Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008983.1 Hibiscus syriacus cultivar Beakdansim tig00112347_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: 1350231
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1341598 original size:36 final size:37
Alignment explanation
Indices: 1341558--1341628 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
1341548 TTGTGATCAT
*
1341558 GTTTGT-TTTGTTTATCATTAAAAGTATTT-ATGTTTG
1 GTTTGTGTTCGTTTATCATTAAAAGT-TTTCATGTTTG
**
1341594 GTTTGTGTTCGTTTATTTTTAAAAGTTTTCATGTT
1 GTTTGTGTTCGTTTATCATTAAAAGTTTTCATGTT
1341629 CGTTCGTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 9 0.30
37 21 0.70
ACGTcount: A:0.20, C:0.04, G:0.17, T:0.59
Consensus pattern (37 bp):
GTTTGTGTTCGTTTATCATTAAAAGTTTTCATGTTTG
Found at i:1341658 original size:23 final size:23
Alignment explanation
Indices: 1341630--1341678 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1341620 TTTCATGTTC
* *
1341630 GTTCGTTTAGCGTTCATGAACAT
1 GTTCGTTTAACATTCATGAACAT
*
1341653 GTTCGTTTAACATTCGTGAACAT
1 GTTCGTTTAACATTCATGAACAT
1341676 GTT
1 GTT
1341679 TTTTTAGTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.41
Consensus pattern (23 bp):
GTTCGTTTAACATTCATGAACAT
Found at i:1341684 original size:23 final size:24
Alignment explanation
Indices: 1341630--1341693 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 24
1341620 TTTCATGTTC
* *
1341630 GTTCGTTTAG-CGTTCATGAACAT
1 GTTCGTTTAGACATTCGTGAACAT
1341653 GTTCGTTTA-ACATTCGTGAACAT
1 GTTCGTTTAGACATTCGTGAACAT
** *
1341676 GTTTTTTTAGTCATTCGT
1 GTTCGTTTAGACATTCGT
1341694 CGGAATGTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 27 0.79
24 7 0.21
ACGTcount: A:0.20, C:0.16, G:0.19, T:0.45
Consensus pattern (24 bp):
GTTCGTTTAGACATTCGTGAACAT
Found at i:1341933 original size:36 final size:37
Alignment explanation
Indices: 1341874--1341985 Score: 154
Period size: 37 Copynumber: 3.0 Consensus size: 37
1341864 CTTTAACATT
*
1341874 ATATATATATATATAATATTTTTTAAAACATTTTGAAAA
1 ATATATATA-ATAT-ATAATTTTTAAAACATTTTGAAAA
*
1341913 CT-TATATAATATATAATTTTTAAAACATTTTGAAAA
1 ATATATATAATATATAATTTTTAAAACATTTTGAAAA
* * *
1341949 ATATATATAATATATAGTTTTGAAAACATTTTTAAAA
1 ATATATATAATATATAATTTTTAAAACATTTTGAAAA
1341986 TATTTTTGAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
36 24 0.36
37 35 0.53
38 6 0.09
39 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (37 bp):
ATATATATAATATATAATTTTTAAAACATTTTGAAAA
Found at i:1341980 original size:11 final size:12
Alignment explanation
Indices: 1341966--1341998 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1341956 TAATATATAG
1341966 TTTTGAAAACAT
1 TTTTGAAAACAT
*
1341978 TTTT-AAAATAT
1 TTTTGAAAACAT
1341989 TTTTGAAAAC
1 TTTTGAAAAC
1341999 TATATAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:1342018 original size:47 final size:49
Alignment explanation
Indices: 1341928--1342035 Score: 168
Period size: 47 Copynumber: 2.3 Consensus size: 49
1341918 ATAATATATA
*
1341928 ATTTTTAAAACA-TTTTGAAAAATATATATAATATATAGTTTTGAAAAC
1 ATTTTTAAAATATTTTTGAAAAATATATATAATATATAGTTTTGAAAAC
* *
1341976 ATTTTTAAAATATTTTTG-AAAA-CTATATAATATATAGTTTTGAAAAT
1 ATTTTTAAAATATTTTTGAAAAATATATATAATATATAGTTTTGAAAAC
1342023 ATTTTTAAAATAT
1 ATTTTTAAAATAT
1342036 ATAATATATA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
47 36 0.64
48 15 0.27
49 5 0.09
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (49 bp):
ATTTTTAAAATATTTTTGAAAAATATATATAATATATAGTTTTGAAAAC
Found at i:1342091 original size:15 final size:15
Alignment explanation
Indices: 1342071--1342113 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1342061 TGAATATATA
1342071 TATTATATAGTTT-TT
1 TATTATAT-GTTTATT
1342086 TATTAT-T-TTTATT
1 TATTATATGTTTATT
1342099 TATTATATGTTTATT
1 TATTATATGTTTATT
1342114 AATTTATTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.12
13 8 0.32
14 2 0.08
15 12 0.48
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (15 bp):
TATTATATGTTTATT
Found at i:1342095 original size:34 final size:34
Alignment explanation
Indices: 1341978--1342084 Score: 171
Period size: 34 Copynumber: 3.1 Consensus size: 34
1341968 TTGAAAACAT
1341978 TTTTAAAATATTTTTGAAAACTATATAATATATAG
1 TTTTAAAATATTTTTGAAAA-TATATAATATATAG
1342013 TTTTGAAAATATTTTT-AAAATATATAATATATAG
1 TTTT-AAAATATTTTTGAAAATATATAATATATAG
* *
1342047 TTTTAAAATATTTTTGAATATATATATTATATAG
1 TTTTAAAATATTTTTGAAAATATATAATATATAG
1342081 TTTT
1 TTTT
1342085 TTATTATTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
33 11 0.16
34 38 0.56
35 8 0.12
36 11 0.16
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (34 bp):
TTTTAAAATATTTTTGAAAATATATAATATATAG
Found at i:1342127 original size:28 final size:28
Alignment explanation
Indices: 1342071--1342127 Score: 64
Period size: 28 Copynumber: 2.0 Consensus size: 28
1342061 TGAATATATA
* *
1342071 TATTATATAGTTTTTTATTATTTTTATT
1 TATTATATAGTTTTTAATTATTTTCATT
1342099 TATTATAT-GTTTATTAATT-TATTTCATT
1 TATTATATAGTTT-TTAATTAT-TTTCATT
1342127 T
1 T
1342128 TATTTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.68
Consensus pattern (28 bp):
TATTATATAGTTTTTAATTATTTTCATT
Found at i:1343404 original size:24 final size:25
Alignment explanation
Indices: 1343377--1343427 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
1343367 AACTTAACTA
*
1343377 TTTTTT-TTGATTTATTTA-ATATT
1 TTTTTTATTTATTTATTTATATATT
* *
1343400 TTTTTTATTTTTTTATTTATTTATT
1 TTTTTTATTTATTTATTTATATATT
1343425 TTT
1 TTT
1343428 CCCTTTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 10 0.43
25 7 0.30
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (25 bp):
TTTTTTATTTATTTATTTATATATT
Found at i:1343421 original size:21 final size:21
Alignment explanation
Indices: 1343370--1343414 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1343360 TCTTCTCAAC
1343370 TTAACTATTTTTTTTGATTTAT
1 TTAA-TATTTTTTTTGATTTAT
*
1343392 TTAATATTTTTTTT-ATTTTT
1 TTAATATTTTTTTTGATTTAT
1343412 TTA
1 TTA
1343415 TTTATTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 10 0.45
22 4 0.18
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TTAATATTTTTTTTGATTTAT
Found at i:1343992 original size:23 final size:23
Alignment explanation
Indices: 1343964--1344012 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1343954 TTTCATGTTC
* *
1343964 GTTCGTTTAGCGTTCATGAACAT
1 GTTCGTTTAACATTCATGAACAT
*
1343987 GTTCGTTTAACATTCGTGAACAT
1 GTTCGTTTAACATTCATGAACAT
1344010 GTT
1 GTT
1344013 TTTAGTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.41
Consensus pattern (23 bp):
GTTCGTTTAACATTCATGAACAT
Found at i:1344025 original size:22 final size:22
Alignment explanation
Indices: 1343980--1344025 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
1343970 TTAGCGTTCA
1343980 TGAACATGTTCGTTTAACATTCG
1 TGAACATGTTC-TTTAACATTCG
*
1344003 TGAACATGTT-TTTAGTCATTCG
1 TGAACATGTTCTTTA-ACATTCG
1344025 T
1 T
1344026 CGGAACGTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 7 0.33
23 10 0.48
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.43
Consensus pattern (22 bp):
TGAACATGTTCTTTAACATTCG
Found at i:1344174 original size:23 final size:22
Alignment explanation
Indices: 1344148--1344230 Score: 85
Period size: 23 Copynumber: 3.7 Consensus size: 22
1344138 TTCGTGTTCA
* *
1344148 TCGTTTAGCATTCATGAACATGT
1 TCGTTTAACATT-ATGAACATAT
*
1344171 TCGTTTAACATTTGTGAACATAT
1 TCGTTTAACA-TTATGAACATAT
* * *
1344194 TCCTTTAACGTTATGAACATAA
1 TCGTTTAACATTATGAACATAT
*
1344216 TAGTTTAACATTATG
1 TCGTTTAACATTATG
1344231 CGACCAACAC
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
22 22 0.45
23 25 0.51
24 2 0.04
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.41
Consensus pattern (22 bp):
TCGTTTAACATTATGAACATAT
Found at i:1345359 original size:12 final size:12
Alignment explanation
Indices: 1345342--1345366 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1345332 TTATATTTTA
1345342 AAAAATAATATT
1 AAAAATAATATT
1345354 AAAAATAATATT
1 AAAAATAATATT
1345366 A
1 A
1345367 TTATTTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAATAATATT
Done.