Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001628.1 Hibiscus syriacus cultivar Beakdansim tig00003241_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: 110542
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:8420 original size:22 final size:22
Alignment explanation
Indices: 8385--8426 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
8375 AGTACGTTCA
*
8385 GGGGGTATCAATTCCCCCCTTG
1 GGGGGAATCAATTCCCCCCTTG
*
8407 GGGGGAATCTATTCCCCCCT
1 GGGGGAATCAATTCCCCCCT
8427 AAAGGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.33, G:0.26, T:0.26
Consensus pattern (22 bp):
GGGGGAATCAATTCCCCCCTTG
Found at i:9249 original size:38 final size:38
Alignment explanation
Indices: 9153--9249 Score: 149
Period size: 38 Copynumber: 2.6 Consensus size: 38
9143 TATAAGACAT
* * *
9153 ATGACAGGTCCTTTGGGACACAGATTACATCCTTCGGG
1 ATGACAGGTCCTTCGGGACATAGATGACATCCTTCGGG
9191 ATGACAGGTCCTTCGGGACATAGATGACATCCTTCGGG
1 ATGACAGGTCCTTCGGGACATAGATGACATCCTTCGGG
* *
9229 ATGATAGGTCATTCGGGACAT
1 ATGACAGGTCCTTCGGGACAT
9250 TTATACGAGC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (38 bp):
ATGACAGGTCCTTCGGGACATAGATGACATCCTTCGGG
Found at i:11707 original size:2 final size:2
Alignment explanation
Indices: 11700--11738 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
11690 ATTTGGATCC
11700 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11739 GATTAAGGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15429 original size:38 final size:38
Alignment explanation
Indices: 15300--15430 Score: 165
Period size: 38 Copynumber: 3.4 Consensus size: 38
15290 TATAAGACAT
** * *
15300 ATGACAGGTTATTCGGGACACAGATTACATCCTTCTGG
1 ATGACAGGTCCTTCGGGACACAGATTACATTCTTCGGG
15338 ATGACAGGTCCTTCGGGACACAGATTACA-TCATTCGGG
1 ATGACAGGTCCTTCGGGACACAGATTACATTC-TTCGGG
** * *
15376 ATGACAATTCATTCGGGACACAGATGACATTCTTCGGG
1 ATGACAGGTCCTTCGGGACACAGATTACATTCTTCGGG
*
15414 ATGATAGGTCCTTCGGG
1 ATGACAGGTCCTTCGGG
15431 GACATTTATA
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
37 1 0.01
38 76 0.96
39 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (38 bp):
ATGACAGGTCCTTCGGGACACAGATTACATTCTTCGGG
Found at i:18190 original size:97 final size:97
Alignment explanation
Indices: 18087--18283 Score: 349
Period size: 97 Copynumber: 2.0 Consensus size: 97
18077 AAAAATAATA
18087 TTTTTATTATTAAAAAATGACAGGCACCTAAATGTATAACTAAAAAAAATATTAGACAACTATTT
1 TTTTTATTATTAAAAAATGACAGGCACCTAAATGTATAACTAAAAAAAATATTAGACAACTATTT
*
18152 TTAGCGAAAAGTTCTTCAGACACAAAAATGTT
66 TTAGCGAAAAGTTCTTCAAACACAAAAATGTT
* * * *
18184 TTTTTATTATTAAAAAATGGCAGGCACCTAAATGTATAATTGAAAAAAATATTAGTCAACTATTT
1 TTTTTATTATTAAAAAATGACAGGCACCTAAATGTATAACTAAAAAAAATATTAGACAACTATTT
18249 TTAGCGAAAAGTTCTTCAAACACAAAAATGTT
66 TTAGCGAAAAGTTCTTCAAACACAAAAATGTT
18281 TTT
1 TTT
18284 CAAGACATAA
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.34
Consensus pattern (97 bp):
TTTTTATTATTAAAAAATGACAGGCACCTAAATGTATAACTAAAAAAAATATTAGACAACTATTT
TTAGCGAAAAGTTCTTCAAACACAAAAATGTT
Found at i:21616 original size:33 final size:33
Alignment explanation
Indices: 21573--21643 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
21563 TTTGATTTTG
* *
21573 CCCCTCATTTTCTATGGTTAATTATACTTTGCC
1 CCCCTAATTTTCTATGATTAATTATACTTTGCC
* *
21606 CCCCTAATTTTCTTTGATTAATTATATTTTGCC
1 CCCCTAATTTTCTATGATTAATTATACTTTGCC
21639 CCCCT
1 CCCCT
21644 TAAGTTAGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.18, C:0.28, G:0.07, T:0.46
Consensus pattern (33 bp):
CCCCTAATTTTCTATGATTAATTATACTTTGCC
Found at i:27885 original size:31 final size:32
Alignment explanation
Indices: 27815--27900 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
27805 GAATTTCAAT
* * * **
27815 AAGTTTAAGGACCATTCTATAATAATTTGAGA
1 AAGTTTAATGACCATTTTGTAACCATTTGAGA
*
27847 AAGTTTAATGACTATTTTGTAACCATTTGAG-
1 AAGTTTAATGACCATTTTGTAACCATTTGAGA
*
27878 AAGTTTAATGACCCTTTTGTAAC
1 AAGTTTAATGACCATTTTGTAAC
27901 TTCCAAAACA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
31 21 0.46
32 25 0.54
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (32 bp):
AAGTTTAATGACCATTTTGTAACCATTTGAGA
Found at i:42911 original size:6 final size:6
Alignment explanation
Indices: 42900--43028 Score: 73
Period size: 6 Copynumber: 20.8 Consensus size: 6
42890 TTGGTGTTCA
* *
42900 GAGAGG GAGAGG GAGAGGGG GAGAGA GAGAGA GAGAGG GAGAGG GAGGGAGG
1 GAGAGG GAGAGG GAGA--GG GAGAGG GAGAGG GAGAGG GAGAGG GA--GAGG
* * * * *
42952 GAGAGAG AGTGAGG GAG-GG G-GAGG GGGAGG GGGAGG GGGAGG GGGAGG
1 GAGAG-G -GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
* * * * * *
43000 GGGGGG GGGGGG GGGAGG GAGGGG GAGAG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAG
43029 AGACTTCATG
Statistics
Matches: 106, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
4 1 0.01
5 6 0.06
6 81 0.76
7 2 0.02
8 16 0.15
ACGTcount: A:0.26, C:0.00, G:0.74, T:0.01
Consensus pattern (6 bp):
GAGAGG
Found at i:42936 original size:32 final size:32
Alignment explanation
Indices: 42899--42986 Score: 124
Period size: 32 Copynumber: 2.8 Consensus size: 32
42889 CTTGGTGTTC
42899 AGAGAGGGAGAGGGAGAGGGGGAGAGAGAGAG
1 AGAGAGGGAGAGGGAGAGGGGGAGAGAGAGAG
*
42931 AGAGAGGGAGAGGGAG-GGAGGGAGAGAGAGTG
1 AGAGAGGGAGAGGGAGAGG-GGGAGAGAGAGAG
* * *
42963 AGGGAGGGGGAGGGGGAGGGGGAG
1 AGAGAGGGAGAGGGAGAGGGGGAG
42987 GGGGAGGGGG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
31 2 0.04
32 46 0.92
33 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.67, T:0.01
Consensus pattern (32 bp):
AGAGAGGGAGAGGGAGAGGGGGAGAGAGAGAG
Found at i:42978 original size:1 final size:1
Alignment explanation
Indices: 42968--43024 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
42958 GAGTGAGGGA
* * * * * * *
42968 GGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGGGGGGGGGGGGGAGGGAGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
43025 AGAGAGACTT
Statistics
Matches: 42, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.12, C:0.00, G:0.88, T:0.00
Consensus pattern (1 bp):
G
Found at i:42985 original size:18 final size:18
Alignment explanation
Indices: 42964--43026 Score: 96
Period size: 18 Copynumber: 3.6 Consensus size: 18
42954 GAGAGAGTGA
42964 GGGAGGGGGAGGGGGAGG
1 GGGAGGGGGAGGGGGAGG
42982 GGGAGGGGGAGGGGGAGG
1 GGGAGGGGGAGGGGGAGG
43000 GGG-GGGGG-GGGGG-GG
1 GGGAGGGGGAGGGGGAGG
43015 AGGGAGGGGGAG
1 -GGGAGGGGGAG
43027 AGAGACTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.05
16 8 0.19
17 10 0.24
18 22 0.52
ACGTcount: A:0.14, C:0.00, G:0.86, T:0.00
Consensus pattern (18 bp):
GGGAGGGGGAGGGGGAGG
Found at i:43172 original size:18 final size:18
Alignment explanation
Indices: 43149--43268 Score: 92
Period size: 18 Copynumber: 6.8 Consensus size: 18
43139 AGGGGGAGGG
43149 GGGAGAGAGAGAGGGGGT
1 GGGAGAGAGAGAGGGGGT
*
43167 GGGAGAGAGAGA--GGGA
1 GGGAGAGAGAGAGGGGGT
43183 GGGAG-G-GAG-GGAGGGT
1 GGGAGAGAGAGAGG-GGGT
43199 GGGAGAGAGAGAGGGAGGGT
1 GGGAGAGAGAGA-GG-GGGT
*
43219 GGGAGGGAGAG-GGAGGGT
1 GGGAGAGAGAGAGG-GGGT
* * *
43237 GGGAGGGAGGGAGAGGG-
1 GGGAGAGAGAGAGGGGGT
* *
43254 AGGAGAGGGAGAGGG
1 GGGAGAGAGAGAGGG
43269 AGAGAGAGGG
Statistics
Matches: 84, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
14 3 0.04
15 1 0.01
16 16 0.19
17 11 0.13
18 35 0.42
19 1 0.01
20 17 0.20
ACGTcount: A:0.28, C:0.00, G:0.69, T:0.03
Consensus pattern (18 bp):
GGGAGAGAGAGAGGGGGT
Found at i:43176 original size:4 final size:4
Alignment explanation
Indices: 43142--43294 Score: 112
Period size: 4 Copynumber: 40.2 Consensus size: 4
43132 GTTGGAGAGG
* * * * *
43142 GGGA GGG- GGGA GAGA GAGA -GG- GGGT GGGA GAGA GAGA GGGA GGGA
1 GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA
* * * *
43187 GGGA GGGA GGGT GGGA GAGA GAGA GGGA GGGT GGGA GGGA --GA GGGA
1 GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA
*
43233 GGGT GGGA GGGA GGGA --GA GGGA GGAGA GGGA --GA GGGA GAGAGA GGGA
1 GGGA GGGA GGGA GGGA GGGA GGGA GG-GA GGGA GGGA GGGA G-G-GA GGGA
43280 --GA GGGA GGGA GGGA G
1 GGGA GGGA GGGA GGGA G
43295 AGACCTCATG
Statistics
Matches: 122, Mismatches: 13, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
2 8 0.07
3 6 0.05
4 99 0.81
5 6 0.05
6 3 0.02
ACGTcount: A:0.28, C:0.00, G:0.69, T:0.03
Consensus pattern (4 bp):
GGGA
Found at i:43176 original size:22 final size:22
Alignment explanation
Indices: 43136--43297 Score: 125
Period size: 22 Copynumber: 7.2 Consensus size: 22
43126 AACAAAGTTG
43136 GAGAGGGGGAGGG-GGGAGAGA
1 GAGAGGGGGAGGGAGGGAGAGA
* *
43157 GAGAGGGGGTGGGAGAGAGAGA
1 GAGAGGGGGAGGGAGGGAGAGA
* *
43179 GGGAGGGAGGGAGGGAGGGTGGGAGA
1 GAGA-GG-GGGAGGGA-GG-GAGAGA
* * *
43205 GAGAGAGGGAGGGTGGGAGGGA
1 GAGAGGGGGAGGGAGGGAGAGA
* *
43227 GAG-GGAGGGTGGGAGGGAGGGA
1 GAGAGG-GGGAGGGAGGGAGAGA
43249 GAG-GGAGGAGAGGGAGAGG-GAGA
1 GAGAGG-GG-GAGGGAG-GGAGAGA
* *
43272 GAGAGGGAGAGGGAGGGAGGGA
1 GAGAGGGGGAGGGAGGGAGAGA
43294 GAGA
1 GAGA
43298 CCTCATGTAA
Statistics
Matches: 113, Mismatches: 18, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
21 15 0.13
22 53 0.47
23 17 0.15
24 18 0.16
25 2 0.02
26 8 0.07
ACGTcount: A:0.29, C:0.00, G:0.69, T:0.02
Consensus pattern (22 bp):
GAGAGGGGGAGGGAGGGAGAGA
Found at i:43297 original size:16 final size:16
Alignment explanation
Indices: 43135--43297 Score: 126
Period size: 16 Copynumber: 10.4 Consensus size: 16
43125 AAACAAAGTT
*
43135 GGAGAGGGGGAGGG-G
1 GGAGAGAGGGAGGGAG
* *
43150 GGAGAGAGAGAGGGGGTG
1 GGAGAGAG-G-GAGGGAG
*
43168 GGAGAGAGAGAGGGAG
1 GGAGAGAGGGAGGGAG
* *
43184 GGAGGGAGGGAGGGTG
1 GGAGAGAGGGAGGGAG
*
43200 GGAGAGAGAGAGGGAG
1 GGAGAGAGGGAGGGAG
* *
43216 GGTGGGAGGGA--GAG
1 GGAGAGAGGGAGGGAG
* *
43230 GGAGGGTGGGAGGGA-
1 GGAGAGAGGGAGGGAG
43245 GG-GAGAGGGA-GGAG
1 GGAGAGAGGGAGGGAG
*
43259 AGG-GAGAGGGAGAGAG
1 -GGAGAGAGGGAGGGAG
43275 AGG-GAGAGGGAGGGAG
1 -GGAGAGAGGGAGGGAG
43291 GGAGAGA
1 GGAGAGA
43298 CCTCATGTAA
Statistics
Matches: 119, Mismatches: 20, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
13 3 0.03
14 18 0.15
15 21 0.18
16 64 0.54
17 4 0.03
18 9 0.08
ACGTcount: A:0.29, C:0.00, G:0.69, T:0.02
Consensus pattern (16 bp):
GGAGAGAGGGAGGGAG
Found at i:43389 original size:266 final size:268
Alignment explanation
Indices: 42900--43401 Score: 764
Period size: 266 Copynumber: 1.9 Consensus size: 268
42890 TTGGTGTTCA
* *
42900 GAGAGGGAGAGGGAGAGGGGGAGAGAGAGAGAGAGAGGGAGAGGGAGGGAGGGAGAGAGAGTGAG
1 GAGAGAGAGAGGGAGAGGGGGAGAGAGAGAGAGAGAGAGAGAGGGAGGGAGGGAGAGAGAG-GAG
* * * * * * * * *
42965 GGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGAGGGGGGGGGGGGGGGGGAGGGAGGGGGAGAGA
65 GGAGGGGGAGAGGGAGGGAGAGGGGGAGAGGGAGAGGGAGAGAGAGGGAGAGGGAGGGGGAGAGA
*
43030 GACTTCATGTAAGCCTTCTTCCTTTAAGCTTTTTTATGTTAATAATGGCTTTTAGGTGGTGAATA
130 GACCTCATGTAAGCCTTCTTCCTTTAAGCTTTTTTATGTTAATAATGGCTTTTAGGTGGTGAATA
43095 TGTTTTCCCCCTTCATCTCATCTGGGTTTTAAACAAAGTTGGAGAGGGGGAGGGGGGAGAGAGAG
195 TGTTTTCCCCCTTCATCTCATCTGGGTTTTAAACAAAGTTGGAGAGGGGGAGGGGGGAGAGAGAG
43160 AGGGGGTGG
260 AGGGGGTGG
* * * * *
43169 GAGAGAGAGAGGGAG-GGAGGGAGGGAGGGTGGGAGAGAGAGAGGGAGGGTGGGAG-G-GA-GAG
1 GAGAGAGAGAGGGAGAGG-GGGAGAGAGAGAGAGAGAGAGAGAGGGAGGGAGGGAGAGAGAGGAG
43230 GGAGGGTGG-GAGGGAGGGAGAGGGAGGAGAGGGAGAGGGAGAGAGAGGGAGAGGGAGGGAGG-G
65 GGAGGG-GGAGAGGGAGGGAGAGGG-GGAGAGGGAGAGGGAGAGAGAGGGAGAGGGAGGG-GGAG
43293 AGAGACCTCATGTAAGCCTTCTTCCTTTAAGCTTTTTTATGTTAATAATGGCTTTTAGGTGGTGA
127 AGAGACCTCATGTAAGCCTTCTTCCTTTAAGCTTTTTTATGTTAATAATGGCTTTTAGGTGGTGA
43358 ATATGTTTTCCCCCTTCATCTCATCTGGGTTTTAAACAAAGTTG
192 ATATGTTTTCCCCCTTCATCTCATCTGGGTTTTAAACAAAGTTG
43402 TAAGATTTAA
Statistics
Matches: 212, Mismatches: 17, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
265 22 0.10
266 138 0.65
267 4 0.02
268 3 0.01
269 45 0.21
ACGTcount: A:0.25, C:0.08, G:0.48, T:0.19
Consensus pattern (268 bp):
GAGAGAGAGAGGGAGAGGGGGAGAGAGAGAGAGAGAGAGAGAGGGAGGGAGGGAGAGAGAGGAGG
GAGGGGGAGAGGGAGGGAGAGGGGGAGAGGGAGAGGGAGAGAGAGGGAGAGGGAGGGGGAGAGAG
ACCTCATGTAAGCCTTCTTCCTTTAAGCTTTTTTATGTTAATAATGGCTTTTAGGTGGTGAATAT
GTTTTCCCCCTTCATCTCATCTGGGTTTTAAACAAAGTTGGAGAGGGGGAGGGGGGAGAGAGAGA
GGGGGTGG
Found at i:48314 original size:12 final size:12
Alignment explanation
Indices: 48297--48329 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
48287 CCCTCAACTA
48297 AGTCGATGAGCC
1 AGTCGATGAGCC
48309 AGTCGATGAGCC
1 AGTCGATGAGCC
*
48321 AGCCGATGA
1 AGTCGATGA
48330 TGATGGTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.33, T:0.15
Consensus pattern (12 bp):
AGTCGATGAGCC
Found at i:50959 original size:44 final size:44
Alignment explanation
Indices: 50910--50993 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
50900 AGTCAAATTC
*
50910 AACAAAAGTGAGGGTAAAAGAAATAAAACAAGTAGTTGAATTTA
1 AACAAAAGTAAGGGTAAAAGAAATAAAACAAGTAGTTGAATTTA
*
50954 AACAAAAGTAAGGGTAAGAGAAATAAAACAAGTAGTTGAA
1 AACAAAAGTAAGGGTAAAAGAAATAAAACAAGTAGTTGAA
50994 GCTGAACAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.56, C:0.05, G:0.21, T:0.18
Consensus pattern (44 bp):
AACAAAAGTAAGGGTAAAAGAAATAAAACAAGTAGTTGAATTTA
Found at i:55739 original size:19 final size:19
Alignment explanation
Indices: 55704--55741 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
55694 GTAAGTTAAT
*
55704 TTTTAATATATTATATTTA
1 TTTTAATATATGATATTTA
55723 TTTT-ATATATGATTATTTA
1 TTTTAATATATGA-TATTTA
55742 GAAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTAATATATGATATTTA
Found at i:62033 original size:22 final size:21
Alignment explanation
Indices: 62008--62064 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
61998 AGGGTTTTAT
62008 TTTACATAATTTTAAGTTAAAA
1 TTTACATAATTTTAA-TTAAAA
*
62030 TTTACACTCAA-TTTAATTTAAA
1 TTTACA-T-AATTTTAATTAAAA
*
62052 TATACATAATTTT
1 TTTACATAATTTT
62065 TTATTATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 2 0.07
21 4 0.13
22 16 0.53
23 6 0.20
24 2 0.07
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (21 bp):
TTTACATAATTTTAATTAAAA
Found at i:63297 original size:2 final size:2
Alignment explanation
Indices: 63292--63329 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
63282 TTTTTTATTA
63292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63330 GACCACTCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66519 original size:2 final size:2
Alignment explanation
Indices: 66512--66575 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
66502 CTGGTGCTGA
66512 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66554 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
66576 CATGATTACT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67790 original size:2 final size:2
Alignment explanation
Indices: 67785--67814 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
67775 TCCAATGGTT
*
67785 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
67815 CAAGGTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:75464 original size:2 final size:2
Alignment explanation
Indices: 75459--75484 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
75449 CTCTCTCTCT
75459 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
75485 GTCCCCTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:77892 original size:22 final size:22
Alignment explanation
Indices: 77845--77893 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
77835 AATTTAATAT
* *
77845 ATAAAATTATTCATAATTAAAT
1 ATAAAATTATTCATAATAAAAA
*
77867 ATAATATTATT-ATATATAAAAA
1 ATAAAATTATTCATA-ATAAAAA
77889 ATAAA
1 ATAAA
77894 TGTAACCGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAAAATTATTCATAATAAAAA
Found at i:98339 original size:15 final size:15
Alignment explanation
Indices: 98316--98364 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
98306 ACCATGACCA
*
98316 CGAGTCGAGTCGAGC
1 CGAGTCGAGCCGAGC
*
98331 CGAGCCGAGCCGAGC
1 CGAGTCGAGCCGAGC
* * *
98346 CGTGTCGTGCCGTGC
1 CGAGTCGAGCCGAGC
98361 CGAG
1 CGAG
98365 ACAGACGGTG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.14, C:0.33, G:0.41, T:0.12
Consensus pattern (15 bp):
CGAGTCGAGCCGAGC
Found at i:102826 original size:6 final size:6
Alignment explanation
Indices: 102815--102870 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
102805 GACACGTATT
* **
102815 ACCACG ACCACG ACCACG A-GACGAG ATGACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCAC--G ACCACG ACCACG ACCACG ACCACG
*
102864 ATCACG A
1 ACCACG A
102871 GACGAGACGG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
5 2 0.05
6 36 0.84
7 2 0.05
8 3 0.07
ACGTcount: A:0.36, C:0.39, G:0.21, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:107541 original size:19 final size:20
Alignment explanation
Indices: 107517--107555 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
107507 AAAATTAAAA
107517 TCCCGA-TTTTCCCGGTTTT
1 TCCCGATTTTTCCCGGTTTT
*
107536 TCCCGATTTTTTCCGGTTTT
1 TCCCGATTTTTCCCGGTTTT
107556 CAGCCGGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.05, C:0.28, G:0.15, T:0.51
Consensus pattern (20 bp):
TCCCGATTTTTCCCGGTTTT
Done.