Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000553.1 Hibiscus syriacus cultivar Beakdansim tig00001079_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: 60212
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1073 original size:43 final size:43
Alignment explanation
Indices: 994--1111 Score: 172
Period size: 43 Copynumber: 2.8 Consensus size: 43
984 CATTCTTCAT
*
994 AACATTAGCGGCATTTGT-A---TAAAATGCCGCAATTTTAAG
1 AACATTAGTGGCATTTGTAATTTTAAAATGCCGCAATTTTAAG
1033 AACATTAGTGGCATTTGTAATTTTAAAATGCCGCAATTTTAAG
1 AACATTAGTGGCATTTGTAATTTTAAAATGCCGCAATTTTAAG
* * *
1076 TACATTAGTGGCGTTTGTAATTTGAAAATGCCGCAA
1 AACATTAGTGGCATTTGTAATTTTAAAATGCCGCAA
1112 CATTTATGTC
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
39 17 0.24
40 1 0.01
43 53 0.75
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.34
Consensus pattern (43 bp):
AACATTAGTGGCATTTGTAATTTTAAAATGCCGCAATTTTAAG
Found at i:2205 original size:30 final size:30
Alignment explanation
Indices: 2169--2229 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2159 TAGTAACTTT
**
2169 AGATAATACGACATAATGTACAAACTATTA
1 AGATAATAAAACATAATGTACAAACTATTA
2199 AGATAATAAAACATAATGTACAAACTATTA
1 AGATAATAAAACATAATGTACAAACTATTA
2229 A
1 A
2230 ACAATGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.54, C:0.11, G:0.08, T:0.26
Consensus pattern (30 bp):
AGATAATAAAACATAATGTACAAACTATTA
Found at i:4816 original size:75 final size:74
Alignment explanation
Indices: 4699--4907 Score: 237
Period size: 75 Copynumber: 2.8 Consensus size: 74
4689 TTGAGTTTAA
* * *
4699 TATTTTTCTAGACTTAATATTATGGGTTGAGTCTT-AAGATTTGACACTTTAATATTATGATTTG
1 TATTATTCTAGACTTAATATTGTGGTTTGAGTCTTGAA-ATTTGA-ACTTTAATATTATGATTTG
4763 ATTATGGATTT
64 ATTATGGATTT
* * * * * * *
4774 TATTATTCTAGAGTTAATTTTGTGGTTTGAATCTTGAAATTTGATATTTTAATATTGTGGTTTGT
1 TATTATTCTAGACTTAATATTGTGGTTTGAGTCTTGAAATTTGA-ACTTTAATATTATGATTTGA
4839 TTATGGATTT
65 TTATGGATTT
* * * *
4849 TACTGTTCTAAACTTAATATTGTGGTTTGAGTCTTGATATTTG-ACTTT-AT-TTATGATTT
1 TATTATTCTAGACTTAATATTGTGGTTTGAGTCTTGAAATTTGAACTTTAATATTATGATTT
4908 TTTATATATA
Statistics
Matches: 112, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
71 7 0.06
72 2 0.02
73 4 0.04
75 97 0.87
76 2 0.02
ACGTcount: A:0.25, C:0.06, G:0.17, T:0.52
Consensus pattern (74 bp):
TATTATTCTAGACTTAATATTGTGGTTTGAGTCTTGAAATTTGAACTTTAATATTATGATTTGAT
TATGGATTT
Found at i:7361 original size:8 final size:8
Alignment explanation
Indices: 7348--7374 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
7338 ATTAAAGTAG
7348 AATAGTTC
1 AATAGTTC
7356 AATAGTTC
1 AATAGTTC
7364 AATAGTTC
1 AATAGTTC
7372 AAT
1 AAT
7375 GATTTATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (8 bp):
AATAGTTC
Found at i:8220 original size:32 final size:32
Alignment explanation
Indices: 8179--8271 Score: 168
Period size: 32 Copynumber: 2.9 Consensus size: 32
8169 GAGTCGAGGG
*
8179 TTACCTATGTCTTTCGAGACATATGGACAAAA
1 TTACCTATGTCTTTCGGGACATATGGACAAAA
*
8211 TTACCTATGTCTTTCGGGACATATGGACATAA
1 TTACCTATGTCTTTCGGGACATATGGACAAAA
8243 TTACCTATGTCTTTCGGGACATATGGACA
1 TTACCTATGTCTTTCGGGACATATGGACA
8272 GTTTCCTATG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.33
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGACAAAA
Found at i:12625 original size:32 final size:32
Alignment explanation
Indices: 12584--12740 Score: 257
Period size: 32 Copynumber: 4.9 Consensus size: 32
12574 GAGTCGAAGG
*
12584 TTACCTATGTCTTTCGGGACATATGGACAGGA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
12616 TTACCTATGTCTTT-GGGACATATGGAC-GTAA
1 TTACCTATGTCTTTCGGGACATATGGACAG-AA
12647 TTACCTATGTCTTTCGGGACATATGGACA-ATA
1 TTACCTATGTCTTTCGGGACATATGGACAGA-A
*
12679 TTACCTATGTCTTTCGGGACATATAGACAGAA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
12711 TTACCTATGTCTTTCGGGACATATGGACAG
1 TTACCTATGTCTTTCGGGACATATGGACAG
12741 TTACTTATGT
Statistics
Matches: 117, Mismatches: 3, Indels: 10
0.90 0.02 0.08
Matches are distributed among these distances:
30 1 0.01
31 29 0.25
32 86 0.74
33 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGACAGAA
Found at i:12662 original size:63 final size:62
Alignment explanation
Indices: 12584--12767 Score: 264
Period size: 63 Copynumber: 2.9 Consensus size: 62
12574 GAGTCGAAGG
12584 TTACCTATGTCTTTCGGGACATATGGACAGGATTACCTATGTCTTTGGGACATATGGAC-GTAA
1 TTACCTATGTCTTTCGGGACATATGGACA-GATTACCTATGTCTTTGGGACATATGGACAG-AA
* *
12647 TTACCTATGTCTTTCGGGACATATGGACAATATTACCTATGTCTTTCGGGACATATAGACAGAA
1 TTACCTATGTCTTTCGGGACATATGGAC-AGATTACCTATGTCTTT-GGGACATATGGACAGAA
* * *
12711 TTACCTATGTCTTTCGGGACATATGGACAG-TTACTTATGTTCTTAGGAACATATGGA
1 TTACCTATGTCTTTCGGGACATATGGACAGATTACCTATG-TCTTTGGGACATATGGA
12768 TAGGTCATTC
Statistics
Matches: 110, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
62 18 0.16
63 48 0.44
64 43 0.39
65 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.34
Consensus pattern (62 bp):
TTACCTATGTCTTTCGGGACATATGGACAGATTACCTATGTCTTTGGGACATATGGACAGAA
Found at i:14238 original size:21 final size:21
Alignment explanation
Indices: 14208--14255 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
14198 AAACTATGAT
*
14208 TTATTATTATGGATTTCAAGA
1 TTATTGTTATGGATTTCAAGA
*
14229 TTATTGTTATGGATTTCAAGT
1 TTATTGTTATGGATTTCAAGA
14250 TTATTG
1 TTATTG
14256 GATAACGCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.04, G:0.17, T:0.52
Consensus pattern (21 bp):
TTATTGTTATGGATTTCAAGA
Found at i:17894 original size:15 final size:14
Alignment explanation
Indices: 17877--17933 Score: 73
Period size: 15 Copynumber: 4.0 Consensus size: 14
17867 CTTAATATTA
17877 ATATTTAATTTTTT
1 ATATTTAATTTTTT
17891 AATAATTTAA-TTTTT
1 -AT-ATTTAATTTTTT
17906 ATATTTAATATTTTT
1 ATATTTAAT-TTTTT
17921 ATATTT-ATTTTTT
1 ATATTTAATTTTTT
17934 TTTAACATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 11 0.28
14 4 0.10
15 18 0.46
16 6 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
ATATTTAATTTTTT
Found at i:17934 original size:15 final size:15
Alignment explanation
Indices: 17877--17966 Score: 69
Period size: 15 Copynumber: 5.9 Consensus size: 15
17867 CTTAATATTA
17877 ATATTTAAT-TTTTT
1 ATATTTAATATTTTT
17891 AATAATTT-A-ATTTTT
1 -AT-ATTTAATATTTTT
17906 ATATTTAATATTTTT
1 ATATTTAATATTTTT
* *
17921 ATATTTATTTTTTTTT
1 ATATTTA-ATATTTTT
* *
17937 AACATTTAAATAATTTT
1 -ATATTT-AATATTTTT
*
17954 ATATTTAAAATTT
1 ATATTTAATATTT
17967 AAAATAATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
13 4 0.07
14 3 0.05
15 26 0.44
16 15 0.25
17 10 0.17
18 1 0.02
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATTTAATATTTTT
Found at i:17934 original size:29 final size:29
Alignment explanation
Indices: 17868--17933 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
17858 TTTTAGATTC
* *
17868 TTAATATTAATATTTAATTTTTTAATAAT
1 TTAATTTTTATATTTAATTTTTTAATAAT
17897 TTAATTTTTATATTTAATATTTTT-AT-AT
1 TTAATTTTTATATTTAAT-TTTTTAATAAT
*
17925 TTATTTTTT
1 TTAATTTTT
17934 TTTAACATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 10 0.30
29 18 0.55
30 5 0.15
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (29 bp):
TTAATTTTTATATTTAATTTTTTAATAAT
Found at i:18140 original size:22 final size:22
Alignment explanation
Indices: 18097--18137 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
18087 ATTATGAGTC
**
18097 ATTATGTTTAACATTGTAAATT
1 ATTATGTTTAACATCATAAATT
18119 ATTATG-TTAACATCATAAA
1 ATTATGTTTAACATCATAAA
18138 ATTTAACGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTATGTTTAACATCATAAATT
Found at i:20073 original size:3 final size:3
Alignment explanation
Indices: 20065--20161 Score: 194
Period size: 3 Copynumber: 32.3 Consensus size: 3
20055 ATAATGTACA
20065 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20113 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
20161 A
1 A
20162 GGTTGGGGAG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:20745 original size:16 final size:17
Alignment explanation
Indices: 20718--20754 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
20708 TATGGGATGA
20718 AAAAATAGTA-TTATTGT
1 AAAAATAGTATTTATT-T
20735 AAAAATA-TATTTATTT
1 AAAAATAGTATTTATTT
20751 AAAA
1 AAAA
20755 TAATATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
AAAAATAGTATTTATTT
Found at i:27143 original size:20 final size:21
Alignment explanation
Indices: 27104--27143 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
27094 TTTTAAAGAT
*
27104 ATTTATTACTCTATTTTTAAG
1 ATTTATTACTCTATTGTTAAG
*
27125 ATTTATTA-TGTATTGTTAA
1 ATTTATTACTCTATTGTTAA
27144 ACTTTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
ATTTATTACTCTATTGTTAAG
Found at i:27217 original size:43 final size:43
Alignment explanation
Indices: 27156--27244 Score: 106
Period size: 43 Copynumber: 2.1 Consensus size: 43
27146 TTTTTTATGA
* * *
27156 TTAGTTATAATATATTAGTTTGGTGTATTTTTAAATTGTTATT
1 TTAGTTATAATATATTAGTTTAGTGTATTTGTAAATTATTATT
* * * * *
27199 TTAGTTGTGATATGTTAGTTTAGTGTGTTTGTATATTATTATT
1 TTAGTTATAATATATTAGTTTAGTGTATTTGTAAATTATTATT
27242 TTA
1 TTA
27245 AAGGTTAGAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.25, C:0.00, G:0.17, T:0.58
Consensus pattern (43 bp):
TTAGTTATAATATATTAGTTTAGTGTATTTGTAAATTATTATT
Found at i:27351 original size:2 final size:2
Alignment explanation
Indices: 27344--27373 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
27334 ATCACTAGAT
27344 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
27374 AAGTAAGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30143 original size:105 final size:105
Alignment explanation
Indices: 30002--30208 Score: 238
Period size: 105 Copynumber: 2.0 Consensus size: 105
29992 TATGGTCAAT
* * * * *
30002 TGAACCTTGGTTTGATGTTAGAGCTTATTGAAGATTCTGATTGACAA-AATTAACTTGGCTCAAG
1 TGAACCTTGATTCGATATTAGAGCTTATTGAAGATTCTGACTGA-AAGAACTAACTTGGCTCAAG
*
30066 GGTACAG-TAAAAGTGGACATCCATCTAACAATATGGCCAGC
65 GATAC-GCTAAAAGTGGACATCCATCTAACAATATGGCCAGC
* * * * *
30107 TGAACCTTGATTCGATATTGGAGTTTGTTGATGATTCTGACTGAAAGAACTAGCTTGGCTCAAGG
1 TGAACCTTGATTCGATATTAGAGCTTATTGAAGATTCTGACTGAAAGAACTAACTTGGCTCAAGG
*** * *
30172 ATACGCTAGGTGTGGGCATCCATTTAACAATATGGCC
66 ATACGCTAAAAGTGGACATCCATCTAACAATATGGCC
30209 TTGAGAAGGT
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
104 3 0.04
105 81 0.96
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (105 bp):
TGAACCTTGATTCGATATTAGAGCTTATTGAAGATTCTGACTGAAAGAACTAACTTGGCTCAAGG
ATACGCTAAAAGTGGACATCCATCTAACAATATGGCCAGC
Found at i:44356 original size:21 final size:21
Alignment explanation
Indices: 44331--44370 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
44321 AAACACGATG
44331 AGTAGTATCAATACTGATGAA
1 AGTAGTATCAATACTGATGAA
**
44352 AGTAGTATTGATACTGATG
1 AGTAGTATCAATACTGATG
44371 TGGAGGTATC
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:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (21 bp):
AGTAGTATCAATACTGATGAA
Found at i:45217 original size:52 final size:52
Alignment explanation
Indices: 45099--45209 Score: 177
Period size: 53 Copynumber: 2.1 Consensus size: 52
45089 ATGTACTTTC
*
45099 GACACTATGTGTGCACCCATGGTATTCAAATGAGTTTGTGAATTACAATTTT
1 GACACTATGTGTGCACCCATGGAATTCAAATGAGTTTGTGAATTACAATTTT
* * *
45151 GGCACTATGTGTGCATCCATGGAATTCATAATGAGTTTGTGAATTACCATTTT
1 GACACTATGTGTGCACCCATGGAATTCA-AATGAGTTTGTGAATTACAATTTT
45204 GACACT
1 GACACT
45210 TAGGTGCAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 25 0.47
53 28 0.53
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (52 bp):
GACACTATGTGTGCACCCATGGAATTCAAATGAGTTTGTGAATTACAATTTT
Found at i:51439 original size:21 final size:21
Alignment explanation
Indices: 51413--51466 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
51403 CCATGAACAA
51413 TATCGATACTGAAAAAAGTAG
1 TATCGATACTGAAAAAAGTAG
*
51434 TATCGATACTGACAAAAGTAG
1 TATCGATACTGAAAAAAGTAG
51455 TATCGATACTGA
1 TATCGATACTGA
51467 TGTGGAGGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (21 bp):
TATCGATACTGAAAAAAGTAG
Found at i:56550 original size:24 final size:25
Alignment explanation
Indices: 56518--56569 Score: 97
Period size: 24 Copynumber: 2.1 Consensus size: 25
56508 CAACATTAAA
56518 GAGAACATTAAGTCATGAA-TGAAT
1 GAGAACATTAAGTCATGAATTGAAT
56542 GAGAACATTAAGTCATGAATTGAAT
1 GAGAACATTAAGTCATGAATTGAAT
56567 GAG
1 GAG
56570 TTAGGAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.70
25 8 0.30
ACGTcount: A:0.44, C:0.08, G:0.23, T:0.25
Consensus pattern (25 bp):
GAGAACATTAAGTCATGAATTGAAT
Done.