Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005317.1 Hibiscus syriacus cultivar Beakdansim tig00012037_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: 37759
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:1793 original size:24 final size:24
Alignment explanation
Indices: 1766--1811 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
1756 CAAAATAGAT
*
1766 ATCATAACAGAATCCAGATCATAA
1 ATCAAAACAGAATCCAGATCATAA
* * *
1790 ATCAAAACGGAATTCAGGTCAT
1 ATCAAAACAGAATCCAGATCAT
1812 GTCAGAACAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATCCAGATCATAA
Found at i:12060 original size:60 final size:59
Alignment explanation
Indices: 11935--12060 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 59
11925 CATGAAGCCA
* * * * * *
11935 AAGTTCAAGTACCTAATTGGATCCAAAAAAGTTTAGGCATCACATTGAATCTTAAAGCC
1 AAGTTCAAGTACCTAATTGGACCCAAAAAAGTTAAGACATCAAATTGAACCTTAAAACC
* * * *
11994 AAGTTCAAGTACCTAATTGGACCCAAAAAATGTTAAGATATTAAATTGCACCTTAAAATC
1 AAGTTCAAGTACCTAATTGGACCCAAAAAA-GTTAAGACATCAAATTGAACCTTAAAACC
12054 AAGTTCA
1 AAGTTCA
12061 GATACTGAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
59 29 0.52
60 27 0.48
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.28
Consensus pattern (59 bp):
AAGTTCAAGTACCTAATTGGACCCAAAAAAGTTAAGACATCAAATTGAACCTTAAAACC
Found at i:15225 original size:20 final size:18
Alignment explanation
Indices: 15196--15312 Score: 108
Period size: 20 Copynumber: 5.9 Consensus size: 18
15186 AAATGACCAA
15196 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACGCGAT-T
* *
15215 CAAATTTCGCAACCCAGGTT
1 CAAA-TTCGCAACGC-GATT
15235 CCAAATTCGCAACGCGATTT
1 -CAAATTCGCAACGCGA-TT
*
15255 TAAGATTCGCAACGCGATAGT
1 CAA-ATTCGCAACGCGAT--T
15276 CAAAATTCGCAACGCGATT
1 C-AAATTCGCAACGCGATT
*
15295 TAAGATTCGCAACGCGAT
1 CAA-ATTCGCAACGCGAT
15313 ACTCCAAAAT
Statistics
Matches: 82, Mismatches: 7, Indels: 18
0.77 0.07 0.17
Matches are distributed among these distances:
18 2 0.02
19 23 0.28
20 34 0.41
21 21 0.26
22 2 0.02
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.23
Consensus pattern (18 bp):
CAAATTCGCAACGCGATT
Found at i:15264 original size:40 final size:40
Alignment explanation
Indices: 15196--15327 Score: 144
Period size: 40 Copynumber: 3.3 Consensus size: 40
15186 AAATGACCAA
* * *
15196 CAAATTCGCAACGCGATCTCAA-ATTTCGCAACCCAGGT-TC
1 CAAATTCGCAACGCGATTTTAAGA-TTCGCAACCC-GATATC
*
15236 CAAATTCGCAACGCGATTTTAAGATTCGCAACGCGATAGTC
1 CAAATTCGCAACGCGATTTTAAGATTCGCAACCCGATA-TC
* *
15277 AAAATTCGCAACGCGA-TTTAAGATTCGCAACGCGATACTC
1 CAAATTCGCAACGCGATTTTAAGATTCGCAACCCGATA-TC
*
15317 CAAAATCGCAA
1 CAAATTCGCAA
15328 TGCATTTGTT
Statistics
Matches: 81, Mismatches: 8, Indels: 6
0.85 0.08 0.06
Matches are distributed among these distances:
39 2 0.02
40 61 0.75
41 18 0.22
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (40 bp):
CAAATTCGCAACGCGATTTTAAGATTCGCAACCCGATATC
Found at i:15292 original size:41 final size:41
Alignment explanation
Indices: 15237--15327 Score: 150
Period size: 40 Copynumber: 2.2 Consensus size: 41
15227 CCCAGGTTCC
*
15237 AAATTCGCAACGCGATTTTAAGATTCGCAACGCGATAGT-CA
1 AAATTCGCAACGCGA-TTTAAGATTCGCAACGCGATACTCCA
15278 AAATTCGCAACGCGATTTAAGATTCGCAACGCGATACTCCA
1 AAATTCGCAACGCGATTTAAGATTCGCAACGCGATACTCCA
15319 AAA-TCGCAA
1 AAATTCGCAA
15328 TGCATTTGTT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
40 28 0.58
41 20 0.42
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (41 bp):
AAATTCGCAACGCGATTTAAGATTCGCAACGCGATACTCCA
Found at i:15303 original size:60 final size:60
Alignment explanation
Indices: 15199--15312 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
15189 TGACCAACAA
* *
15199 ATTCGCAACGCGATCTCAAATTTCGCAACCCAGGTTCCAAATTCGCAACGCGATTTTAAG
1 ATTCGCAACGCGATCTCAAAATTCGCAACCCAGATTCCAAATTCGCAACGCGATTTTAAG
* * *
15259 ATTCGCAACGCGATAGTCAAAATTCGCAACGC-GATT-TAAGATTCGCAACGCGAT
1 ATTCGCAACGCGAT-CTCAAAATTCGCAACCCAGATTCCAA-ATTCGCAACGCGAT
15313 ACTCCAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 2 0.04
60 31 0.66
61 14 0.30
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (60 bp):
ATTCGCAACGCGATCTCAAAATTCGCAACCCAGATTCCAAATTCGCAACGCGATTTTAAG
Found at i:16174 original size:6 final size:6
Alignment explanation
Indices: 16156--16187 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
16146 GTCCCGTCCC
*
16156 GTCGTG GTGGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
16188 AATACGTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.12, G:0.53, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:16282 original size:21 final size:21
Alignment explanation
Indices: 16256--16323 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
16246 AACAAATGCA
*
16256 TTGCGATTTTGGAGTATCGCG
1 TTGCGATTTTGGAATATCGCG
* *
16277 TTGCGAATCTT--AAAATCGCG
1 TTGCG-ATTTTGGAATATCGCG
* *
16297 TTACGATTTTGGACTATCGCG
1 TTGCGATTTTGGAATATCGCG
16318 TTGCGA
1 TTGCGA
16324 ATCTTAAAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 4 0.11
20 11 0.31
21 17 0.47
22 4 0.11
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (21 bp):
TTGCGATTTTGGAATATCGCG
Found at i:16296 original size:20 final size:20
Alignment explanation
Indices: 16271--16345 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
16261 ATTTTGGAGT
16271 ATCGCGTTGCGAATCTTAAA
1 ATCGCGTTGCGAATCTTAAA
* * **
16291 ATCGCGTTACG-ATTTTGGACT
1 ATCGCGTTGCGAATCTT--AAA
16312 ATCGCGTTGCGAATCTTAAA
1 ATCGCGTTGCGAATCTTAAA
*
16332 ATCGCGCTGCGAAT
1 ATCGCGTTGCGAAT
16346 TTGGAACCTG
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
19 4 0.09
20 24 0.56
21 11 0.26
22 4 0.09
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (20 bp):
ATCGCGTTGCGAATCTTAAA
Found at i:16349 original size:41 final size:41
Alignment explanation
Indices: 16257--16350 Score: 152
Period size: 41 Copynumber: 2.3 Consensus size: 41
16247 ACAAATGCAT
* *
16257 TGCGATTTTGGAGTATCGCGTTGCGAATCTTAAAATCGCGT
1 TGCGATTTTGGACTATCGCGTTGCGAATCTTAAAATCGCGC
*
16298 TACGATTTTGGACTATCGCGTTGCGAATCTTAAAATCGCGC
1 TGCGATTTTGGACTATCGCGTTGCGAATCTTAAAATCGCGC
*
16339 TGCGAATTTGGA
1 TGCGATTTTGGA
16351 ACCTGGGTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (41 bp):
TGCGATTTTGGACTATCGCGTTGCGAATCTTAAAATCGCGC
Found at i:20464 original size:18 final size:18
Alignment explanation
Indices: 20409--20465 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
20399 TGAAATTGAT
*
20409 TTTTTCGATTCGGTTCGA
1 TTTTTCGATTCGGTTCGG
** * *
20427 TTTTTTTA-ACGGTTTGGG
1 TTTTTCGATTCGG-TTCGG
20445 TTTTTCGATTCGGTTCGG
1 TTTTTCGATTCGGTTCGG
20463 TTT
1 TTT
20466 ATCGGTTTTT
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
17 3 0.11
18 22 0.79
19 3 0.11
ACGTcount: A:0.09, C:0.12, G:0.25, T:0.54
Consensus pattern (18 bp):
TTTTTCGATTCGGTTCGG
Found at i:22158 original size:4 final size:4
Alignment explanation
Indices: 22151--22178 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
22141 GATGGACCAA
22151 GGAG GGAG GGAG GGAG GGAG GGAG GGAG
1 GGAG GGAG GGAG GGAG GGAG GGAG GGAG
22179 AGGGAGACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (4 bp):
GGAG
Found at i:26170 original size:14 final size:15
Alignment explanation
Indices: 26113--26175 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 15
26103 AAATAAAACC
26113 AATTAAAT-TATTAT
1 AATTAAATATATTAT
26127 --TTAAA-ATCATTACT
1 AATTAAATAT-ATTA-T
26141 AATTAAATATATTAT
1 AATTAAATATATTAT
*
26156 AATTAATTA-ATTAT
1 AATTAAATATATTAT
26170 -ATTAAA
1 AATTAAA
26176 ATCTATATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
12 6 0.15
13 9 0.22
14 6 0.15
15 9 0.22
16 9 0.22
17 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:32255 original size:43 final size:43
Alignment explanation
Indices: 32196--32287 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
32186 AGTTACCCTT
* * *
32196 AAAATATTAAGTGTCTCAATTATAAAGATAGAAAT-AGATATTA
1 AAAAAATTAAGGGTCTCAATTATAAAGATA-AAATGAGAGATTA
* *
32239 AAAAAATTAAGGGTCTCAATTATAAAGGTAAAATGTGAGATTA
1 AAAAAATTAAGGGTCTCAATTATAAAGATAAAATGAGAGATTA
32282 AAAAAA
1 AAAAAA
32288 AATCAGAGGC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.28
Consensus pattern (43 bp):
AAAAAATTAAGGGTCTCAATTATAAAGATAAAATGAGAGATTA
Found at i:36026 original size:6 final size:6
Alignment explanation
Indices: 36010--36051 Score: 52
Period size: 6 Copynumber: 7.0 Consensus size: 6
36000 TCTTTCCTTT
36010 TTTTCC TTTTTCC TTTT-- TTTTCC TTTTTCC TTTTCC TTTTCC
1 TTTTCC -TTTTCC TTTTCC TTTTCC -TTTTCC TTTTCC TTTTCC
36052 GTGTTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.12
6 16 0.50
7 12 0.38
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTCC
Found at i:36029 original size:17 final size:17
Alignment explanation
Indices: 36002--36043 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
35992 CCCAATAATC
36002 TTTCC-TTTTTTTCCTT
1 TTTCCTTTTTTTTCCTT
36018 TTTCCTTTTTTTTCCTT
1 TTTCCTTTTTTTTCCTT
36035 TTTCCTTTT
1 TTTCCTTTT
36044 CCTTTTCCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCCTTTTTTTTCCTT
Done.