Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004930.1 Hibiscus syriacus cultivar Beakdansim tig00011094_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: 97229
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:5738 original size:17 final size:17
Alignment explanation
Indices: 5673--5768 Score: 81
Period size: 17 Copynumber: 5.5 Consensus size: 17
5663 CACTTCGTTG
5673 ATTAAACTAGTTCATTCAA
1 ATTAAACTAGTTCATT--A
*
5692 GATT--ACAAGTTCATTGA
1 -ATTAAACTAGTTCATT-A
*
5709 A-TAAATTTAGTTCATTA
1 ATTAAA-CTAGTTCATTA
*
5726 ATTAAACTAGTTCATTC
1 ATTAAACTAGTTCATTA
* *
5743 ATCAAACTAGTTCATTT
1 ATTAAACTAGTTCATTA
5760 ATTAAACTA
1 ATTAAACTA
5769 ACTTTTAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
15 1 0.02
16 1 0.02
17 36 0.57
18 22 0.35
20 3 0.05
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (17 bp):
ATTAAACTAGTTCATTA
Found at i:12626 original size:21 final size:22
Alignment explanation
Indices: 12601--12641 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
12591 GGAGTGTTTG
12601 GTGAGGTT-TTTCCTTTTATTT
1 GTGAGGTTATTTCCTTTTATTT
*
12622 GTGAGGTTATTTCTTTTTAT
1 GTGAGGTTATTTCCTTTTAT
12642 AACTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.12, C:0.07, G:0.20, T:0.61
Consensus pattern (22 bp):
GTGAGGTTATTTCCTTTTATTT
Found at i:14506 original size:29 final size:29
Alignment explanation
Indices: 14473--14541 Score: 122
Period size: 29 Copynumber: 2.4 Consensus size: 29
14463 TGAAATTAGG
*
14473 AAGGAAATGAAATGATAGTGAAAAGATGA
1 AAGGAAATGAAATGATAATGAAAAGATGA
14502 AAGGAAATGAAATGATAATGAAAAGATGA
1 AAGGAAATGAAATGATAATGAAAAGATGA
14531 AAGGAAA-GAAA
1 AAGGAAATGAAA
14542 AGGTTATCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
28 4 0.10
29 35 0.90
ACGTcount: A:0.59, C:0.00, G:0.26, T:0.14
Consensus pattern (29 bp):
AAGGAAATGAAATGATAATGAAAAGATGA
Found at i:24962 original size:18 final size:17
Alignment explanation
Indices: 24924--24956 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
24914 GTGCAAAAAG
24924 AAAGAAAATCAGAAAATA
1 AAAGAAAA-CAGAAAATA
24942 AAAGAAAA-AGAAAAT
1 AAAGAAAACAGAAAAT
24957 TCAAAAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (17 bp):
AAAGAAAACAGAAAATA
Found at i:28369 original size:23 final size:23
Alignment explanation
Indices: 28329--28373 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
28319 ATATATATAT
28329 ATATGAAAATAACTATCTTATAAC
1 ATATGAAAATAACTATC-TATAAC
28353 ATATG-AAATAAGC-ATCTATAA
1 ATATGAAAATAA-CTATCTATAA
28374 GTATAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.25
23 9 0.45
24 6 0.30
ACGTcount: A:0.51, C:0.11, G:0.07, T:0.31
Consensus pattern (23 bp):
ATATGAAAATAACTATCTATAAC
Found at i:29115 original size:17 final size:17
Alignment explanation
Indices: 29080--29115 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29070 TTACATCGGC
*
29080 TATAGAAATGGTTAGGG
1 TATAGAAATGGATAGGG
*
29097 TATAGAAATGGATATGG
1 TATAGAAATGGATAGGG
29114 TA
1 TA
29116 GGATAGAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (17 bp):
TATAGAAATGGATAGGG
Found at i:29180 original size:16 final size:16
Alignment explanation
Indices: 29144--29195 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
29134 GAGATAAGGT
29144 AAGAAATAAGAAAAGATGA
1 AAGAAA-AAG-AAA-ATGA
*
29163 AAGAAAAAGGAAATGA
1 AAGAAAAAGAAAATGA
* *
29179 AATAAATAGAAAATGA
1 AAGAAAAAGAAAATGA
29195 A
1 A
29196 GATATCTTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 18 0.62
17 2 0.07
18 3 0.10
19 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (16 bp):
AAGAAAAAGAAAATGA
Found at i:29338 original size:25 final size:24
Alignment explanation
Indices: 29310--29362 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
29300 TTTGAGCGTA
*
29310 CTTTGCAACTTT-TTCTTTTCTTTT
1 CTTTG-AACTTTCTTCTTTTATTTT
*
29334 GCTTTGAATTTTCTTCTTTTATTTT
1 -CTTTGAACTTTCTTCTTTTATTTT
29359 CTTT
1 CTTT
29363 CTCTTGTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.09, C:0.17, G:0.06, T:0.68
Consensus pattern (24 bp):
CTTTGAACTTTCTTCTTTTATTTT
Found at i:29403 original size:6 final size:6
Alignment explanation
Indices: 29392--29436 Score: 65
Period size: 6 Copynumber: 7.3 Consensus size: 6
29382 ATGTATGAGT
29392 TTTTTC TTTTTC TTTTTC TTTTTAC -TTTTC TTCTTTC TTTTTC TT
1 TTTTTC TTTTTC TTTTTC TTTTT-C TTTTTC TT-TTTC TTTTTC TT
29437 GTTTGCTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 1 0.03
6 28 0.78
7 7 0.19
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:37056 original size:2 final size:2
Alignment explanation
Indices: 37049--37083 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
37039 AGTTATTTTC
37049 AT AT 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 AT AT A
37084 CCTATAGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39943 original size:17 final size:18
Alignment explanation
Indices: 39916--39951 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
39906 TTGCGTCGGC
*
39916 TATAGGAAATGGTTATGG
1 TATAGGAAATGGATATGG
39934 TATA-GAAATGGATATGG
1 TATAGGAAATGGATATGG
39951 T
1 T
39952 CAAGGTAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (18 bp):
TATAGGAAATGGATATGG
Found at i:40639 original size:35 final size:35
Alignment explanation
Indices: 40600--40715 Score: 160
Period size: 35 Copynumber: 3.3 Consensus size: 35
40590 TTATAAGGGA
*
40600 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
* *
40635 ATGGTGATGATATAGGCATGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
* ** *
40670 ATGGTGATGTTATATACGTGAAAATAGTGATGGAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATGGAAG
40706 ATGGTGATGA
1 ATGGTGATGA
40716 ACAAATAGTA
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
35 48 0.69
36 22 0.31
ACGTcount: A:0.34, C:0.03, G:0.35, T:0.28
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
Found at i:41081 original size:19 final size:19
Alignment explanation
Indices: 41057--41106 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
41047 GAAACCCCTT
**
41057 TGAAAATACATGATTTTTA
1 TGAAAATACATGATTTAAA
*
41076 TGAAAATACATTATTTAAA
1 TGAAAATACATGATTTAAA
*
41095 TGAAGATACATG
1 TGAAAATACATG
41107 GTCTTGGCCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.46, C:0.06, G:0.12, T:0.36
Consensus pattern (19 bp):
TGAAAATACATGATTTAAA
Found at i:45691 original size:17 final size:17
Alignment explanation
Indices: 45669--45706 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
45659 TGGTTGACAG
45669 ATTTTAAAAAATGGCAC
1 ATTTTAAAAAATGGCAC
45686 ATTTTAAAAAATGGCAC
1 ATTTTAAAAAATGGCAC
45703 ATTT
1 ATTT
45707 CATTGCGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (17 bp):
ATTTTAAAAAATGGCAC
Found at i:60137 original size:15 final size:15
Alignment explanation
Indices: 60107--60148 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
60097 GGATAATTAA
60107 GAAAGGAAATTGAAATG
1 GAAA-GAAA-TGAAATG
60124 GAAAGAAATGAAATG
1 GAAAGAAATGAAATG
*
60139 GATAGAAATG
1 GAAAGAAATG
60149 TTATCAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 16 0.67
16 4 0.17
17 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.29, T:0.17
Consensus pattern (15 bp):
GAAAGAAATGAAATG
Found at i:67251 original size:16 final size:15
Alignment explanation
Indices: 67223--67267 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
67213 TTAATTGGAA
67223 AAAAT-GAAAGAAAT
1 AAAATGGAAAGAAAT
* *
67237 AGAATTGATAAGAAAT
1 AAAATGGA-AAGAAAT
67253 AAAATGGAAAGAAAT
1 AAAATGGAAAGAAAT
67268 TATATCAAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 4 0.15
15 9 0.35
16 13 0.50
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (15 bp):
AAAATGGAAAGAAAT
Found at i:67266 original size:15 final size:14
Alignment explanation
Indices: 67223--67267 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
67213 TTAATTGGAA
67223 AAAATGAAAGAAAT
1 AAAATGAAAGAAAT
*
67237 AGAATTGATAAGAAAT
1 A-AAATGA-AAGAAAT
67253 AAAATGGAAAGAAAT
1 AAAAT-GAAAGAAAT
67268 TATATCAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 1 0.04
15 15 0.58
16 10 0.38
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (14 bp):
AAAATGAAAGAAAT
Found at i:68209 original size:19 final size:20
Alignment explanation
Indices: 68168--68218 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
68158 GAAACCCCTT
*
68168 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
68188 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
68207 TGAAGATACATG
1 TGAAAATACATG
68219 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:72397 original size:19 final size:20
Alignment explanation
Indices: 72356--72406 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
72346 GAAACCCCTT
*
72356 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
72376 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
72395 TGAAGATACATG
1 TGAAAATACATG
72407 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:79238 original size:2 final size:2
Alignment explanation
Indices: 79221--79280 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
79211 TCATAATAAC
*
79221 TA TA GA TA TA -A 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
79262 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
79281 GTTAATAACT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:85237 original size:24 final size:25
Alignment explanation
Indices: 85210--85256 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
85200 GATGTAGGAG
* *
85210 TCTTTTTTC-TTTTCTTTTTGTTTT
1 TCTTCTTTCATTTGCTTTTTGTTTT
85234 TCTTCTTTCATTTGCTTTTTGTT
1 TCTTCTTTCATTTGCTTTTTGTT
85257 GCAGCACTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.02, C:0.15, G:0.06, T:0.77
Consensus pattern (25 bp):
TCTTCTTTCATTTGCTTTTTGTTTT
Found at i:89652 original size:15 final size:14
Alignment explanation
Indices: 89608--89655 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 14
89598 TTGGAATTAA
*
89608 GAAATGAAATAAAT
1 GAAATGAAAGAAAT
89622 GGAAATTGATAAGAAAT
1 -GAAA-TGA-AAGAAAT
89639 GAAATGGAAAGAAAT
1 GAAAT-GAAAGAAAT
89654 GA
1 GA
89656 TATCAAGGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 14 0.48
16 9 0.31
17 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (14 bp):
GAAATGAAAGAAAT
Found at i:89652 original size:26 final size:24
Alignment explanation
Indices: 89605--89657 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
89595 TAATTGGAAT
89605 TAAGAAATGAAATAAATGGAAATTGA
1 TAAGAAATGAAATAAA-GGAAA-TGA
89631 TAAGAAATGAAATGGAAA-GAAATGA
1 TAAGAAATGAAAT--AAAGGAAATGA
89656 TA
1 TA
89658 TCAAGGTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 5 0.20
26 17 0.68
28 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.21, T:0.21
Consensus pattern (24 bp):
TAAGAAATGAAATAAAGGAAATGA
Done.