Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000074.1 Hibiscus syriacus cultivar Beakdansim tig00000136_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: 1055225
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:1001557 original size:71 final size:72
Alignment explanation
Indices: 1001468--1001651 Score: 216
Period size: 71 Copynumber: 2.6 Consensus size: 72
1001458 TTTTTTTAAA
* *
1001468 AAAACATGTTGGAAAACATATATATTATATAGTTTTTAAAAAAAGCATTGTAG-A-A-ATAT-AT
1 AAAACAT-TTTGAAAACATATATATTATATAG--TTTAAAAAAAACATTGTAGAATATATATAAT
*
1001529 ATAATTTTTG
63 ATAATTTTCG
* * *
1001539 AAAGCATTTTTGAAAACATATATATTATATAG-TTAAAAAAAACATTTTGGAATATATATAATAT
1 AAAACA-TTTTGAAAACATATATATTATATAGTTTAAAAAAAACATTGTAGAATATATATAATAT
1001603 AATTTTCG
65 AATTTTCG
* * *
1001611 AAAACATTTTAAAAATATATATAATATATAGTTTAAAAAAA
1 AAAACATTTTGAAAACATATATATTATATAGTTTAAAAAAA
1001652 CAGTTTGAAA
Statistics
Matches: 97, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
68 15 0.15
69 1 0.01
70 1 0.01
71 54 0.56
72 26 0.27
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (72 bp):
AAAACATTTTGAAAACATATATATTATATAGTTTAAAAAAAACATTGTAGAATATATATAATATA
ATTTTCG
Found at i:1001603 original size:34 final size:34
Alignment explanation
Indices: 1001462--1001661 Score: 104
Period size: 34 Copynumber: 5.6 Consensus size: 34
1001452 ATATAGTTTT
* *
1001462 TTTAAAAAAACATGTTGGAAAACATATATATTATATAG
1 TTTAAAAAAACAT-TTTG--AA-ATATATATAATATAG
*
1001500 TTTTTAAAAAAAGCATTGTAGAAATATATATAAT-T--
1 --TTTAAAAAAA-CATT-TTGAAATATATATAATATAG
* * *
1001535 TTT--GAAAGCATTTTTGAAAACATATATATTATATAG
1 TTTAAAAAAACA-TTTTG--AA-ATATATATAATATAG
* * *
1001571 TTAAAAAAAACATTTTGGAATATATATAATATAA
1 TTTAAAAAAACATTTTGAAATATATATAATATAG
*** *
1001605 TTTTCGAAAACATTTTAAAAATATATATAATATATAG
1 TTTAAAAAAACATTTT-GAAATATATAT-A-ATATAG
*
1001642 TTTAAAAAAACAGTTTGAAA
1 TTTAAAAAAACATTTTGAAA
1001662 AAATTTATAA
Statistics
Matches: 122, Mismatches: 24, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
30 4 0.03
31 5 0.04
32 2 0.02
33 13 0.11
34 26 0.21
35 10 0.08
36 6 0.05
37 23 0.19
38 15 0.12
39 2 0.02
40 11 0.09
41 5 0.04
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (34 bp):
TTTAAAAAAACATTTTGAAATATATATAATATAG
Found at i:1001640 original size:37 final size:35
Alignment explanation
Indices: 1001525--1001728 Score: 124
Period size: 37 Copynumber: 5.7 Consensus size: 35
1001515 TTGTAGAAAT
* *
1001525 ATATATAATTTTTGAAAGCATTTTTGAAAACATATATA
1 ATATATAA-TTTTGAAAACA-TTTT-AAAAAATATATA
* * *** ** *
1001563 TTATATAGTTAAAAAAAACATTTTGGAATATATAT-
1 ATATATAATT-TTGAAAACATTTTAAAAAATATATA
1001598 A-ATATAATTTTCGAAAACATTTTAAAAATATATATA
1 ATATATAATTTT-GAAAACATTTTAAAAA-ATATATA
* ** * *
1001634 ATATATAGTTTAAAAAAACAGTTTGAAAAAATTTATA
1 ATATATAATTT-TGAAAACA-TTTTAAAAAATATATA
* * * * *
1001671 ATATTTAGTTTTTAAAACATATTAAAAACTATATA
1 ATATATAATTTTGAAAACATTTTAAAAAATATATA
* *
1001706 GTATATGATTTTGAAAACATTTT
1 ATATATAATTTTGAAAACATTTT
1001729 TTTAGAAAGT
Statistics
Matches: 124, Mismatches: 35, Indels: 17
0.70 0.20 0.10
Matches are distributed among these distances:
34 19 0.15
35 35 0.28
36 15 0.12
37 36 0.29
38 19 0.15
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (35 bp):
ATATATAATTTTGAAAACATTTTAAAAAATATATA
Found at i:1001652 original size:71 final size:68
Alignment explanation
Indices: 1001480--1001672 Score: 208
Period size: 71 Copynumber: 2.8 Consensus size: 68
1001470 AACATGTTGG
* * * *
1001480 AAAACATATATATTATATAGTTTTTAAAAAAAGCATTGTAGAAATATATATAATTTTTGAAAGCA
1 AAAACATATATATTATATAG--TTTAAAAAAA-CATTTTGGAAATATATATAATTTTCGAAAACA
*
1001545 TTTTTG
63 TTTTTA
*
1001551 AAAACATATATATTATATAGTTAAAAAAAACATTTTGGAATATATATAATATAATTTTCGAAAAC
1 AAAACATATATATTATATAGTTTAAAAAAACATTTTGG-A-A-ATAT-ATATAATTTTCGAAAAC
1001616 A-TTTTA
62 ATTTTTA
* * * * * *
1001622 AAAATATATATAATATATAGTTTAAAAAAACAGTTTGAAAAAATTTATAAT
1 AAAACATATATATTATATAGTTTAAAAAAACATTTTGGAAATATATATAAT
1001673 ATTTAGTTTT
Statistics
Matches: 105, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
67 6 0.06
68 9 0.09
69 11 0.10
70 2 0.02
71 61 0.58
72 16 0.15
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.38
Consensus pattern (68 bp):
AAAACATATATATTATATAGTTTAAAAAAACATTTTGGAAATATATATAATTTTCGAAAACATTT
TTA
Found at i:1001671 original size:72 final size:70
Alignment explanation
Indices: 1001523--1001705 Score: 188
Period size: 71 Copynumber: 2.5 Consensus size: 70
1001513 CATTGTAGAA
* * * * *
1001523 ATAT-ATATAATTTTTGAAAGCATTTTTGAAAACATATATATTATATAGTTAAAAAAAACATTTT
1 ATATAATATAA-TTTTGAAAACA-TTTTAAAAATATATATAATATATAGTTAAAAAAAACAGTTT
* *
1001587 GGAATAT
64 GAAAAAT
*
1001594 ATATAATATAATTTTCGAAAACATTTTAAAAATATATATAATATATAGTTTAAAAAAACAGTTTG
1 ATATAATATAATTTT-GAAAACATTTTAAAAATATATATAATATATAGTTAAAAAAAACAGTTTG
1001659 AAAAAAT
65 -AAAAAT
* * * *
1001666 TTATAATATTTAGTTTTTAAAACATATTAAAAACTATATA
1 ATATAATA--TAATTTTGAAAACATTTTAAAAA-TATATA
1001706 GTATATGATT
Statistics
Matches: 94, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
71 45 0.48
72 23 0.24
73 14 0.15
74 12 0.13
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (70 bp):
ATATAATATAATTTTGAAAACATTTTAAAAATATATATAATATATAGTTAAAAAAAACAGTTTGA
AAAAT
Found at i:1001812 original size:33 final size:34
Alignment explanation
Indices: 1001749--1001817 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
1001739 ATATATATAT
* * *
1001749 ATATATATAATATTATTTTAAAACGTTATTTGAAA
1 ATATATATAATATGATTTTAAAAC-ATATTTAAAA
*
1001784 ATATATATTATATGATTTTAAAA-ATATTTAAAA
1 ATATATATAATATGATTTTAAAACATATTTAAAA
1001817 A
1 A
1001818 AAACGTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 9 0.30
35 21 0.70
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (34 bp):
ATATATATAATATGATTTTAAAACATATTTAAAA
Found at i:1003324 original size:22 final size:23
Alignment explanation
Indices: 1003292--1003335 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1003282 ATTTTTCTTA
* *
1003292 TTTTATGTTTTTTATTC-TTTAT
1 TTTTATATTTTTAATTCATTTAT
1003314 TTTTATATTTTTAATTCATTTA
1 TTTTATATTTTTAATTCATTTA
1003336 ACTTTTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTATATTTTTAATTCATTTAT
Found at i:1003840 original size:23 final size:23
Alignment explanation
Indices: 1003810--1003854 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1003800 CTTTCTTTAA
1003810 TTAAATGCTAAATTACTAATTTC
1 TTAAATGCTAAATTACTAATTTC
1003833 TTAAATGCTAAATTACTAATTT
1 TTAAATGCTAAATTACTAATTT
1003855 ACACTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.44
Consensus pattern (23 bp):
TTAAATGCTAAATTACTAATTTC
Found at i:1007379 original size:20 final size:19
Alignment explanation
Indices: 1007354--1007395 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1007344 GAAAACACTT
*
1007354 TGAGAGTGAATTGTGAATGC
1 TGAGAGTGAATTGAGAA-GC
*
1007374 TGAGAGTGAGTTGAGAAGC
1 TGAGAGTGAATTGAGAAGC
1007393 TGA
1 TGA
1007396 ATATAGCCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.31, C:0.05, G:0.38, T:0.26
Consensus pattern (19 bp):
TGAGAGTGAATTGAGAAGC
Found at i:1007883 original size:6 final size:6
Alignment explanation
Indices: 1007872--1007896 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1007862 GACACGTATT
1007872 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
1007897 GCTGAGCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1021267 original size:16 final size:16
Alignment explanation
Indices: 1021246--1021276 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1021236 TCTGCTTCAA
1021246 TAATGTGTGATGTCAG
1 TAATGTGTGATGTCAG
1021262 TAATGTGTGATGTCA
1 TAATGTGTGATGTCA
1021277 CAACATTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.39
Consensus pattern (16 bp):
TAATGTGTGATGTCAG
Found at i:1022418 original size:11 final size:11
Alignment explanation
Indices: 1022402--1022433 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1022392 GCCATGTAAT
1022402 TGAATGCAAAA
1 TGAATGCAAAA
*
1022413 TGAATGTAAAA
1 TGAATGCAAAA
1022424 TGAATGCAAA
1 TGAATGCAAA
1022434 TGGAGGTACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.19, T:0.22
Consensus pattern (11 bp):
TGAATGCAAAA
Found at i:1048793 original size:59 final size:59
Alignment explanation
Indices: 1048730--1048842 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 59
1048720 CTTCCTCTTT
* * *
1048730 CATTTTAGCACACGAAGTGCCCTAT-TCGAAAATTCATACCATTAGTATGATTTTGTTAC
1 CATTTTAGCACACAAAATGCCCTATGT-GAAAATCCATACCATTAGTATGATTTTGTTAC
*
1048789 CATTTTAGCACATAAAATGCCCTATGTGAAAATCCATACCATTAGTATGATTTT
1 CATTTTAGCACACAAAATGCCCTATGTGAAAATCCATACCATTAGTATGATTTT
1048843 CTATAGCACC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 48 0.98
60 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (59 bp):
CATTTTAGCACACAAAATGCCCTATGTGAAAATCCATACCATTAGTATGATTTTGTTAC
Found at i:1049441 original size:63 final size:62
Alignment explanation
Indices: 1049364--1049524 Score: 175
Period size: 63 Copynumber: 2.5 Consensus size: 62
1049354 TTCTCTCACA
*
1049364 GATGCATC-AGTGCACAACCTATGCATCGATGCATATATTACATTCGATG-TT-TTCATCTTAAG
1 GATGCATCGA-TGCACAACCTATGCATCGATGCATA-ACTACATTCGATGTTTATTCAT-TTAA-
1049426 G
62 G
* * *
1049427 GATGCATCGATGCACTACCTATGCATCGATGCACTAACTACCTTCGATGTTTATTTATTTAAG
1 GATGCATCGATGCACAACCTATGCATCGATGCA-TAACTACATTCGATGTTTATTCATTTAAG
* * * *
1049490 TATGCATCGGTGCACTCACTTATGCATCGATGCAT
1 GATGCATCGATGCAC-AACCTATGCATCGATGCAT
1049525 CTTGCCCAGA
Statistics
Matches: 85, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
63 56 0.66
64 25 0.29
65 4 0.05
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (62 bp):
GATGCATCGATGCACAACCTATGCATCGATGCATAACTACATTCGATGTTTATTCATTTAAG
Found at i:1054650 original size:3 final size:3
Alignment explanation
Indices: 1054642--1054688 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
1054632 ATGATGGGTG
*
1054642 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1054689 TGATTGAATG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
ATA
Done.