Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008790.1 Hibiscus syriacus cultivar Beakdansim tig00111933_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: 36897
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3991 original size:9 final size:9
Alignment explanation
Indices: 3967--4052 Score: 84
Period size: 9 Copynumber: 9.3 Consensus size: 9
3957 GCTGCTGGAA
*
3967 ACCGGTTTA
1 ACCGGTTTG
*
3976 ACTGGTTTG
1 ACCGGTTTG
3985 ACCGGTTTG
1 ACCGGTTTG
*
3994 ACCGGTTTCA
1 ACCGGTTT-G
*
4004 ACCGGTTCG
1 ACCGGTTTG
4013 AACCGGTTTG
1 -ACCGGTTTG
*
4023 ACCGGTCTG
1 ACCGGTTTG
4032 AACC-GTTTG
1 -ACCGGTTTG
*
4041 ACCGGTCTG
1 ACCGGTTTG
4050 ACC
1 ACC
4053 CGACCCGATC
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
8 3 0.05
9 42 0.67
10 18 0.29
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:4035 original size:29 final size:27
Alignment explanation
Indices: 3984--4052 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 27
3974 TAACTGGTTT
*
3984 GACCGGTTTGACCGGTTTCAACCGGTTC
1 GACCGGTTTGACCGGTCTCAACC-GTTC
* *
4012 GAACCGGTTTGACCGGTCTGAACCGTTT
1 G-ACCGGTTTGACCGGTCTCAACCGTTC
*
4040 GACCGGTCTGACC
1 GACCGGTTTGACC
4053 CGACCCGATC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 11 0.31
28 5 0.14
29 20 0.56
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (27 bp):
GACCGGTTTGACCGGTCTCAACCGTTC
Found at i:4077 original size:22 final size:22
Alignment explanation
Indices: 4049--4091 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4039 TGACCGGTCT
*
4049 GACCCGACCCGATCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
4071 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
4092 GTTGACTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.47, G:0.23, T:0.12
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:10934 original size:54 final size:54
Alignment explanation
Indices: 10852--10956 Score: 192
Period size: 54 Copynumber: 1.9 Consensus size: 54
10842 CACTGGTTCA
* *
10852 TAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTTTGCCCAGATTTTCG
1 TAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGATTTTCG
10906 TAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGATTT
1 TAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGATTT
10957 CTTGTTAGTA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (54 bp):
TAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTGCCCAGATTTTCG
Found at i:13009 original size:7 final size:7
Alignment explanation
Indices: 12997--13190 Score: 185
Period size: 7 Copynumber: 27.7 Consensus size: 7
12987 CTTGATTCAA
12997 TTTCTTT
1 TTTCTTT
13004 TTTCTTCTT
1 TTTC-T-TT
13013 TTTCTTT
1 TTTCTTT
13020 TTTCTCTT
1 TTTCT-TT
13028 TTT-TCTT
1 TTTCT-TT
13035 TTTCTTT
1 TTTCTTT
13042 TTT-TTT
1 TTTCTTT
*
13048 TTTTTTT
1 TTTCTTT
*
13055 TTTTTCTT
1 TTTCT-TT
13063 TTTC-TT
1 TTTCTTT
13069 TTT-TTT
1 TTTCTTT
13075 TTT-TTT
1 TTTCTTT
13081 TTTCTTT
1 TTTCTTT
13088 TTTC-TT
1 TTTCTTT
13094 TTT-TTT
1 TTTCTTT
13100 TTTC-TT
1 TTTCTTT
13106 TTT-TTT
1 TTTCTTT
13112 TTTCTTT
1 TTTCTTT
13119 TTTCTTT
1 TTTCTTT
13126 TTTCTTT
1 TTTCTTT
13133 TTTC-TT
1 TTTCTTT
*
13139 TTT-TTC
1 TTTCTTT
13145 TTTCTTT
1 TTTCTTT
13152 TTTCCTTAT
1 TTT-CTT-T
13161 TTTCTTTTT
1 TTTC--TTT
13170 TTTCTTCT
1 TTTCTT-T
13178 TTTCCTTT
1 TTT-CTTT
13186 TTTCT
1 TTTCT
13191 CTGATGGATG
Statistics
Matches: 164, Mismatches: 3, Indels: 40
0.79 0.01 0.19
Matches are distributed among these distances:
6 51 0.31
7 68 0.41
8 25 0.15
9 18 0.11
10 2 0.01
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTCTTT
Found at i:13076 original size:45 final size:44
Alignment explanation
Indices: 13001--13180 Score: 193
Period size: 46 Copynumber: 4.0 Consensus size: 44
12991 ATTCAATTTC
* * *
13001 TTTTTTCTTCTTTTTCTTTTTTCTCTTTTTTCTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTCTTTTTTTTCTTTTTTCTTTTTCTTTTTT
* *
13045 TTTTTTTTTTTTTTTCTTTTTCTTTTTTTTTTTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTC-TTTT-TTTTCTTTTTTCTTTTTCTTTTTT
*
13091 CTTTTTTTTTTTCTTT-TTTTTTTTCTTTTTTCTTTTTTCTTTTTTCT
1 -TTTTTTTTTTTTTTTCTTTTTTTTCTTTTTTC-TTTTTC-TTTTT-T
* * *
13138 TTTTTTCTTTCTTTTTTCCTTATTTTCTTTTTT-TTCTTCTTTT
1 TTTTTT-TTT-TTTTTTCTTTTTTTTCTTTTTTCTTTTTCTTTT
13181 CCTTTTTTCT
Statistics
Matches: 115, Mismatches: 12, Indels: 16
0.80 0.08 0.11
Matches are distributed among these distances:
44 24 0.21
45 14 0.12
46 36 0.31
47 23 0.20
48 5 0.04
49 13 0.11
ACGTcount: A:0.01, C:0.13, G:0.00, T:0.87
Consensus pattern (44 bp):
TTTTTTTTTTTTTTTCTTTTTTTTCTTTTTTCTTTTTCTTTTTT
Found at i:13172 original size:1 final size:1
Alignment explanation
Indices: 13001--13154 Score: 146
Period size: 1 Copynumber: 154.0 Consensus size: 1
12991 ATTCAATTTC
* * * * * * * *
13001 TTTTTTCTTCTTTTTCTTTTTTCTCTTTTTTCTTTTTCTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * * * *
13066 CTTTTTTTTTTTTTTTTTCTTTTTTCTTTTTTTTTTTCTTTTTTTTTTTCTTTTTTCTTTTTTCT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
13131 TTTTTCTTTTTTTCTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTT
13155 CCTTATTTTC
Statistics
Matches: 117, Mismatches: 36, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 117 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:13181 original size:37 final size:32
Alignment explanation
Indices: 13000--13189 Score: 218
Period size: 31 Copynumber: 6.0 Consensus size: 32
12990 GATTCAATTT
* *
13000 CTTTTTTCTTCTTTTTCTTTTTTCTCTTTTTT-
1 CTTTTTTCTT-TTTTTTTTTTTTTTCTTTTTTC
13032 C-TTTTTC-TTTTTTTTTTTTTTT-TTTTTT-
1 CTTTTTTCTTTTTTTTTTTTTTTTCTTTTTTC
13060 C-TTTTTCTTTTTTTTTTTTTTTTTCTTTTTT-
1 CTTTTTTC-TTTTTTTTTTTTTTTTCTTTTTTC
13091 CTTTTTT-TTTTTCTTTTTTTTTTTCTTTTTT-
1 CTTTTTTCTTTTT-TTTTTTTTTTTCTTTTTTC
13122 CTTTTTTCTTTTTTCTTTTTTTCTTTCTTTTTTC
1 CTTTTTTCTTTTTT-TTTTTTT-TTTCTTTTTTC
* *
13156 CTTATTTTCTTTTTTTTCTTCTTTTCCTTTTTTC
1 CTT-TTTTCTTTTTTTT-TTTTTTTTCTTTTTTC
13190 TCTGATGGAT
Statistics
Matches: 143, Mismatches: 4, Indels: 20
0.86 0.02 0.12
Matches are distributed among these distances:
28 13 0.09
29 12 0.08
30 21 0.15
31 39 0.27
32 18 0.13
33 10 0.07
34 15 0.10
35 15 0.10
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (32 bp):
CTTTTTTCTTTTTTTTTTTTTTTTCTTTTTTC
Found at i:13181 original size:45 final size:44
Alignment explanation
Indices: 12998--13190 Score: 184
Period size: 39 Copynumber: 4.6 Consensus size: 44
12988 TTGATTCAAT
* *
12998 TTCTTTTTTCTTC-TTTTTCTTTTTTCTCTTTTTTCTTTTTCTTTTT
1 TTCTTTTTT-TTCTTTTTTCTTTTTT-TCTTTCTT-TTTTCCTTTTT
13044 TT-TTTTTTTT-TTTTTTC--TTTTTCTTT-TTTTTT--TTTTT
1 TTCTTTTTTTTCTTTTTTCTTTTTTTCTTTCTTTTTTCCTTTTT
*
13081 TT-TCTTTTTTCTTTTTT-TTTTTCTT-TTT-TTTTTT-C-TTTT
1 TTCTTTTTTTTCTTTTTTCTTTTT-TTCTTTCTTTTTTCCTTTTT
*
13120 TTC--TTTTTTCTTTTTTCTTTTTTTCTTTCTTTTTTCCTTATT
1 TTCTTTTTTTTCTTTTTTCTTTTTTTCTTTCTTTTTTCCTTTTT
*
13162 TTCTTTTTTTTCTTCTTTTCCTTTTTTCT
1 TTCTTTTTTTTCTT-TTTTCTTTTTTTCT
13191 CTGATGGATG
Statistics
Matches: 129, Mismatches: 3, Indels: 31
0.79 0.02 0.19
Matches are distributed among these distances:
37 14 0.11
38 21 0.16
39 30 0.23
40 10 0.08
41 6 0.05
42 10 0.08
44 17 0.13
45 19 0.15
46 2 0.02
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (44 bp):
TTCTTTTTTTTCTTTTTTCTTTTTTTCTTTCTTTTTTCCTTTTT
Found at i:13186 original size:53 final size:49
Alignment explanation
Indices: 13001--13190 Score: 195
Period size: 45 Copynumber: 4.0 Consensus size: 49
12991 ATTCAATTTC
* * *
13001 TTTTTTCTTCTTTTTCTTTTTTC--TCTTTT-TTCTTTTTC-TTTTT-T
1 TTTTTTCTTTTTTTTTTTTTTTCTTTTTTTTCTTCTTTTTCTTTTTTCT
* * *
13045 TTTTTT-TTTTTTTTTCTTTTTCTTTTTTTTTTTTTTTTTCTTTTTTCT
1 TTTTTTCTTTTTTTTTTTTTTTCTTTTTTTTCTTCTTTTTCTTTTTTCT
13093 TTTTTT-TTTTCTTTTTTTTTTTC--TTTTTTC-T-TTTTTCTTTTTTCT
1 TTTTTTCTTTT-TTTTTTTTTTTCTTTTTTTTCTTCTTTTTCTTTTTTCT
*
13138 TTTTTTCTTTCTTTTTTCCTTATTTTCTTTTTTTTCTTCTTTTCCTTTTTTCT
1 TTTTTTCTTT-TTTTTT--TT-TTTTCTTTTTTTTCTTCTTTTTCTTTTTTCT
13191 CTGATGGATG
Statistics
Matches: 123, Mismatches: 8, Indels: 21
0.81 0.05 0.14
Matches are distributed among these distances:
43 13 0.11
44 6 0.05
45 25 0.20
46 17 0.14
47 12 0.10
48 13 0.11
49 16 0.13
51 7 0.06
52 1 0.01
53 13 0.11
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.86
Consensus pattern (49 bp):
TTTTTTCTTTTTTTTTTTTTTTCTTTTTTTTCTTCTTTTTCTTTTTTCT
Found at i:19365 original size:2 final size:2
Alignment explanation
Indices: 19358--19391 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
19348 TAAAAAGTAA
19358 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
19392 TTAGGGTTTT
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:19716 original size:2 final size:2
Alignment explanation
Indices: 19709--19740 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19699 TTACAAATCT
19709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19741 ATAGAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20776 original size:3 final size:3
Alignment explanation
Indices: 20768--20806 Score: 69
Period size: 3 Copynumber: 12.7 Consensus size: 3
20758 TCAGTTTACA
20768 TAT TAT TAT TAT TAT TAT TAT ATAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
20807 AATAAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:22171 original size:2 final size:2
Alignment explanation
Indices: 22158--22189 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
22148 TATATTAGTC
*
22158 AT AT AA 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
22190 TTGTTTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:22406 original size:158 final size:168
Alignment explanation
Indices: 22206--22659 Score: 438
Period size: 158 Copynumber: 2.7 Consensus size: 168
22196 AAATAATAAT
* * * *
22206 TATTTATTTATTTTTTATATATAAAGAAAAGGACAGTCTTAAAGCAACTAGATGTCCCATTCTGA
1 TATTTATTTA--TTTTAAATATTAAG-AAAGGATAGTCTTAAAGCAACTAGATGTCCTATTCTGA
*
22271 TATTTTAAAAATAAATAAATATCCTACTTATAAAA-ACCAGA-A-A-ATACATAT-TGT-T-T-T
63 TATTTTAAAAATAAATAAATATCCTACTTATAAAATA-CAGATATATATACATATATATATATAT
22328 ATTTA-AATTATTTTCTTAGGAAAATTA-T-TA-T-TT-TTAA
127 ATTTATAATTATTTT-TTAGGAAAATTATTATATTCTTATTAA
* *
22365 TATTTATTTATTTTCCAAATATTAAGAAAGGATAGTCTTAAAGCAAGTAGATGTCTTATTCTGAT
1 TATTTATTTATTTT--AAATATTAAGAAAGGATAGTCTTAAAGCAACTAGATGTCCTATTCTGAT
* * * * * *
22430 ATTTTAAAAATAAATATATATCATGCTTATAAATATATATATATATATATATATATATATATATA
64 ATTTTAAAAATAAATAAATATCCTACTTATAAA-ATACAGATATATATACATATATATATATATA
* *
22495 TTTACTTCATTATTTTTTAGGGAAATTATTATATTCTTATTAA
128 TTTA--TAATTATTTTTTAGGAAAATTATTATATTCTTATTAA
* *
22538 TATTTATTTATTTATTAATATTAAAGAAA--ATGCAGTCTTAAAGCAACTAGATGTCCTTTTCTG
1 TATTTATTTATTT-TAAATATT-AAGAAAGGAT--AGTCTTAAAGCAACTAGATGTCCTATTCTG
* * * ** * *
22601 ATA-TTTGAAAATAAATAAATATCCTATTTACAAAACCCTAAATATATATATATATATAT
62 ATATTTTAAAAATAAATAAATATCCTACTTATAAAATAC-AGATATATATACATATATAT
22660 TTAATCCTTA
Statistics
Matches: 242, Mismatches: 29, Indels: 35
0.79 0.09 0.11
Matches are distributed among these distances:
157 4 0.02
158 65 0.27
159 21 0.09
160 2 0.01
161 1 0.00
162 7 0.03
163 2 0.01
164 1 0.00
165 1 0.00
166 6 0.02
168 11 0.05
169 9 0.04
170 2 0.01
171 4 0.02
172 52 0.21
173 53 0.22
174 1 0.00
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (168 bp):
TATTTATTTATTTTAAATATTAAGAAAGGATAGTCTTAAAGCAACTAGATGTCCTATTCTGATAT
TTTAAAAATAAATAAATATCCTACTTATAAAATACAGATATATATACATATATATATATATATTT
ATAATTATTTTTTAGGAAAATTATTATATTCTTATTAA
Found at i:22467 original size:2 final size:2
Alignment explanation
Indices: 22457--22495 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
22447 ATATCATGCT
*
22457 TA TA AA 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
22496 TTACTTCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:23118 original size:13 final size:14
Alignment explanation
Indices: 23081--23142 Score: 58
Period size: 13 Copynumber: 4.5 Consensus size: 14
23071 TTCTTTCAAA
23081 ATTTTTATTACTTAT
1 ATTTTTATTA-TTAT
*
23096 AATATTTATTA-TAT
1 -ATTTTTATTATTAT
23110 ATTTTTATTATTA-
1 ATTTTTATTATTAT
* *
23123 ATGTTT-TTATTTT
1 ATTTTTATTATTAT
23136 ATTTTTA
1 ATTTTTA
23143 GATATTAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
12 5 0.13
13 19 0.50
14 5 0.13
16 9 0.24
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (14 bp):
ATTTTTATTATTAT
Found at i:23120 original size:16 final size:16
Alignment explanation
Indices: 23101--23137 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
23091 CTTATAATAT
23101 TTATTATATATTTTTA
1 TTATTATATATTTTTA
*
23117 TTATTA-ATGTTTTTA
1 TTATTATATATTTTTA
23132 TT-TTAT
1 TTATTAT
23138 TTTTAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 3 0.16
15 10 0.53
16 6 0.32
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTATTATATATTTTTA
Found at i:31475 original size:54 final size:54
Alignment explanation
Indices: 31417--31550 Score: 144
Period size: 54 Copynumber: 2.5 Consensus size: 54
31407 GAAAATGATG
* *
31417 AATGTGTTGTCAAATGCTTTATGAACAT-CTGACCAGAAGCCACAAGAAAGGATA
1 AATGTGTTGTCAAATGCTTTACGAACATCCAG-CCAGAAGCCACAAGAAAGGATA
* * * ** * *
31471 AATGTGTTATCAAAAGCTTTACGAAAATCCAGGTAGAAGCCACGAGAAAGGATG
1 AATGTGTTGTCAAATGCTTTACGAACATCCAGCCAGAAGCCACAAGAAAGGATA
* * *
31525 AATGTATTGTCACATGTTTTACGAAC
1 AATGTGTTGTCAAATGCTTTACGAAC
31551 CAATGATTAT
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
54 62 0.97
55 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (54 bp):
AATGTGTTGTCAAATGCTTTACGAACATCCAGCCAGAAGCCACAAGAAAGGATA
Found at i:31940 original size:22 final size:22
Alignment explanation
Indices: 31912--31978 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
31902 TATCTACATC
31912 TACATTCTTCAAAGATGATAGA
1 TACATTCTTCAAAGATGATAGA
*
31934 TACATTCTTTAAAGATGATAGA
1 TACATTCTTCAAAGATGATAGA
* *
31956 TTC-TCTTTTCAAAGATGATAGA
1 TACAT-TCTTCAAAGATGATAGA
31978 T
1 T
31979 TCTCTTTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 1 0.03
22 39 0.98
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.37
Consensus pattern (22 bp):
TACATTCTTCAAAGATGATAGA
Found at i:31979 original size:22 final size:22
Alignment explanation
Indices: 31919--31995 Score: 104
Period size: 22 Copynumber: 3.5 Consensus size: 22
31909 ATCTACATTC
*
31919 TTCAAAGATGATAGATACAT-TCT
1 TTCAAAGATGATAGATTC-TCT-T
31942 TT-AAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
31963 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
31985 TTTAAAGATGA
1 TTCAAAGATGA
31996 AAGCCTTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
21 4 0.08
22 44 0.88
23 2 0.04
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:32891 original size:74 final size:74
Alignment explanation
Indices: 32770--32939 Score: 268
Period size: 74 Copynumber: 2.3 Consensus size: 74
32760 ACCTCAAGGC
* * * * *
32770 CATCCATAAGACCTATAGTGCATGATGTTTTCAAAAATCCTTCGGGAGATTTTTTATATTTAAAG
1 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATATTTAAAG
32835 CCTCCGGGT
66 CCTCCGGGT
*
32844 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAG
1 CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATATTTAAAG
*
32909 CCTTCGGGT
66 CCTCCGGGT
*
32918 CATCTGTAAGACCTACAGTGCA
1 CATCCGTAAGACCTACAGTGCA
32940 AGATTATAAG
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 88 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (74 bp):
CATCCGTAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGATTTTTGATATTTAAAG
CCTCCGGGT
Found at i:33131 original size:3 final size:3
Alignment explanation
Indices: 33118--33174 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
33108 TTAGTTTACA
33118 TAT TA- TAT TAT TA- TAT TAT TAT TAT ATAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
33161 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
33175 AATAAAAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.12
3 41 0.82
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:33131 original size:8 final size:9
Alignment explanation
Indices: 33118--33174 Score: 84
Period size: 8 Copynumber: 6.6 Consensus size: 9
33108 TTAGTTTACA
33118 TATTA-TAT
1 TATTATTAT
33126 TATTA-TAT
1 TATTATTAT
33134 TATTATTAT
1 TATTATTAT
33143 ATATTATTAT
1 -TATTATTAT
33153 TATTA-TAT
1 TATTATTAT
33161 TATTATTAT
1 TATTATTAT
33170 TATTA
1 TATTA
33175 AATAAAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
8 21 0.46
9 16 0.35
10 9 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATTATTAT
Found at i:33965 original size:20 final size:20
Alignment explanation
Indices: 33942--33986 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
33932 AGAGAGAATG
33942 GAGAGTAAATCTCTCCTAGA
1 GAGAGTAAATCTCTCCTAGA
33962 GAGAGTAAATCTCTCCTAGA
1 GAGAGTAAATCTCTCCTAGA
33982 GAGAG
1 GAGAG
33987 AAGAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (20 bp):
GAGAGTAAATCTCTCCTAGA
Found at i:35207 original size:22 final size:22
Alignment explanation
Indices: 35182--35253 Score: 108
Period size: 22 Copynumber: 3.2 Consensus size: 22
35172 CAAATCCCTT
35182 TTTTTATTTCTAAAAAAAATGA
1 TTTTTATTTCTAAAAAAAATGA
**
35204 TTTTTATTTCTAAAAAAAAAAA
1 TTTTTATTTCTAAAAAAAATGA
*
35226 TTTTTATTTCTAAAAAGAATGAA
1 TTTTTATTTCTAAAAAAAATG-A
35249 TTTTT
1 TTTTT
35254 TGTTAAACGC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 38 0.86
23 6 0.14
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (22 bp):
TTTTTATTTCTAAAAAAAATGA
Found at i:35416 original size:18 final size:19
Alignment explanation
Indices: 35366--35415 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
35356 GCTGACTCCT
35366 AAAA-CATTTTTTTAAATC
1 AAAATCATTTTTTTAAATC
35384 AAAATCATTTTTTTAAATC
1 AAAATCATTTTTTTAAATC
35403 AAAATCATTTTTT
1 AAAATCATTTTTT
35416 ATCCACATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 4 0.13
19 27 0.87
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (19 bp):
AAAATCATTTTTTTAAATC
Done.