Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002806.1 Hibiscus syriacus cultivar Beakdansim tig00005775_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: 55205
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1060 original size:22 final size:22
Alignment explanation
Indices: 1035--1086 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
1025 TATATAATGT
1035 ATGAACAATACCATAAACAGTA-
1 ATGAACAA-ACCATAAACAGTAC
* *
1057 ATGAACAAACCGTAAATAGTACC
1 ATGAACAAACCATAAACAGTA-C
1080 ATGAACA
1 ATGAACA
1087 GTGCCGATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
22 8 0.31
23 7 0.27
ACGTcount: A:0.52, C:0.19, G:0.12, T:0.17
Consensus pattern (22 bp):
ATGAACAAACCATAAACAGTAC
Found at i:1886 original size:31 final size:31
Alignment explanation
Indices: 1848--2020 Score: 244
Period size: 31 Copynumber: 5.5 Consensus size: 31
1838 GCTTGTATAA
1848 TAATCTGTCCATATGTCCCGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
*
1879 TAATCTGTCCATATGTCTCGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
* * *
1910 TAATCTGTCCATATATCCTGAAGAAC-TAAG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
*
1940 TAA-CTGTCCATATGTCCTGAAGAACATAGG
1 TAATCTGTCCATATGTCCCGAAGAACATAGG
1970 TAATCCTGTCCATATGTCCCGTAAG-ACATAGG
1 TAAT-CTGTCCATATGTCCCG-AAGAACATAGG
2002 TAATCCTGGTCCATATGTC
1 TAAT-CT-GTCCATATGTC
2021 TTGGAAGACA
Statistics
Matches: 129, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
29 21 0.16
30 12 0.09
31 53 0.41
32 29 0.22
33 14 0.11
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (31 bp):
TAATCTGTCCATATGTCCCGAAGAACATAGG
Found at i:3024 original size:22 final size:23
Alignment explanation
Indices: 2975--3031 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
2965 TGTTTAACGT
2975 AGGTATCGGTACACCCATAACTG
1 AGGTATCGGTACACCCATAACTG
* *
2998 AGGTATCAGTACACCCCTAA-TG
1 AGGTATCGGTACACCCATAACTG
3020 AGGTATCGGTAC
1 AGGTATCGGTAC
3032 CTTCTTAGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (23 bp):
AGGTATCGGTACACCCATAACTG
Found at i:8241 original size:26 final size:26
Alignment explanation
Indices: 8205--8271 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 26
8195 ACATTCGAAC
8205 TCAAGGTGTCGAAGCGACCCATGAAA
1 TCAAGGTGTCGAAGCGACCCATGAAA
8231 TCAAGGTGTCGAGGCGAAGCGACCCATGAAA
1 TCAAGGTGT-----CGAAGCGACCCATGAAA
8262 TCAAGGTGTC
1 TCAAGGTGTC
8272 AATCGACGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
26 10 0.28
31 26 0.72
ACGTcount: A:0.31, C:0.22, G:0.30, T:0.16
Consensus pattern (26 bp):
TCAAGGTGTCGAAGCGACCCATGAAA
Found at i:12768 original size:37 final size:37
Alignment explanation
Indices: 12695--12769 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
12685 GTTGGAAAAT
* *
12695 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
12732 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
12769 A
1 A
12770 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:19217 original size:20 final size:20
Alignment explanation
Indices: 19180--19218 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19170 AACCCCTTAG
*
19180 TATCGATACCCTATGAACAA
1 TATCGATACCCTAAGAACAA
19200 TATCGATACCAC-AAGAACA
1 TATCGATACC-CTAAGAACA
19219 TGATACCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.21
Consensus pattern (20 bp):
TATCGATACCCTAAGAACAA
Found at i:26651 original size:51 final size:51
Alignment explanation
Indices: 26571--26676 Score: 176
Period size: 51 Copynumber: 2.1 Consensus size: 51
26561 AGATTTTTGA
*
26571 ACATCTTAACATAGTTAGGTTGCACGAGGTATATGTTGTTTTAAGTATTGT
1 ACATCTTAACATAGTTAGGTTACACGAGGTATATGTTGTTTTAAGTATTGT
* * *
26622 ACATCTTAACATAGTTAGGTTACATGAGGTATGTGTTGTTTTAATTATTGT
1 ACATCTTAACATAGTTAGGTTACACGAGGTATATGTTGTTTTAAGTATTGT
26673 ACAT
1 ACAT
26677 TGTACTTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.42
Consensus pattern (51 bp):
ACATCTTAACATAGTTAGGTTACACGAGGTATATGTTGTTTTAAGTATTGT
Found at i:26785 original size:2 final size:2
Alignment explanation
Indices: 26780--26817 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
26770 TATATTGTTA
26780 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
26818 TATTCTTGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28124 original size:43 final size:43
Alignment explanation
Indices: 28060--28184 Score: 241
Period size: 43 Copynumber: 2.9 Consensus size: 43
28050 TAAGTGTTTC
28060 AAACAAGATACAAACTTGGAATTTAAGACAAGAAACATGTCTA
1 AAACAAGATACAAACTTGGAATTTAAGACAAGAAACATGTCTA
*
28103 AAACAAGATACAAACTCGGAATTTAAGACAAGAAACATGTCTA
1 AAACAAGATACAAACTTGGAATTTAAGACAAGAAACATGTCTA
28146 AAACAAGATACAAACTTGGAATTTAAGACAAGAAACATG
1 AAACAAGATACAAACTTGGAATTTAAGACAAGAAACATG
28185 AGCGATTAAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 80 1.00
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.19
Consensus pattern (43 bp):
AAACAAGATACAAACTTGGAATTTAAGACAAGAAACATGTCTA
Found at i:28133 original size:25 final size:24
Alignment explanation
Indices: 28062--28178 Score: 69
Period size: 25 Copynumber: 5.2 Consensus size: 24
28052 AGTGTTTCAA
28062 ACAAGATACAAACTTGGAATTTAAG
1 ACAAGATACAAAC-TGGAATTTAAG
* * *
28087 ACAAGA-A-ACA-T-G--TCTAAA
1 ACAAGATACAAACTGGAATTTAAG
28105 ACAAGATACAAACTCGGAATTTAAG
1 ACAAGATACAAACT-GGAATTTAAG
* * *
28130 ACAAGA-A-ACA-T-G--TCTAAA
1 ACAAGATACAAACTGGAATTTAAG
28148 ACAAGATACAAACTTGGAATTTAAG
1 ACAAGATACAAAC-TGGAATTTAAG
28173 ACAAGA
1 ACAAGA
28179 AACATGAGCG
Statistics
Matches: 66, Mismatches: 12, Indels: 28
0.62 0.11 0.26
Matches are distributed among these distances:
18 20 0.30
19 2 0.03
20 6 0.09
21 2 0.03
22 2 0.03
23 6 0.09
24 2 0.03
25 26 0.39
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.20
Consensus pattern (24 bp):
ACAAGATACAAACTGGAATTTAAG
Found at i:29996 original size:21 final size:21
Alignment explanation
Indices: 29967--30026 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
29957 AATGCTAAAG
*
29967 TTTTAAAAATATTTAATTTTT
1 TTTTAAAAATAATTAATTTTT
*
29988 TTTTTAAAATAATTAATTTTT
1 TTTTAAAAATAATTAATTTTT
** *
30009 AATTAAATAAAAATTAAT
1 TTTTAAA-AATAATTAAT
30027 AATTCTTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 23 0.72
22 9 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTTAAAAATAATTAATTTTT
Found at i:30230 original size:18 final size:20
Alignment explanation
Indices: 30195--30231 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
30185 ATAAAATATT
*
30195 TATTTTTATTTTATAATTAG
1 TATTTTTATTTGATAATTAG
30215 TATTTTT-TTTGA-AATTA
1 TATTTTTATTTGATAATTA
30232 TAGAGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 4 0.25
20 7 0.44
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (20 bp):
TATTTTTATTTGATAATTAG
Found at i:31761 original size:128 final size:130
Alignment explanation
Indices: 31583--31843 Score: 454
Period size: 129 Copynumber: 2.0 Consensus size: 130
31573 CGAGTCCGAG
* * *
31583 ATGTCACATTGACTTTTTAAAAACGATGTTCTTACAAGATAACAAAACATTTGAACTCAATTTAA
1 ATGTCACATTGACTTTTTAAAAACAATGTTCTTACAAAATAACAAAACATTTAAACTCAATTTAA
* * *
31648 GAAAATACAATAATATTCT-ATTATATTATGCTTCATTATAAAAATTCAAGTCAAAAATGTATTT
66 GAAAATACAATAATATTATAATTATATTATGATTCATTATAAAAATTCAAGTCAAAAACGTATTT
31712 ATGTCACATTGACTTTTT-AAAACAATGTTCTTACAAAATAACAAAACATTTAAACTCAATTTAA
1 ATGTCACATTGACTTTTTAAAAACAATGTTCTTACAAAATAACAAAACATTTAAACTCAATTTAA
31776 GAAAATACAATAATATTATAATTATATTATGATTCATTATAAAAATTCAAGTCAAAAACGTATTT
66 GAAAATACAATAATATTATAATTATATTATGATTCATTATAAAAATTCAAGTCAAAAACGTATTT
31841 ATG
1 ATG
31844 AACATTACTA
Statistics
Matches: 125, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
128 61 0.49
129 64 0.51
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (130 bp):
ATGTCACATTGACTTTTTAAAAACAATGTTCTTACAAAATAACAAAACATTTAAACTCAATTTAA
GAAAATACAATAATATTATAATTATATTATGATTCATTATAAAAATTCAAGTCAAAAACGTATTT
Found at i:31849 original size:128 final size:129
Alignment explanation
Indices: 31583--31849 Score: 439
Period size: 128 Copynumber: 2.1 Consensus size: 129
31573 CGAGTCCGAG
* * * *
31583 ATGTCACATTGACTTTTTAAAAACGATGTTCTTACAAGATAACAAAACATTTGAACTCAATTTAA
1 ATGTAACATTGACTTTTTAAAAACAATGTTCTTACAAAATAACAAAACATTTAAACTCAATTTAA
* * *
31648 GAAAATACAATAATATTCTATTATATTATGCTTCATTATAAAAATTCAAGTCAAAAATGTATTT
66 GAAAATACAATAATATTATATTATATTATGATTCATTATAAAAATTCAAGTCAAAAACGTATTT
*
31712 ATGTCACATTGACTTTTT-AAAACAATGTTCTTACAAAATAACAAAACATTTAAACTCAATTTAA
1 ATGTAACATTGACTTTTTAAAAACAATGTTCTTACAAAATAACAAAACATTTAAACTCAATTTAA
31776 GAAAATACAATAATATTATAATTATATTATGATTCATTATAAAAATTCAAGTCAAAAACGTATTT
66 GAAAATACAATAATATTAT-ATTATATTATGATTCATTATAAAAATTCAAGTCAAAAACGTATTT
31841 ATG-AACATT
1 ATGTAACATT
31850 ACTATACGGT
Statistics
Matches: 130, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
128 66 0.51
129 64 0.49
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (129 bp):
ATGTAACATTGACTTTTTAAAAACAATGTTCTTACAAAATAACAAAACATTTAAACTCAATTTAA
GAAAATACAATAATATTATATTATATTATGATTCATTATAAAAATTCAAGTCAAAAACGTATTT
Found at i:32329 original size:39 final size:37
Alignment explanation
Indices: 32273--32536 Score: 115
Period size: 38 Copynumber: 7.2 Consensus size: 37
32263 ACAAAAAATG
* ***
32273 GTTTCTGAAAATATATATAATATAGTTTTTTTTAAAAAC
1 GTTTTTGAAAAT-TATATAATATA-TAAGTTTTAAAAAC
32312 GTTTTTGAAAACTTATATACAATATATAAGTTTTAAAAAC
1 GTTTTTGAAAA-TTATAT--AATATATAAGTTTTAAAAAC
* * * * *
32352 -ATTTTGAAAATTATATAACATAT-ATTTTTGAAATC
1 GTTTTTGAAAATTATATAATATATAAGTTTTAAAAAC
* *
32387 -ATTTT-AAAA--ATATAATGTAT-AGTTTAAAATAAAAAC
1 GTTTTTGAAAATTATATAATATATAAGTTT----TAAAAAC
* *
32423 ATTTTTGAAAATTTTATATAATATAT-AGTTTTAAAAAT
1 GTTTTTGAAAA--TTATATAATATATAAGTTTTAAAAAC
* * *
32461 ATTTTGGAAAACTCATAT-A-ATAT---TTTTAAAAATC
1 GTTTTTGAAAA-TTATATAATATATAAGTTTTAAAAA-C
* * ** *
32495 ATTTTTGAAAACTATATGGTATAT-AGTTTTGAAAAC
1 GTTTTTGAAAATTATATAATATATAAGTTTTAAAAAC
*
32531 ATTTTT
1 GTTTTT
32537 AAATATAATA
Statistics
Matches: 181, Mismatches: 26, Indels: 39
0.74 0.11 0.16
Matches are distributed among these distances:
32 13 0.07
33 13 0.07
34 14 0.08
35 22 0.12
36 19 0.10
37 17 0.09
38 26 0.14
39 24 0.13
40 12 0.07
41 6 0.03
42 15 0.08
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (37 bp):
GTTTTTGAAAATTATATAATATATAAGTTTTAAAAAC
Found at i:32493 original size:33 final size:32
Alignment explanation
Indices: 32443--32511 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
32433 ATTTTATATA
32443 ATATATAGTTTTAAAAAT-ATTTTGGAAAACT
1 ATATATAGTTTTAAAAATCATTTTGGAAAACT
* *
32474 CATATAATATTTTTAAAAATCATTTTTGAAAACT
1 -ATAT-ATAGTTTTAAAAATCATTTTGGAAAACT
32508 ATAT
1 ATAT
32512 GGTATATAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 4 0.12
33 17 0.52
34 12 0.36
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (32 bp):
ATATATAGTTTTAAAAATCATTTTGGAAAACT
Found at i:32496 original size:20 final size:21
Alignment explanation
Indices: 32458--32496 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
32448 TAGTTTTAAA
*
32458 AATATTTTGGAAAACTCATAT
1 AATATTTTGGAAAAATCATAT
*
32479 AATATTTT-TAAAAATCAT
1 AATATTTTGGAAAAATCAT
32497 TTTTGAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (21 bp):
AATATTTTGGAAAAATCATAT
Found at i:32637 original size:18 final size:18
Alignment explanation
Indices: 32616--32654 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
32606 ATTATTTCTT
*
32616 TTCATTTTA-TTCACTTTA
1 TTCATTTAATTTCA-TTTA
32634 TTCATTTAATTTCATTTA
1 TTCATTTAATTTCATTTA
32652 TTC
1 TTC
32655 TGTTTATGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.15, G:0.00, T:0.62
Consensus pattern (18 bp):
TTCATTTAATTTCATTTA
Found at i:34474 original size:17 final size:18
Alignment explanation
Indices: 34434--34484 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
34424 TAACAATACT
*
34434 TATCAGTAATCATATTAC
1 TATCATTAATCATATTAC
34452 TATCATTAATTCAT-TTA-
1 TATCATTAA-TCATATTAC
*
34469 TATCATGTAAGCATAT
1 TATCAT-TAATCATAT
34485 ACTGAACCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 9 0.32
18 15 0.54
19 4 0.14
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (18 bp):
TATCATTAATCATATTAC
Found at i:34722 original size:31 final size:31
Alignment explanation
Indices: 34699--34777 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
34689 CATAGATTCT
*
34699 GAAGAACCTAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
34730 GAAGAACATAGGTAAACAATCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
34761 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
34778 CCTCGACCAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.18
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Done.