Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003189.1 Hibiscus syriacus cultivar Beakdansim tig00006706_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: 60407
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3919 original size:18 final size:18
Alignment explanation
Indices: 3898--3934 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3888 CTAATTTTAT
3898 TTAAACATTATATAAAAA
1 TTAAACATTATATAAAAA
**
3916 TTAAATGTTATATAAAAA
1 TTAAACATTATATAAAAA
3934 T
1 T
3935 AATTATGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
TTAAACATTATATAAAAA
Found at i:4926 original size:20 final size:20
Alignment explanation
Indices: 4901--4939 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4891 AATGACCAGT
* *
4901 TGAAAACTGGTAGAACCGGC
1 TGAAAACCGGTAAAACCGGC
4921 TGAAAACCGGTAAAACCGG
1 TGAAAACCGGTAAAACCGG
4940 GGTGAACCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.21, G:0.28, T:0.13
Consensus pattern (20 bp):
TGAAAACCGGTAAAACCGGC
Found at i:21864 original size:12 final size:12
Alignment explanation
Indices: 21847--21877 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
21837 TTAAATATAT
*
21847 ATACCCGGCCCG
1 ATACCCGGCCCA
21859 ATACCCGGCCCA
1 ATACCCGGCCCA
21871 ATACCCG
1 ATACCCG
21878 TTTAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.48, G:0.19, T:0.10
Consensus pattern (12 bp):
ATACCCGGCCCA
Found at i:22023 original size:26 final size:25
Alignment explanation
Indices: 21969--22027 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
21959 ATCCCCACGG
21969 TTTTTTAAACAGGGACGAGTACCGA
1 TTTTTTAAACAGGGACGAGTACCGA
* * * *
21994 TTTTTTAAACAGTGACGGGTACTGG
1 TTTTTTAAACAGGGACGAGTACCGA
22019 TTTTTTAAA
1 TTTTTTAAA
22028 TGGGAACGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (25 bp):
TTTTTTAAACAGGGACGAGTACCGA
Found at i:24139 original size:18 final size:17
Alignment explanation
Indices: 24092--24130 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
24082 GGAGCCAATT
*
24092 TTTTTATTTA-TTTAAA
1 TTTTTATATATTTTAAA
24108 TTTTTATATATTTTAAA
1 TTTTTATATATTTTAAA
24125 TTTTTA
1 TTTTTA
24131 ATTAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTTATATATTTTAAA
Found at i:24155 original size:26 final size:25
Alignment explanation
Indices: 24104--24169 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 25
24094 TTTATTTATT
* *
24104 TAAATTTTTATATATTTTAAATTTTTAA
1 TAAA-TTTTAT-TCTTTTAAAATTTT-A
* *
24132 TTAATTTTTTTCTTTTAAAATTTTA
1 TAAATTTTATTCTTTTAAAATTTTA
24157 TAAATTTTATTCT
1 TAAATTTTATTCT
24170 CTAATATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
25 12 0.38
26 12 0.38
27 5 0.16
28 3 0.09
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (25 bp):
TAAATTTTATTCTTTTAAAATTTTA
Found at i:25983 original size:58 final size:58
Alignment explanation
Indices: 25912--26031 Score: 159
Period size: 58 Copynumber: 2.1 Consensus size: 58
25902 GTTGTTGTCA
* * * **
25912 TGTTGGAGATCTAATTGTTCTTTTTGTCGTGTACGATGTGGTTGATAAAATTTGAAGT
1 TGTTGGAGATCTAATTATTCTTTTTGTCGCGAACGATGTGGTTGATAAAATGGGAAGT
* * * *
25970 TGTTGGGGATCTAATTATTCTTTTTTTGGCGAACGATGTGGTTGATTAAATGGGAAGT
1 TGTTGGAGATCTAATTATTCTTTTTGTCGCGAACGATGTGGTTGATAAAATGGGAAGT
26028 TGTT
1 TGTT
26032 AGTCATGTCG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.22, C:0.07, G:0.28, T:0.44
Consensus pattern (58 bp):
TGTTGGAGATCTAATTATTCTTTTTGTCGCGAACGATGTGGTTGATAAAATGGGAAGT
Found at i:31222 original size:38 final size:37
Alignment explanation
Indices: 31166--31268 Score: 136
Period size: 38 Copynumber: 2.8 Consensus size: 37
31156 TTTTGTATAT
* *
31166 ACATATATATATAATATAGTTTTGAAAACATATTTGAA
1 ACATATATATATTATATAGTTTTTAAAACA-ATTTGAA
* *
31204 ACATCTATATATTATATAGTTTTTAAAACACTTTGAA
1 ACATATATATATTATATAGTTTTTAAAACAATTTGAA
* *
31241 A-ATAAATATAATATATAGTTTTTAAAAC
1 ACATATATATATTATATAGTTTTTAAAAC
31269 GTTTTTAAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 24 0.41
37 7 0.12
38 27 0.47
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.41
Consensus pattern (37 bp):
ACATATATATATTATATAGTTTTTAAAACAATTTGAA
Found at i:31257 original size:36 final size:36
Alignment explanation
Indices: 31170--31403 Score: 158
Period size: 35 Copynumber: 6.4 Consensus size: 36
31160 GTATATACAT
* **
31170 ATATATATAATATAGTTTTGAAAACATATTTGAAACATCT
1 ATATA-AT-ATATAGTTTTTAAAACAT-TTTGAAA-ATAA
* *
31210 ATATATTATATAGTTTTTAAAACACTTTGAAAATAA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
* * *
31246 ATATAATATATAGTTTTTAAAACGTTTTTAAGA-AA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
* ** * *
31281 ATATATTATACGGTTTTAAAAAACATTTTTAAAATAA
1 ATATAATATATAGTTTT-TAAAACATTTTGAAAATAA
* * *
31318 ATATAAT-T-T--TTTTAAAAGAAACATTTTGAAAACAT
1 ATATAATATATAGTTTT--TA-AAACATTTTGAAAATAA
* * *
31353 ATATATTATATAGTTTTGAAATCATTTT-AAAA-AA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
*
31387 CTTATAATATATAGTTT
1 -ATATAATATATAGTTT
31404 AAAAAAAAAA
Statistics
Matches: 158, Mismatches: 27, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
33 4 0.03
34 4 0.03
35 54 0.34
36 53 0.34
37 17 0.11
38 16 0.10
39 5 0.03
40 5 0.03
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.42
Consensus pattern (36 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAATAA
Found at i:31369 original size:72 final size:71
Alignment explanation
Indices: 31174--31408 Score: 182
Period size: 72 Copynumber: 3.3 Consensus size: 71
31164 ATACATATAT
* * *
31174 ATATAATATA-GTTTTGAAAACATATTTG-AAACATCTATATATTATATAGTTTTTAAAACACTT
1 ATATAATATATATTTTAAAAACAT-TTTGAAAACA--TATATATTATATAGTTTTAAAAACACTT
31237 TGAAAATAA
63 TGAAAATAA
* * * ** *
31246 ATATAATATATAGTTTTTAAAACGTTTTTAAGAA-A-ATATATTATACGGTTTTAAAAAACATTT
1 ATATAATATATA-TTTTAAAAACATTTTGAA-AACATATATATTATATAGTTTT-AAAAACACTT
*
31309 TTAAAATAA
63 TGAAAATAA
* *
31318 ATATAAT-T-T-TTTTAAAAGAAACATTTTGAAAACATATATATTATATAGTTTTGAAATCA-TT
1 ATATAATATATATTTT--AA-AAACATTTTGAAAACATATATATTATATAGTTTTAAAAACACTT
*
31379 TTAAAA-AA
63 TGAAAATAA
* *
31387 CTTATAATATATAGTTTAAAAA
1 -ATATAATATATATTTTAAAAA
31409 AAAAACATTT
Statistics
Matches: 131, Mismatches: 18, Indels: 30
0.73 0.10 0.17
Matches are distributed among these distances:
68 4 0.03
69 2 0.02
70 21 0.16
71 35 0.27
72 49 0.37
73 6 0.05
74 12 0.09
75 2 0.02
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.41
Consensus pattern (71 bp):
ATATAATATATATTTTAAAAACATTTTGAAAACATATATATTATATAGTTTTAAAAACACTTTGA
AAATAA
Found at i:31507 original size:66 final size:66
Alignment explanation
Indices: 31353--31499 Score: 160
Period size: 67 Copynumber: 2.2 Consensus size: 66
31343 TTGAAAACAT
* *
31353 ATATATTATATAGTTTTGAAATCATTTTAAAAAACTTATAATATATAGTTTAAAAAAAAAACATT
1 ATATATTATATAGTTTTGAAAACATTTTAAAAAAC-TATAATATATAATTT--AAAAAAAACATT
31418 TTGA
63 TTGA
* * * * *
31422 A-A-ACTATATAATTTTGAAAACGTTTTAAAAATA-TATAATATATAATTT-TAAAATAC-TTTT
1 ATATATTATATAGTTTTGAAAACATTTTAAAAA-ACTATAATATATAATTTAAAAAAAACATTTT
31482 GA
65 GA
31484 ATATATTATATAGTTT
1 ATATATTATATAGTTT
31500 GTAGAAAATA
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
62 7 0.11
63 7 0.11
64 10 0.15
66 14 0.21
67 25 0.38
68 2 0.03
69 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (66 bp):
ATATATTATATAGTTTTGAAAACATTTTAAAAAACTATAATATATAATTTAAAAAAAACATTTTG
A
Found at i:31557 original size:14 final size:15
Alignment explanation
Indices: 31538--31579 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
31528 ATCGTTGTTG
31538 TTTATTTTTATTTA-
1 TTTATTTTTATTTAT
*
31552 TTTATTTTTATTAAT
1 TTTATTTTTATTTAT
*
31567 TTTATTTTCATTT
1 TTTATTTTTATTT
31580 TAATTGTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTTTTATTTAT
Found at i:55929 original size:2 final size:2
Alignment explanation
Indices: 55922--55968 Score: 64
Period size: 2 Copynumber: 24.5 Consensus size: 2
55912 ATCAATTAGT
55922 TA TA TA TA -A TA TA TA T- TA TA TA TA T- 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
55961 TA TCA TA T
1 TA T-A TA T
55969 TATCGTATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.07
2 36 0.88
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55936 original size:9 final size:9
Alignment explanation
Indices: 55922--55968 Score: 69
Period size: 9 Copynumber: 5.3 Consensus size: 9
55912 ATCAATTAGT
*
55922 TATATATAA
1 TATATATTA
55931 TATATATTA
1 TATATATTA
55940 TATATATTA
1 TATATATTA
55949 TATATA-TA
1 TATATATTA
*
55957 TATATATCA
1 TATATATTA
55966 TAT
1 TAT
55969 TATCGTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
8 8 0.23
9 27 0.77
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (9 bp):
TATATATTA
Found at i:55981 original size:33 final size:29
Alignment explanation
Indices: 55922--55986 Score: 76
Period size: 33 Copynumber: 2.1 Consensus size: 29
55912 ATCAATTAGT
*
55922 TATATATAATATATATTATATATATTATA
1 TATATATAATATATATTATATATATTAAA
*
55951 TATATATATATATCATATTATCGTATTATTAAA
1 TATATATA-ATAT-ATATTAT-ATA-TATTAAA
55984 TAT
1 TAT
55987 TCCAAGTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.27
30 4 0.13
31 7 0.23
32 2 0.07
33 9 0.30
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (29 bp):
TATATATAATATATATTATATATATTAAA
Found at i:56601 original size:15 final size:15
Alignment explanation
Indices: 56582--56617 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
56572 ATTTGTTTTT
56582 ATTAATACTTTATAA
1 ATTAATACTTTATAA
* *
56597 TTTAATATTTTATAA
1 ATTAATACTTTATAA
56612 ATTAAT
1 ATTAAT
56618 TTAATAATGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTAATACTTTATAA
Found at i:57244 original size:2 final size:2
Alignment explanation
Indices: 57237--57268 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
57227 TAAATATGAA
57237 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57269 ATACATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:57520 original size:24 final size:25
Alignment explanation
Indices: 57489--57535 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
57479 CAAGTTCAGT
57489 TCTGTTAA-T-GGTTAACGAAAAAA
1 TCTGTTAATTCGGTTAACGAAAAAA
*
57512 TCTGATTAATTCGGTTAATGAAAA
1 TCTG-TTAATTCGGTTAACGAAAA
57536 TTCGGTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 4 0.20
25 1 0.05
26 11 0.55
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (25 bp):
TCTGTTAATTCGGTTAACGAAAAAA
Done.