Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003633.1 Hibiscus syriacus cultivar Beakdansim tig00007693_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: 85776
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:1853 original size:2 final size:2
Alignment explanation
Indices: 1846--1893 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1836 TAATTTTTCA
1846 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
1888 AT AT AT
1 AT AT AT
1894 TTTAAGTTCG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6197 original size:22 final size:21
Alignment explanation
Indices: 6155--6194 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6145 AAGACTATTT
6155 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
6176 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
6195 ATAGAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:8165 original size:18 final size:17
Alignment explanation
Indices: 8111--8159 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
8101 TTGGATCCTT
* *
8111 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
8129 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
8147 AGTGCATTCGATG
1 AGTGCA-TCGATG
8160 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:8267 original size:65 final size:64
Alignment explanation
Indices: 8131--8288 Score: 196
Period size: 65 Copynumber: 2.5 Consensus size: 64
8121 TGCACTAAGA
*
8131 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCATAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCATAGTGCATCGATGCATGGCTG
* * * *
8195 GTGCATCGATGCATCAAATGTATTCGATGTTTTCATAAA-ATCC-TCAGTGCATCGGTGTATGG-
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAT-AGTGCATCGATGCATGGC
*
8257 TAT
63 T-G
*
8260 GTGCATCGATGCATGAAATGCATTCGATG
1 GTGCATCGATGCATCAAATGCATTCGATG
8289 CTCAATTTAT
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 29 0.35
65 50 0.61
66 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCATAGTGCATCGATGCATGGCTG
Found at i:22520 original size:18 final size:18
Alignment explanation
Indices: 22441--22513 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
22431 ATTGAATATT
*
22441 TGTCCCGAAGGGCCACTA
1 TGTCCCGAAGGACCACTA
*
22459 TGTCCCGAAGGAACACTGA
1 TGTCCCGAAGGACCACT-A
* *
22478 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
22497 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
22514 GTTTCCCTCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 30 0.65
19 2 0.04
20 14 0.30
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:24307 original size:16 final size:17
Alignment explanation
Indices: 24275--24307 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
24265 GTTTTTTAAA
24275 TTTTAATGATTTAATTC
1 TTTTAATGATTTAATTC
*
24292 TTTTAAT-ATTTGATTC
1 TTTTAATGATTTAATTC
24308 CAGTTTATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (17 bp):
TTTTAATGATTTAATTC
Found at i:25126 original size:2 final size:2
Alignment explanation
Indices: 25119--25143 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25109 CTCGTAATGA
25119 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
25144 GTGATACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30930 original size:64 final size:64
Alignment explanation
Indices: 30857--31061 Score: 209
Period size: 64 Copynumber: 3.2 Consensus size: 64
30847 TGTTTGAATG
* * **
30857 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTC
1 TGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
30920 A
64 A
* * **
30921 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
* * ** * * * *
30985 TGCATCGATGTATAAGG-AGTGCATCGATGCATCTCAACAATAATACAACATCGAATACATTTTA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
*
31049 TGCACCGATGCAT
1 TGCATCGATGCAT
31062 CTCAACAATA
Statistics
Matches: 117, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
64 109 0.93
65 8 0.07
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:31059 original size:45 final size:45
Alignment explanation
Indices: 31004--31107 Score: 199
Period size: 45 Copynumber: 2.3 Consensus size: 45
30994 GTATAAGGAG
*
31004 TGCATCGATGCATCTCAACAATAATACAACATCGAATACATTTTA
1 TGCACCGATGCATCTCAACAATAATACAACATCGAATACATTTTA
31049 TGCACCGATGCATCTCAACAATAATACAACATCGAATACATTTTA
1 TGCACCGATGCATCTCAACAATAATACAACATCGAATACATTTTA
31094 TGCACCGATGCATC
1 TGCACCGATGCATC
31108 AGTAGTGCAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.27
Consensus pattern (45 bp):
TGCACCGATGCATCTCAACAATAATACAACATCGAATACATTTTA
Found at i:31820 original size:31 final size:31
Alignment explanation
Indices: 31782--31905 Score: 216
Period size: 31 Copynumber: 4.0 Consensus size: 31
31772 AGGGTCGAGG
31782 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
31813 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
31844 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
31875 GTTTACCTA-GATTCTTCGGGATC-TATGGACT
1 GTTTACCTATG-TTCTTCGGGA-CATATGGACT
31906 TGTCCTTCGG
Statistics
Matches: 91, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
30 1 0.01
31 89 0.98
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:40397 original size:64 final size:64
Alignment explanation
Indices: 40324--40547 Score: 231
Period size: 64 Copynumber: 3.5 Consensus size: 64
40314 TGTTTGAATG
* * ** *
40324 TGCACCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGATATCGAATGCAATTC
1 TGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAATTC
40387 A
64 A
* * **
40388 TGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGG
1 TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
* ** * * * *
40452 TGCATCGATGCATAAGG-AGTGCATCGATGCATCTCAACAATAATACAACATCGAATACATTTTA
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
*
40516 TGCACCGATGCATCA-GTAGTGCATCGATGCAT
1 TGCATCGATGCAT-AGGTAGTGCATCGATGCAT
40548 ACCTTCATTA
Statistics
Matches: 135, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
63 1 0.01
64 126 0.93
65 8 0.06
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (64 bp):
TGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCA
Found at i:41239 original size:31 final size:31
Alignment explanation
Indices: 41201--41325 Score: 216
Period size: 31 Copynumber: 4.0 Consensus size: 31
41191 AGGGTCGAGG
41201 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
41232 GTTTACCTATGTTCTTTGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
41263 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
41294 GTTTACCTA-GATTCTTCGGGACATATGGACT
1 GTTTACCTATG-TTCTTCGGGACATATGGACT
41325 G
1 G
41326 GTCCTTCGAG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
30 1 0.01
31 88 0.99
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:43087 original size:29 final size:29
Alignment explanation
Indices: 43050--43113 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
43040 ATCAAACCAA
* *
43050 AATTTATTTGAAAATTATTAATCGAACTG
1 AATTAATTTGAAAATTATTAACCGAACTG
*
43079 AATTAATTTGAAAATTATTAGCCGAACTG
1 AATTAATTTGAAAATTATTAACCGAACTG
43108 AATTAA
1 AATTAA
43114 CCGATTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.38
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCGAACTG
Found at i:50865 original size:2 final size:2
Alignment explanation
Indices: 50858--50888 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
50848 TCATTCAATC
50858 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50889 AATTATGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55813 original size:5 final size:5
Alignment explanation
Indices: 55803--55829 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
55793 CTTAATCCTG
55803 GGGAT GGGAT GGGAT GGGAT GGGAT GG
1 GGGAT GGGAT GGGAT GGGAT GGGAT GG
55830 ATTATATTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.63, T:0.19
Consensus pattern (5 bp):
GGGAT
Found at i:57301 original size:17 final size:17
Alignment explanation
Indices: 57281--57314 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
57271 ATTAAATTTA
*
57281 TATAAAATTGTAATTAT
1 TATAAAACTGTAATTAT
*
57298 TATAACACTGTAATTAT
1 TATAAAACTGTAATTAT
57315 AATTGTATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (17 bp):
TATAAAACTGTAATTAT
Found at i:57403 original size:19 final size:21
Alignment explanation
Indices: 57365--57404 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
57355 ATTTTTAAAA
57365 TTTAATAATCAAAGCAATTAT
1 TTTAATAATCAAAGCAATTAT
*
57386 TTTAAT-AT-AAATCAATTAT
1 TTTAATAATCAAAGCAATTAT
57405 AATTATGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (21 bp):
TTTAATAATCAAAGCAATTAT
Found at i:63192 original size:21 final size:22
Alignment explanation
Indices: 63137--63192 Score: 53
Period size: 25 Copynumber: 2.5 Consensus size: 22
63127 ATAACGATAG
*
63137 TAATAA-TAAGACATTTGTAAT
1 TAATAATTAAGAAATTTGTAAT
*
63158 TAAGAATAGATAAGAAATTTGTAA-
1 TAATAAT---TAAGAAATTTGTAAT
63182 TAATAATTAAG
1 TAATAATTAAG
63193 GACATCCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
21 9 0.32
24 6 0.21
25 13 0.46
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.34
Consensus pattern (22 bp):
TAATAATTAAGAAATTTGTAAT
Found at i:65612 original size:87 final size:87
Alignment explanation
Indices: 65466--65639 Score: 294
Period size: 87 Copynumber: 2.0 Consensus size: 87
65456 TTAGAGAGTG
* * *
65466 ACAGAAAGTAAACTAAATGTTCATGCAACTGTCCCTGCAGATGCGCACGTACTACAAGCTTTACG
1 ACAGAAAGCAAACTAAATGTTCATGCAACTGTCCCTGCAGATGCGCACATACTACAAGCTTTACA
65531 AAGTTAAAAACAATCATATTTA
66 AAGTTAAAAACAATCATATTTA
*
65553 ACAGAAAGCCAACTAAATGTTCATGCAACTGTCCCTGCAGATGCGCACATACTACAAGCTTTACA
1 ACAGAAAGCAAACTAAATGTTCATGCAACTGTCCCTGCAGATGCGCACATACTACAAGCTTTACA
* *
65618 AAGTTAAAAACTATCGTATTTA
66 AAGTTAAAAACAATCATATTTA
65640 TATGGATATC
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 81 1.00
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (87 bp):
ACAGAAAGCAAACTAAATGTTCATGCAACTGTCCCTGCAGATGCGCACATACTACAAGCTTTACA
AAGTTAAAAACAATCATATTTA
Found at i:72373 original size:17 final size:17
Alignment explanation
Indices: 72341--72378 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
72331 ATTACCAATA
72341 AAAATATACATAAAATCT
1 AAAATATACATAAAAT-T
*
72359 AAAATATA-TTAAAATT
1 AAAATATACATAAAATT
72375 AAAA
1 AAAA
72379 AAAAAATAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 6 0.32
18 8 0.42
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATATACATAAAATT
Found at i:72379 original size:17 final size:19
Alignment explanation
Indices: 72339--72379 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
72329 AAATTACCAA
72339 TAAAAATATACATAAAATC
1 TAAAAATATACATAAAATC
*
72358 T-AAAATATA-TTAAAAT-
1 TAAAAATATACATAAAATC
72374 TAAAAA
1 TAAAAA
72380 AAAAATAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.05
17 10 0.50
18 8 0.40
19 1 0.05
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAAATATACATAAAATC
Found at i:80506 original size:2 final size:2
Alignment explanation
Indices: 80499--80531 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
80489 TCATAACTTT
80499 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 T
80532 TGTTTTAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:82622 original size:16 final size:15
Alignment explanation
Indices: 82601--82647 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
82591 ATGAAATTAT
*
82601 TTAAAATTAAAAATA
1 TTAAAAATAAAAATA
82616 TTAAAAA-AAATGAATA
1 TTAAAAATAAA--AATA
82632 TTTAAAAATAAAAATA
1 -TTAAAAATAAAAATA
82648 GTATTAAAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 3 0.11
15 6 0.22
16 8 0.30
17 7 0.26
18 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
TTAAAAATAAAAATA
Found at i:82836 original size:32 final size:34
Alignment explanation
Indices: 82783--82845 Score: 78
Period size: 32 Copynumber: 1.9 Consensus size: 34
82773 TTTAGTATTA
82783 AAAATTTTAAAAAAATAATAAA-T-TTAAAATTT
1 AAAATTTTAAAAAAATAATAAAGTATTAAAATTT
* *
82815 AAAA-TTTAAAAATATTTATAAAGTATTAAAA
1 AAAATTTTAAAAA-AATAATAAAGTATTAAAA
82846 AATTAACAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
31 8 0.31
32 11 0.42
33 1 0.04
34 6 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (34 bp):
AAAATTTTAAAAAAATAATAAAGTATTAAAATTT
Done.