Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006015.1 Hibiscus syriacus cultivar Beakdansim tig00014185_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: 33311
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Found at i:8228 original size:15 final size:15
Alignment explanation
Indices: 8208--8282 Score: 74
Period size: 15 Copynumber: 5.3 Consensus size: 15
8198 ATAAAAAGAT
8208 AAAAAAATGAAAAAG
1 AAAAAAATGAAAAAG
8223 AAAAAAATG---AA-
1 AAAAAAATGAAAAAG
8234 AAAAAAATGAAAAATG
1 AAAAAAATGAAAAA-G
*
8250 AAAAAAA-G-AAATG
1 AAAAAAATGAAAAAG
8263 -AAAAAATGAAAAGAG
1 AAAAAAATGAAAA-AG
8278 AAAAA
1 AAAAA
8283 GGAGGGTTTG
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
11 9 0.18
12 8 0.16
13 2 0.04
14 8 0.16
15 11 0.22
16 11 0.22
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (15 bp):
AAAAAAATGAAAAAG
Found at i:8245 original size:20 final size:19
Alignment explanation
Indices: 8224--8274 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 19
8214 ATGAAAAAGA
8224 AAAAAATGAAAAAAAAATG
1 AAAAAATGAAAAAAAAATG
8243 -AAAAATGAAAAAAAGAAATG
1 AAAAAATG-AAAAAA-AAATG
8263 AAAAAATGAAAA
1 AAAAAATGAAAA
8275 GAGAAAAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.24
19 6 0.21
20 9 0.31
21 7 0.24
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (19 bp):
AAAAAATGAAAAAAAAATG
Found at i:8279 original size:20 final size:19
Alignment explanation
Indices: 8209--8280 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 19
8199 TAAAAAGATA
8209 AAAAAATGAAAAAG--A--
1 AAAAAATGAAAAAGAAATG
*
8224 AAAAAATGAAAAAAAAATG
1 AAAAAATGAAAAAGAAATG
8243 -AAAAATGAAAAAAAGAAATG
1 AAAAAATG--AAAAAGAAATG
8263 AAAAAATGAAAAGAGAAA
1 AAAAAATGAAAA-AGAAA
8281 AAGGAGGGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
15 13 0.28
17 1 0.02
18 7 0.15
19 4 0.09
20 15 0.32
21 7 0.15
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (19 bp):
AAAAAATGAAAAAGAAATG
Found at i:8283 original size:26 final size:25
Alignment explanation
Indices: 8200--8282 Score: 112
Period size: 26 Copynumber: 3.1 Consensus size: 25
8190 GGGAACAAAT
*
8200 AAAAAGATAAAAAAATGAAAAAGAA
1 AAAAAGAAAAAAAAATGAAAAAGAA
8225 AAAAATGAAAAAAAAATGAAAAATGAA
1 AAAAA-GAAAAAAAAATGAAAAA-GAA
8252 AAAAAGAAATGAAAAAATGAAAAGAGAA
1 AAAAAGAAA--AAAAAATGAAAA-AGAA
8280 AAA
1 AAA
8283 GGAGGGTTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 7
0.87 0.02 0.12
Matches are distributed among these distances:
25 5 0.10
26 20 0.38
27 8 0.15
28 18 0.35
29 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.08
Consensus pattern (25 bp):
AAAAAGAAAAAAAAATGAAAAAGAA
Found at i:9403 original size:136 final size:136
Alignment explanation
Indices: 9157--9494 Score: 533
Period size: 136 Copynumber: 2.5 Consensus size: 136
9147 GGTGAACCAG
9157 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
* * *
9222 AGAAGAGCTTGTTAGACCTATCACTCGATTCACGACATTTTGAATCAGTGACACCTTGCTTGAAG
66 AGAAGAGCTTGTTAGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
*
9287 GATCAG
131 GATCAA
*
9293 TATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
* * *
9358 AGAAGAGCTTGTTCGACCTATCACTCGATTCATAACATTTCGAATCAGTGACACCTCGCTTGAGG
66 AGAAGAGCTTGTTAGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
9423 GATCAA
131 GATCAA
* * * *
9429 CATTTCCAGTGAAGAGTTCATAATGAGAAGAACTCGTCCTA-A-A-GGAG-A-AAGTTCATAATG
1 CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
9489 AGAAGA
66 AGAAGA
9495 ACTCGTCCTA
Statistics
Matches: 189, Mismatches: 13, Indels: 5
0.91 0.06 0.02
Matches are distributed among these distances:
131 18 0.10
132 1 0.01
133 4 0.02
134 1 0.01
135 1 0.01
136 164 0.87
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (136 bp):
CATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAATG
AGAAGAGCTTGTTAGACCTATCACTCGATTCACAACATTTCGAATCAGTGACACCTCGCTTGAAG
GATCAA
Found at i:9489 original size:35 final size:35
Alignment explanation
Indices: 9443--9562 Score: 240
Period size: 35 Copynumber: 3.4 Consensus size: 35
9433 TCCAGTGAAG
9443 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
1 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
9478 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
1 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
9513 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
1 AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
9548 AGTTCATAATGAGAA
1 AGTTCATAATGAGAA
9563 AAACATGTTC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 85 1.00
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (35 bp):
AGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
Found at i:9822 original size:3 final size:3
Alignment explanation
Indices: 9807--9855 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
9797 AGTTAAAAAA
* *
9807 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9854 TA
1 TA
9856 AGTGTATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 1 0.02
3 40 0.98
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:11227 original size:14 final size:16
Alignment explanation
Indices: 11203--11235 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
11193 GTTTATTTTG
11203 TTTTAAGTATTT-TAT
1 TTTTAAGTATTTATAT
11218 TTTTAA-TATTTATAT
1 TTTTAAGTATTTATAT
11233 TTT
1 TTT
11236 AGTCACACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTAAGTATTTATAT
Found at i:12022 original size:49 final size:49
Alignment explanation
Indices: 11797--12014 Score: 373
Period size: 49 Copynumber: 4.4 Consensus size: 49
11787 ATATATATAT
* * * **
11797 ATATATTTATTTATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
11846 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
11895 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
*
11944 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTCTTTGTTC
1 ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
*
11993 ATATACATATATATTTGTTTAA
1 ATATATATATATATTTGTTTAA
12015 TGTGTCTTAG
Statistics
Matches: 162, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 162 1.00
ACGTcount: A:0.29, C:0.08, G:0.11, T:0.52
Consensus pattern (49 bp):
ATATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTC
Found at i:12213 original size:51 final size:51
Alignment explanation
Indices: 12083--12205 Score: 219
Period size: 51 Copynumber: 2.4 Consensus size: 51
12073 TTGTTAAACG
*
12083 TATATATATATTTTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATA
1 TATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATA
*
12134 TATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTTTTCATA
1 TATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATA
*
12185 TATATATATATATTTGTTTAA
1 TATATATATATATTTATTTAA
12206 CATGTCTTAG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (51 bp):
TATATATATATATTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATA
Found at i:12237 original size:191 final size:187
Alignment explanation
Indices: 11896--12263 Score: 549
Period size: 191 Copynumber: 1.9 Consensus size: 187
11886 TTTTTGTTCA
* *
11896 TATATATATATATTTGTTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATATATTTG
1 TATATATATATATTTATTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATATATTTA
**
11961 TTTAACATGTCTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTTAATGTGTCTTAGG
66 TTTAACATGTCTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTTAACATGTCTTAGG
*
12026 AAGAATAGCCATTATTTATTTGTTTAACATATAGCTTAGTTGGATATTTGTTAAACG
131 AAGAATAGCCATTATTTATTTGTTTAACATATAGCTTAGCTGGATATTTGTTAAACG
* **
12083 TATATATATATTTTTATTTAATGTGTCTTGGAAACTGATTTTTTGTTCATATATATATATATATT
1 TATATATATATATTTATTTAACATGTCTTGGAAACTGATTTTTTGTTC--ATATATATATATATT
** * * *
12148 TATTTAATGTGTCTTGGAAACTGATTTTTTTTTCATATATATATATATATTTGTTTAACATGTCT
64 TATTTAACATGTCTTGGAAACTGATTCTTTGTTC--ATATACATATATATTTGTTTAACATGTCT
* *
12213 TAGGAAGAATAGGCA-TATTTTATTTGTTTAACGTATAGCTTAGCTGGATAT
127 TAGGAAGAATAGCCATTA-TTTATTTGTTTAACATATAGCTTAGCTGGATAT
12264 ATATATATTT
Statistics
Matches: 161, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
187 44 0.27
189 44 0.27
190 2 0.01
191 71 0.44
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (187 bp):
TATATATATATATTTATTTAACATGTCTTGGAAACTGATTTTTTGTTCATATATATATATATTTA
TTTAACATGTCTTGGAAACTGATTCTTTGTTCATATACATATATATTTGTTTAACATGTCTTAGG
AAGAATAGCCATTATTTATTTGTTTAACATATAGCTTAGCTGGATATTTGTTAAACG
Found at i:14005 original size:50 final size:50
Alignment explanation
Indices: 13928--14025 Score: 178
Period size: 50 Copynumber: 2.0 Consensus size: 50
13918 GTGGGTACTC
* *
13928 AATTAACTTTATAACTCGAATTCTTATTGATACGAACAAAATACGATATA
1 AATTAACTTTATAACTCGAATTATTATTGATACGAAAAAAATACGATATA
13978 AATTAACTTTATAACTCGAATTATTATTGATACGAAAAAAATACGATA
1 AATTAACTTTATAACTCGAATTATTATTGATACGAAAAAAATACGATA
14026 CAACGTCGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (50 bp):
AATTAACTTTATAACTCGAATTATTATTGATACGAAAAAAATACGATATA
Found at i:15399 original size:11 final size:11
Alignment explanation
Indices: 15383--15417 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
15373 ATATAAAAAT
15383 AAATTATTAAA
1 AAATTATTAAA
15394 AAATTATTAAA
1 AAATTATTAAA
* *
15405 AAAATATCAAA
1 AAATTATTAAA
15416 AA
1 AA
15418 GAAAACAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATTATTAAA
Found at i:18942 original size:2 final size:2
Alignment explanation
Indices: 18935--18977 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
18925 ACAAAATGTT
18935 TA TA TA TA TA 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 TA TA TA TA TA
18977 T
1 T
18978 GACTTTAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19603 original size:23 final size:22
Alignment explanation
Indices: 19574--19619 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
19564 TTAATTAGTT
19574 TAAATTTAAATCGAGTTTAAATC
1 TAAATTTAAATCGAG-TTAAATC
* *
19597 TAAATTTTAATTGAGTTAAATC
1 TAAATTTAAATCGAGTTAAATC
19619 T
1 T
19620 GAAAATGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (22 bp):
TAAATTTAAATCGAGTTAAATC
Found at i:23182 original size:3 final size:3
Alignment explanation
Indices: 23174--23233 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
23164 TTTCGTCCCG
*
23174 TTA TTA TTA TTA TTA TTA TTA TCT- TTA TTA TTA TTA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA
*
23219 TTA ATA -TA TT- TTA TT
1 TTA TTA TTA TTA TTA TT
23234 TTTAATTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
2 5 0.10
3 44 0.88
4 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Done.