indices: 87775--87808 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
87765 GTGTCATCTA
87775 TATCATTTTTCTT
1 TATC-TTTTTCTT
*
87788 TTTCTTTTTCTT
1 TATCTTTTTCTT
87800 TATCTTTTT
1 TATCTTTTT
87809 TCCTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 16 0.84
13 3 0.16
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (12 bp):
TATCTTTTTCTT
Found at i:89681 original size:33 final size:33
Alignment explanation
Indices: 89642--89705 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
89632 TCTGTTTTGA
*
89642 GATACATCTGATATCACGTATTTGTACTCTTGG
1 GATACATCCGATATCACGTATTTGTACTCTTGG
*
89675 GATACATCCGATATCATGTATTTGTACTCTT
1 GATACATCCGATATCACGTATTTGTACTCTT
89706 TGTTTTCTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.41
Consensus pattern (33 bp):
GATACATCCGATATCACGTATTTGTACTCTTGG
Found at i:95815 original size:15 final size:15
Alignment explanation
Indices: 95797--95831 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
95787 GGGAGGAGGG
95797 TATCCCTGAGCAGGA
1 TATCCCTGAGCAGGA
* *
95812 TATCCCTGAGGAGGG
1 TATCCCTGAGCAGGA
95827 TATCC
1 TATCC
95832 TTGTGGCGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.26, G:0.29, T:0.23
Consensus pattern (15 bp):
TATCCCTGAGCAGGA
Found at i:109395 original size:24 final size:25
Alignment explanation
Indices: 109368--109425 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
109358 TGGGAAGATA
109368 AATTTTTTAAAATTATTTTT-TACT
1 AATTTTTTAAAATTATTTTTATACT
* * *
109392 AATTTTTTATATTTATTTTTATCCT
1 AATTTTTTAAAATTATTTTTATACT
*
109417 TATTTTTTA
1 AATTTTTTA
109426 TTATACTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 18 0.62
25 11 0.38
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (25 bp):
AATTTTTTAAAATTATTTTTATACT
Found at i:109409 original size:13 final size:13
Alignment explanation
Indices: 109369--109426 Score: 50
Period size: 12 Copynumber: 4.7 Consensus size: 13
109359 GGGAAGATAA
* *
109369 ATTTTTTAAAATT
1 ATTTTTTATACTT
*
109382 A-TTTTT-TACTA
1 ATTTTTTATACTT
*
109393 ATTTTTTATATTT
1 ATTTTTTATACTT
*
109406 A-TTTTTATCCTT
1 ATTTTTTATACTT
109418 ATTTTTTAT
1 ATTTTTTAT
109427 TATACTGTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
11 3 0.09
12 20 0.57
13 12 0.34
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTTTATACTT
Done.